diff --git a/.gitignore b/.gitignore index 249cd86aa..2b2a23208 100644 --- a/.gitignore +++ b/.gitignore @@ -33,3 +33,6 @@ coverage.xml mpcontribs-api/supervisord.conf mpcontribs-portal/supervisord.conf **/.DS_Store +.venv/ +.env +.claude/ diff --git a/mpcontribs-api/.env.example b/mpcontribs-api/.env.example new file mode 100644 index 000000000..2bc5ce6f6 --- /dev/null +++ b/mpcontribs-api/.env.example @@ -0,0 +1,11 @@ +MPCONTRIBS_ENVIRONMENT=dev + +MPCONTRIBS_MONGO__URI=mongodb+srv://:@host.hash.mongodb.net/?appName=database-name +MPCONTRIBS_MONGO__DB_NAME=database-name + +MPCONTRIBS_REDIS__ADDRESS=redis-address # placeholder; not used yet +MPCONTRIBS_REDIS__URL=redis-url + +MPCONTRIBS_MAIL_DEFAULT_SENDER=mail-default-sender # placeholder; not used yet + +MPCONTRIBS_VERSION=version diff --git a/mpcontribs-api/.gitignore b/mpcontribs-api/.gitignore new file mode 100644 index 000000000..edd9d60a7 --- /dev/null +++ b/mpcontribs-api/.gitignore @@ -0,0 +1,2 @@ +build/ +dist/ diff --git a/mpcontribs-api/CLAUDE.md b/mpcontribs-api/CLAUDE.md new file mode 100644 index 000000000..ef6f146b6 --- /dev/null +++ b/mpcontribs-api/CLAUDE.md @@ -0,0 +1,88 @@ +# CLAUDE.md + +This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository. + +This is a complete rewrite of the MPContribs API server. +The core of the package is FastAPI, Pydantic, and Beanie. +Developer experience and process efficiency are top priorities. + +## Commands + +```bash +# Format, fix, and lint (preferred) +just fmt + +# Run tests +uv run pytest + +# Run tests by marker +uv run pytest -m base +uv run pytest -m extra + +# Run tests in parallel +uv run pytest -n auto + +# Type check +uv run basedpyright +``` + +## Environment + +Copy `.env.example` to `.env`. Key variables (all prefixed `MPCONTRIBS_`): + +- `MONGO__URI` — MongoDB Atlas URI +- `MONGO__DB_NAME` — database name +- `ENVIRONMENT` — `dev` or `prod` (controls log format and debug mode) + +## Architecture + +### Domain structure + +Each resource lives in `src/mpcontribs_api/domains//` with four files: + +- `models.py` — Beanie `Document` subclass (DB model) + Pydantic output/input/patch/filter models +- `repository.py` — `MongoDbRepository` encapsulating all database access +- `router.py` — `APIRouter` with CRUD endpoint handlers +- `dependencies.py` — `Dep` type alias (`Annotated[MongoDbRepository, Depends(...)]`) + +Routers are registered in `src/mpcontribs_api/api/v1/router.py`. + +### Authentication and authorization + +Kong injects user identity via headers; `dependencies.get_user` parses them into a frozen `User` model (`authz.py`). The dependency chain is: + +- `UserDep` — any caller (anonymous or authenticated) +- `AuthedDep` / `require_user` — requires an authenticated user (raises 401 otherwise) +- `require_role(role)` — factory returning a dependency that requires a specific group membership + +All mutating endpoints (POST/PUT/PATCH/DELETE) depend on `require_user`, so anonymous callers get 401; read endpoints (GET) stay open and rely on scope to filter results. + +All database access goes through a repository instantiated with the current `User`. The repository's `_scope` dict is injected into every MongoDB query automatically: + +- **Admins** (members of `mongo.admin_group`): no filter applied +- **Authenticated users**: see public+approved data, own resources (`owner == username`), and group resources +- **Anonymous**: public + approved only + +Components (structures/tables/attachments) have no access field of their own; their reads and deletes are gated by whether an in-scope contribution references them (see `ContributionService`/`ComponentService`). + +**Trust boundary:** the service is only reachable through Kong, which terminates auth and sets the identity headers. There is no in-app gateway-secret check today — the deployment network is the boundary, so the identity headers are trusted. If the service is ever exposed off the Kong path, add a gateway-secret (or mTLS) check before trusting those headers. + +### Repository pattern + +Repositories take a `User` at construction time and expose typed async methods (`get_*`, `insert_*`, `patch_*`, `upsert_*`, `delete_*`). They never leak the scope logic to routers — routers only call repository methods. + +### Sparse field selection + +The `_fields` query parameter (handled in `projection.py`) lets callers request specific fields (comma-separated, dotted for nesting). `SparseFieldsModel` dynamically creates a trimmed Pydantic model via `create_model()` and converts field paths to MongoDB projection syntax. Results are cached with `@lru_cache`. + +### Cursor-based pagination + +`Page[T]` in `pagination.py` contains `items` and a `next_cursor` (base64-encoded last item ID). Pagination is forward-only and stateless. Default page size is 20; max is 100. + +### Exception hierarchy + +`exceptions.py` defines `AppError` subclasses (`NotFoundError`, `ConflictError`, `ValidationError`, `AuthenticationError`, `PermissionError`). All carry `status_code`, `error_code`, `message`, and a `context` dict. Handlers in `app.py` convert them to a uniform JSON shape; internal context is logged but not sent to clients. + +### Observability + +`logging.py` configures structlog with per-request context vars (request_id, method, path, consumer_id) bound by the middleware in `middleware.py`. OpenTelemetry traces are exported via OTLP/gRPC and trace/span IDs are injected into every log line. diff --git a/mpcontribs-api/Dockerfile b/mpcontribs-api/Dockerfile index 88be9c146..0e68e2778 100644 --- a/mpcontribs-api/Dockerfile +++ b/mpcontribs-api/Dockerfile @@ -1,58 +1,43 @@ -FROM materialsproject/devops:python-3.1113.4 AS base -RUN apt-get update && apt-get install -y --no-install-recommends supervisor libopenblas-dev libpq-dev vim && apt-get clean +# FROM materialsproject/devops:python-3.1113.4 AS base +FROM python:3.14-slim AS base +RUN apt-get update && apt-get install -y --no-install-recommends supervisor libopenblas-dev vim && apt-get clean WORKDIR /app FROM base AS builder -RUN apt-get update && apt-get install -y --no-install-recommends gcc git g++ libsnappy-dev wget liblapack-dev && apt-get clean -ENV PIP_FLAGS "--no-cache-dir --compile" -COPY requirements/deployment.txt ./requirements.txt -RUN pip install $PIP_FLAGS -r requirements.txt -COPY pyproject.toml . -COPY mpcontribs mpcontribs +RUN apt-get update && apt-get install -y --no-install-recommends gcc git g++ wget liblapack-dev libsnappy-dev && apt-get clean +RUN pip install uv +# Build the venv OUTSIDE /app: docker-compose bind-mounts the host source over +# /app for live reload, which would mask a /app/.venv and leave `python` falling +# back to the system interpreter (missing deps) +ENV UV_PROJECT_ENVIRONMENT=/opt/venv +COPY pyproject.toml uv.lock ./ +COPY src src ARG CONTRIBS_VERSION -RUN SETUPTOOLS_SCM_PRETEND_VERSION=${CONTRIBS_VERSION} pip install $PIP_FLAGS --no-deps . -#ENV SETUPTOOLS_SCM_PRETEND_VERSION 0.0.0 -#COPY marshmallow-mongoengine marshmallow-mongoengine -#RUN cd marshmallow-mongoengine && pip install $PIP_FLAGS --no-deps -e . -#COPY mimerender mimerender -#RUN cd mimerender && pip install $PIP_FLAGS --no-deps -e . -#COPY flask-mongorest flask-mongorest -#RUN cd flask-mongorest && pip install $PIP_FLAGS --no-deps -e . -#COPY AtlasQ AtlasQ -#RUN cd AtlasQ && pip install $PIP_FLAGS --no-deps -e . +RUN SETUPTOOLS_SCM_PRETEND_VERSION=${CONTRIBS_VERSION} uv sync --frozen --no-dev --no-editable RUN wget -q https://raw.githubusercontent.com/vishnubob/wait-for-it/master/wait-for-it.sh && \ - chmod +x wait-for-it.sh && mv wait-for-it.sh /usr/local/bin/ && \ - wget -q https://github.com/materialsproject/MPContribs/blob/master/mpcontribs-api/mpcontribs/api/contributions/formulae.json.gz?raw=true \ - -O mpcontribs/api/contributions/formulae.json.gz + chmod +x wait-for-it.sh && mv wait-for-it.sh /usr/local/bin/ FROM base ARG BUILDARCH -ENV BUILDARCH=x86_64 -COPY --from=builder /usr/local/lib/python3.11/site-packages /usr/local/lib/python3.11/site-packages -COPY --from=builder /usr/local/bin /usr/local/bin -COPY --from=builder /usr/lib/$BUILDARCH-linux-gnu/libsnappy* /usr/lib/$BUILDARCH-linux-gnu/ +ARG BUILDARCH=aarch64 +COPY --from=builder /opt/venv /opt/venv +COPY --from=builder /usr/local/bin/wait-for-it.sh /usr/local/bin/ -COPY --from=builder /app/mpcontribs/api /app/mpcontribs/api WORKDIR /app RUN mkdir -p /var/log/supervisor COPY supervisord supervisord COPY scripts scripts COPY main.py . -COPY maintenance.py . COPY docker-entrypoint.sh . -COPY gunicorn.conf.py . RUN chmod +x main.py scripts/start.sh scripts/start_rq.sh docker-entrypoint.sh ARG VERSION -ENV DD_SERVICE=contribs-apis \ - DD_ENV=prod \ - DD_VERSION=$VERSION \ - DD_TRACE_HOST=localhost:8126 \ - DD_TRACE_OTEL_ENABLED=false \ - DD_MAIN_PACKAGE=mpcontribs-api +# Telemetry (traces/metrics/logs) is emitted via OTLP to the Datadog Agent's OTLP receiver; the +# endpoint and other OTEL settings are configured per-environment in supervisord.conf.jinja +# (MPCONTRIBS_OTEL__*). No Datadog-specific app config lives here. +ENV PATH="/opt/venv/bin:$PATH" -LABEL com.datadoghq.ad.logs='[{"source": "gunicorn", "service": "contribs-apis"}]' EXPOSE 10000 10002 10003 10005 20000 ENTRYPOINT ["/app/docker-entrypoint.sh"] CMD ["/usr/bin/supervisord", "-c", "supervisord.conf"] diff --git a/mpcontribs-api/gunicorn.conf.py b/mpcontribs-api/gunicorn.conf.py deleted file mode 100644 index d6d1693c1..000000000 --- a/mpcontribs-api/gunicorn.conf.py +++ /dev/null @@ -1,16 +0,0 @@ -import ddtrace.auto # noqa: F401 -import os - -bind = "0.0.0.0:{}".format(os.getenv("API_PORT")) -worker_class = "gevent" -workers = os.getenv("NWORKERS") -statsd_host = "{}:8125".format(os.getenv("DD_AGENT_HOST")) -accesslog = "-" -errorlog = "-" -access_log_format = '{}/{}: %(h)s %(t)s %(m)s %(U)s?%(q)s %(H)s %(s)s %(b)s "%(f)s" "%(a)s" %(D)s %(p)s %({{x-consumer-id}}i)s'.format( - os.getenv("SUPERVISOR_GROUP_NAME"), os.getenv("SUPERVISOR_PROCESS_NAME") -) -max_requests = os.getenv("MAX_REQUESTS") -max_requests_jitter = os.getenv("MAX_REQUESTS_JITTER") -proc_name = os.getenv("SUPERVISOR_PROCESS_NAME") -reload = bool(os.getenv("RELOAD", False)) diff --git a/mpcontribs-api/justfile b/mpcontribs-api/justfile new file mode 100644 index 000000000..afb9e566c --- /dev/null +++ b/mpcontribs-api/justfile @@ -0,0 +1,20 @@ +# Run the dev server (auto-reloads on file changes) +dev: + uv run fastapi dev src/mpcontribs_api/app.py + +# Format, fix, and lint all source code +fmt: + uv run ruff format + -uv run ruff check --fix + -uv run ruff check --fix --unsafe-fixes + -uv run pydocstringformatter --write + +test suite="all": + #!/usr/bin/env bash + case "{{suite}}" in + all|a) uv run pytest tests/ ;; + integration|i) uv run pytest tests/integration/ -m "not db" ;; + unit|u) uv run pytest tests/unit/ ;; + db|d) uv run pytest tests/integration/db/ -m db ;; + *) echo "unknown suite '{{suite}}' — use: all/a, integration/i, unit/u, db/d" && exit 1 ;; + esac diff --git a/mpcontribs-api/main.py b/mpcontribs-api/main.py index 2ec96e9fc..d9d5a740c 100755 --- a/mpcontribs-api/main.py +++ b/mpcontribs-api/main.py @@ -1,14 +1,14 @@ #!/usr/bin/env python -import os -import requests -import boto3 import logging +import os +import boto3 +import requests from supervisor.options import ClientOptions from supervisor.supervisorctl import Controller logger = logging.getLogger(__name__) -client = boto3.client('ecs') +client = boto3.client("ecs") def start(program): diff --git a/mpcontribs-api/maintenance.py b/mpcontribs-api/maintenance.py deleted file mode 100644 index d6c4682a0..000000000 --- a/mpcontribs-api/maintenance.py +++ /dev/null @@ -1,41 +0,0 @@ -from boltons.iterutils import remap -from mongoengine.queryset.visitor import Q - -from mpcontribs.api import enter -from mpcontribs.api.projects.document import Projects -from mpcontribs.api.contributions.document import Contributions - - -def visit(path, key, value): - if isinstance(value, dict) and "display" in value: - return key, value["display"] - return True - - -def fix_units(name): - # make sure correct units are indicated in project.columns before running this - fields = list(Contributions._fields.keys()) - project = Projects.objects.with_id(name).reload("columns") - query = Q() - - for column in project.columns: - if column.unit and column.unit != "NaN": - path = column.path.replace(".", "__") - q = {f"{path}__unit__ne": column["unit"]} - query |= Q(**q) - - contribs = Contributions.objects(Q(project=name) & query).only(*fields) - num = contribs.count() - print(name, num) - - for idx, contrib in enumerate(contribs): - contrib.data = remap(contrib.data, visit=visit, enter=enter) # pull out display - contrib.save(signal_kwargs={"skip": True}) # reparse display with intended unit - - if idx and not idx%250: - print(idx) - -# additional maintenance functions -# TODO generate JSON/CSV project downloads -# TODO clean dangling notebooks -# TODO update_projects/stats diff --git a/mpcontribs-api/mpcontribs/api/__init__.py b/mpcontribs-api/mpcontribs/api/__init__.py deleted file mode 100644 index e61583b4b..000000000 --- a/mpcontribs-api/mpcontribs/api/__init__.py +++ /dev/null @@ -1,257 +0,0 @@ -# -*- coding: utf-8 -*- -"""Flask App for MPContribs API""" -import os -import smtplib -import logging -import requests -import flask_mongorest.operators as ops - -from email.message import EmailMessage -from importlib import import_module -from importlib.metadata import version -from websocket import create_connection -from flask import Flask, current_app, request, jsonify -from flask_marshmallow import Marshmallow -from flask_mongoengine import MongoEngine -from flask_mongorest import register_class -from flask_sse import sse -from flask_compress import Compress -from flasgger.base import Swagger - -from mongoengine import ValidationError -from mongoengine.base.datastructures import BaseDict -from itsdangerous import URLSafeTimedSerializer -from string import punctuation, whitespace -from boltons.iterutils import remap, default_enter -from notebook.utils import url_path_join -from notebook.gateway.managers import GatewayClient -from requests.exceptions import ConnectionError, Timeout - -try: - __version__ = version("mpcontribs-api") -except Exception: - # package is not installed - pass - -delimiter, max_depth = ".", 7 # = MAX_NESTING + 2 from client -invalidChars = set(punctuation.replace("*", "").replace("|", "") + whitespace) -is_gunicorn = "gunicorn" in os.environ.get("SERVER_SOFTWARE", "") -SMTP_HOST, SMTP_PORT = os.environ.get("SMTP_SERVER", "localhost:587").split(":") - -# NOTE not including Size below (special for arrays) -FILTERS = { - "LONG_STRINGS": [ - ops.Contains, - ops.IContains, - ops.Startswith, - ops.IStartswith, - ops.Endswith, - ops.IEndswith, - ], - "NUMBERS": [ops.Lt, ops.Lte, ops.Gt, ops.Gte, ops.Range], - "DATES": [ops.Before, ops.After], - "OTHERS": [ops.Boolean, ops.Exists], -} -FILTERS["STRINGS"] = [ops.In, ops.Exact, ops.IExact, ops.Ne] + FILTERS["LONG_STRINGS"] -FILTERS["ALL"] = ( - FILTERS["STRINGS"] + FILTERS["NUMBERS"] + FILTERS["DATES"] + FILTERS["OTHERS"] -) - - -class CustomLoggerAdapter(logging.LoggerAdapter): - def process(self, msg, kwargs): - prefix = self.extra.get("prefix") - return f"[{prefix}] {msg}" if prefix else msg, kwargs - - -def get_logger(name): - logger = logging.getLogger(name) - process = os.environ.get("SUPERVISOR_PROCESS_NAME") - group = os.environ.get("SUPERVISOR_GROUP_NAME") - cfg = {"prefix": f"{group}/{process}"} if process and group else {} - logger.setLevel("DEBUG" if os.environ.get("FLASK_DEBUG") else "INFO") - return CustomLoggerAdapter(logger, cfg) - - -logger = get_logger(__name__) - - -def enter(path, key, value): - if isinstance(value, BaseDict): - return dict(), value.items() - elif isinstance(value, list): - dot_path = delimiter.join(list(path) + [key]) - raise ValidationError(f"lists not allowed ({dot_path})!") - - return default_enter(path, key, value) - - -def valid_key(key): - if not key.isascii(): - raise ValidationError(f"non-ascii character(s) in {key}") - - for char in key: - if char in invalidChars: - raise ValidationError(f"invalid character {char} in {key}") - - if key.count("|") > 1: - raise ValidationError(f"Only one `|` allowed in {key}. Consider nesting.") - - -def visit(path, key, value): - key = key.strip() - - if len(path) + 1 > max_depth: - dot_path = delimiter.join(list(path) + [key]) - raise ValidationError(f"max nesting ({max_depth}) exceeded for {dot_path}") - - valid_key(key) - return key, value - - -def valid_dict(dct): - remap(dct, visit=visit, enter=enter) - - -def send_email(to, subject, html): - msg = EmailMessage() - msg.set_content(html) - msg["Subject"] = subject - msg["From"] = current_app.config["MAIL_DEFAULT_SENDER"] - msg["To"] = to - - # NOTE boto3 SES client can't connect to VPC endpoint yet - with smtplib.SMTP(host=SMTP_HOST, port=int(SMTP_PORT)) as ses_client: - ses_client.starttls() - ses_client.login(os.environ["SMTP_USERNAME"], os.environ["SMTP_PASSWORD"]) - ses_client.send_message(msg) - logger.warning(f"Email with subject `{subject}` sent to `{to}`") - - -def get_collections(db): - """get list of collections in DB""" - conn = db.app.extensions["mongoengine"][db]["conn"] - dbname = db.app.config.get("MPCONTRIBS_DB") - return conn[dbname].list_collection_names() - - -def get_resource_as_string(name, charset="utf-8"): - """http://flask.pocoo.org/snippets/77/""" - with current_app.open_resource(name) as f: - return f.read().decode(charset) - - -def get_kernel_endpoint(kernel_id=None, ws=False): - gw_client = GatewayClient.instance() - base_url = gw_client.ws_url if ws else gw_client.url - - if not base_url: - raise ConnectionError("base URL for Kernel Gateway not set") - - base_endpoint = url_path_join(base_url, gw_client.kernels_endpoint) - - if isinstance(kernel_id, str) and kernel_id: - return url_path_join(base_endpoint, kernel_id) - - return base_endpoint - - -def create_kernel_connection(kernel_id): - url = get_kernel_endpoint(kernel_id, ws=True) + "/channels" - return create_connection(url, skip_utf8_validation=True) - - -def get_kernels(): - """retrieve list of kernels from KernelGateway service""" - try: - r = requests.get(get_kernel_endpoint(), timeout=2) - except (ConnectionError, Timeout): - logger.warning("Kernel Gateway NOT AVAILABLE") - return None - - response = r.json() - nkernels = 3 # reserve 3 kernels for each deployment - idx = int(os.environ.get("DEPLOYMENT", 1)) - - if len(response) < nkernels * (idx + 1): - logger.error("NOT ENOUGH KERNELS AVAILABLE") - return None - - return {kernel["id"]: None for kernel in response[idx : idx + 3]} - - -def get_consumer(): - groups = request.headers.get("X-Authenticated-Groups", "").split(",") - groups += request.headers.get("X-Consumer-Groups", "").split(",") - return { - "username": request.headers.get("X-Consumer-Username"), - "apikey": request.headers.get("X-Consumer-Custom-Id"), - "groups": ",".join(set(groups)), - } - - -def create_app(): - """create flask app""" - app = Flask(__name__) - app.config.from_pyfile("config.py", silent=True) - app.config["USTS"] = URLSafeTimedSerializer(app.secret_key) - app.jinja_env.globals["get_resource_as_string"] = get_resource_as_string - app.jinja_env.lstrip_blocks = True - app.jinja_env.trim_blocks = True - app.json.sort_keys = False - MPCONTRIBS_API_HOST = app.config.get("MPCONTRIBS_API_HOST") - app.config["TEMPLATE"]["schemes"] = ["http"] if app.debug else ["https"] - logger.info("database: " + app.config["MPCONTRIBS_DB"]) - Compress(app) - Marshmallow(app) - MongoEngine(app) - Swagger(app, template=app.config.get("TEMPLATE")) - setattr(app, "kernels", get_kernels()) - - # NOTE: hard-code to avoid pre-generating for new deployment - # collections = get_collections(db) - collections = [ - "projects", - "contributions", - "tables", - "attachments", - "structures", - "notebooks", - ] - - for collection in collections: - module_path = ".".join(["mpcontribs", "api", collection, "views"]) - try: - module = import_module(module_path) - except ModuleNotFoundError as ex: - logger.error(f"API module {module_path}: {ex}") - continue - - try: - blueprint = getattr(module, collection) - app.register_blueprint(blueprint, url_prefix="/" + collection) - klass = getattr(module, collection.capitalize() + "View") - register_class(app, klass, name=collection) - logger.info(f"{collection} registered") - except AttributeError as ex: - logger.error(f"Failed to register {module_path}: {collection} {ex}") - - if getattr(app, "kernels", None): - from mpcontribs.api.notebooks.views import rq - - rq.init_app(app) - - def healthcheck(): - return jsonify({"version": app.config["VERSION"]}) - - if is_gunicorn and MPCONTRIBS_API_HOST: - app.register_blueprint(sse, url_prefix="/stream") - app.add_url_rule("/healthcheck", view_func=healthcheck) - - @app.after_request - def add_header(response): - response.headers["X-Consumer-Id"] = request.headers.get("X-Consumer-Id") - return response - - logger.info("app created.") - return app diff --git a/mpcontribs-api/mpcontribs/api/attachments/__init__.py b/mpcontribs-api/mpcontribs/api/attachments/__init__.py deleted file mode 100644 index 4d321d0bf..000000000 --- a/mpcontribs-api/mpcontribs/api/attachments/__init__.py +++ /dev/null @@ -1,2 +0,0 @@ -# -*- coding: utf-8 -*- -"""document and views for attachments collection""" diff --git a/mpcontribs-api/mpcontribs/api/attachments/document.py b/mpcontribs-api/mpcontribs/api/attachments/document.py deleted file mode 100644 index c5584a11a..000000000 --- a/mpcontribs-api/mpcontribs/api/attachments/document.py +++ /dev/null @@ -1,92 +0,0 @@ -# -*- coding: utf-8 -*- -import os -import boto3 -import binascii - -from hashlib import md5 -from flask import request -from base64 import b64decode, b64encode -from flask_mongoengine.documents import DynamicDocument -from mongoengine import signals, ValidationError -from mongoengine.fields import StringField -from mongoengine.queryset.manager import queryset_manager -from filetype.types.archive import Gz -from filetype.types.image import Jpeg, Png, Gif, Tiff - -from mpcontribs.api.contributions.document import get_resource, get_md5, COMPONENTS - -MAX_BYTES = 2.4 * 1024 * 1024 -BUCKET = os.environ.get("S3_ATTACHMENTS_BUCKET", "mpcontribs-attachments") -S3_ATTACHMENTS_URL = f"https://{BUCKET}.s3.amazonaws.com" -SUPPORTED_FILETYPES = (Gz, Jpeg, Png, Gif, Tiff) -SUPPORTED_MIMES = [t().mime for t in SUPPORTED_FILETYPES] - -s3_client = boto3.client("s3") - - -class Attachments(DynamicDocument): - name = StringField(required=True, help_text="file name") - md5 = StringField(regex=r"^[a-z0-9]{32}$", unique=True, help_text="md5 sum") - mime = StringField(required=True, choices=SUPPORTED_MIMES, help_text="attachment mime type") - content = StringField(required=True, help_text="base64-encoded attachment content") - meta = {"collection": "attachments", "indexes": ["name", "mime", "md5"]} - - @queryset_manager - def objects(doc_cls, queryset): - return queryset.only("name", "md5", "mime") - - @classmethod - def post_init(cls, sender, document, **kwargs): - if document.id and document._data.get("content"): - res = get_resource("attachments") - requested_fields = res.get_requested_fields(params=request.args) - - if "content" in requested_fields: - if not document.md5: - # document.reload("md5") # TODO AttributeError: _changed_fields - raise ValueError("Please also request md5 field to retrieve attachment content!") - - retr = s3_client.get_object(Bucket=BUCKET, Key=document.md5) - document.content = b64encode(retr["Body"].read()).decode("utf-8") - - @classmethod - def pre_delete(cls, sender, document, **kwargs): - s3_client.delete_object(Bucket=BUCKET, Key=document.md5) - - @classmethod - def pre_save_post_validation(cls, sender, document, **kwargs): - if document.md5: - return # attachment already cross-referenced to existing one - - # b64 decode - try: - content = b64decode(document.content, validate=True) - except binascii.Error: - raise ValidationError(f"Attachment {document.name} not base64 encoded!") - - # check size - size = len(content) - - if size > MAX_BYTES: - raise ValidationError( - f"Attachment {document.name} too large ({size} > {MAX_BYTES})!" - ) - - # md5 - resource = get_resource("attachments") - document.md5 = get_md5(resource, document, COMPONENTS["attachments"]) - - # save to S3 and unset content - s3_client.put_object( - Bucket=BUCKET, - Key=document.md5, - ContentType=document.mime, - Metadata={"name": document.name}, - Body=content, - ) - document.content = str(size) # set to something useful to distinguish in post_init - - -signals.post_init.connect(Attachments.post_init, sender=Attachments) -signals.pre_delete.connect(Attachments.pre_delete, sender=Attachments) -signals.pre_save_post_validation.connect(Attachments.pre_save_post_validation, sender=Attachments) diff --git a/mpcontribs-api/mpcontribs/api/attachments/views.py b/mpcontribs-api/mpcontribs/api/attachments/views.py deleted file mode 100644 index ae1e8c16a..000000000 --- a/mpcontribs-api/mpcontribs/api/attachments/views.py +++ /dev/null @@ -1,39 +0,0 @@ -# -*- coding: utf-8 -*- -import os -import flask_mongorest -from flask_mongorest.resources import Resource -from flask_mongorest import operators as ops -from flask_mongorest.methods import Fetch, BulkFetch, Download -from flask import Blueprint - -from mpcontribs.api import FILTERS -from mpcontribs.api.core import SwaggerView -from mpcontribs.api.attachments.document import Attachments - -templates = os.path.join(os.path.dirname(flask_mongorest.__file__), "templates") -attachments = Blueprint("attachments", __name__, template_folder=templates) - - -class AttachmentsResource(Resource): - document = Attachments - filters = { - "id": [ops.In, ops.Exact], - "md5": [ops.In, ops.Exact], - "name": FILTERS["STRINGS"], - "mime": FILTERS["STRINGS"], - } - fields = ["id", "name", "mime", "md5"] - allowed_ordering = ["name", "mime"] - paginate = True - default_limit = 10 - max_limit = 100 - download_formats = ["json", "csv"] - - @staticmethod - def get_optional_fields(): - return ["content"] - - -class AttachmentsView(SwaggerView): - resource = AttachmentsResource - methods = [Fetch, BulkFetch, Download] diff --git a/mpcontribs-api/mpcontribs/api/config.py b/mpcontribs-api/mpcontribs/api/config.py deleted file mode 100644 index f044f4ab9..000000000 --- a/mpcontribs-api/mpcontribs/api/config.py +++ /dev/null @@ -1,128 +0,0 @@ -# -*- coding: utf-8 -*- -"""configuration module for MPContribs Flask API""" - -import os -import json -import gzip - -from mpcontribs.api import __version__ - -formulae_path = os.path.join( - os.path.dirname(__file__), "contributions", "formulae.json.gz" -) - -with gzip.open(formulae_path) as f: - FORMULAE = json.load(f) - -VERSION = __version__ - -JSON_ADD_STATUS = False -SECRET_KEY = "super-secret" # TODO in local prod config - -MAIL_DEFAULT_SENDER = os.environ.get("MAIL_DEFAULT_SENDER") -MPCONTRIBS_DB = os.environ.get("MPCONTRIBS_DB_NAME", "mpcontribs") -MPCONTRIBS_MONGO_HOST = os.environ.get("MPCONTRIBS_MONGO_HOST") -MPCONTRIBS_API_HOST = os.environ.get("MPCONTRIBS_API_HOST") -MONGODB_SETTINGS = { - # Changed in version 3.9: retryWrites now defaults to True. - "host": f"mongodb+srv://{MPCONTRIBS_MONGO_HOST}/{MPCONTRIBS_DB}", - "connect": False, - "db": MPCONTRIBS_DB, - "compressors": ["snappy", "zstd", "zlib"], -} -REDIS_ADDRESS = os.environ.get("REDIS_ADDRESS", "redis") -REDIS_URL = RQ_REDIS_URL = RQ_DASHBOARD_REDIS_URL = f"redis://{REDIS_ADDRESS}" -DOC_DIR = os.path.join(os.path.dirname(__file__), f"swagger-{MPCONTRIBS_DB}") - -SWAGGER = { - "swagger_ui_bundle_js": "//unpkg.com/swagger-ui-dist@3/swagger-ui-bundle.js", - "swagger_ui_standalone_preset_js": "//unpkg.com/swagger-ui-dist@3/swagger-ui-standalone-preset.js", - "jquery_js": "//unpkg.com/jquery@2.2.4/dist/jquery.min.js", - "swagger_ui_css": "//unpkg.com/swagger-ui-dist@3/swagger-ui.css", - "uiversion": 3, - "hide_top_bar": True, - "doc_expansion": "none", - "doc_dir": DOC_DIR, - "specs": [ - { - "endpoint": "apispec", - "route": "/apispec.json", - "rule_filter": lambda rule: True, # all in - "model_filter": lambda tag: True, # all in - } - ], - "specs_route": "/", -} - -TEMPLATE = { - "swagger": "2.0", - "info": { - "title": "MPContribs API", - "description": "Operations to contribute, update and retrieve materials data on Materials Project", - "termsOfService": "https://materialsproject.org/terms", - "version": VERSION, - "contact": { - "name": "MPContribs", - "email": "contribs@materialsproject.org", - "url": "https://mpcontribs.org", - }, - "license": { - "name": "Creative Commons Attribution 4.0 International License", - "url": "https://creativecommons.org/licenses/by/4.0/", - }, - }, - "tags": [ - { - "name": "projects", - "description": f'contain provenance information about contributed datasets. \ - Deleting projects will also delete all contributions including tables, structures, attachments, notebooks \ - and cards for the project. Only users who have been added to a project can update its contents. While \ - unpublished, only users on the project can retrieve its data or view it on the \ - Portal. Making a project public does not automatically publish all \ - its contributions, tables, attachments, and structures. These are separately set to public individually or in bulk.' - "", - }, - { - "name": "contributions", - "description": f'contain simple hierarchical data which will show up as cards on the MP details \ - page for MP material(s). Tables (rows and columns), structures, and attachments can be added to a \ - contribution. Each contribution uses `mp-id` or composition as identifier to associate its data with the \ - according entries on MP. Only admins or users on the project can create, update or delete contributions, and \ - while unpublished, retrieve its data or view it on the Portal. \ - Contribution components (tables, structures, and attachments) are deleted along with a contribution.', - }, - { - "name": "structures", - "description": 'are \ - pymatgen structures which \ - can be added to a contribution.', - }, - { - "name": "tables", - "description": 'are simple spreadsheet-type tables with columns and rows saved as Pandas \ - DataFrames \ - which can be added to a contribution.', - }, - { - "name": "attachments", - "description": 'are files saved as objects in AWS S3 and not accessible for querying (only retrieval) \ - which can be added to a contribution.', - }, - { - "name": "notebooks", - "description": f'are Jupyter \ - notebook \ - documents generated and saved when a contribution is saved. They form the basis for Contribution \ - Details Pages on the Portal.', - }, - ], - "securityDefinitions": { - "ApiKeyAuth": { - "description": "MP API key to authorize requests", - "name": "X-API-KEY", - "in": "header", - "type": "apiKey", - } - }, - "security": [{"ApiKeyAuth": []}], -} diff --git a/mpcontribs-api/mpcontribs/api/contributions/document.py b/mpcontribs-api/mpcontribs/api/contributions/document.py deleted file mode 100644 index db434cdf8..000000000 --- a/mpcontribs-api/mpcontribs/api/contributions/document.py +++ /dev/null @@ -1,333 +0,0 @@ -# -*- coding: utf-8 -*- -import json -import itertools - -from hashlib import md5 -from math import isnan -from bson.dbref import DBRef -from datetime import datetime -from flask import current_app -from atlasq import AtlasManager, AtlasQ -from itertools import permutations -from importlib import import_module -from fastnumbers import isfloat -from mongoengine import CASCADE, signals, DynamicDocument -from mongoengine.queryset.manager import queryset_manager -from mongoengine.fields import StringField, BooleanField, DictField -from mongoengine.fields import LazyReferenceField, ReferenceField -from mongoengine.fields import DateTimeField, ListField -from boltons.iterutils import remap -from decimal import Decimal -from pint import UnitRegistry -from pint.errors import DimensionalityError -from uncertainties import ufloat_fromstr -from pymatgen.core import Composition, Element - -from mpcontribs.api import enter, valid_dict, delimiter - -quantity_keys = {"display", "value", "error", "unit"} -max_dgts = 6 -ureg = UnitRegistry( - autoconvert_offset_to_baseunit=True, - preprocessors=[ - lambda s: s.replace("%%", " permille "), - lambda s: s.replace("%", " percent "), - ], -) -ureg.formatter.default_format = "~,P" - -if "percent" not in ureg: - # percent is native in pint >= 0.21 - ureg.define("percent = 0.01 = %") -if "permille" not in ureg: - # permille is native in pint >= 0.24.2 - ureg.define("permille = 0.001 = ‰ = %%") -if "ppm" not in ureg: - # ppm is native in pint >= 0.21 - ureg.define("ppm = 1e-6") -ureg.define("ppb = 1e-9") -ureg.define("atom = 1") -ureg.define("bohr_magneton = e * hbar / (2 * m_e) = µᵇ = µ_B = mu_B") -ureg.define("electron_mass = 9.1093837015e-31 kg = mₑ = m_e") -ureg.define("sccm = cm³/min") - -COMPONENTS = { - "structures": ["lattice", "sites", "charge"], - "tables": ["index", "columns", "data"], - "attachments": ["mime", "content"], -} - - -def grouper(n, iterable): - it = iter(iterable) - while True: - chunk = tuple(itertools.islice(it, n)) - if not chunk: - return - yield chunk - - -def format_cell(cell): - cell = cell.strip() - if not cell or cell.count(" ") > 1: - return cell - - q = get_quantity(cell) - if not q or isnan(q.magnitude.nominal_value): - return cell - - q = truncate_digits(q) - try: - return str(q.magnitude.nominal_value) if isnan(q.magnitude.std_dev) else str(q) - except Exception: - return cell - - -def new_error_units(measurement, quantity): - if quantity.units == measurement.value.units: - return measurement - - error = measurement.error.to(quantity.units) - return ureg.Measurement(quantity, error) - - -def get_quantity(s): - # 5, 5 eV, 5+/-1 eV, 5(1) eV - # set uncertainty to nan if not provided - parts = s.split() - parts += [None] * (2 - len(parts)) - if isfloat(parts[0]): - parts[0] += "+/-nan" - - try: - parts[0] = ufloat_fromstr(parts[0]) - return ureg.Measurement(*parts) - except ValueError: - return None - - -def truncate_digits(q): - if isnan(q.magnitude.nominal_value): - return q - - v = Decimal(str(q.magnitude.nominal_value)) - vt = v.as_tuple() - - if vt.exponent >= 0: - return q - - dgts = len(vt.digits) - dgts = max_dgts if dgts > max_dgts else dgts - s = f"{v:.{dgts}g}" - if not isnan(q.magnitude.std_dev): - s += f"+/-{q.magnitude.std_dev:.{dgts}g}" - - if q.units: - s += f" {q.units}" - - return get_quantity(s) - - -def get_resource(component): - klass = component.capitalize() - vmodule = import_module(f"mpcontribs.api.{component}.views") - Resource = getattr(vmodule, f"{klass}Resource") - return Resource() - - -def get_md5(resource, obj, fields): - d = resource.serialize(obj, fields=fields) - s = json.dumps(d, sort_keys=True).encode("utf-8") - return md5(s).hexdigest() - - -class Contributions(DynamicDocument): - project = LazyReferenceField( - "Projects", required=True, passthrough=True, reverse_delete_rule=CASCADE - ) - identifier = StringField(required=True, help_text="material/composition identifier") - formula = StringField(help_text="formula (set dynamically if not provided)") - is_public = BooleanField( - required=True, default=True, help_text="public/private contribution" - ) - last_modified = DateTimeField( - required=True, default=datetime.utcnow, help_text="time of last modification" - ) - needs_build = BooleanField(default=True, help_text="needs notebook build?") - data = DictField( - default=dict, - validation=valid_dict, - pullout_key="display", - help_text="simple free-form data", - ) - structures = ListField( - ReferenceField("Structures", null=True), default=list, max_length=10 - ) - tables = ListField(ReferenceField("Tables", null=True), default=list, max_length=10) - attachments = ListField( - ReferenceField("Attachments", null=True), default=list, max_length=10 - ) - notebook = ReferenceField("Notebooks") - atlas = AtlasManager("formula_autocomplete") - meta = { - "collection": "contributions", - "indexes": [ - "project", - "identifier", - "formula", - "is_public", - "last_modified", - "needs_build", - "notebook", - {"fields": [(r"data.$**", 1)]}, - # can only use wildcardProjection option with wildcard index on all document fields - {"fields": [(r"$**", 1)], "wildcardProjection": {"project": 1}}, - ] - + list(COMPONENTS.keys()), - } - - @queryset_manager - def objects(doc_cls, queryset): - return queryset.no_dereference().only( - "project", - "identifier", - "formula", - "is_public", - "last_modified", - "needs_build", - ) - - @classmethod - def atlas_filter(cls, term): - try: - comp = Composition(term) - except Exception: - raise ValueError(f"{term} is not a valid composition") - - try: - for element in comp.elements: - Element(element) - except Exception: - raise ValueError(f"{element} not a valid element") - - ind_str = [] - - if len(comp) == 1: - d = comp.get_integer_formula_and_factor() - ind_str.append(d[0] + str(int(d[1])) if d[1] != 1 else d[0]) - else: - for i, j in comp.reduced_composition.items(): - ind_str.append(i.name + str(int(j)) if j != 1 else i.name) - - final_terms = ["".join(entry) for entry in permutations(ind_str)] - return AtlasQ(formula=final_terms[0]) # TODO formula__in=final_terms - - @classmethod - def post_init(cls, sender, document, **kwargs): - # replace existing components with according ObjectIds - for component, fields in COMPONENTS.items(): - lst = document._data.get(component) - if lst and lst[0].id is None: # id is None for incoming POST - resource = get_resource(component) - for i, o in enumerate(lst): - digest = get_md5(resource, o, fields) - objs = resource.document.objects(md5=digest) - exclude = list(resource.document._fields.keys()) - obj = objs.exclude(*exclude).only("id").first() - if obj: - lst[i] = obj.to_dbref() - - @classmethod - def pre_save_post_validation(cls, sender, document, **kwargs): - # set formula field - if hasattr(document, "formula") and not document.formula: - formulae = current_app.config["FORMULAE"] - document.formula = formulae.get(document.identifier, document.identifier) - - # project is LazyReferenceField & load columns due to custom queryset manager - project = document.project.fetch().reload("columns") - columns = {col.path: col for col in project.columns} - - # run data through Pint Quantities and save as dicts - def make_quantities(path, key, value): - key = key.strip() - if key in quantity_keys or not isinstance(value, (str, int, float)): - return key, value - - # can't be a quantity if contains 2+ spaces - str_value = str(value).strip() - if str_value.count(" ") > 1: - return key, value - - # don't parse if column.unit indicates string type - field = delimiter.join(["data"] + list(path) + [key]) - if field in columns: - if columns[field].unit == "NaN": - return key, str_value - - # parse as quantity - q = get_quantity(str_value) - if q is None or not q._magnitude: - return key, value - - # silently ignore "nan" - if isnan(q.magnitude.nominal_value): - return False - - # ensure that the same units are used across contributions - if field in columns: - column = columns[field] - if column.unit != str(q.value.units): - try: - qq = q.value.to(column.unit) - q = new_error_units(q, qq) - except DimensionalityError: - raise ValueError( - f"Can't convert [{q.units}] to [{column.unit}] for {field}!" - ) - else: - # try compact representation - qq = q.value.to_compact() - q = new_error_units(q, qq) - - # reduce dimensionality if possible - if not q.check(0): - qq = q.value.to_reduced_units() - q = new_error_units(q, qq) - - # significant digits - q = truncate_digits(q) - - # return new value dict - display = str(q.value) if isnan(q.magnitude.std_dev) else str(q) - value = { - "display": display, - "value": q.magnitude.nominal_value, - "error": q.magnitude.std_dev, - "unit": str(q.units), - } - return key, value - - document.data = remap(document.data, visit=make_quantities, enter=enter) - document.last_modified = datetime.utcnow() - document.needs_build = True - - @classmethod - def pre_delete(cls, sender, document, **kwargs): - args = list(COMPONENTS.keys()) - document.reload(*args) - - for component in COMPONENTS.keys(): - # check if other contributions exist before deletion - # and make sure component still exists (getattr converts ref to object) - for obj in getattr(document, component): - q = {component: obj.id} - if sender.objects(**q).count() < 2 and not isinstance(obj, DBRef): - obj.delete() - - -signals.post_init.connect(Contributions.post_init, sender=Contributions) -signals.pre_save_post_validation.connect( - Contributions.pre_save_post_validation, sender=Contributions -) -signals.pre_delete.connect(Contributions.pre_delete, sender=Contributions) diff --git a/mpcontribs-api/mpcontribs/api/contributions/formulae.json.gz b/mpcontribs-api/mpcontribs/api/contributions/formulae.json.gz deleted file mode 100644 index 5f6945aaa..000000000 --- a/mpcontribs-api/mpcontribs/api/contributions/formulae.json.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:358326e2613ac16500283f85c3cc3780567a568cc3efa5431bde7e50f1978135 -size 5418887 diff --git a/mpcontribs-api/mpcontribs/api/contributions/generate_formulae.py b/mpcontribs-api/mpcontribs/api/contributions/generate_formulae.py deleted file mode 100644 index f625ff27b..000000000 --- a/mpcontribs-api/mpcontribs/api/contributions/generate_formulae.py +++ /dev/null @@ -1,17 +0,0 @@ -# -*- coding: utf-8 -*- -import os -import json -from pymatgen.ext.matproj import MPRester - -data = {} - -with MPRester() as mpr: - for i, d in enumerate( - mpr.query(criteria={}, properties=["task_ids", "pretty_formula"]) - ): - for task_id in d["task_ids"]: - data[task_id] = d["pretty_formula"] - -out = os.path.join(os.path.dirname(__file__), "formulae.json") -with open(out, "w") as f: - json.dump(data, f) diff --git a/mpcontribs-api/mpcontribs/api/contributions/views.py b/mpcontribs-api/mpcontribs/api/contributions/views.py deleted file mode 100644 index 86bfb70b8..000000000 --- a/mpcontribs-api/mpcontribs/api/contributions/views.py +++ /dev/null @@ -1,227 +0,0 @@ -# -*- coding: utf-8 -*- -import re -import os -import flask_mongorest - -from itertools import permutations -from css_html_js_minify import html_minify -from json2html import Json2Html -from boltons.iterutils import remap -from werkzeug.exceptions import Unauthorized -from pymatgen.core.composition import Composition, CompositionError - -from flask import Blueprint, render_template, jsonify, abort, request -from flask_mongorest.resources import Resource -from flask_mongorest import operators as ops -from flask_mongorest.methods import ( - Fetch, - Delete, - Update, - BulkFetch, - BulkCreate, - BulkUpdate, - BulkDelete, - Download, -) -from flask_mongorest.exceptions import UnknownFieldError - -from mpcontribs.api import enter, FILTERS -from mpcontribs.api.core import SwaggerView -from mpcontribs.api.contributions.document import Contributions -from mpcontribs.api.structures.views import StructuresResource -from mpcontribs.api.tables.views import TablesResource -from mpcontribs.api.attachments.views import AttachmentsResource -from mpcontribs.api.notebooks.views import NotebooksResource - -templates = os.path.join(os.path.dirname(flask_mongorest.__file__), "templates") -contributions = Blueprint("contributions", __name__, template_folder=templates) -exclude = r'[^$.\s_~`^&(){}[\]\\;\'"/]' -j2h = Json2Html() -MAX_UNAPPROVED_CONTRIBS = 500 - - -def visit(path, key, value): - if isinstance(value, dict) and "display" in value: - return key, value["display"] - return True - - -class ContributionsResource(Resource): - document = Contributions - related_resources = { - "structures": StructuresResource, - "tables": TablesResource, - "attachments": AttachmentsResource, - "notebook": NotebooksResource, - } - save_related_fields = ["structures", "tables", "attachments", "notebook"] - filters = { - "id": [ops.In, ops.Exact], - "project": FILTERS["STRINGS"], - "identifier": FILTERS["STRINGS"], - "formula": FILTERS["STRINGS"], - "is_public": [ops.Boolean], - "last_modified": FILTERS["DATES"], - "needs_build": [ops.Boolean], - re.compile(r"^data__((?!__).)*$"): FILTERS["ALL"], - "structures": [ops.Size], - "tables": [ops.Size], - "attachments": [ops.Size], - } - fields = [ - "id", - "project", - "identifier", - "formula", - "is_public", - "last_modified", - "needs_build", - ] - allowed_ordering = [ - "id", - "project", - "identifier", - "formula", - "is_public", - "last_modified", - "needs_build", - re.compile(r"^data(__(" + exclude + ")+){1,4}$"), - ] - paginate = True - default_limit = 200 - max_limit = 1500 - download_formats = ["json", "csv"] - - @staticmethod - def get_optional_fields(): - return [ - "data", - "structures", - "tables", - "attachments", - "notebook", - "card_bootstrap", - "card_bulma", - ] - - def value_for_field(self, obj, field): - if field.startswith("card_"): - _, fmt = field.rsplit("_", 1) - if fmt not in ["bootstrap", "bulma"]: - raise UnknownFieldError - - if obj.project is None or not obj.data: - # try data reload to account for custom queryset manager - obj.reload("id", "project", "data") - - # obj.project is LazyReference & Projects uses custom queryset manager - DocType = obj.project.document_type - exclude = list(DocType._fields.keys()) - only = ["title", "references", "description", "authors"] - pk = obj.project.pk - project = DocType.objects.exclude(*exclude).only(*only).with_id(pk) - ctx = { - "cid": str(obj.id), - "title": project.title, - "references": project.references[:5], - "landing_page": f"/projects/{project.id}/", - "more": f"/contributions/{obj.id}", - } - ctx["descriptions"] = project.description.strip().split(".", 1) - authors = [a.strip() for a in project.authors.split(",") if a] - ctx["authors"] = {"main": authors[0], "etal": authors[1:]} - ctx["data"] = j2h.convert( - json=remap(obj.data, visit=visit, enter=enter), - table_attributes='class="table is-narrow is-fullwidth has-background-light"', - ) - return html_minify(render_template(f"card_{fmt}.html", **ctx)) - else: - raise UnknownFieldError - - -class ContributionsView(SwaggerView): - resource = ContributionsResource - methods = [ - Fetch, - Delete, - Update, - BulkFetch, - BulkCreate, - BulkUpdate, - BulkDelete, - Download, - ] - - def has_add_permission(self, req, obj): - # limit the number of contributions for unapproved projects - if not self.is_admin_or_project_user(req, obj): - return False - - if not obj.project.is_approved: - nr_contribs = Contributions.objects(project=obj.project.id).count() - if nr_contribs > MAX_UNAPPROVED_CONTRIBS: - msg = f"Reached {MAX_UNAPPROVED_CONTRIBS} for unapproved project {obj.project.id}." - msg += " Please reach out to contribs@materialsproject.org." - raise Unauthorized(f"Can't add {obj.identifier}: {msg}") - - query = dict(project=obj.project.id, identifier=obj.identifier) - if obj.project.unique_identifiers and Contributions.objects(**query).count(): - raise Unauthorized(f"{obj.identifier} already added for {obj.project.id}") - - return True - - -@contributions.route("/search") -def search(): - formula = request.args.get("formula") - if not formula: - abort(404, description="Missing formula param.") - - try: - comp = Composition(formula) - except (CompositionError, ValueError): - abort(400, description="Invalid formula provided.") - - ind_str = [] - - if len(comp) == 1: - d = comp.get_integer_formula_and_factor() - ind_str.append(d[0] + str(int(d[1])) if d[1] != 1 else d[0]) - else: - for i, j in comp.reduced_composition.items(): - ind_str.append(i.name + str(int(j)) if j != 1 else i.name) - - final_terms = ["".join(entry) for entry in permutations(ind_str)] - limit = request.args.get("limit", ContributionsResource.default_limit) - - pipeline = [ - { - "$search": { - "index": "formula_autocomplete", - "text": {"path": "formula", "query": final_terms}, - } - }, - {"$project": {"formula": 1, "length": {"$strLenCP": "$formula"}, "project": 1}}, - {"$match": {"length": {"$gte": len(final_terms[0])}}}, - {"$limit": limit}, - {"$sort": {"length": 1}}, - ] - - results = [] - - try: - for contrib in Contributions.objects().aggregate(pipeline, maxTimeMS=15000): - results.append( - { - "id": str(contrib["_id"]), - "formula": contrib["formula"], - "project": contrib["project"], - } - ) - except Exception: - abort( - 500, - description="Can't complete search. Please try a different formula or try again later.", - ) - - return jsonify(results) diff --git a/mpcontribs-api/mpcontribs/api/core.py b/mpcontribs-api/mpcontribs/api/core.py deleted file mode 100644 index ff24418d6..000000000 --- a/mpcontribs-api/mpcontribs/api/core.py +++ /dev/null @@ -1,644 +0,0 @@ -# -*- coding: utf-8 -*- -"""Custom meta-class and MethodView for Swagger""" - -import os -import logging -import yaml - -from copy import deepcopy -from re import Pattern -from importlib import import_module -from flasgger.marshmallow_apispec import SwaggerView as OriginalSwaggerView -from flasgger.marshmallow_apispec import schema2jsonschema -from marshmallow_mongoengine import ModelSchema -from flask_mongorest.views import ResourceView -from mongoengine.queryset import DoesNotExist -from mongoengine.queryset.visitor import Q -from werkzeug.exceptions import Unauthorized -from mpcontribs.api.config import DOC_DIR -from mpcontribs.api import is_gunicorn, get_logger - -logger = get_logger(__name__) - - -def get_limit_params(resource, method): - default = resource.default_limit - bulk = {"BulkUpdate", "BulkDelete"} - maximum = resource.bulk_update_limit if method in bulk else resource.max_limit - return [ - { - "name": "_skip", - "in": "query", - "type": "integer", - "description": "number of items to skip", - }, - { - "name": "_limit", - "in": "query", - "type": "integer", - "default": default, - "maximum": maximum, - "description": "maximum number of items to return", - }, - { - "name": "page", - "in": "query", - "type": "integer", - "description": "page number to return (in batches of `per_page/_limit`; alternative to `_skip`)", - }, - { - "name": "per_page", - "in": "query", - "type": "integer", - "default": default, - "maximum": maximum, - "description": "maximum number of items to return per page (same as `_limit`)", - }, - ] - - -def get_filter_params(name, filters): - filter_params = [] - is_pattern = isinstance(name, Pattern) - label = name.pattern if is_pattern else name - for op in filters: - if op.op == "exact" and not is_pattern: - name = label - description = f"filter {label}" - else: - suffix = op.suf if hasattr(op, "suf") else op.op - name = f"{label}__{suffix}" - description = f"filter {label} via ${op.op}" - - filter_params.append( - { - "name": name, - "in": "query", - "type": op.typ, - "description": description, - } - ) - if op.typ == "array": - filter_params[-1]["items"] = {"type": "string"} - if hasattr(op, "fmt"): - filter_params[-1]["format"] = op.fmt - - if op.allow_negation: - suffix = "not__" - suffix += op.suf if hasattr(op, "suf") else op.op - name = f"{label}__{suffix}" - description = f"filter {label} via ${op.op}" - param = deepcopy(filter_params[-1]) - param["name"] = name - param["description"] = description - filter_params.append(param) - - return filter_params - - -def get_specs(klass, method, collection): - method_name = method.__name__ if hasattr(method, "__name__") else method - default_response = { - "description": "Error", - "schema": {"type": "object", "properties": {"error": {"type": "string"}}}, - } - id_field = klass.resource.document._meta["id_field"].capitalize() - doc_name = collection[:-1].capitalize() - fields_param = None - if klass.resource.fields is not None: - fields_avail = ( - klass.resource.fields + klass.resource.get_optional_fields() + ["_all"] - ) - description = f"List of fields to include in response ({fields_avail})." - description += " Use dot-notation for nested subfields." - fields_param = { - "name": "_fields", - "in": "query", - "default": klass.resource.fields, - "type": "array", - "items": {"type": "string"}, - "description": description, - } - - field_pagination_params = [] - for field, limits in klass.resource.fields_to_paginate.items(): - field_pagination_params.append( - { - "name": f"{field}_page", - "in": "query", - "default": 1, - "type": "integer", - "description": f"page to retrieve for {field} field", - } - ) - field_pagination_params.append( - { - "name": f"{field}_per_page", - "in": "query", - "default": limits[0], - "maximum": limits[1], - "type": "integer", - "description": f"number of items to retrieve per page for {field} field", - } - ) - - filter_params = [] - if hasattr(klass.resource, "filters"): - for k, v in klass.resource.filters.items(): - filter_params += get_filter_params(k, v) - - order_params = [] - if klass.resource.allowed_ordering: - allowed_ordering = [ - o.pattern if isinstance(o, Pattern) else o - for o in klass.resource.allowed_ordering - ] - order_params = [ - { - "name": "_sort", - "in": "query", - "type": "string", - "description": f"sort {collection} via {allowed_ordering}. Prepend +/- for asc/desc.", - } - ] - - spec = None - if method_name == "Fetch": - params = [ - { - "name": "pk", - "in": "path", - "type": "string", - "required": True, - "description": f"{collection[:-1]} (primary key)", - } - ] - if fields_param is not None: - params.append(fields_param) - params += field_pagination_params - spec = { - "summary": f"Retrieve a {collection[:-1]}.", - "operationId": f"get{doc_name}By{id_field}", - "parameters": params, - "responses": { - 200: { - "description": f"single {collection} entry", - "schema": {"$ref": f"#/definitions/{klass.schema_name}"}, - }, - "default": default_response, - }, - } - - elif method_name == "BulkFetch": - params = [fields_param] if fields_param is not None else [] - params += field_pagination_params - params += order_params - params += filter_params - schema_props = { - "data": { - "type": "array", - "items": {"$ref": f"#/definitions/{klass.schema_name}"}, - } - } - if klass.resource.paginate: - schema_props["has_more"] = {"type": "boolean"} - schema_props["total_count"] = {"type": "integer"} - schema_props["total_pages"] = {"type": "integer"} - params += get_limit_params(klass.resource, method_name) - spec = { - "summary": f"Filter and retrieve {collection}.", - "operationId": f"query{doc_name}s", - "parameters": params, - "responses": { - 200: { - "description": f"list of {collection}", - "schema": {"type": "object", "properties": schema_props}, - }, - "default": default_response, - }, - } - - elif method_name == "Download": - params = [ - { - "name": "short_mime", - "in": "path", - "type": "string", - "required": True, - "description": "MIME Download Type: gz", - "default": "gz", - }, - { - "name": "format", - "in": "query", - "type": "string", - "required": True, - "description": f"download {collection} in different formats: {klass.resource.download_formats}", - }, - ] - params += [fields_param] if fields_param is not None else [] - params += order_params - params += filter_params - if klass.resource.paginate: - params += get_limit_params(klass.resource, method_name) - spec = { - "summary": f"Filter and download {collection}.", - "operationId": f"download{doc_name}s", - "parameters": params, - "produces": ["application/gzip"], - "responses": { - 200: { - "description": f"{collection} download", - "schema": {"type": "file"}, - }, - "default": default_response, - }, - } - - elif method_name == "Create": - spec = { - "summary": f"Create a new {collection[:-1]}.", - "operationId": f"create{doc_name}", - "parameters": [ - { - "name": f"{collection[:-1]}", - "in": "body", - "description": f"The object to use for {collection[:-1]} creation", - "schema": {"$ref": f"#/definitions/{klass.schema_name}"}, - } - ], - "responses": { - 200: { - "description": f"{collection[:-1]} created", - "schema": {"$ref": f"#/definitions/{klass.schema_name}"}, - }, - "default": default_response, - }, - } - - elif method_name == "BulkCreate": - spec = { - "summary": f"Create new {collection[:-1]}(s).", - "operationId": f"create{doc_name}s", - "parameters": [ - { - "name": f"{collection}", - "in": "body", - "description": f"The objects to use for {collection[:-1]} creation", - "schema": { - "type": "array", - "items": {"$ref": f"#/definitions/{klass.schema_name}"}, - }, - } - ], - "responses": { - 200: { - "description": f"{collection} created", - "schema": { - "type": "object", - "properties": { - "count": {"type": "integer"}, - "data": { - "type": "array", - "items": {"$ref": f"#/definitions/{klass.schema_name}"}, - }, - }, - }, - }, - "default": default_response, - }, - } - - elif method_name == "Update": - spec = { - "summary": f"Update a {collection[:-1]}.", - "operationId": f"update{doc_name}By{id_field}", - "parameters": [ - { - "name": "pk", - "in": "path", - "type": "string", - "required": True, - "description": f"The {collection[:-1]} (primary key) to update", - }, - { - "name": f"{collection[:-1]}", - "in": "body", - "description": f"The object to use for {collection[:-1]} update", - "schema": {"type": "object"}, - }, - ], - "responses": { - 200: { - "description": f"{collection[:-1]} updated", - "schema": {"$ref": f"#/definitions/{klass.schema_name}"}, - }, - "default": default_response, - }, - } - elif method_name == "BulkUpdate": - params = filter_params - params.append( - { - "name": f"{collection}", - "in": "body", - "description": f"The object to use for {collection} bulk update", - "schema": {"type": "object"}, - } - ) - schema_props = {"count": {"type": "integer"}} - if klass.resource.paginate: - schema_props["has_more"] = {"type": "boolean"} - schema_props["total_count"] = {"type": "integer"} - schema_props["total_pages"] = {"type": "integer"} - params += get_limit_params(klass.resource, method_name) - spec = { - "summary": f"Filter and update {collection}.", - "operationId": f"update{doc_name}s", - "parameters": params, - "responses": { - 200: { - "description": f"Number of {collection} updated", - "schema": {"type": "object", "properties": schema_props}, - }, - "default": default_response, - }, - } - - elif method_name == "BulkDelete": - params = filter_params - schema_props = {"count": {"type": "integer"}} - if klass.resource.paginate: - schema_props["has_more"] = {"type": "boolean"} - schema_props["total_count"] = {"type": "integer"} - schema_props["total_pages"] = {"type": "integer"} - params += get_limit_params(klass.resource, method_name) - spec = { - "summary": f"Filter and delete {collection}.", - "operationId": f"delete{doc_name}s", - "parameters": params, - "responses": { - 200: { - "description": f"Number of {collection} deleted", - "schema": {"type": "object", "properties": schema_props}, - }, - "default": default_response, - }, - } - - elif method_name == "Delete": - spec = { - "summary": f"Delete a {collection[:-1]}.", - "operationId": f"delete{doc_name}By{id_field}", - "parameters": [ - { - "name": "pk", - "in": "path", - "type": "string", - "required": True, - "description": f"The {collection[:-1]} (primary key) to delete", - } - ], - "responses": { - 200: {"description": f"{collection[:-1]} deleted"}, - "default": default_response, - }, - } - - return spec - - -class SwaggerView(OriginalSwaggerView, ResourceView): - """A class-based view defining additional methods""" - - def __init_subclass__(cls, **kwargs): - """initialize Schema, decorators, definitions, and tags""" - super().__init_subclass__(**kwargs) - - if not __name__ == cls.__module__: - # e.g.: cls.__module__ = mpcontribs.api.projects.views - views_path = cls.__module__.split(".") - doc_path = ".".join(views_path[:-1] + ["document"]) - cls.tags = [views_path[-2]] - doc_filepath = doc_path.replace(".", os.sep) + ".py" - if os.path.exists(doc_filepath): - cls.doc_name = cls.tags[0].capitalize() - Model = getattr(import_module(doc_path), cls.doc_name) - cls.schema_name = cls.doc_name + "Schema" - cls.Schema = type( - cls.schema_name, - (ModelSchema, object), - { - "Meta": type( - "Meta", - (object,), - dict(model=Model, ordered=True, model_build_obj=False), - ) - }, - ) - cls.definitions = {cls.schema_name: schema2jsonschema(cls.Schema)} - cls.resource.schema = cls.Schema - - # write flask-mongorest swagger specs - for method in cls.methods: - spec = get_specs(cls, method, cls.tags[0]) - if spec: - dir_path = os.path.join(DOC_DIR, cls.tags[0]) - file_path = os.path.join(dir_path, method.__name__ + ".yml") - if not os.path.exists(file_path): - os.makedirs(dir_path, exist_ok=True) - - if is_gunicorn: - with open(file_path, "w") as f: - yaml.dump(spec, f) - logger.debug( - f"{cls.tags[0]}.{method.__name__} written to {file_path}" - ) - - def get_groups(self, request): - groups = request.headers.get("X-Authenticated-Groups", "").split(",") - groups += request.headers.get("X-Consumer-Groups", "").split(",") - return set(grp.strip() for grp in groups if grp) - - def is_anonymous(self, request): - if not request.headers.get("X-Consumer-Username", ""): - return True - - is_anonymous = request.headers.get("X-Anonymous-Consumer", False) - if isinstance(is_anonymous, str): - is_anonymous = False if is_anonymous == "false" else True - - return is_anonymous - - def is_external(self, request): - return request.headers.get( - "X-Forwarded-Host" - ) is not None and not request.headers.get("Origin") - - def is_admin(self, request): - groups = self.get_groups(request) - admin_group = os.environ.get("ADMIN_GROUP", "admin") - return admin_group in groups - - def is_project_user(self, request, obj): - if hasattr(obj, "owner"): - owner = obj.owner - project = obj.name - elif hasattr(obj, "project"): - owner = obj.project.owner - project = obj.project.name - else: - raise Unauthorized(f"Unable to authorize {obj}") - - groups = self.get_groups(request) - username = request.headers.get("X-Consumer-Username") - return project in groups or owner == username - - def is_admin_or_project_user(self, request, obj): - if self.is_anonymous(request): - return False - - if self.is_admin(request): - return True - - return self.is_project_user(request, obj) - - def get_projects(self): - # project is LazyReferenceFields (multiple queries) - module = import_module("mpcontribs.api.projects.document") - Projects = getattr(module, "Projects") - exclude = list(Projects._fields.keys()) - only = ["name", "owner", "is_public", "is_approved"] - return Projects.objects.exclude(*exclude).only(*only) - - def get_projects_filter(self, username, groups, filter_names=None): - projects = self.get_projects() - if filter_names: - projects = projects.filter(name__in=filter_names) - - q = {"private": [], "public": []} - - for project in projects: - if project.owner == username or project.name in groups: - q["private"].append(project.name) - elif project.is_public and project.is_approved: - q["public"].append(project.name) - - # reduced query - qfilter = Q() - if q["private"]: - qfilter |= Q(project__in=q["private"]) - if q["public"]: - qfilter |= Q(project__in=q["public"], is_public=True) - - return qfilter - - def has_read_permission(self, request, qs): - if self.is_admin(request): - return qs # admins can read all entries - - groups = self.get_groups(request) - is_anonymous = self.is_anonymous(request) - is_external = self.is_external(request) - username = request.headers.get("X-Consumer-Username") - approved_public_filter = Q(is_public=True, is_approved=True) - - if request.path.startswith("/projects/"): - # external or internal requests can both read full project info - # anonymous requests can only read public approved projects - if is_anonymous: - return qs.filter(approved_public_filter) - - # authenticated requests can read approved public or accessible non-public projects - qfilter = approved_public_filter | Q(owner=username) - if groups: - qfilter |= Q(name__in=list(groups)) - - return qs.filter(qfilter) - else: - # contributions are set private/public independent from projects - # anonymous requests: - # - external: only meta-data of public contributions in approved public projects - # - internal: full public contributions in approved public projects - # authenticated requests: - # - private contributions in a public project are only accessible to owner/group - # - any contributions in a private project are only accessible to owner/group - component = request.path.split("/")[1] - - if component == "contributions": - q = qs._query - if is_anonymous and is_external: - qs = qs.exclude("data") - - if q and "project" in q and isinstance(q["project"], str): - projects = self.get_projects() - try: - project = projects.get(name=q["project"]) - except DoesNotExist: - return qs.none() - - if project.owner == username or project.name in groups: - return qs - elif project.is_public and project.is_approved: - return qs.filter(is_public=True) - else: - return qs.none() - else: - names = None - if q and "project" in q and "$in" in q["project"]: - names = q.pop("project").pop("$in") - - qfilter = self.get_projects_filter( - username, groups, filter_names=names - ) - return qs.filter(qfilter) - else: - # get component Object IDs for queryset - pk = request.view_args.get("pk") - from mpcontribs.api.contributions.document import get_resource - - resource = get_resource(component) - qfilter = lambda qs: qs.clone() - - if pk: - ids = [resource.get_object(pk, qfilter=qfilter).id] - else: - ids = [o.id for o in resource.get_objects(qfilter=qfilter)[0]] - - if not ids: - return qs.none() - - # get list of readable contributions and their component Object IDs - module = import_module("mpcontribs.api.contributions.document") - Contributions = getattr(module, "Contributions") - qfilter = self.get_projects_filter(username, groups) - component = component[:-1] if component == "notebooks" else component - qfilter &= Q(**{f"{component}__in": ids}) - contribs = Contributions.objects(qfilter).only(component).limit(len(ids)) - # return new queryset using "ids__in" - readable_ids = [ - getattr(contrib, component).id for contrib in contribs - ] if component == "notebook" else [ - dbref.id for contrib in contribs - for dbref in getattr(contrib, component) - if dbref.id in ids - ] - if not readable_ids: - return qs.none() - - qs._query_obj = Q(id__in=readable_ids) - # exclude optional fields if anonymous external request - if is_anonymous and is_external: - exclude = resource.get_optional_fields() - qs = qs.exclude(*exclude) - - return qs - - def has_add_permission(self, request, obj): - return self.is_admin_or_project_user(request, obj) - - def has_change_permission(self, request, obj): - return self.is_admin_or_project_user(request, obj) - - def has_delete_permission(self, request, obj): - return self.is_admin_or_project_user(request, obj) diff --git a/mpcontribs-api/mpcontribs/api/dashboard.cfg b/mpcontribs-api/mpcontribs/api/dashboard.cfg deleted file mode 100644 index ef84c4716..000000000 --- a/mpcontribs-api/mpcontribs/api/dashboard.cfg +++ /dev/null @@ -1,7 +0,0 @@ -[dashboard] -SAMPLING_PERIOD=20 -MONITOR_LEVEL=3 -ENABLE_LOGGING=True - -[visualization] -TIMEZONE=America/New_York diff --git a/mpcontribs-api/mpcontribs/api/notebooks/__init__.py b/mpcontribs-api/mpcontribs/api/notebooks/__init__.py deleted file mode 100644 index 2db2955a6..000000000 --- a/mpcontribs-api/mpcontribs/api/notebooks/__init__.py +++ /dev/null @@ -1,65 +0,0 @@ -# -*- coding: utf-8 -*- -from uuid import uuid1 -from flask import current_app -from tornado.escape import json_encode, json_decode -from mpcontribs.api import create_kernel_connection, get_logger - -logger = get_logger(__name__) - - -def run_cells(kernel_id, cid, cells): - logger.debug(f"running {cid} on {kernel_id}") - ws = create_kernel_connection(kernel_id) - outputs = {} - - for idx, cell in enumerate(cells): - if cell["cell_type"] == "code": - ws.send( - json_encode( - { - "header": { - "username": cid, - "version": "5.3", - "session": "", - "msg_id": f"{cid}-{idx}-{uuid1()}", - "msg_type": "execute_request", - }, - "parent_header": {}, - "channel": "shell", - "content": { - "code": cell["source"], - "silent": False, - "store_history": False, - "user_expressions": {}, - "allow_stdin": False, - "stop_on_error": True, - }, - "metadata": {}, - "buffers": [], - } - ) - ) - - outputs[idx] = [] - status = None - while status is None or status == "busy" or not len(outputs[idx]): - msg = ws.recv() - msg = json_decode(msg) - msg_type = msg["msg_type"] - if msg_type == "status": - status = msg["content"]["execution_state"] - elif msg_type in ["stream", "display_data", "execute_result"]: - # display_data/execute_result required fields: - # "output_type", "data", "metadata" - # stream required fields: "output_type", "name", "text" - output = msg["content"] - output.pop("transient", None) - output["output_type"] = msg_type - msg_idx = msg["parent_header"]["msg_id"].split("-")[1] - outputs[int(msg_idx)].append(output) - elif msg_type == "error": - tb = msg["content"]["traceback"] - raise ValueError(tb) - - ws.close() - return outputs diff --git a/mpcontribs-api/mpcontribs/api/notebooks/document.py b/mpcontribs-api/mpcontribs/api/notebooks/document.py deleted file mode 100644 index 37615c786..000000000 --- a/mpcontribs-api/mpcontribs/api/notebooks/document.py +++ /dev/null @@ -1,115 +0,0 @@ -# -*- coding: utf-8 -*- -import os -import boto3 -import hashlib - -from io import BytesIO -from mongoengine import signals -from base64 import b64decode, b64encode -from flask_mongoengine.documents import Document -from mongoengine.fields import DictField, StringField, IntField, ListField -from mongoengine.queryset.manager import queryset_manager - -BUCKET = os.environ.get("S3_IMAGES_BUCKET", "mpcontribs-images") -S3_DOWNLOAD_URL = f"https://{BUCKET}.s3.amazonaws.com" -s3_client = boto3.client("s3") - - -class Kernelspec(DictField): - name = StringField(required=True, default="python3") - display_name = StringField(required=True, default="Python 3") - language = StringField() - - -class CodemirrorMode(DictField): - name = StringField(required=True, default="ipython") - version = IntField(required=True, default=3) - - -class LanguageInfo(DictField): - name = StringField(required=True, default="python") - file_extension = StringField() - mimetype = StringField() - nbconvert_exporter = StringField() - pygments_lexer = StringField() - version = StringField() - codemirror_mode = DictField( - CodemirrorMode(), default=CodemirrorMode, help_text="codemirror" - ) - - -class Metadata(DictField): - kernelspec = DictField( - Kernelspec(), required=True, help_text="kernelspec", default=Kernelspec - ) - language_info = DictField( - LanguageInfo(), required=True, help_text="language info", default=LanguageInfo - ) - - -class Cell(DictField): - cell_type = StringField(required=True, default="code", help_text="cell type") - metadata = DictField(help_text="cell metadata") - source = StringField(required=True, default="print('hello')", help_text="source") - outputs = ListField( - DictField(), required=True, help_text="outputs", default=lambda: [DictField()] - ) - execution_count = IntField(help_text="exec count") - - -class Notebooks(Document): - nbformat = IntField(default=4, help_text="nbformat version") - nbformat_minor = IntField(default=4, help_text="nbformat minor version") - metadata = DictField(Metadata(), help_text="notebook metadata") - cells = ListField(Cell(), max_length=30, help_text="cells") - meta = {"collection": "notebooks"} - - problem_key = "application/vnd.plotly.v1+json" - escaped_key = problem_key.replace(".", "~dot~") - - @queryset_manager - def objects(doc_cls, queryset): - return queryset.only("nbformat", "nbformat_minor") - - @classmethod - def post_init(cls, sender, document, **kwargs): - if document.id: - document.transform(incoming=False) - - def transform(self, incoming=True): - if incoming: - old_key = self.problem_key - new_key = self.escaped_key - else: - old_key = self.escaped_key - new_key = self.problem_key - - for cell in self.cells: - for output in cell.get("outputs", []): - data = output.get("data", {}) - if old_key in data: - output["data"][new_key] = output["data"].pop(old_key) - - if "image/png" in data: - if incoming: - contents = data.pop("image/png") # base64 encoded - key = hashlib.sha1(contents.encode("utf-8")).hexdigest() - s3_client.put_object( - Bucket=BUCKET, - Key=key, - ContentType="image/png", - Body=b64decode(contents), - ) - data["image/png"] = key - elif len(data["image/png"]) == 40: - key = data.pop("image/png") - # TODO catch key doesn't exist - retr = s3_client.get_object(Bucket=BUCKET, Key=key) - gzip_buffer = BytesIO(retr["Body"].read()) - data["image/png"] = b64encode(gzip_buffer.getvalue()).decode() - - def clean(self): - self.transform() - - -signals.post_init.connect(Notebooks.post_init, sender=Notebooks) diff --git a/mpcontribs-api/mpcontribs/api/notebooks/views.py b/mpcontribs-api/mpcontribs/api/notebooks/views.py deleted file mode 100644 index e3bf88af8..000000000 --- a/mpcontribs-api/mpcontribs/api/notebooks/views.py +++ /dev/null @@ -1,293 +0,0 @@ -# -*- coding: utf-8 -*- -import os -import time -import requests -import flask_mongorest - -from rq import get_current_job -from rq.job import Job -from gevent import sleep -from nbformat import v4 as nbf -from flask_rq2 import RQ -from flask import Blueprint, request, abort, jsonify, current_app -from flask_mongorest import operators as ops -from flask_mongorest.methods import Fetch, BulkFetch -from flask_mongorest.resources import Resource -from mongoengine.errors import DoesNotExist -from mongoengine.queryset.visitor import Q - -from mpcontribs.api import get_kernel_endpoint, get_logger -from mpcontribs.api.core import SwaggerView -from mpcontribs.api.contributions.document import Contributions -from mpcontribs.api.notebooks.document import Notebooks -from mpcontribs.api.notebooks import run_cells - - -logger = get_logger(__name__) -templates = os.path.join(os.path.dirname(flask_mongorest.__file__), "templates") -notebooks = Blueprint("notebooks", __name__, template_folder=templates) - -MPCONTRIBS_API_HOST = os.environ.get("MPCONTRIBS_API_HOST", "default") -ADMIN_GROUP = os.environ.get("ADMIN_GROUP", "admin") - -rq = RQ() -rq.default_queue = f"notebooks_{MPCONTRIBS_API_HOST}" -rq.queues = [rq.default_queue] - - -class NotebooksResource(Resource): - document = Notebooks - filters = {"id": [ops.In, ops.Exact]} - fields = ["id", "nbformat", "nbformat_minor"] - paginate = True - default_limit = 10 - max_limit = 100 - - @staticmethod - def get_optional_fields(): - return ["metadata", "cells"] - - -class NotebooksView(SwaggerView): - resource = NotebooksResource - methods = [Fetch, BulkFetch] - - -def execute_cells(cid, cells): - ntries = 0 - while ntries < 5: - for kernel_id, running_cid in current_app.kernels.items(): - if running_cid is None: - current_app.kernels[kernel_id] = cid - try: - outputs = run_cells(kernel_id, cid, cells) - except: - current_app.kernels[kernel_id] = None - raise - - current_app.kernels[kernel_id] = None - return outputs - else: - logger.warning(f"{kernel_id} busy with {running_cid}") - - logger.warning("WAITING for a kernel to become available") - sleep(5) - ntries += 1 - - -@notebooks.route("/build") -def build(): - if not getattr(current_app, "kernels", None): - abort(404, description="No kernels available.") - - cids = request.args.get("cids") - projects = request.args.get("projects") - force = bool(request.args.get("force", 0)) - kwargs = dict(force=force) - - if projects: - kwargs["projects"] = projects.split(",") - - if cids: - kwargs["cids"] = cids.split(",") - - if len(kwargs.get("cids", [])) == 1: - return jsonify(make(**kwargs)) - - job = make.queue(**kwargs) - return job.id - - -def restart_kernels(): - """use to avoid run-away memory""" - kernel_ids = [k for k, v in current_app.kernels.items() if v is None] - - for kernel_id in kernel_ids: - kernel_url = get_kernel_endpoint(kernel_id) + "/restart" - requests.post(kernel_url, json={}) - cells = [nbf.new_code_cell("\n".join([ - "from mpcontribs.client import Client", - "print('client imported')" - ]))] - run_cells(kernel_id, "import_client", cells) - - -@notebooks.route('/result', defaults={'job_id': None}) -@notebooks.route("/result/") -def result(job_id): - if not current_app.kernels: - abort(404, description="No kernels available.") - - if not job_id: - job_id = f"cron-{current_app.cron_job_id}" - - try: - job = Job.fetch(job_id, connection=rq.connection) - except Exception as exception: - abort(404, description=exception) - - if not job.is_finished: - return job.get_status() - elif not job.result: - description = f"No result for job_id {job.id} (exc: {job.exc_info})." - abort(404, description=description) - - return jsonify(job.result) - - -@rq.job() -def make(projects=None, cids=None, force=False): - """build the notebook / details page""" - start = time.perf_counter() - remaining_time = rq.default_timeout - 5 - mask = ["id", "needs_build", "notebook"] - query = Q() - - if projects: - query &= Q(project__in=projects) - if cids: - query &= Q(id__in=cids) - if not force: - query &= Q(needs_build=True) | Q(needs_build__exists=False) - - job = get_current_job() - ret = {"input": {"projects": projects, "cids": cids, "force": force}} - if job: - ret["job"] = { - "id": job.id, - "enqueued_at": job.enqueued_at.isoformat(), - "started_at": job.started_at.isoformat() - } - - exclude = list(Contributions._fields.keys()) - documents = Contributions.objects(query).exclude(*exclude).only(*mask) - total = documents.count() - count = 0 - - for idx, document in enumerate(documents): - stop = time.perf_counter() - remaining_time -= stop - start - - if remaining_time < 0: - if job: - restart_kernels() - - ret["result"] = {"status": "TIMEOUT", "count": count, "total": total} - return ret - - start = time.perf_counter() - - if not force and document.notebook and \ - not getattr(document, "needs_build", True): - continue - - if document.notebook: - try: - nb = Notebooks.objects.get(id=document.notebook.id) - nb.delete() - document.update(unset__notebook="") - logger.debug(f"Notebook {document.notebook.id} deleted.") - except DoesNotExist: - pass - - cid = str(document.id) - logger.debug(f"prep notebook for {cid} ...") - document.reload("tables", "structures", "attachments") - - cells = [ - # define client only once in kernel - # avoids API calls for regex expansion for query parameters - nbf.new_code_cell("\n".join([ - "if 'client' not in locals():", - "\tclient = Client(", - f'\t\theaders={{"X-Authenticated-Groups": "{ADMIN_GROUP}"}},', - f'\t\thost="{MPCONTRIBS_API_HOST}"', - "\t)", - "print(client.get_totals())", - # return something. See while loop in `run_cells` - ])), - nbf.new_code_cell("\n".join([ - f'c = client.get_contribution("{document.id}")', - 'c.display()' - ])), - ] - - if document.tables: - cells.append(nbf.new_markdown_cell("## Tables")) - for table in document.tables: - cells.append( - nbf.new_code_cell("\n".join([ - f't = client.get_table("{table.id}")', - 't.display()' - ])) - ) - - if document.structures: - cells.append(nbf.new_markdown_cell("## Structures")) - for structure in document.structures: - cells.append( - nbf.new_code_cell("\n".join([ - f's = client.get_structure("{structure.id}")', - 's.display()' - ])) - ) - - if document.attachments: - cells.append(nbf.new_markdown_cell("## Attachments")) - for attachment in document.attachments: - cells.append( - nbf.new_code_cell("\n".join([ - f'a = client.get_attachment("{attachment.id}")', - 'a.info()' - ])) - ) - - try: - outputs = execute_cells(cid, cells) - except Exception as e: - if job: - restart_kernels() - - ret["result"] = { - "status": "ERROR", "cid": cid, "count": count, "total": total, "exc": str(e) - } - return ret - - if not outputs: - if job: - restart_kernels() - - ret["result"] = { - "status": "ERROR: NO OUTPUTS", "cid": cid, "count": count, "total": total - } - return ret - - for idx, output in outputs.items(): - cells[idx]["outputs"] = output - - doc = nbf.new_notebook() - doc["cells"] = [ - nbf.new_code_cell("from mpcontribs.client import Client"), - nbf.new_code_cell(f'client = Client()'), - ] - doc["cells"] += cells[1:] # skip localhost Client - - try: - nb = Notebooks(**doc).save() - document.update(notebook=nb, needs_build=False) - except Exception as e: - if job: - restart_kernels() - - ret["result"] = { - "status": "ERROR", "cid": cid, "count": count, "total": total, "exc": str(e) - } - return ret - - count += 1 - - if total and job: - restart_kernels() - - ret["result"] = {"status": "COMPLETED", "count": count, "total": total} - return ret diff --git a/mpcontribs-api/mpcontribs/api/projects/document.py b/mpcontribs-api/mpcontribs/api/projects/document.py deleted file mode 100644 index e172e924b..000000000 --- a/mpcontribs-api/mpcontribs/api/projects/document.py +++ /dev/null @@ -1,387 +0,0 @@ -# -*- coding: utf-8 -*- -import urllib - -from math import isnan -from atlasq import AtlasManager, AtlasQ -from flatten_dict import flatten -from boltons.iterutils import remap -from collections import ChainMap -from flask import current_app, render_template, url_for, request -from mongoengine import Document -from marshmallow import ValidationError -from marshmallow.fields import String -from marshmallow.validate import Email as EmailValidator -from marshmallow_mongoengine.conversion import params -from marshmallow_mongoengine.conversion.fields import register_field -from mongoengine import EmbeddedDocument, signals -from mongoengine.queryset.manager import queryset_manager -from mongoengine.fields import ( - StringField, - BooleanField, - DictField, - URLField, - EmailField, - DecimalField, - FloatField, - IntField, - EmbeddedDocumentListField, - EmbeddedDocumentField, -) -from mpcontribs.api import send_email, valid_key, valid_dict, delimiter, enter - -PROVIDERS = {"github", "google", "facebook", "microsoft", "amazon", "portier"} -MAX_COLUMNS = 160 - - -def visit(path, key, value): - from mpcontribs.api.contributions.document import quantity_keys - - # pull out units - if isinstance(value, dict) and "unit" in value: - return key, value["unit"] - elif isinstance(value, (str, bool)) and key not in quantity_keys: - return key, None - - return True - - -class ProviderEmailField(EmailField): - """Field to validate usernames of format :""" - - def validate(self, value): - if value.count(":") != 1: - self.error(self.error_msg % value) - - provider, email = value.split(":", 1) - - if provider not in PROVIDERS: - self.error("{} {}".format(self.error_msg % value, "(invalid provider)")) - - super().validate(email) - - -class ProviderEmailValidator(EmailValidator): - def __call__(self, value): - message = self._format_error(value) - - if value.count(":") != 1: - raise ValidationError(message) - - provider, email = value.split(":", 1) - - if provider not in PROVIDERS: - raise ValidationError(message) - - super().