From 6a578b0bab9547f2be7586ec797aec8e478e2480 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sun, 21 Jul 2024 16:25:58 +0530 Subject: [PATCH 01/22] feat: create task --- deployment/config.yaml | 72 +++++++++ poetry.lock | 8 +- pyproject.toml | 2 +- tesk/api/ga4gh/tes/controllers.py | 19 ++- tesk/api/ga4gh/tes/task/__init__.py | 1 + tesk/api/ga4gh/tes/task/create_task.py | 77 ++++++++++ tesk/api/kubernetes/__init__.py | 1 + tesk/api/kubernetes/client_wrapper.py | 203 +++++++++++++++++++++++++ tesk/api/kubernetes/constants.py | 132 ++++++++++++++++ tesk/api/kubernetes/converter.py | 133 ++++++++++++++++ tesk/api/kubernetes/template.py | 90 +++++++++++ tesk/app.py | 1 + tesk/custom_config.py | 147 ++++++++++++++++++ tesk/exceptions.py | 10 ++ tesk/utils.py | 191 +++++++++++++++++++++++ 15 files changed, 1080 insertions(+), 7 deletions(-) create mode 100644 tesk/api/ga4gh/tes/task/__init__.py create mode 100644 tesk/api/ga4gh/tes/task/create_task.py create mode 100644 tesk/api/kubernetes/__init__.py create mode 100644 tesk/api/kubernetes/client_wrapper.py create mode 100644 tesk/api/kubernetes/constants.py create mode 100644 tesk/api/kubernetes/converter.py create mode 100644 tesk/api/kubernetes/template.py create mode 100644 tesk/custom_config.py create mode 100644 tesk/utils.py diff --git a/deployment/config.yaml b/deployment/config.yaml index e102bf37..a443b07d 100644 --- a/deployment/config.yaml +++ b/deployment/config.yaml @@ -48,6 +48,78 @@ api: swagger_ui: True serve_spec: True +custom: + taskmaster_template: + apiVersion: batch/v1 + kind: Job + metadata: + name: taskmaster + labels: + app: taskmaster + spec: + template: + metadata: + name: taskmaster + spec: + serviceAccountName: default + containers: + - name: taskmaster + image: eu.gcr.io/tes-wes/taskmaster:v0.0.5.2 + args: + - -f + - /jsoninput/JSON_INPUT.gz + env: + - name: TESK_FTP_USERNAME + valueFrom: + secretKeyRef: + name: ftp-secret + key: username + optional: true + - name: TESK_FTP_PASSWORD + valueFrom: + secretKeyRef: + name: ftp-secret + key: password + optional: true + volumeMounts: + - name: podinfo + mountPath: /podinfo + readOnly: true + - name: jsoninput + mountPath: /jsoninput + readOnly: true + volumes: + - name: podinfo + downwardAPI: + items: + - path: labels + fieldRef: + fieldPath: metadata.labels + restartPolicy: Never + taskmaster_env_properties: + # Taskmaster image name + imageName: eu.gcr.io/tes-wes/taskmaster + # Taskmaster image version + imageVersion: v0.10.0 + # Filer image name + filerImageName: eu.gcr.io/tes-wes/filer + # Filer image version + filerImageVersion: v0.10.0 + # Test FTP account settings + ftp: + # Name of the secret with FTP account credentials + secretName: account-secret + # If FTP account enabled (based on non-emptiness of secretName) + enabled: false + # If verbose (debug) mode of taskmaster is on (passes additional flag to taskmaster and sets image pull policy to Always) + debug: false + # Environment variables, that will be passed to taskmaster + environment: + key: value + # Service Account name for taskmaster + serviceAccountName: default + + # Logging configuration # Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.LogConfig log: diff --git a/poetry.lock b/poetry.lock index 3143c301..90462f06 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1486,13 +1486,13 @@ zookeeper = ["kazoo (>=2.8.0)"] [[package]] name = "kubernetes" -version = "29.0.0" +version = "30.1.0" description = "Kubernetes python client" optional = false python-versions = ">=3.6" files = [ - {file = "kubernetes-29.0.0-py2.py3-none-any.whl", hash = "sha256:ab8cb0e0576ccdfb71886366efb102c6a20f268d817be065ce7f9909c631e43e"}, - {file = "kubernetes-29.0.0.tar.gz", hash = "sha256:c4812e227ae74d07d53c88293e564e54b850452715a59a927e7e1bc6b9a60459"}, + {file = "kubernetes-30.1.0-py2.py3-none-any.whl", hash = "sha256:e212e8b7579031dd2e512168b617373bc1e03888d41ac4e04039240a292d478d"}, + {file = "kubernetes-30.1.0.tar.gz", hash = "sha256:41e4c77af9f28e7a6c314e3bd06a8c6229ddd787cad684e0ab9f69b498e98ebc"}, ] [package.dependencies] @@ -3165,4 +3165,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "f84324e2321c3fc0bd7e89e46294a494af5805b4bc1845adeb7d08d5ffe7fdfb" +content-hash = "76db58e24a3e85e5e7df18c0013cbf61bfce0d94c8fbb3af7bed6206b88ef64c" diff --git a/pyproject.toml b/pyproject.toml index 92cd2d18..b52b9297 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,7 @@ version = "0.1.0" [tool.poetry.dependencies] boto3 = "1.34.104" foca = "^0.13.0" -kubernetes = "^29.0.0" +kubernetes = "^30.1.0" python = "^3.11" requests = ">=2.20.0" urllib3 = "^2.2.1" diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index c92497fe..c2d66b58 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/tesk/api/ga4gh/tes/controllers.py @@ -2,9 +2,15 @@ import logging -# from connexion import request # type: ignore from foca.utils.logging import log_traffic # type: ignore +from tesk.api.kubernetes.template import KubernetesTemplateSupplier +from tesk.api.ga4gh.tes.models import TesTask +from tesk.utils import get_custom_config +from tesk.api.kubernetes.converter import TesKubernetesConverter + +# from tesk.api.ga4gh.tes.task.create_task import CreateTask as TaskCreater + # Get logger instance logger = logging.getLogger(__name__) @@ -24,13 +30,22 @@ def CancelTask(id, *args, **kwargs) -> dict: # type: ignore # POST /tasks @log_traffic -def CreateTask(*args, **kwargs) -> dict: # type: ignore +def CreateTask(**kwargs) -> dict: # type: ignore """Create task. Args: *args: Variable length argument list. **kwargs: Arbitrary keyword arguments. """ + request_body = kwargs["body"] + create_task_request = TesTask(**request_body) + user = { + "username": "test", + "is_member": True, + "any_group": "test_group", + } + tkc = TesKubernetesConverter().from_tes_task_to_k8s_job(create_task_request, user) + print(tkc) pass diff --git a/tesk/api/ga4gh/tes/task/__init__.py b/tesk/api/ga4gh/tes/task/__init__.py new file mode 100644 index 00000000..b8e71d87 --- /dev/null +++ b/tesk/api/ga4gh/tes/task/__init__.py @@ -0,0 +1 @@ +"""Task API controller logic.""" diff --git a/tesk/api/ga4gh/tes/task/create_task.py b/tesk/api/ga4gh/tes/task/create_task.py new file mode 100644 index 00000000..3694718e --- /dev/null +++ b/tesk/api/ga4gh/tes/task/create_task.py @@ -0,0 +1,77 @@ +"""TESK API module for creating a task.""" + +import logging + +from tesk.api.ga4gh.tes.models import TesTask +from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper +from tesk.api.kubernetes.constants import Constants +from tesk.api.kubernetes.converter import TesKubernetesConverter +from tesk.exceptions import KubernetesError + +logger = logging.getLogger(__name__) + + +class CreateTesTask: + """Create TES task.""" + + def __init__(self, task: TesTask, user=None, namespace="default"): + """Initialize the CreateTask class. + + Args: + task: TES task to create. + user: User who creates the task. + namespace: Kubernetes namespace where the task is created. + """ + self.task = task + self.user = user + self.kubernetes_client_wrapper = KubernetesClientWrapper() + self.namespace = namespace + self.tes_kubernetes_converter = TesKubernetesConverter(self.namespace) + self.constants = Constants() + + def create_task(self): + """Create TES task.""" + attempts_no = 0 + while True: + try: + resources = self.task.resources + + if resources and resources.ram_gb: + minimum_ram_gb = self.kubernetes_client_wrapper.minimum_ram_gb() + if resources.ram_gb < minimum_ram_gb: + self.task.resources.ram_gb = minimum_ram_gb + + task_master_job = ( + self.tes_kubernetes_converter.from_tes_task_to_k8s_job( + self.task, self.user + ) + ) + + # TODO: Create ConfigMap + # TODO: Create Job + # TODO Return created job + # task_master_config_map = converter.from_tes_task_to_k8s_config_map( + # task, user, task_master_job + # ) + # created_config_map = kubernetes_client_wrapper.create_config_map( + # task_master_config_map + # ) + # created_job = kubernetes_client_wrapper.create_job(task_master_job) + # return converter.from_k8s_job_to_tes_create_task_response(created_job) + + except KubernetesError as e: + # Handle Kubernetes specific exceptions + if ( + not e.is_object_name_duplicated() + or attempts_no >= self.constants.job_create_attempts_no + ): + raise e + attempts_no += 1 + + except Exception as exc: + logging.error("ERROR: In createTask", exc_info=True) + raise exc + + def response(self) -> dict: + """Create response.""" + return self.create_task() diff --git a/tesk/api/kubernetes/__init__.py b/tesk/api/kubernetes/__init__.py new file mode 100644 index 00000000..ffa7082e --- /dev/null +++ b/tesk/api/kubernetes/__init__.py @@ -0,0 +1 @@ +"""Kubernetes API module.""" diff --git a/tesk/api/kubernetes/client_wrapper.py b/tesk/api/kubernetes/client_wrapper.py new file mode 100644 index 00000000..1854f2e6 --- /dev/null +++ b/tesk/api/kubernetes/client_wrapper.py @@ -0,0 +1,203 @@ +"""Wrapper Abstraction of Kubernetes Python client API for TESK.""" + +import logging +from typing import Optional + +from kubernetes import client, config +from kubernetes.client import V1ConfigMap, V1Job, V1LimitRangeList +from kubernetes.utils.quantity import parse_quantity # type: ignore + +from tesk.exceptions import KubernetesError, NotFound + +logger = logging.getLogger(__name__) + + +class KubernetesClientWrapper: + """Kubernetes client wrapper class.""" + + def __init__(self, namespace="tesk"): + """Initialize the Kubernetes client wrapper. + + Args: + namespace: Namespace to use for Kubernetes. + """ + # NOTE: WE might want to provide config files to load_kube_config + # we can have env variable define this or it can be passed from + # custom in FOCA config. Latter is prefered. + config.load_kube_config() + self.batch_api = client.BatchV1Api() + self.core_api = client.CoreV1Api() + self.namespace = namespace + + def create_job(self, job: V1Job) -> V1Job: + """Create a job in the Kubernetes cluster. + + Returns: + Job object created in the Kubernetes cluster. + """ + try: + v1_job: V1Job = self.batch_api.create_namespaced_job( + namespace=self.namespace, body=job + ) + return v1_job + except KubernetesError as e: + logger.error(f"Exception when creating job: {e}") + raise + + def create_config_map(self, config_map: V1ConfigMap) -> V1ConfigMap: + """Create a config map in the Kubernetes cluster. + + Args: + config_map: ConfigMap object to create. + """ + try: + v1_config_map: V1ConfigMap = self.core_api.create_namespaced_config_map( + namespace=self.namespace, body=config_map + ) + return v1_config_map + except KubernetesError as e: + logger.error(f"Exception when creating config map: {e}") + raise + + def read_taskmaster_job(self, task_id: str) -> V1Job: + """Read a taskmaster job from the Kubernetes cluster. + + task_id: Task identifier. + + Returns: + Job object read from the Kubernetes cluster + + Raises: + Exception: If the task is not found. + """ + try: + job: V1Job = self.batch_api.read_namespaced_job( + name=task_id, namespace=self.namespace + ) + if ( + # TODO: Put all these string in constants.py + "job-type" in job.metadata.labels + and job.metadata.labels["job-type"] == "taskmaster" + ): + return job + except KubernetesError as e: + if e.status != NotFound.code: + logger.error(f"Exception when reading job: {e}") + raise + raise Exception(f"Task {task_id} not found") + + def list_jobs(self, label_selector=None, limit=None): + """List jobs in the Kubernetes cluster. + + Args: + label_selector: Label selector to filter jobs. + limit: Maximum number of jobs to return. + """ + try: + return self.batch_api.list_namespaced_job( + namespace=self.namespace, label_selector=label_selector, limit=limit + ) + except KubernetesError as e: + logger.error(f"Exception when listing jobs: {e}") + raise + + def list_limits(self, label_selector=None, limit=None) -> V1LimitRangeList: + """List limit ranges in the Kubernetes cluster. + + Args: + label_selector: Label selector to filter limit ranges. + limit: Maximum number of limit ranges to return. + """ + try: + return self.core_api.list_namespaced_limit_range( + namespace=self.namespace, label_selector=label_selector, limit=limit + ) + except KubernetesError as e: + logger.error(f"Exception when listing limits: {e}") + raise + + def minimum_ram_gb(self) -> float: + """Get the minimum amount of RAM in the cluster. + + Returns: + Minimum amount of RAM in the cluster in GB. + """ + try: + min_ram = 0 + limits = self.list_limits().items + for limit in limits: + for item in limit.spec.limits: + if "memory" in item.min: + mem_quantity = item.min["memory"] + mem_bytes = self.quantity_to_bytes(mem_quantity) + min_ram = max(min_ram, mem_bytes) + return min_ram / (1024**3) + except Exception as e: + logger.error(f"Error in minimum_ram_gb: {e}") + return 0.0 + + def quantity_to_bytes(self, quantity: str) -> int: + """Convert quantity(resource) to bytes.""" + return parse_quantity(quantity) + + def list_single_job_pods(self, job: V1Job): + """List pods associated with a single job. + + Args: + job: Job object to list pods for. + """ + label_selector = ",".join( + f"{k}={v}" for k, v in job.spec.selector.match_labels.items() + ) + try: + return self.core_api.list_namespaced_pod( + namespace=self.namespace, label_selector=label_selector + ) + except KubernetesError as e: + logger.error(f"Exception when listing pods: {e}") + raise + + def read_pod_log(self, pod_name: str) -> Optional[str]: + """Read logs from a pod. + + Args: + pod_name: Name of the pod to read logs from. + """ + try: + pod_log: str = self.core_api.read_namespaced_pod_log( + name=pod_name, namespace=self.namespace + ) + return pod_log + except KubernetesError as e: + logger.error(f"Exception when reading pod log: {e}") + return None + + def label_job_as_cancelled(self, task_id: str) -> None: + """Label a job as cancelled. + + Args: + task_id: Task identifier. + """ + try: + patch = {"metadata": {"labels": {"status": "cancelled"}}} + self.batch_api.patch_namespaced_job( + name=task_id, namespace=self.namespace, body=patch + ) + except KubernetesError as e: + logger.error(f"Exception when labeling job as cancelled: {e}") + raise + + def label_pod_as_cancelled(self, pod_name: str) -> None: + """Label a pod as cancelled. + + Args: + pod_name: Pod name. + """ + try: + patch = {"metadata": {"labels": {"status": "cancelled"}}} + self.core_api.patch_namespaced_pod( + name=pod_name, namespace=self.namespace, body=patch + ) + except KubernetesError as e: + logger.error(f"Exception when labeling pod as cancelled: {e}") + raise diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py new file mode 100644 index 00000000..5ea8e81c --- /dev/null +++ b/tesk/api/kubernetes/constants.py @@ -0,0 +1,132 @@ +"""Constants for Kubernetes API.""" + +from typing import Set + +from pydantic import BaseModel, Field + + +class Constants(BaseModel): + taskmaster_input: str = Field( + default="JSON_INPUT", + description="ENV var that serves as taskmaster script input (JSON format)", + ) + taskmaster_input_exec_key: str = Field( + default="executors", + description="Key in JSON taskmaster input, which holds list of executors", + ) + volume_name: str = Field("PVC", description="Volume name") + job_create_attempts_no: int = Field( + default=5, + description="Number of attempts of job creation in case of name collision", + ) + job_name_taskm_prefix: str = Field( + default="task-", + description="Constant prefix of taskmaster's job name (== TES task ID)", + ) + job_name_exec_prefix: str = Field( + default="-ex-", + description="Part of executor's job name, that follows taskmaster's name", + ) + job_name_taskm_rand_part_length: int = Field( + default=4, + description="No of bytes of random part of task master's name (which end up encoded to hex)", + ) + job_name_exec_no_length: int = Field( + default=2, + description="No of digits reserved for executor number in executor's job name. Ends up padded with '0' for numbers < 10", + ) + job_name_filer_suf: str = Field( + default="-outputs-filer", description="Output filer name suffix" + ) + ann_testask_name_key: str = Field( + default="tes-task-name", + description="Key of the annotation, that stores name of TES task in both taskmaster's job and executor's jobs", + ) + ann_json_input_key: str = Field( + default="json-input", + description="Key of the annotation, that stores whole input TES task serialized to JSON", + ) + label_testask_id_key: str = Field( + default="taskmaster-name", + description="Key of the label, that stores taskmaster's name (==TES task generated ID) in executor jobs", + ) + label_jobtype_key: str = Field( + default="job-type", + description="Key of the label, that stores type of a job (taskmaster or executor)", + ) + label_jobtype_value_taskm: str = Field( + default="taskmaster", + description="Value of the label with taskmaster's job type", + ) + label_jobtype_value_exec: str = Field( + default="executor", description="Value of the label with executor's job type" + ) + label_execno_key: str = Field( + default="executor-no", + description="Key of the label, that holds executor number for executor jobs", + ) + label_taskstate_key: str = Field( + default="task-status", + description="Key of the label, that holds executor's state", + ) + label_taskstate_value_canc: str = Field( + default="Cancelled", + description="Value of the label, that holds executor's Cancelled state", + ) + label_userid_key: str = Field( + default="creator-user-id", description="Key of the label, that holds user id" + ) + label_groupname_key: str = Field( + default="creator-group-name", + description="Key of the label, that holds user's group name", + ) + absolute_path_regexp: str = Field( + default="^\\/.*", description="Pattern to validate paths" + ) + absolute_path_message: str = Field( + default="must be an absolute path", + description="Message for absolute path validation (to avoid message.properties)", + ) + resource_disk_default: float = Field(0.1, description="Default resource disk value") + completed_states: Set[str] = Field( + default={"CANCELED", "COMPLETE", "EXECUTOR_ERROR", "SYSTEM_ERROR"}, + description="TES task states, indicating task is not running and cannot be cancelled", + ) + ftp_secret_username_env: str = Field( + default="TESK_FTP_USERNAME", + description="Name of taskmaster's ENV variable with username of FTP account used for storage", + ) + ftp_secret_password_env: str = Field( + default="TESK_FTP_PASSWORD", + description="Name of taskmaster's ENV variable with password of FTP account used for storage", + ) + cancel_patch: str = Field( + default='{"metadata":{"labels":{"task-status":"Cancelled"}}}', + description="Patch object passed to job API, when cancelling task", + ) + + +class PodPhase(BaseModel): + code: str = Field(default="Pending", description="The phase code of the pod") + + +class K8sConstants(BaseModel): + k8s_batch_api_version: str = Field( + default="batch/v1", description="Kubernetes Batch API version" + ) + k8s_batch_api_job_type: str = Field( + default="Job", description="Kubernetes Job object type" + ) + job_restart_policy: str = Field( + default="Never", description="Kubernetes Job restart policy" + ) + resource_cpu_key: str = Field("cpu", description="Executor CPU resource label") + resource_mem_key: str = Field( + default="memory", description="Executor memory resource label" + ) + resource_mem_unit: str = Field( + default="Gi", description="Executor memory resource unit" + ) + resource_mem_one_gb: int = Field( + default=1073741824, description="One Gibibyte (Gi) in bytes" + ) diff --git a/tesk/api/kubernetes/converter.py b/tesk/api/kubernetes/converter.py new file mode 100644 index 00000000..8309d00a --- /dev/null +++ b/tesk/api/kubernetes/converter.py @@ -0,0 +1,133 @@ +"""Module for converting TES tasks to Kubernetes jobs.""" + +import gzip +import json +import logging +from io import BytesIO + +from kubernetes.client import ( + V1ConfigMap, + V1ConfigMapVolumeSource, + V1ObjectMeta, + V1Volume, +) +from kubernetes.client.models import V1Job + +from tesk.api.ga4gh.tes.models import TesTask +from tesk.api.kubernetes.constants import Constants, K8sConstants +from tesk.api.kubernetes.template import KubernetesTemplateSupplier +from tesk.custom_config import TaskmasterEnvProperties +from tesk.utils import get_taskmaster_env_property, get_taskmaster_template + +logger = logging.getLogger(__name__) + + +class TesKubernetesConverter: + def __init__(self, namespace="default"): + """Initialize the converter.""" + self.taskmaster_template: V1Job = get_taskmaster_template() + self.taskmaster_env_properties: TaskmasterEnvProperties = ( + get_taskmaster_env_property() + ) + self.constants = Constants() + self.k8s_constants = K8sConstants() + self.namespace = namespace + + def from_tes_task_to_k8s_job(self, task: TesTask, user): + taskmsater_job: V1Job = KubernetesTemplateSupplier( + self.namespace + ).task_master_template() + + if taskmsater_job.metadata is None: + taskmsater_job.metadata = V1ObjectMeta() + + if taskmsater_job.metadata.annotations is None: + taskmsater_job.metadata.annotations = {} + + if taskmsater_job.metadata.labels is None: + taskmsater_job.metadata.labels = {} + + taskmsater_job.metadata.annotations[self.constants.ann_testask_name_key] = ( + task.name + ) + taskmsater_job.metadata.labels[self.constants.label_userid_key] = user[ + "username" + ] + + if task.tags and "GROUP_NAME" in task.tags: + taskmsater_job.metadata.labels[self.constants.label_userid_key] = task[ + "tags" + ]["GROUP_NAME"] + elif user["is_member"]: + taskmsater_job.metadata.labels[self.constants.label_groupname_key] = user[ + "any_group" + ] + + try: + taskmsater_job.metadata.annotations[self.constants.ann_json_input_key] = ( + task.json() + ) + except Exception as ex: + logger.info( + f"Serializing task {taskmsater_job.metadata.name} to JSON failed", ex + ) + + volume = V1Volume( + name="jsoninput", + config_map=V1ConfigMapVolumeSource(name=taskmsater_job.metadata.name), + ) + taskmsater_job.spec.template.spec.volumes.append(volume) + + return taskmsater_job + + # def from_tes_task_to_k8s_config_map(self, task, user, job): + # task_master_config_map = V1ConfigMap( + # metadata=V1ObjectMeta(name=job.metadata.name) + # ) + # task_master_config_map.metadata.annotations[ANN_TESTASK_NAME_KEY] = task["name"] + # task_master_config_map.metadata.labels[LABEL_USERID_KEY] = user["username"] + + # if "tags" in task and "GROUP_NAME" in task["tags"]: + # task_master_config_map.metadata.labels[LABEL_GROUPNAME_KEY] = task["tags"][ + # "GROUP_NAME" + # ] + # elif user["is_member"]: + # task_master_config_map.metadata.labels[LABEL_GROUPNAME_KEY] = user[ + # "any_group" + # ] + + # executors_as_jobs = [ + # self.from_tes_executor_to_k8s_job( + # task_master_config_map.metadata.name, + # task["name"], + # executor, + # idx, + # task["resources"], + # user, + # ) + # for idx, executor in enumerate(task["executors"]) + # ] + + # task_master_input = { + # "inputs": task.get("inputs", []), + # "outputs": task.get("outputs", []), + # "volumes": task.get("volumes", []), + # "resources": {"disk_gb": task["resources"].get("disk_gb", 10.0)}, + # } + # task_master_input[TASKMASTER_INPUT_EXEC_KEY] = executors_as_jobs + + # task_master_input_as_json = json.dumps(task_master_input) + # try: + # with BytesIO() as obj: + # with gzip.GzipFile(fileobj=obj, mode="wb") as gzip_file: + # gzip_file.write(task_master_input_as_json.encode("utf-8")) + # task_master_config_map.binary_data = { + # f"{TASKMASTER_INPUT}.gz": obj.getvalue() + # } + # except Exception as e: + # logger.info( + # f"Compression of task {task_master_config_map.metadata.name} JSON configmap failed", + # e, + # ) + + # return task_master_config_map diff --git a/tesk/api/kubernetes/template.py b/tesk/api/kubernetes/template.py new file mode 100644 index 00000000..842b18f7 --- /dev/null +++ b/tesk/api/kubernetes/template.py @@ -0,0 +1,90 @@ +"""Create tamplates for kubernetes objects.""" + +import logging +import uuid + +from kubernetes.client import ( + V1EnvVar, +) +from kubernetes.client.models import V1Job + +from