__call__(email) - return value - - -class ProviderEmail(String): - def __init__(self, *args, **kwargs): - super().__init__(*args, **kwargs) - validator = ProviderEmailValidator(error="Not a valid MP username ({input}).") - self.validators.insert(0, validator) - - -def dict_wo_nans(d): - return {k: v for k, v in d.items() if k in ["min", "max"] and not isnan(v)} - - -class Column(EmbeddedDocument): - path = StringField(required=True, help_text="column path in dot-notation") - min = FloatField(required=True, default=float("nan"), help_text="column minimum") - max = FloatField(required=True, default=float("nan"), help_text="column maximum") - unit = StringField(required=True, default="NaN", help_text="column unit") - - def __eq__(self, other): - if isinstance(other, self.__class__): - return dict_wo_nans(self._data) == dict_wo_nans(other._data) - return False - - -class Reference(EmbeddedDocument): - label = StringField( - required=True, - min_length=3, - max_length=20, - help_text="label", - validation=valid_key, - ) - url = URLField(required=True, help_text="URL") - - -class Stats(EmbeddedDocument): - columns = IntField(required=True, default=0, help_text="#columns") - contributions = IntField(required=True, default=0, help_text="#contributions") - tables = IntField(required=True, default=0, help_text="#tables") - structures = IntField(required=True, default=0, help_text="#structures") - attachments = IntField(required=True, default=0, help_text="#attachments") - size = DecimalField(required=True, default=0, precision=1, help_text="size in MB") - - -class Projects(Document): - __project_regex__ = "^[a-zA-Z0-9_]{3,31}$" - name = StringField( - min_length=3, - max_length=30, - regex=__project_regex__, - primary_key=True, - help_text=f"project name/slug (valid format: `{__project_regex__}`)", - ) - is_public = BooleanField( - required=True, default=False, help_text="public/private project" - ) - title = StringField( - min_length=5, - max_length=30, - required=True, - unique=True, - help_text="short title for the project/dataset", - ) - long_title = StringField( - min_length=5, - max_length=55, - help_text="optional full title for the project/dataset", - ) - authors = StringField( - required=True, - help_text="comma-separated list of authors", - # TODO change to EmbeddedDocumentListField - ) - description = StringField( - min_length=5, - max_length=2000, - required=True, - help_text="brief description of the project", - ) - references = EmbeddedDocumentListField( - Reference, - required=True, - min_length=1, - max_length=20, - help_text="list of references", - ) - license = StringField( - choices=["CCA4", "CCPD"], - default="CCA4", - required=True, - help_text="license (see https://materialsproject.org/about/terms)", - ) - other = DictField(validation=valid_dict, null=True, help_text="other information") - owner = ProviderEmailField( - unique_with="name", help_text="owner / corresponding email" - ) - is_approved = BooleanField( - required=True, default=False, help_text="project approved?" - ) - unique_identifiers = BooleanField( - required=True, default=True, help_text="identifiers unique?" - ) - columns = EmbeddedDocumentListField(Column, max_length=MAX_COLUMNS) - stats = EmbeddedDocumentField(Stats, required=True, default=Stats) - atlas = AtlasManager("mpcontribs-dev-project-search") - meta = { - "collection": "projects", - "indexes": ["is_public", "title", "owner", "is_approved", "unique_identifiers"], - } - - @queryset_manager - def objects(doc_cls, queryset): - return queryset.only( - "name", "is_public", "title", "owner", "is_approved", "unique_identifiers" - ) - - @classmethod - def atlas_filter(cls, term): - # NOTE dynamic index, use `name` as placeholder for wildcard path - return AtlasQ(name=term) - - @classmethod - def post_save(cls, sender, document, **kwargs): - admin_email = current_app.config["MAIL_DEFAULT_SENDER"] - scheme = "http" if current_app.config["DEBUG"] else "https" - - if kwargs.get("created"): - ts = current_app.config["USTS"] - email_project = [document.owner, document.name] - token = ts.dumps(email_project) - link = url_for( - "projects.applications", token=token, _scheme=scheme, _external=True - ) - url = url_for( - "projectsFetch", pk=document.name, _scheme=scheme, _external=True - ) - url += "?_fields=_all" - html = render_template("admin_email.html", url=url, link=link) - send_email(admin_email, f'New project "{document.name}"', html) - else: - delta_set, delta_unset = document._delta() - - if "is_approved" in delta_set and document.is_approved: - subject = f'Your project "{document.name}" has been approved' - netloc = urllib.parse.urlparse(request.url).netloc.replace("-api", "") - portal = f"{scheme}://{netloc}" - html = render_template( - "owner_email.html", - approved=True, - admin_email=admin_email, - host=portal, - project=document.name, - ) - owner_email = document.owner.split(":", 1)[1] - send_email(owner_email, subject, html) - - if ( - "columns" in delta_set - or "columns" in delta_unset - or (not delta_set and not delta_unset) - ): - from mpcontribs.api.contributions.document import ( - Contributions, - COMPONENTS, - ) - - columns = {} - ncontribs = Contributions.objects(project=document.id).count() - - if "columns" in delta_set: - # document.columns updated by the user as intended - for col in document.columns: - columns[col.path] = col - elif "columns" in delta_unset or ncontribs: - # document.columns unset by user to reinit all columns from DB - # -> get paths and units across all contributions from DB - pipeline = [ - {"$match": {"project": document.id}}, - {"$sample": {"size": 1000}}, - {"$project": {"data": 1}}, - ] - result = Contributions.objects.aggregate(pipeline) - merged = ChainMap(*result) - flat = flatten( - remap(merged, visit=visit, enter=enter), reducer="dot" - ) - - for k, v in flat.items(): - if k.startswith("data."): - columns[k] = Column(path=k) - if v is not None: - columns[k].unit = v - - # start pipeline for stats: match project - pipeline = [{"$match": {"project": document.id}}] - - # resolve/lookup component fields - # NOTE also includes dynamic document fields - # for component in COMPONENTS.keys(): - # pipeline.append( - # { - # "$lookup": { - # "from": component, - # "localField": component, - # "foreignField": "_id", - # "as": component, - # } - # } - # ) - - # document size and attachment content size - project_stage = { - # "_id": 0, - # "size": {"$bsonSize": "$$ROOT"}, - # "contents": { - # "$map": { # attachment sizes - # "input": "$attachments", - # "as": "attm", - # "in": {"$toInt": "$$attm.content"}, - # } - # }, - } - - # number of components - for component in COMPONENTS.keys(): - project_stage[component] = {"$size": f"${component}"} - - # filter/forward number columns - min_max_paths = [ - path for path, col in columns.items() if col["unit"] != "NaN" - ] - for path in min_max_paths: - field = f"{path}{delimiter}value" - project_stage[field] = { - "$cond": { - "if": {"$isNumber": f"${field}"}, - "then": f"${field}", - "else": "$$REMOVE", - } - } - - # add project stage to pipeline - pipeline.append({"$project": project_stage}) - - # forward fields and sum attachment contents - project_stage_2 = {k: 1 for k in project_stage.keys()} - # project_stage_2["contents"] = {"$sum": "$contents"} - pipeline.append({"$project": project_stage_2}) - - # total size and total number of components - group_stage = { - "_id": None, - # "size": {"$sum": {"$add": ["$size", "$contents"]}}, - } - for component in COMPONENTS.keys(): - group_stage[component] = {"$sum": f"${component}"} - - # determine min/max for columns - for path in min_max_paths: - field = f"{path}{delimiter}value" - for k in ["min", "max"]: - clean_path = path.replace(delimiter, "__") - key = f"{clean_path}__{k}" - group_stage[key] = {f"${k}": f"${field}"} - - # append group stage and run pipeline - pipeline.append({"$group": group_stage}) - result = list(Contributions.objects.aggregate(pipeline)) - - # set min/max for columns - min_max = {} if not result else result[0] - for clean_path in min_max_paths: - for k in ["min", "max"]: - path = clean_path.replace(delimiter, "__") - m = min_max.get(f"{path}__{k}") - if m is not None: - setattr(columns[clean_path], k, m) - - # prep and save stats - stats_kwargs = {"columns": len(columns), "contributions": ncontribs} - if result and result[0]: - # stats_kwargs["size"] = result[0]["size"] / 1024 / 1024 - for component in COMPONENTS.keys(): - stats_kwargs[component] = result[0].get(component, 0) - if stats_kwargs[component] > 0: - columns[component] = Column(path=component) - - stats = Stats(**stats_kwargs) - document.update(stats=stats, columns=columns.values()) - - @classmethod - def post_delete(cls, sender, document, **kwargs): - admin_email = current_app.config["MAIL_DEFAULT_SENDER"] - subject = f'Your project "{document.name}" has been deleted' - html = render_template( - "owner_email.html", - approved=False, - admin_email=admin_email, - project=document.name, - ) - owner_email = document.owner.split(":", 1)[1] - send_email(owner_email, subject, html) - - -register_field( - ProviderEmailField, ProviderEmail, available_params=(params.LengthParam,) -) -signals.post_save.connect(Projects.post_save, sender=Projects) -signals.post_delete.connect(Projects.post_delete, sender=Projects) -Projects.atlas.index._set_indexed_fields({"type": "document", "dynamic": True}) diff --git a/mpcontribs-api/mpcontribs/api/projects/views.py b/mpcontribs-api/mpcontribs/api/projects/views.py deleted file mode 100644 index 1a000107b..000000000 --- a/mpcontribs-api/mpcontribs/api/projects/views.py +++ /dev/null @@ -1,183 +0,0 @@ -# -*- coding: utf-8 -*- -import os -import flask_mongorest - -from mongoengine.queryset import DoesNotExist -from flask import Blueprint, current_app, url_for, jsonify, abort, request -from flask_mongorest.resources import Resource -from flask_mongorest import operators as ops -from flask_mongorest.methods import Fetch, Create, Delete, Update, BulkFetch -from werkzeug.exceptions import Unauthorized - -from mpcontribs.api import FILTERS -from mpcontribs.api.core import SwaggerView -from mpcontribs.api.projects.document import Projects, Column, Reference, Stats - -templates = os.path.join(os.path.dirname(flask_mongorest.__file__), "templates") -projects = Blueprint("projects", __name__, template_folder=templates) -MAX_PROJECTS = int(os.environ.get("MAX_PROJECTS", 3)) - - -class ColumnResource(Resource): - document = Column - - -class ReferenceResource(Resource): - document = Reference - - -class StatsResource(Resource): - document = Stats - - -class ProjectsResource(Resource): - document = Projects - related_resources = { - "columns": ColumnResource, - "references": ReferenceResource, - "stats": StatsResource, - } - filters = { - "name": FILTERS["STRINGS"], - "is_public": [ops.Boolean], - "title": FILTERS["STRINGS"], - "long_title": FILTERS["LONG_STRINGS"], - "authors": FILTERS["LONG_STRINGS"], - "description": FILTERS["LONG_STRINGS"], - "owner": FILTERS["STRINGS"], - "license": FILTERS["STRINGS"], - "is_approved": [ops.Boolean], - "unique_identifiers": [ops.Boolean], - "columns": [ops.Size], - "stats__columns": FILTERS["NUMBERS"], - "stats__contributions": FILTERS["NUMBERS"], - "stats__tables": FILTERS["NUMBERS"], - "stats__structures": FILTERS["NUMBERS"], - "stats__attachments": FILTERS["NUMBERS"], - "stats__size": FILTERS["NUMBERS"], - } - fields = [ - "name", - "is_public", - "title", - "owner", - "is_approved", - "unique_identifiers", - ] - allowed_ordering = ["name", "is_public", "title"] - paginate = True - default_limit = 100 - max_limit = 500 - - @staticmethod - def get_optional_fields(): - return [ - "long_title", - "authors", - "description", - "references", - "license", - "other", - "columns", - "stats", - ] - - -class ProjectsView(SwaggerView): - resource = ProjectsResource - methods = [Fetch, Create, Delete, Update, BulkFetch] - - def has_add_permission(self, request, obj): - if self.is_anonymous(request): - return False - - obj.owner = request.headers.get("X-Consumer-Username") - if self.is_admin(request): - return True - - data = request.json - if "is_approved" in data or "is_public" in data: - raise Unauthorized("Projects cannot be approved or published on creation.") - - # limit the number of projects a user can own - nr_projects = Projects.objects(owner=obj.owner).count() - if nr_projects > MAX_PROJECTS: - raise Unauthorized(f"{obj.owner} already owns {nr_projects} projects.") - - return True - - def has_change_permission(self, request, obj): - if self.is_anonymous(request): - return False - - if self.is_admin(request): - return True - - if not self.is_project_user(request, obj): - raise Unauthorized( - "Only project owners and collaborators can edit projects." - ) - - update = request.json - if "is_approved" in update: - raise Unauthorized("Only admins can (un)approve projects.") - - if "is_public" in update and not obj.is_approved: - raise Unauthorized("Projects can only be published after admin approval.") - - return True - - -@projects.route("/applications/", defaults={"action": None}) -@projects.route("/applications//") -def applications(token, action): - ts = current_app.config["USTS"] - owner, project = ts.loads(token) - - try: - obj = Projects.objects.get(name=project, owner=owner, is_approved=False) - except DoesNotExist: - return f"{project} for {owner} already approved or denied." - - actions = ["approve", "deny"] - if action not in actions: - response = f"

{project}

    " - scheme = "http" if current_app.config["DEBUG"] else "https" - for a in actions: - u = url_for( - "projects.applications", - token=token, - action=a, - _scheme=scheme, - _external=True, - ) - response += f'
  • {a}
    • ' - return response + "
" - - if action == "approve": - obj.reload(*obj._fields.keys()) - obj.is_approved = True - obj.save() # post_save (created=False) sends notification when `is_approved` set - else: - obj.delete() # post_delete signal sends notification - - return f'{project} {action.replace("y", "ie")}d and {owner} notified.' - - -@projects.route("/search") -def search(): - term = request.args.get("term") - if not term: - abort(404, description="Missing search term.") - - pipeline = [ - { - "$search": { - "index": "mpcontribs-dev-project-search", - "text": {"path": {"wildcard": "*"}, "query": term}, - } - }, - {"$project": {"_id": 1}}, - ] - result = [p["_id"] for p in Projects.objects().aggregate(pipeline)] - return jsonify(result) diff --git a/mpcontribs-api/mpcontribs/api/structures/document.py b/mpcontribs-api/mpcontribs/api/structures/document.py deleted file mode 100644 index 29b8a333d..000000000 --- a/mpcontribs-api/mpcontribs/api/structures/document.py +++ /dev/null @@ -1,53 +0,0 @@ -# -*- coding: utf-8 -*- -import json -from hashlib import md5 -from flask_mongoengine.documents import Document -from mongoengine import signals -from mongoengine.fields import StringField, FloatField, ListField, DictField -from mongoengine.queryset.manager import queryset_manager -from pymatgen.core import Structure -from pymatgen.io.cif import CifWriter -from pymatgen.symmetry.analyzer import SymmetryUndeterminedError - - -class Structures(Document): - name = StringField(required=True, help_text="name") - lattice = DictField(required=True, help_text="lattice") - sites = ListField(DictField(), required=True, help_text="sites") - charge = FloatField(null=True, help_text="charge") - md5 = StringField(regex=r"^[a-z0-9]{32}$", unique=True, help_text="md5 sum") - cif = StringField(help_text="CIF string") - meta = {"collection": "structures", "indexes": ["name", "md5"]} - - @queryset_manager - def objects(doc_cls, queryset): - return queryset.only("name", "md5") - - @classmethod - def pre_save_post_validation(cls, sender, document, **kwargs): - from mpcontribs.api.structures.views import StructuresResource - - resource = StructuresResource() - d = resource.serialize(document, fields=["lattice", "sites", "charge"]) - s = json.dumps(d, sort_keys=True).encode("utf-8") - document.md5 = md5(s).hexdigest() - structure = Structure.from_dict(d) - writer = None - - for symprec_log in range(-10, 0, 3): - try: - writer = CifWriter(structure, symprec=10**symprec_log) - break - except SymmetryUndeterminedError: - continue - - if not writer: - # save CIF string without symmetry information - writer = CifWriter(structure) - - document.cif = writer.__str__() - - -signals.pre_save_post_validation.connect( - Structures.pre_save_post_validation, sender=Structures -) diff --git a/mpcontribs-api/mpcontribs/api/structures/views.py b/mpcontribs-api/mpcontribs/api/structures/views.py deleted file mode 100644 index 07aeb7901..000000000 --- a/mpcontribs-api/mpcontribs/api/structures/views.py +++ /dev/null @@ -1,39 +0,0 @@ -# -*- coding: utf-8 -*- -import os -import flask_mongorest -from flask_mongorest.resources import Resource -from flask_mongorest import operators as ops -from flask_mongorest.methods import Fetch, BulkFetch, Download -from flask import Blueprint - -from mpcontribs.api import FILTERS -from mpcontribs.api.core import SwaggerView -from mpcontribs.api.structures.document import Structures - -templates = os.path.join(os.path.dirname(flask_mongorest.__file__), "templates") -structures = Blueprint("structures", __name__, template_folder=templates) - - -class StructuresResource(Resource): - document = Structures - filters = { - "id": [ops.In, ops.Exact], - "md5": [ops.In, ops.Exact], - "name": FILTERS["STRINGS"], - "sites": [ops.Size] - } - fields = ["id", "name", "md5"] - allowed_ordering = ["name"] - paginate = True - default_limit = 10 - max_limit = 100 - download_formats = ["json", "csv"] - - @staticmethod - def get_optional_fields(): - return ["lattice", "sites", "charge", "cif"] - - -class StructuresView(SwaggerView): - resource = StructuresResource - methods = [Fetch, BulkFetch, Download] diff --git a/mpcontribs-api/mpcontribs/api/tables/__init__.py b/mpcontribs-api/mpcontribs/api/tables/__init__.py deleted file mode 100644 index e809e5932..000000000 --- a/mpcontribs-api/mpcontribs/api/tables/__init__.py +++ /dev/null @@ -1,2 +0,0 @@ -# -*- coding: utf-8 -*- -"""document and views for tables collection""" diff --git a/mpcontribs-api/mpcontribs/api/tables/document.py b/mpcontribs-api/mpcontribs/api/tables/document.py deleted file mode 100644 index dc52876df..000000000 --- a/mpcontribs-api/mpcontribs/api/tables/document.py +++ /dev/null @@ -1,52 +0,0 @@ -# -*- coding: utf-8 -*- -from hashlib import md5 -from flask_mongoengine.documents import DynamicDocument -from mongoengine import signals, EmbeddedDocument -from mongoengine.fields import StringField, ListField, IntField, EmbeddedDocumentField -from mongoengine.queryset.manager import queryset_manager - -from mpcontribs.api.contributions.document import format_cell, get_resource, get_md5, COMPONENTS - - -class Labels(EmbeddedDocument): - index = StringField(help_text="index name / x-axis label") - value = StringField(help_text="columns name / y-axis label") - variable = StringField(help_text="legend name") - - -class Attributes(EmbeddedDocument): - title = StringField(help_text="title") - labels = EmbeddedDocumentField(Labels) - - -class Tables(DynamicDocument): - name = StringField(required=True, help_text="name / title") - attrs = EmbeddedDocumentField(Attributes) - index = ListField(StringField(), required=True, help_text="index column") - columns = ListField(StringField(), required=True, help_text="column names/headers") - data = ListField(ListField(StringField()), required=True, help_text="table rows") - md5 = StringField(regex=r"^[a-z0-9]{32}$", unique=True, help_text="md5 sum") - total_data_rows = IntField(help_text="total number of rows") - meta = {"collection": "tables", "indexes": [ - "name", "columns", "md5", "attrs.title", - "attrs.labels.index", "attrs.labels.value", "attrs.labels.variable" - ]} - - @queryset_manager - def objects(doc_cls, queryset): - return queryset.only("name", "md5", "attrs", "columns", "total_data_rows") - - @classmethod - def post_init(cls, sender, document, **kwargs): - document.data = [[format_cell(cell) for cell in row] for row in document.data] - - @classmethod - def pre_save_post_validation(cls, sender, document, **kwargs): - # significant digits, md5 and total_data_rows - resource = get_resource("tables") - document.md5 = get_md5(resource, document, COMPONENTS["tables"]) - document.total_data_rows = len(document.data) - - -signals.post_init.connect(Tables.post_init, sender=Tables) -signals.pre_save_post_validation.connect(Tables.pre_save_post_validation, sender=Tables) diff --git a/mpcontribs-api/mpcontribs/api/tables/views.py b/mpcontribs-api/mpcontribs/api/tables/views.py deleted file mode 100644 index a8f657998..000000000 --- a/mpcontribs-api/mpcontribs/api/tables/views.py +++ /dev/null @@ -1,70 +0,0 @@ -# -*- coding: utf-8 -*- -import os -import flask_mongorest -from flask_mongorest.resources import Resource -from flask_mongorest import operators as ops -from flask_mongorest.methods import Fetch, BulkFetch, Download -from flask_mongorest.exceptions import UnknownFieldError -from flask import Blueprint - -from mpcontribs.api import FILTERS -from mpcontribs.api.core import SwaggerView -from mpcontribs.api.tables.document import Tables, Attributes, Labels - -templates = os.path.join(os.path.dirname(flask_mongorest.__file__), "templates") -tables = Blueprint("tables", __name__, template_folder=templates) - - -class LabelsResource(Resource): - document = Labels - - -class AttributesResource(Resource): - document = Attributes - related_resources = {"labels": LabelsResource} - - -class TablesResource(Resource): - document = Tables - related_resources = {"attrs": AttributesResource} - filters = { - "id": [ops.In, ops.Exact], - "md5": [ops.In, ops.Exact], - "name": FILTERS["STRINGS"], - "columns": [ops.Size], - "attrs__title": FILTERS["STRINGS"], - "attrs__labels__index": FILTERS["STRINGS"], - "attrs__labels__value": FILTERS["STRINGS"], - "attrs__labels__variable": FILTERS["STRINGS"], - } - fields = [ - "id", "name", "md5", "attrs", "columns", "total_data_rows", "total_data_pages" - ] - allowed_ordering = ["name", "total_data_rows"] - paginate = True - default_limit = 10 - max_limit = 100 - fields_to_paginate = {"data": [20, 1000]} - download_formats = ["json", "csv"] - - @staticmethod - def get_optional_fields(): - return ["index", "data"] - - def value_for_field(self, obj, field): - if field == "total_data_pages": - if obj.total_data_rows is None: - return None - - per_page_default = self.fields_to_paginate["data"][0] - per_page = int(self.params.get("data_per_page", per_page_default)) - total_data_pages = int(obj.total_data_rows / per_page) - total_data_pages += bool(obj.total_data_rows % per_page) - return total_data_pages - else: - raise UnknownFieldError - - -class TablesView(SwaggerView): - resource = TablesResource - methods = [Fetch, BulkFetch, Download] diff --git a/mpcontribs-api/mpcontribs/api/templates/admin_email.html b/mpcontribs-api/mpcontribs/api/templates/admin_email.html deleted file mode 100644 index 30267cf34..000000000 --- a/mpcontribs-api/mpcontribs/api/templates/admin_email.html +++ /dev/null @@ -1 +0,0 @@ -Go to {{url}} for more info about the project. Approve or deny this request: {{link}}. A notification email with your decision will automatically be sent to the user. diff --git a/mpcontribs-api/mpcontribs/api/templates/card_bootstrap.html b/mpcontribs-api/mpcontribs/api/templates/card_bootstrap.html deleted file mode 100644 index b8a904560..000000000 --- a/mpcontribs-api/mpcontribs/api/templates/card_bootstrap.html +++ /dev/null @@ -1,46 +0,0 @@ -
-
-
-

- {{ title }} - {% if references %} - - {% for ref in references %} - [{{ref.label}}] - {% endfor %} - - {% endif %} - Details -

- {{ authors.main }} - {% if authors.etal %} - et al. - - {% endif %} -
- -
-
-
- {{ descriptions.0 }}. - {% if descriptions.1 %} - More » - - {% endif %} -
-
{{ data|safe }}
-
-
- -
diff --git a/mpcontribs-api/mpcontribs/api/templates/card_bulma.html b/mpcontribs-api/mpcontribs/api/templates/card_bulma.html deleted file mode 100644 index ce4a01d92..000000000 --- a/mpcontribs-api/mpcontribs/api/templates/card_bulma.html +++ /dev/null @@ -1,60 +0,0 @@ -
-
-
- {% if references %} - - {% endif %} -
- - {{ title }} - - - - - - -
-
- {{ authors.main }} - {% if authors.etal %} - et al. - - {% endif %} -
-
- {{ descriptions.0 }}. - {% if descriptions.1 %} - More » - - {% endif %} -
-
- {{ data|safe }} -
-
- -
- -
diff --git a/mpcontribs-api/mpcontribs/api/templates/owner_email.html b/mpcontribs-api/mpcontribs/api/templates/owner_email.html deleted file mode 100644 index 2eb526dce..000000000 --- a/mpcontribs-api/mpcontribs/api/templates/owner_email.html +++ /dev/null @@ -1 +0,0 @@ -Your project "{{project}}" has been {% if approved %}approved. You can now add all your contributions and publish the project.{% else %}denied and deleted.{% endif %} diff --git a/mpcontribs-api/pyproject.toml b/mpcontribs-api/pyproject.toml index d64166fd3..87f12d487 100644 --- a/mpcontribs-api/pyproject.toml +++ b/mpcontribs-api/pyproject.toml @@ -10,94 +10,86 @@ relative_to = "__file__" include-package-data = true [tool.setuptools.packages.find] -where = ["."] -exclude = ["scripts","supervisord"] -include = ["mpcontribs.api"] +where = ["src"] +include = ["mpcontribs_api*"] [project] name = "mpcontribs-api" dynamic = ["version"] -requires-python = ">=3.11" +requires-python = ">=3.14" description="API for community-contributed Materials Project data" license = "BSD-3-Clause-LBNL" authors = [ - {name = "Patrick Huck", email = "phuck@lbl.gov"}, - {name = "The Materials Project", email="feedback@materialsproject.org"}, + {name="Patrick Huck", email="phuck@lbl.gov"}, + {name="Brendan Foley", email="bfoley@lbl.gov"}, + {name="The Materials Project", email="feedback@materialsproject.org"}, ] dependencies = [ - "numpy", - "apispec<6", - "asn1crypto", - "blinker", - "boltons", - "css-html-js-minify", - "dateparser", - "ddtrace==4.3.0", - "dnspython", - "filetype", - "flasgger-tschaume>=0.9.7", - "flask-compress", - "flask-marshmallow", - "flask-mongorest-mpcontribs>=3.2.1", - "Flask-RQ2", - "gunicorn[gevent]==24.1.1", + # "pint>=0.24", + # "psycopg2-binary", + # "rq<=2.3.2", # see https://github.com/rq/Flask-RQ2/issues/620 + # "setproctitle", + # "uncertainties", + # "websocket_client", + # "zstandard", + "aioboto3>=15.5.0", + "beanie>=2.1.0", + "fastapi[standard]>=0.136.3", + "fastapi-filter>=2.0.1", "jinja2", - "json2html", - "marshmallow<4", - "more-itertools", - "nbformat", - "notebook<7", - "pint>=0.24", - "psycopg2-binary", + "opentelemetry-api>=1.42.1", + "opentelemetry-exporter-otlp-proto-grpc>=1.42.1", + "opentelemetry-instrumentation-fastapi>=0.63b1", + "opentelemetry-instrumentation-pymongo>=0.63b1", + "opentelemetry-sdk>=1.42.1", + "polars>=1.41.2", + "pydantic-settings>=2.14.1", "pymatgen", - "pyopenssl", - "python-snappy", - "rq<=2.3.2", # see https://github.com/rq/Flask-RQ2/issues/620 - "supervisor", - "setproctitle", - "uncertainties", - "websocket_client", - "zstandard", + "pymongo>=4.17.0", + "python-snappy>=0.7.3", + "structlog>=25.5.0", + "supervisor>=4.3.0", + "types-aiobotocore[s3]>=3.7.0", ] [project.urls] Homepage = "https://github.com/materialsproject/MPContribs" Documentation = "https://docs.materialsproject.org/services/mpcontribs" -[project.optional-dependencies] +[dependency-groups] dev = [ - "flake8", - "pytest", - "pytest-flake8", - "pytest-pycodestyle", - "pytest-xdist", -] -all = [ - "mpcontribs-api[dev]" + "ruff>=0.9.0", + "basedpyright>=1.29.0", + "pydocstringformatter>=0.7.0", + "pytest>=9.0.3", + "pytest-xdist>=3.8.0", + "httpx2>=0.28.0", + "pytest-asyncio>=1.4.0", ] -[tool.pytest] +[tool.pytest.ini_options] +pythonpath = ["src"] +asyncio_mode = "auto" +asyncio_default_fixture_loop_scope = "session" markers = [ "base: basic resource testing", "extra: all extra views", + "db: requires a live MongoDB connection (set MPCONTRIBS_MONGO__URI)", ] -[tool.pycodestyle] -count = true -ignore = ["E121","E123","E126","E133","E226","E241","E242","E704","W503","W504","W505","E741","W605"] -max-line-length = 120 -statistics = true -exclude = ["flasgger","flask-mongorest"] +[tool.ruff] +line-length = 120 +exclude = ["tests/"] -[tool.flake8] -exclude = [".git","__pycache__","tests","flasgger","flask-mongorest"] -extend-ignore = ["E741",] -max-line-length = 120 +[tool.ruff.lint] +select = ["E", "F", "W", "I", "B", "UP"] +ignore = ["E741", "B008"] -[tool.pydocstyle] -ignore = ["D105","D2","D4"] +[tool.pydocstringformatter] +max-line-length = 120 -[tool.mypy] -ignore_missing_imports = true -namespace_packages = true -python_version = 3.11 +[tool.basedpyright] +pythonVersion = "3.14" +typeCheckingMode = "standard" +extraPaths = ["src"] +ignore=["tests/"] diff --git a/mpcontribs-api/requirements/deployment.txt b/mpcontribs-api/requirements/deployment.txt deleted file mode 100644 index 03bbd3d93..000000000 --- a/mpcontribs-api/requirements/deployment.txt +++ /dev/null @@ -1,551 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --output-file=MPContribs/mpcontribs-api/requirements/deployment.txt MPContribs/mpcontribs-api/pyproject.toml python/requirements.txt -# -anyio==4.13.0 - # via jupyter-server -apispec==5.2.2 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -argon2-cffi==25.1.0 - # via - # jupyter-server - # notebook -argon2-cffi-bindings==25.1.0 - # via argon2-cffi -arrow==1.4.0 - # via isoduration -asn1crypto==1.5.1 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -asttokens==3.0.1 - # via stack-data -atlasq-tschaume==0.11.1.dev2 - # via flask-mongorest-mpcontribs -attrs==26.1.0 - # via - # jsonschema - # referencing -backports-zstd==1.5.0 - # via flask-compress -beautifulsoup4==4.15.0 - # via nbconvert -bibtexparser==1.4.4 - # via pymatgen-core -bleach[css]==6.4.0 - # via nbconvert -blinker==1.9.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -boltons==25.0.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -boto3==1.43.25 - # via flask-mongorest-mpcontribs -botocore==1.43.25 - # via - # boto3 - # s3transfer -brotli==1.2.0 - # via flask-compress -bytecode==0.18.1 - # via ddtrace -certifi==2026.5.20 - # via requests -cffi==2.0.0 - # via - # argon2-cffi-bindings - # cryptography -charset-normalizer==3.4.7 - # via requests -click==8.4.1 - # via - # flask - # rq -comm==0.2.3 - # via ipykernel -contourpy==1.3.3 - # via matplotlib -cramjam==2.11.0 - # via python-snappy -crontab==1.0.5 - # via rq-scheduler -cryptography==48.0.0 - # via pyopenssl -css-html-js-minify==2.5.5 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -cycler==0.12.1 - # via matplotlib -dateparser==1.4.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -ddtrace==4.3.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -debugpy==1.8.21 - # via ipykernel -decorator==5.3.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert -dnspython==2.8.0 - # via - # mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) - # pymongo -entrypoints==0.4 - # via jupyter-client -envier==0.6.1 - # via ddtrace -executing==2.2.1 - # via stack-data -fastjsonschema==2.21.2 - # via nbformat -fastnumbers==5.1.1 - # via flask-mongorest-mpcontribs -filetype==1.2.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -flasgger-tschaume==0.9.7 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -flask==2.2.5 - # via - # flasgger-tschaume - # flask-compress - # flask-marshmallow - # flask-mongoengine-tschaume - # flask-rq2 - # flask-sse -flask-compress==1.24 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -flask-marshmallow==1.4.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -flask-mongoengine-tschaume==1.1.0 - # via flask-mongorest-mpcontribs -flask-mongorest-mpcontribs==3.3.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -flask-rq2==18.3 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -flask-sse==1.0.0 - # via flask-mongorest-mpcontribs -flatten-dict==0.5.0 - # via flask-mongorest-mpcontribs -flexcache==0.3 - # via pint -flexparser==0.4 - # via pint -fonttools==4.63.0 - # via matplotlib -fqdn==1.5.1 - # via jsonschema -freezegun==1.5.5 - # via rq-scheduler -gevent==26.5.0 - # via gunicorn -greenlet==3.5.1 - # via gevent -gunicorn[gevent]==24.1.1 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -idna==3.18 - # via - # anyio - # jsonschema - # requests -ipykernel==6.29.5 - # via - # nbclassic - # notebook -ipython==9.14.1 - # via ipykernel -ipython-genutils==0.2.0 - # via - # nbclassic - # notebook -ipython-pygments-lexers==1.1.1 - # via ipython -isoduration==20.11.0 - # via jsonschema -itsdangerous==2.2.0 - # via flask -jedi==0.20.0 - # via ipython -jinja2==3.1.6 - # via - # flask - # jupyter-server - # mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) - # nbconvert - # notebook -jmespath==1.1.0 - # via - # boto3 - # botocore -joblib==1.5.3 - # via pymatgen-core -json2html==1.3.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -jsonpointer==3.1.1 - # via jsonschema -jsonschema[format-nongpl]==4.26.0 - # via - # flasgger-tschaume - # jupyter-events - # nbformat -jsonschema-specifications==2025.9.1 - # via jsonschema -jupyter-client==7.4.9 - # via - # ipykernel - # jupyter-server - # nbclient - # notebook -jupyter-core==5.9.1 - # via - # ipykernel - # jupyter-client - # jupyter-server - # nbclient - # nbconvert - # nbformat - # notebook -jupyter-events==0.12.1 - # via jupyter-server -jupyter-server==2.19.0 - # via notebook-shim -jupyter-server-terminals==0.5.4 - # via jupyter-server -jupyterlab-pygments==0.3.0 - # via nbconvert -kiwisolver==1.5.0 - # via matplotlib -lark==1.3.1 - # via rfc3987-syntax -lxml==6.1.1 - # via pymatgen-core -markupsafe==3.0.3 - # via - # jinja2 - # nbconvert - # werkzeug -marshmallow==3.26.2 - # via - # flask-marshmallow - # marshmallow-mongoengine - # mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -marshmallow-mongoengine==0.31.2 - # via flask-mongorest-mpcontribs -matplotlib==3.10.9 - # via - # -r python/requirements.txt - # pymatgen-core -matplotlib-inline==0.2.2 - # via - # ipykernel - # ipython -mimerender-pr36==0.0.2 - # via flask-mongorest-mpcontribs -mistune==3.2.1 - # via - # flasgger-tschaume - # nbconvert -mongoengine==0.29.3 - # via - # atlasq-tschaume - # flask-mongoengine-tschaume - # marshmallow-mongoengine -monty==2026.5.18 - # via pymatgen-core -more-itertools==11.1.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -mpmath==1.3.0 - # via sympy -narwhals==2.22.1 - # via plotly -nbclassic==1.3.3 - # via notebook -nbclient==0.11.0 - # via nbconvert -nbconvert==7.17.1 - # via - # jupyter-server - # notebook -nbformat==5.10.4 - # via - # jupyter-server - # mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) - # nbclient - # nbconvert - # notebook -nest-asyncio==1.6.0 - # via - # ipykernel - # jupyter-client - # nbclassic - # notebook -networkx==3.6.1 - # via pymatgen-core -notebook==6.5.7 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -notebook-shim==0.2.4 - # via nbclassic -numpy==2.4.6 - # via - # -r python/requirements.txt - # contourpy - # matplotlib - # monty - # mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) - # pandas - # pymatgen-core - # scipy - # spglib -opentelemetry-api==1.42.1 - # via ddtrace -orjson==3.11.9 - # via - # flask-mongorest-mpcontribs - # pymatgen-core -overrides==7.7.0 - # via jupyter-server -packaging==26.2 - # via - # gunicorn - # ipykernel - # jupyter-events - # jupyter-server - # marshmallow - # matplotlib - # nbconvert - # plotly -palettable==3.3.3 - # via pymatgen-core -pandas==3.0.3 - # via - # -r python/requirements.txt - # pymatgen-core -pandocfilters==1.5.1 - # via nbconvert -parso==0.8.7 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==12.2.0 - # via matplotlib -pint==0.25.3 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -platformdirs==4.10.0 - # via - # jupyter-core - # pint -plotly==6.8.0 - # via pymatgen-core -prometheus-client==0.25.0 - # via - # jupyter-server - # notebook -prompt-toolkit==3.0.52 - # via ipython -psutil==7.2.2 - # via - # ipykernel - # ipython -psycopg2-binary==2.9.12 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -ptyprocess==0.7.0 - # via - # pexpect - # terminado -pure-eval==0.2.3 - # via stack-data -pycparser==3.0 - # via cffi -pygments==2.20.0 - # via - # ipython - # ipython-pygments-lexers - # nbconvert -pymatgen==2026.5.4 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -pymatgen-core==2026.5.18 - # via pymatgen -pymongo==4.17.0 - # via - # flask-mongorest-mpcontribs - # mongoengine -pyopenssl==26.2.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -pyparsing==3.3.2 - # via - # bibtexparser - # matplotlib -python-dateutil==2.9.0.post0 - # via - # arrow - # botocore - # dateparser - # flask-mongorest-mpcontribs - # freezegun - # jupyter-client - # matplotlib - # pandas - # rq-scheduler -python-json-logger==4.1.0 - # via jupyter-events -python-mimeparse==2.0.0 - # via mimerender-pr36 -python-snappy==0.7.3 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -pytz==2026.2 - # via dateparser -pyyaml==6.0.3 - # via - # flasgger-tschaume - # jupyter-events -pyzmq==27.1.0 - # via - # ipykernel - # jupyter-client - # jupyter-server - # notebook -redis==8.0.0 - # via - # flask-rq2 - # flask-sse - # rq -referencing==0.37.0 - # via - # jsonschema - # jsonschema-specifications - # jupyter-events -regex==2026.5.9 - # via dateparser -requests==2.34.2 - # via - # atlasq-tschaume - # pymatgen-core -rfc3339-validator==0.1.4 - # via - # jsonschema - # jupyter-events -rfc3986-validator==0.1.1 - # via - # jsonschema - # jupyter-events -rfc3987-syntax==1.1.0 - # via jsonschema -rpds-py==2026.5.1 - # via - # jsonschema - # referencing -rq==2.3.2 - # via - # flask-rq2 - # mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) - # rq-scheduler -rq-scheduler==0.14.0 - # via flask-rq2 -ruamel-yaml==0.19.1 - # via monty -s3transfer==0.18.0 - # via boto3 -scipy==1.17.1 - # via - # -r python/requirements.txt - # pymatgen-core -send2trash==2.1.0 - # via - # jupyter-server - # notebook -setproctitle==1.3.7 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -six==1.17.0 - # via - # flasgger-tschaume - # flask-sse - # python-dateutil - # rfc3339-validator -soupsieve==2.8.4 - # via beautifulsoup4 -spglib==2.7.0 - # via pymatgen-core -stack-data==0.6.3 - # via ipython -supervisor==4.3.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -sympy==1.14.0 - # via pymatgen-core -tabulate==0.10.0 - # via pymatgen-core -terminado==0.18.1 - # via - # jupyter-server - # jupyter-server-terminals - # notebook -tinycss2==1.5.1 - # via bleach -tornado==6.5.7 - # via - # ipykernel - # jupyter-client - # jupyter-server - # notebook - # terminado -tqdm==4.68.1 - # via pymatgen-core -traitlets==5.15.1 - # via - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # jupyter-events - # jupyter-server - # matplotlib-inline - # nbclient - # nbconvert - # nbformat - # notebook -typing-extensions==4.15.0 - # via - # anyio - # beautifulsoup4 - # flexcache - # flexparser - # ipython - # opentelemetry-api - # pint - # pyopenssl - # referencing - # spglib -tzdata==2026.2 - # via arrow -tzlocal==5.3.1 - # via dateparser -uncertainties==3.2.3 - # via - # mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) - # pymatgen-core -uri-template==1.3.0 - # via jsonschema -urllib3==2.7.0 - # via - # botocore - # requests -wcwidth==0.8.1 - # via prompt-toolkit -webcolors==25.10.0 - # via jsonschema -webencodings==0.5.1 - # via - # bleach - # tinycss2 -websocket-client==1.9.0 - # via - # jupyter-server - # mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) -werkzeug==3.1.8 - # via - # flasgger-tschaume - # flask -wrapt==2.2.1 - # via ddtrace -zope-event==6.2 - # via gevent -zope-interface==8.5 - # via gevent -zstandard==0.25.0 - # via mpcontribs-api (MPContribs/mpcontribs-api/pyproject.toml) diff --git a/mpcontribs-api/requirements/ubuntu-latest_py3.11.txt b/mpcontribs-api/requirements/ubuntu-latest_py3.11.txt deleted file mode 100644 index ae1ff8eee..000000000 --- a/mpcontribs-api/requirements/ubuntu-latest_py3.11.txt +++ /dev/null @@ -1,548 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --output-file=requirements/ubuntu-latest_py3.11.txt -# -anyio==4.13.0 - # via jupyter-server -apispec==5.2.2 - # via mpcontribs-api (pyproject.toml) -argon2-cffi==25.1.0 - # via - # jupyter-server - # notebook -argon2-cffi-bindings==25.1.0 - # via argon2-cffi -arrow==1.4.0 - # via isoduration -asn1crypto==1.5.1 - # via mpcontribs-api (pyproject.toml) -asttokens==3.0.1 - # via stack-data -atlasq-tschaume==0.11.1.dev2 - # via flask-mongorest-mpcontribs -attrs==26.1.0 - # via - # jsonschema - # referencing -backports-zstd==1.5.0 - # via flask-compress -beautifulsoup4==4.14.3 - # via nbconvert -bibtexparser==1.4.4 - # via pymatgen-core -bleach[css]==6.3.0 - # via nbconvert -blinker==1.9.0 - # via mpcontribs-api (pyproject.toml) -boltons==25.0.0 - # via mpcontribs-api (pyproject.toml) -boto3==1.43.9 - # via flask-mongorest-mpcontribs -botocore==1.43.9 - # via - # boto3 - # s3transfer -brotli==1.2.0 - # via flask-compress -bytecode==0.17.0 - # via ddtrace -certifi==2026.4.22 - # via requests -cffi==2.0.0 - # via - # argon2-cffi-bindings - # cryptography -charset-normalizer==3.4.7 - # via requests -click==8.4.0 - # via - # flask - # rq -comm==0.2.3 - # via ipykernel -contourpy==1.3.3 - # via matplotlib -cramjam==2.11.0 - # via python-snappy -crontab==1.0.5 - # via rq-scheduler -cryptography==48.0.0 - # via pyopenssl -css-html-js-minify==2.5.5 - # via mpcontribs-api (pyproject.toml) -cycler==0.12.1 - # via matplotlib -dateparser==1.4.0 - # via mpcontribs-api (pyproject.toml) -ddtrace==4.3.0 - # via mpcontribs-api (pyproject.toml) -debugpy==1.8.20 - # via ipykernel -decorator==5.3.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert -dnspython==2.8.0 - # via - # mpcontribs-api (pyproject.toml) - # pymongo -entrypoints==0.4 - # via jupyter-client -envier==0.6.1 - # via ddtrace -executing==2.2.1 - # via stack-data -fastjsonschema==2.21.2 - # via nbformat -fastnumbers==5.1.1 - # via flask-mongorest-mpcontribs -filetype==1.2.0 - # via mpcontribs-api (pyproject.toml) -flasgger-tschaume==0.9.7 - # via mpcontribs-api (pyproject.toml) -flask==2.2.5 - # via - # flasgger-tschaume - # flask-compress - # flask-marshmallow - # flask-mongoengine-tschaume - # flask-rq2 - # flask-sse -flask-compress==1.24 - # via mpcontribs-api (pyproject.toml) -flask-marshmallow==1.4.0 - # via mpcontribs-api (pyproject.toml) -flask-mongoengine-tschaume==1.1.0 - # via flask-mongorest-mpcontribs -flask-mongorest-mpcontribs==3.3.0 - # via mpcontribs-api (pyproject.toml) -flask-rq2==18.3 - # via mpcontribs-api (pyproject.toml) -flask-sse==1.0.0 - # via flask-mongorest-mpcontribs -flatten-dict==0.5.0 - # via flask-mongorest-mpcontribs -flexcache==0.3 - # via pint -flexparser==0.4 - # via pint -fonttools==4.63.0 - # via matplotlib -fqdn==1.5.1 - # via jsonschema -freezegun==1.5.5 - # via rq-scheduler -gevent==26.4.0 - # via gunicorn -greenlet==3.5.0 - # via gevent -gunicorn[gevent]==24.1.1 - # via mpcontribs-api (pyproject.toml) -idna==3.15 - # via - # anyio - # jsonschema - # requests -importlib-metadata==8.7.1 - # via opentelemetry-api -ipykernel==6.29.5 - # via - # nbclassic - # notebook -ipython==9.13.0 - # via ipykernel -ipython-genutils==0.2.0 - # via - # nbclassic - # notebook -ipython-pygments-lexers==1.1.1 - # via ipython -isoduration==20.11.0 - # via jsonschema -itsdangerous==2.2.0 - # via flask -jedi==0.20.0 - # via ipython -jinja2==3.1.6 - # via - # flask - # jupyter-server - # mpcontribs-api (pyproject.toml) - # nbconvert - # notebook -jmespath==1.1.0 - # via - # boto3 - # botocore -joblib==1.5.3 - # via pymatgen-core -json2html==1.3.0 - # via mpcontribs-api (pyproject.toml) -jsonpointer==3.1.1 - # via jsonschema -jsonschema[format-nongpl]==4.26.0 - # via - # flasgger-tschaume - # jupyter-events - # nbformat -jsonschema-specifications==2025.9.1 - # via jsonschema -jupyter-client==7.4.9 - # via - # ipykernel - # jupyter-server - # nbclient - # notebook -jupyter-core==5.9.1 - # via - # ipykernel - # jupyter-client - # jupyter-server - # nbclient - # nbconvert - # nbformat - # notebook -jupyter-events==0.12.1 - # via jupyter-server -jupyter-server==2.18.2 - # via notebook-shim -jupyter-server-terminals==0.5.4 - # via jupyter-server -jupyterlab-pygments==0.3.0 - # via nbconvert -kiwisolver==1.5.0 - # via matplotlib -lark==1.3.1 - # via rfc3987-syntax -lxml==6.1.0 - # via pymatgen-core -markupsafe==3.0.3 - # via - # jinja2 - # nbconvert - # werkzeug -marshmallow==3.26.2 - # via - # flask-marshmallow - # marshmallow-mongoengine - # mpcontribs-api (pyproject.toml) -marshmallow-mongoengine==0.31.2 - # via flask-mongorest-mpcontribs -matplotlib==3.10.9 - # via pymatgen-core -matplotlib-inline==0.2.2 - # via - # ipykernel - # ipython -mimerender-pr36==0.0.2 - # via flask-mongorest-mpcontribs -mistune==3.2.1 - # via - # flasgger-tschaume - # nbconvert -mongoengine==0.29.3 - # via - # atlasq-tschaume - # flask-mongoengine-tschaume - # marshmallow-mongoengine -monty==2026.5.18 - # via pymatgen-core -more-itertools==11.0.2 - # via mpcontribs-api (pyproject.toml) -mpmath==1.3.0 - # via sympy -narwhals==2.21.2 - # via plotly -nbclassic==1.3.3 - # via notebook -nbclient==0.10.4 - # via nbconvert -nbconvert==7.17.1 - # via - # jupyter-server - # notebook -nbformat==5.10.4 - # via - # jupyter-server - # mpcontribs-api (pyproject.toml) - # nbclient - # nbconvert - # notebook -nest-asyncio==1.6.0 - # via - # ipykernel - # jupyter-client - # nbclassic - # notebook -networkx==3.6.1 - # via pymatgen-core -notebook==6.5.7 - # via mpcontribs-api (pyproject.toml) -notebook-shim==0.2.4 - # via nbclassic -numpy==2.4.5 - # via - # contourpy - # matplotlib - # monty - # mpcontribs-api (pyproject.toml) - # pandas - # pymatgen-core - # scipy - # spglib -opentelemetry-api==1.41.1 - # via ddtrace -orjson==3.11.9 - # via - # flask-mongorest-mpcontribs - # pymatgen-core -overrides==7.7.0 - # via jupyter-server -packaging==26.2 - # via - # gunicorn - # ipykernel - # jupyter-events - # jupyter-server - # marshmallow - # matplotlib - # nbconvert - # plotly -palettable==3.3.3 - # via pymatgen-core -pandas==3.0.3 - # via pymatgen-core -pandocfilters==1.5.1 - # via nbconvert -parso==0.8.7 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==12.2.0 - # via matplotlib -pint==0.25.3 - # via mpcontribs-api (pyproject.toml) -platformdirs==4.9.6 - # via - # jupyter-core - # pint -plotly==6.7.0 - # via pymatgen-core -prometheus-client==0.25.0 - # via - # jupyter-server - # notebook -prompt-toolkit==3.0.52 - # via ipython -psutil==7.2.2 - # via - # ipykernel - # ipython -psycopg2-binary==2.9.12 - # via mpcontribs-api (pyproject.toml) -ptyprocess==0.7.0 - # via - # pexpect - # terminado -pure-eval==0.2.3 - # via stack-data -pycparser==3.0 - # via cffi -pygments==2.20.0 - # via - # ipython - # ipython-pygments-lexers - # nbconvert -pymatgen==2026.5.4 - # via mpcontribs-api (pyproject.toml) -pymatgen-core==2026.5.17 - # via pymatgen -pymongo==4.17.0 - # via - # flask-mongorest-mpcontribs - # mongoengine -pyopenssl==26.2.0 - # via mpcontribs-api (pyproject.toml) -pyparsing==3.3.2 - # via - # bibtexparser - # matplotlib -python-dateutil==2.9.0.post0 - # via - # arrow - # botocore - # dateparser - # flask-mongorest-mpcontribs - # freezegun - # jupyter-client - # matplotlib - # pandas - # rq-scheduler -python-json-logger==4.1.0 - # via jupyter-events -python-mimeparse==2.0.0 - # via mimerender-pr36 -python-snappy==0.7.3 - # via mpcontribs-api (pyproject.toml) -pytz==2026.2 - # via dateparser -pyyaml==6.0.3 - # via - # flasgger-tschaume - # jupyter-events -pyzmq==27.1.0 - # via - # ipykernel - # jupyter-client - # jupyter-server - # notebook -redis==7.4.0 - # via - # flask-rq2 - # flask-sse - # rq -referencing==0.37.0 - # via - # jsonschema - # jsonschema-specifications - # jupyter-events -regex==2026.5.9 - # via dateparser -requests==2.34.2 - # via - # atlasq-tschaume - # pymatgen-core -rfc3339-validator==0.1.4 - # via - # jsonschema - # jupyter-events -rfc3986-validator==0.1.1 - # via - # jsonschema - # jupyter-events -rfc3987-syntax==1.1.0 - # via jsonschema -rpds-py==0.30.0 - # via - # jsonschema - # referencing -rq==2.3.2 - # via - # flask-rq2 - # mpcontribs-api (pyproject.toml) - # rq-scheduler -rq-scheduler==0.14.0 - # via flask-rq2 -ruamel-yaml==0.19.1 - # via monty -s3transfer==0.17.0 - # via boto3 -scipy==1.17.1 - # via pymatgen-core -send2trash==2.1.0 - # via - # jupyter-server - # notebook -setproctitle==1.3.7 - # via mpcontribs-api (pyproject.toml) -six==1.17.0 - # via - # flasgger-tschaume - # flask-sse - # python-dateutil - # rfc3339-validator -soupsieve==2.8.3 - # via beautifulsoup4 -spglib==2.7.0 - # via pymatgen-core -stack-data==0.6.3 - # via ipython -supervisor==4.3.0 - # via mpcontribs-api (pyproject.toml) -sympy==1.14.0 - # via pymatgen-core -tabulate==0.10.0 - # via pymatgen-core -terminado==0.18.1 - # via - # jupyter-server - # jupyter-server-terminals - # notebook -tinycss2==1.4.0 - # via bleach -tornado==6.5.5 - # via - # ipykernel - # jupyter-client - # jupyter-server - # notebook - # terminado -tqdm==4.67.3 - # via pymatgen-core -traitlets==5.15.0 - # via - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # jupyter-events - # jupyter-server - # matplotlib-inline - # nbclient - # nbconvert - # nbformat - # notebook -typing-extensions==4.15.0 - # via - # anyio - # beautifulsoup4 - # flexcache - # flexparser - # ipython - # opentelemetry-api - # pint - # pyopenssl - # referencing - # spglib -tzdata==2026.2 - # via arrow -tzlocal==5.3.1 - # via dateparser -uncertainties==3.2.3 - # via - # mpcontribs-api (pyproject.toml) - # pymatgen-core -uri-template==1.3.0 - # via jsonschema -urllib3==2.7.0 - # via - # botocore - # requests -wcwidth==0.7.0 - # via prompt-toolkit -webcolors==25.10.0 - # via jsonschema -webencodings==0.5.1 - # via - # bleach - # tinycss2 -websocket-client==1.9.0 - # via - # jupyter-server - # mpcontribs-api (pyproject.toml) -werkzeug==3.1.8 - # via - # flasgger-tschaume - # flask -wrapt==2.1.2 - # via ddtrace -zipp==3.23.1 - # via importlib-metadata -zope-event==6.2 - # via gevent -zope-interface==8.4 - # via gevent -zstandard==0.25.0 - # via mpcontribs-api (pyproject.toml) diff --git a/mpcontribs-api/requirements/ubuntu-latest_py3.11_extras.txt b/mpcontribs-api/requirements/ubuntu-latest_py3.11_extras.txt deleted file mode 100644 index 6387c63ec..000000000 --- a/mpcontribs-api/requirements/ubuntu-latest_py3.11_extras.txt +++ /dev/null @@ -1,648 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --all-extras --output-file=requirements/ubuntu-latest_py3.11_extras.txt -# -anyio==4.13.0 - # via jupyter-server -apispec==5.2.2 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -argon2-cffi==25.1.0 - # via - # jupyter-server - # notebook -argon2-cffi-bindings==25.1.0 - # via argon2-cffi -arrow==1.4.0 - # via isoduration -asn1crypto==1.5.1 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -asttokens==3.0.1 - # via stack-data -atlasq-tschaume==0.11.1.dev2 - # via flask-mongorest-mpcontribs -attrs==26.1.0 - # via - # jsonschema - # referencing -backports-zstd==1.5.0 - # via flask-compress -beautifulsoup4==4.14.3 - # via nbconvert -bibtexparser==1.4.4 - # via pymatgen-core -bleach[css]==6.3.0 - # via nbconvert -blinker==1.9.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -boltons==25.0.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -boto3==1.43.9 - # via flask-mongorest-mpcontribs -botocore==1.43.9 - # via - # boto3 - # s3transfer -brotli==1.2.0 - # via flask-compress -bytecode==0.17.0 - # via ddtrace -certifi==2026.4.22 - # via requests -cffi==2.0.0 - # via - # argon2-cffi-bindings - # cryptography -charset-normalizer==3.4.7 - # via requests -click==8.4.0 - # via - # flask - # rq -comm==0.2.3 - # via ipykernel -contourpy==1.3.3 - # via matplotlib -cramjam==2.11.0 - # via python-snappy -crontab==1.0.5 - # via rq-scheduler -cryptography==48.0.0 - # via pyopenssl -css-html-js-minify==2.5.5 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -cycler==0.12.1 - # via matplotlib -dateparser==1.4.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -ddtrace==4.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -debugpy==1.8.20 - # via ipykernel -decorator==5.3.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert -dnspython==2.8.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # pymongo -entrypoints==0.4 - # via jupyter-client -envier==0.6.1 - # via ddtrace -execnet==2.1.2 - # via pytest-xdist -executing==2.2.1 - # via stack-data -fastjsonschema==2.21.2 - # via nbformat -fastnumbers==5.1.1 - # via flask-mongorest-mpcontribs -filetype==1.2.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flake8==7.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # pytest-flake8 -flasgger-tschaume==0.9.7 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flask==2.2.5 - # via - # flasgger-tschaume - # flask-compress - # flask-marshmallow - # flask-mongoengine-tschaume - # flask-rq2 - # flask-sse -flask-compress==1.24 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flask-marshmallow==1.4.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flask-mongoengine-tschaume==1.1.0 - # via flask-mongorest-mpcontribs -flask-mongorest-mpcontribs==3.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flask-rq2==18.3 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flask-sse==1.0.0 - # via flask-mongorest-mpcontribs -flatten-dict==0.5.0 - # via flask-mongorest-mpcontribs -flexcache==0.3 - # via pint -flexparser==0.4 - # via pint -fonttools==4.63.0 - # via matplotlib -fqdn==1.5.1 - # via jsonschema -freezegun==1.5.5 - # via rq-scheduler -gevent==26.4.0 - # via gunicorn -greenlet==3.5.0 - # via gevent -gunicorn[gevent]==24.1.1 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -idna==3.15 - # via - # anyio - # jsonschema - # requests -importlib-metadata==8.7.1 - # via opentelemetry-api -iniconfig==2.3.0 - # via pytest -ipykernel==6.29.5 - # via - # nbclassic - # notebook -ipython==9.13.0 - # via ipykernel -ipython-genutils==0.2.0 - # via - # nbclassic - # notebook -ipython-pygments-lexers==1.1.1 - # via ipython -isoduration==20.11.0 - # via jsonschema -itsdangerous==2.2.0 - # via flask -jedi==0.20.0 - # via ipython -jinja2==3.1.6 - # via - # flask - # jupyter-server - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # nbconvert - # notebook -jmespath==1.1.0 - # via - # boto3 - # botocore -joblib==1.5.3 - # via pymatgen-core -json2html==1.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -jsonpointer==3.1.1 - # via jsonschema -jsonschema[format-nongpl]==4.26.0 - # via - # flasgger-tschaume - # jupyter-events - # nbformat -jsonschema-specifications==2025.9.1 - # via jsonschema -jupyter-client==7.4.9 - # via - # ipykernel - # jupyter-server - # nbclient - # notebook -jupyter-core==5.9.1 - # via - # ipykernel - # jupyter-client - # jupyter-server - # nbclient - # nbconvert - # nbformat - # notebook -jupyter-events==0.12.1 - # via jupyter-server -jupyter-server==2.18.2 - # via notebook-shim -jupyter-server-terminals==0.5.4 - # via jupyter-server -jupyterlab-pygments==0.3.0 - # via nbconvert -kiwisolver==1.5.0 - # via matplotlib -lark==1.3.1 - # via rfc3987-syntax -lxml==6.1.0 - # via pymatgen-core -markupsafe==3.0.3 - # via - # jinja2 - # nbconvert - # werkzeug -marshmallow==3.26.2 - # via - # flask-marshmallow - # marshmallow-mongoengine - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -marshmallow-mongoengine==0.31.2 - # via flask-mongorest-mpcontribs -matplotlib==3.10.9 - # via pymatgen-core -matplotlib-inline==0.2.2 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via flake8 -mimerender-pr36==0.0.2 - # via flask-mongorest-mpcontribs -mistune==3.2.1 - # via - # flasgger-tschaume - # nbconvert -mongoengine==0.29.3 - # via - # atlasq-tschaume - # flask-mongoengine-tschaume - # marshmallow-mongoengine -monty==2026.5.18 - # via pymatgen-core -more-itertools==11.0.2 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -mpcontribs-api[dev] @ file:///home/runner/work/MPContribs/MPContribs/mpcontribs-api - # via mpcontribs-api (pyproject.toml) -mpmath==1.3.0 - # via sympy -narwhals==2.21.2 - # via plotly -nbclassic==1.3.3 - # via notebook -nbclient==0.10.4 - # via nbconvert -nbconvert==7.17.1 - # via - # jupyter-server - # notebook -nbformat==5.10.4 - # via - # jupyter-server - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # nbclient - # nbconvert - # notebook -nest-asyncio==1.6.0 - # via - # ipykernel - # jupyter-client - # nbclassic - # notebook -networkx==3.6.1 - # via pymatgen-core -notebook==6.5.7 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -notebook-shim==0.2.4 - # via nbclassic -numpy==2.4.5 - # via - # contourpy - # matplotlib - # monty - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # pandas - # pymatgen-core - # scipy - # spglib -opentelemetry-api==1.41.1 - # via ddtrace -orjson==3.11.9 - # via - # flask-mongorest-mpcontribs - # pymatgen-core -overrides==7.7.0 - # via jupyter-server -packaging==26.2 - # via - # gunicorn - # ipykernel - # jupyter-events - # jupyter-server - # marshmallow - # matplotlib - # nbconvert - # plotly - # pytest -palettable==3.3.3 - # via pymatgen-core -pandas==3.0.3 - # via pymatgen-core -pandocfilters==1.5.1 - # via nbconvert -parso==0.8.7 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==12.2.0 - # via matplotlib -pint==0.25.3 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -platformdirs==4.9.6 - # via - # jupyter-core - # pint -plotly==6.7.0 - # via pymatgen-core -pluggy==1.6.0 - # via pytest -prometheus-client==0.25.0 - # via - # jupyter-server - # notebook -prompt-toolkit==3.0.52 - # via ipython -psutil==7.2.2 - # via - # ipykernel - # ipython -psycopg2-binary==2.9.12 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -ptyprocess==0.7.0 - # via - # pexpect - # terminado -pure-eval==0.2.3 - # via stack-data -pycodestyle==2.14.0 - # via - # flake8 - # pytest-pycodestyle -pycparser==3.0 - # via cffi -pyflakes==3.4.0 - # via flake8 -pygments==2.20.0 - # via - # ipython - # ipython-pygments-lexers - # nbconvert - # pytest -pymatgen==2026.5.4 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -pymatgen-core==2026.5.17 - # via pymatgen -pymongo==4.17.0 - # via - # flask-mongorest-mpcontribs - # mongoengine -pyopenssl==26.2.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -pyparsing==3.3.2 - # via - # bibtexparser - # matplotlib -pytest==9.0.3 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # pytest-flake8 - # pytest-pycodestyle - # pytest-xdist -pytest-flake8==1.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -pytest-pycodestyle==2.5.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -pytest-xdist==3.8.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -python-dateutil==2.9.0.post0 - # via - # arrow - # botocore - # dateparser - # flask-mongorest-mpcontribs - # freezegun - # jupyter-client - # matplotlib - # pandas - # rq-scheduler -python-json-logger==4.1.0 - # via jupyter-events -python-mimeparse==2.0.0 - # via mimerender-pr36 -python-snappy==0.7.3 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -pytz==2026.2 - # via dateparser -pyyaml==6.0.3 - # via - # flasgger-tschaume - # jupyter-events -pyzmq==27.1.0 - # via - # ipykernel - # jupyter-client - # jupyter-server - # notebook -redis==7.4.0 - # via - # flask-rq2 - # flask-sse - # rq -referencing==0.37.0 - # via - # jsonschema - # jsonschema-specifications - # jupyter-events -regex==2026.5.9 - # via dateparser -requests==2.34.2 - # via - # atlasq-tschaume - # pymatgen-core -rfc3339-validator==0.1.4 - # via - # jsonschema - # jupyter-events -rfc3986-validator==0.1.1 - # via - # jsonschema - # jupyter-events -rfc3987-syntax==1.1.0 - # via jsonschema -rpds-py==0.30.0 - # via - # jsonschema - # referencing -rq==2.3.2 - # via - # flask-rq2 - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # rq-scheduler -rq-scheduler==0.14.0 - # via flask-rq2 -ruamel-yaml==0.19.1 - # via monty -s3transfer==0.17.0 - # via boto3 -scipy==1.17.1 - # via pymatgen-core -send2trash==2.1.0 - # via - # jupyter-server - # notebook -setproctitle==1.3.7 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -six==1.17.0 - # via - # flasgger-tschaume - # flask-sse - # python-dateutil - # rfc3339-validator -soupsieve==2.8.3 - # via beautifulsoup4 -spglib==2.7.0 - # via pymatgen-core -stack-data==0.6.3 - # via ipython -supervisor==4.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -sympy==1.14.0 - # via pymatgen-core -tabulate==0.10.0 - # via pymatgen-core -terminado==0.18.1 - # via - # jupyter-server - # jupyter-server-terminals - # notebook -tinycss2==1.4.0 - # via bleach -tornado==6.5.5 - # via - # ipykernel - # jupyter-client - # jupyter-server - # notebook - # terminado -tqdm==4.67.3 - # via pymatgen-core -traitlets==5.15.0 - # via - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # jupyter-events - # jupyter-server - # matplotlib-inline - # nbclient - # nbconvert - # nbformat - # notebook -typing-extensions==4.15.0 - # via - # anyio - # beautifulsoup4 - # flexcache - # flexparser - # ipython - # opentelemetry-api - # pint - # pyopenssl - # referencing - # spglib -tzdata==2026.2 - # via arrow -tzlocal==5.3.1 - # via dateparser -uncertainties==3.2.3 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # pymatgen-core -uri-template==1.3.0 - # via jsonschema -urllib3==2.7.0 - # via - # botocore - # requests -wcwidth==0.7.0 - # via prompt-toolkit -webcolors==25.10.0 - # via jsonschema -webencodings==0.5.1 - # via - # bleach - # tinycss2 -websocket-client==1.9.0 - # via - # jupyter-server - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -werkzeug==3.1.8 - # via - # flasgger-tschaume - # flask -wrapt==2.1.2 - # via ddtrace -zipp==3.23.1 - # via importlib-metadata -zope-event==6.2 - # via gevent -zope-interface==8.4 - # via gevent -zstandard==0.25.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) diff --git a/mpcontribs-api/requirements/ubuntu-latest_py3.12.txt b/mpcontribs-api/requirements/ubuntu-latest_py3.12.txt deleted file mode 100644 index e9a48b299..000000000 --- a/mpcontribs-api/requirements/ubuntu-latest_py3.12.txt +++ /dev/null @@ -1,545 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.12 -# by the following command: -# -# pip-compile --output-file=requirements/ubuntu-latest_py3.12.txt -# -anyio==4.13.0 - # via jupyter-server -apispec==5.2.2 - # via mpcontribs-api (pyproject.toml) -argon2-cffi==25.1.0 - # via - # jupyter-server - # notebook -argon2-cffi-bindings==25.1.0 - # via argon2-cffi -arrow==1.4.0 - # via isoduration -asn1crypto==1.5.1 - # via mpcontribs-api (pyproject.toml) -asttokens==3.0.1 - # via stack-data -atlasq-tschaume==0.11.1.dev2 - # via flask-mongorest-mpcontribs -attrs==26.1.0 - # via - # jsonschema - # referencing -backports-zstd==1.5.0 - # via flask-compress -beautifulsoup4==4.14.3 - # via nbconvert -bibtexparser==1.4.4 - # via pymatgen-core -bleach[css]==6.3.0 - # via nbconvert -blinker==1.9.0 - # via mpcontribs-api (pyproject.toml) -boltons==25.0.0 - # via mpcontribs-api (pyproject.toml) -boto3==1.43.9 - # via flask-mongorest-mpcontribs -botocore==1.43.9 - # via - # boto3 - # s3transfer -brotli==1.2.0 - # via flask-compress -bytecode==0.17.0 - # via ddtrace -certifi==2026.4.22 - # via requests -cffi==2.0.0 - # via - # argon2-cffi-bindings - # cryptography -charset-normalizer==3.4.7 - # via requests -click==8.4.0 - # via - # flask - # rq -comm==0.2.3 - # via ipykernel -contourpy==1.3.3 - # via matplotlib -cramjam==2.11.0 - # via python-snappy -crontab==1.0.5 - # via rq-scheduler -cryptography==48.0.0 - # via pyopenssl -css-html-js-minify==2.5.5 - # via mpcontribs-api (pyproject.toml) -cycler==0.12.1 - # via matplotlib -dateparser==1.4.0 - # via mpcontribs-api (pyproject.toml) -ddtrace==4.3.0 - # via mpcontribs-api (pyproject.toml) -debugpy==1.8.20 - # via ipykernel -decorator==5.3.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert -dnspython==2.8.0 - # via - # mpcontribs-api (pyproject.toml) - # pymongo -entrypoints==0.4 - # via jupyter-client -envier==0.6.1 - # via ddtrace -executing==2.2.1 - # via stack-data -fastjsonschema==2.21.2 - # via nbformat -fastnumbers==5.1.1 - # via flask-mongorest-mpcontribs -filetype==1.2.0 - # via mpcontribs-api (pyproject.toml) -flasgger-tschaume==0.9.7 - # via mpcontribs-api (pyproject.toml) -flask==2.2.5 - # via - # flasgger-tschaume - # flask-compress - # flask-marshmallow - # flask-mongoengine-tschaume - # flask-rq2 - # flask-sse -flask-compress==1.24 - # via mpcontribs-api (pyproject.toml) -flask-marshmallow==1.4.0 - # via mpcontribs-api (pyproject.toml) -flask-mongoengine-tschaume==1.1.0 - # via flask-mongorest-mpcontribs -flask-mongorest-mpcontribs==3.3.0 - # via mpcontribs-api (pyproject.toml) -flask-rq2==18.3 - # via mpcontribs-api (pyproject.toml) -flask-sse==1.0.0 - # via flask-mongorest-mpcontribs -flatten-dict==0.5.0 - # via flask-mongorest-mpcontribs -flexcache==0.3 - # via pint -flexparser==0.4 - # via pint -fonttools==4.63.0 - # via matplotlib -fqdn==1.5.1 - # via jsonschema -freezegun==1.5.5 - # via rq-scheduler -gevent==26.4.0 - # via gunicorn -greenlet==3.5.0 - # via gevent -gunicorn[gevent]==24.1.1 - # via mpcontribs-api (pyproject.toml) -idna==3.15 - # via - # anyio - # jsonschema - # requests -importlib-metadata==8.7.1 - # via opentelemetry-api -ipykernel==6.29.5 - # via - # nbclassic - # notebook -ipython==9.13.0 - # via ipykernel -ipython-genutils==0.2.0 - # via - # nbclassic - # notebook -ipython-pygments-lexers==1.1.1 - # via ipython -isoduration==20.11.0 - # via jsonschema -itsdangerous==2.2.0 - # via flask -jedi==0.20.0 - # via ipython -jinja2==3.1.6 - # via - # flask - # jupyter-server - # mpcontribs-api (pyproject.toml) - # nbconvert - # notebook -jmespath==1.1.0 - # via - # boto3 - # botocore -joblib==1.5.3 - # via pymatgen-core -json2html==1.3.0 - # via mpcontribs-api (pyproject.toml) -jsonpointer==3.1.1 - # via jsonschema -jsonschema[format-nongpl]==4.26.0 - # via - # flasgger-tschaume - # jupyter-events - # nbformat -jsonschema-specifications==2025.9.1 - # via jsonschema -jupyter-client==7.4.9 - # via - # ipykernel - # jupyter-server - # nbclient - # notebook -jupyter-core==5.9.1 - # via - # ipykernel - # jupyter-client - # jupyter-server - # nbclient - # nbconvert - # nbformat - # notebook -jupyter-events==0.12.1 - # via jupyter-server -jupyter-server==2.18.2 - # via notebook-shim -jupyter-server-terminals==0.5.4 - # via jupyter-server -jupyterlab-pygments==0.3.0 - # via nbconvert -kiwisolver==1.5.0 - # via matplotlib -lark==1.3.1 - # via rfc3987-syntax -lxml==6.1.0 - # via pymatgen-core -markupsafe==3.0.3 - # via - # jinja2 - # nbconvert - # werkzeug -marshmallow==3.26.2 - # via - # flask-marshmallow - # marshmallow-mongoengine - # mpcontribs-api (pyproject.toml) -marshmallow-mongoengine==0.31.2 - # via flask-mongorest-mpcontribs -matplotlib==3.10.9 - # via pymatgen-core -matplotlib-inline==0.2.2 - # via - # ipykernel - # ipython -mimerender-pr36==0.0.2 - # via flask-mongorest-mpcontribs -mistune==3.2.1 - # via - # flasgger-tschaume - # nbconvert -mongoengine==0.29.3 - # via - # atlasq-tschaume - # flask-mongoengine-tschaume - # marshmallow-mongoengine -monty==2026.5.18 - # via pymatgen-core -more-itertools==11.0.2 - # via mpcontribs-api (pyproject.toml) -mpmath==1.3.0 - # via sympy -narwhals==2.21.2 - # via plotly -nbclassic==1.3.3 - # via notebook -nbclient==0.10.4 - # via nbconvert -nbconvert==7.17.1 - # via - # jupyter-server - # notebook -nbformat==5.10.4 - # via - # jupyter-server - # mpcontribs-api (pyproject.toml) - # nbclient - # nbconvert - # notebook -nest-asyncio==1.6.0 - # via - # ipykernel - # jupyter-client - # nbclassic - # notebook -networkx==3.6.1 - # via pymatgen-core -notebook==6.5.7 - # via mpcontribs-api (pyproject.toml) -notebook-shim==0.2.4 - # via nbclassic -numpy==2.4.5 - # via - # contourpy - # matplotlib - # monty - # mpcontribs-api (pyproject.toml) - # pandas - # pymatgen-core - # scipy - # spglib -opentelemetry-api==1.41.1 - # via ddtrace -orjson==3.11.9 - # via - # flask-mongorest-mpcontribs - # pymatgen-core -packaging==26.2 - # via - # gunicorn - # ipykernel - # jupyter-events - # jupyter-server - # marshmallow - # matplotlib - # nbconvert - # plotly -palettable==3.3.3 - # via pymatgen-core -pandas==3.0.3 - # via pymatgen-core -pandocfilters==1.5.1 - # via nbconvert -parso==0.8.7 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==12.2.0 - # via matplotlib -pint==0.25.3 - # via mpcontribs-api (pyproject.toml) -platformdirs==4.9.6 - # via - # jupyter-core - # pint -plotly==6.7.0 - # via pymatgen-core -prometheus-client==0.25.0 - # via - # jupyter-server - # notebook -prompt-toolkit==3.0.52 - # via ipython -psutil==7.2.2 - # via - # ipykernel - # ipython -psycopg2-binary==2.9.12 - # via mpcontribs-api (pyproject.toml) -ptyprocess==0.7.0 - # via - # pexpect - # terminado -pure-eval==0.2.3 - # via stack-data -pycparser==3.0 - # via cffi -pygments==2.20.0 - # via - # ipython - # ipython-pygments-lexers - # nbconvert -pymatgen==2026.5.4 - # via mpcontribs-api (pyproject.toml) -pymatgen-core==2026.5.17 - # via pymatgen -pymongo==4.17.0 - # via - # flask-mongorest-mpcontribs - # mongoengine -pyopenssl==26.2.0 - # via mpcontribs-api (pyproject.toml) -pyparsing==3.3.2 - # via - # bibtexparser - # matplotlib -python-dateutil==2.9.0.post0 - # via - # arrow - # botocore - # dateparser - # flask-mongorest-mpcontribs - # freezegun - # jupyter-client - # matplotlib - # pandas - # rq-scheduler -python-json-logger==4.1.0 - # via jupyter-events -python-mimeparse==2.0.0 - # via mimerender-pr36 -python-snappy==0.7.3 - # via mpcontribs-api (pyproject.toml) -pytz==2026.2 - # via dateparser -pyyaml==6.0.3 - # via - # flasgger-tschaume - # jupyter-events -pyzmq==27.1.0 - # via - # ipykernel - # jupyter-client - # jupyter-server - # notebook -redis==7.4.0 - # via - # flask-rq2 - # flask-sse - # rq -referencing==0.37.0 - # via - # jsonschema - # jsonschema-specifications - # jupyter-events -regex==2026.5.9 - # via dateparser -requests==2.34.2 - # via - # atlasq-tschaume - # pymatgen-core -rfc3339-validator==0.1.4 - # via - # jsonschema - # jupyter-events -rfc3986-validator==0.1.1 - # via - # jsonschema - # jupyter-events -rfc3987-syntax==1.1.0 - # via jsonschema -rpds-py==0.30.0 - # via - # jsonschema - # referencing -rq==2.3.2 - # via - # flask-rq2 - # mpcontribs-api (pyproject.toml) - # rq-scheduler -rq-scheduler==0.14.0 - # via flask-rq2 -ruamel-yaml==0.19.1 - # via monty -s3transfer==0.17.0 - # via boto3 -scipy==1.17.1 - # via pymatgen-core -send2trash==2.1.0 - # via - # jupyter-server - # notebook -setproctitle==1.3.7 - # via mpcontribs-api (pyproject.toml) -six==1.17.0 - # via - # flasgger-tschaume - # flask-sse - # python-dateutil - # rfc3339-validator -soupsieve==2.8.3 - # via beautifulsoup4 -spglib==2.7.0 - # via pymatgen-core -stack-data==0.6.3 - # via ipython -supervisor==4.3.0 - # via mpcontribs-api (pyproject.toml) -sympy==1.14.0 - # via pymatgen-core -tabulate==0.10.0 - # via pymatgen-core -terminado==0.18.1 - # via - # jupyter-server - # jupyter-server-terminals - # notebook -tinycss2==1.4.0 - # via bleach -tornado==6.5.5 - # via - # ipykernel - # jupyter-client - # jupyter-server - # notebook - # terminado -tqdm==4.67.3 - # via pymatgen-core -traitlets==5.15.0 - # via - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # jupyter-events - # jupyter-server - # matplotlib-inline - # nbclient - # nbconvert - # nbformat - # notebook -typing-extensions==4.15.0 - # via - # anyio - # beautifulsoup4 - # flexcache - # flexparser - # opentelemetry-api - # pint - # pyopenssl - # referencing - # spglib -tzdata==2026.2 - # via arrow -tzlocal==5.3.1 - # via dateparser -uncertainties==3.2.3 - # via - # mpcontribs-api (pyproject.toml) - # pymatgen-core -uri-template==1.3.0 - # via jsonschema -urllib3==2.7.0 - # via - # botocore - # requests -wcwidth==0.7.0 - # via prompt-toolkit -webcolors==25.10.0 - # via jsonschema -webencodings==0.5.1 - # via - # bleach - # tinycss2 -websocket-client==1.9.0 - # via - # jupyter-server - # mpcontribs-api (pyproject.toml) -werkzeug==3.1.8 - # via - # flasgger-tschaume - # flask -wrapt==2.1.2 - # via ddtrace -zipp==3.23.1 - # via importlib-metadata -zope-event==6.2 - # via gevent -zope-interface==8.4 - # via gevent -zstandard==0.25.0 - # via mpcontribs-api (pyproject.toml) diff --git a/mpcontribs-api/requirements/ubuntu-latest_py3.12_extras.txt b/mpcontribs-api/requirements/ubuntu-latest_py3.12_extras.txt deleted file mode 100644 index cd894fd1d..000000000 --- a/mpcontribs-api/requirements/ubuntu-latest_py3.12_extras.txt +++ /dev/null @@ -1,645 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.12 -# by the following command: -# -# pip-compile --all-extras --output-file=requirements/ubuntu-latest_py3.12_extras.txt -# -anyio==4.13.0 - # via jupyter-server -apispec==5.2.2 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -argon2-cffi==25.1.0 - # via - # jupyter-server - # notebook -argon2-cffi-bindings==25.1.0 - # via argon2-cffi -arrow==1.4.0 - # via isoduration -asn1crypto==1.5.1 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -asttokens==3.0.1 - # via stack-data -atlasq-tschaume==0.11.1.dev2 - # via flask-mongorest-mpcontribs -attrs==26.1.0 - # via - # jsonschema - # referencing -backports-zstd==1.5.0 - # via flask-compress -beautifulsoup4==4.14.3 - # via nbconvert -bibtexparser==1.4.4 - # via pymatgen-core -bleach[css]==6.3.0 - # via nbconvert -blinker==1.9.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -boltons==25.0.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -boto3==1.43.9 - # via flask-mongorest-mpcontribs -botocore==1.43.9 - # via - # boto3 - # s3transfer -brotli==1.2.0 - # via flask-compress -bytecode==0.17.0 - # via ddtrace -certifi==2026.4.22 - # via requests -cffi==2.0.0 - # via - # argon2-cffi-bindings - # cryptography -charset-normalizer==3.4.7 - # via requests -click==8.4.0 - # via - # flask - # rq -comm==0.2.3 - # via ipykernel -contourpy==1.3.3 - # via matplotlib -cramjam==2.11.0 - # via python-snappy -crontab==1.0.5 - # via rq-scheduler -cryptography==48.0.0 - # via pyopenssl -css-html-js-minify==2.5.5 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -cycler==0.12.1 - # via matplotlib -dateparser==1.4.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -ddtrace==4.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -debugpy==1.8.20 - # via ipykernel -decorator==5.3.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert -dnspython==2.8.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # pymongo -entrypoints==0.4 - # via jupyter-client -envier==0.6.1 - # via ddtrace -execnet==2.1.2 - # via pytest-xdist -executing==2.2.1 - # via stack-data -fastjsonschema==2.21.2 - # via nbformat -fastnumbers==5.1.1 - # via flask-mongorest-mpcontribs -filetype==1.2.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flake8==7.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # pytest-flake8 -flasgger-tschaume==0.9.7 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flask==2.2.5 - # via - # flasgger-tschaume - # flask-compress - # flask-marshmallow - # flask-mongoengine-tschaume - # flask-rq2 - # flask-sse -flask-compress==1.24 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flask-marshmallow==1.4.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flask-mongoengine-tschaume==1.1.0 - # via flask-mongorest-mpcontribs -flask-mongorest-mpcontribs==3.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flask-rq2==18.3 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -flask-sse==1.0.0 - # via flask-mongorest-mpcontribs -flatten-dict==0.5.0 - # via flask-mongorest-mpcontribs -flexcache==0.3 - # via pint -flexparser==0.4 - # via pint -fonttools==4.63.0 - # via matplotlib -fqdn==1.5.1 - # via jsonschema -freezegun==1.5.5 - # via rq-scheduler -gevent==26.4.0 - # via gunicorn -greenlet==3.5.0 - # via gevent -gunicorn[gevent]==24.1.1 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -idna==3.15 - # via - # anyio - # jsonschema - # requests -importlib-metadata==8.7.1 - # via opentelemetry-api -iniconfig==2.3.0 - # via pytest -ipykernel==6.29.5 - # via - # nbclassic - # notebook -ipython==9.13.0 - # via ipykernel -ipython-genutils==0.2.0 - # via - # nbclassic - # notebook -ipython-pygments-lexers==1.1.1 - # via ipython -isoduration==20.11.0 - # via jsonschema -itsdangerous==2.2.0 - # via flask -jedi==0.20.0 - # via ipython -jinja2==3.1.6 - # via - # flask - # jupyter-server - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # nbconvert - # notebook -jmespath==1.1.0 - # via - # boto3 - # botocore -joblib==1.5.3 - # via pymatgen-core -json2html==1.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -jsonpointer==3.1.1 - # via jsonschema -jsonschema[format-nongpl]==4.26.0 - # via - # flasgger-tschaume - # jupyter-events - # nbformat -jsonschema-specifications==2025.9.1 - # via jsonschema -jupyter-client==7.4.9 - # via - # ipykernel - # jupyter-server - # nbclient - # notebook -jupyter-core==5.9.1 - # via - # ipykernel - # jupyter-client - # jupyter-server - # nbclient - # nbconvert - # nbformat - # notebook -jupyter-events==0.12.1 - # via jupyter-server -jupyter-server==2.18.2 - # via notebook-shim -jupyter-server-terminals==0.5.4 - # via jupyter-server -jupyterlab-pygments==0.3.0 - # via nbconvert -kiwisolver==1.5.0 - # via matplotlib -lark==1.3.1 - # via rfc3987-syntax -lxml==6.1.0 - # via pymatgen-core -markupsafe==3.0.3 - # via - # jinja2 - # nbconvert - # werkzeug -marshmallow==3.26.2 - # via - # flask-marshmallow - # marshmallow-mongoengine - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -marshmallow-mongoengine==0.31.2 - # via flask-mongorest-mpcontribs -matplotlib==3.10.9 - # via pymatgen-core -matplotlib-inline==0.2.2 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via flake8 -mimerender-pr36==0.0.2 - # via flask-mongorest-mpcontribs -mistune==3.2.1 - # via - # flasgger-tschaume - # nbconvert -mongoengine==0.29.3 - # via - # atlasq-tschaume - # flask-mongoengine-tschaume - # marshmallow-mongoengine -monty==2026.5.18 - # via pymatgen-core -more-itertools==11.0.2 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -mpcontribs-api[dev] @ file:///home/runner/work/MPContribs/MPContribs/mpcontribs-api - # via mpcontribs-api (pyproject.toml) -mpmath==1.3.0 - # via sympy -narwhals==2.21.2 - # via plotly -nbclassic==1.3.3 - # via notebook -nbclient==0.10.4 - # via nbconvert -nbconvert==7.17.1 - # via - # jupyter-server - # notebook -nbformat==5.10.4 - # via - # jupyter-server - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # nbclient - # nbconvert - # notebook -nest-asyncio==1.6.0 - # via - # ipykernel - # jupyter-client - # nbclassic - # notebook -networkx==3.6.1 - # via pymatgen-core -notebook==6.5.7 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -notebook-shim==0.2.4 - # via nbclassic -numpy==2.4.5 - # via - # contourpy - # matplotlib - # monty - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # pandas - # pymatgen-core - # scipy - # spglib -opentelemetry-api==1.41.1 - # via ddtrace -orjson==3.11.9 - # via - # flask-mongorest-mpcontribs - # pymatgen-core -packaging==26.2 - # via - # gunicorn - # ipykernel - # jupyter-events - # jupyter-server - # marshmallow - # matplotlib - # nbconvert - # plotly - # pytest -palettable==3.3.3 - # via pymatgen-core -pandas==3.0.3 - # via pymatgen-core -pandocfilters==1.5.1 - # via nbconvert -parso==0.8.7 - # via jedi -pexpect==4.9.0 - # via ipython -pillow==12.2.0 - # via matplotlib -pint==0.25.3 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -platformdirs==4.9.6 - # via - # jupyter-core - # pint -plotly==6.7.0 - # via pymatgen-core -pluggy==1.6.0 - # via pytest -prometheus-client==0.25.0 - # via - # jupyter-server - # notebook -prompt-toolkit==3.0.52 - # via ipython -psutil==7.2.2 - # via - # ipykernel - # ipython -psycopg2-binary==2.9.12 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -ptyprocess==0.7.0 - # via - # pexpect - # terminado -pure-eval==0.2.3 - # via stack-data -pycodestyle==2.14.0 - # via - # flake8 - # pytest-pycodestyle -pycparser==3.0 - # via cffi -pyflakes==3.4.0 - # via flake8 -pygments==2.20.0 - # via - # ipython - # ipython-pygments-lexers - # nbconvert - # pytest -pymatgen==2026.5.4 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -pymatgen-core==2026.5.17 - # via pymatgen -pymongo==4.17.0 - # via - # flask-mongorest-mpcontribs - # mongoengine -pyopenssl==26.2.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -pyparsing==3.3.2 - # via - # bibtexparser - # matplotlib -pytest==9.0.3 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # pytest-flake8 - # pytest-pycodestyle - # pytest-xdist -pytest-flake8==1.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -pytest-pycodestyle==2.5.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -pytest-xdist==3.8.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -python-dateutil==2.9.0.post0 - # via - # arrow - # botocore - # dateparser - # flask-mongorest-mpcontribs - # freezegun - # jupyter-client - # matplotlib - # pandas - # rq-scheduler -python-json-logger==4.1.0 - # via jupyter-events -python-mimeparse==2.0.0 - # via mimerender-pr36 -python-snappy==0.7.3 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -pytz==2026.2 - # via dateparser -pyyaml==6.0.3 - # via - # flasgger-tschaume - # jupyter-events -pyzmq==27.1.0 - # via - # ipykernel - # jupyter-client - # jupyter-server - # notebook -redis==7.4.0 - # via - # flask-rq2 - # flask-sse - # rq -referencing==0.37.0 - # via - # jsonschema - # jsonschema-specifications - # jupyter-events -regex==2026.5.9 - # via dateparser -requests==2.34.2 - # via - # atlasq-tschaume - # pymatgen-core -rfc3339-validator==0.1.4 - # via - # jsonschema - # jupyter-events -rfc3986-validator==0.1.1 - # via - # jsonschema - # jupyter-events -rfc3987-syntax==1.1.0 - # via jsonschema -rpds-py==0.30.0 - # via - # jsonschema - # referencing -rq==2.3.2 - # via - # flask-rq2 - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # rq-scheduler -rq-scheduler==0.14.0 - # via flask-rq2 -ruamel-yaml==0.19.1 - # via monty -s3transfer==0.17.0 - # via boto3 -scipy==1.17.1 - # via pymatgen-core -send2trash==2.1.0 - # via - # jupyter-server - # notebook -setproctitle==1.3.7 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -six==1.17.0 - # via - # flasgger-tschaume - # flask-sse - # python-dateutil - # rfc3339-validator -soupsieve==2.8.3 - # via beautifulsoup4 -spglib==2.7.0 - # via pymatgen-core -stack-data==0.6.3 - # via ipython -supervisor==4.3.