tesk.api.kubernetes.constants import Constants, K8sConstants +from tesk.custom_config import TaskmasterEnvProperties +from tesk.utils import get_taskmaster_env_property, get_taskmaster_template + +logger = logging.getLogger(__name__) + + +class KubernetesTemplateSupplier: + """Templates for tasmaster's and executor's job object..""" + + def __init__(self, namespace="default"): + """Initialize the converter.""" + self.taskmaster_template: V1Job = get_taskmaster_template() + self.taskmaster_env_properties: TaskmasterEnvProperties = ( + get_taskmaster_env_property() + ) + self.constants = Constants() + self.k8s_constants = K8sConstants() + self.namespace = namespace + + def get_task_master_name(self) -> str: + """Generate a unique name for the taskmaster job.""" + return self.constants.job_name_taskm_prefix + str(uuid.uuid4()) + + def task_master_template(self) -> V1Job: + """Create a template for the taskmaster job.""" + job: V1Job = self.taskmaster_template + + job.spec.template.spec.service_account_name = ( + self.taskmaster_env_properties.serviceAccountName + ) + + container = job.spec.template.spec.containers[0] + container.image = f"{self.taskmaster_env_properties.imageName}:{self.taskmaster_env_properties.imageVersion}" + container.args.extend( + [ + "-n", + self.namespace, + "-fn", + self.taskmaster_env_properties.filerImageName, + "-fv", + self.taskmaster_env_properties.filerImageVersion, + ] + ) + + if self.taskmaster_env_properties.debug: + container.args.append("-d") + container.image_pull_policy = "Always" + + job.metadata.labels[self.constants.label_jobtype_key] = ( + self.constants.label_jobtype_value_taskm + ) + task_master_name = self.get_task_master_name() + job.metadata.name = task_master_name + + container.env.extend( + [ + V1EnvVar(name=key.upper().replace(".", "_"), value=value) + for key, value in self.taskmaster_env_properties.environment.items() + ] + ) + + ftp_secrets = [ + self.constants.ftp_secret_username_env, + self.constants.ftp_secret_password_env, + ] + container.env = [ + env + for env in container.env + if env.name not in ftp_secrets or self.taskmaster_env_properties.ftp.enabled + ] + + if self.taskmaster_env_properties.ftp.enabled: + for env in container.env: + if env.name in ftp_secrets: + env.value_from.secret_key_ref.name = ( + self.taskmaster_env_properties.ftp.secretName + ) + + return job diff --git a/tesk/app.py b/tesk/app.py index f09e525c..1dd4883a 100644 --- a/tesk/app.py +++ b/tesk/app.py @@ -38,6 +38,7 @@ def init_app() -> FlaskApp: foca = Foca( config_file=config_path, + custom_config_model="tesk.custom_config.CustomConfig", ) return foca.create_app() diff --git a/tesk/custom_config.py b/tesk/custom_config.py new file mode 100644 index 00000000..555e1d0f --- /dev/null +++ b/tesk/custom_config.py @@ -0,0 +1,147 @@ +"""Custom configuration model for the FOCA app.""" + +from typing import Dict, List, Optional + +from pydantic import BaseModel, Field + + +class FtpConfig(BaseModel): + """Ftp configuration model for the TESK.""" + + secretName: Optional[str] = Field( + default=None, description="Name of the secret with FTP account credentials" + ) + enabled: bool = Field( + default=False, + description="If FTP account enabled (based on non-emptiness of secretName)", + ) + + +class TaskmasterEnvProperties(BaseModel): + """Taskmaster environment properties model for the TESK.""" + + imageName: str = Field( + default="eu.gcr.io/tes-wes/taskmaster", description="Taskmaster image name" + ) + imageVersion: str = Field(default="v0.10.0", description="Taskmaster image version") + filerImageName: str = Field( + default="eu.gcr.io/tes-wes/filer", description="Filer image name" + ) + filerImageVersion: str = Field(default="v0.10.0", description="Filer image version") + ftp: FtpConfig = Field(default=None, description="Test FTP account settings") + debug: bool = Field( + default=False, + description="If verbose (debug) mode of taskmaster is on (passes additional " + "flag to taskmaster and sets image pull policy to Always)", + ) + environment: Dict[str, str] = Field( + default={"key": "value"}, + description="Environment variables, that will be passed to taskmaster", + ) + serviceAccountName: str = Field( + default="default", description="Service Account name for taskmaster" + ) + + +class SecretKeyRef(BaseModel): + """Reference to a secret key.""" + + name: str + key: str + optional: Optional[bool] = Field(False, description="If the reference is optional") + + +class EnvVarSource(BaseModel): + """Source for an environment variable.""" + + secretKeyRef: Optional[SecretKeyRef] = None + + +class EnvVar(BaseModel): + """Environment variable.""" + + name: str + valueFrom: Optional[EnvVarSource] = None + + +class VolumeMount(BaseModel): + """Volume mount configuration.""" + + name: str + mountPath: str + readOnly: bool + + +class DownwardAPIItem(BaseModel): + """Downward API item configuration.""" + + path: str + fieldRef: Dict[str, str] + + +class Volume(BaseModel): + """Volume configuration.""" + + name: str + downwardAPI: Optional[Dict[str, List[DownwardAPIItem]]] = None + + +class Container(BaseModel): + """Container configuration.""" + + name: str + image: str + args: List[str] + env: List[EnvVar] + volumeMounts: List[VolumeMount] + + +class PodSpec(BaseModel): + """Pod specification.""" + + serviceAccountName: str + containers: List[Container] + volumes: List[Volume] + restartPolicy: str + + +class PodMetadata(BaseModel): + """Pod metadata.""" + + name: str + + +class PodTemplate(BaseModel): + """Pod template configuration.""" + + metadata: PodMetadata + spec: PodSpec + + +class JobSpec(BaseModel): + """Job specification.""" + + template: PodTemplate + + +class JobMetadata(BaseModel): + """Job metadata.""" + + name: str + labels: Dict[str, str] + + +class Job(BaseModel): + """Kubernetes Job configuration.""" + + apiVersion: str + kind: str + metadata: JobMetadata + spec: JobSpec + + +class CustomConfig(BaseModel): + """Custom configuration model for the FOCA app.""" + + taskmaster_template: Job # This is Pydantic model for V1Job + taskmaster_env_properties: TaskmasterEnvProperties diff --git a/tesk/exceptions.py b/tesk/exceptions.py index 8d00301c..add22fe0 100644 --- a/tesk/exceptions.py +++ b/tesk/exceptions.py @@ -7,12 +7,18 @@ OAuthProblem, Unauthorized, ) +from kubernetes.client.exceptions import ApiException from werkzeug.exceptions import ( BadRequest, InternalServerError, NotFound, ) + +class ConfigNotFoundError(FileNotFoundError): + """Configuration file not found error.""" + + # exceptions raised in app context exceptions = { Exception: { @@ -66,3 +72,7 @@ # exceptions raised outside of app context class ValidationError(Exception): """Value or object is not compatible with required type or schema.""" + + +class KubernetesError(ApiException): + """Kubernetes error.""" diff --git a/tesk/utils.py b/tesk/utils.py new file mode 100644 index 00000000..8fef6e42 --- /dev/null +++ b/tesk/utils.py @@ -0,0 +1,191 @@ +"""Utility functions for the TESK package.""" + +import os +from pathlib import Path +from typing import Optional + +from foca import Foca +from kubernetes.client.models import ( + V1Container, + V1DownwardAPIProjection, + V1DownwardAPIVolumeFile, + V1EnvVar, + V1EnvVarSource, + V1Job, + V1JobSpec, + V1ObjectMeta, + V1PodSpec, + V1PodTemplateSpec, + V1SecretKeySelector, + V1Volume, + V1VolumeMount, +) + +from tesk.custom_config import ( + Container, + CustomConfig, + DownwardAPIItem, + EnvVar, + EnvVarSource, + Job, + JobMetadata, + JobSpec, + PodSpec, + PodTemplate, + TaskmasterEnvProperties, + Volume, + VolumeMount, +) +from tesk.exceptions import ConfigNotFoundError + + +def get_config_path() -> Path: + """Get the configuration path. + + Returns: + The path of the config file. + """ + # Determine the configuration path + if config_path_env := os.getenv("TESK_FOCA_CONFIG_PATH"): + return Path(config_path_env).resolve() + else: + return (Path(__file__).parents[1] / "deployment" / "config.yaml").resolve() + + +def get_custom_config() -> CustomConfig: + """Get the custom configuration. + + Returns: + The custom configuration. + """ + conf = Foca(config_file=get_config_path()).conf + try: + return CustomConfig(**conf.custom) + except AttributeError: + raise ConfigNotFoundError( + "Custom configuration not found in config file." + ) from None + + +def get_taskmaster_template() -> V1Job: + """Get the taskmaster template from the custom configuration. + + Returns: + The taskmaster template. + """ + custom_conf = get_custom_config() + try: + print(custom_conf.taskmaster_template) + return job_to_v1job(custom_conf.taskmaster_template) + except AttributeError: + raise ConfigNotFoundError( + "Custom configuration doesn't seem to have taskmaster_template in config file." + ) from None + + +def get_taskmaster_env_property() -> TaskmasterEnvProperties: + """Get the taskmaster env property from the custom configuration. + + Returns: + The taskmaster env property. + """ + custom_conf = get_custom_config() + try: + return custom_conf.taskmaster_env_properties + except AttributeError: + raise ConfigNotFoundError( + "Custom configuration doesn't seem to have taskmaster_env_properties in config file." + ) from None + + +def job_to_v1job(job: Job) -> V1Job: + """Convert a pydantic job model to a V1Job object. + + Returns: + The V1Job object. + """ + + def convert_env_var_source( + env_var_source: Optional[EnvVarSource], + ) -> Optional[V1EnvVarSource]: + if env_var_source is None: + return None + if env_var_source.secretKeyRef: + return V1EnvVarSource( + secret_key_ref=V1SecretKeySelector( + name=env_var_source.secretKeyRef.name, + key=env_var_source.secretKeyRef.key, + optional=env_var_source.secretKeyRef.optional, + ) + ) + return None + + def convert_downward_api_item( + downward_api_item: DownwardAPIItem, + ) -> V1DownwardAPIVolumeFile: + return V1DownwardAPIVolumeFile( + path=downward_api_item.path, field_ref=downward_api_item.fieldRef + ) + + def convert_volume(volume: Volume) -> V1Volume: + if volume.downwardAPI: + return V1Volume( + name=volume.name, + downward_api=V1DownwardAPIProjection( + items=[ + convert_downward_api_item(item) + for item in volume.downwardAPI["items"] + ] + ), + ) + return V1Volume(name=volume.name) + + def convert_env_var(env_var: EnvVar) -> V1EnvVar: + return V1EnvVar( + name=env_var.name, value_from=convert_env_var_source(env_var.valueFrom) + ) + + def convert_volume_mount(volume_mount: VolumeMount) -> V1VolumeMount: + return V1VolumeMount( + name=volume_mount.name, + mount_path=volume_mount.mountPath, + read_only=volume_mount.readOnly, + ) + + def convert_container(container: Container) -> V1Container: + return V1Container( + name=container.name, + image=container.image, + args=container.args, + env=[convert_env_var(env) for env in container.env], + volume_mounts=[convert_volume_mount(vm) for vm in container.volumeMounts], + ) + + def convert_pod_spec(pod_spec: PodSpec) -> V1PodSpec: + return V1PodSpec( + service_account_name=pod_spec.serviceAccountName, + containers=[ + convert_container(container) for container in pod_spec.containers + ], + volumes=[convert_volume(volume) for volume in pod_spec.volumes], + restart_policy=pod_spec.restartPolicy, + ) + + def convert_pod_template(pod_template: PodTemplate) -> V1PodTemplateSpec: + return V1PodTemplateSpec( + metadata=V1ObjectMeta(name=pod_template.metadata.name), + spec=convert_pod_spec(pod_template.spec), + ) + + def convert_job_spec(job_spec: JobSpec) -> V1JobSpec: + return V1JobSpec(template=convert_pod_template(job_spec.template)) + + def convert_job_metadata(job_metadata: JobMetadata) -> V1ObjectMeta: + return V1ObjectMeta(name=job_metadata.name, labels=job_metadata.labels) + + return V1Job( + api_version=job.apiVersion, + kind=job.kind, + metadata=convert_job_metadata(job.metadata), + spec=convert_job_spec(job.spec), + ) From 4edd2780095d4b80511f08b6400ec1868ea1c6cd Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sun, 21 Jul 2024 16:29:37 +0530 Subject: [PATCH 02/22] chore: update poetry lock --- poetry.lock | 998 +++++++++++++++++++++++++++------------------------- 1 file changed, 514 insertions(+), 484 deletions(-) diff --git a/poetry.lock b/poetry.lock index 90462f06..bcde931c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -92,13 +92,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p [[package]] name = "authlib" -version = "1.3.0" +version = "1.3.1" description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients." optional = false python-versions = ">=3.8" files = [ - {file = "Authlib-1.3.0-py2.py3-none-any.whl", hash = "sha256:9637e4de1fb498310a56900b3e2043a206b03cb11c05422014b0302cbc814be3"}, - {file = "Authlib-1.3.0.tar.gz", hash = "sha256:959ea62a5b7b5123c5059758296122b57cd2585ae2ed1c0622c21b371ffdae06"}, + {file = "Authlib-1.3.1-py2.py3-none-any.whl", hash = "sha256:d35800b973099bbadc49b42b256ecb80041ad56b7fe1216a362c7943c088f377"}, + {file = "authlib-1.3.1.tar.gz", hash = "sha256:7ae843f03c06c5c0debd63c9db91f9fda64fa62a42a77419fa15fbb7e7a58917"}, ] [package.dependencies] @@ -120,13 +120,13 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "bandit" -version = "1.7.8" +version = "1.7.9" description = "Security oriented static analyser for python code." optional = false python-versions = ">=3.8" files = [ - {file = "bandit-1.7.8-py3-none-any.whl", hash = "sha256:509f7af645bc0cd8fd4587abc1a038fc795636671ee8204d502b933aee44f381"}, - {file = "bandit-1.7.8.tar.gz", hash = "sha256:36de50f720856ab24a24dbaa5fee2c66050ed97c1477e0a1159deab1775eab6b"}, + {file = "bandit-1.7.9-py3-none-any.whl", hash = "sha256:52077cb339000f337fb25f7e045995c4ad01511e716e5daac37014b9752de8ec"}, + {file = "bandit-1.7.9.tar.gz", hash = "sha256:7c395a436743018f7be0a4cbb0a4ea9b902b6d87264ddecf8cfdc73b4f78ff61"}, ] [package.dependencies] @@ -174,6 +174,17 @@ files = [ {file = "billiard-4.2.0.tar.gz", hash = "sha256:9a3c3184cb275aa17a732f93f65b20c525d3d9f253722d26a82194803ade5a2c"}, ] +[[package]] +name = "blinker" +version = "1.8.2" +description = "Fast, simple object-to-object and broadcast signaling" +optional = false +python-versions = ">=3.8" +files = [ + {file = "blinker-1.8.2-py3-none-any.whl", hash = "sha256:1779309f71bf239144b9399d06ae925637cf6634cf6bd131104184531bf67c01"}, + {file = "blinker-1.8.2.tar.gz", hash = "sha256:8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83"}, +] + [[package]] name = "boto3" version = "1.34.104" @@ -195,13 +206,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.34.115" -description = "Type annotations for boto3 1.34.115 generated with mypy-boto3-builder 7.24.0" +version = "1.34.145" +description = "Type annotations for boto3 1.34.145 generated with mypy-boto3-builder 7.25.0" optional = false python-versions = ">=3.8" files = [ - {file = "boto3_stubs-1.34.115-py3-none-any.whl", hash = "sha256:fd06dc6cfb2503fcd4314e63d52eae4889f84e06ff4f92dca4a1f6cae68bfb00"}, - {file = "boto3_stubs-1.34.115.tar.gz", hash = "sha256:1d58dde687903e9b8cd01b2680219ace3981aab72f82165b58bb0a56cff2ce3f"}, + {file = "boto3_stubs-1.34.145-py3-none-any.whl", hash = "sha256:1303deb7d749a2c9bd5a30830e1d537c1474b70c5f429e3db9af5d3eaa7b9696"}, + {file = "boto3_stubs-1.34.145.tar.gz", hash = "sha256:2d15ccfc44407baae897d3a531f9eb0826e207d70e92f5268e8703139bec2dba"}, ] [package.dependencies] @@ -214,8 +225,7 @@ accessanalyzer = ["mypy-boto3-accessanalyzer (>=1.34.0,<1.35.0)"] account = ["mypy-boto3-account (>=1.34.0,<1.35.0)"] acm = ["mypy-boto3-acm (>=1.34.0,<1.35.0)"] acm-pca = 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@@ -3165,4 +3195,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "76db58e24a3e85e5e7df18c0013cbf61bfce0d94c8fbb3af7bed6206b88ef64c" +content-hash = "d59553a995b6676426b56df8143cda1a886ae6a58c990a98ff0584ef4df0c95c" From 009ca53571f9283c83de2c166d769cdcf8a215b9 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Tue, 30 Jul 2024 17:20:35 +0530 Subject: [PATCH 03/22] review --- deployment/config.yaml | 10 ++++----- tesk/api/ga4gh/tes/controllers.py | 19 +++++++--------- tesk/api/ga4gh/tes/task/create_task.py | 10 +++++---- tesk/api/kubernetes/client_wrapper.py | 8 +++++-- tesk/api/kubernetes/converter.py | 30 ++++++++++++++------------ tesk/api/kubernetes/template.py | 3 ++- tesk/constants.py | 17 +++++++++++++++ tesk/custom_config.py | 16 ++++++++++---- 8 files changed, 72 insertions(+), 41 deletions(-) create mode 100644 tesk/constants.py diff --git a/deployment/config.yaml b/deployment/config.yaml index a443b07d..62cc514e 100644 --- a/deployment/config.yaml +++ b/deployment/config.yaml @@ -64,7 +64,7 @@ custom: serviceAccountName: default containers: - name: taskmaster - image: eu.gcr.io/tes-wes/taskmaster:v0.0.5.2 + image: docker.io/elixircloud/tesk-core-taskmaster:v0.10.2 args: - -f - /jsoninput/JSON_INPUT.gz @@ -98,13 +98,13 @@ custom: restartPolicy: Never taskmaster_env_properties: # Taskmaster image name - imageName: eu.gcr.io/tes-wes/taskmaster + imageName: docker.io/elixircloud/tesk-core-taskmaster # Taskmaster image version - imageVersion: v0.10.0 + imageVersion: latest # Filer image name - filerImageName: eu.gcr.io/tes-wes/filer + filerImageName: docker.io/elixircloud/tesk-core-filer # Filer image version - filerImageVersion: v0.10.0 + filerImageVersion: latest # Test FTP account settings ftp: # Name of the secret with FTP account credentials diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index c2d66b58..a215203d 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/tesk/api/ga4gh/tes/controllers.py @@ -8,7 +8,7 @@ from tesk.api.ga4gh.tes.models import TesTask from tesk.utils import get_custom_config from tesk.api.kubernetes.converter import TesKubernetesConverter - +from tesk.exceptions import BadRequest, InternalServerError # from tesk.api.ga4gh.tes.task.create_task import CreateTask as TaskCreater # Get logger instance @@ -37,16 +37,13 @@ def CreateTask(**kwargs) -> dict: # type: ignore *args: Variable length argument list. **kwargs: Arbitrary keyword arguments. """ - request_body = kwargs["body"] - create_task_request = TesTask(**request_body) - user = { - "username": "test", - "is_member": True, - "any_group": "test_group", - } - tkc = TesKubernetesConverter().from_tes_task_to_k8s_job(create_task_request, user) - print(tkc) - pass + try: + request_body = kwargs.get("body") + if request_body is None: + logger("Nothing recieved in request body.") + raise BadRequest("No request body recieved.") + except Exception as e: + raise InternalServerError from e # GET /tasks/service-info diff --git a/tesk/api/ga4gh/tes/task/create_task.py b/tesk/api/ga4gh/tes/task/create_task.py index 3694718e..c301d27b 100644 --- a/tesk/api/ga4gh/tes/task/create_task.py +++ b/tesk/api/ga4gh/tes/task/create_task.py @@ -7,6 +7,7 @@ from tesk.api.kubernetes.constants import Constants from tesk.api.kubernetes.converter import TesKubernetesConverter from tesk.exceptions import KubernetesError +from tesk.constants import TeskConstants logger = logging.getLogger(__name__) @@ -14,7 +15,8 @@ class CreateTesTask: """Create TES task.""" - def __init__(self, task: TesTask, user=None, namespace="default"): + # TODO: Add user to the class when auth implemented in FOCA + def __init__(self, task: TesTask, namespace=TeskConstants.tesk_namespace): """Initialize the CreateTask class. Args: @@ -23,7 +25,7 @@ def __init__(self, task: TesTask, user=None, namespace="default"): namespace: Kubernetes namespace where the task is created. """ self.task = task - self.user = user + # self.user = user self.kubernetes_client_wrapper = KubernetesClientWrapper() self.namespace = namespace self.tes_kubernetes_converter = TesKubernetesConverter(self.namespace) @@ -32,7 +34,7 @@ def __init__(self, task: TesTask, user=None, namespace="default"): def create_task(self): """Create TES task.""" attempts_no = 0 - while True: + while attempts_no > self.constants.job_create_attempts_no: try: resources = self.task.resources @@ -46,7 +48,7 @@ def create_task(self): self.task, self.user ) ) - + # TODO: Create ConfigMap # TODO: Create Job # TODO Return created job diff --git a/tesk/api/kubernetes/client_wrapper.py b/tesk/api/kubernetes/client_wrapper.py index 1854f2e6..0d387ad5 100644 --- a/tesk/api/kubernetes/client_wrapper.py +++ b/tesk/api/kubernetes/client_wrapper.py @@ -7,6 +7,7 @@ from kubernetes.client import V1ConfigMap, V1Job, V1LimitRangeList from kubernetes.utils.quantity import parse_quantity # type: ignore +from tesk.constants import TeskConstants from tesk.exceptions import KubernetesError, NotFound logger = logging.getLogger(__name__) @@ -15,7 +16,7 @@ class KubernetesClientWrapper: """Kubernetes client wrapper class.""" - def __init__(self, namespace="tesk"): + def __init__(self, namespace=TeskConstants.tesk_namespace): """Initialize the Kubernetes client wrapper. Args: @@ -132,9 +133,12 @@ def minimum_ram_gb(self) -> float: mem_bytes = self.quantity_to_bytes(mem_quantity) min_ram = max(min_ram, mem_bytes) return min_ram / (1024**3) - except Exception as e: + except (ValueError, TypeError) as e: logger.error(f"Error in minimum_ram_gb: {e}") return 0.0 + except Exception as e: + logger.error(f"Unexpected error in minimum_ram_gb: {e}") + raise def quantity_to_bytes(self, quantity: str) -> int: """Convert quantity(resource) to bytes.""" diff --git a/tesk/api/kubernetes/converter.py b/tesk/api/kubernetes/converter.py index 8309d00a..0e5fee88 100644 --- a/tesk/api/kubernetes/converter.py +++ b/tesk/api/kubernetes/converter.py @@ -16,6 +16,7 @@ from tesk.api.ga4gh.tes.models import TesTask from tesk.api.kubernetes.constants import Constants, K8sConstants from tesk.api.kubernetes.template import KubernetesTemplateSupplier +from tesk.constants import TeskConstants from tesk.custom_config import TaskmasterEnvProperties from tesk.utils import get_taskmaster_env_property, get_taskmaster_template @@ -23,7 +24,7 @@ class TesKubernetesConverter: - def __init__(self, namespace="default"): + def __init__(self, namespace=TeskConstants.tesk_namespace): """Initialize the converter.""" self.taskmaster_template: V1Job = get_taskmaster_template() self.taskmaster_env_properties: TaskmasterEnvProperties = ( @@ -33,7 +34,8 @@ def __init__(self, namespace="default"): self.k8s_constants = K8sConstants() self.namespace = namespace - def from_tes_task_to_k8s_job(self, task: TesTask, user): + # TODO: Add user to the mmethod when auth implemented in FOCA + def from_tes_task_to_k8s_job(self, task: TesTask): taskmsater_job: V1Job = KubernetesTemplateSupplier( self.namespace ).task_master_template() @@ -50,18 +52,18 @@ def from_tes_task_to_k8s_job(self, task: TesTask, user): taskmsater_job.metadata.annotations[self.constants.ann_testask_name_key] = ( task.name ) - taskmsater_job.metadata.labels[self.constants.label_userid_key] = user[ - "username" - ] - - if task.tags and "GROUP_NAME" in task.tags: - taskmsater_job.metadata.labels[self.constants.label_userid_key] = task[ - "tags" - ]["GROUP_NAME"] - elif user["is_member"]: - taskmsater_job.metadata.labels[self.constants.label_groupname_key] = user[ - "any_group" - ] + # taskmsater_job.metadata.labels[self.constants.label_userid_key] = user[ + # "username" + # ] + + # if task.tags and "GROUP_NAME" in task.tags: + # taskmsater_job.metadata.labels[self.constants.label_userid_key] = task[ + # "tags" + # ]["GROUP_NAME"] + # elif user["is_member"]: + # taskmsater_job.metadata.labels[self.constants.label_groupname_key] = user[ + # "any_group" + # ] try: taskmsater_job.metadata.annotations[self.constants.ann_json_input_key] = ( diff --git a/tesk/api/kubernetes/template.py b/tesk/api/kubernetes/template.py index 842b18f7..d4dfc29a 100644 --- a/tesk/api/kubernetes/template.py +++ b/tesk/api/kubernetes/template.py @@ -9,6 +9,7 @@ from kubernetes.client.models import V1Job from tesk.api.kubernetes.constants import Constants, K8sConstants +from tesk.constants import TeskConstants from tesk.custom_config import TaskmasterEnvProperties from tesk.utils import get_taskmaster_env_property, get_taskmaster_template @@ -18,7 +19,7 @@ class KubernetesTemplateSupplier: """Templates for tasmaster's and executor's job