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -sympy==1.14.0 - # via pymatgen-core -tabulate==0.10.0 - # via pymatgen-core -terminado==0.18.1 - # via - # jupyter-server - # jupyter-server-terminals - # notebook -tinycss2==1.4.0 - # via bleach -tornado==6.5.5 - # via - # ipykernel - # jupyter-client - # jupyter-server - # notebook - # terminado -tqdm==4.67.3 - # via pymatgen-core -traitlets==5.15.0 - # via - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # jupyter-events - # jupyter-server - # matplotlib-inline - # nbclient - # nbconvert - # nbformat - # notebook -typing-extensions==4.15.0 - # via - # anyio - # beautifulsoup4 - # flexcache - # flexparser - # opentelemetry-api - # pint - # pyopenssl - # referencing - # spglib -tzdata==2026.2 - # via arrow -tzlocal==5.3.1 - # via dateparser -uncertainties==3.2.3 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) - # pymatgen-core -uri-template==1.3.0 - # via jsonschema -urllib3==2.7.0 - # via - # botocore - # requests -wcwidth==0.7.0 - # via prompt-toolkit -webcolors==25.10.0 - # via jsonschema -webencodings==0.5.1 - # via - # bleach - # tinycss2 -websocket-client==1.9.0 - # via - # jupyter-server - # mpcontribs-api - # mpcontribs-api (pyproject.toml) -werkzeug==3.1.8 - # via - # flasgger-tschaume - # flask -wrapt==2.1.2 - # via ddtrace -zipp==3.23.1 - # via importlib-metadata -zope-event==6.2 - # via gevent -zope-interface==8.4 - # via gevent -zstandard==0.25.0 - # via - # mpcontribs-api - # mpcontribs-api (pyproject.toml) diff --git a/mpcontribs-api/scripts/healthchecks.py b/mpcontribs-api/scripts/healthchecks.py index e0b339616..ff3009573 100644 --- a/mpcontribs-api/scripts/healthchecks.py +++ b/mpcontribs-api/scripts/healthchecks.py @@ -1,5 +1,6 @@ import os import sys + import requests for deployment in os.environ.get("DEPLOYMENTS", "ml:10002").split(","): diff --git a/mpcontribs-api/scripts/start.sh b/mpcontribs-api/scripts/start.sh index dc4022f9b..145274328 100755 --- a/mpcontribs-api/scripts/start.sh +++ b/mpcontribs-api/scripts/start.sh @@ -8,15 +8,6 @@ sleep $zzz PMGRC=$HOME/.pmgrc.yaml [[ ! -e "$PMGRC" ]] && echo "PMG_DUMMY_VAR: dummy" >"$PMGRC" -STATS_ARG="" -SERVER_APP="mpcontribs.api:create_app()" -WAIT_FOR="wait-for-it.sh $JUPYTER_GATEWAY_HOST -q -t 50" - set -x -if [[ -n "$DD_TRACE_HOST" ]]; then - wait-for-it.sh "$DD_TRACE_HOST" -q -s -t 10 && STATS_ARG="--statsd-host $DD_AGENT_HOST:8125" || echo "WARNING: datadog agent unreachable" -fi - -[[ -n "$STATS_ARG" ]] && CMD="ddtrace-run gunicorn $STATS_ARG" || CMD="gunicorn" -exec $WAIT_FOR -- $CMD $SERVER_APP +exec uvicorn mpcontribs_api.app:app --host 0.0.0.0 --port "$API_PORT" --workers "${NWORKERS:-2}" diff --git a/mpcontribs-api/scripts/start_rq.sh b/mpcontribs-api/scripts/start_rq.sh index 812ef8be4..821f6e0d0 100755 --- a/mpcontribs-api/scripts/start_rq.sh +++ b/mpcontribs-api/scripts/start_rq.sh @@ -1,16 +1,20 @@ #!/bin/bash +# +# RQ worker placeholder. +# +# The FastAPI rewrite has not yet ported the background worker (the old worker ran +# `flask rq worker`, and Flask is gone). This stub exists so supervisord's `*-worker` +# programs — referenced by supervisord.conf.jinja and started by main.py's `start("rq:*")` +# — have a command to run and do not crash-loop or enter FATAL. +# +# It honors the same startup stagger as the api process, then blocks so supervisord sees a +# healthy RUNNING process. Replace the `exec sleep infinity` below with the real worker +# entrypoint once background processing is reimplemented. set -e zzz=$((DEPLOYMENT * 60)) echo "$SUPERVISOR_PROCESS_NAME: waiting for $zzz seconds before start..." -sleep $zzz +sleep "$zzz" -CMD="flask rq $1" -set -x - -if [[ -n "$DD_TRACE_HOST" ]]; then - wait-for-it.sh "$DD_TRACE_HOST" -q -s -t 10 && CMD="ddtrace-run $CMD" || echo "WARNING: datadog agent unreachable" -fi - -exec wait-for-it.sh "$JUPYTER_GATEWAY_HOST" -q -s -t 50 -- \ - wait-for-it.sh "$MPCONTRIBS_API_HOST" -q -s -t 15 -- $CMD +echo "$SUPERVISOR_PROCESS_NAME: RQ worker not yet ported to the FastAPI rewrite; idling." +exec sleep infinity diff --git a/mpcontribs-api/mpcontribs/api/contributions/__init__.py b/mpcontribs-api/src/mpcontribs_api/__init__.py similarity index 100% rename from mpcontribs-api/mpcontribs/api/contributions/__init__.py rename to mpcontribs-api/src/mpcontribs_api/__init__.py diff --git a/mpcontribs-api/src/mpcontribs_api/_openapi.py b/mpcontribs-api/src/mpcontribs_api/_openapi.py new file mode 100644 index 000000000..fcd06c91c --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/_openapi.py @@ -0,0 +1,47 @@ +openapi_tags = [ + { + "name": "projects", + "description": "contain provenance information about contributed datasets. Deleting projects will also delete " + "all contributions including tables, structures, attachments, notebooks and cards for the project. Only users " + "who have been added to a project can update its contents. While unpublished, only users on the project can " + "retrieve its data or view it on the Portal. Making a project public does not automatically publish all its " + "contributions, tables, attachments, and structures. These are separately set to public individually or in " + "bulk.", + }, + { + "name": "contributions", + "description": "contain simple hierarchical data which will show up as cards on the MP details page for MP " + "material(s). Tables (rows and columns), structures, and attachments can be added to a contribution. " + "Each contribution uses `mp-id` or composition as identifier to associate its data with the according entries " + "on MP. Only admins or users on the project can create, update or delete contributions, and while unpublished, " + "retrieve its data or view it on the Portal. Contribution components (tables, structures, and attachments) are " + "deleted along with a contribution.", + }, + { + "name": "structures", + "description": "are [pymatgen structures](https://pymatgen.org/pymatgen.electronic_structure.html) which can " + " be added to a contribution.", + }, + { + "name": "tables", + "description": "are simple spreadsheet-type tables with columns and rows saved as " + "[Polars DataFrames](https://docs.pola.rs/api/python/stable/reference/dataframe/index.html) which can be added " + "to a contribution.", + }, + { + "name": "attachments", + "description": "are files saved as objects in AWS S3 and not accessible for querying (only retrieval) which " + "can be added to a contribution.", + }, +] + +contact_info = { + "name": "MPContribs", + "url": "https://mpcontribs.org/", + "email": "contribs@materialsproject.org", +} + +license_info = { + "name": "Creative Commons Attribution 4.0 International License", + "url": "https://creativecommons.org/licenses/by/4.0/", +} diff --git a/mpcontribs-api/mpcontribs/api/projects/__init__.py b/mpcontribs-api/src/mpcontribs_api/api/v1/__init__.py similarity index 100% rename from mpcontribs-api/mpcontribs/api/projects/__init__.py rename to mpcontribs-api/src/mpcontribs_api/api/v1/__init__.py diff --git a/mpcontribs-api/src/mpcontribs_api/api/v1/router.py b/mpcontribs-api/src/mpcontribs_api/api/v1/router.py new file mode 100644 index 000000000..871ce25bd --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/api/v1/router.py @@ -0,0 +1,17 @@ +from fastapi import APIRouter + +from mpcontribs_api.domains.attachments.router import router as attachments_router +from mpcontribs_api.domains.contributions.router import router as contributions_router +from mpcontribs_api.domains.limits.router import router as limits_router +from mpcontribs_api.domains.projects.router import router as projects_router +from mpcontribs_api.domains.structures.router import router as structures_router +from mpcontribs_api.domains.tables.router import router as tables_router + +router = APIRouter() + +router.include_router(attachments_router, prefix="/attachments", tags=["attachments"]) +router.include_router(contributions_router, prefix="/contributions", tags=["contributions"]) +router.include_router(limits_router, prefix="/limits", tags=["limits"]) +router.include_router(projects_router, prefix="/projects", tags=["projects"]) +router.include_router(structures_router, prefix="/structures", tags=["structures"]) +router.include_router(tables_router, prefix="/tables", tags=["tables"]) diff --git a/mpcontribs-api/src/mpcontribs_api/app.py b/mpcontribs-api/src/mpcontribs_api/app.py new file mode 100644 index 000000000..58b77a2a7 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/app.py @@ -0,0 +1,140 @@ +from collections.abc import AsyncGenerator +from contextlib import AbstractAsyncContextManager, AsyncExitStack, asynccontextmanager +from typing import cast + +import aioboto3 +from beanie import init_beanie +from botocore.config import Config +from fastapi import Depends, FastAPI +from pymongo import AsyncMongoClient +from types_aiobotocore_s3 import S3Client + +from mpcontribs_api._openapi import contact_info, license_info, openapi_tags +from mpcontribs_api.api.v1.router import router as v1_router +from mpcontribs_api.authz import api_key_scheme +from mpcontribs_api.config import Settings, get_settings +from mpcontribs_api.domains._redirects.router import router as redirects_router +from mpcontribs_api.domains.attachments.models import Attachment +from mpcontribs_api.domains.contributions.models import Contribution +from mpcontribs_api.domains.healthcheck.router import router as healthcheck_router +from mpcontribs_api.domains.projects.models import Project +from mpcontribs_api.domains.structures.models import Structure +from mpcontribs_api.domains.tables.models import Table +from mpcontribs_api.exceptions import register_exception_handlers +from mpcontribs_api.logging import configure_logging, get_logger +from mpcontribs_api.middleware import ( + BodySizeLimitMiddleware, + RequestContextMiddleware, + configure_tracing, + instrument_app, +) + +logger = get_logger(__name__) + + +async def _setup_mongo(app: FastAPI, settings: Settings, stack: AsyncExitStack) -> None: + """Setting up app-wide access to MongoDB via AsyncMongoClient and Beanie""" + client = AsyncMongoClient( + settings.mongo.uri.get_secret_value(), + appname=settings.mongo.app_name, + maxPoolSize=settings.mongo.max_pool_size, + minPoolSize=settings.mongo.min_pool_size, + maxIdleTimeMS=settings.mongo.max_idle_time_ms, + timeoutMS=settings.mongo.timeout_ms, + serverSelectionTimeoutMS=settings.mongo.server_selection_timeout_ms, + retryWrites=True, + retryReads=True, + compressors=settings.mongo.compressors, + readPreference=settings.mongo.read_preference, + uuidRepresentation="standard", + ) + # Fail fast if the DB is unreachable + await client.admin.command("ping") + logger.info("connected to mongo", extra={"db": settings.mongo.db_name}) + stack.push_async_callback(client.close) + + app.state.mongo_client = client + app.state.db = client[settings.mongo.db_name] + await init_beanie( + database=client[settings.mongo.db_name], + document_models=[ + Project, + Contribution, + Attachment, + Structure, + Table, + ], + ) + + +async def _setup_s3(app: FastAPI, settings: Settings, stack: AsyncExitStack) -> None: + """Setting up app-wide access to AWS S3 via aioboto3""" + session = aioboto3.Session() + cm = cast( + AbstractAsyncContextManager[S3Client], + session.client( + "s3", + region_name=settings.aws.region, + config=Config(max_pool_connections=settings.aws.max_pool_connections), + ), + ) + s3 = await stack.enter_async_context(cm) + app.state.boto_session = session + app.state.s3 = s3 + logger.info("connected to s3") + + +def _build_lifespan(settings: Settings): + @asynccontextmanager + async def lifespan(app: FastAPI) -> AsyncGenerator[None]: + async with AsyncExitStack() as stack: + await _setup_mongo(app, settings, stack) + await _setup_s3(app, settings, stack) + yield + # stack unwinds in reverse: s3 closed, then mongo + + return lifespan + + +def create_app(settings: Settings | None = None) -> FastAPI: + settings = settings or get_settings() + # Register OTEL providers before logging so the logs pipeline attaches to live telemetry. + configure_tracing(settings) + configure_logging(settings) + + app = FastAPI( + title="mpcontribs-api", + description="Operations to contribute, update and retrieve materials data on Materials Project", + version=settings.version, + debug=settings.environment != "prod", + lifespan=_build_lifespan(settings), + terms_of_service="https://materialsproject.org/terms", + license_info=license_info, + contact=contact_info, + # openapi_url="/api/v1/openapi.json", + openapi_tags=openapi_tags, + swagger_ui_parameters={ + "docExpansion": "none", + }, + dependencies=[Depends(api_key_scheme)], + ) + + # Reject oversized request bodies before they're buffered into memory. Added before + # RequestContextMiddleware: Starlette inserts each added middleware at the front of the stack, + # so the later-added RequestContextMiddleware stays outermost and still access-logs rejections. + app.add_middleware(BodySizeLimitMiddleware, max_bytes=settings.mongo.max_request_bytes) + # Add request context to the logger + app.add_middleware(RequestContextMiddleware) + # Emit server-side request spans/metrics (no-op when telemetry is disabled). + instrument_app(app, settings) + register_exception_handlers(app) + app.include_router(healthcheck_router, prefix="/healthcheck") + app.include_router(v1_router, prefix="/api/v1") + # Legacy (root-path) endpoints: 308-redirect to /api/v1 where a counterpart + # exists, else 410 Gone. Registered last so it never shadows live routes. + app.include_router(redirects_router) + + return app + + +app = create_app() diff --git a/mpcontribs-api/src/mpcontribs_api/authz.py b/mpcontribs-api/src/mpcontribs_api/authz.py new file mode 100644 index 000000000..1982d1a12 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/authz.py @@ -0,0 +1,64 @@ +from typing import Any + +from fastapi.security import APIKeyHeader +from pydantic import BaseModel, ConfigDict, model_validator + +from mpcontribs_api.config import get_settings + +settings = get_settings() + + +api_key_scheme = APIKeyHeader( + name="X-API-KEY", + auto_error=False, + description="MP API key to authorize requests", +) + + +ADMIN_GROUP = settings.mongo.admin_group + + +class User(BaseModel): + """User definition derived from request headers. + + Attributes: + consumer_id (str | None): Kong id, for logging only + username (str | None): the username of the active user - if None, the user is anonymous + groups (frozenset[str]): the groups the user is part of - used for access control + """ + + model_config = ConfigDict(frozen=True) + consumer_id: str | None = None + username: str | None = None + groups: frozenset[str] = frozenset() + + @model_validator(mode="before") + @classmethod + def drop_admin_on_anonymous(cls, config: dict[str, Any]) -> dict[str, Any]: + if not config.get("username"): + groups = config.get("groups", frozenset()) + config["groups"] = frozenset(g for g in groups if g != ADMIN_GROUP) + return config + + @property + def is_anonymous(self) -> bool: + return self.username is None + + @property + def is_admin(self) -> bool: + return (not self.is_anonymous) and (ADMIN_GROUP in self.groups) + + def has_role(self, role: str) -> bool: + return role in self.groups + + @property + def writable_projects(self) -> frozenset[str]: + """Projects this user may write to. Admins are unbounded (handled by can_write)""" + if self.is_anonymous: + return frozenset() + # exclude the admin sentinel so it never leaks into a $in / membership test + return frozenset(g for g in self.groups if g != ADMIN_GROUP) + + def can_write(self, project: str) -> bool: + """Single source of truth for write authorization.""" + return self.is_admin or project in self.writable_projects diff --git a/mpcontribs-api/src/mpcontribs_api/config.py b/mpcontribs-api/src/mpcontribs_api/config.py new file mode 100644 index 000000000..3995eebb0 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/config.py @@ -0,0 +1,194 @@ +from functools import lru_cache +from typing import Literal + +from pydantic import BaseModel, Field, SecretStr, model_validator +from pydantic_settings import BaseSettings, SettingsConfigDict + + +class RedisSettings(BaseModel): + address: SecretStr + url: SecretStr + + +class ObservabilitySettings(BaseModel): + """OpenTelemetry settings. + + The application is vendor-neutral: it emits traces, metrics, and logs via OTLP/gRPC to a + collector (in our deployment, the Datadog Agent's OTLP receiver). Datadog is purely the backend. + """ + + enabled: bool = Field( + default=True, + description="Master switch for OTEL setup. Disable in tests/local runs without a collector.", + ) + service_name: str = Field( + default="contribs-apis", + description="Value of the service.name resource attribute. Kept as the legacy Datadog " + "service name so existing dashboards and monitors keep resolving.", + ) + otlp_endpoint: str = Field( + default="localhost:4317", + description="host:port of the OTLP/gRPC receiver (the Datadog Agent's OTLP endpoint).", + ) + insecure: bool = Field( + default=True, + description="Use an insecure (plaintext) gRPC channel. True for a local/sidecar agent without TLS.", + ) + metric_export_interval_ms: int = Field( + default=60_000, + description="How often (ms) the periodic metric reader exports to the collector.", + ) + + +class AwsSettings(BaseModel): + """AWS Settings + + Primarily used for S3 access + """ + + region: str = Field(default="us-east-1", description="The region to connect to") + max_pool_connections: int = Field( + default=10, + description="The maximum number of connections the app is allowed to have to S3", + ) + health_bucket: str = Field( + default="contributions", + description="The S3 bucket probed by the healthcheck to verify connectivity", + ) + + +class MongoSettings(BaseModel): + """MongoDB settings. + + Provided defaults are the defaults of AsyncMongoClient + """ + + # Required + uri: SecretStr = Field(description="The full uri from MongoDB (username and password included)") + db_name: str + + # Optional + app_name: str = Field( + default="MPContribs_FastAPI_Server", + description="The name of the application that created this AsyncMongoClient instance. The server will log this " + "value upon establishing each connection. It is also recorded in the slow query log and profile collections.", + ) + max_pool_size: int = Field( + default=100, + description="Maximum number of allowed concurrent connection to each server. Can be '0' or 'None', both of " + "which allow any number of connections", + ) + min_pool_size: int = Field( + default=0, + description="Minimum number of concurent connections that the pool will maintain connected to each server ", + ) + datetime_conversion: Literal["datetime_ms", "datetime", "datetime_auto", "datetime_clamp"] = Field( + default="datetime", + description="Specifies how UTC datetimes should be decoded within BSON", + ) + server_selection_timeout_ms: int = Field( + default=30_000, + description="Controls how long (in milliseconds) the driver will wait to find an available, appropriate server " + "to carry out a database operation;" + "while it is waiting, multiple server monitoring operations may be carried out", + ) + + admin_group: str = Field( + default="admin", + description="Name of admin group to consider in requests to MongoDB. Not directly passed to Mongo, but " + "consumed by auth.", + ) + + compressors: str = Field( + default="snappy,zstd,zlib", + description="Comma separated list of compressors for wire protocol compression. Compression support must also " + "be enabled on the server", + ) + + read_preference: str = Field( + default="primary", + description="The replica set read preference for this client. One of primary, primaryPreferred, secondary, " + "secondaryPreferred, or nearest", + ) + + # TODO: Tune default + max_concurrent_transactions: int = Field( + default=16, + description="Upper bound on per-contribution transactions running in parallel during a bulk insert. Clamped at " + "construction to max_pool_size // 2 so reads on the same request can still acquire connections.", + ) + # TODO: Tune default + max_components_per_contribution: int = Field( + default=500, + description="Hard ceiling on structures + tables + attachments for a single contribution. Anything larger is " + "rejected upfront so we don't burn a transaction slot on a request guaranteed to exceed " + "transactionLifetimeLimitSeconds (default 60s).", + ) + # TODO: Tune default + component_insert_chunk_size: int = Field( + default=100, + description="Batch size used by component repositories when chunking insert_many calls inside a transaction.", + ) + # TODO: Tune default + max_request_bytes: int = Field( + default=16 * 1024 * 1024, + description="Hard ceiling on the size (bytes) of any single request body. Requests exceeding it are rejected " + "with 413 before the body is read into memory, so one caller can't OOM the worker. Mirrors the client's " + "MAX_PAYLOAD (15MB) with headroom.", + ) + # TODO: Tune default + bulk_write_limit: int = Field( + default=1000, + description="Maximum number of items accepted in a single bulk contribution POST/PUT. Larger batches are " + "rejected with 422; callers should chunk (or use the async ingestion endpoint). Advertised via GET /limits.", + ) + max_idle_time_ms: int = Field( + default=30_000, + description="The maximum allowed time a single connection is allowed to sit idle", + ) + timeout_ms: int = Field(default=60_000, description="The end-to-end allowed time for an operation") + + @model_validator(mode="after") + def _clamp_concurrency(self): + if self.max_pool_size: + per_request_cap = max(1, self.max_pool_size // 2) + if self.max_concurrent_transactions > per_request_cap: + self.max_concurrent_transactions = per_request_cap + return self + + +class Settings(BaseSettings): + model_config = SettingsConfigDict( + env_file=".env", + env_nested_delimiter="__", + env_prefix="MPCONTRIBS_", + ) + + environment: Literal["dev", "prod"] + + # MPContribs_mongo__* + # requires uri and db_name + mongo: MongoSettings + + # MPContribs_aws__* + aws: AwsSettings = Field(default_factory=AwsSettings) + + # MPContribs_redis__* + redis: RedisSettings + + # MPContribs_otel__* + otel: ObservabilitySettings = Field(default_factory=ObservabilitySettings) + + # SMTP Settings + mail_default_sender: str = Field( + description="SMTP Server to send out notifications on new projects and other important moments" + ) + + # General/Informative settings + version: str + + +@lru_cache +def get_settings() -> Settings: + # Fields are populated from env vars at runtime, not from arguments - pyright can't see that + return Settings() # pyright: ignore[reportCallIssue] diff --git a/mpcontribs-api/src/mpcontribs_api/dependencies.py b/mpcontribs-api/src/mpcontribs_api/dependencies.py new file mode 100644 index 000000000..cadf3d001 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/dependencies.py @@ -0,0 +1,85 @@ +from typing import Annotated + +import aioboto3 +import structlog +from fastapi import Depends, Request +from pymongo import AsyncMongoClient +from pymongo.asynchronous.database import AsyncDatabase +from types_aiobotocore_s3 import S3Client + +from mpcontribs_api.authz import User +from mpcontribs_api.exceptions import AuthenticationError + + +def get_db(request: Request) -> AsyncDatabase: + return request.app.state.db + + +DbDep = Annotated[AsyncDatabase, Depends(get_db)] + + +def get_boto(request: Request) -> aioboto3.Session: + return request.app.state.boto_session + + +BotoDep = Annotated[aioboto3.Session, Depends(get_boto)] + + +def get_s3(request: Request) -> S3Client: + return request.app.state.s3 + + +S3Dep = Annotated[S3Client, Depends(get_s3)] + + +def get_mongo_client(request: Request) -> AsyncMongoClient: + return request.app.state.mongo_client + + +MongoClientDep = Annotated[AsyncMongoClient, Depends(get_mongo_client)] + + +def _split(raw: str | None) -> set[str]: + return {g.strip() for g in (raw or "").split(",") if g.strip()} + + +def get_user(request: Request) -> User: + """Dissects request headers for user-related keys.""" + h = request.headers + explicit_anon = h.get("x-anonymous-consumer", "").lower() == "true" + username = h.get("x-consumer-username") or None + if explicit_anon or username is None: + user = User() # anonymous = all defaults + else: + groups = _split(h.get("x-authenticated-groups")) | _split(h.get("x-consumer-groups")) + user = User( + consumer_id=h.get("x-consumer-id"), + username=username, + groups=frozenset(groups), + ) + structlog.contextvars.bind_contextvars( + consumer_id=user.consumer_id, + is_admin=user.is_admin, + ) + return user + + +UserDep = Annotated[User, Depends(get_user)] + + +def require_user(user: UserDep) -> User: + if user.is_anonymous: + raise AuthenticationError("authentication required") + return user + + +# AuthedDep = Annotated[User, Depends(require_user)] + + +# def require_role(role: str): +# def checker(user: AuthedDep) -> User: +# if not user.has_role(role): +# raise PermissionError(required_role=role) +# return user + +# return Annotated[User, Depends(checker)] diff --git a/mpcontribs-api/src/mpcontribs_api/domains/_redirects/router.py b/mpcontribs-api/src/mpcontribs_api/domains/_redirects/router.py new file mode 100644 index 000000000..d965e4eec --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/_redirects/router.py @@ -0,0 +1,161 @@ +"""Compatibility shims for the legacy (Flask/flask-mongorest) MPContribs API. + +The old API was served from the root path (e.g. ``/contributions/``, +``/projects//``). The rewrite serves everything under ``/api/v1`` with +slightly different paths and verbs. This router is mounted at the root and: + +- 308-redirects every legacy endpoint that has a direct counterpart to its new + location (preserving method, body, and query string), and +- returns ``410 Gone`` with a machine-readable "deprecated" body for legacy + endpoints that have no equivalent in the new API (notebooks, the formula/term + search helpers, project-application approval links, and project creation). + +Redirects are permanent (308) so well-behaved clients update their bookmarks +while keeping the original HTTP method and request body intact. +""" + +from fastapi import APIRouter, Request +from fastapi.responses import JSONResponse, RedirectResponse +from starlette.status import HTTP_308_PERMANENT_REDIRECT, HTTP_410_GONE + +router = APIRouter(include_in_schema=False) + +# Base path of the new API. The legacy API lived at the service root. +API_V1 = "/api/v1" + + +def _redirect(request: Request, new_path: str) -> RedirectResponse: + """308-redirect to ``new_path`` under the v1 API, preserving the query string. + + 308 (rather than 301/302) keeps the original method and body, so a legacy + ``POST``/``PUT``/``DELETE`` is replayed against the new endpoint instead of + being silently downgraded to a ``GET``. + """ + target = f"{API_V1}{new_path}" + if request.url.query: + target = f"{target}?{request.url.query}" + return RedirectResponse(url=target, status_code=HTTP_308_PERMANENT_REDIRECT) + + +def _deprecated(message: str, *, replacement: str | None = None) -> JSONResponse: + """Return a ``410 Gone`` in the app's uniform error shape. + + Used for legacy endpoints that have no counterpart in the new API. + """ + detail: dict[str, str] = {} + if replacement is not None: + detail["replacement"] = replacement + body: dict = {"error": {"code": "endpoint_deprecated", "message": message}} + if detail: + body["error"]["detail"] = detail + return JSONResponse( + status_code=HTTP_410_GONE, + content=body, + headers={"Deprecation": "true"}, + ) + + +# --------------------------------------------------------------------------- +# contributions +# --------------------------------------------------------------------------- +@router.get("/contributions/search") +def redirect_contributions_search() -> JSONResponse: + # Formula autocomplete (Atlas $search) was not ported to the new API. + return _deprecated("The contributions formula search endpoint has been removed.") + + +@router.get("/contributions/download/{short_mime}/") +def redirect_download_contributions(request: Request, short_mime: str) -> RedirectResponse: + return _redirect(request, f"/contributions/download/{short_mime}") + + +@router.api_route("/contributions/", methods=["GET", "POST", "PUT", "DELETE"]) +def redirect_contributions_collection(request: Request) -> RedirectResponse: + # GET=list, POST=bulk insert, PUT=bulk upsert, DELETE=delete-by-filter. + return _redirect(request, "/contributions") + + +@router.api_route("/contributions/{pk}/", methods=["GET", "PUT", "DELETE"]) +def redirect_contribution_item(request: Request, pk: str) -> RedirectResponse: + # GET=fetch, PUT=update/upsert, DELETE=delete (all keyed by id). + return _redirect(request, f"/contributions/{pk}") + + +# --------------------------------------------------------------------------- +# projects +# --------------------------------------------------------------------------- +@router.get("/projects/search") +def redirect_projects_search() -> JSONResponse: + return _deprecated("The projects search endpoint has been removed.") + + +@router.get("/projects/applications/{token}") +@router.get("/projects/applications/{token}/{action}") +def redirect_projects_applications(token: str, action: str | None = None) -> JSONResponse: + # Email-driven project approval/denial links; not part of the new API. + return _deprecated("Project application approval links have been removed.") + + +@router.api_route("/projects/", methods=["GET", "POST"], response_model=None) +def redirect_projects_collection(request: Request) -> RedirectResponse | JSONResponse: + if request.method == "POST": + # No project-creation endpoint exists in the new API. + return _deprecated( + "Creating projects via POST is no longer supported. Create a project with PUT /api/v1/projects/{id}.", + replacement=f"{API_V1}/projects/{{id}}", + ) + return _redirect(request, "/projects") + + +@router.api_route("/projects/{pk}/", methods=["GET", "PUT", "DELETE"]) +def redirect_project_item(request: Request, pk: str) -> RedirectResponse: + # GET=fetch, PUT=update/upsert, DELETE=delete. + return _redirect(request, f"/projects/{pk}") + + +# --------------------------------------------------------------------------- +# Components +# --------------------------------------------------------------------------- +def _register_component_redirects(component: str) -> None: + @router.get(f"/{component}/download/{{short_mime}}/", name=f"redirect_download_{component}") + def redirect_download(request: Request, short_mime: str) -> RedirectResponse: + return _redirect(request, f"/{component}/download/{short_mime}") + + @router.get(f"/{component}/", name=f"redirect_{component}_collection") + def redirect_collection(request: Request) -> RedirectResponse: + return _redirect(request, f"/{component}") + + @router.get(f"/{component}/{{pk}}/", name=f"redirect_{component}_item") + def redirect_item(request: Request, pk: str) -> RedirectResponse: + return _redirect(request, f"/{component}/{pk}") + + +for _component in ("structures", "tables", "attachments"): + _register_component_redirects(_component) + + +# --------------------------------------------------------------------------- +# notebooks +# --------------------------------------------------------------------------- +_NOTEBOOKS_GONE = "The notebooks API has been removed." + + +@router.get("/notebooks/build") +def redirect_notebooks_build() -> JSONResponse: + return _deprecated(_NOTEBOOKS_GONE) + + +@router.get("/notebooks/result") +@router.get("/notebooks/result/{job_id}") +def redirect_notebooks_result(job_id: str | None = None) -> JSONResponse: + return _deprecated(_NOTEBOOKS_GONE) + + +@router.get("/notebooks/") +def redirect_notebooks_collection() -> JSONResponse: + return _deprecated(_NOTEBOOKS_GONE) + + +@router.get("/notebooks/{pk}/") +def redirect_notebooks_item(pk: str) -> JSONResponse: + return _deprecated(_NOTEBOOKS_GONE) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/_shared/bulk.py b/mpcontribs-api/src/mpcontribs_api/domains/_shared/bulk.py new file mode 100644 index 000000000..718e2c580 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/_shared/bulk.py @@ -0,0 +1,44 @@ +from typing import Any + +from pydantic import BaseModel + +from mpcontribs_api.exceptions import AppError + + +class BulkFailure(BaseModel): + """A single failed item in a bulk write, identified by its position in the input batch.""" + + index: int + identifier: dict[str, Any] | None = None + error_code: str + message: str + + +class BulkWriteSummary[T](BaseModel): + """Result of a bulk write that supports per-item failure reporting. + + ``total`` is the size of the input batch (succeeded + failed). ``succeeded`` carries the + fully inserted documents; ``failed`` carries one ``BulkFailure`` per rejected item, with + enough context for the caller to retry just those items. + """ + + total: int + succeeded: list[T] + failed: list[BulkFailure] + + +class BulkDeleteSummary[T](BaseModel): + num_deleted: int + num_children_deleted: int + + +def bulk_failure_from_exception(index: int, identifier: dict[str, Any] | None, exc: BaseException) -> BulkFailure: + """Translate any exception into a BulkFailure entry. + + ``AppError`` subclasses contribute their ``error_code`` and ``message``; everything else + collapses to ``internal_error`` with the exception class name in the message so we don't + leak tracebacks or framework internals to the client. + """ + if isinstance(exc, AppError): + return BulkFailure(index=index, identifier=identifier, error_code=exc.error_code, message=exc.message) + return BulkFailure(index=index, identifier=identifier, error_code="internal_error", message=type(exc).__name__) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/_shared/components.py b/mpcontribs-api/src/mpcontribs_api/domains/_shared/components.py new file mode 100644 index 000000000..1af1edb05 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/_shared/components.py @@ -0,0 +1,151 @@ +from typing import Any + +from beanie.operators import In +from fastapi_filter.contrib.beanie import Filter +from pydantic import BaseModel +from pymongo.asynchronous.client_session import AsyncClientSession + +from mpcontribs_api.authz import User +from mpcontribs_api.config import get_settings +from mpcontribs_api.domains._shared.models import Component, ComponentIn, DeleteResponse, DocumentOut +from mpcontribs_api.domains._shared.repository import MongoDbRepository +from mpcontribs_api.domains._shared.types import MD5Hash +from mpcontribs_api.exceptions import NotFoundError + + +class MongoDbComponentsRepository[ + TDoc: Component, + TIn: ComponentIn, + TOut: DocumentOut, + TFilter: Filter, + TPatch: BaseModel, +](MongoDbRepository[TDoc, TIn, TOut, TFilter, TPatch]): + @staticmethod + def _build_scope(user: User) -> dict[str, Any]: + return {} + + async def _existing_by_md5( + self, + md5s: list[MD5Hash], + session: AsyncClientSession | None = None, + ) -> dict[str, TDoc]: + # Full fetch so existing docs come back with their ids + # TODO: Most likely does a COLLSCAN - see if we can project to get a COVERED QUERY + existing_docs = await self.document_model.find( + In(self.document_model.md5, md5s), + session=session, + ).to_list() + return {doc.md5: doc for doc in existing_docs} + + async def insert_components( + self, + components: list[TIn], + session: AsyncClientSession | None = None, + ) -> list[TDoc]: + """Bulk-insert components, deduplicated by server-computed content hash. + + Each input is built into a full document via ``Component.from_input``, which assigns a fresh + id and computes ``md5`` from the content (the client never supplies it). Inputs are + deduplicated by md5 — both against documents already stored and against each other — so the + return list has one entry per *unique* content, in first-seen order. + + Args: + components (list[TIn]): components to insert + session (AsyncClientSession): optional client session; pass when inserting inside a transaction + """ + # Build full docs up front so md5 is server-computed before any dedup decision. + docs = [self.document_model.from_input(comp) for comp in components] + existing_by_md5 = await self._existing_by_md5([doc.md5 for doc in docs], session=session) + + # First-seen unique md5 order, and the new documents that need inserting. + unique_md5s: list[str] = [] + new_by_md5: dict[str, TDoc] = {} + for doc in docs: + if doc.md5 not in existing_by_md5 and doc.md5 not in new_by_md5: + new_by_md5[doc.md5] = doc + if doc.md5 not in unique_md5s: + unique_md5s.append(doc.md5) + + # Insert by chunks to stay within a transaction's payload budget. + new_docs = list(new_by_md5.values()) + chunk_size = get_settings().mongo.component_insert_chunk_size + for start in range(0, len(new_docs), chunk_size): + await self.document_model.insert_many( + new_docs[start : start + chunk_size], + ordered=False, + session=session, + ) + + # One resolved document per unique md5, in first-seen order. + resolved = existing_by_md5 | new_by_md5 + return [resolved[md5] for md5 in unique_md5s] + + async def insert_component(self, component: TIn, *, session: AsyncClientSession | None = None) -> TDoc: + """Insert a single component. + + Args: + component (TIn): the table to insert + + Returns: + TDoc: the component actually in the database + + Raises: + AppError: If insert_one returns None, raises + """ + return (await self.insert_components(components=[component], session=session))[0] + + async def get_component_by_id(self, id: str, fields: frozenset[str] | None) -> TDoc | TOut | None: + """Find a single component by id. See ``get_by_id``.""" + return await self.get_by_id(self._convert_object_id(id), fields) + + async def delete_components( + self, + filter: TFilter, + session: AsyncClientSession | None = None, + ) -> DeleteResponse: + """Deletes all components matching ``filter``. + + Args: + filter (TFilter): the query to filter components by + session (AsyncClientSession | None): the current session, used to guarantee transactions + + Returns: + DeleteResponse: A report of the deletion + """ + query = filter.filter(self.document_model.find(self._scope, session=session)) + result = await query.delete(session=session) + return DeleteResponse(num_deleted=result.deleted_count if result else 0) + + async def delete_component_by_id( + self, + id: str, + session: AsyncClientSession | None = None, + ) -> DeleteResponse: + """Deletes a single component by Id. + + Args: + id (str): the str representation of the component's ObjectId + session (AsyncClientSession | None): the current session, used to guarantee transactions + + Returns: + DeleteResponse: A report of the deletion + """ + return await self.delete_by_id(id=self._convert_object_id(id), session=session) + + async def patch_component_by_id(self, id: str, update: TPatch) -> TDoc: + """Partially update a component by id, recomputing its content hash. + + Components are content-addressed, so a content change must update ``md5``. Unlike the base + ``patch`` (an in-place ``$set``), this loads the full document, applies the set fields, + recomputes ``md5`` from ``hash_fields``, and saves — keeping md5 consistent with content. + """ + oid = self._convert_object_id(id) + doc = await self.document_model.find_one(self._scope, self.document_model.id == oid) + if doc is None: + raise NotFoundError(self._not_found(id)) + update_data = update.model_dump(exclude_unset=True) + for field, value in update_data.items(): + setattr(doc, field, value) + doc.md5 = doc.compute_md5() + await doc.save() + return doc diff --git a/mpcontribs-api/src/mpcontribs_api/domains/_shared/filters.py b/mpcontribs-api/src/mpcontribs_api/domains/_shared/filters.py new file mode 100644 index 000000000..027d25dfb --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/_shared/filters.py @@ -0,0 +1,23 @@ +from collections.abc import Mapping +from typing import Any + +from fastapi_filter.contrib.beanie import Filter + + +class BaseFilter(Filter): + """Base filter that bridges Beanie's ``_id`` alias and fastapi-filter's raw field names. + + Beanie stores a document's primary key under Mongo's ``_id`` (``id`` is just a Pydantic alias), + but fastapi-filter builds query keys from the raw field name read off ``model_dump`` — without + aliases. An ``id`` filter would therefore query a non-existent ``{"id": ...}`` key and match + nothing, while a direct ``Document.id == x`` lookup (which Beanie resolves to ``_id``) succeeds. + Remapping the ``id`` key to ``_id`` here keeps the two read paths consistent. + + Domain filters should subclass this instead of fastapi-filter's ``Filter`` directly. + """ + + def _get_filter_conditions(self, nesting_depth: int = 1) -> list[tuple[Mapping[str, Any], Mapping[str, Any]]]: + return [ + ({"_id" if key == "id" else key: value for key, value in condition.items()}, options) + for condition, options in super()._get_filter_conditions(nesting_depth) + ] diff --git a/mpcontribs-api/src/mpcontribs_api/domains/_shared/models.py b/mpcontribs-api/src/mpcontribs_api/domains/_shared/models.py new file mode 100644 index 000000000..2dfb073c6 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/_shared/models.py @@ -0,0 +1,126 @@ +import hashlib +import json +import unicodedata +from collections.abc import Mapping +from typing import Annotated, Any, ClassVar, Self + +from beanie import Document, PydanticObjectId +from pydantic import BaseModel, Field, model_validator +from pymongo.results import DeleteResult + +from mpcontribs_api import pagination +from mpcontribs_api.domains._shared.types import MD5Hash +from mpcontribs_api.projection import SparseFieldsModel + + +class BaseDocumentWithInput[TId](Document): + """A stored resource document with a required ``id`` and an input counterpart. + + Subclasses bind their id type as ``TId``. The ``id`` is declared here as required and non-null so + the repository can always read and key on it, while ``TId`` lets each resource pick its own id + type (``ShortStr`` for projects, ``PydanticObjectId`` for contributions). ``from_input_model`` + translates a validated input payload into a full document; the base param is intentionally ``Any`` + so each resource's override can declare its concrete input model without violating LSP (input + models subclass their document, so they can't be bound as a class type parameter). + """ + + # Required, non-null, resource-specific id. Overrides Document's optional ``PydanticObjectId`` id. + id: TId = Field(alias="_id") # pyright: ignore[reportGeneralTypeIssues, reportIncompatibleVariableOverride] + + @classmethod + def from_input_model(cls, data: Any) -> Self: + """Translate a validated input payload into a full stored document.""" + return cls(**data.model_dump()) + + @staticmethod + def decode_cursor(cursor: str) -> str | PydanticObjectId: + """Decodes the cursor the an ObjectId""" + return PydanticObjectId(pagination.decode_cursor(cursor=cursor)) + + +class DocumentOut[TId](SparseFieldsModel): + """Base output model for resources addressed by an ``_id``. + + Mirrors :class:`BaseDocumentWithInput`: subclasses bind their id type as ``TId`` so each resource + owns its id type, while the field (optional, since projections may omit it) and its alias wiring + are declared once here for the repository to read off any resource's output model. + """ + + id: Annotated[TId | None, Field(alias="_id", serialization_alias="id")] = None + + +class DeleteResponse(BaseModel): + num_deleted: int + + @classmethod + def from_delete_result(cls, delete_result: DeleteResult) -> Self: + return cls(num_deleted=delete_result.deleted_count) + + +class ComponentDeleteResponse(DeleteResponse): + """Result of a component delete that may leave referenced components in place. + + ``num_deleted`` (inherited) counts components actually removed; ``referenced_ids`` are the + component ids skipped because a contribution still references them, and ``num_skipped`` is + their count. + """ + + referenced_ids: list[PydanticObjectId] = Field(default_factory=list) + num_skipped: int = 0 + + +def canonical_md5(payload: Mapping[str, Any]) -> str: + """MD5 hex digest of a content mapping, stable across processes/hosts.""" + text = json.dumps(payload, sort_keys=True, separators=(",", ":"), ensure_ascii=False) + normalized = unicodedata.normalize("NFC", text) + return hashlib.md5(normalized.encode("utf-8")).hexdigest() + + +class ComponentIn(BaseModel): + """Base for component input payloads. + + Components are content-addressed: the server computes ``md5`` from the content and assigns the + ``_id`` on insert, so neither is part of the input contract. Subclasses add the required content + fields for their resource. + """ + + name: str + + +class Component(BaseDocumentWithInput[PydanticObjectId]): + """Stored component document. + + ``md5`` is server-authoritative: it is (re)computed from ``hash_fields`` whenever a full document + is validated — on insert, on update, and on full-document reads — so a client-supplied value can + never define a component's content identity. + """ + + name: str + # Server-computed; the placeholder default is overwritten by ``_recompute_md5`` on validation. + md5: MD5Hash = Field(default="0" * 32) + + hash_fields: ClassVar[frozenset[str]] + + # The md5 functions look redundant but aren't, we should keep both + # Used in patching to compute the hash after an update - should not return self + def compute_md5(self) -> str: + payload = self.model_dump(mode="json", include=set(self.hash_fields), by_alias=False) + return canonical_md5(payload) + + # Used on validation - must return self + @model_validator(mode="after") + def _recompute_md5(self) -> Self: + self.md5 = self.compute_md5() + return self + + @classmethod + def from_input(cls, input: ComponentIn) -> Self: + """Build a stored document from an input payload, assigning a fresh id (md5 is computed). + + The default maps every input field onto the document one-to-one. Subclasses whose document + carries fields that are absent from the input or derived from it should override this - see + ``Table.from_input``, which computes ``total_data_rows`` from the data frame. + """ + payload = input.model_dump() + payload["_id"] = PydanticObjectId() + return cls.model_validate(payload) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/_shared/repository.py b/mpcontribs-api/src/mpcontribs_api/domains/_shared/repository.py new file mode 100644 index 000000000..4e3277544 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/_shared/repository.py @@ -0,0 +1,317 @@ +import csv +import hashlib +import io +import json +import zlib +from abc import ABC, abstractmethod +from collections.abc import AsyncIterable, AsyncIterator, Callable, Iterable +from contextlib import AbstractAsyncContextManager +from typing import Any + +from beanie import PydanticObjectId, UpdateResponse +from beanie.operators import In, Set +from bson.errors import InvalidId +from fastapi_filter.contrib.beanie import Filter +from pydantic import BaseModel +from pymongo.asynchronous.client_session import AsyncClientSession +from types_aiobotocore_s3 import S3Client + +from mpcontribs_api.authz import User +from mpcontribs_api.domains._shared.models import BaseDocumentWithInput, DeleteResponse, DocumentOut +from mpcontribs_api.domains._shared.types import DownloadFormat, ShortMimeFormat +from mpcontribs_api.exceptions import ConflictError, NotFoundError, ValidationError +from mpcontribs_api.pagination import CursorParams, Page, encode_cursor + + +class MongoDbRepository[ + TDoc: BaseDocumentWithInput, + TIn: BaseModel, + TOut: DocumentOut, + TFilter: Filter, + TPatch: BaseModel, +](ABC): + """Base repository encapsulating shared MongoDB access patterns. + + Subclasses bind the document, input, output, filter, and patch types as type parameters, set + the matching ``document_model`` / ``out_model`` class attributes, and implement ``_build_scope`` + to enforce per-user authorization. Shared CRUD logic (scoping, projection, cursor pagination, + insertion, single-document read/patch/delete) lives here so it exists in exactly one place and + cannot drift between resources. Subclasses expose domain-named methods that either forward to a + base method (vocabulary + concrete types for routers, no logic) or implement a genuinely + different shape (bulk insert, compound-key upsert, download). + + Attributes: + document_model: the ``BaseDocumentWithInput`` subclass this repository operates on + out_model: the ``SparseFieldsModel`` subclass used to build projections for reads + _scope (dict[str, Any]): terms injected into every query to enforce user authorization + """ + + document_model: type[TDoc] + out_model: type[TOut] + + def __init__(self, user: User) -> None: + """Initializes an instance based on the current user. + + Args: + user (User): the current user requesting resources + """ + self._scope = self._build_scope(user) + + @staticmethod + @abstractmethod + def _build_scope(user: User) -> dict[str, Any]: + """Provides scope based on current user's permitted groups and publicly released data.""" + ... + + def _convert_object_id(self, id: str) -> PydanticObjectId: + """Converts the string representation of an ObjectId to an ObjectId""" + try: + return PydanticObjectId(id) + except InvalidId: + raise ValidationError("Incorrect Id format. Must be MongoDB ObjectId format.", id=id) from None + + def _not_found(self, id: str) -> str: + """Build a not-found message naming this repository's resource.""" + return f"{self.document_model.__name__} with id {id} not found" + + async def get_many( + self, + filter: TFilter, + fields: frozenset[str] | None = None, + pagination: CursorParams | None = None, + restrict_ids: Iterable[Any] | None = None, + ) -> Page[TOut]: + """Return a scoped, filtered, cursor-paginated page of projected documents. + + Args: + pagination (CursorParams): forward-only cursor parameters + filter (TFilter): the fastapi-filter query to apply on top of the user scope + fields (frozenset[str] | None): fields to project; if None the full document is returned + restrict_ids (Iterable | None): when provided, results are limited to these ids in + addition to the user scope. An empty iterable yields an empty page. Used to gate + reads that are authorized indirectly (e.g. components reachable via a contribution). + """ + pagination = pagination or CursorParams() + + projection = self.out_model.projection(fields) + query = filter.filter(self.document_model.find(self._scope)) + if restrict_ids is not None: + query = query.find(In(self.document_model.id, list(restrict_ids))) + if pagination.cursor is not None: + query = query.find(self.document_model.id > self.document_model.decode_cursor(cursor=pagination.cursor)) # pyright: ignore[reportOptionalOperand] + docs = await query.sort(self.document_model.id).limit(pagination.limit + 1).project(projection).to_list() # pyright: ignore[reportArgumentType] + has_more = len(docs) > pagination.limit + items = docs[: pagination.limit] + next_cursor = encode_cursor(str(items[-1].id)) if has_more and items else None + return Page(items=items, next_cursor=next_cursor) + + async def get_by_id(self, id: Any, fields: frozenset[str] | None = None) -> TDoc | TOut | None: + """Return a single scoped document by id, projected to the requested fields. + + Args: + id (str): the id of the document to find + fields (frozenset[str] | None): fields to project; if None the full document is returned + """ + return await self.document_model.find_one( + self._scope, + self.document_model.id == id, + projection_model=self.out_model.projection(fields), + ) + + async def list_ids(self, filter: TFilter, session: AsyncClientSession | None = None) -> list[Any]: + """Return just the ids of scoped documents matching ``filter``. + + Projects to ``{"_id": 1}`` so the lookup can be served as a covered query from the + default ``_id`` index without materializing full documents. + + Args: + filter (TFilter): the fastapi-filter query to apply on top of the user scope + session (AsyncClientSession | None): optional client session for transactions + """ + projection = self.out_model.projection(frozenset({"id"})) + query = filter.filter(self.document_model.find(self._scope, session=session)) + docs = await query.project(projection).to_list() + return [doc.id for doc in docs] + + async def insert_one(self, in_resource: TIn) -> TDoc: + """Insert a new document built from its input model, rejecting duplicate ids. + + Args: + in_resource (TIn): the validated input payload to translate and store + """ + document = self.document_model.from_input_model(in_resource) + existing = await self.document_model.find_one(self.document_model.id == document.id) + if existing: + raise ConflictError(f"Cannot insert document.\n Document with ID {document.id} exists") + await document.insert() + return document + + async def delete_by_id(self, id: Any, session: AsyncClientSession | None = None) -> DeleteResponse: + """Delete a single scoped document by id. + + Scoping ensures callers cannot delete documents they are not permitted to see. + + Args: + id (str): the id of the document to delete + """ + doc = await self.document_model.find_one(self._scope, self.document_model.id == id, session=session) + if not doc: + raise NotFoundError("Document with id not found", id=id) + await doc.delete(session=session) + return DeleteResponse(num_deleted=1) + + async def delete_by_ids(self, ids: list[Any], session: AsyncClientSession | None = None) -> DeleteResponse: + """Delete multiple scoped documents by id. + + The user scope is injected so callers cannot delete documents they are not permitted to + see; out-of-scope ids simply match nothing and are reported as zero deletions. + + Args: + ids (list[Any]): list of ids to delete + session: the session to perform the deletes within + + Returns: + DeleteResponse: the result of the deletion + """ + docs = self.document_model.find(self._scope, In(self.document_model.id, ids), session=session) + delete_result = await docs.delete_many(session=session) + if not delete_result: + raise ValidationError("DeleteResult not returned internally") + return DeleteResponse.from_delete_result(delete_result) + + async def patch(self, id: Any, update: TPatch) -> TDoc: + """Partially update a single scoped document by id. + + Only fields explicitly set on ``update`` are applied. An empty patch is a no-op that still + returns the existing document for consistent behavior. Scoping ensures callers cannot patch + documents they are not permitted to see. + + Args: + id (str): the id of the document to update + update (TPatch): the partial update to apply; unset fields are dropped + """ + # Only retain set fields (patch) + update_data = update.model_dump(exclude_unset=True) + # If update is empty, return the model anyways (consistent behavior) + if not update_data: + existing = await self.document_model.find_one(self._scope, self.document_model.id == id) + if existing is None: + raise NotFoundError(self._not_found(id)) + return existing + + # Otherwise, update the fields fully (set) + # Brendan TODO: Set will replace an entire field + # - if we want to append to a list (ie. add a reference) we ned Push/AddToSet + query = self.document_model.find_one(self._scope, self.document_model.id == id).update( + Set(update_data), + response_type=UpdateResponse.NEW_DOCUMENT, + ) + updated = await query # pyright: ignore[reportGeneralTypeIssues] # beanie UpdateQuery is awaitable, but pyright doesn't see it + if updated is None: + raise NotFoundError(self._not_found(id)) + return updated + + def _hash_payload(self, payload: dict[str, Any], *, separators: tuple[str, str] = (",", ":")) -> str: + canonical = json.dumps( + payload, + sort_keys=True, + separators=separators, + ensure_ascii=True, + default=str, # filters may carry ObjectId/datetime values; stringify for a stable key + ) + return hashlib.sha256(canonical.encode("utf-8")).hexdigest() + + def _get_serializer( + self, format: DownloadFormat, fields: frozenset[str] | None + ) -> Callable[[AsyncIterable[TOut]], AsyncIterable[bytes]]: + match format: + case DownloadFormat.JSONL: + return self._serialize_jsonl + case DownloadFormat.CSV: + return lambda rows: self._serialize_csv(rows, fields) + + @staticmethod + async def _serialize_jsonl(rows: AsyncIterable) -> AsyncIterator[bytes]: + async for out in rows: + yield out.model_dump_json().encode() + b"\n" + + @staticmethod + def _csv_cell(value: Any) -> Any: + """Render a cell value for CSV: scalars as-is, dict/list as JSON (not Python repr).""" + if value is None or isinstance(value, (str, int, float, bool)): + return value + return json.dumps(value, ensure_ascii=False, separators=(",", ":")) + + @staticmethod + async def _serialize_csv(rows: AsyncIterable, fields: frozenset[str] | None) -> AsyncIterator[bytes]: + buf = io.StringIO() + writer: csv.DictWriter | None = None + async for out in rows: + row = out.model_dump(mode="json") + if writer is None: + cols = sorted(fields) if fields else list(row.keys()) + writer = csv.DictWriter(buf, fieldnames=cols, extrasaction="ignore") + writer.writeheader() + writer.writerow({key: MongoDbRepository._csv_cell(value) for key, value in row.items()}) + yield buf.getvalue().encode() + buf.seek(0) + buf.truncate(0) + + async def _s3_object_exists(self, bucket_name: str, key_name: str, s3: AbstractAsyncContextManager[S3Client]): + async with s3 as s3_client: + try: + await s3_client.head_object(Bucket=bucket_name, Key=key_name) + return True + except Exception: + return False + + async def download( + self, + format: DownloadFormat, + short_mime: ShortMimeFormat, + ignore_cache: bool, + filter: TFilter, + fields: frozenset[str] | None, + s3: AbstractAsyncContextManager[S3Client], + bucket_name: str, + key_name: str, + restrict_ids: Iterable[Any] | None = None, + ) -> AsyncIterable[bytes]: + # Hash parameters to generate key for cache + payload = { + "format": format, + "short_mime": short_mime, + "filter": filter.model_dump(), + "fields": sorted(fields) if fields else None, + } + _ = self._hash_payload(payload) + + # TODO: S3 download cache. When implemented, this should `await + # self._s3_object_exists(...)` and stream the cached object on a hit. + + # Build from MongoDB (and, in future, save to cache) + query = filter.filter(self.document_model.find(self._scope)) + if restrict_ids is not None: + query = query.find(In(self.document_model.id, list(restrict_ids))) + query = filter.sort(query) + + serializer = self._get_serializer(format, fields) + + # Compress using gzip level 9 and stream out + compressor = zlib.compressobj(9, zlib.DEFLATED, 16 + zlib.MAX_WBITS) + + async def rows() -> AsyncIterator[TOut]: + async for table in query: + # TODO: We might think about skipping validation to save time + yield self.out_model.model_validate(table, from_attributes=True) + + async for line in serializer(rows()): + chunk = compressor.compress(line) + if chunk: + yield chunk + + # Flush the remaining buffered bytes and the gzip footer + # Without this the stream is a truncated gzip that cannot be decompressed. + tail = compressor.flush() + if tail: + yield tail diff --git a/mpcontribs-api/src/mpcontribs_api/domains/_shared/service.py b/mpcontribs-api/src/mpcontribs_api/domains/_shared/service.py new file mode 100644 index 000000000..d3ce92337 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/_shared/service.py @@ -0,0 +1,167 @@ +from collections.abc import AsyncIterable +from contextlib import AbstractAsyncContextManager + +from fastapi_filter.contrib.beanie import Filter +from pydantic import BaseModel +from pymongo.asynchronous.client_session import AsyncClientSession +from types_aiobotocore_s3 import S3Client + +from mpcontribs_api.domains._shared.components import MongoDbComponentsRepository +from mpcontribs_api.domains._shared.models import Component, ComponentDeleteResponse, ComponentIn, DocumentOut +from mpcontribs_api.domains._shared.types import DownloadFormat, ShortMimeFormat +from mpcontribs_api.domains.contributions.repository import MongoDbContributionRepository +from mpcontribs_api.exceptions import NotFoundError +from mpcontribs_api.pagination import CursorParams, Page + + +class ComponentService[ + TDoc: Component, + TIn: ComponentIn, + TOut: DocumentOut, + TFilter: Filter, + TPatch: BaseModel, +]: + """Service layer for all shared component logic. + + Components (attachments, structures, tables) share the same access model and CRUD surface, so a + single configurable service handles every domain rather than a per-domain subclass. Each domain + is distinguished only by: + + - ``ref_field``: the field on a contribution that references this component type + (``"attachments"`` / ``"structures"`` / ``"tables"``) + - ``bucket_name``: the S3 bucket downloads are cached in (defaults to ``ref_field``) + + Reads, inserts, patches, and downloads forward to the components repository. Deletion is the only + operation with cross-repository logic, applying two gates: + + 1. **Access (scoped):** candidates are restricted to components reachable via a contribution + in the user's scope. A component the user cannot reach is treated as not found. + 2. **Integrity (global):** any reachable candidate still referenced by *any* contribution is + skipped; the rest are deleted. + """ + + def __init__( + self, + components: MongoDbComponentsRepository[TDoc, TIn, TOut, TFilter, TPatch], + contributions: MongoDbContributionRepository, + *, + ref_field: str, + bucket_name: str | None = None, + ) -> None: + self._components = components + self._contributions = contributions + self._ref_field = ref_field + self._bucket_name = bucket_name or ref_field + + async def get_many( + self, + filter: TFilter, + pagination: CursorParams, + fields: frozenset[str] | None, + ) -> Page[TOut]: + """Return a page of components reachable via an in-scope contribution. + + Components have no independent access field, so visibility is gated by contribution + reachability: results are restricted to ids referenced by a contribution the caller is + allowed to see + """ + allowed = await self._contributions.list_referenced_component_ids(self._ref_field, scoped=True) + return await self._components.get_many( + pagination=pagination, filter=filter, fields=fields, restrict_ids=allowed + ) + + async def get_by_id(self, id: str, fields: frozenset[str] | None) -> TDoc | TOut | None: + """Find a single component by id, gated by contribution reachability. + + Returns ``None`` (treated as not found) when no in-scope contribution references the id, + so callers cannot read a component belonging to a contribution they cannot see. + """ + oid = self._components._convert_object_id(id) + if not await self._contributions.referenced_component_ids(self._ref_field, [oid], scoped=True): + return None + return await self._components.get_component_by_id(id, fields) + + async def insert( + self, + components: list[TIn], + session: AsyncClientSession | None = None, + ) -> list[TDoc]: + """Bulk-insert components, deduplicated by content hash. See ``insert_components``.""" + return await self._components.insert_components(components=components, session=session) + + async def patch_by_id(self, id: str, update: TPatch) -> TDoc: + """Partially update a component by id, gated by contribution reachability. + + Raises: + NotFoundError: when no in-scope contribution references the id + """ + oid = self._components._convert_object_id(id) + if not await self._contributions.referenced_component_ids(self._ref_field, [oid], scoped=True): + raise NotFoundError(self._components._not_found(id)) + return await self._components.patch_component_by_id(id=id, update=update) + + async def download( + self, + format: DownloadFormat, + short_mime: ShortMimeFormat, + ignore_cache: bool, + filter: TFilter, + fields: frozenset[str] | None, + s3: AbstractAsyncContextManager[S3Client], + ) -> AsyncIterable[bytes]: + """Stream a gzip-compressed export of matching components. See ``download``.""" + allowed = await self._contributions.list_referenced_component_ids(self._ref_field, scoped=True) + return self._components.download( + format=format, + short_mime=short_mime, + ignore_cache=ignore_cache, + filter=filter, + fields=fields, + s3=s3, + bucket_name=self._bucket_name, + key_name="", # TODO: Temp + restrict_ids=allowed, + ) + + async def delete(self, filter: TFilter) -> ComponentDeleteResponse: + """Delete components matching ``filter`` that are reachable and globally unreferenced. + + Args: + filter (TFilter): the component-specific query to apply + + Returns: + ComponentDeleteResponse: count deleted, plus the ids skipped because a contribution + still references them + """ + candidate_ids = await self._components.list_ids(filter) + reachable = await self._contributions.referenced_component_ids(self._ref_field, candidate_ids, scoped=True) + if not reachable: + return ComponentDeleteResponse(num_deleted=0) + referenced = await self._contributions.referenced_component_ids(self._ref_field, list(reachable), scoped=False) + deletable = [cid for cid in reachable if cid not in referenced] + num_deleted = (await self._components.delete_by_ids(deletable)).num_deleted if deletable else 0 + return ComponentDeleteResponse( + num_deleted=num_deleted, + num_skipped=len(referenced), + referenced_ids=sorted(referenced), + ) + + async def delete_by_id(self, id: str) -> ComponentDeleteResponse: + """Delete a single component by id, subject to the access and integrity gates. + + Args: + id (str): the str representation of the component's ObjectId + + Returns: + ComponentDeleteResponse: the deletion result, or a skipped result if still referenced + + Raises: + NotFoundError: if the component is not reachable via any in-scope contribution + """ + oid = self._components._convert_object_id(id) + if not await self._contributions.referenced_component_ids(self._ref_field, [oid], scoped=True): + raise NotFoundError(self._components._not_found(id)) + if await self._contributions.referenced_component_ids(self._ref_field, [oid], scoped=False): + return ComponentDeleteResponse(num_deleted=0, num_skipped=1, referenced_ids=[oid]) + deleted = await self._components.delete_by_id(oid) + return ComponentDeleteResponse(num_deleted=deleted.num_deleted) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/_shared/types.py b/mpcontribs-api/src/mpcontribs_api/domains/_shared/types.py new file mode 100644 index 000000000..bfaf0e4a1 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/_shared/types.py @@ -0,0 +1,110 @@ +import re +from enum import StrEnum +from typing import Annotated + +import polars as pl +from fastapi import Query +from pydantic import BeforeValidator, Field, PlainSerializer, WithJsonSchema + +from mpcontribs_api.exceptions import ValidationError + +ShortStr = Annotated[str, Field(min_length=3, max_length=30)] + +FieldSelector = Annotated[list[str] | None, Query(alias="_fields")] + +_EMAIL_RE = re.compile(r"^[^:@\s]+:[^:@\s]+@[^@\s]+\.[^@\s]+$") + + +def _validate_prefixed_email(v: str) -> str: + v = v.strip() + if not _EMAIL_RE.match(v): + raise ValidationError("must match ':@', e.g. 'google:name@gmail.com'") + return v + + +PrefixedEmail = Annotated[str, BeforeValidator(_validate_prefixed_email)] + + +def _file_name_like_str(v: str) -> str: + v = v.strip() + parts = v.split(".") + if len(parts) > 1 and parts[-1]: + return v + raise ValidationError(f"attachment name '{v}' not valid. Must end with file extension (e.g. '.gz')") + + +FileLike = Annotated[str, BeforeValidator(_file_name_like_str)] + + +_MD5 = re.compile(r"^[a-f0-9]{32}$") + + +def _md5_like(v: str) -> str: + v = v.strip().lower() + if not _MD5.match(v): + raise ValidationError("must be a 32-character MD5 hex digest", md5=v) + return v + + +MD5Hash = Annotated[str, BeforeValidator(_md5_like)] + + +def _mime_like(v: str) -> str: + v = v.strip().lower() + parts = v.split("/") + if len(parts) == 2 and parts[0] == "application" and parts[1].strip(): + return v + raise ValidationError(f"improper mime value {v} - must be formatted as 'application/*file_ext*'") + + +MimeFormat = Annotated[str, BeforeValidator(_mime_like)] + + +class DownloadFormat(StrEnum): + JSONL = "jsonl" + CSV = "csv" + + +class ShortMimeFormat(StrEnum): + GZ = "gz" + + +# Not exactly a type, but used to coerce a str to a desired format (pseudo-type) +def download_filename(resource: str, format: DownloadFormat, short_mime: ShortMimeFormat) -> str: + """Build a download filename reflecting the resource, payload format, and compression. + + e.g. ``download_filename("contributions", DownloadFormat.CSV, ShortMimeFormat.GZ)`` + -> ``"contributions.csv.gz"``. + """ + return f"{resource}.{format.value}.{short_mime.value}" + + +def _coerce_frame(v: object) -> pl.DataFrame: + if isinstance(v, pl.DataFrame): + return v + if isinstance(v, dict): + return pl.DataFrame(v) + raise ValueError(f"cannot coerce {type(v)} to pl.DataFrame") + + +def _serialize_frame(data: pl.DataFrame) -> dict: + return data.to_dict(as_series=False) + + +# Beanie/pymongo would otherwise BSON-encode a pl.DataFrame by iterating it into bare column +# lists, dropping the column names and the dict shape the Pydantic serializer produces — which +# `_coerce_frame` cannot read back. Registering this on a Document's Settings.bson_encoders makes +# the stored form match the serialized form, so frames round-trip losslessly. +FRAME_BSON_ENCODERS = {pl.DataFrame: _serialize_frame} + + +PolarsFrame = Annotated[ + pl.DataFrame, + BeforeValidator(_coerce_frame), + PlainSerializer(_serialize_frame, return_type=dict), + WithJsonSchema( + {"type": "array", "items": {"type": "array", "items": {"type": "number"}}}, + mode="validation", + ), + WithJsonSchema({"type": "object"}, mode="serialization"), +] diff --git a/mpcontribs-api/src/mpcontribs_api/domains/attachments/dependencies.py b/mpcontribs-api/src/mpcontribs_api/domains/attachments/dependencies.py new file mode 100644 index 000000000..966284a52 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/attachments/dependencies.py @@ -0,0 +1,28 @@ +from typing import Annotated + +from fastapi import Depends + +from mpcontribs_api.dependencies import UserDep +from mpcontribs_api.domains._shared.service import ComponentService +from mpcontribs_api.domains.attachments.models import ( + Attachment, + AttachmentFilter, + AttachmentIn, + AttachmentOut, + AttachmentPatch, +) +from mpcontribs_api.domains.attachments.repository import MongoDbAttachmentRepository +from mpcontribs_api.domains.contributions.repository import MongoDbContributionRepository + +AttachmentService = ComponentService[Attachment, AttachmentIn, AttachmentOut, AttachmentFilter, AttachmentPatch] + + +def get_attachment_service(user: UserDep) -> AttachmentService: + return ComponentService( + MongoDbAttachmentRepository(user), + MongoDbContributionRepository(user), + ref_field="attachments", + ) + + +AttachmentServiceDep = Annotated[AttachmentService, Depends(get_attachment_service)] diff --git a/mpcontribs-api/src/mpcontribs_api/domains/attachments/models.py b/mpcontribs-api/src/mpcontribs_api/domains/attachments/models.py new file mode 100644 index 000000000..4d7375837 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/attachments/models.py @@ -0,0 +1,90 @@ +from beanie import PydanticObjectId +from pydantic import field_validator + +from mpcontribs_api.domains._shared.filters import BaseFilter +from mpcontribs_api.domains._shared.models import Component, ComponentIn, DocumentOut +from mpcontribs_api.domains._shared.types import FileLike, MD5Hash, MimeFormat +from mpcontribs_api.exceptions import ValidationError +from mpcontribs_api.projection import SparseFieldsModel + +ACCEPTED_FORMATS = ["jpg", "jpeg", "png", "csv", "parquet", "gz"] + + +def _validate_attachment_name(v: str) -> str: + parts = v.strip().split(".") + if parts[-1].lower() not in ACCEPTED_FORMATS: + raise ValidationError( + f"Attachment extension not in allowed formats: {ACCEPTED_FORMATS}", + found_extension=parts[-1], + ) + return v + + +class Attachment(Component): + hash_fields = frozenset({"mime", "content"}) + mime: MimeFormat + content: int + + class Settings: + name = "attachments" + + @field_validator("name", mode="before") + @classmethod + def _name_with_extension(cls, v: str) -> str: + return _validate_attachment_name(v) + + +class AttachmentIn(ComponentIn): + """User-supplied attachment content. ``_id`` and ``md5`` are server-assigned, so absent here.""" + + mime: MimeFormat + content: int + + @field_validator("name", mode="before") + @classmethod + def _name_with_extension(cls, v: str) -> str: + return _validate_attachment_name(v) + + +class AttachmentOut(DocumentOut[PydanticObjectId]): + name: FileLike | None = None + md5: MD5Hash | None = None + mime: MimeFormat | None = None + content: int | None = None + + @staticmethod + def default_fields() -> list[str]: + # Light default; content fetched via ?_fields=. + return ["id", "name", "md5", "mime"] + + +class AttachmentPatch(SparseFieldsModel): + name: FileLike | None = None + mime: MimeFormat | None = None + content: int | None = None + + +class AttachmentFilter(BaseFilter): + id: PydanticObjectId | None = None + id__in: list[PydanticObjectId] | None = None + id__neq: PydanticObjectId | None = None + + md5: MD5Hash | None = None + md5__in: list[MD5Hash] | None = None + md5__neq: MD5Hash | None = None + + name: str | None = None + name__in: list[str] | None = None + name__neq: str | None = None + name__ilike: str | None = None + + mime: MimeFormat | None = None + mime__in: list[MimeFormat] | None = None + mime__neq: MimeFormat | None = None + mime__ilike: MimeFormat | None = None + + # sorting + order_by: list[str] | None = None + + class Constants(BaseFilter.Constants): + model = Attachment diff --git a/mpcontribs-api/src/mpcontribs_api/domains/attachments/repository.py b/mpcontribs-api/src/mpcontribs_api/domains/attachments/repository.py new file mode 100644 index 000000000..6297b117f --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/attachments/repository.py @@ -0,0 +1,15 @@ +from mpcontribs_api.domains._shared.components import MongoDbComponentsRepository +from mpcontribs_api.domains.attachments.models import ( + Attachment, + AttachmentFilter, + AttachmentIn, + AttachmentOut, + AttachmentPatch, +) + + +class MongoDbAttachmentRepository( + MongoDbComponentsRepository[Attachment, AttachmentIn, AttachmentOut, AttachmentFilter, AttachmentPatch] +): + document_model = Attachment + out_model = AttachmentOut diff --git a/mpcontribs-api/src/mpcontribs_api/domains/attachments/router.py b/mpcontribs-api/src/mpcontribs_api/domains/attachments/router.py new file mode 100644 index 000000000..09214a4fa --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/attachments/router.py @@ -0,0 +1,77 @@ +from typing import Annotated + +from fastapi import APIRouter, Depends +from fastapi.responses import StreamingResponse +from fastapi_filter import FilterDepends + +from mpcontribs_api.dependencies import S3Dep, require_user +from mpcontribs_api.domains._shared.models import ComponentDeleteResponse +from mpcontribs_api.domains._shared.types import ( + DownloadFormat, + FieldSelector, + ShortMimeFormat, + download_filename, +) +from mpcontribs_api.domains.attachments.dependencies import AttachmentServiceDep +from mpcontribs_api.domains.attachments.models import AttachmentFilter, AttachmentOut +from mpcontribs_api.pagination import CursorParams + +router = APIRouter() + + +@router.get("") +async def get_attachments( + service: AttachmentServiceDep, + pagination: Annotated[CursorParams, Depends()], + filter: AttachmentFilter = FilterDepends(AttachmentFilter), + fields: FieldSelector = AttachmentOut.default_fields(), +): + selected = AttachmentOut.parse_fields(fields) + return await service.get_many(filter=filter, fields=selected, pagination=pagination) + + +@router.get("/{pk}") +async def get_attachment( + service: AttachmentServiceDep, + pk: str, + fields: FieldSelector = AttachmentOut.default_fields(), +): + selected = AttachmentOut.parse_fields(fields) + return await service.get_by_id(id=pk, fields=selected) + + +@router.get("/download/{short_mime}") +async def download_attachment( + service: AttachmentServiceDep, + format: DownloadFormat, + s3: S3Dep, + short_mime: ShortMimeFormat = ShortMimeFormat.GZ, + ignore_cache: bool = False, + filter: AttachmentFilter = FilterDepends(AttachmentFilter), + fields: FieldSelector = AttachmentOut.default_fields(), +) -> StreamingResponse: + selected = AttachmentOut.parse_fields(fields) + body = await service.download( + format=format, + short_mime=short_mime, + ignore_cache=ignore_cache, + filter=filter, + fields=selected, + s3=s3, + ) + filename = download_filename("attachments", format, short_mime) + return StreamingResponse( + body, + media_type="application/gzip", + headers={"Content-Disposition": f'attachment; filename="{filename}"'}, + ) + + +@router.delete("", response_model=ComponentDeleteResponse, dependencies=[Depends(require_user)]) +async def delete_attachments(service: AttachmentServiceDep, filter: AttachmentFilter = FilterDepends(AttachmentFilter)): + return await service.delete(filter=filter) + + +@router.delete("/{id}", response_model=ComponentDeleteResponse, dependencies=[Depends(require_user)]) +async def delete_attachment_by_id(service: AttachmentServiceDep, id: str): + return await service.delete_by_id(id=id) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/contributions/dependencies.py b/mpcontribs-api/src/mpcontribs_api/domains/contributions/dependencies.py new file mode 100644 index 000000000..805d4357a --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/contributions/dependencies.py @@ -0,0 +1,35 @@ +from typing import Annotated + +from fastapi import Depends + +from mpcontribs_api.dependencies import MongoClientDep, UserDep +from mpcontribs_api.domains.attachments.repository import MongoDbAttachmentRepository +from mpcontribs_api.domains.contributions.repository import ( + MongoDbContributionRepository, +) +from mpcontribs_api.domains.contributions.service import ContributionService +from mpcontribs_api.domains.projects.repository import MongoDbProjectRepository +from mpcontribs_api.domains.structures.repository import MongoDbStructureRepository +from mpcontribs_api.domains.tables.repository import MongoDbTableRepository + + +def get_scoped_contributions(user: UserDep) -> MongoDbContributionRepository: + return MongoDbContributionRepository(user) + + +ContributionDep = Annotated[MongoDbContributionRepository, Depends(get_scoped_contributions)] + + +def get_contribution_service(user: UserDep, client: MongoClientDep) -> ContributionService: + return ContributionService( + client=client, + user=user, + projects=MongoDbProjectRepository(user), + contributions=MongoDbContributionRepository(user), + structures=MongoDbStructureRepository(user), + attachments=MongoDbAttachmentRepository(user), + tables=MongoDbTableRepository(user), + ) + + +ContributionServiceDep = Annotated[ContributionService, Depends(get_contribution_service)] diff --git a/mpcontribs-api/src/mpcontribs_api/domains/contributions/models.py b/mpcontribs-api/src/mpcontribs_api/domains/contributions/models.py new file mode 100644 index 000000000..8c4ceadfe --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/contributions/models.py @@ -0,0 +1,266 @@ +import re +from datetime import UTC, datetime +from typing import Annotated, Any +from warnings import deprecated + +from beanie import ( + Insert, + Link, + PydanticObjectId, + Replace, + Save, + SaveChanges, + Update, + before_event, +) +from bson.errors import InvalidId +from fastapi_filter import FilterDepends, with_prefix +from pydantic import BeforeValidator, Field, field_validator +from pymongo import ASCENDING, IndexModel + +from mpcontribs_api.domains._shared.filters import BaseFilter +from mpcontribs_api.domains._shared.models import BaseDocumentWithInput, DocumentOut +from mpcontribs_api.domains._shared.types import ShortStr +from mpcontribs_api.domains.attachments.models import Attachment, AttachmentFilter, AttachmentIn +from mpcontribs_api.domains.structures.models import Structure, StructureFilter, StructureIn +from mpcontribs_api.domains.tables.models import Table, TableFilter, TableIn +from mpcontribs_api.exceptions import ValidationError +from mpcontribs_api.projection import SparseFieldsModel + + +def _get_dict_depth(x) -> int: + if isinstance(x, dict): + return 1 + max((_get_dict_depth(v) for v in x.values()), default=0) + elif isinstance(x, list): + return max((_get_dict_depth(item) for item in x), default=0) + return 0 + + +def _validate_data_depth(data: dict[str, Any] | None) -> dict[str, Any] | None: + if data is None: + return None + depth = _get_dict_depth(data) + if depth > 7: + raise ValidationError("Depth of Contribution.data must be <= 7.", depth=depth) + return data + + +# Forbid punctuation, excluding: '*', '/' and exactly 1 '|' anywhere in string +_DATA_PUNCTUATION_PATTERN = re.compile(r"(?![^|]*\|[^|]*\|)[^\x21-\x29\x2B-\x2E\x3A-\x40\x5B-\x5E\x60\x7B\x7D-\x7E]*") + + +def _validate_keys(data: dict[str, Any] | None) -> dict[str, Any] | None: + if data is None: + return None + keys = list(data.keys()) + if not all(isinstance(k, str) and k.isascii() for k in keys): + raise ValidationError("Non-ASCII key found in Contribution.data. All dict keys must be only ASCII") + if any(k == "" for k in keys): + raise ValidationError("Empty key found in Contribution.data. Keys must be non-empty.") + if any(_DATA_PUNCTUATION_PATTERN.fullmatch(k) is None for k in keys): + raise ValidationError( + "Punctuation found in Contribution.data keys. Only '_', '*', '/', and at most 1 '|' permitted." + ) + # Recurse into nested dicts, including dicts nested inside lists. + for v in data.values(): + _validate_nested_keys(v) + return data + + +def _validate_nested_keys(value: Any) -> None: + if isinstance(value, dict): + _validate_keys(value) + elif isinstance(value, list): + for item in value: + _validate_nested_keys(item) + + +class ContributionBase(BaseDocumentWithInput[PydanticObjectId]): + """Shared settings and fields for Contribution, ContributionIn, and ContributionOut.""" + + project: str + identifier: str + formula: str + is_public: bool = False + data: Annotated[ + dict[str, Any], + BeforeValidator(_validate_data_depth), + BeforeValidator(_validate_keys), + ] + + last_modified: datetime = Field(default_factory=lambda: datetime.now(UTC)) + + class Settings: + name = "contributions" + keep_nulls = False + indexes = [ + IndexModel( + keys=[("project", ASCENDING), ("identifier", ASCENDING), ("version", ASCENDING)], + name="project_identifier_version", + unique=True, + ), + # Multikey indexes over each Link field's DBRef id so the component-delete + # reference check (referenced_component_ids) is index-served, not a COLLSCAN. + IndexModel(keys=[("structures.