object..""" - def __init__(self, namespace="default"): + def __init__(self, namespace=TeskConstants.tesk_namespace): """Initialize the converter.""" self.taskmaster_template: V1Job = get_taskmaster_template() self.taskmaster_env_properties: TaskmasterEnvProperties = ( diff --git a/tesk/constants.py b/tesk/constants.py new file mode 100644 index 00000000..641df53d --- /dev/null +++ b/tesk/constants.py @@ -0,0 +1,17 @@ +"""Tesk scoped constants.""" + +import os + + +class TeskConstants: + """Tesk scoped constants.""" + + filer_image_name: str = os.getenv( + "FILER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-filer" + ) + filer_image_version: str = os.getenv("FILER_IMAGE_VERSION", "latest") + taskmaster_image_name: str = os.getenv( + "TASKMASTER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-taskmaster" + ) + taskmaster_image_version: str = os.getenv("TASKMASTER_IMAGE_VERSION", "latest") + tesk_namespace: str = os.getenv("TESK_NAMESPACE", "tesk") diff --git a/tesk/custom_config.py b/tesk/custom_config.py index 555e1d0f..a2e0c0b7 100644 --- a/tesk/custom_config.py +++ b/tesk/custom_config.py @@ -4,6 +4,8 @@ from pydantic import BaseModel, Field +from tesk.constants import TeskConstants + class FtpConfig(BaseModel): """Ftp configuration model for the TESK.""" @@ -21,13 +23,19 @@ class TaskmasterEnvProperties(BaseModel): """Taskmaster environment properties model for the TESK.""" imageName: str = Field( - default="eu.gcr.io/tes-wes/taskmaster", description="Taskmaster image name" + default=TeskConstants.taskmaster_image_name, + description="Taskmaster image name", + ) + imageVersion: str = Field( + default=TeskConstants.taskmaster_image_version, + description="Taskmaster image version", ) - imageVersion: str = Field(default="v0.10.0", description="Taskmaster image version") filerImageName: str = Field( - default="eu.gcr.io/tes-wes/filer", description="Filer image name" + default=TeskConstants.filer_image_name, description="Filer image name" + ) + filerImageVersion: str = Field( + default=TeskConstants.filer_image_version, description="Filer image version" ) - filerImageVersion: str = Field(default="v0.10.0", description="Filer image version") ftp: FtpConfig = Field(default=None, description="Test FTP account settings") debug: bool = Field( default=False, From 2429b0fdfc89f02a73af16191ecc358b8307014b Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Thu, 1 Aug 2024 16:55:00 +0530 Subject: [PATCH 04/22] WIP --- README.md | 26 ++ deployment/charts/tesk/values.yaml | 2 +- poetry.lock | 369 ++++++++++++------------- tesk/api/ga4gh/tes/controllers.py | 2 + tesk/api/ga4gh/tes/task/create_task.py | 6 +- tesk/api/kubernetes/converter.py | 159 +++++++---- tesk/api/kubernetes/template.py | 57 +++- tesk/constants.py | 25 +- tesk/custom_config.py | 29 ++ 9 files changed, 427 insertions(+), 248 deletions(-) diff --git a/README.md b/README.md index 0dd388ec..8f8b6ad6 100644 --- a/README.md +++ b/README.md @@ -55,6 +55,32 @@ After the last executor, the `filer` is called once more to process the outputs and push them to remote locations from the PVC. The PVC is the scrubbed, deleted and the taskmaster ends, completing the task. +┌─────────────────────────────────────────────────────────┐ +│ Kubernetes │ +│ │ +│ ┌────────────────────────────┐ ┌───────────────────┐ │ +│ │ Secret: ftp-secret │ │ ConfigMap/PVC │ │ +│ │ - username │ │ - JSON_INPUT.gz │ │ +│ │ - password │ │ │ │ +│ └──────────▲─────────────────┘ └───────▲───────────┘ │ +│ │ | │ +│ │ | │ +│ │ | │ +│ ┌─────────┴────────────────────────────┴────────────┐ │ +│ │ Job: taskmaster │ │ +│ │ ┌───────────────────────────────────────────────┐ │ │ +│ │ │ Pod: taskmaster │ │ │ +│ │ │ - Container: taskmaster │ │ │ +│ │ │ - Env: TESK_FTP_USERNAME │ │ │ +│ │ │ - Env: TESK_FTP_PASSWORD │ │ │ +│ │ │ - Args: -f /jsoninput/JSON_INPUT.gz │ │ │ +│ │ │ - Mounts: /podinfo │ │ │ +│ │ │ /jsoninput │ │ │ +│ │ └───────────────────────────────────────────────┘ │ │ +│ └───────────────────────────────────────────────────┘ │ +│ │ +└─────────────────────────────────────────────────────────┘ + ## Requirements - A working [Kubernetes](https://kubernetes.io/) cluster version 1.9 and later. diff --git a/deployment/charts/tesk/values.yaml b/deployment/charts/tesk/values.yaml index dae8b617..e2a957c2 100644 --- a/deployment/charts/tesk/values.yaml +++ b/deployment/charts/tesk/values.yaml @@ -9,7 +9,7 @@ host_name: "" # # 'openstack' or 's3' -storage: none +storage: s3 # Configurable storage class. storageClass: diff --git a/poetry.lock b/poetry.lock index 717f28e5..3c52b3b5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "added-value" @@ -206,13 +206,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.34.145" -description = "Type annotations for boto3 1.34.145 generated with mypy-boto3-builder 7.25.0" +version = "1.34.151" +description = "Type annotations for boto3 1.34.151 generated with mypy-boto3-builder 7.25.0" optional = false python-versions = ">=3.8" files = [ - {file = "boto3_stubs-1.34.145-py3-none-any.whl", hash = "sha256:1303deb7d749a2c9bd5a30830e1d537c1474b70c5f429e3db9af5d3eaa7b9696"}, - {file = "boto3_stubs-1.34.145.tar.gz", hash = "sha256:2d15ccfc44407baae897d3a531f9eb0826e207d70e92f5268e8703139bec2dba"}, + {file = "boto3_stubs-1.34.151-py3-none-any.whl", hash = "sha256:7c74775d5bca4693c9695526b95c80a572d6e1bf8059249698abff9596268671"}, + {file = "boto3_stubs-1.34.151.tar.gz", hash = "sha256:8422368138fb74afb7c11965677726000c4d24b7b3b872d414f5c706372bf94f"}, ] [package.dependencies] @@ -225,7 +225,7 @@ accessanalyzer = 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"5360faeac82607ad994db4eac1f2a80dc823b930ba697b84e0bba299b9cac893" ->>>>>>> main +content-hash = "58ff8e56ad701a8cda42215ba47057dd79e85b0d989a6b274ca7b7aa9c616620" diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index 9b9f01a2..73dc388d 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/tesk/api/ga4gh/tes/controllers.py @@ -6,6 +6,7 @@ from tesk.api.ga4gh.tes.models import TesTask from tesk.api.ga4gh.tes.service_info.service_info import ServiceInfo +from tesk.api.ga4gh.tes.task.create_task import CreateTesTask from tesk.api.kubernetes.converter import TesKubernetesConverter from tesk.api.kubernetes.template import KubernetesTemplateSupplier from tesk.exceptions import BadRequest, InternalServerError @@ -42,6 +43,7 @@ def CreateTask(**kwargs) -> dict: # type: ignore if request_body is None: logger("Nothing recieved in request body.") raise BadRequest("No request body recieved.") + CreateTesTask(TesTask(**request_body)).create_task() except Exception as e: raise InternalServerError from e diff --git a/tesk/api/ga4gh/tes/task/create_task.py b/tesk/api/ga4gh/tes/task/create_task.py index c301d27b..a6f76398 100644 --- a/tesk/api/ga4gh/tes/task/create_task.py +++ b/tesk/api/ga4gh/tes/task/create_task.py @@ -21,7 +21,6 @@ def __init__(self, task: TesTask, namespace=TeskConstants.tesk_namespace): Args: task: TES task to create. - user: User who creates the task. namespace: Kubernetes namespace where the task is created. """ self.task = task @@ -45,10 +44,13 @@ def create_task(self): task_master_job = ( self.tes_kubernetes_converter.from_tes_task_to_k8s_job( - self.task, self.user + self.task, + # self.user ) ) + print(task_master_job) + # TODO: Create ConfigMap # TODO: Create Job # TODO Return created job diff --git a/tesk/api/kubernetes/converter.py b/tesk/api/kubernetes/converter.py index 0e5fee88..54fc9630 100644 --- a/tesk/api/kubernetes/converter.py +++ b/tesk/api/kubernetes/converter.py @@ -13,7 +13,7 @@ ) from kubernetes.client.models import V1Job -from tesk.api.ga4gh.tes.models import TesTask +from tesk.api.ga4gh.tes.models import TesExecutor, TesResources, TesTask from tesk.api.kubernetes.constants import Constants, K8sConstants from tesk.api.kubernetes.template import KubernetesTemplateSupplier from tesk.constants import TeskConstants @@ -26,7 +26,6 @@ class TesKubernetesConverter: def __init__(self, namespace=TeskConstants.tesk_namespace): """Initialize the converter.""" - self.taskmaster_template: V1Job = get_taskmaster_template() self.taskmaster_env_properties: TaskmasterEnvProperties = ( get_taskmaster_env_property() ) @@ -82,54 +81,108 @@ def from_tes_task_to_k8s_job(self, task: TesTask): return taskmsater_job - # def from_tes_task_to_k8s_config_map(self, task, user, job): - # task_master_config_map = V1ConfigMap( - # metadata=V1ObjectMeta(name=job.metadata.name) - # ) - # task_master_config_map.metadata.annotations[ANN_TESTASK_NAME_KEY] = task["name"] - # task_master_config_map.metadata.labels[LABEL_USERID_KEY] = user["username"] - - # if "tags" in task and "GROUP_NAME" in task["tags"]: - # task_master_config_map.metadata.labels[LABEL_GROUPNAME_KEY] = task["tags"][ - # "GROUP_NAME" - # ] - # elif user["is_member"]: - # task_master_config_map.metadata.labels[LABEL_GROUPNAME_KEY] = user[ - # "any_group" - # ] - - # executors_as_jobs = [ - # self.from_tes_executor_to_k8s_job( - # task_master_config_map.metadata.name, - # task["name"], - # executor, - # idx, - # task["resources"], - # user, - # ) - # for idx, executor in enumerate(task["executors"]) - # ] - - # task_master_input = { - # "inputs": task.get("inputs", []), - # "outputs": task.get("outputs", []), - # "volumes": task.get("volumes", []), - # "resources": {"disk_gb": task["resources"].get("disk_gb", 10.0)}, - # } - # task_master_input[TASKMASTER_INPUT_EXEC_KEY] = executors_as_jobs - - # task_master_input_as_json = json.dumps(task_master_input) - # try: - # with BytesIO() as obj: - # with gzip.GzipFile(fileobj=obj, mode="wb") as gzip_file: - # gzip_file.write(task_master_input_as_json.encode("utf-8")) - # task_master_config_map.binary_data = { - # f"{TASKMASTER_INPUT}.gz": obj.getvalue() - # } - # except Exception as e: - # logger.info( - # f"Compression of task {task_master_config_map.metadata.name} JSON configmap failed", - # e, - # ) - - # return task_master_config_map + def from_tes_task_to_k8s_config_map( + self, + task: TesTask, + # user, + job, + ): + task_master_config_map = V1ConfigMap( + metadata=V1ObjectMeta(name=job.metadata.name) + ) + task_master_config_map.metadata.annotations[ + self.constants.ann_testask_name_key + ] = task["name"] + # task_master_config_map.metadata.labels[self.constants.label_userid_key] = user["username"] + + if "tags" in task and "GROUP_NAME" in task["tags"]: + task_master_config_map.metadata.labels[ + self.constants.label_groupname_key + ] = task["tags"]["GROUP_NAME"] + # elif user["is_member"]: + # task_master_config_map.metadata.labels[self.constants.label_groupname_key] = user[ + # "any_group" + # ] + + executors_as_jobs = [ + self.from_tes_executor_to_k8s_job( + task_master_config_map.metadata.name, + task["name"], + executor, + idx, + task["resources"], + # user, + ) + for idx, executor in enumerate(task["executors"]) + ] + + task_master_input = { + "inputs": task.inputs or [], + "outputs": task.outputs or [], + "volumes": task.volumes or [], + "resources": {"disk_gb": task.resources.disk_gb or 10.0}, + } + task_master_input[self.constants.taskmaster_input_exec_key] = executors_as_jobs + + task_master_input_as_json = json.dumps(task_master_input) + try: + with BytesIO() as obj: + with gzip.GzipFile(fileobj=obj, mode="wb") as gzip_file: + gzip_file.write(task_master_input_as_json.encode("utf-8")) + task_master_config_map.binary_data = { + f"{self.constants.taskmaster_input}.gz": obj.getvalue() + } + except Exception as e: + logger.info( + f"Compression of task {task_master_config_map.metadata.name} JSON configmap failed", + e, + ) + + return task_master_config_map + + + def from_tes_executor_to_k8s_job( + self, + generated_task_id: str, + tes_task_name: str, + executor: TesExecutor, + executor_index: int, + resources: TesResources, + # user: User + ) -> V1Job: + # Get new template executor Job object + job = self.executor_template_supplier() + + # Set executors name based on taskmaster's job name + Job(job).change_job_name(Task(generated_task_id).get_executor_name(executor_index)) + + # Put arbitrary