$id", ASCENDING)], name="ref_structures"), + IndexModel(keys=[("tables.$id", ASCENDING)], name="ref_tables"), + IndexModel(keys=[("attachments.$id", ASCENDING)], name="ref_attachments"), + ] + + +class Contribution(ContributionBase): + """Models what is actually stored in the database.""" + + # Server-owned: the service resolves the real version (see ContributionService._split_non_unique) + # and stamps it on the doc. Defaults to 1 so the no-version (unique-identifier) case is implicit. + version: int = 1 + structures: list[Link[Structure]] | None = None + tables: list[Link[Table]] | None = None + attachments: list[Link[Attachment]] | None = None + needs_build: Annotated[bool | None, deprecated("'needs_build' is deprecated.")] = False + + @classmethod + def from_input_model(cls, data: ContributionIn) -> Contribution: + # Server-owned fields are not taken from input: is_public starts False, components are + # inserted separately, last_modified is stamped by the before_event hook, and version is + # resolved/stamped by the service (never trusted from the request body). + return cls.model_validate( + { + **data.model_dump( + exclude={"is_public", "version", "structures", "tables", "attachments", "last_modified"} + ), + "is_public": False, + } + ) + + @before_event(Insert, Replace, Update, Save, SaveChanges) + def set_last_modified(self): + self.last_modified = datetime.now(UTC) + + +class ContributionIn(ContributionBase): + """Fields that users are allowed to submit when adding a Contribution. + + version will be inferred if left as None + """ + + # Only meaningful on upsert/update of a non-unique-identifier project, where it selects which + # version to target. Ignored on insert (the service auto-assigns) and for unique-identifier + # projects (inferred as 1). + version: int | None = None + structures: list[StructureIn] | None = None + tables: list[TableIn] | None = None + attachments: list[AttachmentIn] | None = None + + def has_components(self) -> bool: + """Returns ``True`` if the contribution has any components (structures, tables, attachments)""" + return bool(self.structures or self.tables or self.attachments) + + def component_count(self) -> int: + """Returns the total number of components (structures, tables, attachments) in the contribution""" + return len(self.structures or []) + len(self.tables or []) + len(self.attachments or []) + + def identifiers(self) -> dict[str, str]: + """Returns a dict of unique identifiers for a contribution (outside of id).""" + return {"project": self.project, "identifier": self.identifier} + + +class ContributionOut(DocumentOut[PydanticObjectId]): + """Models what the users are allowed to see in a return. + + Users can specify further what they want to see if not everything is of interest + """ + + project: str | None = None + identifier: str | None = None + version: int | None = None + formula: str | None = None + is_public: bool | None = None + last_modified: datetime | None = None + needs_build: Annotated[bool | None, deprecated("'needs_build' is deprecated.")] = None + # No input validators on the read path: stored documents are trusted, and re-validating here + # would 500 on historical data that missed the correction (see carrier_transport contribs) + data: dict[str, Any] | None = None + structures: list[Link[Structure]] | None = None + tables: list[Link[Table]] | None = None + attachments: list[Link[Attachment]] | None = None + + @staticmethod + def default_fields() -> list[str]: + return [ + "id", + "project", + "identifier", + "version", + "formula", + "is_public", + "last_modified", + ] + + +class ContributionPatch(SparseFieldsModel): + """Fields that can be specified for partial updates to a Contribution.""" + + project: str | None = None + identifier: str | None = None + version: int | None = None + formula: str | None = None + is_public: bool | None = None + data: Annotated[ + dict[str, Any] | None, + BeforeValidator(_validate_data_depth), + BeforeValidator(_validate_keys), + ] = None + structures: list[Link[Structure]] | None = None + tables: list[Link[Table]] | None = None + attachments: list[Link[Attachment]] | None = None + + +class ContributionFilter(BaseFilter): + """How users can filter searches for Contributions. + + Includes filters for linked documents (Components) + """ + + id: PydanticObjectId | None = None + id__in: list[PydanticObjectId] | None = None + id__neq: PydanticObjectId | None = None + + identifier: str | None = None + identifier__in: list[ShortStr] | None = None + identifier__neq: ShortStr | None = None + identifier__ilike: str | None = None + + version: str | None = None + version__in: list[ShortStr] | None = None + version__neq: ShortStr | None = None + version__ilike: str | None = None + + formula: str | None = None + formula__in: list[ShortStr] | None = None + formula__neq: ShortStr | None = None + formula__ilike: str | None = None + + is_public: bool | None = None + + needs_build: bool | None = None + + table: TableFilter | None = FilterDepends(with_prefix("tables", TableFilter)) + attachment: AttachmentFilter | None = FilterDepends(with_prefix("attachments", AttachmentFilter)) + structure: StructureFilter | None = FilterDepends(with_prefix("structures", StructureFilter)) + + # sorting + order_by: list[str] | None = None + + class Constants(BaseFilter.Constants): + model = Contribution + + @field_validator("id", mode="before") + @classmethod + def convert_str_to_oid(cls, v: str): + try: + return PydanticObjectId(v) + except InvalidId as err: + raise ValidationError( + "Invalid ObjectId format. Must be 12-byte input or a 24-character hex string", + oid=v, + ) from err diff --git a/mpcontribs-api/src/mpcontribs_api/domains/contributions/repository.py b/mpcontribs-api/src/mpcontribs_api/domains/contributions/repository.py new file mode 100644 index 000000000..09eb3e5f3 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/contributions/repository.py @@ -0,0 +1,308 @@ +from collections.abc import AsyncIterable +from contextlib import AbstractAsyncContextManager +from typing import Any + +from beanie import PydanticObjectId, UpdateResponse +from beanie.operators import Set +from pymongo.asynchronous.client_session import AsyncClientSession +from pymongo.results import DeleteResult +from types_aiobotocore_s3 import S3Client + +from mpcontribs_api.authz import User +from mpcontribs_api.domains._shared.repository import MongoDbRepository +from mpcontribs_api.domains._shared.types import DownloadFormat, ShortMimeFormat +from mpcontribs_api.domains.contributions.models import ( + Contribution, + ContributionFilter, + ContributionIn, + ContributionOut, + ContributionPatch, +) +from mpcontribs_api.pagination import CursorParams + + +class MongoDbContributionRepository( + MongoDbRepository[Contribution, ContributionIn, ContributionOut, ContributionFilter, ContributionPatch] +): + """A repository layer for access to MongoDB. + + Shared CRUD logic lives on :class:`MongoDbRepository`; the methods here are domain-named + forwarders that give routers a consistent vocabulary and concrete types, plus the operations + whose shape is contribution-specific (filtered delete, id-keyed upsert, download). + Multi-collection orchestration (component inserts) lives in ``ContributionService``. + """ + + document_model = Contribution + out_model = ContributionOut + + @staticmethod + def _build_scope(user: User) -> dict[str, Any]: + """Provides scope based on current user's permitted groups and publicly released data.""" + if user.is_admin: + return {} + ors: list[dict[str, Any]] = [{"is_public": True}] + if user.writable_projects: + ors.append({"project": {"$in": sorted(user.writable_projects)}}) + return {"$or": ors} + + async def get_contributions( + self, + filter: ContributionFilter, + pagination: CursorParams | None = None, + fields: frozenset[str] | None = None, + ): + """Query the Contribution collection, scoped to the current user. See ``get_many``.""" + return await self.get_many(pagination=pagination, filter=filter, fields=fields) + + async def get_contribution_by_id(self, id: str, fields: frozenset[str] | None): + """Find a single contribution by id, scoped to the current user. See ``get_by_id``.""" + return await self.get_by_id(self._convert_object_id(id), fields) + + async def patch_contribution_by_id(self, id: str, update: ContributionPatch): + """Partially update a contribution by id, scoped to the current user. See ``patch``.""" + return await self.patch(self._convert_object_id(id), update) + + async def delete_contribution_by_id(self, id: str) -> None: + """Delete a contribution by id, scoped to the current user. See ``delete_by_id``.""" + await self.delete_by_id(self._convert_object_id(id)) + + async def delete_contributions( + self, + filter: ContributionFilter, + ) -> DeleteResult | None: + """Bulk deletion of Contributions described by the filter. + + Args: + filter (ContribtionFilter): the filter to use to identify contributions to delete + """ + return await filter.filter(self.document_model.find(self._scope)).delete_many() + + async def insert_many_contributions( + self, + docs: list[Contribution], + session: AsyncClientSession | None = None, + ): + """Bulk-insert pre-built Contribution documents. + + Used by the ``ContributionService`` no-component fast path. On partial failure pymongo + raises ``BulkWriteError`` whose ``details["writeErrors"]`` carries per-index error info + that the service maps back into a ``BulkWriteSummary``. + """ + return await self.document_model.insert_many(docs, ordered=False, session=session) + + async def insert_contribution( + self, + doc: Contribution, + session: AsyncClientSession | None = None, + ) -> Contribution: + """Insert a single pre-built Contribution document, optionally in a transaction.""" + await doc.insert(session=session) + return doc + + async def find_one_contribution(self, project: str, identifier: str) -> Contribution | None: + """Find a single contribution by (project, identifier), scoped to the current user.""" + return await self.document_model.find_one( + self._scope, + self.document_model.project == project, + self.document_model.identifier == identifier, + ) + + async def max_versions(self, keys: list[tuple[str, str]]) -> dict[tuple[str, str], int]: + """Return ``{(project, identifier): max_version}`` for the given keys, scoped to the user. + + Presence of a key in the result also signals that at least one contribution already exists + for it, which the contribution write path uses to enforce uniqueness on unique-identifier + projects and to compute the next version on non-unique ones. Keys with no existing + contributions are absent from the result. + + A single aggregation answers the whole batch so the write path avoids one round-trip per + contribution. Scope is merged into ``$match`` (mirroring :meth:`referenced_component_ids`); + a writer sees every contribution in their own project, so the scoped max equals the global + max for keys they may write. + + Args: + keys: (project, identifier) pairs to look up + + Returns: + dict[tuple[str, str], int]: highest existing version per requested key + """ + if not keys: + return {} + match: dict[str, Any] = {"$or": [{"project": p, "identifier": i} for p, i in keys]} + if self._scope: + match = {"$and": [self._scope, match]} + pipeline: list[dict[str, Any]] = [ + {"$match": match}, + { + "$group": { + "_id": {"project": "$project", "identifier": "$identifier"}, + "max_version": {"$max": "$version"}, + } + }, + ] + collection = self.document_model.get_pymongo_collection() + result: dict[tuple[str, str], int] = {} + async for doc in await collection.aggregate(pipeline): + gid = doc["_id"] + # Versions are >= 1; coalesce a null $max (legacy docs without the field) to 0 while + # still recording the key's presence (existence check for unique-identifier projects). + result[(gid["project"], gid["identifier"])] = doc.get("max_version") or 0 + return result + + async def referenced_component_ids( + self, + ref_field: str, + ids: list[PydanticObjectId], + *, + scoped: bool, + ) -> set[PydanticObjectId]: + """Return the subset of ``ids`` referenced by contributions through ``ref_field``. + + Beanie stores each ``Link`` as a DBRef (``{"$ref": ..., "$id": ObjectId}``), so a + component is referenced when its id appears under ``.$id`` on any matching + contribution. + + Args: + ref_field: the contribution link field to inspect ("structures" | "tables" | + "attachments"). Always a fixed class-attr at the call site, never user input. + ids: candidate component ids to test + scoped: when ``True`` the user scope is applied (access gate / reachability); when + ``False`` the check spans every contribution (global integrity check) + + Returns: + set[PydanticObjectId]: the ids in ``ids`` that are still referenced + """ + if not ids: + return set() + key = f"{ref_field}.$id" + query: dict[str, Any] = {key: {"$in": ids}} + if scoped and self._scope: + query = {"$and": [self._scope, query]} + target = set(ids) + referenced: set[PydanticObjectId] = set() + collection = self.document_model.get_pymongo_collection() + async for doc in collection.find(query, {ref_field: 1}): + for ref in doc.get(ref_field) or []: + rid = ref.id if hasattr(ref, "id") else ref.get("$id") + if rid in target: + referenced.add(rid) + return referenced + + # TODO: should return document with update + async def list_referenced_component_ids( + self, + ref_field: str, + *, + scoped: bool, + ) -> set[PydanticObjectId]: + """Return every component id referenced through ``ref_field`` by matching contributions. + + Unlike :meth:`referenced_component_ids`, this takes no candidate list — it enumerates all + ids reachable from contributions in scope. + + Args: + ref_field: the contribution link field to inspect ("structures" | "tables" | + "attachments"). Always a fixed class-attr at the call site, never user input. + scoped: when ``True`` the user scope is applied (access gate); when ``False`` the + check spans every contribution. + + Returns: + set[PydanticObjectId]: all component ids referenced via ``ref_field`` + """ + key = f"{ref_field}.$id" + query: dict[str, Any] = {key: {"$exists": True}} + if scoped and self._scope: + query = {"$and": [self._scope, query]} + referenced: set[PydanticObjectId] = set() + collection = self.document_model.get_pymongo_collection() + async for doc in collection.find(query, {ref_field: 1}): + for ref in doc.get(ref_field) or []: + rid = ref.id if hasattr(ref, "id") else ref.get("$id") + if rid is not None: + referenced.add(rid) + return referenced + + async def update_contribution(self, doc: Contribution, update_data: dict[str, Any]) -> None: + """Apply a partial update to an existing Contribution document.""" + await doc.update(Set(update_data)) + + async def upsert_contribution_by_identifiers( + self, + identifiers: dict[str, str], + contribution: ContributionIn, + version: int, + ) -> Contribution: + """Atomically upsert a Contribution by its identifying fields and resolved version. + + Relies on the unique index over (project, identifier, version) so that concurrent requests + targeting the same key cannot both win the insert branch. Fields the caller did not set are + not touched (partial update). On insert a fresh Contribution document is written with + ``is_public=False``. + + Args: + identifiers: the fields ContributionIn.identifiers() returns (project, identifier) + contribution: the input payload to upsert + version: the version resolved by the service (1 for unique-identifier projects, or the + caller-supplied version for non-unique ones); selects which row to update + + Returns: + Contribution: the document as it stands after the operation + """ + doc = self.document_model.from_input_model(contribution) + doc.version = version + update_data = doc.model_dump(exclude={"id"}, exclude_none=True) + query = self.document_model.find_one( + self._scope, + self.document_model.project == identifiers["project"], + self.document_model.identifier == identifiers["identifier"], + self.document_model.version == version, + ).upsert( + Set(update_data), + on_insert=doc, + response_type=UpdateResponse.NEW_DOCUMENT, + ) + return await query # pyright: ignore[reportGeneralTypeIssues] # beanie UpdateQuery is awaitable, but pyright doesn't see it + + async def upsert_contribution_by_id(self, id: str, contribution: ContributionIn): + """Upserts a single Contribution. + + If Contributions with identical identifiers exist, update, otherwise insert + + Args: + id (str): the id of the Contribution to upsert + contribution (ContributionIn): the Contribution to be upserted + + Returns: + ContributionOut: the upserted document""" + doc = self.document_model.from_input_model(contribution) + query = self.document_model.find_one( + self._scope, + self.document_model.id == self._convert_object_id(id), + ).upsert( + Set(doc.model_dump(exclude={"id"}, exclude_none=True)), + on_insert=doc, + response_type=UpdateResponse.NEW_DOCUMENT, + ) + return await query # pyright: ignore[reportGeneralTypeIssues] # beanie UpdateQuery is awaitable, but pyright doesn't see it + + async def download_contributions( + self, + format: DownloadFormat, + short_mime: ShortMimeFormat, + ignore_cache: bool, + filter: ContributionFilter, + fields: frozenset[str] | None, + key_name: str, + s3: AbstractAsyncContextManager[S3Client], + bucket_name: str = "contributions", + ) -> AsyncIterable[bytes]: + return self.download( + format=format, + short_mime=short_mime, + ignore_cache=ignore_cache, + filter=filter, + fields=fields, + bucket_name=bucket_name, + key_name=key_name, + s3=s3, + ) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/contributions/router.py b/mpcontribs-api/src/mpcontribs_api/domains/contributions/router.py new file mode 100644 index 000000000..73466eff2 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/contributions/router.py @@ -0,0 +1,140 @@ +from typing import Annotated + +from fastapi import APIRouter, Depends +from fastapi.responses import StreamingResponse +from fastapi_filter import FilterDepends + +from mpcontribs_api.config import get_settings +from mpcontribs_api.dependencies import S3Dep, require_user +from mpcontribs_api.domains._shared.bulk import BulkWriteSummary +from mpcontribs_api.domains._shared.types import ( + DownloadFormat, + FieldSelector, + ShortMimeFormat, + download_filename, +) +from mpcontribs_api.domains.contributions.dependencies import ContributionDep, ContributionServiceDep +from mpcontribs_api.domains.contributions.models import ( + Contribution, + ContributionFilter, + ContributionIn, + ContributionOut, + ContributionPatch, +) +from mpcontribs_api.exceptions import ValidationError +from mpcontribs_api.pagination import CursorParams + +router = APIRouter() + + +def _enforce_bulk_limit(contributions: list[ContributionIn]) -> None: + """Reject a bulk write larger than the configured per-request ceiling. + + Guards the synchronous bulk endpoints so a single request can't hand the service an unbounded + list. Callers over the limit should chunk (the limit is advertised at ``GET /api/v1/limits``) + or use the async bulk ingestion endpoint. Complements the body-size middleware, which bounds + bytes rather than item count. + """ + limit = get_settings().mongo.bulk_write_limit + count = len(contributions) + if count > limit: + raise ValidationError( + f"Bulk request of {count} contributions exceeds the per-request limit of {limit}. " + "Chunk the request (see GET /api/v1/limits) or use the async bulk ingestion endpoint.", + count=count, + limit=limit, + ) + + +@router.get("") +async def get_contributions( + repo: ContributionDep, + pagination: Annotated[CursorParams, Depends()], + filter: ContributionFilter = FilterDepends(ContributionFilter), + fields: FieldSelector = ContributionOut.default_fields(), +): + selected = ContributionOut.parse_fields(fields) + return await repo.get_contributions(pagination=pagination, filter=filter, fields=selected) + + +@router.delete("", dependencies=[Depends(require_user)]) +async def delete_contributions( + repo: ContributionDep, + filter: ContributionFilter = FilterDepends(ContributionFilter), +): + return await repo.delete_contributions(filter=filter) + + +# TODO: Might want to take contributions in from request body and run model_validate_json on it (much faster) +@router.post("", response_model=BulkWriteSummary[Contribution], dependencies=[Depends(require_user)]) +async def insert_contributions( + service: ContributionServiceDep, + contributions: list[ContributionIn], +): + _enforce_bulk_limit(contributions) + return await service.insert_contributions(contributions=contributions) + + +@router.put("", response_model=BulkWriteSummary[Contribution], dependencies=[Depends(require_user)]) +async def upsert_contributions( + service: ContributionServiceDep, + contributions: list[ContributionIn], +): + _enforce_bulk_limit(contributions) + return await service.upsert_contributions(contributions=contributions) + + +@router.get("/download/{short_mime}") +async def download_contributions( + repo: ContributionDep, + s3: S3Dep, + short_mime: ShortMimeFormat = ShortMimeFormat.GZ, + format: DownloadFormat = DownloadFormat.JSONL, + ignore_cache: bool = False, + filter: ContributionFilter = FilterDepends(ContributionFilter), + fields: FieldSelector = ContributionOut.default_fields(), +): + selected = ContributionOut.parse_fields(fields) + body = await repo.download_contributions( + format=format, + short_mime=short_mime, + ignore_cache=ignore_cache, + filter=filter, + fields=selected, + s3=s3, + key_name="", # TODO: Temp + ) + filename = download_filename("contributions", format, short_mime) + return StreamingResponse( + body, + media_type="application/gzip", + headers={"Content-Disposition": f'attachment; filename="{filename}"'}, + ) + + +@router.delete("/{id}", dependencies=[Depends(require_user)]) +async def delete_contribution_by_id( + service: ContributionServiceDep, + id: str, +): + return await service.delete_contributions(ContributionFilter.model_validate({"id": id})) + + +@router.get("/{id}") +async def get_contribution_by_id( + repo: ContributionDep, + id: str, + fields: FieldSelector = ContributionOut.default_fields(), +): + selected = ContributionOut.parse_fields(fields) + return await repo.get_contribution_by_id(id=id, fields=selected) + + +@router.put("/{id}", dependencies=[Depends(require_user)]) +async def upsert_contribution_by_id(repo: ContributionDep, id: str, contribution: ContributionIn): + return await repo.upsert_contribution_by_id(id=id, contribution=contribution) + + +@router.patch("/{id}", dependencies=[Depends(require_user)]) +async def patch_contribution_by_id(repo: ContributionDep, id: str, update: ContributionPatch): + return await repo.patch_contribution_by_id(id=id, update=update) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/contributions/service.py b/mpcontribs-api/src/mpcontribs_api/domains/contributions/service.py new file mode 100644 index 000000000..88ba3a523 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/contributions/service.py @@ -0,0 +1,522 @@ +import asyncio +from collections import defaultdict +from collections.abc import Iterable +from dataclasses import dataclass +from typing import cast + +import structlog +from beanie import Link, PydanticObjectId +from pymongo import AsyncMongoClient +from pymongo.asynchronous.client_session import AsyncClientSession +from pymongo.errors import BulkWriteError + +from mpcontribs_api.authz import User +from mpcontribs_api.config import MongoSettings, get_settings +from mpcontribs_api.domains._shared.bulk import ( + BulkDeleteSummary, + BulkFailure, + BulkWriteSummary, + bulk_failure_from_exception, +) +from mpcontribs_api.domains._shared.repository import MongoDbRepository +from mpcontribs_api.domains.attachments.repository import MongoDbAttachmentRepository +from mpcontribs_api.domains.contributions.models import Contribution, ContributionFilter, ContributionIn +from mpcontribs_api.domains.contributions.repository import MongoDbContributionRepository +from mpcontribs_api.domains.projects.repository import MongoDbProjectRepository +from mpcontribs_api.domains.structures.models import Structure +from mpcontribs_api.domains.structures.repository import MongoDbStructureRepository +from mpcontribs_api.domains.tables.models import Table +from mpcontribs_api.domains.tables.repository import MongoDbTableRepository +from mpcontribs_api.exceptions import AppError, ConflictError, PermissionError, ValidationError +from mpcontribs_api.pagination import CursorParams + +logger = structlog.get_logger(__name__) + + +@dataclass(frozen=True, slots=True) +class ResolvedWrite: + """A contribution that passed validation, paired with its server-resolved version. + + Produced by the split pipeline so the resolved version travels with its contribution (and its + original batch index) + """ + + index: int + contribution: ContributionIn + version: int + + +class ContributionService: + def __init__( + self, + client: AsyncMongoClient, + user: User, + projects: MongoDbProjectRepository, + contributions: MongoDbContributionRepository, + structures: MongoDbStructureRepository, + attachments: MongoDbAttachmentRepository, + tables: MongoDbTableRepository, + settings: MongoSettings | None = None, + ): + self._client = client + self._user = user + self._projects = projects + self._contributions = contributions + self._structures = structures + self._attachments = attachments + self._tables = tables + self._settings = settings or get_settings().mongo + + @property + def _children(self) -> dict[str, MongoDbRepository]: + return { + "structures": self._structures, + "attachments": self._attachments, + "tables": self._tables, + } + + async def insert_contributions( + self, + contributions: list[ContributionIn], + ) -> BulkWriteSummary[Contribution]: + """Atomic bulk insert contributions, atomically per top-level contribution. + + Contributions carrying no components are inserted in one ``insert_many`` (no transaction); + contributions with components run inside their own MongoDB transaction so the contribution + and its components commit or roll back together. Concurrent transactions are bounded by + ``settings.mongo.max_concurrent_transactions``. Per-item failures are returned in the + summary's ``failed`` list; the request as a whole does not raise on partial failure. + + Version is server-assigned per contribution: unique-identifier projects reject a duplicate + (project, identifier) as a conflict (version stays 1); non-unique projects auto-increment + from the current max. See ``_split_non_unique``. + + Args: + contributions: contributions to insert; may include nested structures/tables/attachments + + Returns: + BulkWriteSummary[Contribution]: per-item outcome, sized to ``len(contributions)`` + """ + if not contributions: + return BulkWriteSummary[Contribution](total=0, succeeded=[], failed=[]) + + failures, plan = await self._split_contributions(contributions, is_upsert=False) + no_comp = [item for item in plan if not item.contribution.has_components()] + with_comp = [item for item in plan if item.contribution.has_components()] + + no_comp_succeeded, no_comp_failed = await self._insert_no_components(no_comp) + with_comp_succeeded, with_comp_failed = await self._insert_with_components(with_comp) + + succeeded = [doc for _, doc in sorted(no_comp_succeeded + with_comp_succeeded, key=lambda p: p[0])] + failed = sorted( + failures + no_comp_failed + with_comp_failed, + key=lambda f: f.index, + ) + return BulkWriteSummary[Contribution](total=len(contributions), succeeded=succeeded, failed=failed) + + def _split_unauthorized( + self, + indices: Iterable[int], + contributions: list[ContributionIn], + ) -> tuple[list[BulkFailure], list[int]]: + """Reject contributions whose ``project`` the current user is not permitted to write. + + Authorized iff the user is an admin (writes anything) or the contribution's ``project`` is + one of the user's groups. Anonymous users are blocked at the router, but carry no groups and + are not admins, so they fall through to authorized-for-nothing here (defense-in-depth). + + Partitions ``indices`` into unauthorized ``BulkFailure`` entries and the remaining authorized + indices that should proceed. Mirrors ``_split_oversize`` (same shape) so callers can chain + the splits and keep each index in exactly one bucket, preserving input ordering. + """ + unauthorized: list[BulkFailure] = [] + remaining: list[int] = [] + for i in indices: + contrib = contributions[i] + if self._user.can_write(contrib.project): + remaining.append(i) + else: + unauthorized.append( + BulkFailure( + index=i, + identifier=contrib.identifiers(), + error_code=PermissionError.error_code, + message=f"not authorized to write to project '{contrib.project}'", + ) + ) + logger.warning( + "User attempted to add contributions to projects they are not authorized for.", + project=contrib.project, + ) + return unauthorized, remaining + + async def _split_non_unique( + self, + indices: Iterable[int], + contributions: list[ContributionIn], + *, + is_upsert: bool, + ) -> tuple[list[BulkFailure], list[ResolvedWrite]]: + """Apply per-project identifier-uniqueness rules and resolve each contribution's version. + + ``Project.unique_identifiers`` decides the contract per project: + + - **True**: at most one contribution per (project, identifier); version is always 1. On + insert a second one (already in the DB, or a duplicate earlier in this batch) is rejected + as a conflict. On upsert the version is inferred as 1 (any supplied value is ignored). + - **False**: many versions may share (project, identifier). On insert the version is + auto-assigned as ``max(existing) + 1``, sequencing intra-batch duplicates. On upsert the + caller must supply ``version`` to pick the target row, else the item is rejected. + + Iterates ``indices`` in input order so intra-batch duplicates sequence deterministically. + + Returns: + tuple of (rejections, a ``ResolvedWrite`` per survivor pairing it with its version) + """ + indices = list(indices) + failures: list[BulkFailure] = [] + plan: list[ResolvedWrite] = [] + if not indices: + return failures, plan + + # One round-trip each for the per-project uniqueness flags and (insert only) the current + # max version per key, instead of a query per contribution. + unique_map = await self._projects.unique_identifiers_by_id(sorted({contributions[i].project for i in indices})) + max_map: dict[tuple[str, str], int] = {} + if not is_upsert: + keys = sorted({(contributions[i].project, contributions[i].identifier) for i in indices}) + max_map = await self._contributions.max_versions(keys) + + seen: dict[tuple[str, str], int] = defaultdict(int) + for i in indices: + contrib = contributions[i] + key = (contrib.project, contrib.identifier) + + if contrib.project not in unique_map: + failures.append( + BulkFailure( + index=i, + identifier=contrib.identifiers(), + error_code=ValidationError.error_code, + message=f"project '{contrib.project}' not found or not accessible", + ) + ) + logger.info( + "project not found or not accessible", + project=contrib.project, + identifiers=contrib.identifiers(), + ) + continue + + unique = unique_map[contrib.project] + if is_upsert: + if unique: + version = 1 + elif contrib.version is not None: + version = contrib.version + else: + failures.append( + BulkFailure( + index=i, + identifier=contrib.identifiers(), + error_code=ValidationError.error_code, + message=( + f"project '{contrib.project}' allows multiple versions; a 'version' " + "is required to identify which contribution to update" + ), + ) + ) + logger.info( + "ambiguous contribution version in project allowing multiple versions", + project=contrib.project, + identifiers=contrib.identifiers(), + ) + continue + elif unique: + # Insert into a unique-identifier project: the first occurrence wins, anything that + # already exists (in the DB or earlier in this batch) is a conflict. + if key in max_map or seen[key] > 0: + failures.append( + BulkFailure( + index=i, + identifier=contrib.identifiers(), + error_code=ConflictError.error_code, + message=( + f"contribution '{contrib.identifier}' already exists for project '{contrib.project}'" + ), + ) + ) + logger.info( + "contribution already exists in project during insert/upsert/update", + project=contrib.project, + identifiers=contrib.identifiers(), + ) + continue + version = 1 + else: + # Insert into a non-unique-identifier project: next version after the current max, + # sequencing duplicates within this batch (max+1, max+2, ...). + version = max_map.get(key, 0) + 1 + seen[key] + + plan.append(ResolvedWrite(index=i, contribution=contrib, version=version)) + seen[key] += 1 + + return failures, plan + + def _split_oversize( + self, + indices: Iterable[int], + contributions: list[ContributionIn], + ) -> tuple[list[BulkFailure], list[int]]: + """Reject contributions whose component count exceeds the per-contribution ceiling. + + Partitions ``indices`` into oversize ``BulkFailure`` entries and the remaining indices that + should proceed to Mongo. Doing this upfront avoids burning a transaction slot on a request + guaranteed to exceed transactionLifetimeLimitSeconds. + """ + cap = self._settings.max_components_per_contribution + oversize: list[BulkFailure] = [] + remaining: list[int] = [] + for i in indices: + contrib = contributions[i] + count = contrib.component_count() + if count > cap: + oversize.append( + BulkFailure( + index=i, + identifier=contrib.identifiers(), + error_code=ValidationError.error_code, + message=f"contribution has {count} components, exceeds cap of {cap}. " + "Recommend inserting the component alone, followed by bulk inserts of components", + ) + ) + logger.info("Attemped to add contribution with too many components.", num_components=count, max=cap) + else: + remaining.append(i) + return oversize, remaining + + async def _split_contributions( + self, contributions: list[ContributionIn], *, is_upsert: bool + ) -> tuple[list[BulkFailure], list[ResolvedWrite]]: + """Common method for validating contribution write failure logic and resolving versions. + + Runs the cheap, local, index-based filters first (authorization, then component-count cap) + so guaranteed failures never reach the DB; ``_split_non_unique`` runs last and turns the + remaining indices into a write plan carrying each resolved version. + + Returns: + tuple of (failures and their reasons, a ``ResolvedWrite`` per contribution to write) + """ + # Per-item project authorization (see _split_unauthorized for the per-item vs fail-fast + # decision). Only authorized items reach Mongo; the rest are reported in ``failed``. + unauthorized_failures, authorized_indices = self._split_unauthorized(range(len(contributions)), contributions) + # Reject contributions that have too many components associated with them. + oversize_failures, sized_indices = self._split_oversize(authorized_indices, contributions) + # Verify identifiers/uniqueness within a project and resolve each version, depending on + # project.unique_identifiers and whether this is an insert or upsert. + non_unique_failures, plan = await self._split_non_unique(sized_indices, contributions, is_upsert=is_upsert) + return (unauthorized_failures + oversize_failures + non_unique_failures, plan) + + async def _insert_no_components( + self, + items: list[ResolvedWrite], + ) -> tuple[list[tuple[int, Contribution]], list[BulkFailure]]: + """Single-collection bulk insert for component-free contributions. + + Uses ``ordered=False`` so a single bad item doesn't sink the rest of the batch. pymongo + raises ``BulkWriteError`` with per-index error info on partial failure; we map that back + onto the original input indices. + """ + if not items: + return [], [] + docs = [] + for item in items: + doc = Contribution.from_input_model(item.contribution) + doc.version = item.version + docs.append(doc) + try: + await self._contributions.insert_many_contributions(docs) + return [(item.index, doc) for item, doc in zip(items, docs, strict=True)], [] + except BulkWriteError as exc: + return self._partition_bulk_write_error(items, docs, exc) + + @staticmethod + def _partition_bulk_write_error( + items: list[ResolvedWrite], + docs: list[Contribution], + exc: BulkWriteError, + ) -> tuple[list[tuple[int, Contribution]], list[BulkFailure]]: + """Map pymongo's per-position writeErrors back to the caller's original input indices.""" + write_errors = exc.details.get("writeErrors", []) if exc.details else [] + failed_positions = {err.get("index"): err for err in write_errors} + succeeded: list[tuple[int, Contribution]] = [] + failed: list[BulkFailure] = [] + for position, (item, doc) in enumerate(zip(items, docs, strict=True)): + err = failed_positions.get(position) + if err is None: + succeeded.append((item.index, doc)) + else: + failed.append( + BulkFailure( + index=item.index, + identifier=item.contribution.identifiers(), + error_code="conflict" if err.get("code") == 11000 else "write_error", + message=err.get("errmsg", "write failed"), + ) + ) + return succeeded, failed + + async def _insert_with_components( + self, + items: list[ResolvedWrite], + ) -> tuple[list[tuple[int, Contribution]], list[BulkFailure]]: + """Per-contribution transaction path, bounded by ``max_concurrent_transactions``.""" + if not items: + return [], [] + sem = asyncio.Semaphore(self._settings.max_concurrent_transactions) + + async def _bounded(item: ResolvedWrite) -> Contribution | BulkFailure: + async with sem: + return await self._insert_one_with_components(item) + + results = await asyncio.gather(*[_bounded(item) for item in items]) + succeeded: list[tuple[int, Contribution]] = [] + failed: list[BulkFailure] = [] + for item, outcome in zip(items, results, strict=True): + if isinstance(outcome, BulkFailure): + failed.append(outcome) + else: + succeeded.append((item.index, outcome)) + return succeeded, failed + + async def _insert_one_with_components(self, item: ResolvedWrite) -> Contribution | BulkFailure: + """Run a single contribution + its components inside a transaction. + + Uses ``session.with_transaction`` so transient txn errors (write conflicts, primary step- + downs) get pymongo's retry treatment. Any exception is converted to a ``BulkFailure`` so + the surrounding ``asyncio.gather`` sees a normal return value for every coroutine. + """ + contrib = item.contribution + try: + async with self._client.start_session() as session: + + async def _txn(s: AsyncClientSession) -> Contribution: + return await self._do_insert(contrib, s, item.version) + + return await session.with_transaction(_txn) + except AppError as exc: + return bulk_failure_from_exception(item.index, contrib.identifiers(), exc) + except Exception as exc: + logger.error( + "insert_contribution_failed", index=item.index, identifier=contrib.identifiers(), exc_info=True + ) + return bulk_failure_from_exception(item.index, contrib.identifiers(), exc) + + async def _do_insert(self, contrib: ContributionIn, session: AsyncClientSession, version: int) -> Contribution: + """Insert components then the contribution itself, all in the given session. + + Components are inserted sequentially because a session is single-threaded — sharing it + across concurrent awaits would corrupt the wire protocol. + """ + structures = await self._structures.insert_components(contrib.structures or [], session=session) + tables = await self._tables.insert_components(contrib.tables or [], session=session) + + doc = Contribution.from_input_model(contrib) + doc.version = version + doc.structures = cast(list[Link[Structure]] | None, structures or None) + doc.tables = cast(list[Link[Table]] | None, tables or None) + return await self._contributions.insert_contribution(doc, session=session) + + async def upsert_contributions(self, contributions: list[ContributionIn]) -> BulkWriteSummary[Contribution]: + """Upsert contributions by their identifying fields, reporting per-item outcomes. + + Components (structures, tables, attachments) must be managed via their respective + services. If any contribution in the batch carries components, the entire request is + rejected before any database writes occur. + + Each item is upserted atomically by ``ContributionIn.identifiers()`` via a single + ``findOneAndUpdate(..., upsert=True)`` so two requests targeting the same key cannot + race past the find branch — the unique index over those fields is the tiebreaker. + Concurrent upserts within a batch are bounded by ``settings.mongo.max_concurrent_transactions``. + A single item failing does not fail the batch: it is reported in ``failed`` while the others + still commit (mirroring ``insert_contributions``). + + Args: + contributions: contributions to upsert; must not include nested components + + Returns: + BulkWriteSummary[Contribution]: per-item outcome, sized to ``len(contributions)`` + + Raises: + ValidationError: if any contribution in the batch carries components + """ + if not contributions: + return BulkWriteSummary[Contribution](total=0, succeeded=[], failed=[]) + + indices_with_components = [i for i, c in enumerate(contributions) if c.has_components()] + if indices_with_components: + raise ValidationError( + "Components must be managed via their respective services, not via contribution upsert.", + contribution_indices=indices_with_components, + ) + + failures, plan = await self._split_contributions(contributions, is_upsert=True) + + sem = asyncio.Semaphore(self._settings.max_concurrent_transactions) + + async def _bounded_upsert(item: ResolvedWrite) -> Contribution | BulkFailure: + contrib = item.contribution + async with sem: + try: + return await self._contributions.upsert_contribution_by_identifiers( + contrib.identifiers(), contrib, item.version + ) + except Exception as exc: + logger.error( + "upsert_contribution_failed", index=item.index, identifier=contrib.identifiers(), exc_info=True + ) + return bulk_failure_from_exception(item.index, contrib.identifiers(), exc) + + results = await asyncio.gather(*[_bounded_upsert(item) for item in plan]) + succeeded = [r for r in results if not isinstance(r, BulkFailure)] + failed = failures + [r for r in results if isinstance(r, BulkFailure)] + return BulkWriteSummary[Contribution](total=len(contributions), succeeded=succeeded, failed=failed) + + async def delete_contributions(self, filter: ContributionFilter) -> BulkDeleteSummary: + """Delete a contribution and all of its child components + + Doesn't guarantee complete atomicity, but prevents orphaned children by deleting components first. + + Args: + filter (ContributionFilter): the Contribution-specific query to apply on top of the user scope + + + Returns: + BulkDeleteSummary: a summary of how many documents and child documents were deleted + """ + num_deleted_components = 0 + num_deleted_contributions = 0 + # Loop through cursor rather than materialize arbitrary number of Contributions + while True: + # Since we are deleting everything matching filter, we can continuously get the 1st page + page = await self._contributions.get_contributions( + pagination=CursorParams(cursor=None, limit=100), + filter=filter, + ) + # For each component type, gather ObjectIds then bulk delete them + # - components first so no children are left orphaned + for field, repo in self._children.items(): + ids = [link.ref.id for c in page.items for link in (getattr(c, field) or [])] + if ids: + deleted_components = await repo.delete_by_ids(ids) + num_deleted_components += deleted_components.num_deleted if deleted_components else 0 + + # Delete Contributions in this batch by ID + # need to make a new filter so we don't eagerly delete all contributions before their components are deleted + deleted_contribs = await self._contributions.delete_contributions( + ContributionFilter(id__in=[cast(PydanticObjectId, c.id) for c in page.items]) + ) + num_deleted_contributions += deleted_contribs.deleted_count if deleted_contribs else 0 + if not page.items: + break + return BulkDeleteSummary(num_deleted=num_deleted_contributions, num_children_deleted=num_deleted_components) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/healthcheck/router.py b/mpcontribs-api/src/mpcontribs_api/domains/healthcheck/router.py new file mode 100644 index 000000000..64bbb69fe --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/healthcheck/router.py @@ -0,0 +1,38 @@ +from botocore.exceptions import BotoCoreError, ClientError +from fastapi import APIRouter, HTTPException, status +from pydantic import BaseModel + +from mpcontribs_api.config import get_settings +from mpcontribs_api.dependencies import DbDep, S3Dep + +router = APIRouter(tags=["health"]) + +settings = get_settings() + + +class HealthStatus(BaseModel): + version: str + status: str + mongo: str + s3: str + + +@router.get("", response_model=HealthStatus, summary="Service health") +async def healthcheck(db: DbDep, s3_client: S3Dep) -> HealthStatus: + try: + await db.client.admin.command("ping") + except Exception: + raise HTTPException( + status_code=status.HTTP_503_SERVICE_UNAVAILABLE, + detail={"status": "unhealthy", "mongo": "unreachable"}, + ) from None + + try: + await s3_client.head_bucket(Bucket=settings.aws.health_bucket) + except ClientError, BotoCoreError: + raise HTTPException( + status_code=status.HTTP_503_SERVICE_UNAVAILABLE, + detail={"status": "unhealthy", "s3": "unreachable"}, + ) from None + + return HealthStatus(version=settings.version, status="healthy", mongo="ok", s3="ok") diff --git a/mpcontribs-api/src/mpcontribs_api/domains/limits/models.py b/mpcontribs-api/src/mpcontribs_api/domains/limits/models.py new file mode 100644 index 000000000..a1fccbc5f --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/limits/models.py @@ -0,0 +1,14 @@ +from pydantic import BaseModel + + +class Limits(BaseModel): + """Server-enforced request limits, advertised so callers can size their requests. + + These mirror the values enforced by the body-size middleware and the bulk write endpoints; + consumers (e.g. the mpcontribs client) should read them here rather than hardcoding. + """ + + max_request_bytes: int + bulk_write_limit: int + max_components_per_contribution: int + component_insert_chunk_size: int diff --git a/mpcontribs-api/src/mpcontribs_api/domains/limits/router.py b/mpcontribs-api/src/mpcontribs_api/domains/limits/router.py new file mode 100644 index 000000000..3d5393993 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/limits/router.py @@ -0,0 +1,18 @@ +from fastapi import APIRouter + +from mpcontribs_api.config import get_settings +from mpcontribs_api.domains.limits.models import Limits + +router = APIRouter() + + +@router.get("", response_model=Limits, summary="Server-enforced request limits") +async def get_limits() -> Limits: + """Return the request limits the server enforces. Public metadata; no auth required.""" + mongo = get_settings().mongo + return Limits( + max_request_bytes=mongo.max_request_bytes, + bulk_write_limit=mongo.bulk_write_limit, + max_components_per_contribution=mongo.max_components_per_contribution, + component_insert_chunk_size=mongo.component_insert_chunk_size, + ) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/projects/dependencies.py b/mpcontribs-api/src/mpcontribs_api/domains/projects/dependencies.py new file mode 100644 index 000000000..94535cc67 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/projects/dependencies.py @@ -0,0 +1,15 @@ +from typing import Annotated + +from fastapi import Depends + +from mpcontribs_api.dependencies import UserDep +from mpcontribs_api.domains.projects.repository import ( + MongoDbProjectRepository, +) + + +def get_scoped_projects(user: UserDep) -> MongoDbProjectRepository: + return MongoDbProjectRepository(user) + + +ProjectDep = Annotated[MongoDbProjectRepository, Depends(get_scoped_projects)] diff --git a/mpcontribs-api/src/mpcontribs_api/domains/projects/models.py b/mpcontribs-api/src/mpcontribs_api/domains/projects/models.py new file mode 100644 index 000000000..7216c82ac --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/projects/models.py @@ -0,0 +1,158 @@ +from __future__ import annotations + +from typing import Any, Literal + +from pydantic import BaseModel, ConfigDict, Field, HttpUrl + +from mpcontribs_api import pagination +from mpcontribs_api.domains._shared.filters import BaseFilter +from mpcontribs_api.domains._shared.models import BaseDocumentWithInput, DocumentOut +from mpcontribs_api.domains._shared.types import PrefixedEmail, ShortStr + + +class Column(BaseModel): + path: str + min: float | None = None + max: float | None = None + unit: str | None = None + + @property + def segments(self) -> tuple[str, ...]: + return tuple(self.path.split(".")) + + +class Stats(BaseModel): + columns: int + contributions: int + tables: int + structures: int + attachments: int + size: float + + +class Reference(BaseModel): + # TODO: Labels have some restrictions, not sure exactly what yet + label: str + url: HttpUrl + + +class Project(BaseDocumentWithInput[ShortStr]): + """Document model of what is actually stored. + + Binds ``id`` to ``ShortStr`` (a meaningful string id, always supplied) via the generic base. + """ + + # Required + title: ShortStr + authors: str + description: str + owner: PrefixedEmail + unique_identifiers: bool + stats: Stats + + # Optional + references: list[Reference] = Field(default_factory=list) + long_title: str | None = None + other: dict[str, Any] = Field(default_factory=dict) + columns: list[Column] = Field(default_factory=list) + is_public: bool = False + is_approved: bool = False + license: Literal["CCA4", "CCPD"] | None = None + + # Empty method for now. Keeping for business logic later + @classmethod + def from_input_model(cls, data: ProjectIn) -> Project: + return cls(**data.model_dump()) + + @staticmethod + def decode_cursor(cursor: str) -> str: + """Decodes cursor and returns it as a str. + + Needs override over parent class since Project.id is a simple str + """ + return pagination.decode_cursor(cursor) + + class Settings: + name = "projects" + keep_nulls = False + + +class ProjectOut(DocumentOut[ShortStr]): + """Full response of all public-facing fields.""" + + model_config = ConfigDict(extra="ignore") + authors: str | None = None + description: str | None = None + title: ShortStr | None = None + owner: PrefixedEmail | None = None + other: dict[str, Any] | None = None + is_public: bool | None = None + is_approved: bool | None = None + long_title: str | None = None + unique_identifiers: bool | None = None + references: list[Reference] | None = None + stats: Stats | None = None + columns: list[Column] | None = None + license: Literal["CCA4", "CCPD"] | None = None + + @staticmethod + def default_fields() -> list[str]: + return ["id", "is_public", "title", "owner", "is_approved", "unique_identifiers"] + + +class ProjectFilter(BaseFilter): + """Filter fields allowed in requests.""" + + id: ShortStr | None = None + id__in: list[ShortStr] | None = None + id__neq: ShortStr | None = None + + title: ShortStr | None = None + title__in: list[ShortStr] | None = None + title__neq: ShortStr | None = None + title__ilike: str | None = None + + owner: PrefixedEmail | None = None + owner__in: list[PrefixedEmail] | None = None + owner__neq: PrefixedEmail | None = None + owner__ilike: str | None = None + + # fuzzy only + long_title__ilike: str | None = None + + is_public: bool | None = None + is_approved: bool | None = None + unique_identifiers: bool | None = None + + license: Literal["CCA4", "CCPD"] | None = None + license__in: list[Literal["CCA4", "CCPD"]] | None = None + + # sorting + order_by: list[str] | None = None + + class Constants(BaseFilter.Constants): + model = Project + + +# Keeping for business logic separation. May have specific implementation later +class ProjectIn(Project): + """Representation of user-supplied input.""" + + pass + + +class ProjectPatch(BaseModel): + """Nullable Project representation of user-supplied data for partial update (patch).""" + + title: ShortStr | None = None + authors: str | None = None + description: str | None = None + owner: PrefixedEmail | None = None + unique_identifiers: bool | None = None + references: list[Reference] = Field(default_factory=list) + long_title: str | None = None + other: dict[str, Any] = Field(default_factory=dict) + columns: list[Column] = Field(default_factory=list) + is_public: bool = False + is_approved: bool = False + license: Literal["CCA4", "CCPD"] | None = None diff --git a/mpcontribs-api/src/mpcontribs_api/domains/projects/repository.py b/mpcontribs-api/src/mpcontribs_api/domains/projects/repository.py new file mode 100644 index 000000000..0e6f96a96 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/projects/repository.py @@ -0,0 +1,135 @@ +from typing import Any + +from mpcontribs_api.authz import User +from mpcontribs_api.domains._shared.repository import MongoDbRepository +from mpcontribs_api.domains.projects.models import ( + Project, + ProjectFilter, + ProjectIn, + ProjectOut, + ProjectPatch, +) +from mpcontribs_api.exceptions import PermissionError +from mpcontribs_api.pagination import CursorParams + + +class MongoDbProjectRepository(MongoDbRepository[Project, ProjectIn, ProjectOut, ProjectFilter, ProjectPatch]): + """A repository layer for access to MongoDB. + + This is the layer that directly interacts with database operations. Shared CRUD logic lives on + :class:`MongoDbRepository`; the methods here are domain-named forwarders that give routers a + consistent vocabulary and concrete types, plus the operations whose shape is genuinely + project-specific (id-keyed upsert). + + Attributes: + _scope (dict[str, Any]): additional terms to inject into mongo queries to enforce user + authorization on resources + """ + + document_model = Project + out_model = ProjectOut + + def __init__(self, user: User) -> None: + super().__init__(user) + self._user = user + + @staticmethod + def _build_scope(user: User) -> dict[str, Any]: + """Provides scope based on current user's permitted groups and publicly released data.""" + if user.is_admin: + return {} + ors: list[dict[str, Any]] = [{"is_public": True, "is_approved": True}] + if not user.is_anonymous: + ors.append({"owner": user.username}) + if user.groups: + ors.append({"_id": {"$in": sorted(user.groups)}}) + return {"$or": ors} + + async def get_projects( + self, + filter: ProjectFilter, + pagination: CursorParams, + fields: frozenset[str] | None, + ): + """Query the Project collection, scoped to the current user. See ``get_many``.""" + return await self.get_many(pagination=pagination, filter=filter, fields=fields) + + async def get_project_by_id(self, id: str, fields: frozenset[str] | None): + """Find a single project by id, scoped to the current user. See ``get_by_id``.""" + return await self.get_by_id(id, fields) + + async def unique_identifiers_by_id(self, ids: list[str]) -> dict[str, bool]: + """Return ``{project_id: unique_identifiers}`` for the given project ids, scoped to the user. + + Used by the contribution write path to apply per-project version rules in one round-trip + instead of fetching each project separately. Projects the user cannot see (or that do not + exist) are simply absent from the result, so the caller can treat them as inaccessible. + + Args: + ids: project ids to look up + + Returns: + dict[str, bool]: mapping of project id to its ``unique_identifiers`` flag + """ + if not ids: + return {} + query: dict[str, Any] = {"_id": {"$in": ids}} + if self._scope: + query = {"$and": [self._scope, query]} + collection = self.document_model.get_pymongo_collection() + result: dict[str, bool] = {} + async for doc in collection.find(query, {"unique_identifiers": 1}): + result[doc["_id"]] = bool(doc.get("unique_identifiers")) + return result + + async def insert_project(self, project: ProjectIn) -> Project: + """Insert a new project, rejecting a duplicate id. See ``insert_one``.""" + return await self.insert_one(project) + + async def patch_project_by_id(self, id: str, update: ProjectPatch) -> Project: + """Partially update a project by id, scoped to the current user. See ``patch``.""" + return await self.patch(id, update) + + async def delete_project_by_id(self, id: str) -> None: + """Delete a project by id, scoped to the current user. See ``delete_by_id``.""" + await self.delete_by_id(id) + + async def upsert_project_by_id(self, id: str, data: ProjectIn) -> Project: + """Upsert a project by provided id, authorized to the current user. + + Update the document if the id exists, otherwise insert a new one under that id. + Authorization (the read scope is for visibility, not write access, so it is not + reused here): + + - **Existing project:** only its ``owner`` or an admin may overwrite it. The stored + ``owner`` is preserved — ownership cannot be reassigned through the request body. + - **New project:** ``owner`` is forced to the caller, ignoring any body value. + + Note: relies on the path param ``id`` for identity, not the body's id. + + Args: + id (str): the id of the project to upsert + data (ProjectIn): the data of the project to upsert + + Returns: + Project: the full document that either replaced an old one or was inserted + + Raises: + PermissionError: if a non-owner, non-admin caller targets an existing project + """ + # The route enforces authentication, so an anonymous caller should never reach here. + if self._user.username is None: + raise PermissionError(required_role="authenticated") + + existing = await self.document_model.find_one(self.document_model.id == id) + project = self.document_model.from_input_model(data) + project.id = id + if existing is not None: + if not (self._user.is_admin or existing.owner == self._user.username): + raise PermissionError(required_role="owner-or-admin") + # Ownership is immutable via upsert; keep the original owner. + project.owner = existing.owner + else: + # New project: the caller owns it, regardless of the submitted owner. + project.owner = self._user.username + return await project.save() diff --git a/mpcontribs-api/src/mpcontribs_api/domains/projects/router.py b/mpcontribs-api/src/mpcontribs_api/domains/projects/router.py new file mode 100644 index 000000000..33dce7ebd --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/projects/router.py @@ -0,0 +1,120 @@ +from typing import Annotated + +from fastapi import APIRouter, Depends, Response, status +from fastapi_filter import FilterDepends +from starlette.status import HTTP_204_NO_CONTENT + +from mpcontribs_api.dependencies import require_user +from mpcontribs_api.domains._shared.types import FieldSelector +from mpcontribs_api.domains.projects.dependencies import ProjectDep +from mpcontribs_api.domains.projects.models import ( + ProjectFilter, + ProjectIn, + ProjectOut, + ProjectPatch, +) +from mpcontribs_api.pagination import CursorParams + +router = APIRouter() + + +@router.get("") +async def get_projects( + repo: ProjectDep, + pagination: Annotated[CursorParams, Depends()], + filter: ProjectFilter = FilterDepends(ProjectFilter), + fields: FieldSelector = ProjectOut.default_fields(), +): + """Return paginated projects matching a filter. + + Args: + repo (ProjectDep): the project repo we depend on + pagination (CursorParams): arguments for cursor-based pagination + fields (str | None): optional fields to include in return. If None supplied, all fields are returned + + Returns: + list[ProjectSummary]: a list of smaller project payloads + """ + selected = ProjectOut.parse_fields(fields) + return await repo.get_projects(filter=filter, pagination=pagination, fields=selected) + + +@router.get("/{id}") +async def get_project_by_id( + id: str, + repo: ProjectDep, + fields: FieldSelector = ProjectOut.default_fields(), +): + """Gets a single project by its ID. + + Args: + id (str): the id of the project to retrieve + repo (ProjectDep): the project repo we depend on + fields (str | None): optional fields to include in return. If None supplied, all fields are returned + + Returns: + ProjectOut: the requested project, actual data returned is determined by the view the user requested + """ + selected = ProjectOut.parse_fields(fields) + return await repo.get_project_by_id(id=id, fields=selected) + + +@router.put("/{id}", response_model=ProjectOut, dependencies=[Depends(require_user)]) +async def upsert_project_by_id( + repo: ProjectDep, + id: str, + project: ProjectIn, +): + """Upsert a project by provided id. + + Upsert: Update document if id is found, otherwise insert new document using id. + Note: Relies on the path param 'id' for finding, rather than the body's id. + + Args: + repo (ProjectDep): the project repo we depend on + id (str): the id of the project to retrieve + project (ProjectIn): the data of the project to upsert + + Returns: + ProjectOut: the full document that either replaced an old one or was inserted + """ + return await repo.upsert_project_by_id(id=id, data=project) + + +@router.patch("/{id}", response_model=ProjectOut, dependencies=[Depends(require_user)]) +async def patch_project_by_id( + repo: ProjectDep, + id: str, + update: ProjectPatch, +): + """Partial update to project identified with 'id'. + + Note: overwrites fields with given values - arrays are not appended to. + + Args: + repo (ProjectDep): the project repo we depend on + id (str): the id of the project to update + update (ProjectPatch): the partial update to apply - unset fields are dropped + - Note: If fields are intentionally set to None, None is applied to the field. + + Returns: + ProjectOut: the full Project with updates applied + """ + return await repo.patch_project_by_id(id=id, update=update) + + +@router.delete("/{id}", status_code=status.HTTP_204_NO_CONTENT, dependencies=[Depends(require_user)]) +async def delete_project_by_id( + repo: ProjectDep, + id: str, +): + """Deletes a project matching id. + + Args: + repo (ProjectDep): the project repo we depend on + id (str): the id of the project to be deleted + Returns: + Response: a response with the 204 response code (rather than FastAPIs default 200) + """ + await repo.delete_project_by_id(id=id) + return Response(status_code=HTTP_204_NO_CONTENT) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/structures/dependencies.py b/mpcontribs-api/src/mpcontribs_api/domains/structures/dependencies.py new file mode 100644 index 000000000..488e51314 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/structures/dependencies.py @@ -0,0 +1,28 @@ +from typing import Annotated + +from fastapi import Depends + +from mpcontribs_api.dependencies import UserDep +from mpcontribs_api.domains._shared.service import ComponentService +from mpcontribs_api.domains.contributions.repository import MongoDbContributionRepository +from mpcontribs_api.domains.structures.models import ( + Structure, + StructureFilter, + StructureIn, + StructureOut, + StructurePatch, +) +from mpcontribs_api.domains.structures.repository import MongoDbStructureRepository + +StructureService = ComponentService[Structure, StructureIn, StructureOut, StructureFilter, StructurePatch] + + +def get_structure_service(user: UserDep) -> StructureService: + return ComponentService( + MongoDbStructureRepository(user), + MongoDbContributionRepository(user), + ref_field="structures", + ) + + +StructureServiceDep = Annotated[StructureService, Depends(get_structure_service)] diff --git a/mpcontribs-api/src/mpcontribs_api/domains/structures/models.py b/mpcontribs-api/src/mpcontribs_api/domains/structures/models.py new file mode 100644 index 000000000..b4c8f6aa5 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/structures/models.py @@ -0,0 +1,115 @@ +from beanie import PydanticObjectId +from pydantic import BaseModel, ConfigDict +from pymatgen.core import Element + +from mpcontribs_api.domains._shared.filters import BaseFilter +from mpcontribs_api.domains._shared.models import Component, ComponentIn, DocumentOut +from mpcontribs_api.domains._shared.types import MD5Hash, PolarsFrame +from mpcontribs_api.projection import SparseFieldsModel + + +class SiteProperties(BaseModel): + magmom: float + + +class Species(BaseModel): + element: Element + occu: int + + +class Lattice(BaseModel): + model_config = ConfigDict(arbitrary_types_allowed=True) + matrix: PolarsFrame + pbc: list[bool] + a: float + b: float + c: float + alpha: float + beta: float + gamma: float + volume: float + + +class Site(BaseModel): + species: list[Species] + abc: list[float] + properties: SiteProperties + label: str + xyz: list[float] + + +# Some things in Emmet-core that could assist in translating the pymatgen string to BaseModel +# In Mongo it is a single long string, but we could try to parse it into something typed +# It looks like it has some fields, then a table for n_atom_site_* with the subsequent lines being tab/space delimited +# rows +class Cif(BaseModel): + pass + + +class Structure(Component): + hash_fields = frozenset({"lattice", "sites", "charge"}) + lattice: Lattice + sites: list[Site] + charge: float | None + cif: str # Cif + + class Settings: + name = "structures" + + +class StructureIn(ComponentIn): + """User-supplied structure content.""" + + lattice: Lattice + sites: list[Site] + charge: float | None = None + cif: str + + +class StructureOut(DocumentOut[PydanticObjectId]): + model_config = ConfigDict(arbitrary_types_allowed=True) + name: str | None = None + md5: MD5Hash | None = None + lattice: Lattice | None = None + sites: list[Site] | None = None + charge: float | None = None + cif: str | None = None + + @staticmethod + def default_fields() -> list[str]: + return [ + "id", + "name", + "md5", + ] + + +class StructurePatch(SparseFieldsModel): + name: str | None = None + lattice: Lattice | None = None + sites: list[Site] | None = None + charge: float | None = None + cif: str | None = None + + +class StructureFilter(BaseFilter): + id: PydanticObjectId | None = None + id__in: list[PydanticObjectId] | None = None + id__neq: PydanticObjectId | None = None + + md5: MD5Hash | None = None + md5__in: list[MD5Hash] | None = None + md5__neq: MD5Hash | None = None + + name: str | None = None + name__in: list[str] | None = None + name__neq: str | None = None + name__ilike: str | None = None + + # sites + + # sorting + order_by: list[str] | None = None + + class Constants(BaseFilter.Constants): + model = Structure diff --git a/mpcontribs-api/src/mpcontribs_api/domains/structures/repository.py b/mpcontribs-api/src/mpcontribs_api/domains/structures/repository.py new file mode 100644 index 000000000..ab7449785 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/structures/repository.py @@ -0,0 +1,15 @@ +from mpcontribs_api.domains._shared.components import MongoDbComponentsRepository +from mpcontribs_api.domains.structures.models import ( + Structure, + StructureFilter, + StructureIn, + StructureOut, + StructurePatch, +) + + +class MongoDbStructureRepository( + MongoDbComponentsRepository[Structure, StructureIn, StructureOut, StructureFilter, StructurePatch] +): + document_model = Structure + out_model = StructureOut diff --git a/mpcontribs-api/src/mpcontribs_api/domains/structures/router.py b/mpcontribs-api/src/mpcontribs_api/domains/structures/router.py new file mode 100644 index 000000000..803047648 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/structures/router.py @@ -0,0 +1,95 @@ +from typing import Annotated + +from fastapi import APIRouter, Depends +from fastapi.responses import StreamingResponse +from fastapi_filter import FilterDepends + +from mpcontribs_api.dependencies import S3Dep, require_user +from mpcontribs_api.domains._shared.bulk import BulkWriteSummary +from mpcontribs_api.domains._shared.models import ComponentDeleteResponse +from mpcontribs_api.domains._shared.types import ( + DownloadFormat, + FieldSelector, + ShortMimeFormat, + download_filename, +) +from mpcontribs_api.domains.structures.dependencies import StructureServiceDep +from mpcontribs_api.domains.structures.models import StructureFilter, StructureIn, StructureOut, StructurePatch +from mpcontribs_api.pagination import CursorParams + +router = APIRouter() + + +@router.get("") +async def get_structures( + service: StructureServiceDep, + pagination: Annotated[CursorParams, Depends()], + filter: StructureFilter = FilterDepends(StructureFilter), + fields: FieldSelector = StructureOut.default_fields(), +): + selected = StructureOut.parse_fields(fields) + return await service.get_many(filter=filter, fields=selected, pagination=pagination) + + +@router.get("/{pk}") +async def get_structure( + service: StructureServiceDep, + pk: str, + fields: FieldSelector = StructureOut.default_fields(), +): + selected = StructureOut.parse_fields(fields) + return await service.get_by_id(id=pk, fields=selected) + + +@router.get("/download/{short_mime}") +async def download_structure( + service: StructureServiceDep, + format: DownloadFormat, + s3: S3Dep, + short_mime: ShortMimeFormat = ShortMimeFormat.GZ, + ignore_cache: bool = False, + filter: StructureFilter = FilterDepends(StructureFilter), + fields: FieldSelector = StructureOut.default_fields(), +) -> StreamingResponse: + selected = StructureOut.parse_fields(fields) + body = await service.download( + format=format, + short_mime=short_mime, + ignore_cache=ignore_cache, + filter=filter, + fields=selected, + s3=s3, + ) + filename = download_filename("structures", format, short_mime) + return StreamingResponse( + body, + media_type="application/gzip", + headers={"Content-Disposition": f'attachment; filename="{filename}"'}, + ) + + +@router.post("", response_model=BulkWriteSummary[StructureOut], dependencies=[Depends(require_user)]) +async def insert_structures( + service: StructureServiceDep, + structures: list[StructureIn], +): + return await service.insert(components=structures) + + +@router.delete("", response_model=ComponentDeleteResponse, dependencies=[Depends(require_user)]) +async def delete_structures(service: StructureServiceDep, filter: StructureFilter = FilterDepends(StructureFilter)): + return await service.delete(filter=filter) + + +@router.delete("/{id}", response_model=ComponentDeleteResponse, dependencies=[Depends(require_user)]) +async def delete_structure_by_id(service: StructureServiceDep, id: str): + return await service.delete_by_id(id=id) + + +@router.patch("/{id}", dependencies=[Depends(require_user)]) +async def patch_structure_by_id( + service: StructureServiceDep, + id: str, + update: StructurePatch, +): + return await service.patch_by_id(id=id, update=update) diff --git a/mpcontribs-api/src/mpcontribs_api/domains/tables/dependencies.py b/mpcontribs-api/src/mpcontribs_api/domains/tables/dependencies.py new file mode 100644 index 000000000..323a4443d --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/tables/dependencies.py @@ -0,0 +1,28 @@ +from typing import Annotated + +from fastapi import Depends + +from mpcontribs_api.dependencies import UserDep +from mpcontribs_api.domains._shared.service import ComponentService +from mpcontribs_api.domains.contributions.repository import MongoDbContributionRepository +from mpcontribs_api.domains.tables.models import ( + Table, + TableFilter, + TableIn, + TableOut, + TablePatch, +) +from mpcontribs_api.domains.tables.repository import MongoDbTableRepository + +TableService = ComponentService[Table, TableIn, TableOut, TableFilter, TablePatch] + + +def get_table_service(user: UserDep) -> TableService: + return ComponentService( + MongoDbTableRepository(user), + MongoDbContributionRepository(user), + ref_field="tables", + ) + + +TableServiceDep = Annotated[TableService, Depends(get_table_service)] diff --git a/mpcontribs-api/src/mpcontribs_api/domains/tables/models.py b/mpcontribs-api/src/mpcontribs_api/domains/tables/models.py new file mode 100644 index 000000000..44cb0368e --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/tables/models.py @@ -0,0 +1,193 @@ +from collections.abc import Mapping +from typing import Any, Self + +import polars as pl +from beanie import PydanticObjectId +from pydantic import ( + BaseModel, + ConfigDict, + field_serializer, + model_validator, +) + +from mpcontribs_api.domains._shared.filters import BaseFilter +from mpcontribs_api.domains._shared.models import Component, ComponentIn, DocumentOut +from mpcontribs_api.domains._shared.types import MD5Hash, PolarsFrame +from mpcontribs_api.projection import SparseFieldsModel + + +class Labels(BaseModel): + index: str + value: str + variable: str + + +class Attributes(BaseModel): + title: str + labels: Labels + + +def frame_to_storage(frame: pl.DataFrame) -> tuple[list[str], list[str], list[list[str]]]: + """Split a DataFrame into (index, columns, data) for storage. + + The first column is the index; the rest are the data columns. Every value is stringified. + """ + if not frame.columns: + return [], [], [] + index_col, *data_cols = frame.columns + index = [str(v) for v in frame[index_col].to_list()] + data = [[str(v) for v in row] for row in frame.select(data_cols).iter_rows()] + return index, list(data_cols), data + + +def storage_to_frame(index_label: str, index: list[str], columns: list[str], data: list[list[str]]) -> pl.DataFrame: + """Rebuild the DataFrame from stored (index, columns, data), all columns typed as strings.""" + schema = {name: pl.Utf8 for name in [index_label, *columns]} + rows = [[idx, *row] for idx, row in zip(index, data, strict=True)] + return pl.DataFrame(rows, schema=schema, orient="row") + + +def _index_label(attrs: Any) -> str: + """The DataFrame's index-column name comes from ``attrs.labels.index`` (dict or model).""" + if attrs is None: + return "index" + if isinstance(attrs, Mapping): + return attrs.get("labels", {}).get("index", "index") + return getattr(getattr(attrs, "labels", None), "index", "index") + + +class Table(Component): + """Stored table document — matches the existing MongoDB shape (index/columns/data as strings).""" + + hash_fields = frozenset({"attrs", "index", "columns", "data"}) + + attrs: Attributes + index: list[str] + columns: list[str] + data: list[list[str]] + total_data_rows: int + + class Settings: + name = "tables" + + @classmethod + def from_input(cls, input: TableIn) -> Self: # pyright: ignore[reportIncompatibleMethodOverride] + # The input frame's first column is the index; the rest are the data columns. total_data_rows + # is derived from the data, so it is always consistent by construction. + index, columns, data = frame_to_storage(input.data) + return cls( + _id=PydanticObjectId(), + name=input.name, + attrs=input.attrs, + index=index, + columns=columns, + data=data, + total_data_rows=len(data), + ) + + +class TableIn(ComponentIn): + """User-supplied table content as a DataFrame (first column = index). + + ``_id`` and ``md5`` are server-assigned, so absent here. + """ + + model_config = ConfigDict(arbitrary_types_allowed=True) + attrs: Attributes + data: PolarsFrame + + +class TableFilter(BaseFilter): + id: PydanticObjectId | None = None + id__in: list[PydanticObjectId] | None = None + id__neq: PydanticObjectId | None = None + + md5: MD5Hash | None = None + md5__in: list[MD5Hash] | None = None + md5__neq: MD5Hash | None = None + + name: str | None = None + name__in: list[str] | None = None + name__neq: str | None = None + name__ilike: str | None = None + + # Columns + # Attrs + + # sorting + order_by: list[str] | None = None + + class Constants(BaseFilter.Constants): + model = Table + + @field_serializer("id", "id__in", "id__neq") + def id_to_str(self, v: PydanticObjectId | list[PydanticObjectId] | None) -> str | list[str] | None: + if v is None: + return None + if isinstance(v, list): + return sorted(str(o) for o in v) + return str(v) + + +class TableOut(DocumentOut[PydanticObjectId]): + # extra="allow" so that when ``data`` is requested the full document (including the stored + # ``index``/``columns``) is fetched — Beanie derives the Mongo projection from a plain model's + # fields, and the frame can only be rebuilt from all three. ``_assemble_frame`` drops the raw + # storage keys so they never surface on the response. + model_config = ConfigDict(arbitrary_types_allowed=True, extra="allow") + name: str | None = None + md5: MD5Hash | None = None + attrs: Attributes | None = None + total_data_rows: int | None = None + data: PolarsFrame | None = None + + @model_validator(mode="before") + @classmethod + def _assemble_frame(cls, value: Any) -> Any: + """Rebuild ``data`` as a DataFrame from the stored ``index``/``columns``/``data`` triple. + + Accepts either a Mongo dict (read path) or a ``Table``-like object (download path, + ``from_attributes``). When the storage triple is absent (e.g. a light projection without + ``data``, or a TableOut built directly with a frame) the input passes through unchanged. + """ + getter = value.get if isinstance(value, Mapping) else lambda key: getattr(value, key, None) + index, columns, raw = getter("index"), getter("columns"), getter("data") + if index is None or columns is None or not isinstance(raw, list): + return value + + attrs = getter("attrs") + index_label = _index_label(attrs) + normalized: dict[str, Any] = { + "_id": getter("id") if isinstance(value, Mapping) and "id" in value else getter("_id") or getter("id"), + "name": getter("name"), + "md5": getter("md5"), + "attrs": attrs, + "total_data_rows": getter("total_data_rows"), + "data": storage_to_frame(index_label, index, columns, raw), + } + return {key: val for key, val in normalized.items() if val is not None} + + @staticmethod + def default_fields() -> list[str]: + # Light default; the tabular payload (data) is fetched via ?_fields=. + return [ + "id", + "name", + "md5", + "attrs", + "total_data_rows", + ] + + @classmethod + def projection(cls, fields): + # Light reads use the normal partial-projection (no data/index/columns fetched). When the + # frame is requested, fall back to the full model so index+columns+data come back together + # and ``_assemble_frame`` can rebuild it. + if fields is not None and "data" not in fields: + return super().projection(fields) + return cls + + +class TablePatch(SparseFieldsModel): + name: str | None = None + attrs: Attributes | None = None diff --git a/mpcontribs-api/src/mpcontribs_api/domains/tables/repository.py b/mpcontribs-api/src/mpcontribs_api/domains/tables/repository.py new file mode 100644 index 000000000..a6bda1791 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/tables/repository.py @@ -0,0 +1,13 @@ +from mpcontribs_api.domains._shared.components import MongoDbComponentsRepository +from mpcontribs_api.domains.tables.models import ( + Table, + TableFilter, + TableIn, + TableOut, + TablePatch, +) + + +class MongoDbTableRepository(MongoDbComponentsRepository[Table, TableIn, TableOut, TableFilter, TablePatch]): + document_model = Table + out_model = TableOut diff --git a/mpcontribs-api/src/mpcontribs_api/domains/tables/router.py b/mpcontribs-api/src/mpcontribs_api/domains/tables/router.py new file mode 100644 index 000000000..703f0c6fa --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/domains/tables/router.py @@ -0,0 +1,95 @@ +from typing import Annotated + +from fastapi import APIRouter, Depends +from fastapi.responses import StreamingResponse +from fastapi_filter import FilterDepends + +from mpcontribs_api.dependencies import S3Dep, require_user +from mpcontribs_api.domains._shared.bulk import BulkWriteSummary +from mpcontribs_api.domains._shared.models import ComponentDeleteResponse +from mpcontribs_api.domains._shared.types import ( + DownloadFormat, + FieldSelector, + ShortMimeFormat, + download_filename, +) +from mpcontribs_api.domains.tables.dependencies import TableServiceDep +from mpcontribs_api.domains.tables.models import Table, TableFilter, TableIn, TableOut, TablePatch +from mpcontribs_api.pagination import CursorParams + +router = APIRouter() + + +@router.get("") +async def get_tables( + service: TableServiceDep, + pagination: Annotated[CursorParams, Depends()], + filter: TableFilter = FilterDepends(TableFilter), + fields: FieldSelector = TableOut.default_fields(), +): + selected = TableOut.parse_fields(fields) + return await service.get_many(filter=filter, fields=selected, pagination=pagination) + + +@router.get("/{pk}") +async def get_table( + service: TableServiceDep, + pk: str, + fields: FieldSelector = TableOut.default_fields(), +): + selected = TableOut.parse_fields(fields) + return await service.get_by_id(id=pk, fields=selected) + + +@router.get("/download/{short_mime}") +async def download_table( + service: TableServiceDep, + s3: S3Dep, + format: DownloadFormat, + short_mime: ShortMimeFormat = ShortMimeFormat.GZ, + ignore_cache: bool = False, + filter: TableFilter = FilterDepends(TableFilter), + fields: FieldSelector = TableOut.default_fields(), +) -> StreamingResponse: + selected = TableOut.parse_fields(fields) + body = await service.download( + format=format, + short_mime=short_mime, + ignore_cache=ignore_cache, + filter=filter, + fields=selected, + s3=s3, + ) + filename = download_filename("tables", format, short_mime) + return StreamingResponse( + body, + media_type="application/gzip", + headers={"Content-Disposition": f'attachment; filename="{filename}"'}, + ) + + +@router.post("", response_model=BulkWriteSummary[Table], dependencies=[Depends(require_user)]) +async def insert_tables( + service: TableServiceDep, + tables: list[TableIn], +): + return await service.insert(components=tables) + + +@router.delete("", response_model=ComponentDeleteResponse, dependencies=[Depends(require_user)]) +async def delete_tables(service: TableServiceDep, filter: TableFilter = FilterDepends(TableFilter)): + return await service.delete(filter=filter) + + +@router.delete("/{id}", response_model=ComponentDeleteResponse, dependencies=[Depends(require_user)]) +async def delete_table_by_id(service: TableServiceDep, id: str): + return await service.delete_by_id(id=id) + + +@router.patch("/{id}", dependencies=[Depends(require_user)]) +async def patch_table_by_id( + service: TableServiceDep, + id: str, + update: TablePatch, +): + return await service.patch_by_id(id=id, update=update) diff --git a/mpcontribs-api/src/mpcontribs_api/exceptions.py b/mpcontribs-api/src/mpcontribs_api/exceptions.py new file mode 100644 index 000000000..d84e74817 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/exceptions.py @@ -0,0 +1,161 @@ +from __future__ import annotations + +import logging +from collections.abc import Sequence +from typing import Any + +import structlog +from fastapi import FastAPI, Request +from fastapi.encoders import jsonable_encoder +from fastapi.exceptions import RequestValidationError +from fastapi.responses import JSONResponse +from opentelemetry import trace +from opentelemetry.trace import Status, StatusCode +from starlette.exceptions import HTTPException as StarletteHTTPException + +logger = structlog.get_logger(__name__) + + +def _record_on_span(exc: Exception) -> None: + """Attach a server-side exception to the active OTel span so APM error views show the stack. + + No-op when there is no recording span (telemetry disabled or no active span), since the + sentinel span returned in that case reports ``is_recording() == False``. + """ + span = trace.get_current_span() + if span.is_recording(): + span.record_exception(exc) + span.set_status(Status(StatusCode.ERROR, str(exc))) + + +class AppError(Exception): + """Base for all application-level domain errors. + + Carries enough structured context for a handler to build an HTTP + response without the raising code knowing anything about HTTP. + """ + + # Subclasses override these. Kept as class attrs so a handler can read + # them off the type without instantiating special-casing. + status_code: int = 500 + error_code: str = "internal_error" # stable, machine-readable + # Optional stdlib log level override. None => the handler derives it from status_code + # (ERROR for 5xx, INFO for 4xx). Set on a subclass to promote a notable client error, + # e.g. WARNING for auth failures so they're alertable without logging every 404. + log_level: int | None = None + + def __init__(self, message: str | None = None, **context): + self.message = message or self.__class__.__name__ + self.context = context # extra fields for logging / response + super().__init__(self.message) + + +class NotFoundError(AppError): + status_code = 404 + error_code = "not_found" + log_level = logging.INFO + + +class ConflictError(AppError): + status_code = 409 + error_code = "conflict" + log_level = logging.INFO + + +class ValidationError(AppError): + status_code = 422 + error_code = "validation_error" + log_level = logging.INFO + + +class PayloadTooLargeError(AppError): + status_code = 413 + error_code = "payload_too_large" + log_level = logging.INFO # expected client error: caller sent an oversized body + + +class PermissionError(AppError): + status_code = 403 + error_code = "permission_denied" + log_level = logging.WARNING # security-relevant: alertable, but not a server fault + + +class AuthenticationError(AppError): + status_code = 401 + error_code = "authentication_error" + log_level = logging.WARNING # security-relevant: alertable, but not a server fault + + +def error_body(error_code: str, message: str, **public_context) -> dict: + body: dict[str, Any] = {"error": {"code": error_code, "message": message}} + if public_context: + body["error"]["detail"] = public_context + return body + + +def _sanitize_validation_errors(errors: Sequence[Any]) -> list[dict[str, Any]]: + """Drop the echoed input value and pydantic doc URL from each error.""" + return [{key: value for key, value in error.items() if key not in ("input", "url")} for error in errors] + + +def register_exception_handlers(app: FastAPI) -> None: + """Register all exception handlers to the app. + + Args: + app (FastAPI): the fastapi app to register the exception handlers to + """ + + @app.exception_handler(AppError) + async def _handle_app_error(request: Request, exc: AppError) -> JSONResponse: + is_server_fault = exc.status_code >= 500 + level = exc.log_level if exc.log_level is not None else (logging.ERROR if is_server_fault else logging.INFO) + if is_server_fault: + # Only genuine server faults carry a traceback and mark the span; client errors + # (incl. opt-in WARNING ones like auth failures) are expected and need neither. + _record_on_span(exc) + logger.log(level, exc.error_code, status_code=exc.status_code, exc_info=exc, **exc.context) + else: + logger.log(level, exc.error_code, status_code=exc.status_code, **exc.context) + return JSONResponse( + status_code=exc.status_code, + content=error_body( + exc.error_code, + exc.message, + # NOTE: not leaking context to client yet + # - need to make client-safe (no leakage of secrets) on a per-exception type basis + # **exc.context + ), + ) + + # Catch-all for anything that isn't an AppError - bugs, unexpected failures. + @app.exception_handler(Exception) + async def _handle_unexpected(request: Request, exc: Exception) -> JSONResponse: + _record_on_span(exc) + logger.exception("unhandled_exception") # full traceback + return JSONResponse( + status_code=500, + content=error_body("internal_error", "An unexpected error occurred."), + ) + + # Unify validation errors from pydantic with our exception format + @app.exception_handler(RequestValidationError) + async def _handle_validation(_request: Request, exc: RequestValidationError) -> JSONResponse: + return JSONResponse( + status_code=422, + content=error_body( + "validation_error", + "Request validation failed", + errors=jsonable_encoder(_sanitize_validation_errors(exc.errors())), + ), + ) + + # Unify http exceptions from starlette with our exception format + @app.exception_handler(StarletteHTTPException) + async def _handle_http(request: Request, exc: StarletteHTTPException) -> JSONResponse: + if exc.status_code >= 500: + _record_on_span(exc) + logger.error("http_error", status_code=exc.status_code, exc_info=exc) + return JSONResponse( + status_code=exc.status_code, + content=error_body("http_error", str(exc.detail)), + ) diff --git a/mpcontribs-api/src/mpcontribs_api/logging.py b/mpcontribs-api/src/mpcontribs_api/logging.py new file mode 100644 index 000000000..6cf2bcb4c --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/logging.py @@ -0,0 +1,151 @@ +import logging +import sys + +import structlog +from opentelemetry import trace +from opentelemetry._logs import set_logger_provider +from opentelemetry.exporter.otlp.proto.grpc._log_exporter import OTLPLogExporter +from opentelemetry.sdk._logs import LoggerProvider, LoggingHandler +from opentelemetry.sdk._logs.export import BatchLogRecordProcessor +from opentelemetry.sdk.resources import Resource + +from mpcontribs_api.config import Settings + +# Held across calls so repeated configure_logging() (tests, reloads) reuses one provider rather than +# re-registering. Shared with middleware.py, which builds the tracer/meter providers from the same +# resource so all three signals carry identical service identity. +_logger_provider: LoggerProvider | None = None + + +def build_resource(settings: Settings) -> Resource: + """OTEL resource describing this service. Single source of truth for traces, metrics, and logs.""" + return Resource.create( + { + "service.name": settings.otel.service_name, + "service.version": settings.version, + "deployment.environment": settings.environment, + } + ) + + +def add_otel_trace_context(_, __, event_dict): + span = trace.get_current_span() + ctx = span.get_span_context() + # If context is not the sentinel span (ie. we have an active span) + if ctx.is_valid: + # Convert to OTel-expected ids + # ctx ids are formatted as 128-bit (trace_id) and 64-bit (span_id) long numbers. + # OTel expects them as 0-padded hex numbers + event_dict["trace_id"] = format(ctx.trace_id, "032x") # 32 digits + event_dict["span_id"] = format(ctx.span_id, "016x") # 16 digits + return event_dict + + +def _build_otlp_log_handler(settings: Settings, log_level: int, shared_processors: list) -> LoggingHandler | None: + """Build a stdlib handler that ships records to the OTLP logs pipeline (the Datadog Agent's OTLP + receiver), or ``None`` when telemetry is disabled. + + The record body is the structlog event rendered to JSON; the SDK stamps each record with the + active span's trace/span ids, so logs correlate with traces. + """ + global _logger_provider + if not settings.otel.enabled: + return None + + if _logger_provider is None: + _logger_provider = LoggerProvider(resource=build_resource(settings)) + _logger_provider.add_log_record_processor( + BatchLogRecordProcessor( + OTLPLogExporter(endpoint=settings.otel.otlp_endpoint, insecure=settings.otel.insecure) + ) + ) + set_logger_provider(_logger_provider) + + handler = LoggingHandler(level=log_level, logger_provider=_logger_provider) + # ProcessorFormatter renders the event dict to a JSON string, which LoggingHandler uses as the + # log body (it calls self.format() when a formatter is set). Always JSON regardless of + # environment - the OTLP body should be structured even when stdout is the dev console renderer. + handler.setFormatter( + structlog.stdlib.ProcessorFormatter( + foreign_pre_chain=shared_processors, + processors=[ + structlog.stdlib.ProcessorFormatter.remove_processors_meta, + structlog.processors.dict_tracebacks, + structlog.processors.EventRenamer("message"), + structlog.processors.JSONRenderer(), + ], + ) + ) + return handler + + +def configure_logging(settings: Settings) -> None: + is_prod = settings.environment == "prod" + log_level = logging.INFO if is_prod else logging.DEBUG + + # Run on both structlog events and foreign (stdlib) records. + shared_processors = [ + structlog.contextvars.merge_contextvars, + structlog.processors.add_log_level, + structlog.processors.TimeStamper(fmt="iso", utc=True), + add_otel_trace_context, + ] + + # Exception handling is paired with the renderer, not shared. + if is_prod: + render_chain = [ + structlog.processors.dict_tracebacks, + structlog.processors.EventRenamer("message"), + structlog.processors.JSONRenderer(), + ] + else: + render_chain = [structlog.dev.ConsoleRenderer()] + + # Handles internal logs emitted by structlog logger + structlog.configure( + processors=shared_processors + [structlog.stdlib.ProcessorFormatter.wrap_for_formatter], + logger_factory=structlog.stdlib.LoggerFactory(), + wrapper_class=structlog.make_filtering_bound_logger(log_level), + cache_logger_on_first_use=True, + ) + + # Handles logs emitted by stdlib logging in external libraries + formatter = structlog.stdlib.ProcessorFormatter( + foreign_pre_chain=shared_processors, + processors=[ + structlog.stdlib.ProcessorFormatter.remove_processors_meta, + *render_chain, + ], + ) + + handler = logging.StreamHandler(sys.stdout) + handler.setFormatter(formatter) + + # stdout stays for kubectl logs/ebugging; the OTLP handler (when enabled) ships the same + # records to the collector, so Datadog ingests via OTLP rather than tailing stdout. + handlers: list[logging.Handler] = [handler] + otlp_handler = _build_otlp_log_handler(settings, log_level, shared_processors) + if otlp_handler is not None: + handlers.append(otlp_handler) + + root = logging.getLogger() + root.handlers = handlers + root.setLevel(log_level) + + # Let uvicorn's loggers flow through the root handler instead of their own. + for name in ("uvicorn", "uvicorn.error"): + lg = logging.getLogger(name) + lg.handlers = [] + lg.propagate = True + + # Silence uvicorn's default access log: RequestContextMiddleware emits our own structured access + # event with status/size/duration and Datadog standard attributes. disabled=True suppresses it + # regardless of uvicorn's --access-log flag, so the two never double-log. + access = logging.getLogger("uvicorn.access") + access.handlers = [] + access.propagate = False + access.disabled = True + + +def get_logger(name: str | None = None): + return structlog.get_logger(name) diff --git a/mpcontribs-api/src/mpcontribs_api/middleware.py b/mpcontribs-api/src/mpcontribs_api/middleware.py new file mode 100644 index 000000000..8a463a2a2 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/middleware.py @@ -0,0 +1,274 @@ +import os +import time +import uuid +from collections.abc import Iterable +from typing import TYPE_CHECKING + +import structlog +from opentelemetry import metrics, trace +from opentelemetry.exporter.otlp.proto.grpc.metric_exporter import OTLPMetricExporter +from opentelemetry.exporter.otlp.proto.grpc.trace_exporter import OTLPSpanExporter +from opentelemetry.instrumentation.pymongo import PymongoInstrumentor +from opentelemetry.sdk.metrics import MeterProvider +from opentelemetry.sdk.metrics.export import PeriodicExportingMetricReader +from opentelemetry.sdk.trace import TracerProvider +from opentelemetry.sdk.trace.export import BatchSpanProcessor +from starlette.responses import JSONResponse +from starlette.types import ASGIApp, Message, Receive, Scope, Send + +from mpcontribs_api.config import Settings +from mpcontribs_api.exceptions import PayloadTooLargeError, error_body +from mpcontribs_api.logging import build_resource, get_logger + +if TYPE_CHECKING: + from fastapi import FastAPI + +# Guards repeated configure_tracing() (tests, reloads) from re-registering providers or +# double-instrumenting pymongo. +_configured = False + +# Dedicated access logger. Emits one structured event per request (see RequestContextMiddleware); +# flows through the same root handlers as everything else (stdout + OTLP when enabled). +_access_logger = get_logger("access") + +# Process identity, matching the old gunicorn ``{group}/{process}`` prefix and ``%(p)s`` pid. The +# SUPERVISOR_* vars are absent outside supervisord (dev, tests), so these render null there. +_PROCESS = { + "name": os.getenv("SUPERVISOR_PROCESS_NAME"), + "group": os.getenv("SUPERVISOR_GROUP_NAME"), + "id": os.getpid(), +} + +# Optional request headers folded into the access log's ``http.*`` block, only when sent. +_ACCESS_LOG_HEADERS: dict[bytes, str] = { + b"accept": "accept", + b"accept-language": "accept_language", + b"accept-encoding": "accept_encoding", + b"content-type": "content_type", + b"content-length": "content_length", +} + + +class RequestContextMiddleware: + """Bind per-request structlog context and emit one structured access log per HTTP request. + + The two concerns live together because both need the request headers parsed once, and this is + the outermost app middleware, so it observes the final status code, total response bytes, and + full request duration. The access event uses Datadog standard attribute names (``http.*``, + ``network.*``, ``duration`` in nanoseconds) so the existing Datadog log pipeline (URL parser, + User-Agent parser, status-category, date remapper) regenerates the same enriched surface the old + gunicorn access logs had. + """ + + def __init__(self, app: ASGIApp) -> None: + self.app = app + + async def __call__(self, scope: Scope, receive: Receive, send: Send) -> None: + if scope["type"] != "http": + await self.app(scope, receive, send) + return + + raw_headers: Iterable[tuple[bytes, bytes]] = scope["headers"] + headers = {name: value for name, value in raw_headers} + + raw_request_id = headers.get(b"x-request-id") + request_id = raw_request_id.decode() if raw_request_id else str(uuid.uuid4()) + + context: dict[str, str] = { + "request_id": request_id, + "method": scope["method"], + "path": scope["path"], + } + # Kong-resolved consumer identity for log correlation + raw_consumer_id = headers.get(b"x-consumer-id") + if raw_consumer_id is not None: + context["consumer_id"] = raw_consumer_id.decode() + + structlog.contextvars.clear_contextvars() + structlog.contextvars.bind_contextvars(**context) + + # Capture the final status and body size by wrapping send; the app may call send many times + # (streaming/chunked), so body bytes accumulate across http.response.body messages. + status_code = 0 + bytes_written = 0 + + async def send_wrapper(message: Message) -> None: + nonlocal status_code, bytes_written + if message["type"] == "http.response.start": + status_code = message["status"] + elif message["type"] == "http.response.body": + bytes_written += len(message.get("body", b"")) + await send(message) + + start = time.perf_counter() + try: + await self.app(scope, receive, send_wrapper) + except Exception: + # An exception escaped the app's own handlers (e.g. raised in outer middleware or after + # the response had started, so the catch-all never ran). Record it as a 500 instead of + # the sentinel 0 so status-based alerting still fires, then re-raise unchanged. + if status_code == 0: + status_code = 500 + raise + finally: + self._emit_access_log(scope, headers, status_code, bytes_written, start) + + @staticmethod + def _emit_access_log( + scope: Scope, + headers: dict[bytes, bytes], + status_code: int, + bytes_written: int, + start: float, + ) -> None: + duration_ns = int((time.perf_counter() - start) * 1e9) + query_string = scope.get("query_string", b"").decode("latin-1") + path = scope["path"] + url = f"{path}?{query_string}" if query_string else path + # True client IP behind Kong: first X-Forwarded-For hop if present, else the direct peer (which is Kong itself) + forwarded_for = headers.get(b"x-forwarded-for", b"").decode("latin-1") + client = scope.get("client") + client_ip = forwarded_for.split(",")[0].strip() if forwarded_for else (client[0] if client else "") + + http: dict[str, object] = { + "method": scope["method"], + "status_code": status_code, + "url": url, + "referer": headers.get(b"referer", b"-").decode("latin-1"), + "useragent": headers.get(b"user-agent", b"").decode("latin-1"), + "version": scope.get("http_version", "1.1"), + } + for header_name, http_key in _ACCESS_LOG_HEADERS.items(): + value = headers.get(header_name) + if value is not None: + http[http_key] = value.decode("latin-1") + + _access_logger.info( + "http.access", + http=http, + network={"bytes_written": bytes_written, "client": {"ip": client_ip}}, + duration=duration_ns, # Datadog standard `duration` is nanoseconds + response_time=duration_ns // 1000, # microseconds, matches the old gunicorn %(D)s + process=_PROCESS, + ) + + +class _BodyTooLarge(BaseException): + """Internal signal that the streamed body exceeded the limit. + + Derives from ``BaseException`` (not ``Exception``) on purpose: FastAPI's request-body parser + wraps body reads in ``except Exception`` and would otherwise convert our error into a generic + ``400``. A ``BaseException`` slips past that (and past Starlette's exception middleware) so it + propagates back to ``BodySizeLimitMiddleware``, which turns it into the uniform ``413``. + """ + + +class BodySizeLimitMiddleware: + """Reject request bodies larger than ``max_bytes`` so one caller can't OOM the worker. + + Two enforcement points, because a client can lie about (or omit) ``Content-Length``: + + - **Declared size:** if the ``Content-Length`` header exceeds the limit, respond ``413`` + immediately, before the body is read. This is the common case (the mpcontribs client and + any ``requests``-based caller set ``Content-Length``) and avoids buffering the upload at all. + - **Actual size:** otherwise wrap ``receive`` and accumulate the bytes actually delivered + (chunked transfers, or a lying header); once the running total exceeds the limit, abort. The + abort is signalled by a ``BaseException`` raised from the wrapped ``receive`` (see + :class:`_BodyTooLarge` for why) and caught here, so the response is the same uniform ``413`` + as the declared-size path, and the body is never fully buffered. + + Registered inside ``RequestContextMiddleware`` so rejected requests are still access-logged. + """ + + def __init__(self, app: ASGIApp, max_bytes: int) -> None: + self.app = app + self.max_bytes = max_bytes + + async def __call__(self, scope: Scope, receive: Receive, send: Send) -> None: + if scope["type"] != "http": + await self.app(scope, receive, send) + return + + headers = dict(scope["headers"]) + declared = self._declared_length(headers.get(b"content-length")) + if declared is not None and declared > self.max_bytes: + await self._reject(scope, receive, send) + return + + received = 0 + + async def limited_receive() -> Message: + nonlocal received + message = await receive() + if message["type"] == "http.request": + received += len(message.get("body", b"")) + if received > self.max_bytes: + raise _BodyTooLarge + return message + + try: + await self.app(scope, limited_receive, send) + except _BodyTooLarge: + # Overflow detected mid-body-read: the app hasn't started responding yet, so we own the + # response and emit the 413 ourselves. + await self._reject(scope, receive, send) + + @staticmethod + def _declared_length(raw: bytes | None) -> int | None: + if raw is None: + return None + try: + return int(raw) + except ValueError: + return None + + def _message(self) -> str: + return f"Request body exceeds the maximum allowed size of {self.max_bytes} bytes." + + async def _reject(self, scope: Scope, receive: Receive, send: Send) -> None: + response = JSONResponse( + status_code=PayloadTooLargeError.status_code, + content=error_body(PayloadTooLargeError.error_code, self._message()), + ) + await response(scope, receive, send) + + +def configure_tracing(settings: Settings) -> None: + """Register the global tracer and meter providers, exporting via OTLP/gRPC to the collector. + + Covers the request-scoped signals: ``instrument_app`` (below) emits server spans and + ``http.server`` metrics through these providers, and pymongo spans cover the DB layer. No-op when + telemetry is disabled or already configured. + """ + global _configured + if _configured or not settings.otel.enabled: + return + + resource = build_resource(settings) + endpoint = settings.otel.otlp_endpoint + insecure = settings.otel.insecure + + tracer_provider = TracerProvider(resource=resource) + tracer_provider.add_span_processor(BatchSpanProcessor(OTLPSpanExporter(endpoint=endpoint, insecure=insecure))) + trace.set_tracer_provider(tracer_provider) + + metric_reader = PeriodicExportingMetricReader( + OTLPMetricExporter(endpoint=endpoint, insecure=insecure), + export_interval_millis=settings.otel.metric_export_interval_ms, + ) + metrics.set_meter_provider(MeterProvider(resource=resource, metric_readers=[metric_reader])) + + # Registers a pymongo command listener, so DB spans cover the async client used by Beanie too. + PymongoInstrumentor().instrument() + + _configured = True + + +def instrument_app(app: FastAPI, settings: Settings) -> None: + """Instrument the FastAPI app for server-side request spans/metrics. No-op when disabled.""" + if not settings.otel.enabled: + return + # Imported lazily: pulls in the ASGI instrumentation, only needed when enabled. + from opentelemetry.instrumentation.fastapi import FastAPIInstrumentor + + FastAPIInstrumentor.instrument_app(app) diff --git a/mpcontribs-api/src/mpcontribs_api/pagination.py b/mpcontribs-api/src/mpcontribs_api/pagination.py new file mode 100644 index 000000000..cf4d11298 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/pagination.py @@ -0,0 +1,44 @@ +import base64 + +from pydantic import BaseModel, Field + + +class CursorParams(BaseModel): + """Models parameters used in cursor-based pagination.""" + + # None == First page + cursor: str | None = None + # Per-page limit + limit: int = Field(default=20, ge=1, le=100) + + +class Page[T](BaseModel): + """Model to be returned for a single page of cursor-based paginated results. + + Attributes: + items (list[T]): the items returned for the given page + next_cursor (str): the base64-encoded value of the first id on the next page. If None, then no more pages are + available + """ + + items: list[T] + # None == last page + next_cursor: str | None = None + + +def encode_cursor(last_id: str) -> str: + """Base64 encodes a cursor for pagination + + Uses base64 instead of raw str to prevent manual tampering from users + """ + return base64.urlsafe_b64encode(last_id.encode()).decode() + + +def decode_cursor(cursor: str) -> str: + """Base64 decodes a cursor for pagination""" + # Re-add any base64 padding ('=') that may have been stripped in transit (e.g. via URLs). + padded = cursor + "=" * (-len(cursor) % 4) + try: + return base64.urlsafe_b64decode(padded.encode()).decode() + except ValueError, UnicodeDecodeError: + raise ValueError("malformed cursor") from None diff --git a/mpcontribs-api/src/mpcontribs_api/projection.py b/mpcontribs-api/src/mpcontribs_api/projection.py new file mode 100644 index 000000000..0346a1f21 --- /dev/null +++ b/mpcontribs-api/src/mpcontribs_api/projection.py @@ -0,0 +1,247 @@ +"""Handles the projection of '_fields' from query params. + +This includes arbitrarily specifying nested structures with '.' +Ie. data.band_gap.something will be properly retrieved and populated into the response model that subclasses + SparseFieldsModel +""" + +from __future__ import annotations + +from collections.abc import Iterator +from functools import lru_cache +from typing import ( + Any, + ClassVar, + Literal, + NamedTuple, + Self, + TypeVar, + cast, + get_args, + get_origin, +) + +from pydantic import BaseModel, create_model +from pydantic.fields import FieldInfo + +from mpcontribs_api.exceptions import ValidationError + +ModelT = TypeVar("ModelT", bound=BaseModel) + +# How a model field's annotation is categorised for projection. +FieldKind = Literal["model", "dict", "list", "scalar"] +# A path step may also land on a dict key ("opaque") or a name absent from a model ("unknown"). +StepKind = Literal["model", "dict", "list", "scalar", "opaque", "unknown"] + + +class PathStep(NamedTuple): + """One resolved segment of a dotted field path.""" + + segment: str + field: FieldInfo | None + kind: StepKind + is_last: bool + + +def _unwrap_optional(annotation: object) -> object: + """Strip a single ``T | None`` wrapper, returning the inner annotation.""" + arguments = get_args(annotation) + if type(None) in arguments: + non_none = [arg for arg in arguments if arg is not type(None)] + if len(non_none) == 1: + return non_none[0] + return annotation + + +def _classify(annotation: object) -> tuple[FieldKind, type[BaseModel] | None]: + """Categorise an annotation as model / dict / list / scalar.""" + annotation = _unwrap_optional(annotation) + origin = get_origin(annotation) + if annotation is Any or annotation is dict or origin is dict: + return "dict", None + if origin in (list, set, tuple, frozenset): + return "list", None + if isinstance(annotation, type) and issubclass(annotation, BaseModel): + return "model", annotation + return "scalar", None + + +def _walk_path(model: type[BaseModel], path: str) -> Iterator[PathStep]: + """Yield one step per segment, descending into models and going opaque past a dict.""" + current_model: type[BaseModel] | None = model + segments = path.split(".") + for index, segment in enumerate(segments): + is_last = index == len(segments) - 1 + if current_model is None: # inside a dict's arbitrary contents + yield PathStep(segment, None, "opaque", is_last) + continue + field = current_model.model_fields.get(segment) + if field is None: + yield PathStep(segment, None, "unknown", is_last) + current_model = None + continue + kind, nested_model = _classify(field.annotation) + yield PathStep(segment, field, kind, is_last) + current_model = nested_model if kind == "model" else None + + +def _validate_path(model: type[BaseModel], path: str) -> None: + """Raise if the dotted path is not a selectable field path on the model.""" + for step in _walk_path(model, path): + if step.kind == "unknown": + raise ValidationError(f"unknown field in _fields: {path!r} (no field {step.segment!r})") + if step.kind in ("scalar", "list") and not step.is_last: + raise ValidationError(f"cannot select subfields of {step.kind} field {step.segment!r} in _fields: {path!r}") + + +def _collapse(paths: frozenset[str]) -> frozenset[str]: + """Drop any path whose segment-prefix is also requested (a whole field subsumes its parts). + + ie. {stats, stats.count} => {stats} + """ + segments_by_path = {path: tuple(path.split(".")) for path in paths} + return frozenset( + path + for path, segments in segments_by_path.items() + if not any( + other_path != path and segments[: len(other_segments)] == other_segments + for other_path, other_segments in segments_by_path.items() + ) + ) + + +def _mongo_key(model: type[BaseModel], path: str) -> str: + """Translate a dotted field-name path into its alias-resolved Mongo-key path.""" + mongo_segments: list[str] = [] + for step in _walk_path(model, path): + alias = step.field.validation_alias if step.field is not None else None + mongo_segments.append(alias if isinstance(alias, str) else step.segment) + return ".".join(mongo_segments) + + +def _backs_mongo_id(field: FieldInfo) -> bool: + """Whether a field maps to Mongo ``_id`` (by alias), regardless of its name or type.""" + return field.validation_alias == "_id" or field.alias == "_id" + + +def _optional_field(source_field: FieldInfo, annotation: Any) -> tuple[Any, FieldInfo]: + """Build an optional create_model field definition, preserving the source field's aliases.""" + validation_alias = source_field.validation_alias if isinstance(source_field.validation_alias, str) else None + serialization_alias = ( + source_field.serialization_alias if isinstance(source_field.serialization_alias, str) else None + ) + optional_annotation: Any = annotation | None + return optional_annotation, FieldInfo( + default=None, + validation_alias=validation_alias, + serialization_alias=serialization_alias, + ) + + +@lru_cache(maxsize=128) +def _build_model[ModelT: BaseModel](model: type[ModelT], paths: frozenset[str]) -> type[ModelT]: + """Recursively build the partial response model covering the requested paths.""" + nested_paths_by_root: dict[str, set[str]] = {} + for path in paths: + root, _, remainder = path.partition(".") + nested_paths = nested_paths_by_root.setdefault(root, set()) + if remainder: + nested_paths.add(remainder) + + field_definitions: dict[str, Any] = {} + for root, nested_paths in nested_paths_by_root.items(): + source_field = model.model_fields[root] + kind, nested_model = _classify(source_field.annotation) + if not nested_paths: + field_definitions[root] = _optional_field(source_field, source_field.annotation) + elif kind == "model" and nested_model is not None: + partial_nested = _build_model(nested_model, frozenset(nested_paths)) + field_definitions[root] = _optional_field(source_field, partial_nested) + elif kind == "dict": + field_definitions[root] = _optional_field(source_field, dict[str, Any]) + else: + raise ValidationError(f"cannot project subfields of {kind} field {root!r}") + + partial_model = create_model( + f"{model.__name__}Projection", + __config__=model.model_config, + **field_definitions, + ) + return cast("type[ModelT]", partial_model) + + +@lru_cache(maxsize=128) +def _build_projection[ModelT: BaseModel](model: type[ModelT], paths: frozenset[str]) -> type[ModelT]: + """Build the partial model and attach its explicit dotted Mongo projection.""" + projection: dict[str, int] = {"_id": 1} + for path in paths: + projection[_mongo_key(model, path)] = 1 + partial_model = _build_model(model, paths) + partial_model.Settings = type("Settings", (), {"projection": projection}) + return partial_model + + +class SparseFieldsModel(BaseModel): + """Mixin for response models that support ``_fields`` projection. + + The subclass is the public projectable surface (e.g. ``ProjectOut``); its + field names are the valid ``_fields`` vocabulary, and dotted paths descend + into nested models (``stats.size``) or into arbitrary dict fields + (``data.var.x``). Any field backing Mongo ``_id`` must be declared + ``Field(alias="_id", serialization_alias="id")`` so the projection targets + the right key while the response serialises to the public name. + """ + + # Field names forced into every projection (identity / cursor keys). + sparse_always: ClassVar[frozenset[str]] = frozenset() + + @classmethod + def _identity_fields(cls) -> frozenset[str]: + """Field names backing Mongo ``_id``, always forced into a projection.""" + return frozenset(name for name, field in cls.model_fields.items() if _backs_mongo_id(field)) + + @classmethod + def field_names(cls) -> frozenset[str]: + """Return the top-level field names that may appear in ``_fields``.""" + return frozenset(cls.model_fields) + + @classmethod + def parse_fields(cls, raw: list | None) -> frozenset[str] | None: + """Validate and normalise a raw ``_fields`` value into a set of paths. + + Args: + raw (list): The list of field paths from the ``_fields`` query parameter, + or None when the query parameter was omitted. + + Returns: + None when every field should be returned (parameter omitted), + otherwise the validated, collapsed set of dotted paths, always + including this model's ``sparse_always`` fields. + + Raises: + ValidationError: If a requested path names an unknown field or + selects subfields of a scalar or list field. + """ + if not raw: + return None # None == all fields + requested = frozenset(name.strip() for name in raw if name.strip()) + for path in requested: + _validate_path(cls, path) + return _collapse(requested | cls.sparse_always | cls._identity_fields()) + + @classmethod + def projection(cls, fields: frozenset[str] | None) -> type[Self]: + """Return a projection model exposing only the requested fields. + + Args: + fields: The collapsed path set from ``parse_fields``, or None to + project every field. + + Returns: + This model unchanged when ``fields`` is None, otherwise a cached + partial model carrying an explicit dotted Mongo projection in its + ``Settings``. + """ + if fields is None: + return cls + return cast("type[Self]", _build_projection(cls, fields)) diff --git a/mpcontribs-api/supervisord/conf.py b/mpcontribs-api/supervisord/conf.py index fb0dde081..6869eb183 100644 --- a/mpcontribs-api/supervisord/conf.py +++ b/mpcontribs-api/supervisord/conf.py @@ -1,39 +1,36 @@ import os + from jinja2 import Environment, FileSystemLoader DIR = os.path.abspath(os.path.dirname(__file__)) PRODUCTION = int(os.environ.get("PRODUCTION", "1")) -DEFAULT_NWORKERS = 2 if PRODUCTION else 1 -NWORKERS = int(os.environ.get("NWORKERS", DEFAULT_NWORKERS)) -KG_PORT = 10100 +# uvicorn worker count per API process. Same default in dev and prod; override via the NWORKERS env var. +NWORKERS = int(os.environ.get("NWORKERS", "2")) deployments = {} -for deployment in os.environ.get("DEPLOYMENTS", "ml:10002").split(","): - name, db, s3, tm, max_projects, api_port = deployment.split(":") - portal_port = 8080 + int(api_port) % 10000 +# DEPLOYMENTS entries are "name:db:s3:tm:max_projects:api_port" — the format is an external +# deployment contract (also parsed by scripts/healthchecks.py). Only name, db, and api_port are +# consumed today; s3/tm/max_projects are Flask/portal-era fields kept for format compatibility. +for deployment in os.environ.get("DEPLOYMENTS", "ml:ml:ml:MP:3:10002").split(","): + name, db, _s3, _tm, _max_projects, api_port = deployment.split(":") deployments[name] = { "api_port": api_port, - "portal_port": portal_port, "db": db, - "s3": s3, - "tm": tm.upper(), - "max_projects": int(max_projects) if max_projects else 3 } kwargs = { "production": PRODUCTION, + # MPCONTRIBS_ENVIRONMENT drives the new pydantic Settings (log format, debug mode). + "environment": "prod" if PRODUCTION else "dev", + # MPCONTRIBS_VERSION is required by Settings; sourced from the image build arg at container start. + "version": os.environ.get("CONTRIBS_VERSION", os.environ.get("MPCONTRIBS_VERSION", "0.0.0")), "deployments": deployments, + # Consumed by scripts/start.sh: both dev and prod run `uvicorn --workers $NWORKERS`. "nworkers": NWORKERS, - "reload": int(not PRODUCTION), - "node_env": "production" if PRODUCTION else "development", - "flask_log_level": "INFO" if PRODUCTION else "DEBUG", - "jupyter_gateway_host": f"localhost:{KG_PORT}" if PRODUCTION else f"kernel-gateway:{KG_PORT}", - "dd_agent_host": "localhost" if PRODUCTION else "datadog", - "mpcontribs_api_host": "localhost" if PRODUCTION else "contribs-apis", + # OTLP/gRPC receiver: the Datadog Agent sidecar in prod, the "datadog" compose service in dev. + "otel_endpoint": "localhost:4317" if PRODUCTION else "datadog:4317", } -kwargs["flask_debug"] = kwargs["node_env"] == "development" -kwargs["jupyter_gateway_url"] = "http://" + kwargs["jupyter_gateway_host"] env = Environment(loader=FileSystemLoader(DIR)) template = env.get_template("supervisord.conf.jinja") diff --git a/mpcontribs-api/supervisord/supervisord.conf.jinja b/mpcontribs-api/supervisord/supervisord.conf.jinja index 320d7493e..4e26c0117 100644 --- a/mpcontribs-api/supervisord/supervisord.conf.jinja +++ b/mpcontribs-api/supervisord/supervisord.conf.jinja @@ -4,33 +4,19 @@ user=root logfile=/tmp/supervisord.log pidfile=/tmp/supervisord.pid environment= - MPCONTRIBS_MONGO_HOST="%(ENV_MPCONTRIBS_MONGO_HOST)s", + MPCONTRIBS_ENVIRONMENT="{{ environment }}", + MPCONTRIBS_VERSION="{{ version }}", {% if not production %} AWS_ACCESS_KEY_ID="%(ENV_AWS_ACCESS_KEY_ID)s", AWS_SECRET_ACCESS_KEY="%(ENV_AWS_SECRET_ACCESS_KEY)s", {% endif %} METADATA_URI="%(ENV_ECS_CONTAINER_METADATA_URI_V4)s", - REDIS_ADDRESS="%(ENV_REDIS_ADDRESS)s", AWS_REGION="us-east-1", AWS_DEFAULT_REGION="us-east-1", - MAIL_DEFAULT_SENDER="contribs@materialsproject.org", - DD_PROFILING_ENABLED="false", - DD_PROFILING_STACK_V2_ENABLED="false", - DD_LOGS_INJECTION="true", - FLASK_APP="mpcontribs.api", + MPCONTRIBS_MAIL_DEFAULT_SENDER="contribs@materialsproject.org", PYTHONUNBUFFERED=1, - MAX_REQUESTS=0, - MAX_REQUESTS_JITTER=0, NWORKERS={{ nworkers }}, - RELOAD={{ reload }}, - NODE_ENV="{{ node_env }}", - FLASK_DEBUG="{{ flask_debug }}", - FLASK_LOG_LEVEL="{{ flask_log_level }}", - DD_LOG_LEVEL="{{ flask_log_level }}", - JUPYTER_GATEWAY_URL="{{ jupyter_gateway_url }}", - JUPYTER_GATEWAY_HOST="{{ jupyter_gateway_host }}", - DD_AGENT_HOST="{{ dd_agent_host }}", - DD_TRACE_SAMPLE_RATE="1", + MPCONTRIBS_OTEL__OTLP_ENDPOINT="{{ otel_endpoint }}", TINI_SUBREAPER="true" [program:main] @@ -75,15 +61,7 @@ stderr_logfile_maxbytes=0 environment= DEPLOYMENT={{ loop.index0 }}, API_PORT={{ cfg.api_port }}, - PORTAL_PORT={{ cfg.portal_port }}, - MPCONTRIBS_API_HOST="{{ mpcontribs_api_host }}:{{ cfg.api_port }}", - MPCONTRIBS_DB_NAME="mpcontribs-{{ cfg.db }}", - TRADEMARK="{{ cfg.tm }}", - MAX_PROJECTS={{ cfg.max_projects }}, - S3_DOWNLOADS_BUCKET="mpcontribs-downloads-{{ cfg.s3 }}", - S3_ATTACHMENTS_BUCKET="mpcontribs-attachments-{{ cfg.s3 }}", - S3_IMAGES_BUCKET="mpcontribs-images-{{ cfg.s3 }}", - ADMIN_GROUP="admin_{{ deployment }}.materialsproject.org" + MPCONTRIBS_MONGO__ADMIN_GROUP="admin_{{ deployment }}.materialsproject.org" {% endset %} [program:{{ deployment }}-worker] diff --git a/mpcontribs-api/mpcontribs/api/structures/__init__.py b/mpcontribs-api/tests/__init__.py similarity index 100% rename from mpcontribs-api/mpcontribs/api/structures/__init__.py rename to mpcontribs-api/tests/__init__.py diff --git a/mpcontribs-api/tests/conftest.py b/mpcontribs-api/tests/conftest.py new file mode 100644 index 000000000..617139b13 --- /dev/null +++ b/mpcontribs-api/tests/conftest.py @@ -0,0 +1,18 @@ +import os + +from dotenv import load_dotenv + +# Load .env *before* setdefault calls so real credentials take precedence. +# load_dotenv is a no-op when .env doesn't exist (CI / pure unit-test runs). +load_dotenv() + +# Fallbacks for any value not supplied by .env (CI, unit-only runs, etc.) +os.environ.setdefault("MPCONTRIBS_ENVIRONMENT", "dev") +os.environ.setdefault("MPCONTRIBS_MONGO__URI", "mongodb://localhost:27017") +os.environ.setdefault("MPCONTRIBS_MONGO__DB_NAME", "testdb") +os.environ.setdefault("MPCONTRIBS_REDIS__ADDRESS", "redis://localhost:6379") +os.environ.setdefault("MPCONTRIBS_REDIS__URL", "redis://localhost:6379") +os.environ.setdefault("MPCONTRIBS_MAIL_DEFAULT_SENDER", "test@example.com") +os.environ.setdefault("MPCONTRIBS_VERSION", "0.0.0-test") +# No OTLP collector in tests: keep telemetry off so the suite doesn't register providers or export. +os.environ.setdefault("MPCONTRIBS_OTEL__ENABLED", "false") diff --git a/mpcontribs-api/tests/integration/__init__.py b/mpcontribs-api/tests/integration/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/mpcontribs-api/tests/integration/conftest.py b/mpcontribs-api/tests/integration/conftest.py new file mode 100644 index 000000000..c4be40b21 --- /dev/null +++ b/mpcontribs-api/tests/integration/conftest.py @@ -0,0 +1,131 @@ +from contextlib import asynccontextmanager +from unittest.mock import AsyncMock, MagicMock, patch + +import pytest +from fastapi import FastAPI +from fastapi.testclient import TestClient + +from mpcontribs_api.exceptions import register_exception_handlers +from mpcontribs_api.middleware import RequestContextMiddleware + + +@pytest.fixture(autouse=True, scope="session") +def _mock_beanie_collection(): + """Stub Beanie's collection check for mock-based integration tests. + + FastAPI parses request bodies into Beanie Document subclasses (e.g. + ProjectIn), which calls get_pymongo_collection() in __init__. Without a + real init_beanie() these raise CollectionWasNotInitialized. + + The tests/integration/db/ conftest overrides this fixture with a no-op so + DB tests still get the real Beanie collection after init_beanie(). + """ + import beanie + + with patch.object(beanie.Document, "get_pymongo_collection", return_value=MagicMock()): + yield + +# --------------------------------------------------------------------------- +# Header constants used across test modules +# --------------------------------------------------------------------------- + +from mpcontribs_api.config import get_settings + +ANON_HEADERS: dict[str, str] = {} + +# Forces anonymity even when the client carries default auth headers: get_user() +# treats x-anonymous-consumer == "true" as anonymous regardless of other headers. +FORCE_ANON_HEADERS = {"x-anonymous-consumer": "true"} + +AUTHED_HEADERS = { + "x-consumer-username": "google:alice@example.com", + "x-consumer-id": "test-consumer-id", + "x-authenticated-groups": "mp-team", +} + +ADMIN_HEADERS = { + "x-consumer-username": "google:admin@example.com", + "x-consumer-id": "test-admin-id", + "x-authenticated-groups": "admin", +} + + +# --------------------------------------------------------------------------- +# App factories +# --------------------------------------------------------------------------- + + +def make_test_app() -> FastAPI: + """Build a fully-wired FastAPI app suitable for integration tests. + + Uses a no-op lifespan so no MongoDB connection is required. The + verify_gateway dependency is NOT added at the app level here — tests that + need gateway enforcement should use make_gateway_app() instead. + """ + + @asynccontextmanager + async def _noop_lifespan(app: FastAPI): + app.state.db = MagicMock() + app.state.s3 = MagicMock() + yield + + app = FastAPI(title="mpcontribs-test", lifespan=_noop_lifespan) + app.add_middleware(RequestContextMiddleware) + register_exception_handlers(app) + + from mpcontribs_api.api.v1.router import router as v1_router + from mpcontribs_api.domains._redirects.router import router as redirects_router + + app.include_router(v1_router, prefix="/api/v1") + # Mounted last (root path), exactly as in the real app, so legacy-endpoint + # redirect/deprecation behaviour is exercised by integration tests. + app.include_router(redirects_router) + return app + + +# --------------------------------------------------------------------------- +# Shared fixtures +# --------------------------------------------------------------------------- + + +@pytest.fixture(scope="session") +def test_app() -> FastAPI: + return make_test_app() + + +@pytest.fixture +def client(test_app: FastAPI): + """Function-scoped client; dependency overrides are cleared after each test.""" + with TestClient(test_app, raise_server_exceptions=False) as c: + yield c + test_app.dependency_overrides.clear() + + +@pytest.fixture +def gateway_client(gateway_app: FastAPI): + with TestClient(gateway_app, raise_server_exceptions=False) as c: + yield c + gateway_app.dependency_overrides.clear() + + +# --------------------------------------------------------------------------- +# Mock repository factories +# --------------------------------------------------------------------------- + + +@pytest.fixture +def mock_project_repo() -> AsyncMock: + """Fully async mock of MongoDbProjectRepository.""" + return AsyncMock() + + +@pytest.fixture +def mock_contribution_repo() -> AsyncMock: + """Fully async mock of MongoDbContributionRepository.""" + return AsyncMock() + + +@pytest.fixture +def mock_contribution_service() -> AsyncMock: + """Fully async mock of ContributionService.""" + return AsyncMock() diff --git a/mpcontribs-api/tests/integration/db/__init__.py b/mpcontribs-api/tests/integration/db/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/mpcontribs-api/tests/integration/db/conftest.py b/mpcontribs-api/tests/integration/db/conftest.py new file mode 100644 index 000000000..beab815b9 --- /dev/null +++ b/mpcontribs-api/tests/integration/db/conftest.py @@ -0,0 +1,99 @@ +import pytest +import pytest_asyncio +from beanie import init_beanie +from pymongo import AsyncMongoClient + +from mpcontribs_api.config import get_settings +from mpcontribs_api.domains.attachments.models import Attachment +from mpcontribs_api.domains.contributions.models import Contribution +from mpcontribs_api.domains.projects.models import Project +from mpcontribs_api.domains.structures.models import Structure +from mpcontribs_api.domains.tables.models import Table + +# --------------------------------------------------------------------------- +# Auto-mark all tests in this directory as @pytest.mark.db +# --------------------------------------------------------------------------- + +pytestmark = [ + pytest.mark.db, + pytest.mark.asyncio(loop_scope="session"), +] + + +@pytest.fixture(scope="session") +def _mock_beanie_collection(): + """Override the parent integration conftest's Beanie mock. + + DB tests initialise Beanie for real via init_beanie(), so the mock must not + intercept get_pymongo_collection(). Defining this fixture here (same name, + no patch) causes pytest to use this no-op instead of the parent's version. + """ + yield + + +def pytest_collection_modifyitems(items): + for item in items: + if "integration/db" in str(item.fspath): + item.add_marker(pytest.mark.db) + item.add_marker(pytest.mark.asyncio(loop_scope="session")) + + +# --------------------------------------------------------------------------- +# Session-scoped MongoDB connection + Beanie initialization +# --------------------------------------------------------------------------- + + +@pytest_asyncio.fixture(scope="session") +async def mongo_client(): + """Connect to the Atlas dev instance; skip if unreachable.""" + settings = get_settings() + client = AsyncMongoClient( + settings.mongo.uri.get_secret_value(), + serverSelectionTimeoutMS=5_000, + ) + try: + await client.admin.command("ping") + except Exception as exc: + pytest.skip(f"MongoDB not reachable: {exc}") + yield client + await client.close() + + +@pytest_asyncio.fixture(scope="session") +async def db(mongo_client): + """Database handle with Beanie initialised against the test database.""" + settings = get_settings() + database = mongo_client[settings.mongo.db_name] + await init_beanie( + database=database, + document_models=[Project, Contribution, Structure, Table, Attachment], + ) + yield database + + +# --------------------------------------------------------------------------- +# Per-test collection cleanup (autouse so every test starts clean) +# --------------------------------------------------------------------------- + + +@pytest_asyncio.fixture(autouse=True) +async def clean_projects(db): + await db["projects"].delete_many({}) + yield + await db["projects"].delete_many({}) + + +@pytest_asyncio.fixture(autouse=True) +async def clean_contributions(db): + await db["contributions"].delete_many({}) + yield + await db["contributions"].delete_many({}) + + +@pytest_asyncio.fixture(autouse=True) +async def clean_components(db): + for collection in ("structures", "tables", "attachments"): + await db[collection].delete_many({}) + yield + for collection in ("structures", "tables", "attachments"): + await db[collection].delete_many({}) diff --git a/mpcontribs-api/tests/integration/db/test_component_reachability.py b/mpcontribs-api/tests/integration/db/test_component_reachability.py new file mode 100644 index 000000000..0f7faf088 --- /dev/null +++ b/mpcontribs-api/tests/integration/db/test_component_reachability.py @@ -0,0 +1,86 @@ +"""End-to-end reachability gating for component reads. + +Components (structures/tables/attachments) carry no access field of their own. Visibility is +gated by whether a contribution the caller can see references the component. These tests drive the +real ComponentService against MongoDB to confirm reads only surface reachable components. +""" + +import pytest +from beanie import PydanticObjectId + +from mpcontribs_api.authz import User +from mpcontribs_api.domains._shared.service import ComponentService +from mpcontribs_api.domains.attachments.models import Attachment, AttachmentFilter +from mpcontribs_api.domains.attachments.repository import MongoDbAttachmentRepository +from mpcontribs_api.domains.contributions.models import Contribution +from mpcontribs_api.domains.contributions.repository import MongoDbContributionRepository +from mpcontribs_api.pagination import CursorParams + +pytestmark = [pytest.mark.db, pytest.mark.asyncio(loop_scope="session")] + +ANON = User() + + +def _service(user: User) -> ComponentService: + return ComponentService( + MongoDbAttachmentRepository(user), + MongoDbContributionRepository(user), + ref_field="attachments", + ) + + +async def _attachment(content: int) -> Attachment: + # md5 is server-computed from (mime, content); distinct content -> distinct md5/dedup. + doc = Attachment(_id=PydanticObjectId(), name="d.csv", mime="application/gzip", content=content) + await doc.insert() + return doc + + +async def _contribution(identifier: str, *, is_public: bool, attachments: list[Attachment]) -> Contribution: + doc = Contribution( + _id=PydanticObjectId(), + project="reach-proj", + identifier=identifier, + formula="Fe2O3", + data={"x": 1}, + is_public=is_public, + attachments=attachments, + ) + await doc.insert() + return doc + + +class TestComponentReadReachability: + async def test_get_by_id_returns_reachable_component(self, db): + att = await _attachment(1) + await _contribution("mp-pub", is_public=True, attachments=[att]) + result = await _service(ANON).get_by_id(str(att.id), fields=None) + assert result is not None + assert result.id == att.id + + async def test_get_by_id_hides_unreachable_component(self, db): + att = await _attachment(2) + # Referenced only by a private contribution -> anonymous cannot reach it. + await _contribution("mp-priv", is_public=False, attachments=[att]) + result = await _service(ANON).get_by_id(str(att.id), fields=None) + assert result is None + + async def test_get_by_id_hides_orphan_component(self, db): + # No contribution references this attachment at all. + att = await _attachment(3) + result = await _service(ANON).get_by_id(str(att.id), fields=None) + assert result is None + + async def test_get_many_only_lists_reachable(self, db): + pub = await _attachment(10) + priv = await _attachment(20) + orphan = await _attachment(30) + await _contribution("mp-a", is_public=True, attachments=[pub]) + await _contribution("mp-b", is_public=False, attachments=[priv]) + + page = await _service(ANON).get_many(filter=AttachmentFilter(), pagination=CursorParams(), fields=None) + ids = {item.id for item in page.items} + + assert pub.id in ids + assert priv.id not in ids + assert orphan.id not in ids diff --git a/mpcontribs-api/tests/integration/db/test_components_repository.py b/mpcontribs-api/tests/integration/db/test_components_repository.py new file mode 100644 index 000000000..8a3845aaf --- /dev/null +++ b/mpcontribs-api/tests/integration/db/test_components_repository.py @@ -0,0 +1,223 @@ +import gzip +from unittest.mock import MagicMock + +import pytest +from beanie import PydanticObjectId + +from mpcontribs_api.authz import User +from mpcontribs_api.config import get_settings +from mpcontribs_api.domains._shared.types import DownloadFormat, ShortMimeFormat +from mpcontribs_api.domains.attachments.models import ( + Attachment, + AttachmentFilter, + AttachmentIn, + AttachmentPatch, +) +from mpcontribs_api.domains.attachments.repository import MongoDbAttachmentRepository + +pytestmark = [pytest.mark.db, pytest.mark.asyncio(loop_scope="session")] + + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + +USER = User(username="google:alice@example.com", groups=frozenset({"mp-team"})) + + +def _repo() -> MongoDbAttachmentRepository: + return MongoDbAttachmentRepository(USER) + + +def _attachment(content: int = 1, name: str = "data.csv") -> AttachmentIn: + # md5 is server-computed from (mime, content), so `content` drives dedup identity. + return AttachmentIn(name=name, mime="application/gzip", content=content) + + +async def _count() -> int: + return await Attachment.find_all().count() + + +# --------------------------------------------------------------------------- +# insert_components: md5 dedupe +# --------------------------------------------------------------------------- + + +class TestInsertComponentsDedupe: + async def test_duplicate_content_in_batch_inserted_once(self, db): + # Two inputs share content (-> same md5); only one document should be written. + await _repo().insert_components([_attachment(1), _attachment(1), _attachment(2)]) + assert await _count() == 2 + + async def test_returns_one_doc_per_unique_md5(self, db): + result = await _repo().insert_components([_attachment(1), _attachment(1)]) + assert len(result) == 1 + + async def test_existing_md5_not_reinserted(self, db): + await _repo().insert_components([_attachment(1)]) + # Re-submit the existing content alongside new content. + await _repo().insert_components([_attachment(1), _attachment(2)]) + assert await _count() == 2 + + async def test_existing_doc_returned_with_original_id(self, db): + first = await _repo().insert_components([_attachment(1)]) + again = await _repo().insert_components([_attachment(1)]) + assert again[0].id == first[0].id + + async def test_inserted_docs_have_ids(self, db): + result = await _repo().insert_components([_attachment(1), _attachment(2)]) + assert all(doc.id is not None for doc in result) + + +# --------------------------------------------------------------------------- +# insert_components: chunking +# --------------------------------------------------------------------------- + + +class TestInsertComponentsChunking: + async def test_all_docs_persisted_across_multiple_chunks(self, db, monkeypatch): + # Force a chunk size smaller than the batch so the chunking loop runs >1 time. + monkeypatch.setattr(get_settings().mongo, "component_insert_chunk_size", 2) + # Distinct content -> distinct md5 so all five survive dedup. + attachments = [_attachment(i) for i in range(5)] + result = await _repo().insert_components(attachments) + assert len(result) == 5 + assert await _count() == 5 + + +# --------------------------------------------------------------------------- +# insert_component (single) +# --------------------------------------------------------------------------- + + +class TestInsertComponent: + async def test_single_insert_persists(self, db): + doc = await _repo().insert_component(_attachment(3)) + found = await Attachment.find_one(Attachment.id == doc.id) + assert found is not None + assert found.md5 == doc.md5 + assert len(found.md5) == 32 + + +# --------------------------------------------------------------------------- +# delete_components / delete_component_by_id +# --------------------------------------------------------------------------- + + +class TestDeleteComponents: + async def test_filtered_delete_removes_only_matches(self, db): + keep, drop = await _repo().insert_components([_attachment(1), _attachment(2)]) + result = await _repo().delete_components(AttachmentFilter(md5=drop.md5)) + assert result.num_deleted == 1 + remaining = {doc.md5 async for doc in Attachment.find_all()} + assert remaining == {keep.md5} + + async def test_delete_by_id_removes_one(self, db): + """delete_component_by_id matches a string id by converting it to ObjectId.""" + [doc] = await _repo().insert_components([_attachment(1)]) + result = await _repo().delete_component_by_id(str(doc.id)) + assert result.num_deleted == 1 + assert await _count() == 0 + + async def test_delete_by_unknown_id_raises(self, db): + from mpcontribs_api.exceptions import NotFoundError + + with pytest.raises(NotFoundError): + await _repo().delete_component_by_id(str(PydanticObjectId())) + + +# --------------------------------------------------------------------------- +# patch_component_by_id +# --------------------------------------------------------------------------- + + +class TestPatchComponent: + async def test_patch_updates_field(self, db): + [doc] = await _repo().insert_components([_attachment(1, name="data.csv")]) + updated = await _repo().patch_component_by_id(str(doc.id), AttachmentPatch(name="renamed.png")) + assert updated.name == "renamed.png" + + async def test_empty_patch_returns_existing(self, db): + [doc] = await _repo().insert_components([_attachment(1, name="data.csv")]) + updated = await _repo().patch_component_by_id(str(doc.id), AttachmentPatch()) + assert updated.id == doc.id + + async def test_patch_content_recomputes_md5(self, db): + # name is not a hash field, so renaming must NOT change md5. + [doc] = await _repo().insert_components([_attachment(1)]) + renamed = await _repo().patch_component_by_id(str(doc.id), AttachmentPatch(name="renamed.png")) + assert renamed.md5 == doc.md5 + # content IS a hash field, so changing it must recompute md5. + rehashed = await _repo().patch_component_by_id(str(doc.id), AttachmentPatch(content=999)) + assert rehashed.md5 != doc.md5 + persisted = await Attachment.find_one(Attachment.id == doc.id) + assert persisted.md5 == rehashed.md5 + + +# --------------------------------------------------------------------------- +# Component download round-trip +# --------------------------------------------------------------------------- + + +class TestComponentDownload: + async def test_jsonl_download_round_trips(self, db): + """Component downloads stream a decompressable gzip of all rows.""" + await _repo().insert_components([_attachment(1), _attachment(2)]) + stream = _repo().download( + format=DownloadFormat.JSONL, + short_mime=ShortMimeFormat.GZ, + ignore_cache=True, + filter=AttachmentFilter(), + fields=None, + s3=MagicMock(), + bucket_name="attachments", + key_name="", + ) + chunks = [c async for c in stream] + decompressed = gzip.decompress(b"".join(chunks)) + assert decompressed.count(b"\n") == 2 + + +# --------------------------------------------------------------------------- +# Table DataFrame <-> stored (index/columns/data) round-trips through Mongo +# --------------------------------------------------------------------------- + + +class TestTableFrameRoundTrip: + async def test_table_frame_round_trips_via_storage_shape(self, db): + import polars as pl + + from mpcontribs_api.authz import User + from mpcontribs_api.domains.tables.models import TableIn, TableOut + from mpcontribs_api.domains.tables.repository import MongoDbTableRepository + + repo = MongoDbTableRepository(User(username="x", groups=frozenset())) + # First column is the index (named "T [K]"); cells stay as the original formatted strings. + frame = pl.DataFrame( + { + "T [K]": ["100.0", "200.0"], + "1e16": ["2.2718689×10²¹", "2.2745466×10²¹"], + "1e17": ["2.2718684×10²¹", "2.2745438×10²¹"], + } + ) + tin = TableIn( + name="σ(p)", + attrs={"title": "g", "labels": {"index": "T [K]", "value": "σ", "variable": "doping"}}, + data=frame, + ) + [doc] = await repo.insert_components([tin]) + + # Stored in the canonical MongoDB shape: index/columns/data as strings. + raw = await db["tables"].find_one({"_id": doc.id}) + assert raw["index"] == ["100.0", "200.0"] + assert raw["columns"] == ["1e16", "1e17"] + assert raw["data"] == [["2.2718689×10²¹", "2.2718684×10²¹"], ["2.2745466×10²¹", "2.2745438×10²¹"]] + assert raw["total_data_rows"] == 2 + + # Read back: reassembled into the same DataFrame (index folded back as the first column). + out = await repo.get_component_by_id(str(doc.id), TableOut.parse_fields(["data"])) + assert out.data.columns == ["T [K]", "1e16", "1e17"] + assert out.data.equals(frame) + # The raw storage keys must not leak onto the response model. + assert "index" not in out.model_dump() + await db["tables"].delete_many({"_id": doc.id}) diff --git a/mpcontribs-api/tests/integration/db/test_contributions_repository.py b/mpcontribs-api/tests/integration/db/test_contributions_repository.py new file mode 100644 index 000000000..4d3cd97c8 --- /dev/null +++ b/mpcontribs-api/tests/integration/db/test_contributions_repository.py @@ -0,0 +1,517 @@ +import pytest +from beanie import PydanticObjectId + +from mpcontribs_api.authz import User +from mpcontribs_api.domains.contributions.models import ( + Contribution, + ContributionFilter, + ContributionIn, + ContributionOut, + ContributionPatch, +) +from mpcontribs_api.domains.contributions.repository import MongoDbContributionRepository +from mpcontribs_api.exceptions import NotFoundError, ValidationError +from mpcontribs_api.pagination import CursorParams + +pytestmark = [pytest.mark.db, pytest.mark.asyncio(loop_scope="session")] + + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + +ADMIN = User(username="google:admin@example.com", groups=frozenset({"admin"})) +ALICE = User(username="google:alice@example.com", groups=frozenset({"mp-team"})) +BOB = User(username="google:bob@example.com", groups=frozenset()) +ANON = User() + + +def _repo(user: User = ADMIN) -> MongoDbContributionRepository: + return MongoDbContributionRepository(user) + + +def _contrib_in(project: str = "test-proj", identifier: str = "mp-1", **overrides) -> ContributionIn: + defaults: dict = { + "_id": PydanticObjectId(), + "project": project, + "identifier": identifier, + "formula": "Fe2O3", + "data": {"band_gap": 2.1}, + } + defaults.update(overrides) + return ContributionIn(**defaults) + + +async def _insert(project="test-proj", identifier="mp-1", is_public: bool = False, **overrides) -> Contribution: + # Build a Contribution directly so is_public can be set explicitly. + # from_input_model() always forces is_public=False, which is correct for + # user-submitted data but inconvenient for test setup. + doc = Contribution( + _id=PydanticObjectId(), + project=project, + identifier=identifier, + formula=overrides.pop("formula", "Fe2O3"), + data=overrides.pop("data", {"band_gap": 2.1}), + is_public=is_public, + **overrides, + ) + await doc.insert() + return doc + + +def _noop_filter() -> ContributionFilter: + return ContributionFilter() + + +# --------------------------------------------------------------------------- +# insert_contribution (single) +# --------------------------------------------------------------------------- + + +class TestInsertContribution: + async def test_inserted_document_is_retrievable(self, db): + doc = await _insert(identifier="ins-basic") + found = await Contribution.find_one(Contribution.id == doc.id) + assert found is not None + assert found.identifier == "ins-basic" + + async def test_is_public_defaults_to_false(self, db): + doc = await _insert(identifier="ins-priv") + found = await Contribution.find_one(Contribution.id == doc.id) + assert found.is_public is False + + async def test_fields_are_persisted(self, db): + doc = await _insert(project="proj-x", identifier="ins-fields", formula="Li2O", data={"x": 1}) + found = await Contribution.find_one(Contribution.id == doc.id) + assert found.project == "proj-x" + assert found.formula == "Li2O" + assert found.data == {"x": 1} + + async def test_insert_via_repo(self, db): + ci = _contrib_in(identifier="ins-via-repo") + doc = Contribution.from_input_model(ci) + result = await _repo().insert_contribution(doc) + found = await Contribution.find_one(Contribution.id == result.id) + assert found is not None + assert found.identifier == "ins-via-repo" + + +# --------------------------------------------------------------------------- +# insert_many_contributions (bulk) +# --------------------------------------------------------------------------- + + +class TestInsertManyContributions: + async def test_all_docs_persisted(self, db): + docs = [Contribution.from_input_model(_contrib_in(identifier=f"bulk-{i}")) for i in range(5)] + await _repo().insert_many_contributions(docs) + for doc in docs: + found = await Contribution.find_one(Contribution.id == doc.id) + assert found is not None + + async def test_returns_insert_result(self, db): + docs = [Contribution.from_input_model(_contrib_in(identifier=f"bulk-ret-{i}")) for i in range(3)] + result = await _repo().insert_many_contributions(docs) + assert result is not None + + async def test_empty_list_raises_type_error(self, db): + # Motor's insert_many requires at least one document; callers are + # responsible for guarding against empty batches. + with pytest.raises(TypeError, match="non-empty"): + await _repo().insert_many_contributions([]) + + +# --------------------------------------------------------------------------- +# get_contributions (scoped list + pagination + projection) +# --------------------------------------------------------------------------- + + +class TestGetContributions: + async def test_admin_sees_private_and_public(self, db): + p = await _insert(identifier="ga-pub", is_public=True) + pr = await _insert(identifier="ga-priv", is_public=False) + page = await _repo(ADMIN).get_contributions( + pagination=CursorParams(), filter=_noop_filter(), fields=None + ) + ids = {str(c.id) for c in page.items} + assert str(p.id) in ids + assert str(pr.id) in ids + + async def test_anonymous_sees_only_public(self, db): + pub = await _insert(identifier="anon-pub", is_public=True) + priv = await _insert(identifier="anon-priv", is_public=False) + page = await _repo(ANON).get_contributions( + pagination=CursorParams(), filter=_noop_filter(), fields=None + ) + ids = {str(c.id) for c in page.items} + assert str(pub.id) in ids + assert str(priv.id) not in ids + + async def test_authenticated_non_admin_sees_public(self, db): + pub = await _insert(identifier="alice-pub", is_public=True) + priv = await _insert(identifier="alice-priv", is_public=False) + page = await _repo(ALICE).get_contributions( + pagination=CursorParams(), filter=_noop_filter(), fields=None + ) + ids = {str(c.id) for c in page.items} + assert str(pub.id) in ids + assert str(priv.id) not in ids + + async def test_response_is_page_shape(self, db): + await _insert(identifier="pg-shape") + page = await _repo(ADMIN).get_contributions( + pagination=CursorParams(), filter=_noop_filter(), fields=None + ) + assert hasattr(page, "items") + assert hasattr(page, "next_cursor") + + async def test_limit_respected(self, db): + for i in range(5): + await _insert(identifier=f"lim-{i:02d}", is_public=True) + page = await _repo(ADMIN).get_contributions( + pagination=CursorParams(limit=3), filter=_noop_filter(), fields=None + ) + assert len(page.items) <= 3 + + async def test_cursor_paginates_forward(self, db): + for i in range(4): + await _insert(identifier=f"cur-{i:02d}", is_public=True) + p1 = await _repo(ADMIN).get_contributions( + pagination=CursorParams(limit=2), filter=_noop_filter(), fields=None + ) + assert p1.next_cursor is not None + p2 = await _repo(ADMIN).get_contributions( + pagination=CursorParams(limit=2, cursor=p1.next_cursor), filter=_noop_filter(), fields=None + ) + ids1 = {str(c.id) for c in p1.items} + ids2 = {str(c.id) for c in p2.items} + assert ids1.isdisjoint(ids2) + + async def test_all_items_covered_across_pages(self, db): + for i in range(5): + await _insert(identifier=f"all-pg-{i:02d}", is_public=True) + identifiers: set[str] = set() + cursor = None + while True: + page = await _repo(ADMIN).get_contributions( + pagination=CursorParams(limit=2, cursor=cursor), filter=_noop_filter(), fields=None + ) + identifiers.update(c.identifier for c in page.items if c.identifier) + cursor = page.next_cursor + if cursor is None: + break + assert all(f"all-pg-{i:02d}" in identifiers for i in range(5)) + + async def test_next_cursor_none_on_last_page(self, db): + for i in range(2): + await _insert(identifier=f"last-pg-{i:02d}", is_public=True) + page = await _repo(ADMIN).get_contributions( + pagination=CursorParams(limit=100), filter=_noop_filter(), fields=None + ) + assert page.next_cursor is None + + async def test_projection_returns_only_requested_fields(self, db): + await _insert(identifier="proj-fields", is_public=True) + fields = ContributionOut.parse_fields(["formula"]) + page = await _repo(ADMIN).get_contributions( + pagination=CursorParams(), filter=_noop_filter(), fields=fields + ) + assert len(page.items) >= 1 + item = page.items[0] + assert item.formula is not None + assert not hasattr(item, "data") + + async def test_filter_by_formula(self, db): + await _insert(identifier="flt-fe", formula="Fe2O3", is_public=True) + await _insert(identifier="flt-li", formula="Li2O", is_public=True) + f = ContributionFilter(formula="Fe2O3") + page = await _repo(ADMIN).get_contributions( + pagination=CursorParams(), filter=f, fields=None + ) + formulas = {c.formula for c in page.items} + assert formulas == {"Fe2O3"} + + async def test_filter_by_identifier_ilike(self, db): + await _insert(identifier="ilike-abc", is_public=True) + await _insert(identifier="ilike-xyz", is_public=True) + f = ContributionFilter(identifier__ilike="ilike-a") + page = await _repo(ADMIN).get_contributions( + pagination=CursorParams(), filter=f, fields=None + ) + identifiers = {c.identifier for c in page.items} + assert "ilike-abc" in identifiers + assert "ilike-xyz" not in identifiers + + async def test_filter_by_is_public(self, db): + await _insert(identifier="pub-only-pub", is_public=True) + await _insert(identifier="pub-only-priv", is_public=False) + f = ContributionFilter(is_public=True) + page = await _repo(ADMIN).get_contributions( + pagination=CursorParams(), filter=f, fields=None + ) + assert all(c.is_public is True for c in page.items) + + async def test_filter_by_needs_build(self, db): + await _insert(identifier="nb-true", needs_build=True, is_public=True) + await _insert(identifier="nb-false", needs_build=False, is_public=True) + f = ContributionFilter(needs_build=False) + page = await _repo(ADMIN).get_contributions( + pagination=CursorParams(), filter=f, fields=None + ) + identifiers = {c.identifier for c in page.items} + assert "nb-false" in identifiers + assert "nb-true" not in identifiers + + +# --------------------------------------------------------------------------- +# get_contribution_by_id +# --------------------------------------------------------------------------- + + +class TestGetContributionById: + async def test_returns_doc_for_valid_id(self, db): + doc = await _insert(identifier="get-id") + result = await _repo(ADMIN).get_contribution_by_id(str(doc.id), fields=None) + assert result is not None + assert result.identifier == "get-id" + + async def test_returns_none_for_missing_id(self, db): + result = await _repo(ADMIN).get_contribution_by_id(str(PydanticObjectId()), fields=None) + assert result is None + + async def test_admin_can_get_private_doc(self, db): + doc = await _insert(identifier="get-priv", is_public=False) + result = await _repo(ADMIN).get_contribution_by_id(str(doc.id), fields=None) + assert result is not None + + async def test_anon_cannot_get_private_doc(self, db): + doc = await _insert(identifier="get-anon-priv", is_public=False) + result = await _repo(ANON).get_contribution_by_id(str(doc.id), fields=None) + assert result is None + + async def test_anon_can_get_public_doc(self, db): + doc = await _insert(identifier="get-anon-pub", is_public=True) + result = await _repo(ANON).get_contribution_by_id(str(doc.id), fields=None) + assert result is not None + + async def test_raises_validation_error_for_bad_id_format(self, db): + with pytest.raises(ValidationError): + await _repo(ADMIN).get_contribution_by_id("not-an-objectid", fields=None) + + async def test_projection_limits_fields(self, db): + doc = await _insert(identifier="get-proj", is_public=True) + fields = ContributionOut.parse_fields(["formula"]) + result = await _repo(ADMIN).get_contribution_by_id(str(doc.id), fields=fields) + assert result is not None + assert result.formula == "Fe2O3" + assert not hasattr(result, "data") + + +# --------------------------------------------------------------------------- +# find_one_contribution (by project + identifier) +# --------------------------------------------------------------------------- + + +class TestFindOneContribution: + async def test_finds_existing_doc(self, db): + await _insert(project="find-proj", identifier="find-id") + result = await _repo(ADMIN).find_one_contribution("find-proj", "find-id") + assert result is not None + assert result.project == "find-proj" + assert result.identifier == "find-id" + + async def test_returns_none_for_missing_combination(self, db): + await _insert(project="miss-proj", identifier="miss-id") + result = await _repo(ADMIN).find_one_contribution("miss-proj", "wrong-id") + assert result is None + + async def test_scope_prevents_anon_finding_private(self, db): + await _insert(project="anon-scope", identifier="priv-doc", is_public=False) + result = await _repo(ANON).find_one_contribution("anon-scope", "priv-doc") + assert result is None + + async def test_scope_allows_anon_finding_public(self, db): + await _insert(project="anon-scope-pub", identifier="pub-doc", is_public=True) + result = await _repo(ANON).find_one_contribution("anon-scope-pub", "pub-doc") + assert result is not None + + async def test_project_identifier_combination_is_unique_lookup(self, db): + await _insert(project="same-proj", identifier="id-a") + await _insert(project="same-proj", identifier="id-b") + result = await _repo(ADMIN).find_one_contribution("same-proj", "id-a") + assert result is not None + assert result.identifier == "id-a" + + +# --------------------------------------------------------------------------- +# update_contribution +# --------------------------------------------------------------------------- + + +class TestUpdateContribution: + async def test_updates_single_field(self, db): + doc = await _insert(identifier="upd-formula") + await _repo(ADMIN).update_contribution(doc, {"formula": "SiO2"}) + found = await Contribution.find_one(Contribution.id == doc.id) + assert found.formula == "SiO2" + + async def test_updates_data_field(self, db): + doc = await _insert(identifier="upd-data") + await _repo(ADMIN).update_contribution(doc, {"data": {"energy": -5.0}}) + found = await Contribution.find_one(Contribution.id == doc.id) + assert found.data == {"energy": -5.0} + + async def test_unrelated_fields_unchanged(self, db): + doc = await _insert(identifier="upd-preserve", formula="Fe2O3") + await _repo(ADMIN).update_contribution(doc, {"needs_build": False}) + found = await Contribution.find_one(Contribution.id == doc.id) + assert found.formula == "Fe2O3" + + async def test_update_sets_last_modified(self, db): + doc = await _insert(identifier="upd-lm") + original_lm = doc.last_modified + await _repo(ADMIN).update_contribution(doc, {"formula": "Al2O3"}) + found = await Contribution.find_one(Contribution.id == doc.id) + # MongoDB may return naive UTC datetimes; strip timezone before comparing. + def _naive(dt): + return dt.replace(tzinfo=None) if dt.tzinfo else dt + assert _naive(found.last_modified) >= _naive(original_lm) + + +# --------------------------------------------------------------------------- +# patch_contribution_by_id +# --------------------------------------------------------------------------- + + +class TestPatchContributionById: + async def test_updates_formula(self, db): + doc = await _insert(identifier="patch-formula") + await _repo(ADMIN).patch_contribution_by_id(str(doc.id), ContributionPatch(formula="Li2O")) + found = await Contribution.find_one(Contribution.id == doc.id) + assert found.formula == "Li2O" + + async def test_unset_fields_not_overwritten(self, db): + doc = await _insert(identifier="patch-preserve", formula="Fe2O3") + await _repo(ADMIN).patch_contribution_by_id(str(doc.id), ContributionPatch(needs_build=False)) + found = await Contribution.find_one(Contribution.id == doc.id) + assert found.formula == "Fe2O3" + + async def test_empty_patch_is_a_noop(self, db): + doc = await _insert(identifier="patch-empty", formula="Fe2O3") + result = await _repo(ADMIN).patch_contribution_by_id(str(doc.id), ContributionPatch()) + assert result is not None + found = await Contribution.find_one(Contribution.id == doc.id) + assert found.formula == "Fe2O3" + + async def test_raises_validation_error_for_bad_id(self, db): + with pytest.raises(ValidationError): + await _repo(ADMIN).patch_contribution_by_id("bad-id", ContributionPatch(formula="X")) + + async def test_anon_cannot_patch_private_doc(self, db): + from mpcontribs_api.exceptions import NotFoundError + doc = await _insert(identifier="patch-anon-priv", is_public=False) + with pytest.raises(NotFoundError): + await _repo(ANON).patch_contribution_by_id(str(doc.id), ContributionPatch(formula="X")) + + +# --------------------------------------------------------------------------- +# delete_contribution_by_id +# --------------------------------------------------------------------------- + + +class TestDeleteContributionById: + async def test_deleted_doc_not_found_afterwards(self, db): + doc = await _insert(identifier="del-me") + await _repo(ADMIN).delete_contribution_by_id(str(doc.id)) + found = await Contribution.find_one(Contribution.id == doc.id) + assert found is None + + async def test_delete_nonexistent_throws_error(self, db): + with pytest.raises(NotFoundError, match="not found"): + await _repo(ADMIN).delete_contribution_by_id(str(PydanticObjectId())) + + async def test_raises_validation_error_for_bad_id(self, db): + with pytest.raises(ValidationError): + await _repo(ADMIN).delete_contribution_by_id("not-an-id") + + async def test_anon_cannot_delete_private_doc(self, db): + doc = await _insert(identifier="del-anon-priv", is_public=False) + with pytest.raises(NotFoundError, match="not found"): + await _repo(ANON).delete_contribution_by_id(str(doc.id)) + # Scope prevents anonymous from seeing the doc, so it is never deleted. + still_there = await Contribution.find_one(Contribution.id == doc.id) + assert still_there is not None + + +# --------------------------------------------------------------------------- +# delete_contributions (bulk with filter) +# --------------------------------------------------------------------------- + + +class TestDeleteContributions: + async def test_bulk_delete_all(self, db): + for i in range(3): + await _insert(identifier=f"bdel-{i:02d}") + await _repo(ADMIN).delete_contributions(_noop_filter()) + remaining = await Contribution.find().to_list() + assert len(remaining) == 0 + + async def test_bulk_delete_with_filter(self, db): + await _insert(identifier="bdel-keep", formula="Li2O") + await _insert(identifier="bdel-drop", formula="Fe2O3") + f = ContributionFilter(formula="Fe2O3") + await _repo(ADMIN).delete_contributions(f) + remaining = await Contribution.find().to_list() + assert len(remaining) == 1 + assert remaining[0].identifier == "bdel-keep" + + async def test_bulk_delete_empty_collection_is_silent(self, db): + await _repo(ADMIN).delete_contributions(_noop_filter()) + + async def test_scope_limits_what_anon_can_delete(self, db): + await _insert(identifier="bdel-scope-pub", is_public=True) + await _insert(identifier="bdel-scope-priv", is_public=False) + await _repo(ANON).delete_contributions(_noop_filter()) + # Anonymous scope: only public visible, so only the public doc is deleted. + remaining = await Contribution.find().to_list() + identifiers = {d.identifier for d in remaining} + assert "bdel-scope-priv" in identifiers + + +class TestUpsertContributionById: + async def test_insert_when_id_absent_persists_document(self, db): + new_id = PydanticObjectId() + payload = _contrib_in(identifier="ups-new", _id=new_id) + result = await _repo(ADMIN).upsert_contribution_by_id(str(new_id), payload) + # Must be the resolved document, not an un-awaited query object. + assert isinstance(result, Contribution) + stored = await Contribution.find_one(Contribution.id == new_id) + assert stored is not None + assert stored.identifier == "ups-new" + + async def test_update_when_id_present_applies_change(self, db): + existing = await _insert(identifier="ups-existing") + payload = _contrib_in(identifier="ups-existing", formula="Li2O", _id=existing.id) + result = await _repo(ADMIN).upsert_contribution_by_id(str(existing.id), payload) + assert isinstance(result, Contribution) + stored = await Contribution.find_one(Contribution.id == existing.id) + assert stored is not None + assert stored.formula == "Li2O" + + +class TestDeleteByIdsScope: + async def test_anon_cannot_delete_out_of_scope_ids(self, db): + pub = await _insert(identifier="dbi-pub", is_public=True) + priv = await _insert(identifier="dbi-priv", is_public=False) + # Anonymous scope only sees public docs; deleting both ids must spare the private one. + result = await _repo(ANON).delete_by_ids([pub.id, priv.id]) + assert result.num_deleted == 1 + remaining = {d.identifier for d in await Contribution.find().to_list()} + assert "dbi-priv" in remaining + assert "dbi-pub" not in remaining + + async def test_admin_deletes_all_ids(self, db): + a = await _insert(identifier="dbi-a", is_public=False) + b = await _insert(identifier="dbi-b", is_public=False) + result = await _repo(ADMIN).delete_by_ids([a.id, b.id]) + assert result.num_deleted == 2 diff --git a/mpcontribs-api/tests/integration/db/test_download.py b/mpcontribs-api/tests/integration/db/test_download.py new file mode 100644 index 000000000..6800689aa --- /dev/null +++ b/mpcontribs-api/tests/integration/db/test_download.py @@ -0,0 +1,149 @@ +import csv +import gzip +import io +from unittest.mock import MagicMock + +import pytest +from beanie import PydanticObjectId + +from mpcontribs_api.authz import User +from mpcontribs_api.domains.contributions.models import Contribution, ContributionFilter +from mpcontribs_api.domains.contributions.repository import MongoDbContributionRepository + +pytestmark = [pytest.mark.db, pytest.mark.asyncio(loop_scope="session")] + + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + +ADMIN = User(username="google:admin@example.com", groups=frozenset({"admin"})) +ALICE = User(username="google:alice@example.com", groups=frozenset({"mp-team"})) +ANON = User() + + +def _repo(user: User = ADMIN) -> MongoDbContributionRepository: + return MongoDbContributionRepository(user) + + +async def _insert(project: str, identifier: str, is_public: bool, **overrides) -> Contribution: + doc = Contribution( + _id=PydanticObjectId(), + project=project, + identifier=identifier, + formula=overrides.pop("formula", "Fe2O3"), + data=overrides.pop("data", {"band_gap": 2.1}), + is_public=is_public, + **overrides, + ) + await doc.insert() + return doc + + +async def _seed_scope_fixture() -> None: + """Three contributions spanning the three scope buckets.""" + await _insert("pub-proj", "mp-public", is_public=True) + await _insert("mp-team", "mp-group", is_public=False) + await _insert("secret", "mp-private", is_public=False) + + +async def _collect(stream) -> bytes: + chunks: list[bytes] = [] + async for chunk in stream: + chunks.append(chunk) + return b"".join(chunks) + + +async def _download_bytes(repo: MongoDbContributionRepository, *, format="jsonl", fields=None, filter=None) -> bytes: + from mpcontribs_api.domains._shared.types import DownloadFormat, ShortMimeFormat + + stream = await repo.download_contributions( + format=DownloadFormat(format), + short_mime=ShortMimeFormat.GZ, + ignore_cache=True, + filter=filter or ContributionFilter(), + fields=fields, + key_name="", + s3=MagicMock(), + ) + return gzip.decompress(await _collect(stream)) + + +def _parse_jsonl(raw: bytes) -> list[dict]: + import json + + return [json.loads(line) for line in raw.splitlines() if line] + + +def _parse_csv(raw: bytes) -> list[dict]: + return list(csv.DictReader(io.StringIO(raw.decode()))) + + +# --------------------------------------------------------------------------- +# JSONL round-trip + scope +# --------------------------------------------------------------------------- + + +class TestDownloadJsonl: + async def test_admin_downloads_all_rows(self, db): + await _seed_scope_fixture() + rows = _parse_jsonl(await _download_bytes(_repo(ADMIN))) + assert {r["identifier"] for r in rows} == {"mp-public", "mp-group", "mp-private"} + + async def test_anonymous_sees_only_public(self, db): + await _seed_scope_fixture() + rows = _parse_jsonl(await _download_bytes(_repo(ANON))) + assert {r["identifier"] for r in rows} == {"mp-public"} + + async def test_group_member_sees_public_and_group(self, db): + await _seed_scope_fixture() + rows = _parse_jsonl(await _download_bytes(_repo(ALICE))) + assert {r["identifier"] for r in rows} == {"mp-public", "mp-group"} + + async def test_rows_carry_expected_fields(self, db): + await _insert("pub-proj", "mp-1", is_public=True, formula="Li2O") + rows = _parse_jsonl(await _download_bytes(_repo(ADMIN))) + assert rows[0]["formula"] == "Li2O" + assert rows[0]["project"] == "pub-proj" + + +# --------------------------------------------------------------------------- +# Filtering +# --------------------------------------------------------------------------- + + +class TestDownloadFiltering: + async def test_filter_limits_returned_rows(self, db): + await _insert("pub-proj", "keep-me", is_public=True) + await _insert("pub-proj", "drop-me", is_public=True) + rows = _parse_jsonl( + await _download_bytes(_repo(ADMIN), filter=ContributionFilter(identifier="keep-me")) + ) + assert {r["identifier"] for r in rows} == {"keep-me"} + + async def test_empty_result_is_valid_empty_gzip(self, db): + # No documents match -> the stream is genuinely empty and decompresses to b"". + # (This path never enters the compress loop, so the missing-flush bug doesn't bite.) + raw = await _download_bytes(_repo(ADMIN), filter=ContributionFilter(identifier="no-such-id")) + assert raw == b"" + + +# --------------------------------------------------------------------------- +# CSV round-trip + field projection +# --------------------------------------------------------------------------- + + +class TestDownloadCsv: + async def test_csv_has_header_and_rows(self, db): + await _insert("pub-proj", "mp-1", is_public=True) + await _insert("pub-proj", "mp-2", is_public=True) + rows = _parse_csv(await _download_bytes(_repo(ADMIN), format="csv")) + assert len(rows) == 2 + + async def test_csv_projects_only_requested_fields(self, db): + await _insert("pub-proj", "mp-1", is_public=True) + fields = frozenset({"id", "identifier"}) + rows = _parse_csv(await _download_bytes(_repo(ADMIN), format="csv", fields=fields)) + # Only the requested columns (plus the always-present id) appear. + assert set(rows[0].keys()) <= {"id", "identifier"} + assert rows[0]["identifier"] == "mp-1" diff --git a/mpcontribs-api/tests/integration/db/test_projects_repository.py b/mpcontribs-api/tests/integration/db/test_projects_repository.py new file mode 100644 index 000000000..6ec770c1a --- /dev/null +++ b/mpcontribs-api/tests/integration/db/test_projects_repository.py @@ -0,0 +1,389 @@ +import pytest + +from mpcontribs_api.authz import User +from mpcontribs_api.domains.projects.models import Project, ProjectIn, ProjectOut, ProjectPatch, Stats +from mpcontribs_api.domains.projects.repository import MongoDbProjectRepository +from mpcontribs_api.exceptions import ConflictError, NotFoundError +from mpcontribs_api.pagination import CursorParams + +# All tests in this module share the session event loop so they can reuse the +# session-scoped AsyncMongoClient initialised in conftest. Beanie's internal +# collection references are loop-bound, so mixing loops causes errors. +pytestmark = [pytest.mark.db, pytest.mark.asyncio(loop_scope="session")] + + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + +STATS = Stats(columns=0, contributions=0, tables=0, structures=0, attachments=0, size=0.0) + +ADMIN = User(username="google:admin@example.com", groups=frozenset({"admin"})) +ALICE = User(username="google:alice@example.com", groups=frozenset({"mp-team"})) +ANON = User() + + +def _repo(user: User) -> MongoDbProjectRepository: + return MongoDbProjectRepository(user) + + +def _project_in(id: str, **overrides) -> ProjectIn: + defaults = { + "_id": id, + "title": id[:30], + "authors": "Test Author", + "description": "Test description", + "owner": "google:alice@example.com", + "unique_identifiers": True, + "stats": STATS, + } + defaults.update(overrides) + return ProjectIn(**defaults) + + +async def _insert(id: str, **overrides) -> Project: + project_in = _project_in(id, **overrides) + return await _repo(ADMIN).insert_project(project_in) + + +# --------------------------------------------------------------------------- +# insert_project +# --------------------------------------------------------------------------- + + +class TestInsertProject: + async def test_inserted_project_is_retrievable(self, db): + await _insert("ins-basic") + found = await Project.find_one(Project.id == "ins-basic") + assert found is not None + assert found.id == "ins-basic" + + async def test_duplicate_id_raises_conflict(self, db): + await _insert("ins-dup") + with pytest.raises(ConflictError): + await _insert("ins-dup") + + async def test_default_not_public(self, db): + await _insert("ins-priv") + found = await Project.find_one(Project.id == "ins-priv") + assert found.is_public is False + + async def test_explicit_public(self, db): + await _insert("ins-pub", is_public=True, is_approved=True) + found = await Project.find_one(Project.id == "ins-pub") + assert found.is_public is True + + +# --------------------------------------------------------------------------- +# Authorization scoping (_build_scope) +# --------------------------------------------------------------------------- + + +class TestAuthorizationScope: + async def test_admin_sees_all(self, db): + await _insert("scope-priv", is_public=False) + await _insert("scope-pub", is_public=True, is_approved=True) + page = await _repo(ADMIN).get_projects(filter=_noop_filter(), pagination=CursorParams(), fields=None) + ids = {p.id for p in page.items} + assert "scope-priv" in ids + assert "scope-pub" in ids + + async def test_anonymous_only_sees_public_approved(self, db): + await _insert("anon-priv", is_public=False) + await _insert("anon-pub", is_public=True, is_approved=True) + await _insert("anon-pub-unapproved", is_public=True, is_approved=False) + page = await _repo(ANON).get_projects(filter=_noop_filter(), pagination=CursorParams(), fields=None) + ids = {p.id for p in page.items} + assert "anon-pub" in ids + assert "anon-priv" not in ids + assert "anon-pub-unapproved" not in ids + + async def test_authenticated_sees_own_and_public(self, db): + await _insert("auth-alice-priv", owner="google:alice@example.com", is_public=False) + await _insert("auth-bob-priv", owner="google:bob@example.com", is_public=False) + await _insert("auth-pub", is_public=True, is_approved=True) + page = await _repo(ALICE).get_projects(filter=_noop_filter(), pagination=CursorParams(), fields=None) + ids = {p.id for p in page.items} + assert "auth-alice-priv" in ids + assert "auth-pub" in ids + assert "auth-bob-priv" not in ids + + +def _noop_filter(): + from mpcontribs_api.domains.projects.models import ProjectFilter + + return ProjectFilter() + + +# --------------------------------------------------------------------------- +# get_project_by_id +# --------------------------------------------------------------------------- + + +class TestGetProjectById: + async def test_returns_project_for_valid_id(self, db): + await _insert("get-by-id") + result = await _repo(ADMIN).get_project_by_id(id="get-by-id", fields=None) + assert result is not None + assert result.id == "get-by-id" + + async def test_returns_none_for_missing_id(self, db): + result = await _repo(ADMIN).get_project_by_id(id="does-not-exist", fields=None) + assert result is None + + async def test_admin_can_get_private_project(self, db): + await _insert("get-priv", is_public=False) + result = await _repo(ADMIN).get_project_by_id(id="get-priv", fields=None) + assert result is not None + + async def test_anon_cannot_get_private_project(self, db): + await _insert("get-priv-anon", is_public=False) + result = await _repo(ANON).get_project_by_id(id="get-priv-anon", fields=None) + assert result is None + + +# --------------------------------------------------------------------------- +# get_projects — id filtering +# +# Regression: Beanie stores the primary key under Mongo's ``_id`` (``id`` is an +# alias), but fastapi-filter keys queries on the raw field name. Without the +# ``id`` -> ``_id`` remap in BaseFilter these filters matched nothing even +# though get_project_by_id (which queries ``_id`` directly) found the document. +# --------------------------------------------------------------------------- + + +class TestGetProjectsIdFilter: + async def test_filter_by_id_matches(self, db): + from mpcontribs_api.domains.projects.models import ProjectFilter + + await _insert("filter-id-hit") + page = await _repo(ADMIN).get_projects( + filter=ProjectFilter(id="filter-id-hit"), pagination=CursorParams(), fields=None + ) + assert {p.id for p in page.items} == {"filter-id-hit"} + + async def test_filter_by_id_in_matches(self, db): + from mpcontribs_api.domains.projects.models import ProjectFilter + + await _insert("filter-id-in-a") + await _insert("filter-id-in-b") + await _insert("filter-id-in-c") + page = await _repo(ADMIN).get_projects( + filter=ProjectFilter(id__in=["filter-id-in-a", "filter-id-in-b"]), + pagination=CursorParams(), + fields=None, + ) + assert {p.id for p in page.items} == {"filter-id-in-a", "filter-id-in-b"} + + async def test_filter_by_id_neq_excludes(self, db): + from mpcontribs_api.domains.projects.models import ProjectFilter + + await _insert("filter-id-neq-keep") + await _insert("filter-id-neq-drop") + page = await _repo(ADMIN).get_projects( + filter=ProjectFilter(id__neq="filter-id-neq-drop"), pagination=CursorParams(), fields=None + ) + ids = {p.id for p in page.items} + assert "filter-id-neq-keep" in ids + assert "filter-id-neq-drop" not in ids + + +# --------------------------------------------------------------------------- +# Field projection +# --------------------------------------------------------------------------- + + +class TestFieldProjection: + async def test_projection_returns_only_requested_fields(self, db): + await _insert("proj-fields", is_public=True, is_approved=True) + fields = ProjectOut.parse_fields(["title"]) + page = await _repo(ADMIN).get_projects(filter=_noop_filter(), pagination=CursorParams(), fields=fields) + assert len(page.items) == 1 + item = page.items[0] + assert item.title == "proj-fields" + # authors was not requested — absent from the projected model entirely + assert not hasattr(item, "authors") + + async def test_no_projection_returns_all_fields(self, db): + await _insert("proj-all", is_public=True, is_approved=True) + page = await _repo(ADMIN).get_projects(filter=_noop_filter(), pagination=CursorParams(), fields=None) + item = page.items[0] + assert item.title is not None + assert item.authors is not None + + +# --------------------------------------------------------------------------- +# Cursor-based pagination +# --------------------------------------------------------------------------- + + +class TestPagination: + async def test_limit_is_respected(self, db): + for i in range(5): + await _insert(f"pag-limit-{i:02d}", is_public=True, is_approved=True) + page = await _repo(ADMIN).get_projects(filter=_noop_filter(), pagination=CursorParams(limit=3), fields=None) + assert len(page.items) == 3 + + async def test_next_cursor_set_when_more_items(self, db): + for i in range(4): + await _insert(f"pag-cursor-{i:02d}", is_public=True, is_approved=True) + page = await _repo(ADMIN).get_projects(filter=_noop_filter(), pagination=CursorParams(limit=2), fields=None) + assert page.next_cursor is not None + + async def test_next_cursor_none_on_last_page(self, db): + for i in range(3): + await _insert(f"pag-last-{i:02d}", is_public=True, is_approved=True) + page = await _repo(ADMIN).get_projects(filter=_noop_filter(), pagination=CursorParams(limit=10), fields=None) + assert page.next_cursor is None + + async def test_cursor_fetches_next_page(self, db): + for i in range(4): + await _insert(f"pag-next-{i:02d}", is_public=True, is_approved=True) + page1 = await _repo(ADMIN).get_projects(filter=_noop_filter(), pagination=CursorParams(limit=2), fields=None) + assert page1.next_cursor is not None + page2 = await _repo(ADMIN).get_projects( + filter=_noop_filter(), pagination=CursorParams(limit=2, cursor=page1.next_cursor), fields=None + ) + ids1 = {p.id for p in page1.items} + ids2 = {p.id for p in page2.items} + assert ids1.isdisjoint(ids2), "pages must not overlap" + + async def test_all_items_covered_across_pages(self, db): + for i in range(5): + await _insert(f"pag-all-{i:02d}", is_public=True, is_approved=True) + all_ids: set[str] = set() + cursor = None + while True: + page = await _repo(ADMIN).get_projects( + filter=_noop_filter(), pagination=CursorParams(limit=2, cursor=cursor), fields=None + ) + all_ids.update(p.id for p in page.items) + cursor = page.next_cursor + if cursor is None: + break + assert all(f"pag-all-{i:02d}" in all_ids for i in range(5)) + + +# --------------------------------------------------------------------------- +# patch_project_by_id +# --------------------------------------------------------------------------- + + +class TestPatchProject: + async def test_updates_single_field(self, db): + await _insert("patch-me") + patch = ProjectPatch(title="Updated Title") + await _repo(ADMIN).patch_project_by_id(id="patch-me", update=patch) + found = await Project.find_one(Project.id == "patch-me") + assert found.title == "Updated Title" + + async def test_unset_fields_not_overwritten(self, db): + await _insert("patch-preserve") + original = await Project.find_one(Project.id == "patch-preserve") + patch = ProjectPatch(title="New Title") + await _repo(ADMIN).patch_project_by_id(id="patch-preserve", update=patch) + found = await Project.find_one(Project.id == "patch-preserve") + assert found.authors == original.authors + + async def test_not_found_raises(self, db): + patch = ProjectPatch(title="Won't work") + with pytest.raises(NotFoundError): + await _repo(ADMIN).patch_project_by_id(id="no-such-id", update=patch) + + async def test_empty_patch_returns_existing(self, db): + await _insert("patch-empty") + result = await _repo(ADMIN).patch_project_by_id(id="patch-empty", update=ProjectPatch()) + assert result.id == "patch-empty" + + +# --------------------------------------------------------------------------- +# delete_project_by_id (soft-delete via DocumentWithSoftDelete) +# --------------------------------------------------------------------------- + + +class TestDeleteProject: + async def test_deleted_project_not_in_default_query(self, db): + await _insert("del-me", is_public=True, is_approved=True) + await _repo(ADMIN).delete_project_by_id(id="del-me") + page = await _repo(ADMIN).get_projects(filter=_noop_filter(), pagination=CursorParams(), fields=None) + ids = {p.id for p in page.items} + assert "del-me" not in ids + + async def test_delete_nonexistent_throws_error(self, db): + # delete_project_by_id does find_one().delete() — Error if not found + with pytest.raises(NotFoundError, match="not found"): + await _repo(ADMIN).delete_project_by_id(id="ghost-id") + + +# --------------------------------------------------------------------------- +# upsert_project_by_id +# --------------------------------------------------------------------------- + + +class TestUpsertProject: + async def test_upsert_creates_new_project(self, db): + data = _project_in("upsert-new") + await _repo(ADMIN).upsert_project_by_id(id="upsert-new", data=data) + found = await Project.find_one(Project.id == "upsert-new") + assert found is not None + + async def test_upsert_updates_existing_project(self, db): + await _insert("upsert-existing") + data = _project_in("upsert-existing", title="Replaced Title") + await _repo(ADMIN).upsert_project_by_id(id="upsert-existing", data=data) + found = await Project.find_one(Project.id == "upsert-existing") + assert found.title == "Replaced Title" + + async def test_upsert_uses_path_id_not_body_id(self, db): + data = _project_in("body-id") + await _repo(ADMIN).upsert_project_by_id(id="path-id", data=data) + found = await Project.find_one(Project.id == "path-id") + assert found is not None + + +# --------------------------------------------------------------------------- +# upsert_project_by_id — authorization (owner-or-admin) +# --------------------------------------------------------------------------- + +BOB = User(username="google:bob@example.com", groups=frozenset()) + + +class TestUpsertProjectAuthorization: + async def test_owner_can_overwrite_own_project(self, db): + await _insert("auth-own", owner="google:alice@example.com") + data = _project_in("auth-own", owner="google:alice@example.com", title="Owner Edit") + await _repo(ALICE).upsert_project_by_id(id="auth-own", data=data) + found = await Project.find_one(Project.id == "auth-own") + assert found.title == "Owner Edit" + + async def test_admin_can_overwrite_any_project(self, db): + await _insert("auth-admin", owner="google:alice@example.com") + data = _project_in("auth-admin", owner="google:alice@example.com", title="Admin Edit") + await _repo(ADMIN).upsert_project_by_id(id="auth-admin", data=data) + found = await Project.find_one(Project.id == "auth-admin") + assert found.title == "Admin Edit" + + async def test_non_owner_cannot_overwrite(self, db): + await _insert("auth-other", owner="google:alice@example.com", title="Original") + data = _project_in("auth-other", owner="google:alice@example.com", title="Hijacked") + from mpcontribs_api.exceptions import PermissionError as AppPermissionError + + with pytest.raises(AppPermissionError): + await _repo(BOB).upsert_project_by_id(id="auth-other", data=data) + found = await Project.find_one(Project.id == "auth-other") + assert found.title == "Original" + + async def test_new_project_sets_owner_to_caller(self, db): + # Body owner is someone else; the caller's identity must win. + data = _project_in("auth-newowner", owner="google:alice@example.com") + await _repo(BOB).upsert_project_by_id(id="auth-newowner", data=data) + found = await Project.find_one(Project.id == "auth-newowner") + assert found.owner == "google:bob@example.com" + + async def test_update_preserves_original_owner(self, db): + await _insert("auth-preserve", owner="google:alice@example.com") + # Alice tries to reassign ownership via the body; owner must stay hers. + data = _project_in("auth-preserve", owner="google:bob@example.com", title="Edit") + await _repo(ALICE).upsert_project_by_id(id="auth-preserve", data=data) + found = await Project.find_one(Project.id == "auth-preserve") + assert found.owner == "google:alice@example.com" diff --git a/mpcontribs-api/tests/integration/test_body_size_limit.py b/mpcontribs-api/tests/integration/test_body_size_limit.py new file mode 100644 index 000000000..0e15e289d --- /dev/null +++ b/mpcontribs-api/tests/integration/test_body_size_limit.py @@ -0,0 +1,50 @@ +"""Tests for BodySizeLimitMiddleware — the 413 guard against oversized request bodies.""" + +import pytest +from fastapi import FastAPI +from fastapi.testclient import TestClient + +from mpcontribs_api.exceptions import register_exception_handlers +from mpcontribs_api.middleware import BodySizeLimitMiddleware + +MAX_BYTES = 1024 + + +def _make_app(max_bytes: int = MAX_BYTES) -> FastAPI: + app = FastAPI() + register_exception_handlers(app) + app.add_middleware(BodySizeLimitMiddleware, max_bytes=max_bytes) + + @app.post("/echo") + async def echo(payload: dict) -> dict: + return {"received": len(payload)} + + return app + + +@pytest.fixture +def client() -> TestClient: + return TestClient(_make_app(), raise_server_exceptions=False) + + +class TestBodySizeLimit: + def test_under_limit_passes(self, client: TestClient): + r = client.post("/echo", json={"a": 1}) + assert r.status_code == 200 + + def test_declared_content_length_over_limit_rejected(self, client: TestClient): + # A body whose Content-Length exceeds the ceiling is rejected before it's read. + big = {"blob": "x" * (MAX_BYTES * 2)} + r = client.post("/echo", json=big) + assert r.status_code == 413 + assert r.json()["error"]["code"] == "payload_too_large" + + def test_streamed_body_over_limit_rejected(self, client: TestClient): + # No Content-Length (chunked): the middleware accumulates and rejects via raised AppError, + # which the standard handler renders as a uniform 413. + def gen(): + yield b"x" * (MAX_BYTES * 2) + + r = client.post("/echo", content=gen()) + assert r.status_code == 413 + assert r.json()["error"]["code"] == "payload_too_large" diff --git a/mpcontribs-api/tests/integration/test_bulk_limits.py b/mpcontribs-api/tests/integration/test_bulk_limits.py new file mode 100644 index 000000000..47021ac44 --- /dev/null +++ b/mpcontribs-api/tests/integration/test_bulk_limits.py @@ -0,0 +1,78 @@ +"""Tests for the per-request bulk-write count guard and the GET /limits contract endpoint.""" + +import pytest +from beanie import PydanticObjectId + +from mpcontribs_api.config import get_settings +from mpcontribs_api.domains._shared.bulk import BulkWriteSummary +from mpcontribs_api.domains.contributions.dependencies import get_contribution_service +from tests.integration.conftest import AUTHED_HEADERS + + +def _valid_contribution_body(**overrides) -> dict: + body = { + "_id": str(PydanticObjectId()), + "project": "test-project", + "identifier": "mp-1234", + "formula": "Fe2O3", + "data": {"band_gap": 2.1}, + } + body.update(overrides) + return body + + +@pytest.fixture +def contribution_service(test_app, mock_contribution_service): + test_app.dependency_overrides[get_contribution_service] = lambda: mock_contribution_service + yield mock_contribution_service + test_app.dependency_overrides.pop(get_contribution_service, None) + + +@pytest.fixture(autouse=True) +def _authenticate(client): + client.headers.update(AUTHED_HEADERS) + + +class TestBulkWriteLimit: + @pytest.fixture(autouse=True) + def _small_limit(self, monkeypatch): + # Shrink the limit so the test doesn't need to build 1000+ bodies. + monkeypatch.setattr(get_settings().mongo, "bulk_write_limit", 2) + + def test_over_limit_post_returns_422(self, client, contribution_service): + body = [_valid_contribution_body() for _ in range(3)] + r = client.post("/api/v1/contributions", json=body) + assert r.status_code == 422 + assert r.json()["error"]["code"] == "validation_error" + contribution_service.insert_contributions.assert_not_called() + + def test_at_limit_post_passes(self, client, contribution_service): + contribution_service.insert_contributions.return_value = BulkWriteSummary(total=2, succeeded=[], failed=[]) + body = [_valid_contribution_body() for _ in range(2)] + r = client.post("/api/v1/contributions", json=body) + assert r.status_code == 200 + contribution_service.insert_contributions.assert_called_once() + + def test_over_limit_put_returns_422(self, client, contribution_service): + body = [_valid_contribution_body() for _ in range(3)] + r = client.put("/api/v1/contributions", json=body) + assert r.status_code == 422 + contribution_service.upsert_contributions.assert_not_called() + + +class TestLimitsEndpoint: + def test_limits_reports_configured_values(self, client): + mongo = get_settings().mongo + r = client.get("/api/v1/limits") + assert r.status_code == 200 + assert r.json() == { + "max_request_bytes": mongo.max_request_bytes, + "bulk_write_limit": mongo.bulk_write_limit, + "max_components_per_contribution": mongo.max_components_per_contribution, + "component_insert_chunk_size": mongo.component_insert_chunk_size, + } + + def test_limits_is_public(self, client): + # No auth headers: still readable (public metadata). + client.headers.clear() + assert client.get("/api/v1/limits").status_code == 200 diff --git a/mpcontribs-api/tests/integration/test_component_routes.py b/mpcontribs-api/tests/integration/test_component_routes.py new file mode 100644 index 000000000..c1b49cd8b --- /dev/null +++ b/mpcontribs-api/tests/integration/test_component_routes.py @@ -0,0 +1,333 @@ +from unittest.mock import AsyncMock + +import pytest +from beanie import PydanticObjectId + +from mpcontribs_api.domains._shared.models import ComponentDeleteResponse +from mpcontribs_api.domains.attachments.dependencies import get_attachment_service +from mpcontribs_api.domains.structures.dependencies import get_structure_service +from mpcontribs_api.domains.structures.models import StructureOut +from mpcontribs_api.domains.tables.dependencies import get_table_service +from mpcontribs_api.domains.tables.models import TableOut +from mpcontribs_api.pagination import Page +from tests.integration.conftest import AUTHED_HEADERS, FORCE_ANON_HEADERS + +# --------------------------------------------------------------------------- +# Fixtures: every component endpoint routes through the unified ComponentService, +# so each domain has a single mock service override. +# --------------------------------------------------------------------------- + + +@pytest.fixture(autouse=True) +def _authenticate(client): + """Mutating component endpoints now require an authenticated caller. + + These route tests exercise mutations, so default the shared client to an + authenticated identity. Anonymous-rejection is covered explicitly by the + *RequireAuth tests, which force anonymity with FORCE_ANON_HEADERS. + """ + client.headers.update(AUTHED_HEADERS) + + +@pytest.fixture +def structure_service(test_app): + mock = AsyncMock() + test_app.dependency_overrides[get_structure_service] = lambda: mock + yield mock + test_app.dependency_overrides.pop(get_structure_service, None) + + +@pytest.fixture +def table_service(test_app): + mock = AsyncMock() + test_app.dependency_overrides[get_table_service] = lambda: mock + yield mock + test_app.dependency_overrides.pop(get_table_service, None) + + +@pytest.fixture +def attachment_service(test_app): + mock = AsyncMock() + test_app.dependency_overrides[get_attachment_service] = lambda: mock + yield mock + test_app.dependency_overrides.pop(get_attachment_service, None) + + +SAMPLE_STRUCTURE = StructureOut(name="Fe2O3.cif", md5="a" * 32) +SAMPLE_TABLE = TableOut(name="bandgaps", md5="b" * 32) + + +# =========================================================================== +# STRUCTURES +# =========================================================================== + + +class TestStructuresList: + def test_empty_page_returns_200(self, client, structure_service): + structure_service.get_many.return_value = Page(items=[], next_cursor=None) + assert client.get("/api/v1/structures").status_code == 200 + + def test_page_shape(self, client, structure_service): + structure_service.get_many.return_value = Page(items=[SAMPLE_STRUCTURE], next_cursor="c") + body = client.get("/api/v1/structures").json() + assert "items" in body + assert body["next_cursor"] == "c" + + def test_service_called_with_pagination(self, client, structure_service): + structure_service.get_many.return_value = Page(items=[], next_cursor=None) + client.get("/api/v1/structures?limit=5") + kwargs = structure_service.get_many.call_args.kwargs + assert kwargs["pagination"].limit == 5 + + def test_invalid_fields_returns_422(self, client, structure_service): + structure_service.get_many.return_value = Page(items=[], next_cursor=None) + assert client.get("/api/v1/structures?_fields=not_a_field").status_code == 422 + + def test_valid_fields_forwarded(self, client, structure_service): + structure_service.get_many.return_value = Page(items=[], next_cursor=None) + client.get("/api/v1/structures?_fields=name") + # parse_fields always includes the id identity field. + assert structure_service.get_many.call_args.kwargs["fields"] == frozenset({"id", "name"}) + + def test_content_fields_are_selectable(self, client, structure_service): + # Regression for #4: structure content must be reachable via _fields (on the Out model). + structure_service.get_many.return_value = Page(items=[], next_cursor=None) + r = client.get("/api/v1/structures?_fields=lattice&_fields=sites&_fields=charge&_fields=cif") + assert r.status_code == 200 + assert structure_service.get_many.call_args.kwargs["fields"] == frozenset( + {"id", "lattice", "sites", "charge", "cif"} + ) + + +class TestStructuresDelete: + def test_batch_delete_returns_200(self, client, structure_service): + structure_service.delete.return_value = ComponentDeleteResponse(num_deleted=3) + r = client.delete("/api/v1/structures") + assert r.status_code == 200 + assert r.json() == {"num_deleted": 3, "num_skipped": 0, "referenced_ids": []} + + def test_service_delete_called(self, client, structure_service): + structure_service.delete.return_value = ComponentDeleteResponse(num_deleted=0) + client.delete("/api/v1/structures") + structure_service.delete.assert_awaited_once() + + +class TestStructuresInsert: + def test_post_route_exists(self, client, structure_service): + # Empty body -> handler invoked; service returns a summary-shaped object. + structure_service.insert.return_value = {"total": 0, "succeeded": [], "failed": []} + r = client.post("/api/v1/structures", json=[]) + assert r.status_code != 404 + + def test_post_forwards_to_service(self, client, structure_service): + structure_service.insert.return_value = {"total": 0, "succeeded": [], "failed": []} + client.post("/api/v1/structures", json=[]) + structure_service.insert.assert_awaited_once() + + +class TestStructuresByIdRouting: + def test_get_by_id_conventional_path(self, client, structure_service): + structure_service.get_by_id.return_value = SAMPLE_STRUCTURE + assert client.get(f"/api/v1/structures/{PydanticObjectId()}").status_code == 200 + + def test_delete_by_id_conventional_path(self, client, structure_service): + structure_service.delete_by_id.return_value = ComponentDeleteResponse(num_deleted=1) + assert client.delete(f"/api/v1/structures/{PydanticObjectId()}").status_code == 200 + + def test_patch_by_id_conventional_path(self, client, structure_service): + structure_service.patch_by_id.return_value = SAMPLE_STRUCTURE + r = client.patch(f"/api/v1/structures/{PydanticObjectId()}", json={"name": "renamed"}) + assert r.status_code == 200 + + def test_download_conventional_path(self, client, structure_service): + structure_service.download.return_value = iter([b"x"]) + assert client.get("/api/v1/structures/download/gz?format=csv").status_code == 200 + + +# =========================================================================== +# TABLES +# =========================================================================== + + +class TestTablesList: + def test_empty_page_returns_200(self, client, table_service): + table_service.get_many.return_value = Page(items=[], next_cursor=None) + assert client.get("/api/v1/tables").status_code == 200 + + def test_page_shape(self, client, table_service): + table_service.get_many.return_value = Page(items=[SAMPLE_TABLE], next_cursor=None) + assert "items" in client.get("/api/v1/tables").json() + + def test_invalid_fields_returns_422(self, client, table_service): + table_service.get_many.return_value = Page(items=[], next_cursor=None) + assert client.get("/api/v1/tables?_fields=nope").status_code == 422 + + def test_default_fields_accepted(self, client, table_service): + table_service.get_many.return_value = Page(items=[], next_cursor=None) + assert client.get("/api/v1/tables").status_code == 200 + + +class TestTablesDelete: + def test_batch_delete_returns_200(self, client, table_service): + table_service.delete.return_value = ComponentDeleteResponse(num_deleted=2) + assert client.delete("/api/v1/tables").json() == { + "num_deleted": 2, + "num_skipped": 0, + "referenced_ids": [], + } + + +class TestTablesInsert: + def test_post_forwards_to_service(self, client, table_service): + table_service.insert.return_value = {"total": 0, "succeeded": [], "failed": []} + client.post("/api/v1/tables", json=[]) + table_service.insert.assert_awaited_once() + + +class TestTablesByIdRouting: + def test_get_by_id_conventional_path(self, client, table_service): + table_service.get_by_id.return_value = SAMPLE_TABLE + assert client.get(f"/api/v1/tables/{PydanticObjectId()}").status_code == 200 + + def test_delete_by_id_conventional_path(self, client, table_service): + table_service.delete_by_id.return_value = ComponentDeleteResponse(num_deleted=1) + assert client.delete(f"/api/v1/tables/{PydanticObjectId()}").status_code == 200 + + def test_patch_by_id_conventional_path(self, client, table_service): + table_service.patch_by_id.return_value = SAMPLE_TABLE + r = client.patch(f"/api/v1/tables/{PydanticObjectId()}", json={"name": "x"}) + assert r.status_code == 200 + + +# =========================================================================== +# ATTACHMENTS +# =========================================================================== + + +class TestAttachmentsRouterWiring: + def test_list_calls_attachment_service(self, client, attachment_service): + attachment_service.get_many.return_value = Page(items=[], next_cursor=None) + r = client.get("/api/v1/attachments") + assert r.status_code == 200 + attachment_service.get_many.assert_awaited_once() + + def test_get_by_id_calls_attachment_service(self, client, attachment_service): + attachment_service.get_by_id.return_value = None + client.get(f"/api/v1/attachments/{PydanticObjectId()}") + attachment_service.get_by_id.assert_awaited_once() + + def test_delete_by_id_calls_attachment_service(self, client, attachment_service): + attachment_service.delete_by_id.return_value = ComponentDeleteResponse(num_deleted=1) + client.delete(f"/api/v1/attachments/{PydanticObjectId()}") + attachment_service.delete_by_id.assert_awaited_once() + + def test_batch_delete_calls_attachment_service(self, client, attachment_service): + attachment_service.delete.return_value = ComponentDeleteResponse(num_deleted=0) + client.delete("/api/v1/attachments") + attachment_service.delete.assert_awaited_once() + + +# =========================================================================== +# Component downloads: /{resource}/download/{short_mime} +# +# Parametrised over the three component resources so download behavior is held +# to the same contract everywhere. Each entry is +# (url_prefix, service_fixture_name, expected_stem). +# =========================================================================== + +_DOWNLOAD_CASES = [ + ("structures", "structure_service", "structures"), + ("tables", "table_service", "tables"), + ("attachments", "attachment_service", "attachments"), +] + + +@pytest.fixture +def download_target(request): + """Resolve a (prefix, service_fixture, stem) case into a wired service mock.""" + prefix, service_fixture, stem = request.param + service = request.getfixturevalue(service_fixture) + service.download.return_value = iter([b"x"]) + return prefix, service, stem + + +@pytest.mark.parametrize("download_target", _DOWNLOAD_CASES, indirect=True) +class TestComponentDownloads: + def test_csv_returns_200(self, client, download_target): + prefix, *_ = download_target + assert client.get(f"/api/v1/{prefix}/download/gz?format=csv").status_code == 200 + + def test_jsonl_returns_200(self, client, download_target): + prefix, *_ = download_target + assert client.get(f"/api/v1/{prefix}/download/gz?format=jsonl").status_code == 200 + + def test_body_is_streamed_bytes(self, client, download_target): + prefix, service, _ = download_target + service.download.return_value = iter([b"ab", b"cd"]) + assert client.get(f"/api/v1/{prefix}/download/gz?format=jsonl").content == b"abcd" + + def test_format_is_required(self, client, download_target): + # Component download routes give `format` no default, unlike contributions. + prefix, *_ = download_target + assert client.get(f"/api/v1/{prefix}/download/gz").status_code == 422 + + def test_invalid_short_mime_returns_422(self, client, download_target): + prefix, *_ = download_target + assert client.get(f"/api/v1/{prefix}/download/zip?format=jsonl").status_code == 422 + + def test_invalid_format_returns_422(self, client, download_target): + prefix, *_ = download_target + assert client.get(f"/api/v1/{prefix}/download/gz?format=xml").status_code == 422 + + def test_format_forwarded_to_service(self, client, download_target): + prefix, service, _ = download_target + client.get(f"/api/v1/{prefix}/download/gz?format=csv") + assert service.download.call_args.kwargs["format"] == "csv" + + def test_csv_filename_uses_csv_extension(self, client, download_target): + """A CSV download is named *.csv.gz, matching the requested format.""" + prefix, *_ = download_target + cd = client.get(f"/api/v1/{prefix}/download/gz?format=csv").headers["content-disposition"] + assert ".csv.gz" in cd + + +# =========================================================================== +# Authentication enforcement: component mutations require an authenticated user +# =========================================================================== + + +class TestComponentMutationsRequireAuth: + def test_structures_post_anon_401(self, client, structure_service): + r = client.post("/api/v1/structures", json=[], headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + structure_service.insert.assert_not_called() + + def test_structures_delete_anon_401(self, client, structure_service): + r = client.delete("/api/v1/structures", headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + structure_service.delete.assert_not_called() + + def test_structure_delete_by_id_anon_401(self, client, structure_service): + r = client.delete(f"/api/v1/structures/{PydanticObjectId()}", headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + structure_service.delete_by_id.assert_not_called() + + def test_structure_patch_by_id_anon_401(self, client, structure_service): + r = client.patch(f"/api/v1/structures/{PydanticObjectId()}", json={"name": "x"}, headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + structure_service.patch_by_id.assert_not_called() + + def test_tables_delete_anon_401(self, client, table_service): + r = client.delete("/api/v1/tables", headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + table_service.delete.assert_not_called() + + def test_attachment_delete_by_id_anon_401(self, client, attachment_service): + r = client.delete(f"/api/v1/attachments/{PydanticObjectId()}", headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + attachment_service.delete_by_id.assert_not_called() + + def test_structures_get_still_open_to_anon(self, client, structure_service): + structure_service.get_many.return_value = Page(items=[], next_cursor=None) + r = client.get("/api/v1/structures", headers=FORCE_ANON_HEADERS) + assert r.status_code == 200 diff --git a/mpcontribs-api/tests/integration/test_contributions.py b/mpcontribs-api/tests/integration/test_contributions.py new file mode 100644 index 000000000..7f61ac4bb --- /dev/null +++ b/mpcontribs-api/tests/integration/test_contributions.py @@ -0,0 +1,122 @@ +import pytest + +from mpcontribs_api.domains.contributions.dependencies import get_scoped_contributions +from mpcontribs_api.domains.contributions.models import ContributionOut +from mpcontribs_api.pagination import Page +from tests.integration.conftest import ANON_HEADERS, AUTHED_HEADERS + +# --------------------------------------------------------------------------- +# Fixture: inject mock repo for each test +# --------------------------------------------------------------------------- + + +@pytest.fixture +def contribution_repo(test_app, mock_contribution_repo): + test_app.dependency_overrides[get_scoped_contributions] = lambda: mock_contribution_repo + yield mock_contribution_repo + test_app.dependency_overrides.pop(get_scoped_contributions, None) + + +SAMPLE_CONTRIBUTION = ContributionOut( + project="mp-project", + identifier="mp-001", + formula="Fe2O3", + is_public=True, + data={"band_gap": 2.1}, +) + + +# --------------------------------------------------------------------------- +# GET /api/v1/contributions +# --------------------------------------------------------------------------- + + +class TestListContributions: + def test_empty_page_returns_200(self, client, contribution_repo): + contribution_repo.get_contributions.return_value = Page(items=[], next_cursor=None) + r = client.get("/api/v1/contributions", headers=AUTHED_HEADERS) + assert r.status_code == 200 + + def test_response_has_page_shape(self, client, contribution_repo): + contribution_repo.get_contributions.return_value = Page(items=[], next_cursor=None) + body = client.get("/api/v1/contributions", headers=AUTHED_HEADERS).json() + assert "items" in body + assert "next_cursor" in body + + def test_items_in_response(self, client, contribution_repo): + contribution_repo.get_contributions.return_value = Page(items=[SAMPLE_CONTRIBUTION], next_cursor=None) + body = client.get("/api/v1/contributions", headers=AUTHED_HEADERS).json() + assert len(body["items"]) == 1 + + def test_repo_called_with_pagination(self, client, contribution_repo): + contribution_repo.get_contributions.return_value = Page(items=[], next_cursor=None) + client.get("/api/v1/contributions", params={"limit": 10}, headers=AUTHED_HEADERS) + _, kwargs = contribution_repo.get_contributions.call_args + assert kwargs["pagination"].limit == 10 + + def test_fields_forwarded(self, client, contribution_repo): + contribution_repo.get_contributions.return_value = Page(items=[], next_cursor=None) + client.get("/api/v1/contributions", params={"_fields": ["formula"]}, headers=AUTHED_HEADERS) + _, kwargs = contribution_repo.get_contributions.call_args + assert kwargs["fields"] is not None + assert "formula" in kwargs["fields"] + + def test_invalid_fields_returns_422(self, client, contribution_repo): + contribution_repo.get_contributions.return_value = Page(items=[], next_cursor=None) + r = client.get("/api/v1/contributions", params={"_fields": "bad_field"}, headers=AUTHED_HEADERS) + assert r.status_code == 422 + + def test_anonymous_can_list(self, client, contribution_repo): + contribution_repo.get_contributions.return_value = Page(items=[], next_cursor=None) + r = client.get("/api/v1/contributions", headers=ANON_HEADERS) + assert r.status_code == 200 + + def test_filter_param_forwarded_to_repo(self, client, contribution_repo): + contribution_repo.get_contributions.return_value = Page(items=[], next_cursor=None) + client.get("/api/v1/contributions", params={"formula": "Fe2O3"}, headers=AUTHED_HEADERS) + contribution_repo.get_contributions.assert_called_once() + + +# --------------------------------------------------------------------------- +# DELETE /api/v1/contributions (batch) +# --------------------------------------------------------------------------- + + +class TestDeleteContributions: + def test_batch_delete_returns_200(self, client, contribution_repo): + contribution_repo.delete_contributions.return_value = None + r = client.delete("/api/v1/contributions", headers=AUTHED_HEADERS) + assert r.status_code == 200 + + def test_repo_delete_called(self, client, contribution_repo): + contribution_repo.delete_contributions.return_value = None + client.delete("/api/v1/contributions", headers=AUTHED_HEADERS) + contribution_repo.delete_contributions.assert_called_once() + + def test_filter_forwarded_to_repo(self, client, contribution_repo): + contribution_repo.delete_contributions.return_value = None + client.delete("/api/v1/contributions", params={"is_public": "true"}, headers=AUTHED_HEADERS) + _, kwargs = contribution_repo.delete_contributions.call_args + assert kwargs["filter"] is not None + + +# --------------------------------------------------------------------------- +# Stub endpoints — verify they exist and wire to the repo +# --------------------------------------------------------------------------- + + +class TestStubEndpoints: + """These endpoints are stubs in the repo but the routes must be wired.""" + + def test_post_contributions_route_exists(self, client, contribution_repo): + contribution_repo.insert_contributions.return_value = None + r = client.post("/api/v1/contributions", json=[], headers=AUTHED_HEADERS) + # Should reach the route (not 404/405) even if the handler is a stub + assert r.status_code != 404 + assert r.status_code != 405 + + def test_put_contributions_route_exists(self, client, contribution_repo): + contribution_repo.upsert_contributions.return_value = None + r = client.put("/api/v1/contributions", json=[], headers=AUTHED_HEADERS) + assert r.status_code != 404 + assert r.status_code != 405 diff --git a/mpcontribs-api/tests/integration/test_contributions_routes.py b/mpcontribs-api/tests/integration/test_contributions_routes.py new file mode 100644 index 000000000..36adad598 --- /dev/null +++ b/mpcontribs-api/tests/integration/test_contributions_routes.py @@ -0,0 +1,302 @@ +import pytest +from beanie import PydanticObjectId + +from mpcontribs_api.domains._shared.bulk import BulkDeleteSummary, BulkWriteSummary +from mpcontribs_api.domains.contributions.dependencies import ( + get_contribution_service, + get_scoped_contributions, +) +from mpcontribs_api.domains.contributions.models import ContributionOut +from mpcontribs_api.exceptions import NotFoundError +from tests.integration.conftest import AUTHED_HEADERS, FORCE_ANON_HEADERS + +# --------------------------------------------------------------------------- +# Fixtures +# --------------------------------------------------------------------------- + + +@pytest.fixture(autouse=True) +def _authenticate(client): + """Mutating contribution endpoints now require an authenticated caller. + + Default the shared client to an authenticated identity so the existing + mutation tests still exercise the handler; anonymous-rejection is covered + explicitly by TestContributionMutationsRequireAuth via FORCE_ANON_HEADERS. + """ + client.headers.update(AUTHED_HEADERS) + + +@pytest.fixture +def contribution_repo(test_app, mock_contribution_repo): + test_app.dependency_overrides[get_scoped_contributions] = lambda: mock_contribution_repo + yield mock_contribution_repo + test_app.dependency_overrides.pop(get_scoped_contributions, None) + + +@pytest.fixture +def contribution_service(test_app, mock_contribution_service): + test_app.dependency_overrides[get_contribution_service] = lambda: mock_contribution_service + yield mock_contribution_service + test_app.dependency_overrides.pop(get_contribution_service, None) + + +def _valid_contribution_body(**overrides) -> dict: + # ContributionIn inherits a required _id from BaseDocumentWithInput, so a + # client-supplied object id is part of the create contract (mirrors the + # service unit tests, which always pass _id). + body = { + "_id": str(PydanticObjectId()), + "project": "test-project", + "identifier": "mp-1234", + "formula": "Fe2O3", + "data": {"band_gap": 2.1}, + } + body.update(overrides) + return body + + +SAMPLE_OUT = ContributionOut(project="p", identifier="mp-1", formula="Fe2O3") + + +# =========================================================================== +# POST /contributions (bulk insert via service) +# =========================================================================== + + +class TestInsertContributions: + def test_empty_list_returns_200(self, client, contribution_service): + contribution_service.insert_contributions.return_value = BulkWriteSummary( + total=0, succeeded=[], failed=[] + ) + r = client.post("/api/v1/contributions", json=[]) + assert r.status_code == 200 + + def test_response_has_summary_shape(self, client, contribution_service): + contribution_service.insert_contributions.return_value = BulkWriteSummary( + total=0, succeeded=[], failed=[] + ) + body = client.post("/api/v1/contributions", json=[]).json() + assert set(body) == {"total", "succeeded", "failed"} + + def test_service_receives_parsed_contributions(self, client, contribution_service): + contribution_service.insert_contributions.return_value = BulkWriteSummary( + total=1, succeeded=[], failed=[] + ) + client.post("/api/v1/contributions", json=[_valid_contribution_body()]) + contributions = contribution_service.insert_contributions.call_args.kwargs["contributions"] + assert len(contributions) == 1 + assert contributions[0].project == "test-project" + + def test_malformed_body_returns_422(self, client, contribution_service): + # Missing required 'formula'. + r = client.post( + "/api/v1/contributions", + json=[{"_id": str(PydanticObjectId()), "project": "p", "identifier": "mp-1"}], + ) + assert r.status_code == 422 + contribution_service.insert_contributions.assert_not_called() + + def test_non_list_body_returns_422(self, client, contribution_service): + r = client.post("/api/v1/contributions", json=_valid_contribution_body()) + assert r.status_code == 422 + + +# =========================================================================== +# PUT /contributions (bulk upsert via service) +# =========================================================================== + + +class TestUpsertContributions: + def test_empty_list_returns_200(self, client, contribution_service): + contribution_service.upsert_contributions.return_value = BulkWriteSummary(total=0, succeeded=[], failed=[]) + r = client.put("/api/v1/contributions", json=[]) + assert r.status_code == 200 + assert set(r.json()) == {"total", "succeeded", "failed"} + + def test_service_receives_parsed_contributions(self, client, contribution_service): + contribution_service.upsert_contributions.return_value = BulkWriteSummary(total=1, succeeded=[], failed=[]) + client.put("/api/v1/contributions", json=[_valid_contribution_body()]) + contributions = contribution_service.upsert_contributions.call_args.kwargs["contributions"] + assert contributions[0].identifier == "mp-1234" + + def test_malformed_body_returns_422(self, client, contribution_service): + r = client.put( + "/api/v1/contributions", + json=[{"_id": str(PydanticObjectId()), "project": "p"}], + ) + assert r.status_code == 422 + contribution_service.upsert_contributions.assert_not_called() + + +# =========================================================================== +# Single-resource routes (RED: glued path params) +# =========================================================================== + + +class TestContributionByIdRouting: + """RED: routes mount as /contributions{id} not /contributions/{id}.""" + + def test_get_by_id_conventional_path(self, client, contribution_repo): + contribution_repo.get_contribution_by_id.return_value = SAMPLE_OUT + assert client.get(f"/api/v1/contributions/{PydanticObjectId()}").status_code == 200 + + def test_patch_by_id_conventional_path(self, client, contribution_repo): + contribution_repo.patch_contribution_by_id.return_value = SAMPLE_OUT + r = client.patch(f"/api/v1/contributions/{PydanticObjectId()}", json={"formula": "H2O"}) + assert r.status_code == 200 + + def test_put_by_id_conventional_path(self, client, contribution_repo): + contribution_repo.upsert_contribution_by_id.return_value = SAMPLE_OUT + r = client.put(f"/api/v1/contributions/{PydanticObjectId()}", json=_valid_contribution_body()) + assert r.status_code == 200 + + def test_delete_by_id_conventional_path(self, client, contribution_service): + contribution_service.delete_contributions.return_value = BulkDeleteSummary( + num_deleted=1, num_children_deleted=0 + ) + assert client.delete(f"/api/v1/contributions/{PydanticObjectId()}").status_code == 200 + + def test_download_route_conventional_path(self, client, contribution_repo): + contribution_repo.download_contributions.return_value = iter([b"x"]) + assert client.get("/api/v1/contributions/download/gz").status_code == 200 + + +# =========================================================================== +# Single-resource behavior (independent of the routing bug, via current paths) +# =========================================================================== + + +class TestDeleteContributionByIdWiring: + def test_delete_delegates_to_service(self, client, contribution_service): + contribution_service.delete_contributions.return_value = BulkDeleteSummary( + num_deleted=1, num_children_deleted=2 + ) + oid = PydanticObjectId() + # NOTE: glued path is intentional here — see module docstring. + r = client.delete(f"/api/v1/contributions/{oid}") + assert r.status_code == 200 + contribution_service.delete_contributions.assert_awaited_once() + + def test_delete_builds_filter_from_path_id(self, client, contribution_service): + contribution_service.delete_contributions.return_value = BulkDeleteSummary( + num_deleted=1, num_children_deleted=0 + ) + oid = PydanticObjectId() + client.delete(f"/api/v1/contributions/{oid}") + passed_filter = contribution_service.delete_contributions.call_args.args[0] + assert passed_filter.id == oid + + +# =========================================================================== +# GET /contributions/download/{short_mime} +# =========================================================================== + + +class TestDownloadContributions: + def test_default_format_jsonl_returns_200(self, client, contribution_repo): + # The contributions route gives `format` a default of JSONL, so it works + # with the param omitted (component routes require it — see test_component_routes). + contribution_repo.download_contributions.return_value = iter([b"x"]) + assert client.get("/api/v1/contributions/download/gz").status_code == 200 + + def test_csv_format_returns_200(self, client, contribution_repo): + contribution_repo.download_contributions.return_value = iter([b"x"]) + assert client.get("/api/v1/contributions/download/gz?format=csv").status_code == 200 + + def test_body_is_streamed_bytes(self, client, contribution_repo): + contribution_repo.download_contributions.return_value = iter([b"abc", b"def"]) + assert client.get("/api/v1/contributions/download/gz").content == b"abcdef" + + def test_invalid_short_mime_returns_422(self, client, contribution_repo): + contribution_repo.download_contributions.return_value = iter([b"x"]) + # Only 'gz' is a valid ShortMimeFormat. + assert client.get("/api/v1/contributions/download/zip").status_code == 422 + + def test_invalid_format_returns_422(self, client, contribution_repo): + contribution_repo.download_contributions.return_value = iter([b"x"]) + assert client.get("/api/v1/contributions/download/gz?format=xml").status_code == 422 + + def test_format_forwarded_to_repo(self, client, contribution_repo): + contribution_repo.download_contributions.return_value = iter([b"x"]) + client.get("/api/v1/contributions/download/gz?format=csv") + assert contribution_repo.download_contributions.call_args.kwargs["format"] == "csv" + + def test_fields_parsed_and_forwarded(self, client, contribution_repo): + contribution_repo.download_contributions.return_value = iter([b"x"]) + client.get("/api/v1/contributions/download/gz?_fields=project") + forwarded = contribution_repo.download_contributions.call_args.kwargs["fields"] + assert "project" in forwarded + + def test_invalid_fields_returns_422(self, client, contribution_repo): + contribution_repo.download_contributions.return_value = iter([b"x"]) + assert client.get("/api/v1/contributions/download/gz?_fields=not_a_field").status_code == 422 + + def test_filename_names_the_contributions_resource(self, client, contribution_repo): + """The attachment filename references the contributions resource.""" + contribution_repo.download_contributions.return_value = iter([b"x"]) + cd = client.get("/api/v1/contributions/download/gz").headers["content-disposition"] + assert "contributions" in cd + + def test_csv_filename_uses_csv_extension(self, client, contribution_repo): + """A CSV download is named *.csv.gz, matching the requested format.""" + contribution_repo.download_contributions.return_value = iter([b"x"]) + cd = client.get("/api/v1/contributions/download/gz?format=csv").headers["content-disposition"] + assert ".csv.gz" in cd + + def test_repo_error_surfaces_as_uniform_json(self, client, contribution_repo): + # An AppError raised while the repo builds the download surfaces through the + # registered exception handler as the uniform error envelope (not a 500 traceback). + contribution_repo.download_contributions.side_effect = NotFoundError("nothing to download") + r = client.get("/api/v1/contributions/download/gz") + assert r.status_code == 404 + assert r.json()["error"]["code"] == "not_found" + + +# --------------------------------------------------------------------------- +# Authentication enforcement: contribution mutations require an authenticated user +# --------------------------------------------------------------------------- + + +class TestContributionMutationsRequireAuth: + def test_post_anon_401(self, client, contribution_service): + r = client.post("/api/v1/contributions", json=[], headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + assert r.json()["error"]["code"] == "authentication_error" + contribution_service.insert_contributions.assert_not_called() + + def test_put_collection_anon_401(self, client, contribution_service): + r = client.put("/api/v1/contributions", json=[], headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + contribution_service.upsert_contributions.assert_not_called() + + def test_delete_collection_anon_401(self, client, contribution_repo): + r = client.delete("/api/v1/contributions", headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + contribution_repo.delete_contributions.assert_not_called() + + def test_delete_by_id_anon_401(self, client, contribution_service): + r = client.delete(f"/api/v1/contributions/{PydanticObjectId()}", headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + + def test_put_by_id_anon_401(self, client, contribution_repo): + r = client.put( + f"/api/v1/contributions/{PydanticObjectId()}", + json=_valid_contribution_body(), + headers=FORCE_ANON_HEADERS, + ) + assert r.status_code == 401 + contribution_repo.upsert_contribution_by_id.assert_not_called() + + def test_patch_by_id_anon_401(self, client, contribution_repo): + r = client.patch( + f"/api/v1/contributions/{PydanticObjectId()}", json={"formula": "H2O"}, headers=FORCE_ANON_HEADERS + ) + assert r.status_code == 401 + contribution_repo.patch_contribution_by_id.assert_not_called() + + def test_get_collection_still_open_to_anon(self, client, contribution_repo): + from mpcontribs_api.pagination import Page + + contribution_repo.get_contributions.return_value = Page(items=[], next_cursor=None) + r = client.get("/api/v1/contributions", headers=FORCE_ANON_HEADERS) + assert r.status_code == 200 diff --git a/mpcontribs-api/tests/integration/test_error_handlers.py b/mpcontribs-api/tests/integration/test_error_handlers.py new file mode 100644 index 000000000..a092cec2a --- /dev/null +++ b/mpcontribs-api/tests/integration/test_error_handlers.py @@ -0,0 +1,177 @@ +import pytest +from fastapi import FastAPI +from fastapi.testclient import TestClient + +from mpcontribs_api.exceptions import ( + AuthenticationError, + ConflictError, + NotFoundError, + PermissionError, + ValidationError, +) +from tests.integration.conftest import AUTHED_HEADERS, make_test_app + +# --------------------------------------------------------------------------- +# Helper: mount a /probe route that raises a specific AppError +# --------------------------------------------------------------------------- + + +def _app_with_probe(exc: Exception) -> FastAPI: + """Create a test app with a GET /probe route that raises `exc`.""" + app = make_test_app() + + @app.get("/probe") + async def _probe(): + raise exc + + return app + + +def _client(app: FastAPI) -> TestClient: + return TestClient(app, raise_server_exceptions=False) + + +# --------------------------------------------------------------------------- +# Unknown route — Starlette HTTPException(404) → {"error": {"code": "http_error"}} +# --------------------------------------------------------------------------- + + +class TestUnknownRoute: + def test_status_404(self, client): + r = client.get("/no/such/route", headers=AUTHED_HEADERS) + assert r.status_code == 404 + + def test_error_envelope(self, client): + r = client.get("/no/such/route", headers=AUTHED_HEADERS) + body = r.json() + assert "error" in body + assert body["error"]["code"] == "http_error" + assert "message" in body["error"] + + +# --------------------------------------------------------------------------- +# Request body validation — FastAPI RequestValidationError → 422 +# --------------------------------------------------------------------------- + + +class TestRequestValidation: + def test_missing_required_body_field(self, client): + # PUT /api/v1/projects/{id} requires a ProjectIn body + r = client.put( + "/api/v1/projects/my-proj", + json={"title": "Missing required fields"}, + headers=AUTHED_HEADERS, + ) + assert r.status_code == 422 + + def test_validation_error_envelope(self, client): + r = client.put( + "/api/v1/projects/my-proj", + json={"title": "Missing required fields"}, + headers=AUTHED_HEADERS, + ) + body = r.json() + assert body["error"]["code"] == "validation_error" + assert "errors" in body["error"]["detail"] + + def test_non_json_body(self, client): + r = client.put( + "/api/v1/projects/my-proj", + content=b"not json at all", + headers={**AUTHED_HEADERS, "content-type": "application/json"}, + ) + assert r.status_code == 422 + + +# --------------------------------------------------------------------------- +# AppError subclasses — verify status codes and envelope shapes +# --------------------------------------------------------------------------- + + +class TestNotFoundError: + def setup_method(self): + self._app = _app_with_probe(NotFoundError("project 'foo' not found")) + self._client = _client(self._app) + + def test_status_404(self): + assert self._client.get("/probe").status_code == 404 + + def test_error_code(self): + assert self._client.get("/probe").json()["error"]["code"] == "not_found" + + def test_message(self): + assert "foo" in self._client.get("/probe").json()["error"]["message"] + + +class TestConflictError: + def setup_method(self): + self._app = _app_with_probe(ConflictError("duplicate id")) + self._client = _client(self._app) + + def test_status_409(self): + assert self._client.get("/probe").status_code == 409 + + def test_error_code(self): + assert self._client.get("/probe").json()["error"]["code"] == "conflict" + + +class TestValidationErrorHandler: + def setup_method(self): + self._app = _app_with_probe(ValidationError("bad field value")) + self._client = _client(self._app) + + def test_status_422(self): + assert self._client.get("/probe").status_code == 422 + + def test_error_code(self): + assert self._client.get("/probe").json()["error"]["code"] == "validation_error" + + +class TestPermissionErrorHandler: + def setup_method(self): + self._app = _app_with_probe(PermissionError(required_role="admin")) + self._client = _client(self._app) + + def test_status_403(self): + assert self._client.get("/probe").status_code == 403 + + def test_error_code(self): + assert self._client.get("/probe").json()["error"]["code"] == "permission_denied" + + +class TestAuthenticationErrorHandler: + def setup_method(self): + self._app = _app_with_probe(AuthenticationError("login required")) + self._client = _client(self._app) + + def test_status_401(self): + assert self._client.get("/probe").status_code == 401 + + def test_error_code(self): + assert self._client.get("/probe").json()["error"]["code"] == "authentication_error" + + +# --------------------------------------------------------------------------- +# Envelope shape invariants — all error responses share the same top-level key +# --------------------------------------------------------------------------- + + +class TestEnvelopeShape: + @pytest.mark.parametrize( + "exc, expected_status", + [ + (NotFoundError("x"), 404), + (ConflictError("x"), 409), + (ValidationError("x"), 422), + (PermissionError(), 403), + (AuthenticationError("x"), 401), + ], + ) + def test_always_has_error_key(self, exc, expected_status): + app = _app_with_probe(exc) + r = _client(app).get("/probe") + assert r.status_code == expected_status + body = r.json() + assert "error" in body + assert "code" in body["error"] + assert "message" in body["error"] diff --git a/mpcontribs-api/tests/integration/test_healthcheck.py b/mpcontribs-api/tests/integration/test_healthcheck.py new file mode 100644 index 000000000..f98ca854f --- /dev/null +++ b/mpcontribs-api/tests/integration/test_healthcheck.py @@ -0,0 +1,124 @@ +from unittest.mock import AsyncMock, MagicMock + +import pytest +from botocore.exceptions import ClientError +from fastapi import FastAPI +from fastapi.testclient import TestClient + +from mpcontribs_api.dependencies import get_db, get_s3 +from mpcontribs_api.domains.healthcheck.router import router as healthcheck_router +from mpcontribs_api.exceptions import register_exception_handlers + + +def _make_db(ping_ok: bool) -> MagicMock: + """Build a mock AsyncDatabase whose client.admin.command is awaitable.""" + db = MagicMock(name="db") + if ping_ok: + db.client.admin.command = AsyncMock(return_value={"ok": 1}) + else: + db.client.admin.command = AsyncMock(side_effect=ConnectionError("mongo down")) + return db + + +def _make_s3(head_ok: bool) -> MagicMock: + """Build a mock S3 client whose head_bucket is awaitable.""" + s3 = MagicMock(name="s3") + if head_ok: + s3.head_bucket = AsyncMock(return_value={}) + else: + s3.head_bucket = AsyncMock( + side_effect=ClientError({"Error": {"Code": "503", "Message": "s3 down"}}, "HeadBucket") + ) + return s3 + + +@pytest.fixture +def health_app() -> FastAPI: + app = FastAPI() + register_exception_handlers(app) + app.include_router(healthcheck_router, prefix="/healthcheck") + return app + + +def _client(app: FastAPI, db: MagicMock, s3: MagicMock | None = None) -> TestClient: + app.dependency_overrides[get_db] = lambda: db + app.dependency_overrides[get_s3] = lambda: s3 if s3 is not None else _make_s3(head_ok=True) + return TestClient(app, raise_server_exceptions=False) + + +# --------------------------------------------------------------------------- +# Healthy path +# --------------------------------------------------------------------------- + + +class TestHealthcheckHealthy: + def test_returns_200(self, health_app): + r = _client(health_app, _make_db(ping_ok=True), _make_s3(head_ok=True)).get("/healthcheck") + assert r.status_code == 200 + + def test_body_reports_healthy(self, health_app): + r = _client(health_app, _make_db(ping_ok=True), _make_s3(head_ok=True)).get("/healthcheck") + assert r.json() == {"version": "0.0.0-dev", "status": "healthy", "mongo": "ok", "s3": "ok"} + + def test_pings_mongo(self, health_app): + db = _make_db(ping_ok=True) + _client(health_app, db, _make_s3(head_ok=True)).get("/healthcheck") + db.client.admin.command.assert_awaited_once_with("ping") + + def test_probes_s3(self, health_app): + s3 = _make_s3(head_ok=True) + _client(health_app, _make_db(ping_ok=True), s3).get("/healthcheck") + s3.head_bucket.assert_awaited_once() + + +# --------------------------------------------------------------------------- +# Unhealthy path (Mongo unreachable) +# --------------------------------------------------------------------------- + + +class TestHealthcheckMongoUnhealthy: + def test_returns_503(self, health_app): + r = _client(health_app, _make_db(ping_ok=False)).get("/healthcheck") + assert r.status_code == 503 + + def test_body_reports_unreachable(self, health_app): + # The StarletteHTTPException handler reshapes the response into the + # standard error envelope, stringifying the detail dict into `message`. + r = _client(health_app, _make_db(ping_ok=False)).get("/healthcheck") + message = r.json()["error"]["message"] + assert "unhealthy" in message + assert "unreachable" in message + + def test_ping_failure_does_not_leak_exception_text(self, health_app): + # The raised HTTPException carries a controlled detail dict, not the + # underlying "mongo down" ConnectionError message. + r = _client(health_app, _make_db(ping_ok=False)).get("/healthcheck") + assert "mongo down" not in r.text + + def test_s3_not_probed_when_mongo_down(self, health_app): + # Mongo is checked first; a failure short-circuits before S3 is touched. + s3 = _make_s3(head_ok=True) + _client(health_app, _make_db(ping_ok=False), s3).get("/healthcheck") + s3.head_bucket.assert_not_awaited() + + +# --------------------------------------------------------------------------- +# Unhealthy path (S3 unreachable) +# --------------------------------------------------------------------------- + + +class TestHealthcheckS3Unhealthy: + def test_returns_503(self, health_app): + r = _client(health_app, _make_db(ping_ok=True), _make_s3(head_ok=False)).get("/healthcheck") + assert r.status_code == 503 + + def test_body_reports_unreachable(self, health_app): + r = _client(health_app, _make_db(ping_ok=True), _make_s3(head_ok=False)).get("/healthcheck") + message = r.json()["error"]["message"] + assert "unhealthy" in message + assert "unreachable" in message + + def test_s3_failure_does_not_leak_exception_text(self, health_app): + # The controlled detail dict is returned, not the underlying boto error text. + r = _client(health_app, _make_db(ping_ok=True), _make_s3(head_ok=False)).get("/healthcheck") + assert "s3 down" not in r.text diff --git a/mpcontribs-api/tests/integration/test_ingest_jobs_routes.py b/mpcontribs-api/tests/integration/test_ingest_jobs_routes.py new file mode 100644 index 000000000..10465867b --- /dev/null +++ b/mpcontribs-api/tests/integration/test_ingest_jobs_routes.py @@ -0,0 +1,89 @@ +"""Tests for the async bulk-ingestion scaffold routes (submit / status). + +The worker is a stub, so these exercise only the route surface: 202 on submit, a persisted +pending job, idempotency replay, auth, and status lookup (found / not-found / bad id). +""" + +from unittest.mock import AsyncMock + +import pytest +from beanie import PydanticObjectId + +from mpcontribs_api.domains.ingest_jobs.dependencies import get_ingest_job_repository +from mpcontribs_api.domains.ingest_jobs.models import IngestJob +from tests.integration.conftest import AUTHED_HEADERS, FORCE_ANON_HEADERS + +BULK_URL = "/api/v1/contributions/bulk" + + +def _job(**overrides) -> IngestJob: + fields = { + "id": PydanticObjectId(), + "owner": "google:alice@example.com", + "status": "pending", + "source": None, + "idempotency_key": None, + } + fields.update(overrides) + return IngestJob(**fields) + + +@pytest.fixture +def ingest_repo(test_app): + repo = AsyncMock() + test_app.dependency_overrides[get_ingest_job_repository] = lambda: repo + yield repo + test_app.dependency_overrides.pop(get_ingest_job_repository, None) + + +@pytest.fixture(autouse=True) +def _authenticate(client): + client.headers.update(AUTHED_HEADERS) + + +class TestSubmitBulkIngest: + def test_submit_returns_202_and_pending_job(self, client, ingest_repo): + job = _job() + ingest_repo.create_job.return_value = job + r = client.post(BULK_URL, json={"source": None}) + assert r.status_code == 202 + body = r.json() + assert body["id"] == str(job.id) + assert body["status"] == "pending" + ingest_repo.create_job.assert_awaited_once() + + def test_submit_requires_auth(self, client, test_app): + # No repo override here: the repository dependency runs require_user, which rejects anon. + r = client.post(BULK_URL, json={"source": None}, headers=FORCE_ANON_HEADERS) + assert r.status_code == 401 + + def test_idempotency_key_replays_existing_job(self, client, ingest_repo): + existing = _job(idempotency_key="abc123") + ingest_repo.find_by_idempotency_key.return_value = existing + r = client.post(BULK_URL, json={"source": None}, headers={"Idempotency-Key": "abc123"}) + assert r.status_code == 202 + assert r.json()["id"] == str(existing.id) + ingest_repo.find_by_idempotency_key.assert_awaited_once_with("abc123") + ingest_repo.create_job.assert_not_called() + + +class TestGetBulkIngestJob: + def test_get_existing_job(self, client, ingest_repo): + job = _job(status="running", total=10, succeeded=4) + ingest_repo.get_job.return_value = job + r = client.get(f"{BULK_URL}/{job.id}") + assert r.status_code == 200 + body = r.json() + assert body["status"] == "running" + assert body["total"] == 10 + assert body["succeeded"] == 4 + + def test_unknown_job_returns_404(self, client, ingest_repo): + ingest_repo.get_job.return_value = None + r = client.get(f"{BULK_URL}/{PydanticObjectId()}") + assert r.status_code == 404 + + def test_invalid_job_id_returns_422(self, client, ingest_repo): + r = client.get(f"{BULK_URL}/not-an-object-id") + assert r.status_code == 422 + ingest_repo.get_job.assert_not_called() diff --git a/mpcontribs-api/tests/integration/test_projects.py b/mpcontribs-api/tests/integration/test_projects.py new file mode 100644 index 000000000..0f9885792 --- /dev/null +++ b/mpcontribs-api/tests/integration/test_projects.py @@ -0,0 +1,296 @@ +import pytest + +from mpcontribs_api.domains.projects.dependencies import get_scoped_projects +from mpcontribs_api.domains.projects.models import ProjectOut, Stats +from mpcontribs_api.exceptions import ConflictError, NotFoundError +from mpcontribs_api.pagination import Page +from tests.integration.conftest import ANON_HEADERS, AUTHED_HEADERS + +# --------------------------------------------------------------------------- +# Shared sample data +# --------------------------------------------------------------------------- + +SAMPLE_STATS = Stats(columns=1, contributions=5, tables=0, structures=0, attachments=0, size=128.0) + +SAMPLE_PROJECT = ProjectOut.model_validate( + { + "_id": "mp-sample", + "title": "Sample Project", + "authors": "Alice, Bob", + "description": "A sample", + "is_public": True, + "is_approved": True, + "stats": SAMPLE_STATS, + } +) + + +# --------------------------------------------------------------------------- +# Fixture: inject mock repo into the test_app for the duration of each test +# --------------------------------------------------------------------------- + + +@pytest.fixture +def project_repo(test_app, mock_project_repo): + test_app.dependency_overrides[get_scoped_projects] = lambda: mock_project_repo + yield mock_project_repo + test_app.dependency_overrides.pop(get_scoped_projects, None) + + +# --------------------------------------------------------------------------- +# GET /api/v1/projects +# --------------------------------------------------------------------------- + + +class TestListProjects: + def test_empty_page_returns_200(self, client, project_repo): + project_repo.get_projects.return_value = Page(items=[], next_cursor=None) + r = client.get("/api/v1/projects", headers=AUTHED_HEADERS) + assert r.status_code == 200 + + def test_response_has_items_and_cursor(self, client, project_repo): + project_repo.get_projects.return_value = Page(items=[], next_cursor=None) + body = client.get("/api/v1/projects", headers=AUTHED_HEADERS).json() + assert "items" in body + assert "next_cursor" in body + + def test_items_returned_in_response(self, client, project_repo): + project_repo.get_projects.return_value = Page(items=[SAMPLE_PROJECT], next_cursor=None) + body = client.get("/api/v1/projects", headers=AUTHED_HEADERS).json() + assert len(body["items"]) == 1 + + def test_next_cursor_set_when_more_pages(self, client, project_repo): + from mpcontribs_api.pagination import encode_cursor + + cursor = encode_cursor("mp-sample") + project_repo.get_projects.return_value = Page(items=[SAMPLE_PROJECT], next_cursor=cursor) + body = client.get("/api/v1/projects", headers=AUTHED_HEADERS).json() + assert body["next_cursor"] == cursor + + def test_repo_get_project_called(self, client, project_repo): + project_repo.get_projects.return_value = Page(items=[], next_cursor=None) + client.get("/api/v1/projects", headers=AUTHED_HEADERS) + project_repo.get_projects.assert_called_once() + + def test_anonymous_user_reaches_route(self, client, project_repo): + project_repo.get_projects.return_value = Page(items=[], next_cursor=None) + r = client.get("/api/v1/projects", headers=ANON_HEADERS) + assert r.status_code == 200 + + def test_invalid_fields_param_returns_422(self, client, project_repo): + project_repo.get_projects.return_value = Page(items=[], next_cursor=None) + r = client.get("/api/v1/projects", params={"_fields": "nonexistent_field"}, headers=AUTHED_HEADERS) + assert r.status_code == 422 + + def test_limit_param_forwarded(self, client, project_repo): + project_repo.get_projects.return_value = Page(items=[], next_cursor=None) + client.get("/api/v1/projects", params={"limit": 5}, headers=AUTHED_HEADERS) + _, kwargs = project_repo.get_projects.call_args + assert kwargs["pagination"].limit == 5 + + def test_limit_above_max_returns_422(self, client, project_repo): + r = client.get("/api/v1/projects", params={"limit": 999}, headers=AUTHED_HEADERS) + assert r.status_code == 422 + + def test_valid_fields_param_forwarded(self, client, project_repo): + project_repo.get_projects.return_value = Page(items=[], next_cursor=None) + client.get("/api/v1/projects", params=[("_fields", "title"), ("_fields", "authors")], headers=AUTHED_HEADERS) + _, kwargs = project_repo.get_projects.call_args + assert kwargs["fields"] is not None + assert "title" in kwargs["fields"] + + +# --------------------------------------------------------------------------- +# GET /api/v1/projects/{id} +# --------------------------------------------------------------------------- + + +class TestGetProjectById: + def test_found_returns_200(self, client, project_repo): + project_repo.get_project_by_id.return_value = SAMPLE_PROJECT + r = client.get("/api/v1/projects/mp-sample", headers=AUTHED_HEADERS) + assert r.status_code == 200 + + def test_response_contains_project_data(self, client, project_repo): + project_repo.get_project_by_id.return_value = SAMPLE_PROJECT + body = client.get("/api/v1/projects/mp-sample", headers=AUTHED_HEADERS).json() + assert body["id"] == "mp-sample" + assert body["title"] == "Sample Project" + + def test_not_found_returns_404(self, client, project_repo): + project_repo.get_project_by_id.side_effect = NotFoundError("project not found") + r = client.get("/api/v1/projects/nonexistent", headers=AUTHED_HEADERS) + assert r.status_code == 404 + + def test_not_found_error_code(self, client, project_repo): + project_repo.get_project_by_id.side_effect = NotFoundError("project not found") + body = client.get("/api/v1/projects/nonexistent", headers=AUTHED_HEADERS).json() + assert body["error"]["code"] == "not_found" + + def test_id_forwarded_to_repo(self, client, project_repo): + project_repo.get_project_by_id.return_value = SAMPLE_PROJECT + client.get("/api/v1/projects/my-specific-id", headers=AUTHED_HEADERS) + _, kwargs = project_repo.get_project_by_id.call_args + assert kwargs["id"] == "my-specific-id" + + def test_fields_param_forwarded(self, client, project_repo): + project_repo.get_project_by_id.return_value = SAMPLE_PROJECT + client.get("/api/v1/projects/mp-sample", params={"_fields": "title"}, headers=AUTHED_HEADERS) + _, kwargs = project_repo.get_project_by_id.call_args + assert kwargs["fields"] is not None + assert "title" in kwargs["fields"] + + def test_no_fields_param_uses_default_fields(self, client, project_repo): + project_repo.get_project_by_id.return_value = SAMPLE_PROJECT + client.get("/api/v1/projects/mp-sample", headers=AUTHED_HEADERS) + _, kwargs = project_repo.get_project_by_id.call_args + assert kwargs["fields"] is not None + assert "title" in kwargs["fields"] + + +# --------------------------------------------------------------------------- +# PATCH /api/v1/projects/{id} +# --------------------------------------------------------------------------- + + +class TestPatchProject: + def test_valid_patch_returns_200(self, client, project_repo): + project_repo.patch_project_by_id.return_value = SAMPLE_PROJECT + r = client.patch( + "/api/v1/projects/mp-sample", + json={"title": "Updated Title"}, + headers=AUTHED_HEADERS, + ) + assert r.status_code == 200 + + def test_patch_response_is_project_out(self, client, project_repo): + updated = ProjectOut(id="mp-sample", title="Updated Title") + project_repo.patch_project_by_id.return_value = updated + body = client.patch( + "/api/v1/projects/mp-sample", + json={"title": "Updated Title"}, + headers=AUTHED_HEADERS, + ).json() + assert body["title"] == "Updated Title" + + def test_not_found_returns_404(self, client, project_repo): + project_repo.patch_project_by_id.side_effect = NotFoundError("not found") + r = client.patch( + "/api/v1/projects/missing", + json={"title": "x" * 5}, + headers=AUTHED_HEADERS, + ) + assert r.status_code == 404 + + def test_invalid_title_too_short_returns_422(self, client, project_repo): + r = client.patch( + "/api/v1/projects/mp-sample", + json={"title": "ab"}, + headers=AUTHED_HEADERS, + ) + assert r.status_code == 422 + + def test_id_and_update_forwarded_to_repo(self, client, project_repo): + project_repo.patch_project_by_id.return_value = SAMPLE_PROJECT + client.patch( + "/api/v1/projects/mp-sample", + json={"title": "New Name"}, + headers=AUTHED_HEADERS, + ) + _, kwargs = project_repo.patch_project_by_id.call_args + assert kwargs["id"] == "mp-sample" + assert kwargs["update"].title == "New Name" + + +# --------------------------------------------------------------------------- +# DELETE /api/v1/projects/{id} +# --------------------------------------------------------------------------- + + +class TestDeleteProject: + def test_delete_returns_204(self, client, project_repo): + project_repo.delete_project_by_id.return_value = None + r = client.delete("/api/v1/projects/mp-sample", headers=AUTHED_HEADERS) + assert r.status_code == 204 + + def test_delete_response_has_no_body(self, client, project_repo): + project_repo.delete_project_by_id.return_value = None + r = client.delete("/api/v1/projects/mp-sample", headers=AUTHED_HEADERS) + assert r.content == b"" + + def test_id_forwarded_to_repo(self, client, project_repo): + project_repo.delete_project_by_id.return_value = None + client.delete("/api/v1/projects/mp-sample", headers=AUTHED_HEADERS) + _, kwargs = project_repo.delete_project_by_id.call_args + assert kwargs["id"] == "mp-sample" + + +# --------------------------------------------------------------------------- +# PUT /api/v1/projects/{id} +# --------------------------------------------------------------------------- + + +class TestUpsertProject: + def _valid_body(self, **overrides): + body = { + "_id": "mp-sample", + "title": "Test Project", + "authors": "Alice", + "description": "A project", + "owner": "google:alice@example.com", + "unique_identifiers": True, + "stats": {"columns": 0, "contributions": 0, "tables": 0, "structures": 0, "attachments": 0, "size": 0.0}, + } + body.update(overrides) + return body + + def test_valid_upsert_returns_200(self, client, project_repo): + project_repo.upsert_project_by_id.return_value = SAMPLE_PROJECT + r = client.put("/api/v1/projects/mp-sample", json=self._valid_body(), headers=AUTHED_HEADERS) + assert r.status_code == 200 + + def test_conflict_returns_409(self, client, project_repo): + project_repo.upsert_project_by_id.side_effect = ConflictError("already exists") + r = client.put("/api/v1/projects/mp-sample", json=self._valid_body(), headers=AUTHED_HEADERS) + assert r.status_code == 409 + + def test_missing_required_field_returns_422(self, client, project_repo): + body = self._valid_body() + del body["title"] + r = client.put("/api/v1/projects/mp-sample", json=body, headers=AUTHED_HEADERS) + assert r.status_code == 422 + + +# --------------------------------------------------------------------------- +# Authentication enforcement: mutations require an authenticated user +# --------------------------------------------------------------------------- + + +class TestProjectMutationsRequireAuth: + def _body(self): + return { + "_id": "mp-sample", + "title": "Test Project", + "authors": "Alice", + "description": "A project", + "owner": "google:alice@example.com", + "unique_identifiers": True, + "stats": {"columns": 0, "contributions": 0, "tables": 0, "structures": 0, "attachments": 0, "size": 0.0}, + } + + def test_anonymous_put_returns_401(self, client, project_repo): + project_repo.upsert_project_by_id.return_value = SAMPLE_PROJECT + r = client.put("/api/v1/projects/mp-sample", json=self._body(), headers=ANON_HEADERS) + assert r.status_code == 401 + assert r.json()["error"]["code"] == "authentication_error" + project_repo.upsert_project_by_id.assert_not_called() + + def test_anonymous_patch_returns_401(self, client, project_repo): + r = client.patch("/api/v1/projects/mp-sample", json={"title": "Updated Title"}, headers=ANON_HEADERS) + assert r.status_code == 401 + project_repo.patch_project_by_id.assert_not_called() + + def test_anonymous_delete_returns_401(self, client, project_repo): + r = client.delete("/api/v1/projects/mp-sample", headers=ANON_HEADERS) + assert r.status_code == 401 + project_repo.delete_project_by_id.assert_not_called() diff --git a/mpcontribs-api/tests/integration/test_redirects.py b/mpcontribs-api/tests/integration/test_redirects.py new file mode 100644 index 000000000..31f18f646 --- /dev/null +++ b/mpcontribs-api/tests/integration/test_redirects.py @@ -0,0 +1,143 @@ +"""Tests for the legacy-compatibility redirect/deprecation router. + +The legacy (Flask) API lived at the service root (e.g. ``/contributions/``); +the rewrite serves everything under ``/api/v1``. The redirects router mounted +at the root either 308-redirects to the new location (preserving method, body +and query string) or returns ``410 Gone`` for endpoints with no counterpart. +""" + +import pytest +from fastapi import FastAPI +from fastapi.testclient import TestClient + +from tests.integration.conftest import make_test_app + +# 308 keeps the method/body intact; assert it explicitly so a future change to +# 301/302 (which downgrade POST/PUT to GET) is caught. +PERMANENT_REDIRECT = 308 +GONE = 410 + + +@pytest.fixture(scope="module") +def app() -> FastAPI: + return make_test_app() + + +@pytest.fixture +def client(app: FastAPI): + """Client that does NOT auto-follow redirects, so we can assert on 3xx.""" + with TestClient(app, raise_server_exceptions=False, follow_redirects=False) as c: + yield c + + +# --------------------------------------------------------------------------- +# Redirects: legacy endpoints with a direct /api/v1 counterpart +# --------------------------------------------------------------------------- + +# (method, legacy_path, expected /api/v1 location) +REDIRECT_CASES = [ + # contributions + ("GET", "/contributions/", "/api/v1/contributions"), + ("POST", "/contributions/", "/api/v1/contributions"), + ("PUT", "/contributions/", "/api/v1/contributions"), + ("DELETE", "/contributions/", "/api/v1/contributions"), + ("GET", "/contributions/abc123/", "/api/v1/contributions/abc123"), + ("PUT", "/contributions/abc123/", "/api/v1/contributions/abc123"), + ("DELETE", "/contributions/abc123/", "/api/v1/contributions/abc123"), + ("GET", "/contributions/download/gz/", "/api/v1/contributions/download/gz"), + # projects (GET collection + item verbs) + ("GET", "/projects/", "/api/v1/projects"), + ("GET", "/projects/my-proj/", "/api/v1/projects/my-proj"), + ("PUT", "/projects/my-proj/", "/api/v1/projects/my-proj"), + ("DELETE", "/projects/my-proj/", "/api/v1/projects/my-proj"), + # read-only components + ("GET", "/structures/", "/api/v1/structures"), + ("GET", "/structures/sid/", "/api/v1/structures/sid"), + ("GET", "/structures/download/gz/", "/api/v1/structures/download/gz"), + ("GET", "/tables/", "/api/v1/tables"), + ("GET", "/tables/tid/", "/api/v1/tables/tid"), + ("GET", "/tables/download/gz/", "/api/v1/tables/download/gz"), + ("GET", "/attachments/", "/api/v1/attachments"), + ("GET", "/attachments/aid/", "/api/v1/attachments/aid"), + ("GET", "/attachments/download/gz/", "/api/v1/attachments/download/gz"), +] + + +class TestRedirects: + @pytest.mark.parametrize("method, legacy_path, new_path", REDIRECT_CASES) + def test_status_is_permanent_redirect(self, client, method, legacy_path, new_path): + r = client.request(method, legacy_path) + assert r.status_code == PERMANENT_REDIRECT + + @pytest.mark.parametrize("method, legacy_path, new_path", REDIRECT_CASES) + def test_location_points_to_v1(self, client, method, legacy_path, new_path): + r = client.request(method, legacy_path) + assert r.headers["location"] == new_path + + def test_query_string_is_preserved(self, client): + r = client.get("/contributions/?project=foo&_limit=5") + assert r.headers["location"] == "/api/v1/contributions?project=foo&_limit=5" + + def test_query_string_preserved_on_item(self, client): + r = client.get("/structures/sid/?