labels and annotations + job.metadata.labels = job.metadata.labels or {} + job.metadata.labels["taskId"] = generated_task_id + job.metadata.labels["execNo"] = str(executor_index) + job.metadata.labels["userId"] = user.username + + job.metadata.annotations = job.metadata.annotations or {} + job.metadata.annotations["tesTaskName"] = tes_task_name + + container = job.spec.template.spec.containers[0] + + # Convert potential TRS URI into docker image + container.image = self.trs_client.get_docker_image_for_tool_version_uri(executor.image) + + # Map executor's command to job container's command + for command in ExecutorCommandWrapper(executor).get_commands_with_stream_redirects(): + container.add_command_item(command) + + if executor.env: + container.env = [V1EnvVar(name=key, value=value) for key, value in executor.env.items()] + + container.working_dir = executor.workdir + + if resources.cpu_cores: + container.resources.requests['cpu'] = QuantityFormatter().parse(str(resources.cpu_cores)) + + if resources.ram_gb: + container.resources.requests['memory'] = QuantityFormatter().parse(f"{resources.ram_gb:.6f}Gi") + + return job diff --git a/tesk/api/kubernetes/template.py b/tesk/api/kubernetes/template.py index d4dfc29a..d38cbb40 100644 --- a/tesk/api/kubernetes/template.py +++ b/tesk/api/kubernetes/template.py @@ -4,7 +4,16 @@ import uuid from kubernetes.client import ( + V1Container, V1EnvVar, + V1JobSpec, + V1ObjectMeta, + V1PodSpec, + V1PodTemplateSpec, + V1ResourceRequirements, + V1SecretVolumeSource, + V1Volume, + V1VolumeMount, ) from kubernetes.client.models import V1Job @@ -19,7 +28,7 @@ class KubernetesTemplateSupplier: """Templates for tasmaster's and executor's job object..""" - def __init__(self, namespace=TeskConstants.tesk_namespace): + def __init__(self, namespace=TeskConstants.tesk_namespace, security_context = None): """Initialize the converter.""" self.taskmaster_template: V1Job = get_taskmaster_template() self.taskmaster_env_properties: TaskmasterEnvProperties = ( @@ -28,6 +37,7 @@ def __init__(self, namespace=TeskConstants.tesk_namespace): self.constants = Constants() self.k8s_constants = K8sConstants() self.namespace = namespace + self.security_context= security_context def get_task_master_name(self) -> str: """Generate a unique name for the taskmaster job.""" @@ -89,3 +99,48 @@ def task_master_template(self) -> V1Job: ) return job + + def executor_template(self): + container = V1Container(resources=V1ResourceRequirements()) + + if self.taskmaster_env_properties.executorSecret is not None: + container.volume_mounts = [ + V1VolumeMount( + read_only=True, + name=self.taskmaster_env_properties.executorSecret.name, + mount_path=self.taskmaster_env_properties.executorSecret.mountPath, + ) + ] + + pod_spec = V1PodSpec( + containers=[container], + restart_policy=self.k8s_constants.job_restart_policy, + ) + + if self.security_context: + pod_spec.security_context = self.security_context + + job = V1Job( + api_version=self.k8s_constants.k8s_batch_api_version, + kind=self.k8s_constants.k8s_batch_api_job_type, + metadata=V1ObjectMeta( + labels={ + self.constants.label_jobtype_key: self.constants.label_jobtype_value_exec + } + ), + spec=V1JobSpec( + template=V1PodTemplateSpec(metadata=V1ObjectMeta(), spec=pod_spec) + ), + ) + + if self.taskmaster_env_properties.executorSecret is not None: + job.spec.template.spec.volumes = [ + V1Volume( + name=self.taskmaster_env_properties.executorSecret.name, + secret=V1SecretVolumeSource( + secret_name=self.taskmaster_env_properties.executorSecret.name + ), + ) + ] + + return job diff --git a/tesk/constants.py b/tesk/constants.py index 641df53d..6ffaafae 100644 --- a/tesk/constants.py +++ b/tesk/constants.py @@ -4,14 +4,27 @@ class TeskConstants: - """Tesk scoped constants.""" + """Tesk's K8s scoped constants.""" filer_image_name: str = os.getenv( - "FILER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-filer" + "TESK_API_TASKMASTER_FILER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-filer" + ) + filer_image_version: str = os.getenv( + "TESK_API_TASKMASTER_FILER_IMAGE_VERSION", "latest" ) - filer_image_version: str = os.getenv("FILER_IMAGE_VERSION", "latest") taskmaster_image_name: str = os.getenv( - "TASKMASTER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-taskmaster" + "TESK_API_TASKMASTER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-taskmaster" + ) + taskmaster_image_version: str = os.getenv( + "TESK_API_TASKMASTER_IMAGE_VERSION", "latest" + ) + tesk_namespace: str = os.getenv("TESK_API_K8S_NAMESPACE", "tesk") + taskmaster_service_account_name: str = os.getenv( + "TESK_API_TASKMASTER_SERVICE_ACCOUNT_NAME", "taskmaster" + ) + taskmaster_environement_executor_backoff_limit: str = os.getenv( + "ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT", "2" + ) + filer_environment_filer_backoff_limit: str = os.getenv( + "TESK_API_TASKMASTER_ENVIRONMENT_FILER_BACKOFF_LIMIT", "2" ) - taskmaster_image_version: str = os.getenv("TASKMASTER_IMAGE_VERSION", "latest") - tesk_namespace: str = os.getenv("TESK_NAMESPACE", "tesk") diff --git a/tesk/custom_config.py b/tesk/custom_config.py index 279ebffd..112daf3e 100644 --- a/tesk/custom_config.py +++ b/tesk/custom_config.py @@ -20,6 +20,26 @@ class FtpConfig(BaseModel): ) +class ExecutorSecret(BaseModel): + """Executor secret configuration.""" + + name: Optional[str] = Field( + default=None, + description=( + "Name of a secret that will be mounted as volume to each executor. The same" + " name will be used for the secret and the volume" + ), + ) + mountPath: Optional[str] = Field( + default=None, + alias="mountPath", + description="The path where the secret will be mounted to executors", + ) + enabled: bool = Field( + default=False, description="Indicates whether the secret is enabled" + ) + + class TaskmasterEnvProperties(BaseModel): """Taskmaster environment properties model for the TESK.""" @@ -50,6 +70,15 @@ class TaskmasterEnvProperties(BaseModel): serviceAccountName: str = Field( default="default", description="Service Account name for taskmaster" ) + debug: bool = Field( + default=False, + description="If verbose (debug) mode of taskmaster is on (passes additional " + "flag to taskmaster and sets image pull policy to Always)", + ) + executorSecret: Optional[ExecutorSecret] = Field( + default=None, + description="Executor secret configuration" + ) class SecretKeyRef(BaseModel): From cebb7b299c22a4bb326272337537a0153959dc62 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sat, 3 Aug 2024 21:46:00 +0530 Subject: [PATCH 05/22] create task --- poetry.lock | 1033 ++++++++--------- pyproject.toml | 2 +- tesk/api/ga4gh/tes/controllers.py | 9 +- tesk/api/ga4gh/tes/task/create_task.py | 34 +- tesk/api/kubernetes/convert/__init__.py | 0 .../api/kubernetes/{ => convert}/converter.py | 147 ++- tesk/api/kubernetes/convert/data/__init__.py | 0 tesk/api/kubernetes/convert/data/job.py | 48 + tesk/api/kubernetes/convert/data/task.py | 65 ++ .../convert/executor_command_wrapper.py | 60 + .../convert/taskmaster_env_properties.py | 79 ++ tesk/api/kubernetes/{ => convert}/template.py | 6 +- tesk/custom_config.py | 77 +- tesk/exceptions.py | 5 + tesk/utils.py | 11 +- 15 files changed, 899 insertions(+), 677 deletions(-) create mode 100644 tesk/api/kubernetes/convert/__init__.py rename tesk/api/kubernetes/{ => convert}/converter.py (55%) create mode 100644 tesk/api/kubernetes/convert/data/__init__.py create mode 100644 tesk/api/kubernetes/convert/data/job.py create mode 100644 tesk/api/kubernetes/convert/data/task.py create mode 100644 tesk/api/kubernetes/convert/executor_command_wrapper.py create mode 100644 tesk/api/kubernetes/convert/taskmaster_env_properties.py rename tesk/api/kubernetes/{ => convert}/template.py (96%) diff --git a/poetry.lock b/poetry.lock index 3c52b3b5..c1d873ae 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "added-value" @@ -92,13 +92,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p [[package]] name = "authlib" -version = "1.3.1" +version = "1.3.0" description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients." optional = false python-versions = ">=3.8" files = [ - {file = "Authlib-1.3.1-py2.py3-none-any.whl", hash = "sha256:d35800b973099bbadc49b42b256ecb80041ad56b7fe1216a362c7943c088f377"}, - {file = "authlib-1.3.1.tar.gz", hash = "sha256:7ae843f03c06c5c0debd63c9db91f9fda64fa62a42a77419fa15fbb7e7a58917"}, + {file = "Authlib-1.3.0-py2.py3-none-any.whl", hash = "sha256:9637e4de1fb498310a56900b3e2043a206b03cb11c05422014b0302cbc814be3"}, + {file = "Authlib-1.3.0.tar.gz", hash = "sha256:959ea62a5b7b5123c5059758296122b57cd2585ae2ed1c0622c21b371ffdae06"}, ] [package.dependencies] @@ -120,13 +120,13 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "bandit" -version = "1.7.9" +version = "1.7.8" description = "Security oriented static analyser for python code." optional = false python-versions = ">=3.8" files = [ - {file = "bandit-1.7.9-py3-none-any.whl", hash = "sha256:52077cb339000f337fb25f7e045995c4ad01511e716e5daac37014b9752de8ec"}, - {file = "bandit-1.7.9.tar.gz", hash = "sha256:7c395a436743018f7be0a4cbb0a4ea9b902b6d87264ddecf8cfdc73b4f78ff61"}, + {file = "bandit-1.7.8-py3-none-any.whl", hash = "sha256:509f7af645bc0cd8fd4587abc1a038fc795636671ee8204d502b933aee44f381"}, + {file = "bandit-1.7.8.tar.gz", hash = "sha256:36de50f720856ab24a24dbaa5fee2c66050ed97c1477e0a1159deab1775eab6b"}, ] [package.dependencies] @@ -174,17 +174,6 @@ files = [ {file = "billiard-4.2.0.tar.gz", hash = "sha256:9a3c3184cb275aa17a732f93f65b20c525d3d9f253722d26a82194803ade5a2c"}, ] -[[package]] -name = "blinker" -version = "1.8.2" -description = "Fast, simple object-to-object and broadcast signaling" -optional = false -python-versions = ">=3.8" -files = [ - {file = "blinker-1.8.2-py3-none-any.whl", hash = "sha256:1779309f71bf239144b9399d06ae925637cf6634cf6bd131104184531bf67c01"}, - {file = "blinker-1.8.2.tar.gz", hash = "sha256:8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83"}, -] - [[package]] name = "boto3" version = "1.34.104" @@ -206,13 +195,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.34.151" -description = "Type annotations for boto3 1.34.151 generated with mypy-boto3-builder 7.25.0" +version = "1.34.115" +description = "Type annotations for boto3 1.34.115 generated with mypy-boto3-builder 7.24.0" optional = false python-versions = ">=3.8" files = [ - {file = "boto3_stubs-1.34.151-py3-none-any.whl", hash = "sha256:7c74775d5bca4693c9695526b95c80a572d6e1bf8059249698abff9596268671"}, - {file = "boto3_stubs-1.34.151.tar.gz", hash = "sha256:8422368138fb74afb7c11965677726000c4d24b7b3b872d414f5c706372bf94f"}, + {file = "boto3_stubs-1.34.115-py3-none-any.whl", hash = "sha256:fd06dc6cfb2503fcd4314e63d52eae4889f84e06ff4f92dca4a1f6cae68bfb00"}, + {file = "boto3_stubs-1.34.115.tar.gz", hash = "sha256:1d58dde687903e9b8cd01b2680219ace3981aab72f82165b58bb0a56cff2ce3f"}, ] [package.dependencies] @@ -225,7 +214,8 @@ accessanalyzer = ["mypy-boto3-accessanalyzer (>=1.34.0,<1.35.0)"] account = ["mypy-boto3-account (>=1.34.0,<1.35.0)"] acm = ["mypy-boto3-acm (>=1.34.0,<1.35.0)"] acm-pca = ["mypy-boto3-acm-pca (>=1.34.0,<1.35.0)"] -all = ["mypy-boto3-accessanalyzer (>=1.34.0,<1.35.0)", "mypy-boto3-account (>=1.34.0,<1.35.0)", "mypy-boto3-acm (>=1.34.0,<1.35.0)", "mypy-boto3-acm-pca (>=1.34.0,<1.35.0)", "mypy-boto3-amp (>=1.34.0,<1.35.0)", "mypy-boto3-amplify (>=1.34.0,<1.35.0)", "mypy-boto3-amplifybackend (>=1.34.0,<1.35.0)", "mypy-boto3-amplifyuibuilder (>=1.34.0,<1.35.0)", "mypy-boto3-apigateway (>=1.34.0,<1.35.0)", "mypy-boto3-apigatewaymanagementapi (>=1.34.0,<1.35.0)", "mypy-boto3-apigatewayv2 (>=1.34.0,<1.35.0)", "mypy-boto3-appconfig (>=1.34.0,<1.35.0)", 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-3169,20 +3136,20 @@ test = ["websockets"] [[package]] name = "werkzeug" -version = "2.3.8" +version = "2.2.3" description = "The comprehensive WSGI web application library." optional = false -python-versions = ">=3.8" +python-versions = ">=3.7" files = [ - {file = "werkzeug-2.3.8-py3-none-any.whl", hash = "sha256:bba1f19f8ec89d4d607a3bd62f1904bd2e609472d93cd85e9d4e178f472c3748"}, - {file = "werkzeug-2.3.8.tar.gz", hash = "sha256:554b257c74bbeb7a0d254160a4f8ffe185243f52a52035060b761ca62d977f03"}, + {file = "Werkzeug-2.2.3-py3-none-any.whl", hash = "sha256:56433961bc1f12533306c624f3be5e744389ac61d722175d543e1751285da612"}, + {file = "Werkzeug-2.2.3.tar.gz", hash = "sha256:2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe"}, ] [package.dependencies] MarkupSafe = ">=2.1.1" [package.extras] -watchdog = ["watchdog (>=2.3)"] +watchdog = ["watchdog"] [[package]] name = "xmltodict" @@ -3198,4 +3165,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "58ff8e56ad701a8cda42215ba47057dd79e85b0d989a6b274ca7b7aa9c616620" +content-hash = "5360faeac82607ad994db4eac1f2a80dc823b930ba697b84e0bba299b9cac893" diff --git a/pyproject.toml b/pyproject.toml index 1f5b98d7..49795030 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,7 @@ version = "0.1.0" [tool.poetry.dependencies] boto3 = "1.34.104" foca = "^0.13.0" -kubernetes = "^30.1.0" +kubernetes = "^29.0.0" python = "^3.11" requests = ">=2.20.0" urllib3 = "^2.2.2" diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index 73dc388d..109e4092 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/tesk/api/ga4gh/tes/controllers.py @@ -7,8 +7,8 @@ from tesk.api.ga4gh.tes.models import TesTask from tesk.api.ga4gh.tes.service_info.service_info import ServiceInfo from tesk.api.ga4gh.tes.task.create_task import CreateTesTask -from tesk.api.kubernetes.converter import TesKubernetesConverter -from tesk.api.kubernetes.template import KubernetesTemplateSupplier +from tesk.api.kubernetes.convert.converter import TesKubernetesConverter +from tesk.api.kubernetes.convert.template import KubernetesTemplateSupplier from tesk.exceptions import BadRequest, InternalServerError from tesk.utils import get_custom_config @@ -43,7 +43,10 @@ def CreateTask(**kwargs) -> dict: # type: ignore if request_body is None: logger("Nothing recieved in request body.") raise BadRequest("No request body recieved.") - CreateTesTask(TesTask(**request_body)).create_task() + tes_task = TesTask(**request_body) + namespace = "tesk" + task_creater = CreateTesTask(tes_task, namespace) + task_creater.response() except Exception as e: raise InternalServerError from e diff --git a/tesk/api/ga4gh/tes/task/create_task.py b/tesk/api/ga4gh/tes/task/create_task.py index a6f76398..3fb29b38 100644 --- a/tesk/api/ga4gh/tes/task/create_task.py +++ b/tesk/api/ga4gh/tes/task/create_task.py @@ -5,9 +5,9 @@ from tesk.api.ga4gh.tes.models import TesTask from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper from tesk.api.kubernetes.constants import Constants -from tesk.api.kubernetes.converter import TesKubernetesConverter -from tesk.exceptions import KubernetesError +from tesk.api.kubernetes.convert.converter import TesKubernetesConverter from tesk.constants import TeskConstants +from tesk.exceptions import KubernetesError logger = logging.getLogger(__name__) @@ -33,8 +33,9 @@ def __init__(self, task: TesTask, namespace=TeskConstants.tesk_namespace): def create_task(self): """Create TES task.""" attempts_no = 0 - while attempts_no > self.constants.job_create_attempts_no: + while attempts_no < self.constants.job_create_attempts_no: try: + attempts_no += 1 resources = self.task.resources if resources and resources.ram_gb: @@ -49,28 +50,27 @@ def create_task(self): ) ) + task_master_config_map = ( + self.tes_kubernetes_converter.from_tes_task_to_k8s_config_map( + self.task, + task_master_job, + # user + ) + ) + _ = self.kubernetes_client_wrapper.create_config_map( + task_master_config_map + ) + created_job = self.kubernetes_client_wrapper.create_job(task_master_job) + print(task_master_config_map) print(task_master_job) - - # TODO: Create ConfigMap - # TODO: Create Job - # TODO Return created job - # task_master_config_map = converter.from_tes_task_to_k8s_config_map( - # task, user, task_master_job - # ) - # created_config_map = kubernetes_client_wrapper.create_config_map( - # task_master_config_map - # ) - # created_job = kubernetes_client_wrapper.create_job(task_master_job) - # return converter.from_k8s_job_to_tes_create_task_response(created_job) + return created_job.metadata.name except KubernetesError as e: - # Handle Kubernetes specific exceptions if ( not e.is_object_name_duplicated() or attempts_no >= self.constants.job_create_attempts_no ): raise e - attempts_no += 1 except Exception as exc: logging.error("ERROR: In createTask", exc_info=True) diff --git a/tesk/api/kubernetes/convert/__init__.py b/tesk/api/kubernetes/convert/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/tesk/api/kubernetes/converter.py b/tesk/api/kubernetes/convert/converter.py similarity index 55% rename from tesk/api/kubernetes/converter.py rename to tesk/api/kubernetes/convert/converter.py index 54fc9630..fac4889b 100644 --- a/tesk/api/kubernetes/converter.py +++ b/tesk/api/kubernetes/convert/converter.py @@ -1,40 +1,57 @@ """Module for converting TES tasks to Kubernetes jobs.""" +import base64 import gzip import json import logging +from decimal import Decimal from io import BytesIO +from typing import Any from kubernetes.client import ( V1ConfigMap, V1ConfigMapVolumeSource, + V1Container, + V1EnvVar, V1ObjectMeta, + V1ResourceRequirements, V1Volume, ) from kubernetes.client.models import V1Job +from kubernetes.utils.quantity import parse_quantity # type: ignore from tesk.api.ga4gh.tes.models import TesExecutor, TesResources, TesTask from tesk.api.kubernetes.constants import Constants, K8sConstants -from tesk.api.kubernetes.template import KubernetesTemplateSupplier +from tesk.api.kubernetes.convert.data.job import Job +from tesk.api.kubernetes.convert.data.task import Task +from tesk.api.kubernetes.convert.executor_command_wrapper import ExecutorCommandWrapper +from tesk.api.kubernetes.convert.template import KubernetesTemplateSupplier from tesk.constants import TeskConstants from tesk.custom_config import TaskmasterEnvProperties -from tesk.utils import get_taskmaster_env_property, get_taskmaster_template +from tesk.utils import get_taskmaster_env_property, pydantic_model_list_json logger = logging.getLogger(__name__) class TesKubernetesConverter: + """Convert TES requests to Kubernetes resources.""" + def __init__(self, namespace=TeskConstants.tesk_namespace): """Initialize the converter.""" self.taskmaster_env_properties: TaskmasterEnvProperties = ( get_taskmaster_env_property() ) + self.template_supplier = KubernetesTemplateSupplier( + namespace=namespace + # security_context=security_context + ) self.constants = Constants() self.k8s_constants = K8sConstants() self.namespace = namespace - # TODO: Add user to the mmethod when auth implemented in FOCA + # TODO: Add user to the method when auth implemented in FOCA def from_tes_task_to_k8s_job(self, task: TesTask): + """Convert TES task to Kubernetes job.""" taskmsater_job: V1Job = KubernetesTemplateSupplier( self.namespace ).task_master_template() @@ -48,6 +65,8 @@ def from_tes_task_to_k8s_job(self, task: TesTask): if taskmsater_job.metadata.labels is None: taskmsater_job.metadata.labels = {} + # taskmsater_job.metadata.name = task.name + taskmsater_job.metadata.annotations[self.constants.ann_testask_name_key] = ( task.name ) @@ -84,21 +103,30 @@ def from_tes_task_to_k8s_job(self, task: TesTask): def from_tes_task_to_k8s_config_map( self, task: TesTask, + job: V1Job, # user, - job, - ): + ) -> V1ConfigMap: + """Create a Kubernetes ConfigMap from a TES task.""" task_master_config_map = V1ConfigMap( metadata=V1ObjectMeta(name=job.metadata.name) ) + + task_master_config_map.metadata.labels = ( + task_master_config_map.metadata.labels or {} + ) + task_master_config_map.metadata.annotations = ( + task_master_config_map.metadata.annotations or {} + ) + task_master_config_map.metadata.annotations[ self.constants.ann_testask_name_key - ] = task["name"] + ] = task.name # task_master_config_map.metadata.labels[self.constants.label_userid_key] = user["username"] - if "tags" in task and "GROUP_NAME" in task["tags"]: + if "tags" in task and "GROUP_NAME" in task.tags: task_master_config_map.metadata.labels[ self.constants.label_groupname_key - ] = task["tags"]["GROUP_NAME"] + ] = task.tags["GROUP_NAME"] # elif user["is_member"]: # task_master_config_map.metadata.labels[self.constants.label_groupname_key] = user[ # "any_group" @@ -107,30 +135,42 @@ def from_tes_task_to_k8s_config_map( executors_as_jobs = [ self.from_tes_executor_to_k8s_job( task_master_config_map.metadata.name, - task["name"], + task.name, executor, idx, - task["resources"], + task.resources, # user, ) - for idx, executor in enumerate(task["executors"]) + for idx, executor in enumerate(task.executors) ] - task_master_input = { - "inputs": task.inputs or [], - "outputs": task.outputs or [], + task_master_input: dict[str, Any] = { + "inputs": pydantic_model_list_json(task.inputs) or [], + "outputs": pydantic_model_list_json(task.outputs) or [], "volumes": task.volumes or [], - "resources": {"disk_gb": task.resources.disk_gb or 10.0}, + "resources": {"disk_gb": float(task.resources.disk_gb) or 10.0}, } - task_master_input[self.constants.taskmaster_input_exec_key] = executors_as_jobs + task_master_input[self.constants.taskmaster_input_exec_key] = [ + exec_job.to_dict() for exec_job in executors_as_jobs + ] + + def decimal_to_float(obj): + if isinstance(obj, Decimal): + return float(obj) + raise TypeError - task_master_input_as_json = json.dumps(task_master_input) + taskmaster_input_as_json = json.loads( + json.dumps(task_master_input, default=decimal_to_float) + ) try: with BytesIO() as obj: with gzip.GzipFile(fileobj=obj, mode="wb") as gzip_file: - gzip_file.write(task_master_input_as_json.encode("utf-8")) + json_data = json.dumps(taskmaster_input_as_json) + gzip_file.write(json_data.encode("utf-8")) task_master_config_map.binary_data = { - f"{self.constants.taskmaster_input}.gz": obj.getvalue() + f"{self.constants.taskmaster_input}.gz": base64.b64encode( + obj.getvalue() + ).decode("utf-8") } except Exception as e: logger.info( @@ -140,7 +180,6 @@ def from_tes_task_to_k8s_config_map( return task_master_config_map - def from_tes_executor_to_k8s_job( self, generated_task_id: str, @@ -151,38 +190,58 @@ def from_tes_executor_to_k8s_job( # user: User ) -> V1Job: # Get new template executor Job object - job = self.executor_template_supplier() - + job: V1Job = self.template_supplier.executor_template() + # Set executors name based on taskmaster's job name - Job(job).change_job_name(Task(generated_task_id).get_executor_name(executor_index)) - + Job(job).change_job_name( + # Task(job, generated_task_id).get_executor_name(executor_index) + "newname" + ) + # Put arbitrary labels and annotations job.metadata.labels = job.metadata.labels or {} - job.metadata.labels["taskId"] = generated_task_id - job.metadata.labels["execNo"] = str(executor_index) - job.metadata.labels["userId"] = user.username - + job.metadata.labels[self.constants.label_testask_id_key] = generated_task_id + job.metadata.labels[self.constants.label_execno_key] = str(executor_index) + # job.metadata.labels[self.constants.label_userid_key] = user.username + job.metadata.annotations = job.metadata.annotations or {} - job.metadata.annotations["tesTaskName"] = tes_task_name - - container = job.spec.template.spec.containers[0] - + job.metadata.annotations[self.constants.ann_testask_name_key] = tes_task_name + + container: V1Container = job.spec.template.spec.containers[0] + + # TODO: Not sure what to do with this # Convert potential TRS URI into docker image - container.image = self.trs_client.get_docker_image_for_tool_version_uri(executor.image) - + # container.image = self.trs_client.get_docker_image_for_tool_version_uri( + # executor.image + # ) + + if not container.command: + container.command = [] # Map executor's command to job container's command - for command in ExecutorCommandWrapper(executor).get_commands_with_stream_redirects(): - container.add_command_item(command) - + for command in