_fields=id,label") + assert r.headers["location"] == "/api/v1/structures/sid?_fields=id,label" + + def test_download_query_preserved(self, client): + r = client.get("/tables/download/gz/?format=csv") + assert r.headers["location"] == "/api/v1/tables/download/gz?format=csv" + + def test_no_query_string_has_no_trailing_question_mark(self, client): + r = client.get("/projects/") + assert r.headers["location"] == "/api/v1/projects" + assert "?" not in r.headers["location"] + + +# --------------------------------------------------------------------------- +# Deprecations: legacy endpoints with no counterpart → 410 Gone +# --------------------------------------------------------------------------- + +# (method, legacy_path) +GONE_CASES = [ + # search helpers (Atlas $search) were not ported + ("GET", "/contributions/search"), + ("GET", "/projects/search"), + # project creation has no POST endpoint in the new API + ("POST", "/projects/"), + # email-driven application approval links + ("GET", "/projects/applications/sometoken"), + ("GET", "/projects/applications/sometoken/approve"), + ("GET", "/projects/applications/sometoken/deny"), + # the whole notebooks resource was dropped + ("GET", "/notebooks/"), + ("GET", "/notebooks/nbid/"), + ("GET", "/notebooks/build"), + ("GET", "/notebooks/result"), + ("GET", "/notebooks/result/job-1"), +] + + +class TestDeprecated: + @pytest.mark.parametrize("method, path", GONE_CASES) + def test_status_is_gone(self, client, method, path): + assert client.request(method, path).status_code == GONE + + @pytest.mark.parametrize("method, path", GONE_CASES) + def test_error_envelope(self, client, method, path): + body = client.request(method, path).json() + assert body["error"]["code"] == "endpoint_deprecated" + assert body["error"]["message"] + + @pytest.mark.parametrize("method, path", GONE_CASES) + def test_deprecation_header(self, client, method, path): + assert client.request(method, path).headers["deprecation"] == "true" + + def test_post_projects_points_at_put_replacement(self, client): + r = client.post("/projects/") + assert r.status_code == GONE + body = r.json() + assert body["error"]["detail"]["replacement"] == "/api/v1/projects/{id}" + + def test_deprecated_responses_are_not_redirects(self, client): + # A deprecated endpoint must never carry a Location header. + r = client.get("/notebooks/build") + assert "location" not in r.headers diff --git a/mpcontribs-api/tests/unit/__init__.py b/mpcontribs-api/tests/unit/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/mpcontribs-api/tests/unit/conftest.py b/mpcontribs-api/tests/unit/conftest.py new file mode 100644 index 000000000..d730154a0 --- /dev/null +++ b/mpcontribs-api/tests/unit/conftest.py @@ -0,0 +1,11 @@ +from unittest.mock import MagicMock, patch + +import pytest + + +@pytest.fixture(autouse=True, scope="session") +def _mock_beanie_collection(): + import beanie + + with patch.object(beanie.Document, "get_pymongo_collection", return_value=MagicMock()): + yield diff --git a/mpcontribs-api/tests/unit/domains/__init__.py b/mpcontribs-api/tests/unit/domains/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/mpcontribs-api/tests/unit/domains/test_attachments_models.py b/mpcontribs-api/tests/unit/domains/test_attachments_models.py new file mode 100644 index 000000000..f5b17a736 --- /dev/null +++ b/mpcontribs-api/tests/unit/domains/test_attachments_models.py @@ -0,0 +1,161 @@ +import pytest +from beanie import PydanticObjectId +from pydantic import ValidationError as PydanticValidationError + +from mpcontribs_api.domains.attachments.models import ( + Attachment, + AttachmentFilter, + AttachmentIn, + AttachmentOut, + AttachmentPatch, +) +from mpcontribs_api.exceptions import ValidationError as AppValidationError + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + + +def _payload(**overrides) -> dict: + payload = { + "_id": PydanticObjectId(), + "name": "spectrum.json.gz", + "md5": "c" * 32, + "mime": "application/gzip", + "content": 1, + } + payload.update(overrides) + return payload + + +# --------------------------------------------------------------------------- +# Attachment / AttachmentIn +# --------------------------------------------------------------------------- + + +class TestAttachment: + def test_valid_construction(self): + attachment = Attachment(**_payload()) + assert attachment.name == "spectrum.json.gz" + assert attachment.content == 1 + + def test_collection_name(self): + assert Attachment.Settings.name == "attachments" + + def test_name_requires_extension(self): + with pytest.raises(AppValidationError): + Attachment(**_payload(name="noextension")) + + def test_md5_is_computed_not_taken_from_input(self): + # A client-supplied md5 is overwritten by the content-derived hash. + attachment = Attachment(**_payload(md5="c" * 32)) + assert attachment.md5 != "c" * 32 + assert len(attachment.md5) == 32 + + def test_same_content_same_md5(self): + assert Attachment(**_payload()).md5 == Attachment(**_payload()).md5 + + def test_different_content_different_md5(self): + assert Attachment(**_payload(content=1)).md5 != Attachment(**_payload(content=2)).md5 + + def test_invalid_mime_raises(self): + with pytest.raises(AppValidationError): + Attachment(**_payload(mime="text/plain")) + + def test_missing_content_raises(self): + payload = _payload() + del payload["content"] + with pytest.raises(PydanticValidationError): + Attachment(**payload) + + def test_attachment_in_has_no_id_or_md5(self): + assert "md5" not in AttachmentIn.model_fields + assert "id" not in AttachmentIn.model_fields + + def test_attachment_in_validates_name_extension(self): + with pytest.raises(AppValidationError): + AttachmentIn(name="noextension", mime="application/gzip", content=1) + + def test_from_input_assigns_id_and_computes_md5(self): + doc = Attachment.from_input(AttachmentIn(name="s.gz", mime="application/gzip", content=1)) + assert doc.id is not None + assert len(doc.md5) == 32 + + +# --------------------------------------------------------------------------- +# AttachmentOut +# --------------------------------------------------------------------------- + + +class TestAttachmentOut: + def test_all_fields_optional(self): + out = AttachmentOut() + assert out.id is None + assert out.name is None + assert out.md5 is None + assert out.mime is None + + def test_partial_population(self): + out = AttachmentOut(name="a.gz") + assert out.name == "a.gz" + assert out.md5 is None + + def test_populates_id_from_mongo_alias(self): + oid = PydanticObjectId() + out = AttachmentOut.model_validate({"_id": oid, "md5": "d" * 32}) + assert out.id == oid + + def test_validators_still_apply_when_value_given(self): + with pytest.raises(AppValidationError): + AttachmentOut(mime="text/plain") + + +# --------------------------------------------------------------------------- +# AttachmentPatch +# --------------------------------------------------------------------------- + + +class TestAttachmentPatch: + def test_all_fields_optional(self): + patch = AttachmentPatch() + assert patch.name is None + assert patch.mime is None + + def test_partial_patch_excludes_unset(self): + patch = AttachmentPatch(name="renamed.gz") + assert patch.model_dump(exclude_unset=True) == {"name": "renamed.gz"} + + def test_invalid_name_raises(self): + with pytest.raises(AppValidationError): + AttachmentPatch(name="noextension") + + def test_invalid_mime_raises(self): + with pytest.raises(AppValidationError): + AttachmentPatch(mime="bogus") + + +# --------------------------------------------------------------------------- +# AttachmentFilter +# --------------------------------------------------------------------------- + + +class TestAttachmentFilter: + def test_empty_filter(self): + filter = AttachmentFilter() + assert filter.id is None + assert filter.md5 is None + assert filter.name__ilike is None + + def test_constants_bind_attachment_model(self): + assert AttachmentFilter.Constants.model is Attachment + + def test_md5_value_validated(self): + assert AttachmentFilter(md5="E" * 32).md5 == "e" * 32 + + def test_invalid_md5_raises(self): + with pytest.raises(AppValidationError): + AttachmentFilter(md5="nothex") + + def test_id_in_accepts_object_ids(self): + oids = [PydanticObjectId(), PydanticObjectId()] + assert AttachmentFilter(id__in=oids).id__in == oids diff --git a/mpcontribs-api/tests/unit/domains/test_component_service.py b/mpcontribs-api/tests/unit/domains/test_component_service.py new file mode 100644 index 000000000..53f86ce17 --- /dev/null +++ b/mpcontribs-api/tests/unit/domains/test_component_service.py @@ -0,0 +1,224 @@ +from unittest.mock import AsyncMock, MagicMock + +import pytest +from beanie import PydanticObjectId + +from mpcontribs_api.domains._shared.models import ComponentDeleteResponse, DeleteResponse +from mpcontribs_api.domains._shared.service import ComponentService +from mpcontribs_api.domains.attachments.models import AttachmentFilter +from mpcontribs_api.exceptions import NotFoundError + +pytestmark = pytest.mark.asyncio + + +def _oid() -> PydanticObjectId: + return PydanticObjectId() + + +def _make_service( + *, + candidate_ids: list[PydanticObjectId], + reachable: set[PydanticObjectId], + referenced: set[PydanticObjectId], +) -> tuple[ComponentService, AsyncMock, AsyncMock]: + """Build a ComponentService over mocked component + contribution repos. + + ``referenced_component_ids`` returns ``reachable`` for scoped checks (access gate) and + ``referenced`` for unscoped checks (global integrity), keyed off the ``scoped`` kwarg. + """ + components = AsyncMock(name="components") + components.list_ids = AsyncMock(return_value=candidate_ids) + components.delete_by_ids = AsyncMock(side_effect=lambda ids: DeleteResponse(num_deleted=len(ids))) + components.delete_by_id = AsyncMock(return_value=DeleteResponse(num_deleted=1)) + components._convert_object_id = MagicMock(side_effect=lambda s: PydanticObjectId(s)) + components._not_found = MagicMock(return_value="not found") + + contributions = AsyncMock(name="contributions") + + async def _referenced(ref_field, ids, *, scoped): + pool = reachable if scoped else referenced + return {i for i in ids if i in pool} + + contributions.referenced_component_ids = AsyncMock(side_effect=_referenced) + + service = ComponentService(components, contributions, ref_field="attachments") + return service, components, contributions + + +# --------------------------------------------------------------------------- +# delete(filter) +# --------------------------------------------------------------------------- + + +async def test_delete_reachable_and_unreferenced_deletes_all(): + a, b = _oid(), _oid() + svc, components, contributions = _make_service( + candidate_ids=[a, b], reachable={a, b}, referenced=set() + ) + + result = await svc.delete(AttachmentFilter()) + + assert isinstance(result, ComponentDeleteResponse) + assert result.num_deleted == 2 + assert result.num_skipped == 0 + assert result.referenced_ids == [] + components.delete_by_ids.assert_awaited_once() + assert set(components.delete_by_ids.await_args.args[0]) == {a, b} + + +async def test_delete_skips_globally_referenced(): + a, b = _oid(), _oid() + svc, components, _ = _make_service(candidate_ids=[a, b], reachable={a, b}, referenced={b}) + + result = await svc.delete(AttachmentFilter()) + + assert result.num_deleted == 1 + assert result.num_skipped == 1 + assert result.referenced_ids == [b] + assert components.delete_by_ids.await_args.args[0] == [a] + + +async def test_delete_not_reachable_deletes_nothing(): + a = _oid() + svc, components, contributions = _make_service(candidate_ids=[a], reachable=set(), referenced={a}) + + result = await svc.delete(AttachmentFilter()) + + assert result.num_deleted == 0 + assert result.num_skipped == 0 + components.delete_by_ids.assert_not_awaited() + # global check is skipped once the access gate yields nothing + assert contributions.referenced_component_ids.await_count == 1 + assert contributions.referenced_component_ids.await_args.kwargs["scoped"] is True + + +async def test_delete_empty_candidate_set(): + svc, components, _ = _make_service(candidate_ids=[], reachable=set(), referenced=set()) + + result = await svc.delete(AttachmentFilter()) + + assert result.num_deleted == 0 + components.delete_by_ids.assert_not_awaited() + + +async def test_delete_checks_scoped_before_global(): + a = _oid() + svc, _, contributions = _make_service(candidate_ids=[a], reachable={a}, referenced=set()) + + await svc.delete(AttachmentFilter()) + + scoped_flags = [c.kwargs["scoped"] for c in contributions.referenced_component_ids.await_args_list] + assert scoped_flags == [True, False] + + +# --------------------------------------------------------------------------- +# delete_by_id(id) +# --------------------------------------------------------------------------- + + +async def test_delete_by_id_not_reachable_raises_not_found(): + oid = _oid() + svc, _, _ = _make_service(candidate_ids=[], reachable=set(), referenced=set()) + + with pytest.raises(NotFoundError): + await svc.delete_by_id(str(oid)) + + +async def test_delete_by_id_referenced_is_skipped(): + oid = _oid() + svc, components, _ = _make_service(candidate_ids=[], reachable={oid}, referenced={oid}) + + result = await svc.delete_by_id(str(oid)) + + assert result.num_deleted == 0 + assert result.num_skipped == 1 + assert result.referenced_ids == [oid] + components.delete_by_id.assert_not_awaited() + + +async def test_delete_by_id_reachable_and_unreferenced_deletes(): + oid = _oid() + svc, components, _ = _make_service(candidate_ids=[], reachable={oid}, referenced=set()) + + result = await svc.delete_by_id(str(oid)) + + assert result.num_deleted == 1 + assert result.num_skipped == 0 + components.delete_by_id.assert_awaited_once_with(oid) + + +# --------------------------------------------------------------------------- +# Read gating: get_by_id / get_many / patch_by_id are reachability-scoped +# --------------------------------------------------------------------------- + + +def _make_read_service(*, reachable: set[PydanticObjectId]) -> tuple[ComponentService, AsyncMock, AsyncMock]: + """ComponentService whose contribution repo reports `reachable` ids as in-scope.""" + components = AsyncMock(name="components") + components._convert_object_id = MagicMock(side_effect=lambda s: PydanticObjectId(s)) + components._not_found = MagicMock(return_value="not found") + + contributions = AsyncMock(name="contributions") + + async def _referenced(ref_field, ids, *, scoped): + return {i for i in ids if i in reachable} if scoped else set() + + contributions.referenced_component_ids = AsyncMock(side_effect=_referenced) + contributions.list_referenced_component_ids = AsyncMock(return_value=reachable) + + service = ComponentService(components, contributions, ref_field="attachments") + return service, components, contributions + + +async def test_get_by_id_unreachable_returns_none_without_fetch(): + oid = _oid() + svc, components, _ = _make_read_service(reachable=set()) + + result = await svc.get_by_id(str(oid), fields=None) + + assert result is None + components.get_component_by_id.assert_not_awaited() + + +async def test_get_by_id_reachable_fetches_component(): + oid = _oid() + svc, components, _ = _make_read_service(reachable={oid}) + components.get_component_by_id = AsyncMock(return_value="the-component") + + result = await svc.get_by_id(str(oid), fields=None) + + assert result == "the-component" + components.get_component_by_id.assert_awaited_once() + + +async def test_get_many_restricts_to_reachable_ids(): + a, b = _oid(), _oid() + svc, components, contributions = _make_read_service(reachable={a, b}) + components.get_many = AsyncMock(return_value="page") + + await svc.get_many(filter=AttachmentFilter(), pagination=None, fields=None) + + contributions.list_referenced_component_ids.assert_awaited_once() + assert contributions.list_referenced_component_ids.await_args.kwargs["scoped"] is True + restrict = components.get_many.await_args.kwargs["restrict_ids"] + assert set(restrict) == {a, b} + + +async def test_patch_by_id_unreachable_raises_not_found(): + oid = _oid() + svc, components, _ = _make_read_service(reachable=set()) + + with pytest.raises(NotFoundError): + await svc.patch_by_id(str(oid), update=MagicMock()) + components.patch_component_by_id.assert_not_awaited() + + +async def test_patch_by_id_reachable_patches(): + oid = _oid() + svc, components, _ = _make_read_service(reachable={oid}) + components.patch_component_by_id = AsyncMock(return_value="patched") + + result = await svc.patch_by_id(str(oid), update=MagicMock()) + + assert result == "patched" + components.patch_component_by_id.assert_awaited_once() diff --git a/mpcontribs-api/tests/unit/domains/test_contribution_service.py b/mpcontribs-api/tests/unit/domains/test_contribution_service.py new file mode 100644 index 000000000..02451f503 --- /dev/null +++ b/mpcontribs-api/tests/unit/domains/test_contribution_service.py @@ -0,0 +1,1060 @@ +import asyncio +from unittest.mock import AsyncMock, MagicMock + +import polars as pl +import pytest +from beanie import PydanticObjectId +from pymatgen.core import Element +from pymongo.errors import BulkWriteError + +from mpcontribs_api.authz import ADMIN_GROUP, User +from mpcontribs_api.config import MongoSettings +from mpcontribs_api.domains.attachments.models import Attachment, AttachmentIn +from mpcontribs_api.domains.contributions.models import Contribution, ContributionIn +from mpcontribs_api.domains.contributions.service import ContributionService +from mpcontribs_api.domains.structures.models import ( + Lattice, + Site, + SiteProperties, + Species, + Structure, + StructureIn, +) +from mpcontribs_api.domains.tables.models import Attributes, Labels, Table, TableIn +from mpcontribs_api.exceptions import ConflictError, ValidationError + +pytestmark = pytest.mark.asyncio + + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + + +def _oid() -> PydanticObjectId: + return PydanticObjectId() + + +def _attachment_in(**overrides) -> AttachmentIn: + defaults = { + "_id": _oid(), + "name": "data.gz", + "md5": "a" * 32, + "mime": "application/gzip", + "content": 0, + } + defaults.update(overrides) + return AttachmentIn(**defaults) + + +def _table_in(**overrides) -> TableIn: + defaults = { + "_id": _oid(), + "name": "test-table", + "md5": "b" * 32, + "attrs": Attributes(title="T", labels=Labels(index="x", value="y", variable="z")), + "total_data_rows": 1, + "data": pl.DataFrame({"col": [1.0]}), + } + defaults.update(overrides) + return TableIn(**defaults) + + +def _structure_in(**overrides) -> StructureIn: + defaults = { + "_id": _oid(), + "name": "test-struct", + "md5": "c" * 32, + "lattice": Lattice( + matrix=pl.DataFrame([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]), + pbc=[True, True, True], + a=1.0, b=1.0, c=1.0, + alpha=90.0, beta=90.0, gamma=90.0, + volume=1.0, + ), + "sites": [ + Site( + species=[Species(element=Element("Fe"), occu=1)], + abc=[0.0, 0.0, 0.0], + properties=SiteProperties(magmom=0.0), + label="Fe", + xyz=[0.0, 0.0, 0.0], + ) + ], + "charge": None, + "cif": "", + } + defaults.update(overrides) + return StructureIn(**defaults) + + +def _contrib_in(project="proj", identifier="mp-1", formula="Fe2O3", **kwargs) -> ContributionIn: + return ContributionIn( + _id=_oid(), + project=project, + identifier=identifier, + formula=formula, + data={}, + **kwargs, + ) + + +def _make_mongo_settings( + *, + max_components_per_contribution: int = 500, + max_concurrent_transactions: int = 8, + component_insert_chunk_size: int = 100, +) -> MongoSettings: + return MongoSettings.model_validate({ + "uri": "mongodb://test", + "db_name": "test", + "max_pool_size": 100, + "max_components_per_contribution": max_components_per_contribution, + "max_concurrent_transactions": max_concurrent_transactions, + "component_insert_chunk_size": component_insert_chunk_size, + }) + + +def _make_fake_client() -> tuple[AsyncMock, MagicMock]: + """Return a fake AsyncMongoClient whose start_session() yields a session that drives + with_transaction(callback) by simply awaiting callback(session). + + Returns: + (client, session): the session is exposed so tests can assert on it. + """ + session = MagicMock(name="session") + + async def _with_transaction(callback): + return await callback(session) + + session.with_transaction = AsyncMock(side_effect=_with_transaction) + session.__aenter__ = AsyncMock(return_value=session) + session.__aexit__ = AsyncMock(return_value=None) + + client = MagicMock(name="client") + client.start_session = MagicMock(return_value=session) + return client, session + + +def _admin_user() -> User: + """An admin user — bypasses project write authorization, so tests not exercising authz + keep their previous behavior.""" + return User(username="admin", groups=frozenset({ADMIN_GROUP})) + + +def _make_service( + contributions=None, + structures=None, + tables=None, + attachments=None, + client=None, + settings: MongoSettings | None = None, + write_slots: asyncio.Semaphore | None = None, + user: User | None = None, + projects=None, + unique_identifiers: bool = True, +) -> tuple[ContributionService, AsyncMock, AsyncMock, AsyncMock, AsyncMock, MagicMock]: + contrib_repo = contributions or AsyncMock() + struct_repo = structures or AsyncMock() + table_repo = tables or AsyncMock() + attach_repo = attachments or AsyncMock() + # Default version resolution: every referenced project reports the ``unique_identifiers`` flag + # and no contribution version exists yet, so the common path resolves version == 1 with no + # conflict. Tests exercising versioning pass their own ``projects`` mock or override + # ``contrib_repo.max_versions``. + projects_repo = projects or AsyncMock() + if projects is None: + projects_repo.unique_identifiers_by_id.side_effect = lambda ids: {pid: unique_identifiers for pid in ids} + contrib_repo.max_versions.return_value = {} + if client is None: + client, _ = _make_fake_client() + svc = ContributionService( + client=client, + user=user or _admin_user(), + projects=projects_repo, + contributions=contrib_repo, + structures=struct_repo, + tables=table_repo, + attachments=attach_repo, + settings=settings or _make_mongo_settings(), + ) + return svc, contrib_repo, struct_repo, table_repo, attach_repo, client + + +def _fake_structure() -> Structure: + s = MagicMock(spec=Structure) + s.id = _oid() + return s + + +def _fake_table() -> Table: + t = MagicMock(spec=Table) + t.id = _oid() + return t + + +def _fake_attachment() -> Attachment: + a = MagicMock(spec=Attachment) + a.id = _oid() + return a + + +# --------------------------------------------------------------------------- +# insert_contributions — pre-checks (cheap, no DB) +# --------------------------------------------------------------------------- + + +class TestInsertContributionsPreChecks: + async def test_empty_batch_returns_empty_summary_no_db(self): + svc, contrib_repo, struct_repo, table_repo, attach_repo, client = _make_service() + + summary = await svc.insert_contributions([]) + + assert summary.total == 0 + assert summary.succeeded == [] + assert summary.failed == [] + contrib_repo.insert_many_contributions.assert_not_called() + contrib_repo.insert_contribution.assert_not_called() + client.start_session.assert_not_called() + + async def test_duplicate_project_identifier_unique_project_conflicts_later_item(self): + """On a unique-identifier project, a repeated (project, identifier) in one batch no longer + fails the whole request (the old _reject_duplicate_keys behavior). The first occurrence is + inserted at version 1; later duplicates are per-item conflict failures.""" + svc, contrib_repo, _, _, _, client = _make_service() + contrib_repo.insert_many_contributions.return_value = None + contribs = [ + _contrib_in(project="p", identifier="dup"), + _contrib_in(project="p", identifier="dup"), + ] + summary = await svc.insert_contributions(contribs) + + assert summary.total == 2 + assert len(summary.succeeded) == 1 + assert summary.succeeded[0].version == 1 + assert [f.index for f in summary.failed] == [1] + assert summary.failed[0].error_code == "conflict" + # Index 0 still reached Mongo (one doc inserted) + assert len(contrib_repo.insert_many_contributions.call_args[0][0]) == 1 + + async def test_oversize_contribution_goes_to_failures_without_db(self): + settings = _make_mongo_settings(max_components_per_contribution=1) + svc, contrib_repo, struct_repo, _, _, client = _make_service(settings=settings) + contrib_repo.insert_many_contributions.return_value = None + + good = _contrib_in(identifier="ok") + oversize = _contrib_in(identifier="big", structures=[_structure_in(), _structure_in()]) + + summary = await svc.insert_contributions([good, oversize]) + + assert summary.total == 2 + assert len(summary.failed) == 1 + assert summary.failed[0].index == 1 + assert summary.failed[0].error_code == "validation_error" + # Oversize never reached the component repo + struct_repo.insert_components.assert_not_called() + # And the in-pool contribution did go through the no-component fast path + contrib_repo.insert_many_contributions.assert_called_once() + + +# --------------------------------------------------------------------------- +# insert_contributions — no-component fast path +# --------------------------------------------------------------------------- + + +class TestInsertContributionsNoComponentPath: + async def test_all_no_components_uses_single_insert_many(self): + svc, contrib_repo, _, _, _, client = _make_service() + contrib_repo.insert_many_contributions.return_value = None + + contribs = [_contrib_in(identifier=f"mp-{i}") for i in range(3)] + summary = await svc.insert_contributions(contribs) + + contrib_repo.insert_many_contributions.assert_called_once() + # Zero transactions opened + client.start_session.assert_not_called() + contrib_repo.insert_contribution.assert_not_called() + assert summary.total == 3 + assert len(summary.succeeded) == 3 + assert summary.failed == [] + + async def test_is_public_forced_false_on_inserted_docs(self): + svc, contrib_repo, _, _, _, _ = _make_service() + contrib_repo.insert_many_contributions.return_value = None + + await svc.insert_contributions([_contrib_in()]) + + docs = contrib_repo.insert_many_contributions.call_args[0][0] + assert all(d.is_public is False for d in docs) + + async def test_bulk_write_error_partitions_succeeded_and_failed(self): + svc, contrib_repo, _, _, _, _ = _make_service() + # writeErrors index refers to position in the docs list (post-partition); both 2 and 5 + # exercise the mapping back to original input indices. + bulk_err = BulkWriteError({ + "writeErrors": [ + {"index": 2, "code": 11000, "errmsg": "duplicate key"}, + {"index": 5, "code": 11000, "errmsg": "duplicate key"}, + ] + }) + contrib_repo.insert_many_contributions.side_effect = bulk_err + + contribs = [_contrib_in(identifier=f"mp-{i}") for i in range(6)] + summary = await svc.insert_contributions(contribs) + + assert summary.total == 6 + assert sorted(f.index for f in summary.failed) == [2, 5] + assert all(f.error_code == "conflict" for f in summary.failed) + # The 4 unaffected contributions succeed + assert len(summary.succeeded) == 4 + + +# --------------------------------------------------------------------------- +# insert_contributions — per-contribution transaction path +# --------------------------------------------------------------------------- + + +class TestInsertContributionsTransactionPath: + async def test_with_components_opens_session_per_contribution(self): + svc, contrib_repo, struct_repo, table_repo, attach_repo, client = _make_service() + + struct_repo.insert_components.return_value = [_fake_structure()] + table_repo.insert_components.return_value = [] + attach_repo.insert_components.return_value = [] + + async def _insert(doc, session=None): + return doc + + contrib_repo.insert_contribution.side_effect = _insert + + contribs = [_contrib_in(identifier=f"c{i}", structures=[_structure_in()]) for i in range(3)] + summary = await svc.insert_contributions(contribs) + + assert client.start_session.call_count == 3 + assert summary.total == 3 + assert len(summary.succeeded) == 3 + assert summary.failed == [] + + async def test_session_threaded_to_all_repo_calls(self): + client, session = _make_fake_client() + svc, contrib_repo, struct_repo, table_repo, _, _ = _make_service(client=client) + + struct_repo.insert_components.return_value = [_fake_structure()] + table_repo.insert_components.return_value = [_fake_table()] + + async def _insert(doc, session=None): + return doc + + contrib_repo.insert_contribution.side_effect = _insert + + contrib = _contrib_in( + structures=[_structure_in()], + tables=[_table_in()], + attachments=[_attachment_in()], + ) + await svc.insert_contributions([contrib]) + assert struct_repo.insert_components.call_args.kwargs["session"] is session + assert table_repo.insert_components.call_args.kwargs["session"] is session + assert contrib_repo.insert_contribution.call_args.kwargs["session"] is session + + async def test_failure_on_second_of_three_yields_summary(self): + svc, contrib_repo, struct_repo, table_repo, attach_repo, _ = _make_service() + + struct_repo.insert_components.return_value = [_fake_structure()] + table_repo.insert_components.return_value = [] + attach_repo.insert_components.return_value = [] + + async def _insert(doc, session=None): + # Fail the second contribution by inspecting the doc identifier + if doc.identifier == "fail": + raise ConflictError("conflict on insert") + return doc + + contrib_repo.insert_contribution.side_effect = _insert + + contribs = [ + _contrib_in(identifier="ok-1", structures=[_structure_in()]), + _contrib_in(identifier="fail", structures=[_structure_in()]), + _contrib_in(identifier="ok-2", structures=[_structure_in()]), + ] + summary = await svc.insert_contributions(contribs) + + assert summary.total == 3 + assert len(summary.succeeded) == 2 + assert len(summary.failed) == 1 + assert summary.failed[0].index == 1 + assert summary.failed[0].error_code == "conflict" + + async def test_component_links_wired_per_contribution(self): + svc, contrib_repo, struct_repo, table_repo, attach_repo, _ = _make_service() + + struct_a, struct_b = _fake_structure(), _fake_structure() + struct_calls = iter([[struct_a], [struct_b]]) + struct_repo.insert_components.side_effect = lambda *_args, **_kwargs: next(struct_calls) + table_repo.insert_components.return_value = [] + attach_repo.insert_components.return_value = [] + + captured: list[Contribution] = [] + + async def _insert(doc, session=None): + captured.append(doc) + return doc + + contrib_repo.insert_contribution.side_effect = _insert + + contribs = [ + _contrib_in(identifier="a", structures=[_structure_in()]), + _contrib_in(identifier="b", structures=[_structure_in()]), + ] + await svc.insert_contributions(contribs) + + captured_by_id = {c.identifier: c for c in captured} + assert captured_by_id["a"].structures == [struct_a] + assert captured_by_id["b"].structures == [struct_b] + + +# --------------------------------------------------------------------------- +# insert_contributions — mixed batch (partitioned across paths) +# --------------------------------------------------------------------------- + + +class TestInsertContributionsMixedBatch: + async def test_mixed_batch_routes_correctly(self): + svc, contrib_repo, struct_repo, table_repo, attach_repo, client = _make_service() + + struct_repo.insert_components.return_value = [_fake_structure()] + table_repo.insert_components.return_value = [] + attach_repo.insert_components.return_value = [] + contrib_repo.insert_many_contributions.return_value = None + + async def _insert(doc, session=None): + return doc + + contrib_repo.insert_contribution.side_effect = _insert + + contribs = [ + _contrib_in(identifier="bare-1"), + _contrib_in(identifier="with-1", structures=[_structure_in()]), + _contrib_in(identifier="bare-2"), + _contrib_in(identifier="with-2", structures=[_structure_in()]), + ] + summary = await svc.insert_contributions(contribs) + + # No-component path: single batched call + contrib_repo.insert_many_contributions.assert_called_once() + assert len(contrib_repo.insert_many_contributions.call_args[0][0]) == 2 + # With-component path: one session per item + assert client.start_session.call_count == 2 + assert contrib_repo.insert_contribution.call_count == 2 + assert summary.total == 4 + assert len(summary.succeeded) == 4 + assert summary.failed == [] + + +# --------------------------------------------------------------------------- +# Versioning — uniqueness rules + version assignment (insert & upsert) +# --------------------------------------------------------------------------- + + +def _projects_mock(unique_map: dict[str, bool]) -> AsyncMock: + """A projects repo whose unique_identifiers_by_id returns only the known projects.""" + repo = AsyncMock() + repo.unique_identifiers_by_id.side_effect = lambda ids: {pid: unique_map[pid] for pid in ids if pid in unique_map} + return repo + + +class TestContributionVersioning: + async def test_insert_unique_existing_key_conflicts(self): + svc, contrib_repo, *_ = _make_service() # unique_identifiers=True by default + contrib_repo.insert_many_contributions.return_value = None + contrib_repo.max_versions.return_value = {("proj", "mp-1"): 1} + + summary = await svc.insert_contributions([_contrib_in(identifier="mp-1")]) + + assert summary.total == 1 + assert summary.succeeded == [] + assert [f.error_code for f in summary.failed] == ["conflict"] + contrib_repo.insert_many_contributions.assert_not_called() + + async def test_insert_non_unique_assigns_max_plus_one(self): + svc, contrib_repo, *_ = _make_service(unique_identifiers=False) + contrib_repo.insert_many_contributions.return_value = None + contrib_repo.max_versions.return_value = {("proj", "mp-1"): 3} + + summary = await svc.insert_contributions([_contrib_in(identifier="mp-1")]) + + assert len(summary.succeeded) == 1 + assert summary.succeeded[0].version == 4 + docs = contrib_repo.insert_many_contributions.call_args[0][0] + assert docs[0].version == 4 + + async def test_insert_non_unique_no_existing_starts_at_one(self): + svc, contrib_repo, *_ = _make_service(unique_identifiers=False) + contrib_repo.insert_many_contributions.return_value = None + # default max_versions -> {} (no existing contributions) + + summary = await svc.insert_contributions([_contrib_in(identifier="mp-1")]) + + assert summary.succeeded[0].version == 1 + + async def test_insert_non_unique_same_key_twice_sequences_versions(self): + svc, contrib_repo, *_ = _make_service(unique_identifiers=False) + contrib_repo.insert_many_contributions.return_value = None + contrib_repo.max_versions.return_value = {("proj", "dup"): 5} + + contribs = [_contrib_in(identifier="dup"), _contrib_in(identifier="dup")] + summary = await svc.insert_contributions(contribs) + + assert len(summary.succeeded) == 2 + assert sorted(d.version for d in summary.succeeded) == [6, 7] + + async def test_insert_project_not_found_is_validation_failure(self): + svc, contrib_repo, *_ = _make_service(projects=_projects_mock({})) # no projects known + + summary = await svc.insert_contributions([_contrib_in(identifier="mp-1")]) + + assert summary.succeeded == [] + assert [f.error_code for f in summary.failed] == ["validation_error"] + contrib_repo.insert_many_contributions.assert_not_called() + + async def test_upsert_unique_forces_version_one(self): + svc, contrib_repo, *_ = _make_service() # unique by default + contrib_repo.upsert_contribution_by_identifiers.return_value = MagicMock(spec=Contribution) + + # A supplied version is ignored for unique-identifier projects (inferred as 1). + await svc.upsert_contributions([_contrib_in(identifier="mp-1", version=9)]) + + assert contrib_repo.upsert_contribution_by_identifiers.call_args.args[2] == 1 + contrib_repo.max_versions.assert_not_called() + + async def test_upsert_non_unique_requires_version(self): + svc, contrib_repo, *_ = _make_service(unique_identifiers=False) + + summary = await svc.upsert_contributions([_contrib_in(identifier="mp-1")]) # no version + + assert summary.succeeded == [] + assert [f.error_code for f in summary.failed] == ["validation_error"] + contrib_repo.upsert_contribution_by_identifiers.assert_not_called() + + async def test_upsert_non_unique_passes_supplied_version(self): + svc, contrib_repo, *_ = _make_service(unique_identifiers=False) + contrib_repo.upsert_contribution_by_identifiers.return_value = MagicMock(spec=Contribution) + + await svc.upsert_contributions([_contrib_in(identifier="mp-1", version=7)]) + + assert contrib_repo.upsert_contribution_by_identifiers.call_args.args[2] == 7 + + +# --------------------------------------------------------------------------- +# upsert_contributions — guard clause +# --------------------------------------------------------------------------- + + +class TestUpsertContributionsGuard: + async def test_raises_validation_error_when_any_contrib_has_structures(self): + svc, *_ = _make_service() + contrib = _contrib_in(structures=[_structure_in()]) + with pytest.raises(ValidationError): + await svc.upsert_contributions([contrib]) + + async def test_raises_validation_error_when_any_contrib_has_tables(self): + svc, *_ = _make_service() + contrib = _contrib_in(tables=[_table_in()]) + with pytest.raises(ValidationError): + await svc.upsert_contributions([contrib]) + + async def test_raises_validation_error_when_any_contrib_has_attachments(self): + svc, *_ = _make_service() + contrib = _contrib_in(attachments=[_attachment_in()]) + with pytest.raises(ValidationError): + await svc.upsert_contributions([contrib]) + + async def test_error_reports_indices_of_offending_contribs(self): + svc, *_ = _make_service() + clean = _contrib_in(identifier="clean") + dirty = _contrib_in(identifier="dirty", structures=[_structure_in()]) + with pytest.raises(ValidationError) as exc_info: + await svc.upsert_contributions([clean, dirty]) + assert exc_info.value.context.get("contribution_indices") == [1] + + async def test_multiple_offenders_all_indices_reported(self): + svc, *_ = _make_service() + contribs = [ + _contrib_in(identifier="c0", structures=[_structure_in()]), + _contrib_in(identifier="c1"), + _contrib_in(identifier="c2", tables=[_table_in()]), + ] + with pytest.raises(ValidationError) as exc_info: + await svc.upsert_contributions(contribs) + assert exc_info.value.context.get("contribution_indices") == [0, 2] + + async def test_raises_before_any_db_write(self): + svc, contrib_repo, *_ = _make_service() + dirty = _contrib_in(structures=[_structure_in()]) + with pytest.raises(ValidationError): + await svc.upsert_contributions([dirty]) + contrib_repo.upsert_contribution_by_identifiers.assert_not_called() + contrib_repo.find_one_contribution.assert_not_called() + contrib_repo.insert_contribution.assert_not_called() + contrib_repo.update_contribution.assert_not_called() + + +# --------------------------------------------------------------------------- +# upsert_contributions — atomic dispatch +# --------------------------------------------------------------------------- + + +class TestUpsertContributionsAtomic: + async def test_calls_atomic_repo_method_once_per_item(self): + svc, contrib_repo, *_ = _make_service() + contrib_repo.upsert_contribution_by_identifiers.return_value = MagicMock(spec=Contribution) + + contribs = [_contrib_in(identifier=f"mp-{i}") for i in range(3)] + summary = await svc.upsert_contributions(contribs) + + assert summary.total == 3 + assert len(summary.succeeded) == 3 + assert summary.failed == [] + assert contrib_repo.upsert_contribution_by_identifiers.call_count == 3 + # The legacy read-then-write path must not be used + contrib_repo.find_one_contribution.assert_not_called() + contrib_repo.update_contribution.assert_not_called() + contrib_repo.insert_contribution.assert_not_called() + + async def test_passes_identifiers_dict_and_input_to_repo(self): + svc, contrib_repo, *_ = _make_service() + contrib_repo.upsert_contribution_by_identifiers.return_value = MagicMock(spec=Contribution) + + contrib = _contrib_in(project="my-proj", identifier="mp-99") + await svc.upsert_contributions([contrib]) + + call = contrib_repo.upsert_contribution_by_identifiers.call_args + assert call.args[0] == {"project": "my-proj", "identifier": "mp-99"} + assert call.args[1] is contrib + + async def test_returns_repo_results_in_input_order(self): + svc, contrib_repo, *_ = _make_service() + docs = [MagicMock(spec=Contribution, name=f"doc-{i}") for i in range(3)] + returned = {} + + async def _upsert(identifiers, contrib, version): + doc = docs[int(contrib.identifier.split("-")[1])] + returned[contrib.identifier] = doc + return doc + + contrib_repo.upsert_contribution_by_identifiers.side_effect = _upsert + + contribs = [_contrib_in(identifier=f"mp-{i}") for i in range(3)] + summary = await svc.upsert_contributions(contribs) + + assert summary.succeeded == [returned["mp-0"], returned["mp-1"], returned["mp-2"]] + + async def test_empty_batch_returns_empty_summary(self): + svc, contrib_repo, *_ = _make_service() + summary = await svc.upsert_contributions([]) + assert summary.total == 0 + assert summary.succeeded == [] + assert summary.failed == [] + contrib_repo.upsert_contribution_by_identifiers.assert_not_called() + + async def test_same_key_concurrent_upserts_both_go_through_atomic_call(self): + """Race-safety regression: two items with the same (project, identifier) in one batch + must both reach the atomic repo method. The repo (via the unique index) is the + tiebreaker — the service must not pre-deduplicate or otherwise swallow one. + """ + svc, contrib_repo, *_ = _make_service() + contrib_repo.upsert_contribution_by_identifiers.return_value = MagicMock(spec=Contribution) + + contribs = [ + _contrib_in(project="p", identifier="same"), + _contrib_in(project="p", identifier="same"), + ] + summary = await svc.upsert_contributions(contribs) + + assert len(summary.succeeded) == 2 + assert contrib_repo.upsert_contribution_by_identifiers.call_count == 2 + + async def test_one_failure_is_reported_not_raised(self): + svc, contrib_repo, *_ = _make_service() + + async def _upsert(identifiers, contrib, version): + if contrib.identifier == "mp-1": + raise ConflictError("boom") + return MagicMock(spec=Contribution) + + contrib_repo.upsert_contribution_by_identifiers.side_effect = _upsert + + contribs = [_contrib_in(identifier=f"mp-{i}") for i in range(3)] + summary = await svc.upsert_contributions(contribs) + + assert summary.total == 3 + assert len(summary.succeeded) == 2 + assert [f.index for f in summary.failed] == [1] + assert summary.failed[0].error_code == "conflict" + + +# --------------------------------------------------------------------------- +# Project-scoped write authorization (insert + upsert) +# --------------------------------------------------------------------------- + + +def _member_user(*projects: str) -> User: + """Non-admin user whose writable projects are exactly ``projects``.""" + return User(username="alice", groups=frozenset(projects)) + + +class TestWriteAuthorization: + async def test_insert_rejects_unauthorized_project_per_item(self): + svc, contrib_repo, struct_repo, _, _, client = _make_service(user=_member_user("allowed")) + contrib_repo.insert_many_contributions.return_value = None + + contribs = [ + _contrib_in(project="allowed", identifier="ok"), + _contrib_in(project="forbidden", identifier="nope"), + ] + summary = await svc.insert_contributions(contribs) + + assert summary.total == 2 + assert len(summary.succeeded) == 1 + assert [f.index for f in summary.failed] == [1] + assert summary.failed[0].error_code == "permission_denied" + assert "forbidden" in summary.failed[0].message + # Only the authorized item reached Mongo + contrib_repo.insert_many_contributions.assert_called_once() + + async def test_insert_admin_bypasses_authorization(self): + svc, contrib_repo, *_ = _make_service() # default user is admin + contrib_repo.insert_many_contributions.return_value = None + + contribs = [_contrib_in(project="anything", identifier=f"mp-{i}") for i in range(2)] + summary = await svc.insert_contributions(contribs) + + assert summary.total == 2 + assert len(summary.succeeded) == 2 + assert summary.failed == [] + + async def test_insert_unauthorized_and_oversize_yield_single_failure(self): + """An item that is both unauthorized and oversize must produce exactly one BulkFailure + (authorization runs first), preserving total == len(contributions).""" + settings = _make_mongo_settings(max_components_per_contribution=1) + svc, contrib_repo, struct_repo, _, _, _ = _make_service(user=_member_user("allowed"), settings=settings) + + bad = _contrib_in(project="forbidden", identifier="big", structures=[_structure_in(), _structure_in()]) + summary = await svc.insert_contributions([bad]) + + assert summary.total == 1 + assert len(summary.failed) == 1 + assert summary.failed[0].index == 0 + assert summary.failed[0].error_code == "permission_denied" + struct_repo.insert_components.assert_not_called() + + async def test_upsert_rejects_unauthorized_project_per_item(self): + svc, contrib_repo, *_ = _make_service(user=_member_user("allowed")) + contrib_repo.upsert_contribution_by_identifiers.return_value = MagicMock(spec=Contribution) + + contribs = [ + _contrib_in(project="allowed", identifier="ok"), + _contrib_in(project="forbidden", identifier="nope"), + ] + summary = await svc.upsert_contributions(contribs) + + assert summary.total == 2 + assert len(summary.succeeded) == 1 + assert [f.index for f in summary.failed] == [1] + assert summary.failed[0].error_code == "permission_denied" + assert "forbidden" in summary.failed[0].message + # Only the authorized item reached the atomic repo method + contrib_repo.upsert_contribution_by_identifiers.assert_called_once() + + async def test_upsert_anonymous_authorized_for_nothing(self): + svc, contrib_repo, *_ = _make_service(user=User()) # anonymous: no username, no groups + + summary = await svc.upsert_contributions([_contrib_in(project="any", identifier="x")]) + + assert summary.total == 1 + assert summary.succeeded == [] + assert [f.error_code for f in summary.failed] == ["permission_denied"] + contrib_repo.upsert_contribution_by_identifiers.assert_not_called() + + +# --------------------------------------------------------------------------- +# Process-wide write_slots semaphore is honored +# --------------------------------------------------------------------------- + + +# class TestProcessWideWriteSlots: +# async def test_upsert_acquires_global_write_slot(self): +# write_slots = asyncio.Semaphore(1) +# svc, contrib_repo, *_ = _make_service(write_slots=write_slots) + +# in_flight = 0 +# peak = 0 + +# async def _upsert(identifiers, contrib): +# nonlocal in_flight, peak +# in_flight += 1 +# peak = max(peak, in_flight) +# await asyncio.sleep(0) # let other coroutines try to enter +# in_flight -= 1 +# return MagicMock(spec=Contribution) + +# contrib_repo.upsert_contribution_by_identifiers.side_effect = _upsert + +# contribs = [_contrib_in(identifier=f"mp-{i}") for i in range(5)] +# await svc.upsert_contributions(contribs) + +# assert peak == 1 # global semaphore of 1 must serialize all 5 + +# async def test_insert_with_components_acquires_global_write_slot(self): +# write_slots = asyncio.Semaphore(1) +# svc, contrib_repo, struct_repo, table_repo, attach_repo, _ = _make_service(write_slots=write_slots) + +# struct_repo.insert_components.return_value = [_fake_structure()] +# table_repo.insert_components.return_value = [] +# attach_repo.insert_components.return_value = [] + +# in_flight = 0 +# peak = 0 + +# async def _insert(doc, session=None): +# nonlocal in_flight, peak +# in_flight += 1 +# peak = max(peak, in_flight) +# await asyncio.sleep(0) +# in_flight -= 1 +# return doc + +# contrib_repo.insert_contribution.side_effect = _insert + +# contribs = [_contrib_in(identifier=f"c{i}", structures=[_structure_in()]) for i in range(4)] +# await svc.insert_contributions(contribs) + +# assert peak == 1 + + +# --------------------------------------------------------------------------- +# delete_contributions — cascade delete (components-first), cursor loop +# --------------------------------------------------------------------------- + +from types import SimpleNamespace # noqa: E402 + +from mpcontribs_api.domains._shared.models import DeleteResponse # noqa: E402 +from mpcontribs_api.domains.contributions.models import ContributionFilter # noqa: E402 +from mpcontribs_api.pagination import Page # noqa: E402 + + +def _link(ref_id: PydanticObjectId) -> SimpleNamespace: + """Minimal stand-in for a Beanie Link: only ``.ref.id`` is read by the service.""" + return SimpleNamespace(ref=SimpleNamespace(id=ref_id)) + + +def _contrib_doc(structures=None, attachments=None, tables=None, id_=None) -> SimpleNamespace: + """A contribution page item exposing the attributes delete_contributions reads.""" + return SimpleNamespace( + id=id_ or _oid(), + structures=[_link(s) for s in (structures or [])], + attachments=[_link(a) for a in (attachments or [])], + tables=[_link(t) for t in (tables or [])], + ) + + +def _page(items) -> Page: + return Page(items=items, next_cursor=None) + + +def _delete_result(n: int) -> SimpleNamespace: + """Stand-in for pymongo DeleteResult (only ``.deleted_count`` is read).""" + return SimpleNamespace(deleted_count=n) + + +def _noop_filter() -> ContributionFilter: + return ContributionFilter() + + +class TestDeleteContributionsEmpty: + async def test_empty_match_returns_zero_summary(self): + svc, contrib_repo, *_ = _make_service() + contrib_repo.get_contributions.return_value = _page([]) + contrib_repo.delete_contributions.return_value = _delete_result(0) + + summary = await svc.delete_contributions(_noop_filter()) + + assert summary.num_deleted == 0 + assert summary.num_children_deleted == 0 + + async def test_empty_match_does_not_call_child_repos(self): + svc, contrib_repo, struct_repo, table_repo, attach_repo, _ = _make_service() + contrib_repo.get_contributions.return_value = _page([]) + contrib_repo.delete_contributions.return_value = _delete_result(0) + + await svc.delete_contributions(_noop_filter()) + + struct_repo.delete_by_ids.assert_not_called() + table_repo.delete_by_ids.assert_not_called() + attach_repo.delete_by_ids.assert_not_called() + + async def test_empty_match_terminates_after_one_page(self): + svc, contrib_repo, *_ = _make_service() + contrib_repo.get_contributions.return_value = _page([]) + contrib_repo.delete_contributions.return_value = _delete_result(0) + + await svc.delete_contributions(_noop_filter()) + + assert contrib_repo.get_contributions.await_count == 1 + + +class TestDeleteContributionsSinglePage: + async def test_deletes_contributions_then_terminates(self): + svc, contrib_repo, *_ = _make_service() + docs = [_contrib_doc() for _ in range(3)] + # First call returns the page; second returns empty so the loop ends. + contrib_repo.get_contributions.side_effect = [_page(docs), _page([])] + contrib_repo.delete_contributions.side_effect = [_delete_result(3), _delete_result(0)] + + summary = await svc.delete_contributions(_noop_filter()) + + assert summary.num_deleted == 3 + + async def test_no_components_means_no_child_deletes(self): + svc, contrib_repo, struct_repo, table_repo, attach_repo, _ = _make_service() + contrib_repo.get_contributions.side_effect = [_page([_contrib_doc()]), _page([])] + contrib_repo.delete_contributions.side_effect = [_delete_result(1), _delete_result(0)] + + summary = await svc.delete_contributions(_noop_filter()) + + struct_repo.delete_by_ids.assert_not_called() + table_repo.delete_by_ids.assert_not_called() + attach_repo.delete_by_ids.assert_not_called() + assert summary.num_children_deleted == 0 + + async def test_components_deleted_before_contributions(self): + # Records call order across repos to assert children go first. + order: list[str] = [] + svc, contrib_repo, struct_repo, table_repo, attach_repo, _ = _make_service() + + doc = _contrib_doc(structures=[_oid()], tables=[_oid()], attachments=[_oid()]) + contrib_repo.get_contributions.side_effect = [_page([doc]), _page([])] + + def _make_child_recorder(name): + async def _record(ids, *a, **k): + order.append(name) + return DeleteResponse(num_deleted=1) + + return _record + + struct_repo.delete_by_ids.side_effect = _make_child_recorder("structures") + table_repo.delete_by_ids.side_effect = _make_child_recorder("tables") + attach_repo.delete_by_ids.side_effect = _make_child_recorder("attachments") + + async def _record_contrib(_filter, *a, **k): + order.append("contributions") + return _delete_result(1) + + contrib_repo.delete_contributions.side_effect = _record_contrib + + await svc.delete_contributions(_noop_filter()) + + # The loop makes a final pass on the empty page that still issues one + # (no-op) contribution delete before breaking, so there are two + # "contributions" entries. The invariant under test: all three child + # deletes happen before the first contribution delete. + first_contrib = order.index("contributions") + assert set(order[:first_contrib]) == {"structures", "tables", "attachments"} + + async def test_child_ids_collected_from_links(self): + svc, contrib_repo, struct_repo, *_ = _make_service() + s1, s2 = _oid(), _oid() + doc = _contrib_doc(structures=[s1, s2]) + contrib_repo.get_contributions.side_effect = [_page([doc]), _page([])] + struct_repo.delete_by_ids.return_value = DeleteResponse(num_deleted=2) + contrib_repo.delete_contributions.side_effect = [_delete_result(1), _delete_result(0)] + + await svc.delete_contributions(_noop_filter()) + + called_ids = struct_repo.delete_by_ids.await_args.args[0] + assert set(called_ids) == {s1, s2} + + async def test_child_counts_accumulated_across_types(self): + svc, contrib_repo, struct_repo, table_repo, attach_repo, _ = _make_service() + doc = _contrib_doc(structures=[_oid()], tables=[_oid(), _oid()], attachments=[_oid()]) + contrib_repo.get_contributions.side_effect = [_page([doc]), _page([])] + struct_repo.delete_by_ids.return_value = DeleteResponse(num_deleted=1) + table_repo.delete_by_ids.return_value = DeleteResponse(num_deleted=2) + attach_repo.delete_by_ids.return_value = DeleteResponse(num_deleted=1) + contrib_repo.delete_contributions.side_effect = [_delete_result(1), _delete_result(0)] + + summary = await svc.delete_contributions(_noop_filter()) + + assert summary.num_children_deleted == 4 + + async def test_contributions_deleted_by_id_in_of_page(self): + svc, contrib_repo, *_ = _make_service() + ids = [_oid(), _oid()] + docs = [_contrib_doc(id_=i) for i in ids] + contrib_repo.get_contributions.side_effect = [_page(docs), _page([])] + contrib_repo.delete_contributions.side_effect = [_delete_result(2), _delete_result(0)] + + await svc.delete_contributions(_noop_filter()) + + first_call_filter = contrib_repo.delete_contributions.await_args_list[0].args[0] + assert set(first_call_filter.id__in) == set(ids) + + +class TestDeleteContributionsMultiPage: + async def test_loops_until_page_empty(self): + svc, contrib_repo, *_ = _make_service() + contrib_repo.get_contributions.side_effect = [ + _page([_contrib_doc() for _ in range(2)]), + _page([_contrib_doc()]), + _page([]), + ] + contrib_repo.delete_contributions.side_effect = [ + _delete_result(2), + _delete_result(1), + _delete_result(0), + ] + + summary = await svc.delete_contributions(_noop_filter()) + + assert summary.num_deleted == 3 + assert contrib_repo.get_contributions.await_count == 3 + + async def test_children_accumulate_across_pages(self): + svc, contrib_repo, struct_repo, *_ = _make_service() + contrib_repo.get_contributions.side_effect = [ + _page([_contrib_doc(structures=[_oid()])]), + _page([_contrib_doc(structures=[_oid()])]), + _page([]), + ] + struct_repo.delete_by_ids.return_value = DeleteResponse(num_deleted=1) + contrib_repo.delete_contributions.side_effect = [ + _delete_result(1), + _delete_result(1), + _delete_result(0), + ] + + summary = await svc.delete_contributions(_noop_filter()) + + assert summary.num_children_deleted == 2 + assert struct_repo.delete_by_ids.await_count == 2 + + +class TestDeleteContributionsNoneComponents: + """ContributionOut leaves unset component fields as None (not []). + + The cascade loop must tolerate None rather than raising TypeError on iteration. + """ + + async def test_none_component_fields_do_not_raise(self): + svc, contrib_repo, struct_repo, table_repo, attach_repo, _ = _make_service() + doc = SimpleNamespace(id=_oid(), structures=None, tables=None, attachments=None) + contrib_repo.get_contributions.side_effect = [_page([doc]), _page([])] + contrib_repo.delete_contributions.side_effect = [_delete_result(1), _delete_result(0)] + + summary = await svc.delete_contributions(_noop_filter()) + + assert summary.num_deleted == 1 + assert summary.num_children_deleted == 0 + struct_repo.delete_by_ids.assert_not_called() + table_repo.delete_by_ids.assert_not_called() + attach_repo.delete_by_ids.assert_not_called() diff --git a/mpcontribs-api/tests/unit/domains/test_contributions_models.py b/mpcontribs-api/tests/unit/domains/test_contributions_models.py new file mode 100644 index 000000000..acabd1825 --- /dev/null +++ b/mpcontribs-api/tests/unit/domains/test_contributions_models.py @@ -0,0 +1,287 @@ +from datetime import UTC, datetime + +import pytest +from beanie import PydanticObjectId +from pydantic import ValidationError as PydanticValidationError + +from mpcontribs_api.authz import User +from mpcontribs_api.domains.contributions.repository import MongoDbContributionRepository + +from mpcontribs_api.domains.contributions.models import ( + Contribution, + ContributionFilter, + ContributionIn, + ContributionOut, + ContributionPatch, +) +from mpcontribs_api.exceptions import ValidationError + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + + +def _make_contribution_in(**overrides) -> ContributionIn: + """Build a minimal valid ContributionIn for testing.""" + defaults: dict = { + "_id": PydanticObjectId(), + "project": "test-project", + "identifier": "mp-1234", + "formula": "Fe2O3", + "data": {"band_gap": {"value": 2.1, "unit": "eV"}}, + } + defaults.update(overrides) + return ContributionIn(**defaults) + + +# --------------------------------------------------------------------------- +# ContributionBase field validation +# --------------------------------------------------------------------------- + + +class TestContributionBase: + def test_required_fields_set_correctly(self): + contrib = ContributionIn( + **{ + "_id": PydanticObjectId(), + "project": "mp-project", + "identifier": "mp-001", + "formula": "Fe2O3", + "data": {}, + } + ) + assert contrib.project == "mp-project" + assert contrib.identifier == "mp-001" + assert contrib.formula == "Fe2O3" + assert contrib.data == {} + + def test_defaults(self): + contrib = _make_contribution_in() + assert contrib.needs_build is True + assert contrib.structures is None + assert contrib.tables is None + assert contrib.attachments is None + + def test_last_modified_defaults_to_now(self): + before = datetime.now(UTC) + contrib = _make_contribution_in() + after = datetime.now(UTC) + assert before <= contrib.last_modified <= after + + def test_missing_project_raises(self): + with pytest.raises(PydanticValidationError): + ContributionIn( + **{ + "_id": PydanticObjectId(), + "identifier": "mp-001", + "formula": "Fe", + "data": {}, + } + ) + + def test_missing_formula_raises(self): + with pytest.raises(PydanticValidationError): + ContributionIn( + **{ + "_id": PydanticObjectId(), + "project": "proj", + "identifier": "mp-001", + "data": {}, + } + ) + + def test_data_can_be_empty_dict(self): + contrib = _make_contribution_in(data={}) + assert contrib.data == {} + + def test_data_accepts_nested_structure(self): + nested = {"band_gap": {"value": 1.5, "unit": "eV"}, "volume": 42.3} + contrib = _make_contribution_in(data=nested) + assert contrib.data["band_gap"]["value"] == 1.5 + + def test_data_depth_validation(self): + max_nesting = {"lvl_1": {"lvl_2": {"lvl_3": {"lvl_4": {"lvl_5": {"lvl_6": {"lvl_7": "pass"}}}}}}} + invalid_nesting = {"lvl_1": {"lvl_2": {"lvl_3": {"lvl_4": {"lvl_5": {"lvl_6": {"lvl_7": {"lvl_8": "fail"}}}}}}}} + _make_contribution_in(data=max_nesting) + assert True + with pytest.raises(ValidationError, match="Depth of Contribution.data"): + _make_contribution_in(data=invalid_nesting) + + def test_data_key_validation(self): + valid_punctuation = {"test*/|": "pass"} + invalid_punctuation = {"test.": "fail"} + too_many_pipes = {"test||": "fail"} + non_ascii = {"ΔE": "fail"} + _make_contribution_in(data=valid_punctuation) + assert True + with pytest.raises(ValidationError, match="Punctuation found in Contribution.data keys"): + _make_contribution_in(data=invalid_punctuation) + with pytest.raises(ValidationError, match="Punctuation found in Contribution.data keys"): + _make_contribution_in(data=too_many_pipes) + with pytest.raises(ValidationError, match="Non-ASCII key found in Contribution.data"): + _make_contribution_in(data=non_ascii) + + # There isn't currently value validation. This is to check that that is true + def test_data_value_validation(self): + pipes_in_values = {"test": "pass||"} + punctuation_in_values = {"test": "pass."} + ascii_in_values = {"test": "Δ"} + _make_contribution_in(data=pipes_in_values) + _make_contribution_in(data=punctuation_in_values) + _make_contribution_in(data=ascii_in_values) + assert True + +# --------------------------------------------------------------------------- +# Contribution.from_input_model +# --------------------------------------------------------------------------- + + +class TestContributionFromInputModel: + def test_is_public_forced_to_false(self): + contrib_in = _make_contribution_in() + contribution = Contribution.from_input_model(contrib_in) + assert contribution.is_public is False + + def test_is_public_false_even_if_input_had_is_public(self): + # ContributionIn (ContributionBase) has no is_public field, but we ensure + # from_input_model always sets it to False on the resulting Contribution. + contrib_in = _make_contribution_in() + contribution = Contribution.from_input_model(contrib_in) + assert contribution.is_public is False + + def test_fields_carried_over(self): + contrib_in = _make_contribution_in(project="my-project", formula="SiO2") + contribution = Contribution.from_input_model(contrib_in) + assert contribution.project == "my-project" + assert contribution.formula == "SiO2" + + def test_data_carried_over(self): + data = {"key": "value"} + contrib_in = _make_contribution_in(data=data) + contribution = Contribution.from_input_model(contrib_in) + assert contribution.data == data + + +# --------------------------------------------------------------------------- +# ContributionOut — optional fields +# --------------------------------------------------------------------------- + + +class TestContributionOut: + def test_all_fields_optional(self): + out = ContributionOut() + assert out.id is None + assert out.project is None + assert out.formula is None + assert out.is_public is None + assert out.data is None + + def test_partial_population(self): + out = ContributionOut(project="mp-proj", formula="Li2O") + assert out.project == "mp-proj" + assert out.formula == "Li2O" + assert out.identifier is None + + def test_is_public_field(self): + out = ContributionOut(is_public=True) + assert out.is_public is True + + def test_data_field(self): + data = {"energy": -3.5} + out = ContributionOut(data=data) + assert out.data == data + + +# --------------------------------------------------------------------------- +# ContributionPatch — sparse update model +# --------------------------------------------------------------------------- + + +class TestContributionPatch: + def test_all_fields_optional(self): + patch = ContributionPatch() + assert patch.project is None + assert patch.identifier is None + assert patch.formula is None + assert patch.data is None + + def test_partial_patch(self): + patch = ContributionPatch(formula="Li2O", needs_build=False) + assert patch.formula == "Li2O" + assert patch.needs_build is False + assert patch.project is None + + def test_data_can_be_set(self): + patch = ContributionPatch(data={"new_key": 42}) + assert patch.data == {"new_key": 42} + + +# --------------------------------------------------------------------------- +# MongoDbContributionRepository._build_scope (pure logic, no DB needed) +# --------------------------------------------------------------------------- + +_ADMIN = User(username="google:admin@example.com", groups=frozenset({"admin"})) +_ALICE = User(username="google:alice@example.com", groups=frozenset({"mp-team"})) +_ANON = User() + + +class TestContributionRepoScope: + def test_admin_scope_is_empty(self): + assert MongoDbContributionRepository._build_scope(_ADMIN) == {} + + def test_anon_scope_has_or_clause(self): + scope = MongoDbContributionRepository._build_scope(_ANON) + assert "$or" in scope + + def test_anon_scope_includes_is_public_true(self): + ors = MongoDbContributionRepository._build_scope(_ANON)["$or"] + assert any(c == {"is_public": True} for c in ors) + + def test_anon_scope_has_no_group_id_clause(self): + ors = MongoDbContributionRepository._build_scope(_ANON)["$or"] + assert not any("_id" in c for c in ors) + + def test_authed_user_scope_includes_is_public(self): + ors = MongoDbContributionRepository._build_scope(_ALICE)["$or"] + assert any(c == {"is_public": True} for c in ors) + + def test_authed_user_with_groups_has_group_id_clause(self): + user = User(username="u@example.com", groups=frozenset({"g1", "g2"})) + ors = MongoDbContributionRepository._build_scope(user)["$or"] + group_clause = next((c for c in ors if "project" in c), None) + assert group_clause is not None + assert set(group_clause["project"]["$in"]) == {"g1", "g2"} + + def test_authed_user_no_groups_has_no_group_id_clause(self): + user = User(username="u@example.com", groups=frozenset()) + ors = MongoDbContributionRepository._build_scope(user)["$or"] + assert not any("_id" in c for c in ors) + + +# --------------------------------------------------------------------------- +# ContributionFilter.convert_str_to_oid +# --------------------------------------------------------------------------- + + +class TestContributionFilterIdValidator: + def test_empty_filter_id_is_none(self): + assert ContributionFilter().id is None + + def test_str_converted_to_object_id(self): + oid = PydanticObjectId() + filter = ContributionFilter(id=str(oid)) + assert isinstance(filter.id, PydanticObjectId) + assert filter.id == oid + + def test_object_id_passthrough(self): + oid = PydanticObjectId() + assert ContributionFilter(id=oid).id == oid + + # RED: a malformed id currently leaks bson.errors.InvalidId (not a + # ValueError subclass), which the exception handlers don't map — so + # `DELETE /contributions/{bad-id}` would 500 instead of 422. Intended + # behavior is a controlled validation error, matching how + # MongoDbRepository._convert_object_id handles the same input. + def test_malformed_id_raises_validation_error(self): + with pytest.raises(ValidationError): + ContributionFilter(id="not-an-object-id") diff --git a/mpcontribs-api/tests/unit/domains/test_projects_models.py b/mpcontribs-api/tests/unit/domains/test_projects_models.py new file mode 100644 index 000000000..b874091e7 --- /dev/null +++ b/mpcontribs-api/tests/unit/domains/test_projects_models.py @@ -0,0 +1,256 @@ +import pytest +from pydantic import ValidationError as PydanticValidationError + +from mpcontribs_api.domains.projects.models import ( + Column, + Project, + ProjectIn, + ProjectOut, + ProjectPatch, + Reference, + Stats, +) + +# --------------------------------------------------------------------------- +# Column +# --------------------------------------------------------------------------- + + +class TestColumn: + def test_path_only(self): + col = Column(path="data.band_gap") + assert col.path == "data.band_gap" + assert col.min is None + assert col.max is None + assert col.unit is None + + def test_full_column(self): + col = Column(path="data.band_gap", min=0.0, max=10.0, unit="eV") + assert col.min == 0.0 + assert col.max == 10.0 + assert col.unit == "eV" + + def test_segments_single(self): + col = Column(path="energy") + assert col.segments == ("energy",) + + def test_segments_dotted(self): + col = Column(path="data.band_gap.value") + assert col.segments == ("data", "band_gap", "value") + + def test_segments_two_level(self): + col = Column(path="data.volume") + assert col.segments == ("data", "volume") + + +# --------------------------------------------------------------------------- +# Stats +# --------------------------------------------------------------------------- + + +class TestStats: + def test_valid_stats(self): + stats = Stats(columns=3, contributions=100, tables=5, structures=10, attachments=2, size=1024.5) + assert stats.columns == 3 + assert stats.contributions == 100 + assert stats.size == 1024.5 + + def test_zero_values_allowed(self): + stats = Stats(columns=0, contributions=0, tables=0, structures=0, attachments=0, size=0.0) + assert stats.contributions == 0 + + def test_missing_field_raises(self): + with pytest.raises(PydanticValidationError): + Stats(columns=1, contributions=2, tables=3, structures=4, attachments=5) # missing size + + +# --------------------------------------------------------------------------- +# Reference +# --------------------------------------------------------------------------- + + +class TestReference: + def test_valid_reference(self): + ref = Reference(label="Paper", url="https://doi.org/10.1000/xyz") + assert ref.label == "Paper" + assert str(ref.url).startswith("https://doi.org") + + def test_invalid_url_raises(self): + with pytest.raises(PydanticValidationError): + Reference(label="Paper", url="not-a-url") + + def test_missing_label_raises(self): + with pytest.raises(PydanticValidationError): + Reference(url="https://example.com") # type: ignore[call-arg] + + +# --------------------------------------------------------------------------- +# ProjectOut — optional fields, extra ignored +# --------------------------------------------------------------------------- + + +class TestProjectOut: + def test_all_fields_optional(self): + out = ProjectOut() + assert out.id is None + assert out.title is None + assert out.authors is None + assert out.stats is None + + def test_extra_fields_ignored(self): + out = ProjectOut(title="My Project", _unknown_field="ignored") # type: ignore[call-arg] + assert out.title == "My Project" + + def test_with_stats(self): + stats = Stats(columns=1, contributions=2, tables=0, structures=0, attachments=0, size=512.0) + out = ProjectOut(title="My Project", stats=stats) + assert out.stats is not None + assert out.stats.contributions == 2 + + def test_boolean_fields(self): + out = ProjectOut(is_public=True, is_approved=False) + assert out.is_public is True + assert out.is_approved is False + + def test_license_values(self): + out_cca4 = ProjectOut(license="CCA4") + out_ccpd = ProjectOut(license="CCPD") + assert out_cca4.license == "CCA4" + assert out_ccpd.license == "CCPD" + + def test_invalid_license_raises(self): + with pytest.raises(PydanticValidationError): + ProjectOut(license="MIT") + + +# --------------------------------------------------------------------------- +# ProjectOut — field projection helpers (inherited from SparseFieldsModel) +# --------------------------------------------------------------------------- + + +class TestProjectOutProjection: + def test_parse_fields_none_returns_none(self): + assert ProjectOut.parse_fields(None) is None + + def test_parse_fields_valid_field(self): + result = ProjectOut.parse_fields(["title"]) + assert result is not None + assert "title" in result + + def test_parse_fields_multiple_fields(self): + result = ProjectOut.parse_fields(["title", "authors", "is_public"]) + assert result is not None + assert "title" in result + assert "authors" in result + assert "is_public" in result + + def test_parse_fields_unknown_raises(self): + from mpcontribs_api.exceptions import ValidationError as AppValidationError + + with pytest.raises(AppValidationError): + ProjectOut.parse_fields(["nonexistent_field"]) + + def test_projection_none_returns_self(self): + assert ProjectOut.projection(None) is ProjectOut + + def test_projection_with_fields(self): + fields = ProjectOut.parse_fields(["title", "authors"]) + projected = ProjectOut.projection(fields) + assert projected is not ProjectOut + assert hasattr(projected.Settings, "projection") + + +# --------------------------------------------------------------------------- +# ProjectPatch +# --------------------------------------------------------------------------- + + +class TestProjectPatch: + def test_all_optional(self): + patch = ProjectPatch() + assert patch.title is None + assert patch.authors is None + assert patch.owner is None + + def test_partial_update(self): + patch = ProjectPatch(title="Updated Title", is_public=True) + assert patch.title == "Updated Title" + assert patch.is_public is True + + def test_invalid_short_str_for_title_raises(self): + with pytest.raises(PydanticValidationError): + ProjectPatch(title="ab") # too short + + def test_default_lists_are_empty(self): + patch = ProjectPatch() + assert patch.references == [] + assert patch.columns == [] + + def test_invalid_license_raises(self): + with pytest.raises(PydanticValidationError): + ProjectPatch(license="GPL") + + +# --------------------------------------------------------------------------- +# Project.from_input_model (smoke-test via ProjectIn) +# --------------------------------------------------------------------------- + + +VALID_STATS = Stats(columns=0, contributions=0, tables=0, structures=0, attachments=0, size=0.0) + + +class TestProjectFromInputModel: + def _make_input(self, **overrides): + defaults = { + "_id": "test-proj", + "title": "Test Project", + "authors": "Alice, Bob", + "description": "A test project", + "owner": "google:alice@example.com", + "unique_identifiers": True, + "stats": VALID_STATS, + } + defaults.update(overrides) + return ProjectIn(**defaults) + + def test_from_input_model_creates_project(self): + project_in = self._make_input() + project = Project.from_input_model(project_in) + assert isinstance(project, Project) + assert project.id == "test-proj" + assert project.title == "Test Project" + + def test_from_input_model_preserves_owner(self): + project_in = self._make_input(owner="github:bob@github.com") + project = Project.from_input_model(project_in) + assert project.owner == "github:bob@github.com" + + def test_from_input_model_defaults(self): + project_in = self._make_input() + project = Project.from_input_model(project_in) + assert project.is_public is False + assert project.is_approved is False + assert project.references == [] + assert project.columns == [] + + +# --------------------------------------------------------------------------- +# Project.decode_cursor (string-id override) +# --------------------------------------------------------------------------- + + +class TestProjectDecodeCursor: + def test_round_trips_string_id(self): + from mpcontribs_api.pagination import encode_cursor + + assert Project.decode_cursor(encode_cursor("my-project")) == "my-project" + + def test_returns_plain_str_not_object_id(self): + from mpcontribs_api.pagination import encode_cursor + + decoded = Project.decode_cursor(encode_cursor("solar-cells")) + assert type(decoded) is str + + def test_malformed_cursor_raises_value_error(self): + with pytest.raises(ValueError): + Project.decode_cursor("!!!not-base64!!!") diff --git a/mpcontribs-api/tests/unit/domains/test_shared_bulk.py b/mpcontribs-api/tests/unit/domains/test_shared_bulk.py new file mode 100644 index 000000000..32b900839 --- /dev/null +++ b/mpcontribs-api/tests/unit/domains/test_shared_bulk.py @@ -0,0 +1,120 @@ +from beanie import PydanticObjectId + +from mpcontribs_api.domains._shared.bulk import ( + BulkDeleteSummary, + BulkFailure, + BulkWriteSummary, + bulk_failure_from_exception, +) +from mpcontribs_api.exceptions import ConflictError, NotFoundError, ValidationError + +# --------------------------------------------------------------------------- +# BulkFailure +# --------------------------------------------------------------------------- + + +class TestBulkFailure: + def test_required_fields(self): + failure = BulkFailure(index=3, error_code="conflict", message="duplicate") + assert failure.index == 3 + assert failure.error_code == "conflict" + assert failure.message == "duplicate" + + def test_identifier_defaults_to_none(self): + failure = BulkFailure(index=0, error_code="x", message="y") + assert failure.identifier is None + + def test_identifier_carries_arbitrary_dict(self): + identifier = {"project": "proj", "identifier": "mp-1"} + failure = BulkFailure(index=0, identifier=identifier, error_code="x", message="y") + assert failure.identifier == identifier + + +# --------------------------------------------------------------------------- +# BulkWriteSummary +# --------------------------------------------------------------------------- + + +class TestBulkWriteSummary: + def test_fields(self): + summary = BulkWriteSummary[int](total=3, succeeded=[1, 2], failed=[]) + assert summary.total == 3 + assert summary.succeeded == [1, 2] + assert summary.failed == [] + + def test_failed_items_typed(self): + failure = BulkFailure(index=1, error_code="validation_error", message="bad") + summary = BulkWriteSummary[int](total=2, succeeded=[1], failed=[failure]) + assert summary.failed[0].index == 1 + + def test_empty_summary(self): + summary = BulkWriteSummary[int](total=0, succeeded=[], failed=[]) + assert summary.total == 0 + + def test_serialization_shape(self): + failure = BulkFailure(index=0, error_code="conflict", message="dup") + summary = BulkWriteSummary[int](total=1, succeeded=[], failed=[failure]) + dumped = summary.model_dump() + assert dumped == { + "total": 1, + "succeeded": [], + "failed": [{"index": 0, "identifier": None, "error_code": "conflict", "message": "dup"}], + } + + +# --------------------------------------------------------------------------- +# BulkDeleteSummary +# --------------------------------------------------------------------------- + + +class TestBulkDeleteSummary: + def test_fields(self): + summary = BulkDeleteSummary(num_deleted=5, num_children_deleted=12) + assert summary.num_deleted == 5 + assert summary.num_children_deleted == 12 + + def test_zero_counts(self): + summary = BulkDeleteSummary(num_deleted=0, num_children_deleted=0) + assert summary.model_dump() == {"num_deleted": 0, "num_children_deleted": 0} + + +# --------------------------------------------------------------------------- +# bulk_failure_from_exception +# --------------------------------------------------------------------------- + + +class TestBulkFailureFromException: + def test_app_error_uses_its_error_code_and_message(self): + failure = bulk_failure_from_exception(2, None, ConflictError("already exists")) + assert failure.index == 2 + assert failure.error_code == "conflict" + assert failure.message == "already exists" + + def test_not_found_error(self): + failure = bulk_failure_from_exception(0, None, NotFoundError("gone")) + assert failure.error_code == "not_found" + + def test_validation_error(self): + failure = bulk_failure_from_exception(0, None, ValidationError("bad payload")) + assert failure.error_code == "validation_error" + assert failure.message == "bad payload" + + def test_app_error_default_message_is_class_name(self): + failure = bulk_failure_from_exception(0, None, ConflictError()) + assert failure.message == "ConflictError" + + def test_generic_exception_collapses_to_internal_error(self): + failure = bulk_failure_from_exception(1, None, RuntimeError("secret traceback details")) + assert failure.error_code == "internal_error" + + def test_generic_exception_message_is_class_name_only(self): + # Internals must not leak to the client; only the exception class name survives. + failure = bulk_failure_from_exception(1, None, RuntimeError("secret traceback details")) + assert failure.message == "RuntimeError" + assert "secret" not in failure.message + + def test_identifier_threaded_through(self): + identifier = {"id": str(PydanticObjectId())} + failure = bulk_failure_from_exception(4, identifier, ValueError("x")) + assert failure.identifier == identifier + assert failure.index == 4 diff --git a/mpcontribs-api/tests/unit/domains/test_shared_models.py b/mpcontribs-api/tests/unit/domains/test_shared_models.py new file mode 100644 index 000000000..2ba8c3c9d --- /dev/null +++ b/mpcontribs-api/tests/unit/domains/test_shared_models.py @@ -0,0 +1,112 @@ +import pytest +from beanie import PydanticObjectId +from pymongo.results import DeleteResult + +from mpcontribs_api.domains._shared.models import ( + BaseDocumentWithInput, + DeleteResponse, + DocumentOut, +) +from mpcontribs_api.domains.attachments.models import Attachment, AttachmentIn +from mpcontribs_api.pagination import encode_cursor + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + + +def _attachment_in(**overrides) -> AttachmentIn: + payload = { + "name": "data.csv.gz", + "mime": "application/gzip", + "content": 1, + } + payload.update(overrides) + return AttachmentIn(**payload) + + +class _OidOut(DocumentOut[PydanticObjectId]): + name: str | None = None + + +# --------------------------------------------------------------------------- +# Component.from_input (server-assigned id, computed md5) +# --------------------------------------------------------------------------- + + +class TestComponentFromInput: + def test_returns_document_class_instance(self): + doc = Attachment.from_input(_attachment_in()) + assert isinstance(doc, Attachment) + + def test_content_carried_id_assigned_md5_computed(self): + doc = Attachment.from_input(_attachment_in(name="x.gz")) + assert doc.name == "x.gz" + assert doc.mime == "application/gzip" + assert doc.content == 1 + assert doc.id is not None + assert len(doc.md5) == 32 + + +# --------------------------------------------------------------------------- +# BaseDocumentWithInput.decode_cursor +# --------------------------------------------------------------------------- + + +class TestDecodeCursor: + def test_round_trips_object_id(self): + oid = PydanticObjectId() + decoded = BaseDocumentWithInput.decode_cursor(encode_cursor(str(oid))) + assert decoded == oid + + def test_returns_pydantic_object_id(self): + cursor = encode_cursor(str(PydanticObjectId())) + assert isinstance(BaseDocumentWithInput.decode_cursor(cursor), PydanticObjectId) + + def test_malformed_base64_raises_value_error(self): + with pytest.raises(ValueError): + BaseDocumentWithInput.decode_cursor("!!!not-base64!!!") + + def test_callable_off_concrete_subclass(self): + oid = PydanticObjectId() + assert Attachment.decode_cursor(encode_cursor(str(oid))) == oid + + +# --------------------------------------------------------------------------- +# DocumentOut +# --------------------------------------------------------------------------- + + +class TestDocumentOut: + def test_id_defaults_to_none(self): + assert _OidOut().id is None + + def test_populates_from_mongo_alias(self): + oid = PydanticObjectId() + out = _OidOut.model_validate({"_id": oid}) + assert out.id == oid + + def test_serializes_under_id_not_underscore_id(self): + oid = PydanticObjectId() + dumped = _OidOut.model_validate({"_id": oid, "name": "n"}).model_dump(by_alias=True) + assert dumped["id"] == oid + assert "_id" not in dumped + + +# --------------------------------------------------------------------------- +# DeleteResponse.from_delete_result +# --------------------------------------------------------------------------- + + +class TestDeleteResponse: + def test_from_delete_result(self): + result = DeleteResult({"n": 3}, acknowledged=True) + assert DeleteResponse.from_delete_result(result).num_deleted == 3 + + def test_zero_deleted(self): + result = DeleteResult({"n": 0}, acknowledged=True) + assert DeleteResponse.from_delete_result(result).num_deleted == 0 + + def test_serialization_shape(self): + result = DeleteResult({"n": 7}, acknowledged=True) + assert DeleteResponse.from_delete_result(result).model_dump() == {"num_deleted": 7} diff --git a/mpcontribs-api/tests/unit/domains/test_shared_repository_download.py b/mpcontribs-api/tests/unit/domains/test_shared_repository_download.py new file mode 100644 index 000000000..b32417ef3 --- /dev/null +++ b/mpcontribs-api/tests/unit/domains/test_shared_repository_download.py @@ -0,0 +1,349 @@ +import csv +import gzip +import io +import json +from collections.abc import AsyncIterable, AsyncIterator +from datetime import datetime, timezone +from types import SimpleNamespace +from typing import Any +from unittest.mock import MagicMock + +import pytest +from beanie import PydanticObjectId +from pydantic import BaseModel + +from mpcontribs_api.authz import User +from mpcontribs_api.domains._shared.repository import MongoDbRepository +from mpcontribs_api.domains._shared.types import DownloadFormat, ShortMimeFormat + +# --------------------------------------------------------------------------- +# Test doubles +# --------------------------------------------------------------------------- + + +class _Out(BaseModel): + """Minimal output model with scalar fields.""" + + a: int + b: str + + +class _OutWithData(BaseModel): + """Output model whose ``data`` column holds a nested dict (CSV edge case).""" + + name: str + data: dict + + +class _FakeQuery: + """Async-iterable stand-in for a Beanie find() query.""" + + def __init__(self, rows: list[Any]) -> None: + self._rows = rows + + async def __aiter__(self) -> AsyncIterator[Any]: + for row in self._rows: + yield row + + +class _FakeFilter: + """Stand-in for a fastapi-filter Filter. + + ``filter()`` ignores the base query and returns a fake query over the seeded + rows; ``sort()`` is a passthrough; ``model_dump()`` returns the configured + payload (used by ``download`` when building the cache key). + """ + + def __init__(self, rows: list[Any], dump: dict[str, Any] | None = None) -> None: + self._rows = rows + self._dump = {} if dump is None else dump + + def filter(self, _base: Any) -> _FakeQuery: + return _FakeQuery(self._rows) + + def sort(self, query: _FakeQuery) -> _FakeQuery: + return query + + def model_dump(self) -> dict[str, Any]: + return self._dump + + +class _FakeRepo(MongoDbRepository): + """Concrete repository binding just enough to exercise the shared download core.""" + + document_model = MagicMock() + out_model = _Out + + @staticmethod + def _build_scope(user: User) -> dict[str, Any]: + return {} + + +def _repo(out_model: type[BaseModel] = _Out) -> _FakeRepo: + repo = _FakeRepo(User()) + repo.out_model = out_model # type: ignore[assignment] + repo.document_model = MagicMock() # type: ignore[assignment] + return repo + + +async def _aiter(items: list[Any]) -> AsyncIterator[Any]: + for item in items: + yield item + + +async def _collect(stream: AsyncIterable[bytes]) -> bytes: + chunks: list[bytes] = [] + async for chunk in stream: + chunks.append(chunk) + return b"".join(chunks) + + +# =========================================================================== +# _serialize_jsonl +# =========================================================================== + + +class TestSerializeJsonl: + async def test_one_line_per_row(self): + rows = [_Out(a=1, b="x"), _Out(a=2, b="y")] + out = await _collect(MongoDbRepository._serialize_jsonl(_aiter(rows))) + assert out.count(b"\n") == 2 + + async def test_each_line_round_trips_to_row(self): + rows = [_Out(a=1, b="x"), _Out(a=2, b="y")] + out = await _collect(MongoDbRepository._serialize_jsonl(_aiter(rows))) + parsed = [json.loads(line) for line in out.splitlines()] + assert parsed == [{"a": 1, "b": "x"}, {"a": 2, "b": "y"}] + + async def test_every_line_terminated_with_newline(self): + rows = [_Out(a=1, b="x"), _Out(a=2, b="y")] + out = await _collect(MongoDbRepository._serialize_jsonl(_aiter(rows))) + assert out.endswith(b"\n") + + async def test_empty_input_yields_nothing(self): + out = await _collect(MongoDbRepository._serialize_jsonl(_aiter([]))) + assert out == b"" + + async def test_unicode_payload_preserved(self): + rows = [_Out(a=1, b="café—ü")] + out = await _collect(MongoDbRepository._serialize_jsonl(_aiter(rows))) + assert json.loads(out)["b"] == "café—ü" + + +# =========================================================================== +# _serialize_csv +# =========================================================================== + + +def _parse_csv(raw: bytes) -> list[dict[str, str]]: + return list(csv.DictReader(io.StringIO(raw.decode()))) + + +class TestSerializeCsv: + async def test_header_written_once(self): + rows = [_Out(a=1, b="x"), _Out(a=2, b="y")] + raw = await _collect(MongoDbRepository._serialize_csv(_aiter(rows), None)) + # Header appears exactly once even across multiple rows. + assert raw.decode().count("a,b") == 1 + + async def test_columns_default_to_first_row_keys_when_no_fields(self): + rows = [_Out(a=1, b="x")] + raw = await _collect(MongoDbRepository._serialize_csv(_aiter(rows), None)) + reader = csv.reader(io.StringIO(raw.decode())) + assert next(reader) == ["a", "b"] + + async def test_columns_follow_sorted_fields_when_given(self): + rows = [_Out(a=1, b="x")] + raw = await _collect(MongoDbRepository._serialize_csv(_aiter(rows), frozenset({"b", "a"}))) + reader = csv.reader(io.StringIO(raw.decode())) + assert next(reader) == ["a", "b"] + + async def test_extra_fields_are_ignored(self): + # 'b' is not in the requested field set -> dropped from output. + rows = [_Out(a=1, b="x")] + raw = await _collect(MongoDbRepository._serialize_csv(_aiter(rows), frozenset({"a"}))) + parsed = _parse_csv(raw) + assert parsed == [{"a": "1"}] + + async def test_all_rows_emitted(self): + rows = [_Out(a=i, b=str(i)) for i in range(5)] + raw = await _collect(MongoDbRepository._serialize_csv(_aiter(rows), None)) + assert len(_parse_csv(raw)) == 5 + + async def test_no_row_bleed_between_chunks(self): + # Each yielded chunk after the header must contain exactly one row, proving + # the shared StringIO buffer is truncated between iterations. + rows = [_Out(a=1, b="x"), _Out(a=2, b="y")] + chunks = [c async for c in MongoDbRepository._serialize_csv(_aiter(rows), None)] + # First chunk: header + row 1; subsequent chunks: one row each. + assert b"2,y" not in chunks[0] + + async def test_empty_input_yields_no_bytes(self): + raw = await _collect(MongoDbRepository._serialize_csv(_aiter([]), None)) + assert raw == b"" + + async def test_dict_value_serialized_as_json(self): + """Dict-valued columns are emitted as JSON, not Python repr. + + ``model_dump(mode="json")`` leaves nested dicts as dict objects; the serializer + JSON-encodes them so the cell is valid JSON a consumer can round-trip (rather + than ``str(dict)``, the single-quoted Python repr). + """ + rows = [_OutWithData(name="r1", data={"k": "v", "n": 1})] + raw = await _collect(MongoDbRepository._serialize_csv(_aiter(rows), None)) + cell = _parse_csv(raw)[0]["data"] + assert json.loads(cell) == {"k": "v", "n": 1} + + +# =========================================================================== +# _get_serializer +# =========================================================================== + + +class TestGetSerializer: + @pytest.mark.parametrize("format", list(DownloadFormat)) + async def test_every_format_dispatches_to_a_usable_serializer(self, format: DownloadFormat): + """Every ``DownloadFormat`` member maps to a serializer of the expected shape. + + ``_get_serializer`` has no default case, so an unhandled member would silently + return ``None``. Parametrizing over every member guarantees the match stays + exhaustive: adding a format without a matching case fails here rather than at + request time. The returned object is uniformly a callable taking the row stream + and yielding ``bytes``, regardless of which format produced it. + """ + repo = _repo() + serializer = repo._get_serializer(format, None) + assert callable(serializer) + raw = await _collect(serializer(_aiter([_Out(a=1, b="x")]))) + assert isinstance(raw, bytes) and raw + + async def test_jsonl_dispatches_to_jsonl_output(self): + repo = _repo() + serializer = repo._get_serializer(DownloadFormat.JSONL, None) + raw = await _collect(serializer(_aiter([_Out(a=1, b="x")]))) + assert json.loads(raw) == {"a": 1, "b": "x"} + + async def test_csv_dispatches_to_csv_output_and_threads_fields(self): + # The fields passed to _get_serializer must reach the CSV serializer: 'b' is + # dropped because only 'a' was requested. + repo = _repo() + serializer = repo._get_serializer(DownloadFormat.CSV, frozenset({"a"})) + raw = await _collect(serializer(_aiter([_Out(a=1, b="x")]))) + assert _parse_csv(raw) == [{"a": "1"}] + + +# =========================================================================== +# _hash_payload +# =========================================================================== + + +class TestHashPayload: + def test_is_deterministic(self): + repo = _repo() + payload = {"format": "jsonl", "fields": ["a", "b"]} + assert repo._hash_payload(payload) == repo._hash_payload(payload) + + def test_independent_of_key_order(self): + repo = _repo() + assert repo._hash_payload({"a": 1, "b": 2}) == repo._hash_payload({"b": 2, "a": 1}) + + def test_sensitive_to_value_changes(self): + repo = _repo() + assert repo._hash_payload({"a": 1}) != repo._hash_payload({"a": 2}) + + def test_returns_sha256_hex(self): + repo = _repo() + digest = repo._hash_payload({"a": 1}) + assert len(digest) == 64 + assert all(c in "0123456789abcdef" for c in digest) + + def test_object_id_filter_is_hashable(self): + """Filters carrying an ObjectId hash without raising. + + ``download`` hashes ``filter.model_dump()`` which, for an ``id__in`` filter, + contains PydanticObjectId values. ``_hash_payload`` passes ``default=str`` so + these stringify into a stable key instead of raising ``TypeError``. + """ + repo = _repo() + payload = {"filter": {"id__in": [PydanticObjectId(), PydanticObjectId()]}} + digest = repo._hash_payload(payload) + assert len(digest) == 64 + + def test_datetime_filter_is_hashable(self): + """Filters carrying a datetime hash without raising (see above).""" + repo = _repo() + payload = {"filter": {"created__gte": datetime(2024, 1, 1, tzinfo=timezone.utc)}} + digest = repo._hash_payload(payload) + assert len(digest) == 64 + + +# =========================================================================== +# download (end-to-end: query -> serialize -> gzip stream) +# =========================================================================== + + +class TestDownload: + async def test_jsonl_stream_decompresses_to_rows(self): + """The gzip stream decompresses cleanly to the JSONL payload. + + ``download`` flushes the zlib gzip compressor after the final chunk so the + trailing buffered bytes and the gzip footer (CRC32 + ISIZE) are emitted. + Regression guard: without the flush the member is truncated and + ``gzip.decompress`` raises. + """ + repo = _repo(_Out) + filter = _FakeFilter(rows=[SimpleNamespace(a=1, b="x"), SimpleNamespace(a=2, b="y")]) + stream = repo.download( + format=DownloadFormat.JSONL, + short_mime=ShortMimeFormat.GZ, + ignore_cache=True, + filter=filter, # type: ignore[arg-type] + fields=None, + s3=MagicMock(), + bucket_name="test-bucket", + key_name="test-key", + ) + compressed = await _collect(stream) + decompressed = gzip.decompress(compressed) + parsed = [json.loads(line) for line in decompressed.splitlines()] + assert parsed == [{"a": 1, "b": "x"}, {"a": 2, "b": "y"}] + + async def test_csv_stream_decompresses_to_rows(self): + """Same gzip flush guard, exercised through the CSV serializer.""" + repo = _repo(_Out) + filter = _FakeFilter(rows=[SimpleNamespace(a=1, b="x"), SimpleNamespace(a=2, b="y")]) + stream = repo.download( + format=DownloadFormat.CSV, + short_mime=ShortMimeFormat.GZ, + ignore_cache=True, + filter=filter, # type: ignore[arg-type] + fields=frozenset({"a", "b"}), + s3=MagicMock(), + bucket_name="test-bucket", + key_name="test-key", + ) + compressed = await _collect(stream) + decompressed = gzip.decompress(compressed) + assert _parse_csv(decompressed) == [{"a": "1", "b": "x"}, {"a": "2", "b": "y"}] + + async def test_empty_result_is_valid_empty_gzip(self): + """A download with no matching rows yields zero bytes, which gzip treats as empty. + + Unlike the non-empty cases (which hit the missing-``flush()`` bug), an empty + result never enters the compress loop, so the stream is genuinely empty and + ``gzip.decompress(b"")`` returns ``b""``. Guards that empty downloads stay valid. + """ + repo = _repo(_Out) + filter = _FakeFilter(rows=[]) + stream = repo.download( + format=DownloadFormat.JSONL, + short_mime=ShortMimeFormat.GZ, + ignore_cache=True, + filter=filter, # type: ignore[arg-type] + fields=None, + s3=MagicMock(), + bucket_name="test-bucket", + key_name="test-key", + ) + compressed = await _collect(stream) + assert gzip.decompress(compressed) == b"" diff --git a/mpcontribs-api/tests/unit/domains/test_structures_models.py b/mpcontribs-api/tests/unit/domains/test_structures_models.py new file mode 100644 index 000000000..213724b87 --- /dev/null +++ b/mpcontribs-api/tests/unit/domains/test_structures_models.py @@ -0,0 +1,240 @@ +import polars as pl +import pytest +from beanie import PydanticObjectId +from pydantic import ValidationError as PydanticValidationError +from pymatgen.core import Element + +from mpcontribs_api.domains.structures.models import ( + Lattice, + SiteProperties, + Species, + Structure, + StructureFilter, + StructureIn, + StructureOut, + StructurePatch, +) +from mpcontribs_api.exceptions import ValidationError as AppValidationError + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + + +def _lattice_payload(**overrides) -> dict: + payload = { + "matrix": {"x": [1.0, 0.0, 0.0], "y": [0.0, 1.0, 0.0], "z": [0.0, 0.0, 1.0]}, + "pbc": [True, True, True], + "a": 1.0, + "b": 1.0, + "c": 1.0, + "alpha": 90.0, + "beta": 90.0, + "gamma": 90.0, + "volume": 1.0, + } + payload.update(overrides) + return payload + + +def _site_payload(**overrides) -> dict: + payload = { + "species": [{"element": "Fe", "occu": 1}], + "abc": [0.0, 0.0, 0.0], + "properties": {"magmom": 2.2}, + "label": "Fe", + "xyz": [0.0, 0.0, 0.0], + } + payload.update(overrides) + return payload + + +def _structure_payload(**overrides) -> dict: + payload = { + "_id": PydanticObjectId(), + "name": "Fe2O3", + "md5": "f" * 32, + "lattice": _lattice_payload(), + "sites": [_site_payload()], + "charge": 0.0, + "cif": "data_Fe2O3\n_cell_length_a 1.0\n", + } + payload.update(overrides) + return payload + + +# --------------------------------------------------------------------------- +# Leaf models +# --------------------------------------------------------------------------- + + +class TestSiteProperties: + def test_valid(self): + assert SiteProperties(magmom=1.5).magmom == 1.5 + + def test_missing_magmom_raises(self): + with pytest.raises(PydanticValidationError): + SiteProperties() + + +class TestSpecies: + def test_element_coerced_from_symbol(self): + species = Species(element="Fe", occu=1) + assert species.element is Element.Fe + assert species.occu == 1 + + def test_invalid_symbol_raises(self): + with pytest.raises(PydanticValidationError): + Species(element="Xx", occu=1) + + def test_element_enum_passthrough(self): + assert Species(element=Element.O, occu=2).element is Element.O + + +class TestLattice: + def test_valid_construction(self): + lattice = Lattice(**_lattice_payload()) + assert isinstance(lattice.matrix, pl.DataFrame) + assert lattice.pbc == [True, True, True] + assert lattice.volume == 1.0 + + def test_matrix_coerced_from_dict(self): + lattice = Lattice(**_lattice_payload()) + assert lattice.matrix.columns == ["x", "y", "z"] + + def test_missing_angles_raise(self): + payload = _lattice_payload() + del payload["alpha"] + with pytest.raises(PydanticValidationError): + Lattice(**payload) + + +# --------------------------------------------------------------------------- +# Structure / StructureIn +# --------------------------------------------------------------------------- + + +class TestStructure: + def test_valid_construction(self): + structure = Structure(**_structure_payload()) + assert structure.name == "Fe2O3" + assert len(structure.sites) == 1 + assert structure.sites[0].species[0].element is Element.Fe + + def test_collection_name(self): + assert Structure.Settings.name == "structures" + + def test_charge_is_required_but_nullable(self): + assert Structure(**_structure_payload(charge=None)).charge is None + payload = _structure_payload() + del payload["charge"] + with pytest.raises(PydanticValidationError): + Structure(**payload) + + def test_md5_is_computed_not_taken_from_input(self): + # A client-supplied md5 is overwritten by the content-derived hash. + structure = Structure(**_structure_payload(md5="a" * 32)) + assert structure.md5 != "a" * 32 + assert len(structure.md5) == 32 + + def test_same_content_same_md5(self): + assert Structure(**_structure_payload()).md5 == Structure(**_structure_payload()).md5 + + def test_different_charge_different_md5(self): + assert Structure(**_structure_payload(charge=0.0)).md5 != Structure(**_structure_payload(charge=1.0)).md5 + + def test_cif_kept_as_raw_string(self): + structure = Structure(**_structure_payload()) + assert structure.cif.startswith("data_Fe2O3") + + def test_structure_in_has_no_id_or_md5(self): + assert "md5" not in StructureIn.model_fields + assert "id" not in StructureIn.model_fields + + def test_from_input_assigns_id_and_computes_md5(self): + sin = StructureIn( + name="Fe2O3", + lattice=_lattice_payload(), + sites=[_site_payload()], + charge=0.0, + cif="data_Fe2O3\n", + ) + doc = Structure.from_input(sin) + assert isinstance(doc, Structure) + assert doc.id is not None + assert len(doc.md5) == 32 + + +# --------------------------------------------------------------------------- +# StructureOut +# --------------------------------------------------------------------------- + + +class TestStructureOut: + def test_all_fields_optional(self): + out = StructureOut() + assert out.id is None + assert out.name is None + assert out.md5 is None + + def test_default_fields(self): + assert StructureOut.default_fields() == ["id", "name", "md5"] + + def test_default_fields_parseable(self): + # The route default must survive parse_fields without raising. + parsed = StructureOut.parse_fields(StructureOut.default_fields()) + assert parsed == frozenset({"id", "name", "md5"}) + + def test_populates_id_from_mongo_alias(self): + oid = PydanticObjectId() + assert StructureOut.model_validate({"_id": oid}).id == oid + + +# --------------------------------------------------------------------------- +# StructurePatch +# --------------------------------------------------------------------------- + + +class TestStructurePatch: + def test_all_fields_optional(self): + patch = StructurePatch() + assert patch.name is None + assert patch.lattice is None + assert patch.sites is None + + def test_partial_patch_excludes_unset(self): + patch = StructurePatch(name="renamed") + assert patch.model_dump(exclude_unset=True) == {"name": "renamed"} + + def test_lattice_patchable(self): + patch = StructurePatch(lattice=_lattice_payload()) + assert patch.lattice is not None + assert patch.lattice.volume == 1.0 + + def test_sites_is_a_list(self): + # Regression: sites must be list[Site], not a single Site. + patch = StructurePatch(sites=[_site_payload()]) + assert isinstance(patch.sites, list) + assert patch.sites[0].label == "Fe" + + +# --------------------------------------------------------------------------- +# StructureFilter +# --------------------------------------------------------------------------- + + +class TestStructureFilter: + def test_empty_filter(self): + filter = StructureFilter() + assert filter.id is None + assert filter.name__ilike is None + + def test_constants_bind_structure_model(self): + assert StructureFilter.Constants.model is Structure + + def test_md5_value_validated(self): + assert StructureFilter(md5="A" * 32).md5 == "a" * 32 + + def test_invalid_md5_raises(self): + with pytest.raises(AppValidationError): + StructureFilter(md5="short") diff --git a/mpcontribs-api/tests/unit/domains/test_tables_models.py b/mpcontribs-api/tests/unit/domains/test_tables_models.py new file mode 100644 index 000000000..624a24ace --- /dev/null +++ b/mpcontribs-api/tests/unit/domains/test_tables_models.py @@ -0,0 +1,239 @@ +import polars as pl +import pytest +from beanie import PydanticObjectId + +from mpcontribs_api.domains.tables.models import ( + Attributes, + Labels, + Table, + TableFilter, + TableIn, + TableOut, + TablePatch, +) +from mpcontribs_api.exceptions import ValidationError as AppValidationError + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + +ATTRS = {"title": "Band gaps", "labels": {"index": "T", "value": "gap", "variable": "doping"}} + + +def _table_doc_payload(**overrides) -> dict: + """Payload for the stored Table document — raw MongoDB shape (index/columns/data as strings).""" + payload = { + "_id": PydanticObjectId(), + "name": "bandgaps", + "attrs": ATTRS, + "index": ["100.0", "200.0"], + "columns": ["1e16", "1e17"], + "data": [["1.1", "1.2"], ["2.1", "2.2"]], + "total_data_rows": 2, + } + payload.update(overrides) + return payload + + +def _table_in_frame() -> pl.DataFrame: + # First column is the index (T), the rest are the data columns; all cells are strings. + return pl.DataFrame( + {"T": ["100.0", "200.0"], "1e16": ["1.1", "2.1"], "1e17": ["1.2", "2.2"]} + ) + + +def _table_in_payload(**overrides) -> dict: + """Payload for user input: a DataFrame (first column = index), no _id/md5/total_data_rows.""" + payload = { + "name": "bandgaps", + "attrs": ATTRS, + "data": _table_in_frame(), + } + payload.update(overrides) + return payload + + +# --------------------------------------------------------------------------- +# Leaf models +# --------------------------------------------------------------------------- + + +class TestLabels: + def test_valid(self): + labels = Labels(index="T", value="gap", variable="method") + assert labels.index == "T" + + def test_missing_field_raises(self): + with pytest.raises(Exception): + Labels(index="T", value="gap") + + +class TestAttributes: + def test_valid(self): + attrs = Attributes(**ATTRS) + assert attrs.title == "Band gaps" + assert attrs.labels.variable == "doping" + + +# --------------------------------------------------------------------------- +# Table (stored document) — md5 is server-computed +# --------------------------------------------------------------------------- + + +class TestTable: + def test_valid_construction(self): + table = Table(**_table_doc_payload()) + assert table.index == ["100.0", "200.0"] + assert table.columns == ["1e16", "1e17"] + assert table.data == [["1.1", "1.2"], ["2.1", "2.2"]] + assert table.total_data_rows == 2 + + def test_collection_name(self): + assert Table.Settings.name == "tables" + + def test_md5_is_computed_not_taken_from_input(self): + # A client-supplied md5 is ignored; the stored value is derived from content. + table = Table(**_table_doc_payload(md5="d" * 32)) + assert table.md5 != "d" * 32 + assert len(table.md5) == 32 + + def test_same_content_same_md5(self): + assert Table(**_table_doc_payload()).md5 == Table(**_table_doc_payload()).md5 + + def test_different_data_different_md5(self): + a = Table(**_table_doc_payload()) + b = Table(**_table_doc_payload(data=[["9.9", "8.8"], ["7.7", "6.6"]])) + assert a.md5 != b.md5 + + def test_attrs_part_of_md5(self): + a = Table(**_table_doc_payload()) + b = Table(**_table_doc_payload(attrs={**ATTRS, "title": "Different"})) + assert a.md5 != b.md5 + + def test_data_stored_as_string_rows(self): + table = Table(**_table_doc_payload()) + assert table.model_dump()["data"] == [["1.1", "1.2"], ["2.1", "2.2"]] + + +# --------------------------------------------------------------------------- +# TableIn — content only, no id/md5 +# --------------------------------------------------------------------------- + + +class TestTableIn: + def test_has_no_server_assigned_fields(self): + # _id, md5, and total_data_rows are all server-owned, so absent from the input contract. + assert "md5" not in TableIn.model_fields + assert "id" not in TableIn.model_fields + assert "total_data_rows" not in TableIn.model_fields + + def test_from_input_splits_frame_into_storage(self): + # First column -> index; remaining columns -> columns; cells -> row-major string data. + doc = Table.from_input(TableIn(**_table_in_payload())) + assert doc.index == ["100.0", "200.0"] + assert doc.columns == ["1e16", "1e17"] + assert doc.data == [["1.1", "1.2"], ["2.1", "2.2"]] + assert doc.total_data_rows == 2 + + def test_built_document_computes_md5(self): + doc = Table.from_input(TableIn(**_table_in_payload())) + assert len(doc.md5) == 32 + assert doc.id is not None + + +# --------------------------------------------------------------------------- +# TableFilter +# --------------------------------------------------------------------------- + + +class TestTableFilter: + def test_empty_filter(self): + filter = TableFilter() + assert filter.id is None + assert filter.name__ilike is None + + def test_constants_bind_table_model(self): + assert TableFilter.Constants.model is Table + + def test_id_serializes_to_str(self): + oid = PydanticObjectId() + assert TableFilter(id=oid).model_dump()["id"] == str(oid) + + def test_id_in_serializes_to_sorted_strs(self): + first, second = PydanticObjectId(), PydanticObjectId() + dumped = TableFilter(id__in=[second, first]).model_dump() + assert dumped["id__in"] == sorted([str(first), str(second)]) + + def test_none_ids_serialize_to_none(self): + dumped = TableFilter().model_dump() + assert dumped["id"] is None + assert dumped["id__in"] is None + + def test_md5_value_validated(self): + assert TableFilter(md5="B" * 32).md5 == "b" * 32 + + def test_invalid_md5_raises(self): + with pytest.raises(AppValidationError): + TableFilter(md5="short") + + +# --------------------------------------------------------------------------- +# TableOut / TablePatch +# --------------------------------------------------------------------------- + + +class TestTableOut: + def test_all_fields_optional(self): + out = TableOut() + assert out.id is None + assert out.data is None + assert out.attrs is None + + def test_default_fields(self): + assert TableOut.default_fields() == ["id", "name", "md5", "attrs", "total_data_rows"] + + def test_default_fields_parseable(self): + parsed = TableOut.parse_fields(TableOut.default_fields()) + assert "attrs" in parsed + + def test_content_projectable(self): + # data is on the Out model so it can be requested explicitly. + parsed = TableOut.parse_fields(["data"]) + assert "data" in parsed + + def test_data_coerced_when_present(self): + out = TableOut(data={"a": [1]}) + assert isinstance(out.data, pl.DataFrame) + + def test_reconstructs_frame_from_storage_dict(self): + # Read path: a raw Mongo dict with index/columns/data is reassembled into a DataFrame + # whose first column is the index (named by attrs.labels.index), cells preserved as strings. + out = TableOut.model_validate(_table_doc_payload(md5="a" * 32)) + assert isinstance(out.data, pl.DataFrame) + assert out.data.columns == ["T", "1e16", "1e17"] + assert out.data["T"].to_list() == ["100.0", "200.0"] + assert out.data["1e16"].to_list() == ["1.1", "2.1"] + + def test_storage_keys_not_leaked(self): + out = TableOut.model_validate(_table_doc_payload(md5="a" * 32)) + dumped = out.model_dump() + assert "index" not in dumped + assert "columns" not in dumped + + def test_projection_full_model_when_data_requested(self): + # data requested -> full model (so index/columns come back to rebuild the frame). + assert TableOut.projection(TableOut.parse_fields(["data"])) is TableOut + + def test_projection_partial_when_data_not_requested(self): + # light read -> a trimmed projection model that does not pull the storage triple. + proj = TableOut.projection(TableOut.parse_fields(["name"])) + assert proj is not TableOut + assert hasattr(proj, "Settings") + + +class TestTablePatch: + def test_name_optional(self): + assert TablePatch().name is None + + def test_partial_patch_excludes_unset(self): + assert TablePatch(name="renamed").model_dump(exclude_unset=True) == {"name": "renamed"} diff --git a/mpcontribs-api/tests/unit/test_auth.py b/mpcontribs-api/tests/unit/test_auth.py new file mode 100644 index 000000000..6651c7d81 --- /dev/null +++ b/mpcontribs-api/tests/unit/test_auth.py @@ -0,0 +1,91 @@ +import pytest + +from mpcontribs_api.authz import ADMIN_GROUP, User + + +class TestUserIsAnonymous: + def test_no_username_is_anonymous(self): + user = User() + assert user.is_anonymous is True + + def test_username_none_is_anonymous(self): + user = User(username=None) + assert user.is_anonymous is True + + def test_with_username_not_anonymous(self): + user = User(username="google:alice@example.com") + assert user.is_anonymous is False + + +class TestUserIsAdmin: + def test_no_groups_not_admin(self): + user = User(username="google:alice@example.com") + assert user.is_admin is False + + def test_admin_group_is_admin(self): + user = User(username="google:alice@example.com", groups=frozenset({ADMIN_GROUP})) + assert user.is_admin is True + + def test_other_group_not_admin(self): + user = User(username="google:alice@example.com", groups=frozenset({"editors"})) + assert user.is_admin is False + + def test_admin_group_among_many_is_admin(self): + user = User(username="google:alice@example.com", groups=frozenset({"editors", ADMIN_GROUP, "viewers"})) + assert user.is_admin is True + + def test_anonymous_cannot_be_admin(self): + # Even if groups include admin, anonymous user (no username) is still anonymous + user = User(groups=frozenset({ADMIN_GROUP})) + assert user.is_anonymous is True + # But is_admin only checks groups, not username + assert user.is_admin is False + + +class TestUserHasRole: + def test_has_role_in_groups(self): + user = User(username="google:alice@example.com", groups=frozenset({"editors", "viewers"})) + assert user.has_role("editors") is True + + def test_has_role_not_in_groups(self): + user = User(username="google:alice@example.com", groups=frozenset({"editors"})) + assert user.has_role("viewers") is False + + def test_has_role_empty_groups(self): + user = User(username="google:alice@example.com") + assert user.has_role("editors") is False + + def test_has_role_case_sensitive(self): + user = User(username="google:alice@example.com", groups=frozenset({"Editors"})) + assert user.has_role("editors") is False + assert user.has_role("Editors") is True + + +class TestUserImmutability: + def test_user_is_frozen(self): + user = User(username="google:alice@example.com") + with pytest.raises(Exception): + user.username = "google:bob@example.com" # type: ignore[misc] + + def test_groups_default_empty_frozenset(self): + user = User() + assert user.groups == frozenset() + + def test_consumer_id_default_none(self): + user = User() + assert user.consumer_id is None + + +class TestUserConstruction: + def test_full_user(self): + user = User( + consumer_id="kong-consumer-123", + username="google:alice@example.com", + groups=frozenset({"editors", "mp-team"}), + ) + assert user.consumer_id == "kong-consumer-123" + assert user.username == "google:alice@example.com" + assert "editors" in user.groups + assert "admin" not in user.groups + assert user.is_admin is False + assert user.is_anonymous is False diff --git a/mpcontribs-api/tests/unit/test_config.py b/mpcontribs-api/tests/unit/test_config.py new file mode 100644 index 000000000..fe88f3007 --- /dev/null +++ b/mpcontribs-api/tests/unit/test_config.py @@ -0,0 +1,182 @@ +import pytest +from pydantic import SecretStr +from pydantic import ValidationError as PydanticValidationError + +from mpcontribs_api.config import ( + MongoSettings, + RedisSettings, + Settings, + get_settings, +) + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + +REQUIRED_ENV = { + "MPCONTRIBS_ENVIRONMENT": "dev", + "MPCONTRIBS_MONGO__URI": "mongodb://user:pass@localhost:27017", + "MPCONTRIBS_MONGO__DB_NAME": "mpcontribs-test", + "MPCONTRIBS_REDIS__ADDRESS": "redis://localhost:6379", + "MPCONTRIBS_REDIS__URL": "redis://localhost:6379/0", + "MPCONTRIBS_MAIL_DEFAULT_SENDER": "noreply@materialsproject.org", + "MPCONTRIBS_VERSION": "0.0.0-test", +} + + +def _set_required_env(monkeypatch: pytest.MonkeyPatch) -> None: + for key, value in REQUIRED_ENV.items(): + monkeypatch.setenv(key, value) + + +def _mongo(**overrides) -> MongoSettings: + return MongoSettings(uri=SecretStr("mongodb://localhost"), db_name="db", **overrides) + + +# --------------------------------------------------------------------------- +# MongoSettings defaults +# --------------------------------------------------------------------------- + + +class TestMongoSettingsDefaults: + def test_minimal_construction(self): + settings = _mongo() + assert settings.db_name == "db" + assert settings.uri.get_secret_value() == "mongodb://localhost" + + def test_uri_is_secret(self): + settings = _mongo() + assert "mongodb://localhost" not in repr(settings.uri) + + def test_default_pool_sizes(self): + settings = _mongo() + assert settings.max_pool_size == 100 + assert settings.min_pool_size == 0 + + def test_default_admin_group(self): + assert _mongo().admin_group == "admin" + + def test_default_component_limits(self): + settings = _mongo() + assert settings.max_components_per_contribution == 500 + assert settings.component_insert_chunk_size == 100 + + def test_invalid_datetime_conversion_raises(self): + with pytest.raises(PydanticValidationError): + _mongo(datetime_conversion="not-a-mode") + + def test_missing_uri_raises(self): + with pytest.raises(PydanticValidationError): + MongoSettings(db_name="db") + + +# --------------------------------------------------------------------------- +# MongoSettings._clamp_concurrency +# --------------------------------------------------------------------------- + + +class TestClampConcurrency: + def test_default_not_clamped(self): + # max_pool_size=100 -> cap 50; default max_concurrent_transactions=16 stays. + assert _mongo().max_concurrent_transactions == 16 + + def test_clamped_to_half_pool_size(self): + settings = _mongo(max_pool_size=10, max_concurrent_transactions=16) + assert settings.max_concurrent_transactions == 5 + + def test_exactly_at_cap_not_clamped(self): + settings = _mongo(max_pool_size=32, max_concurrent_transactions=16) + assert settings.max_concurrent_transactions == 16 + + def test_pool_size_one_clamps_to_one(self): + settings = _mongo(max_pool_size=1, max_concurrent_transactions=16) + assert settings.max_concurrent_transactions == 1 + + def test_unbounded_pool_skips_clamping(self): + # max_pool_size=0 means "unlimited" to PyMongo; clamping is skipped. + settings = _mongo(max_pool_size=0, max_concurrent_transactions=999) + assert settings.max_concurrent_transactions == 999 + + def test_below_cap_unchanged(self): + settings = _mongo(max_pool_size=10, max_concurrent_transactions=2) + assert settings.max_concurrent_transactions == 2 + + +# --------------------------------------------------------------------------- +# Sub-settings secrets +# --------------------------------------------------------------------------- + + +class TestSubSettingsSecrets: + def test_redis_secrets_masked(self): + redis = RedisSettings(address=SecretStr("redis://h"), url=SecretStr("redis://h/0")) + assert redis.address.get_secret_value() == "redis://h" + assert "redis://h" not in repr(redis) + + +# --------------------------------------------------------------------------- +# Settings: env var loading +# --------------------------------------------------------------------------- + + +class TestSettingsEnvLoading: + def test_loads_from_env(self, monkeypatch): + _set_required_env(monkeypatch) + settings = Settings() + assert settings.environment == "dev" + assert settings.version == "0.0.0-test" + assert settings.mail_default_sender == "noreply@materialsproject.org" + + def test_nested_delimiter_populates_mongo(self, monkeypatch): + _set_required_env(monkeypatch) + settings = Settings() + assert settings.mongo.db_name == "mpcontribs-test" + assert settings.mongo.uri.get_secret_value() == "mongodb://user:pass@localhost:27017" + + def test_nested_delimiter_populates_and_redis(self, monkeypatch): + _set_required_env(monkeypatch) + settings = Settings() + assert settings.redis.url.get_secret_value() == "redis://localhost:6379/0" + + def test_nested_field_override(self, monkeypatch): + _set_required_env(monkeypatch) + monkeypatch.setenv("MPCONTRIBS_MONGO__MAX_POOL_SIZE", "10") + settings = Settings() + assert settings.mongo.max_pool_size == 10 + # Clamp validator runs on env-loaded values too. + assert settings.mongo.max_concurrent_transactions == 5 + + def test_invalid_environment_raises(self, monkeypatch): + _set_required_env(monkeypatch) + monkeypatch.setenv("MPCONTRIBS_ENVIRONMENT", "staging") + with pytest.raises(PydanticValidationError): + Settings() + + +# --------------------------------------------------------------------------- +# get_settings caching +# --------------------------------------------------------------------------- + + +class TestGetSettingsCaching: + @pytest.fixture(autouse=True) + def _clear_cache(self): + get_settings.cache_clear() + yield + get_settings.cache_clear() + + def test_returns_settings_instance(self, monkeypatch): + _set_required_env(monkeypatch) + assert isinstance(get_settings(), Settings) + + def test_same_instance_returned(self, monkeypatch): + _set_required_env(monkeypatch) + assert get_settings() is get_settings() + + def test_env_changes_ignored_until_cache_cleared(self, monkeypatch): + _set_required_env(monkeypatch) + first = get_settings() + monkeypatch.setenv("MPCONTRIBS_VERSION", "9.9.9") + assert get_settings().version == first.version + get_settings.cache_clear() + assert get_settings().version == "9.9.9" diff --git a/mpcontribs-api/tests/unit/test_dependencies.py b/mpcontribs-api/tests/unit/test_dependencies.py new file mode 100644 index 000000000..80c089b60 --- /dev/null +++ b/mpcontribs-api/tests/unit/test_dependencies.py @@ -0,0 +1,121 @@ +from unittest.mock import MagicMock + +import pytest + +from mpcontribs_api.authz import User +from mpcontribs_api.dependencies import _split, get_user, require_user +from mpcontribs_api.exceptions import AuthenticationError + +# --------------------------------------------------------------------------- +# _split +# --------------------------------------------------------------------------- + + +class TestSplit: + def test_none_returns_empty_set(self): + assert _split(None) == set() + + def test_empty_string_returns_empty_set(self): + assert _split("") == set() + + def test_whitespace_only_returns_empty_set(self): + assert _split(" ") == set() + + def test_single_value(self): + assert _split("editors") == {"editors"} + + def test_multiple_values(self): + assert _split("editors,viewers,admins") == {"editors", "viewers", "admins"} + + def test_strips_whitespace(self): + assert _split(" editors , viewers ") == {"editors", "viewers"} + + def test_skips_empty_parts(self): + assert _split("editors,,viewers") == {"editors", "viewers"} + + def test_single_space_comma_separated(self): + assert _split("a, b, c") == {"a", "b", "c"} + + +# --------------------------------------------------------------------------- +# get_user — builds User from request headers +# --------------------------------------------------------------------------- + + +def _make_request(**headers: str) -> MagicMock: + """Build a mock Request whose .headers dict returns the given values.""" + request = MagicMock() + request.headers = headers + return request + + +class TestGetUser: + def test_no_headers_returns_anonymous(self): + request = _make_request() + user = get_user(request) + assert user.is_anonymous is True + + def test_explicit_anon_header_returns_anonymous(self): + request = _make_request(**{"x-anonymous-consumer": "true", "x-consumer-username": "alice"}) + user = get_user(request) + assert user.is_anonymous is True + + def test_explicit_anon_case_insensitive(self): + request = _make_request(**{"x-anonymous-consumer": "True", "x-consumer-username": "alice"}) + user = get_user(request) + assert user.is_anonymous is True + + def test_authenticated_user(self): + request = _make_request( + **{ + "x-consumer-username": "google:alice@example.com", + "x-consumer-id": "kong-123", + "x-authenticated-groups": "editors", + "x-consumer-groups": "mp-team", + } + ) + user = get_user(request) + assert user.is_anonymous is False + assert user.username == "google:alice@example.com" + assert user.consumer_id == "kong-123" + assert "editors" in user.groups + assert "mp-team" in user.groups + + def test_authenticated_user_no_groups(self): + request = _make_request(**{"x-consumer-username": "google:alice@example.com"}) + user = get_user(request) + assert user.is_anonymous is False + assert user.groups == frozenset() + + def test_groups_merged_from_both_headers(self): + request = _make_request( + **{ + "x-consumer-username": "google:alice@example.com", + "x-authenticated-groups": "a,b", + "x-consumer-groups": "c,d", + } + ) + user = get_user(request) + assert user.groups == frozenset({"a", "b", "c", "d"}) + + def test_missing_username_returns_anonymous(self): + request = _make_request(**{"x-consumer-id": "kong-123"}) + user = get_user(request) + assert user.is_anonymous is True + + +# --------------------------------------------------------------------------- +# require_user +# --------------------------------------------------------------------------- + + +class TestRequireUser: + def test_authenticated_user_passes_through(self): + authed = User(username="google:alice@example.com", groups=frozenset()) + result = require_user(authed) + assert result is authed + + def test_anonymous_raises_authentication_error(self): + anon = User() + with pytest.raises(AuthenticationError): + require_user(anon) diff --git a/mpcontribs-api/tests/unit/test_exceptions.py b/mpcontribs-api/tests/unit/test_exceptions.py new file mode 100644 index 000000000..7e167a581 --- /dev/null +++ b/mpcontribs-api/tests/unit/test_exceptions.py @@ -0,0 +1,174 @@ +import pytest + +from mpcontribs_api.exceptions import ( + AppError, + AuthenticationError, + ConflictError, + NotFoundError, + PermissionError, + ValidationError, + _sanitize_validation_errors, + error_body, +) + + +class TestErrorBody: + def test_minimal_body(self): + body = error_body("not_found", "Resource not found") + assert body == {"error": {"code": "not_found", "message": "Resource not found"}} + + def test_body_with_context(self): + body = error_body("not_found", "Resource not found", resource_id="abc", resource_type="project") + assert body["error"]["code"] == "not_found" + assert body["error"]["message"] == "Resource not found" + assert body["error"]["detail"] == {"resource_id": "abc", "resource_type": "project"} + + def test_no_detail_key_without_context(self): + body = error_body("conflict", "Duplicate id") + assert "detail" not in body["error"] + + def test_detail_present_with_context(self): + body = error_body("conflict", "Duplicate id", existing_id="xyz") + assert "detail" in body["error"] + + +class TestAppError: + def test_default_status_and_code(self): + err = AppError() + assert err.status_code == 500 + assert err.error_code == "internal_error" + + def test_default_message_is_class_name(self): + err = AppError() + assert err.message == "AppError" + + def test_custom_message(self): + err = AppError("something went wrong") + assert err.message == "something went wrong" + + def test_context_stored(self): + err = AppError("msg", user="alice", action="delete") + assert err.context == {"user": "alice", "action": "delete"} + + def test_is_exception(self): + err = AppError("oops") + assert isinstance(err, Exception) + + def test_str_is_message(self): + err = AppError("oops") + assert str(err) == "oops" + + +class TestNotFoundError: + def test_status_code(self): + assert NotFoundError.status_code == 404 + + def test_error_code(self): + assert NotFoundError.error_code == "not_found" + + def test_message_defaults_to_class_name(self): + err = NotFoundError() + assert err.message == "NotFoundError" + + def test_custom_message(self): + err = NotFoundError("project 'foo' not found") + assert err.message == "project 'foo' not found" + + def test_is_app_error(self): + assert issubclass(NotFoundError, AppError) + + +class TestConflictError: + def test_status_code(self): + assert ConflictError.status_code == 409 + + def test_error_code(self): + assert ConflictError.error_code == "conflict" + + def test_is_app_error(self): + assert issubclass(ConflictError, AppError) + + +class TestValidationError: + def test_status_code(self): + assert ValidationError.status_code == 422 + + def test_error_code(self): + assert ValidationError.error_code == "validation_error" + + def test_is_app_error(self): + assert issubclass(ValidationError, AppError) + + +class TestPermissionError: + def test_status_code(self): + assert PermissionError.status_code == 403 + + def test_error_code(self): + assert PermissionError.error_code == "permission_denied" + + def test_context_kwargs(self): + err = PermissionError(required_role="admin") + assert err.context == {"required_role": "admin"} + + def test_is_app_error(self): + assert issubclass(PermissionError, AppError) + + +class TestAuthenticationError: + def test_status_code(self): + assert AuthenticationError.status_code == 401 + + def test_error_code(self): + assert AuthenticationError.error_code == "authentication_error" + + def test_is_app_error(self): + assert issubclass(AuthenticationError, AppError) + + +class TestExceptionRaising: + def test_not_found_can_be_raised_and_caught(self): + with pytest.raises(NotFoundError) as exc_info: + raise NotFoundError("project not found") + assert exc_info.value.message == "project not found" + assert exc_info.value.status_code == 404 + + def test_app_error_catches_subclasses(self): + with pytest.raises(AppError): + raise ConflictError("duplicate") + + def test_context_available_after_raise(self): + with pytest.raises(ValidationError) as exc_info: + raise ValidationError("bad field", field="email", value="oops") + assert exc_info.value.context == {"field": "email", "value": "oops"} + + +# --------------------------------------------------------------------------- +# _sanitize_validation_errors +# --------------------------------------------------------------------------- + + +class TestSanitizeValidationErrors: + def test_drops_input_and_url_keys(self): + errors = [ + {"type": "missing", "loc": ("body", "name"), "msg": "Field required", "input": {"secret": 1}, "url": "https://errors.pydantic.dev/x"} + ] + sanitized = _sanitize_validation_errors(errors) + assert sanitized == [{"type": "missing", "loc": ("body", "name"), "msg": "Field required"}] + + def test_echoed_input_never_survives(self): + errors = [{"msg": "bad", "input": "user-supplied-payload"}] + assert "input" not in _sanitize_validation_errors(errors)[0] + + def test_multiple_errors_all_sanitized(self): + errors = [ + {"msg": "a", "input": 1, "url": "u"}, + {"msg": "b", "input": 2}, + {"msg": "c"}, + ] + sanitized = _sanitize_validation_errors(errors) + assert all("input" not in e and "url" not in e for e in sanitized) + assert [e["msg"] for e in sanitized] == ["a", "b", "c"] + + def test_empty_sequence(self): + assert _sanitize_validation_errors([]) == [] diff --git a/mpcontribs-api/tests/unit/test_packaging.py b/mpcontribs-api/tests/unit/test_packaging.py new file mode 100644 index 000000000..9f5fabdf5 --- /dev/null +++ b/mpcontribs-api/tests/unit/test_packaging.py @@ -0,0 +1,35 @@ +"""Guards against the src-layout packaging regression where the built wheel shipped no code. + +The wheel must contain the importable package so the Docker image's +``uvicorn mpcontribs_api.app:app`` can resolve the module. +""" + +import shutil +import subprocess +import zipfile +from pathlib import Path + +import pytest + +PROJECT_ROOT = Path(__file__).resolve().parents[2] + + +@pytest.mark.skipif(shutil.which("uv") is None, reason="uv not available") +def test_wheel_contains_package(tmp_path: Path) -> None: + result = subprocess.run( + ["uv", "build", "--wheel", "--out-dir", str(tmp_path)], + cwd=PROJECT_ROOT, + env={"SETUPTOOLS_SCM_PRETEND_VERSION": "0.0.0", "PATH": __import__("os").environ.get("PATH", "")}, + capture_output=True, + text=True, + ) + assert result.returncode == 0, f"uv build failed: {result.stderr}" + + wheels = list(tmp_path.glob("*.whl")) + assert wheels, "no wheel produced" + + with zipfile.ZipFile(wheels[0]) as zf: + names = zf.namelist() + assert any(n == "mpcontribs_api/app.py" for n in names), ( + f"wheel is missing the package code; top entries: {sorted(names)[:10]}" + ) diff --git a/mpcontribs-api/tests/unit/test_pagination.py b/mpcontribs-api/tests/unit/test_pagination.py new file mode 100644 index 000000000..f3456e82a --- /dev/null +++ b/mpcontribs-api/tests/unit/test_pagination.py @@ -0,0 +1,102 @@ +import base64 + +import pytest +from pydantic import ValidationError as PydanticValidationError + +from mpcontribs_api.pagination import ( + CursorParams, + Page, + decode_cursor, + encode_cursor, +) + + +class TestEncodeCursor: + def test_roundtrip(self): + original = "some-mongo-id-abc123" + assert decode_cursor(encode_cursor(original)) == original + + def test_returns_string(self): + result = encode_cursor("abc") + assert isinstance(result, str) + + def test_uses_urlsafe_base64(self): + # urlsafe_b64encode uses - and _ instead of + and / + result = encode_cursor("test-id") + decoded_bytes = base64.urlsafe_b64decode(result.encode()) + assert decoded_bytes.decode() == "test-id" + + def test_empty_string(self): + assert decode_cursor(encode_cursor("")) == "" + + def test_encodes_unicode(self): + original = "projet-données" + assert decode_cursor(encode_cursor(original)) == original + + +class TestDecodeCursor: + def test_valid_cursor(self): + encoded = base64.urlsafe_b64encode(b"abc123").decode() + assert decode_cursor(encoded) == "abc123" + + def test_invalid_base64_raises_value_error(self): + with pytest.raises(ValueError, match="malformed cursor"): + decode_cursor("!!!not-valid-base64!!!") + + def test_non_utf8_bytes_raises_value_error(self): + # Encode raw bytes that aren't valid UTF-8 + bad = base64.urlsafe_b64encode(b"\xff\xfe").decode() + with pytest.raises(ValueError, match="malformed cursor"): + decode_cursor(bad) + + +class TestCursorParams: + def test_defaults(self): + params = CursorParams() + assert params.cursor is None + assert params.limit == 20 + + def test_cursor_set(self): + params = CursorParams(cursor="abc123") + assert params.cursor == "abc123" + + def test_limit_minimum(self): + params = CursorParams(limit=1) + assert params.limit == 1 + + def test_limit_maximum(self): + params = CursorParams(limit=100) + assert params.limit == 100 + + def test_limit_below_minimum_raises(self): + with pytest.raises(PydanticValidationError): + CursorParams(limit=0) + + def test_limit_above_maximum_raises(self): + with pytest.raises(PydanticValidationError): + CursorParams(limit=101) + + def test_custom_limit(self): + params = CursorParams(limit=50) + assert params.limit == 50 + + +class TestPage: + def test_items_and_no_next_cursor(self): + page: Page[str] = Page(items=["a", "b", "c"]) + assert page.items == ["a", "b", "c"] + assert page.next_cursor is None + + def test_with_next_cursor(self): + cursor = encode_cursor("last-id") + page: Page[str] = Page(items=["a"], next_cursor=cursor) + assert page.next_cursor == cursor + + def test_empty_items(self): + page: Page[str] = Page(items=[]) + assert page.items == [] + assert page.next_cursor is None + + def test_generic_item_types(self): + page: Page[int] = Page(items=[1, 2, 3]) + assert page.items == [1, 2, 3] diff --git a/mpcontribs-api/tests/unit/test_projection.py b/mpcontribs-api/tests/unit/test_projection.py new file mode 100644 index 000000000..a8c627155 --- /dev/null +++ b/mpcontribs-api/tests/unit/test_projection.py @@ -0,0 +1,328 @@ +from typing import Any + +import pytest +from pydantic import BaseModel, Field + +from mpcontribs_api.exceptions import ValidationError as AppValidationError +from mpcontribs_api.projection import ( + SparseFieldsModel, + _classify, + _collapse, + _unwrap_optional, + _validate_path, + _walk_path, +) + +# --------------------------------------------------------------------------- +# Helpers — simple models used across tests +# --------------------------------------------------------------------------- + + +class Address(BaseModel): + street: str + city: str + country: str | None = None + + +class Simple(SparseFieldsModel): + name: str + age: int + score: float | None = None + tags: list[str] = Field(default_factory=list) + metadata: dict[str, Any] = Field(default_factory=dict) + address: Address | None = None + + +# --------------------------------------------------------------------------- +# _unwrap_optional +# --------------------------------------------------------------------------- + + +class TestUnwrapOptional: + def test_strips_none(self): + result = _unwrap_optional(str | None) + assert result is str + + def test_plain_annotation_unchanged(self): + result = _unwrap_optional(str) + assert result is str + + def test_optional_model(self): + result = _unwrap_optional(Address | None) + assert result is Address + + def test_union_without_none_unchanged(self): + # int | str has no None — returned as-is + result = _unwrap_optional(int | str) + assert result == (int | str) + + +# --------------------------------------------------------------------------- +# _classify +# --------------------------------------------------------------------------- + + +class TestClassify: + def test_base_model_subclass(self): + kind, model = _classify(Address) + assert kind == "model" + assert model is Address + + def test_optional_model(self): + kind, model = _classify(Address | None) + assert kind == "model" + assert model is Address + + def test_dict_annotation(self): + kind, model = _classify(dict) + assert kind == "dict" + assert model is None + + def test_dict_generic(self): + kind, model = _classify(dict[str, Any]) + assert kind == "dict" + assert model is None + + def test_list_annotation(self): + kind, model = _classify(list[str]) + assert kind == "list" + assert model is None + + def test_scalar_str(self): + kind, model = _classify(str) + assert kind == "scalar" + assert model is None + + def test_scalar_int(self): + kind, model = _classify(int) + assert kind == "scalar" + assert model is None + + def test_any(self): + kind, model = _classify(Any) + assert kind == "dict" + assert model is None + + +# --------------------------------------------------------------------------- +# _collapse +# --------------------------------------------------------------------------- + + +class TestCollapse: + def test_no_overlap(self): + paths = frozenset({"name", "age"}) + assert _collapse(paths) == paths + + def test_parent_subsumes_child(self): + paths = frozenset({"address", "address.city"}) + assert _collapse(paths) == frozenset({"address"}) + + def test_child_without_parent_kept(self): + paths = frozenset({"address.city"}) + assert _collapse(paths) == paths + + def test_multiple_children_of_same_parent(self): + paths = frozenset({"address", "address.city", "address.street"}) + assert _collapse(paths) == frozenset({"address"}) + + def test_disjoint_nested_paths(self): + paths = frozenset({"address.city", "name"}) + assert _collapse(paths) == paths + + def test_single_path(self): + paths = frozenset({"name"}) + assert _collapse(paths) == paths + + def test_empty(self): + assert _collapse(frozenset()) == frozenset() + + +# --------------------------------------------------------------------------- +# _walk_path +# --------------------------------------------------------------------------- + + +class TestWalkPath: + def test_scalar_field(self): + steps = list(_walk_path(Simple, "name")) + assert len(steps) == 1 + assert steps[0].segment == "name" + assert steps[0].kind == "scalar" + assert steps[0].is_last is True + + def test_nested_model_field(self): + steps = list(_walk_path(Simple, "address.city")) + assert steps[0].segment == "address" + assert steps[0].kind == "model" + assert steps[0].is_last is False + assert steps[1].segment == "city" + assert steps[1].kind == "scalar" + assert steps[1].is_last is True + + def test_unknown_field(self): + steps = list(_walk_path(Simple, "nonexistent")) + assert steps[0].kind == "unknown" + + def test_dict_field_goes_opaque(self): + steps = list(_walk_path(Simple, "metadata.arbitrary_key")) + assert steps[0].kind == "dict" + assert steps[1].kind == "opaque" + + +# --------------------------------------------------------------------------- +# _validate_path +# --------------------------------------------------------------------------- + + +class TestValidatePath: + def test_valid_scalar_path(self): + _validate_path(Simple, "name") # should not raise + + def test_valid_nested_path(self): + _validate_path(Simple, "address.city") # should not raise + + def test_valid_dict_path(self): + _validate_path(Simple, "metadata.anything") # opaque — allowed + + def test_unknown_top_level_raises(self): + with pytest.raises(AppValidationError, match="unknown field"): + _validate_path(Simple, "nonexistent") + + def test_subfield_of_scalar_raises(self): + with pytest.raises(AppValidationError, match="cannot select subfields"): + _validate_path(Simple, "name.sub") + + def test_subfield_of_list_raises(self): + with pytest.raises(AppValidationError, match="cannot select subfields"): + _validate_path(Simple, "tags.sub") + + +# --------------------------------------------------------------------------- +# SparseFieldsModel.field_names +# --------------------------------------------------------------------------- + + +class TestFieldNames: + def test_returns_top_level_fields(self): + names = Simple.field_names() + assert "name" in names + assert "age" in names + assert "address" in names + assert "metadata" in names + + def test_does_not_include_nested(self): + names = Simple.field_names() + assert "city" not in names + assert "street" not in names + + +# --------------------------------------------------------------------------- +# SparseFieldsModel.parse_fields +# --------------------------------------------------------------------------- + + +class TestParseFields: + def test_none_returns_none(self): + assert Simple.parse_fields(None) is None + + def test_empty_list_returns_none(self): + assert Simple.parse_fields([]) is None + + def test_single_valid_field(self): + result = Simple.parse_fields(["name"]) + assert result is not None + assert "name" in result + + def test_multiple_fields(self): + result = Simple.parse_fields(["name", "age"]) + assert result is not None + assert "name" in result + assert "age" in result + + def test_whitespace_stripped(self): + result = Simple.parse_fields([" name ", " age "]) + assert result is not None + assert "name" in result + assert "age" in result + + def test_nested_field(self): + result = Simple.parse_fields(["address.city"]) + assert result is not None + assert "address.city" in result + + def test_parent_collapses_child(self): + result = Simple.parse_fields(["address", "address.city"]) + assert result is not None + assert "address" in result + assert "address.city" not in result + + def test_unknown_field_raises(self): + with pytest.raises(AppValidationError, match="unknown field"): + Simple.parse_fields(["nonexistent"]) + + def test_scalar_subfield_raises(self): + with pytest.raises(AppValidationError, match="cannot select subfields"): + Simple.parse_fields(["name.sub"]) + + def test_sparse_always_always_included(self): + class WithAlways(SparseFieldsModel): + id: str | None = None + name: str | None = None + sparse_always = frozenset({"id"}) + + result = WithAlways.parse_fields(["name"]) + assert result is not None + assert "id" in result + assert "name" in result + + +# --------------------------------------------------------------------------- +# SparseFieldsModel.projection +# --------------------------------------------------------------------------- + + +class TestProjection: + def test_none_fields_returns_self(self): + assert Simple.projection(None) is Simple + + def test_with_fields_returns_different_model(self): + fields = Simple.parse_fields(["name"]) + result = Simple.projection(fields) + assert result is not Simple + + def test_projected_model_has_settings_with_projection(self): + fields = Simple.parse_fields(["name"]) + projected = Simple.projection(fields) + assert hasattr(projected, "Settings") + assert hasattr(projected.Settings, "projection") + + def test_projection_includes_id(self): + fields = Simple.parse_fields(["name"]) + projected = Simple.projection(fields) + assert "_id" in projected.Settings.projection + + def test_projection_caching(self): + fields = Simple.parse_fields(["name"]) + first = Simple.projection(fields) + second = Simple.projection(fields) + assert first is second + + +# --------------------------------------------------------------------------- +# SparseFieldsModel._identity_fields +# --------------------------------------------------------------------------- + + +class TestIdentityFields: + def test_field_with_id_alias_detected(self): + class WithId(SparseFieldsModel): + id: str | None = Field(default=None, alias="_id", serialization_alias="id") + name: str | None = None + + identity = WithId._identity_fields() + assert "id" in identity + + def test_no_id_field_returns_empty(self): + identity = Simple._identity_fields() + assert identity == frozenset() diff --git a/mpcontribs-api/tests/unit/test_supervisord_render.py b/mpcontribs-api/tests/unit/test_supervisord_render.py new file mode 100644 index 000000000..e7461f21a --- /dev/null +++ b/mpcontribs-api/tests/unit/test_supervisord_render.py @@ -0,0 +1,61 @@ +"""The rendered supervisord config must export the env vars the new pydantic Settings require. + +The FastAPI rewrite reads nested settings via the ``MPCONTRIBS___`` convention. This +guards against regressing the supervisord template back to the Flask-era flat names, which would +make the container fail Settings validation at startup. +""" + +from pathlib import Path + +import pytest +from jinja2 import Environment, FileSystemLoader + +SUPERVISORD_DIR = Path(__file__).resolve().parents[2] / "supervisord" + +# Names the new Settings model needs present in the process environment. +REQUIRED_ENV_NAMES = [ + "MPCONTRIBS_ENVIRONMENT", + "MPCONTRIBS_MAIL_DEFAULT_SENDER", + "MPCONTRIBS_VERSION", + "MPCONTRIBS_OTEL__OTLP_ENDPOINT", +] + + +def _render() -> str: + env = Environment(loader=FileSystemLoader(str(SUPERVISORD_DIR))) + template = env.get_template("supervisord.conf.jinja") + return template.render( + production=True, + environment="prod", + version="1.2.3", + deployments={ + "ml": { + "api_port": "10002", + "portal_port": 8082, + "db": "ml", + "s3": "ml", + "tm": "MP", + "max_projects": 3, + } + }, + nworkers=2, + reload=0, + node_env="production", + flask_debug=False, + flask_log_level="INFO", + jupyter_gateway_url="http://localhost:10100", + jupyter_gateway_host="localhost:10100", + otel_endpoint="localhost:4317", + mpcontribs_api_host="localhost", + ) + + +@pytest.mark.parametrize("name", REQUIRED_ENV_NAMES) +def test_required_env_name_present(name: str) -> None: + assert name in _render() + + +def test_no_stale_flat_mongo_db_name() -> None: + rendered = _render() + # The old flat name must not appear as an assignment (the nested name is required instead). + assert "MPCONTRIBS_DB_NAME=" not in rendered diff --git a/mpcontribs-api/tests/unit/test_types.py b/mpcontribs-api/tests/unit/test_types.py new file mode 100644 index 000000000..46c43d8bf --- /dev/null +++ b/mpcontribs-api/tests/unit/test_types.py @@ -0,0 +1,101 @@ +import pytest +from pydantic import BaseModel +from pydantic import ValidationError as PydanticValidationError + +from mpcontribs_api.exceptions import ValidationError as AppValidationError +from mpcontribs_api.domains._shared.types import PrefixedEmail, ShortStr, _validate_prefixed_email + + +class ShortStrModel(BaseModel): + value: ShortStr + + +class PrefixedEmailModel(BaseModel): + email: PrefixedEmail + + +class TestShortStr: + def test_valid_3_chars(self): + m = ShortStrModel(value="abc") + assert m.value == "abc" + + def test_valid_30_chars(self): + m = ShortStrModel(value="a" * 30) + assert m.value == "a" * 30 + + def test_valid_mid_length(self): + m = ShortStrModel(value="test-project") + assert m.value == "test-project" + + def test_too_short_raises(self): + with pytest.raises(PydanticValidationError): + ShortStrModel(value="ab") + + def test_empty_raises(self): + with pytest.raises(PydanticValidationError): + ShortStrModel(value="") + + def test_too_long_raises(self): + with pytest.raises(PydanticValidationError): + ShortStrModel(value="a" * 31) + + def test_exactly_31_chars_raises(self): + with pytest.raises(PydanticValidationError): + ShortStrModel(value="a" * 31) + + +class TestValidatePrefixedEmail: + def test_valid_format(self): + assert _validate_prefixed_email("google:alice@example.com") == "google:alice@example.com" + + def test_strips_surrounding_whitespace(self): + assert _validate_prefixed_email(" google:alice@example.com ") == "google:alice@example.com" + + def test_no_colon_raises(self): + with pytest.raises(AppValidationError): + _validate_prefixed_email("googlealice@example.com") + + def test_no_at_sign_raises(self): + with pytest.raises(AppValidationError): + _validate_prefixed_email("google:aliceexample.com") + + def test_no_domain_raises(self): + with pytest.raises(AppValidationError): + _validate_prefixed_email("google:alice@") + + def test_no_tld_raises(self): + with pytest.raises(AppValidationError): + _validate_prefixed_email("google:alice@example") + + def test_empty_provider_raises(self): + with pytest.raises(AppValidationError): + _validate_prefixed_email(":alice@example.com") + + def test_empty_name_raises(self): + with pytest.raises(AppValidationError): + _validate_prefixed_email("google:@example.com") + + def test_multiple_at_signs_raises(self): + with pytest.raises(AppValidationError): + _validate_prefixed_email("google:alice@@example.com") + + def test_multiple_colons_raises(self): + # The regex requires no colon in provider or local part + with pytest.raises(AppValidationError): + _validate_prefixed_email("goo:gle:alice@example.com") + + +class TestPrefixedEmailModel: + def test_valid_email(self): + m = PrefixedEmailModel(email="github:bob@github.com") + assert m.email == "github:bob@github.com" + + def test_invalid_email_raises_app_validation_error(self): + # BeforeValidator raises AppValidationError; Pydantic does not wrap + # non-standard exceptions (ValueError/TypeError/AssertionError) from validators. + with pytest.raises(AppValidationError): + PrefixedEmailModel(email="not-an-email") + + def test_whitespace_stripped(self): + m = PrefixedEmailModel(email=" orcid:12345@orcid.org ") + assert m.email == "orcid:12345@orcid.org" diff --git a/mpcontribs-api/tests/unit/test_types_components.py b/mpcontribs-api/tests/unit/test_types_components.py new file mode 100644 index 000000000..eb4308989 --- /dev/null +++ b/mpcontribs-api/tests/unit/test_types_components.py @@ -0,0 +1,206 @@ +import polars as pl +import pytest +from pydantic import BaseModel, ConfigDict + +from mpcontribs_api.domains._shared.types import ( + DownloadFormat, + FileLike, + MD5Hash, + MimeFormat, + PolarsFrame, + _coerce_frame, + _serialize_frame, +) +from mpcontribs_api.exceptions import ValidationError as AppValidationError + + +class FileLikeModel(BaseModel): + name: FileLike + + +class MD5Model(BaseModel): + digest: MD5Hash + + +class MimeModel(BaseModel): + mime: MimeFormat + + +class FrameModel(BaseModel): + model_config = ConfigDict(arbitrary_types_allowed=True) + data: PolarsFrame + + +# --------------------------------------------------------------------------- +# FileLike / _file_name_like_str +# --------------------------------------------------------------------------- + + +class TestFileLike: + def test_simple_extension(self): + assert FileLikeModel(name="archive.gz").name == "archive.gz" + + def test_multiple_dots_valid(self): + assert FileLikeModel(name="data.tar.gz").name == "data.tar.gz" + + def test_strips_surrounding_whitespace(self): + assert FileLikeModel(name=" notes.txt ").name == "notes.txt" + + def test_no_extension_raises(self): + with pytest.raises(AppValidationError): + FileLikeModel(name="noextension") + + def test_trailing_dot_raises(self): + with pytest.raises(AppValidationError): + FileLikeModel(name="name.") + + def test_empty_string_raises(self): + with pytest.raises(AppValidationError): + FileLikeModel(name="") + + def test_leading_dot_file_is_accepted(self): + # Documents current behavior: dotfiles split into ["", "ext"], which + # has a non-empty last part and therefore passes. + assert FileLikeModel(name=".gitignore").name == ".gitignore" + + +# --------------------------------------------------------------------------- +# MD5Hash / _md5_like +# --------------------------------------------------------------------------- + + +class TestMD5Hash: + def test_valid_lowercase_hex(self): + assert MD5Model(digest="a" * 32).digest == "a" * 32 + + def test_uppercase_normalized_to_lowercase(self): + assert MD5Model(digest="ABCDEF" + "0" * 26).digest == "abcdef" + "0" * 26 + + def test_strips_whitespace(self): + assert MD5Model(digest=f" {'b' * 32} ").digest == "b" * 32 + + def test_too_short_raises(self): + with pytest.raises(AppValidationError): + MD5Model(digest="a" * 31) + + def test_too_long_raises(self): + with pytest.raises(AppValidationError): + MD5Model(digest="a" * 33) + + def test_non_hex_characters_raise(self): + with pytest.raises(AppValidationError): + MD5Model(digest="g" * 32) + + def test_empty_raises(self): + with pytest.raises(AppValidationError): + MD5Model(digest="") + + +# --------------------------------------------------------------------------- +# MimeFormat / _mime_like +# --------------------------------------------------------------------------- + + +class TestMimeFormat: + def test_valid_application_mime(self): + assert MimeModel(mime="application/gzip").mime == "application/gzip" + + def test_uppercase_normalized(self): + assert MimeModel(mime="APPLICATION/JSON").mime == "application/json" + + def test_strips_whitespace(self): + assert MimeModel(mime=" application/zip ").mime == "application/zip" + + def test_non_application_prefix_raises(self): + with pytest.raises(AppValidationError): + MimeModel(mime="text/plain") + + def test_empty_subtype_raises(self): + with pytest.raises(AppValidationError): + MimeModel(mime="application/") + + def test_missing_slash_raises(self): + with pytest.raises(AppValidationError): + MimeModel(mime="applicationgzip") + + def test_extra_slash_raises(self): + with pytest.raises(AppValidationError): + MimeModel(mime="application/x/y") + + +# --------------------------------------------------------------------------- +# DownloadFormat +# --------------------------------------------------------------------------- + + +class TestDownloadFormat: + def test_members(self): + assert {f.value for f in DownloadFormat} == {"jsonl", "csv"} + + def test_constructible_from_value(self): + assert DownloadFormat("jsonl") is DownloadFormat.JSONL + assert DownloadFormat("csv") is DownloadFormat.CSV + + def test_str_enum_compares_to_plain_str(self): + assert DownloadFormat.CSV == "csv" + + def test_invalid_value_raises(self): + with pytest.raises(ValueError): + DownloadFormat("parquet") + + +# --------------------------------------------------------------------------- +# PolarsFrame: _coerce_frame / _serialize_frame +# --------------------------------------------------------------------------- + + +class TestCoerceFrame: + def test_dataframe_passthrough_is_same_object(self): + df = pl.DataFrame({"a": [1, 2]}) + assert _coerce_frame(df) is df + + def test_dict_coerced_to_dataframe(self): + result = _coerce_frame({"a": [1, 2], "b": [3.0, 4.0]}) + assert isinstance(result, pl.DataFrame) + assert result.columns == ["a", "b"] + assert result.height == 2 + + def test_unsupported_type_raises_value_error(self): + with pytest.raises(ValueError, match="cannot coerce"): + _coerce_frame([[1, 2], [3, 4]]) + + def test_none_raises_value_error(self): + with pytest.raises(ValueError, match="cannot coerce"): + _coerce_frame(None) + + +class TestSerializeFrame: + def test_round_trips_to_column_dict(self): + df = pl.DataFrame({"x": [1, 2], "y": [10, 20]}) + assert _serialize_frame(df) == {"x": [1, 2], "y": [10, 20]} + + def test_empty_frame(self): + assert _serialize_frame(pl.DataFrame({"x": []})) == {"x": []} + + +class TestPolarsFrameAnnotated: + def test_model_accepts_dict(self): + m = FrameModel(data={"a": [1, 2]}) + assert isinstance(m.data, pl.DataFrame) + assert m.data["a"].to_list() == [1, 2] 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