ExecutorCommandWrapper( + executor + ).get_commands_with_stream_redirects(): + container.command.append(command) + if executor.env: - container.env = [V1EnvVar(name=key, value=value) for key, value in executor.env.items()] - + container.env = [ + V1EnvVar(name=key, value=value) for key, value in executor.env.items() + ] + else: + container.env = [] + container.working_dir = executor.workdir - + + container.resources = V1ResourceRequirements(requests={}) + if resources.cpu_cores: - container.resources.requests['cpu'] = QuantityFormatter().parse(str(resources.cpu_cores)) - + container.resources.requests["cpu"] = parse_quantity( + str(resources.cpu_cores) + ) + if resources.ram_gb: - container.resources.requests['memory'] = QuantityFormatter().parse(f"{resources.ram_gb:.6f}Gi") - + container.resources.requests["memory"] = parse_quantity( + f"{resources.ram_gb:.6f}Gi" + ) + return job diff --git a/tesk/api/kubernetes/convert/data/__init__.py b/tesk/api/kubernetes/convert/data/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/tesk/api/kubernetes/convert/data/job.py b/tesk/api/kubernetes/convert/data/job.py new file mode 100644 index 00000000..5df1c2ac --- /dev/null +++ b/tesk/api/kubernetes/convert/data/job.py @@ -0,0 +1,48 @@ +"""A container for a single Kubernetes job object (can be both a taskmaster and an executor) and its list of worker pods (Kubernetes Pod objects).""" + +from typing import List, Optional + +from kubernetes.client import V1Job, V1Pod + + +class Job: + """A container for a single Kubernetes job object (can be both a taskmaster and an executor) and its list of worker pods (Kubernetes Pod objects)""" + + def __init__(self, job: V1Job): + """Initializes the Job with a Kubernetes job object.""" + self.job: V1Job = job + self.pods: List[V1Pod] = [] + + def get_job(self) -> V1Job: + """Returns the Kubernetes job object.""" + return self.job + + def add_pod(self, pod: V1Pod): + """Adds a single pod to the list (without any duplication checks).""" + # TODO: This doesn't take care of duplication, use set on id or name + self.pods.append(pod) + + def has_pods(self) -> bool: + """Checks if the job has any pods.""" + return bool(self.pods) + + def get_first_pod(self) -> Optional[V1Pod]: + """Returns arbitrarily chosen pod from the list (currently the first one added) or None if the job has no pods.""" + if not self.has_pods(): + return None + return self.pods[0] + + def get_pods(self) -> List[V1Pod]: + """Returns the list of job pods in the order of addition to the list or an empty list if no pods.""" + return self.pods + + def change_job_name(self, new_name: str): + """Changes the job name, as well as the names in its metadata and container specs.""" + self.job.metadata.name = new_name + self.job.spec.template.metadata.name = new_name + if self.job.spec.template.spec.containers: + self.job.spec.template.spec.containers[0].name = new_name + + def get_job_name(self) -> Optional[str]: + """Returns the job name.""" + return self.job.metadata.name diff --git a/tesk/api/kubernetes/convert/data/task.py b/tesk/api/kubernetes/convert/data/task.py new file mode 100644 index 00000000..67058769 --- /dev/null +++ b/tesk/api/kubernetes/convert/data/task.py @@ -0,0 +1,65 @@ +"""A composite that represents Kubernetes object's graph of a single TES task. + +- Taskmaster job with its pods. +- Executor jobs with its pods. +""" + +import re +from typing import Dict, List, Optional + +from kubernetes.client.models import V1Job, V1ObjectMeta + +from tesk.api.kubernetes.constants import Constants +from tesk.api.kubernetes.convert.data.job import Job + + +class Task: + """Task is a composite that represents Kubernetes object's graph of a single TES task.""" + + def __init__( + self, taskmaster: Optional[Job] = None, taskmaster_name: Optional[str] = None + ): + if taskmaster: + self.taskmaster = taskmaster + elif taskmaster_name: + job = V1Job(metadata=V1ObjectMeta(name=taskmaster_name)) + self.taskmaster = Job(job) + else: + raise ValueError("Either taskmaster or taskmaster_name must be provided") + + self.executors_by_name: Dict[str, Job] = {} + self.output_filer: Optional[Job] = None + self.constants = Constants() + + def add_executor(self, executor: Job): + self.executors_by_name.setdefault(executor.get_job().metadata.name, executor) + + def set_output_filer(self, filer: Job): + self.output_filer = filer + + def get_taskmaster(self) -> Job: + return self.taskmaster + + def get_executors(self) -> List[Job]: + return sorted(self.executors_by_name.values(), key=self.extract_executor_number) + + def get_last_executor(self) -> Optional[Job]: + if not self.executors_by_name: + return None + executors = self.get_executors() + return executors[-1] if executors else None + + def get_output_filer(self) -> Optional[Job]: + return self.output_filer + + def extract_executor_number(self, executor: Job) -> int: + taskmaster_name = self.taskmaster.get_job_name() + prefix = taskmaster_name + self.constants.job_name_exec_prefix + match = re.match(f"{re.escape(prefix)}(\d+)", executor.get_job_name()) + if match: + return int(match.group(1)) + return float("inf") + + def get_executor_name(self, executor_index: int) -> str: + taskmaster_name = self.taskmaster.get_job_name() + return f"{taskmaster_name}{self.constants.job_name_exec_prefix}{str(executor_index).zfill(self.constants.job_name_exec_no_length)}" diff --git a/tesk/api/kubernetes/convert/executor_command_wrapper.py b/tesk/api/kubernetes/convert/executor_command_wrapper.py new file mode 100644 index 00000000..6fa088b0 --- /dev/null +++ b/tesk/api/kubernetes/convert/executor_command_wrapper.py @@ -0,0 +1,60 @@ +"""Wraps list of executor's command. + +Such that: +- If any of executor's stdin/stdout/stderr params is set, the command runs in shell +- Each part of the original command (single command/argument) that contained shell + special chars is surrounded by single quotes, plus single quote inside such string + are replaced with '"'"' sequence +- `stdin`, `stdout`, `stderr` streams are redirected to paths according to executors + params +""" + +import re +from typing import List + +from tesk.api.ga4gh.tes.models import TesExecutor + + +class ExecutorCommandWrapper: + SPECIAL_CHARS = re.compile(r"[ !\"#$&'()*;<>?\[\\`{|~\t\n]") + + def __init__(self, executor: TesExecutor): + self.executor = executor + + def get_commands_with_stream_redirects(self) -> List[str]: + result = [] + + if ( + not self.executor.stdin + and not self.executor.stdout + and not self.executor.stderr + ): + return self.executor.command + + result.append("/bin/sh") + result.append("-c") + + command_parts = [] + + for command_part in self.executor.command: + if self.SPECIAL_CHARS.search(command_part): + if "'" in command_part: + command_part = command_part.replace("'", "'\"'\"'") + command_part = f"'{command_part}'" + command_parts.append(command_part) + + if self.executor.stdin: + command_parts.append("<") + command_parts.append(self.executor.stdin) + + if self.executor.stdout: + command_parts.append(">") + command_parts.append(self.executor.stdout) + + if self.executor.stderr: + command_parts.append("2>") + command_parts.append(self.executor.stderr) + + result.append(" ".join(command_parts)) + + return result diff --git a/tesk/api/kubernetes/convert/taskmaster_env_properties.py b/tesk/api/kubernetes/convert/taskmaster_env_properties.py new file mode 100644 index 00000000..d0f7ef7d --- /dev/null +++ b/tesk/api/kubernetes/convert/taskmaster_env_properties.py @@ -0,0 +1,79 @@ +"""Taskmaster environment properties model for the TESK.""" + +from typing import Dict, Optional + +from pydantic import BaseModel, Field + +from tesk.constants import TeskConstants + + +class FtpConfig(BaseModel): + """Ftp configuration model for the TESK.""" + + secretName: Optional[str] = Field( + default=None, description="Name of the secret with FTP account credentials" + ) + enabled: bool = Field( + default=False, + description="If FTP account enabled (based on non-emptiness of secretName)", + ) + + +class ExecutorSecret(BaseModel): + """Executor secret configuration.""" + + name: Optional[str] = Field( + default=None, + description=( + "Name of a secret that will be mounted as volume to each executor. The same" + " name will be used for the secret and the volume" + ), + ) + mountPath: Optional[str] = Field( + default=None, + alias="mountPath", + description="The path where the secret will be mounted to executors", + ) + enabled: bool = Field( + default=False, description="Indicates whether the secret is enabled" + ) + + +class TaskmasterEnvProperties(BaseModel): + """Taskmaster environment properties model for the TESK.""" + + imageName: str = Field( + default=TeskConstants.taskmaster_image_name, + description="Taskmaster image name", + ) + imageVersion: str = Field( + default=TeskConstants.taskmaster_image_version, + description="Taskmaster image version", + ) + filerImageName: str = Field( + default=TeskConstants.filer_image_name, description="Filer image name" + ) + filerImageVersion: str = Field( + default=TeskConstants.filer_image_version, description="Filer image version" + ) + ftp: FtpConfig = Field(default=None, description="Test FTP account settings") + debug: bool = Field( + default=False, + description="If verbose (debug) mode of taskmaster is on (passes additional " + "flag to taskmaster and sets image pull policy to Always)", + ) + environment: Dict[str, str] = Field( + default={"key": "value"}, + description="Environment variables, that will be passed to taskmaster", + ) + serviceAccountName: str = Field( + default="default", description="Service Account name for taskmaster" + ) + debug: bool = Field( + default=False, + description="If verbose (debug) mode of taskmaster is on (passes additional " + "flag to taskmaster and sets image pull policy to Always)", + ) + executorSecret: Optional[ExecutorSecret] = Field( + default=None, description="Executor secret configuration" + ) diff --git a/tesk/api/kubernetes/template.py b/tesk/api/kubernetes/convert/template.py similarity index 96% rename from tesk/api/kubernetes/template.py rename to tesk/api/kubernetes/convert/template.py index d38cbb40..45b7f1f4 100644 --- a/tesk/api/kubernetes/template.py +++ b/tesk/api/kubernetes/convert/template.py @@ -28,7 +28,7 @@ class KubernetesTemplateSupplier: """Templates for tasmaster's and executor's job object..""" - def __init__(self, namespace=TeskConstants.tesk_namespace, security_context = None): + def __init__(self, namespace=TeskConstants.tesk_namespace, security_context=None): """Initialize the converter.""" self.taskmaster_template: V1Job = get_taskmaster_template() self.taskmaster_env_properties: TaskmasterEnvProperties = ( @@ -37,7 +37,7 @@ def __init__(self, namespace=TeskConstants.tesk_namespace, security_context = No self.constants = Constants() self.k8s_constants = K8sConstants() self.namespace = namespace - self.security_context= security_context + self.security_context = security_context def get_task_master_name(self) -> str: """Generate a unique name for the taskmaster job.""" @@ -101,7 +101,7 @@ def task_master_template(self) -> V1Job: return job def executor_template(self): - container = V1Container(resources=V1ResourceRequirements()) + container = V1Container(name="executor", resources=V1ResourceRequirements()) if self.taskmaster_env_properties.executorSecret is not None: container.volume_mounts = [ diff --git a/tesk/custom_config.py b/tesk/custom_config.py index 112daf3e..78a285db 100644 --- a/tesk/custom_config.py +++ b/tesk/custom_config.py @@ -5,80 +5,9 @@ from pydantic import BaseModel, Field from tesk.api.ga4gh.tes.models import Service -from tesk.constants import TeskConstants - - -class FtpConfig(BaseModel): - """Ftp configuration model for the TESK.""" - - secretName: Optional[str] = Field( - default=None, description="Name of the secret with FTP account credentials" - ) - enabled: bool = Field( - default=False, - description="If FTP account enabled (based on non-emptiness of secretName)", - ) - - -class ExecutorSecret(BaseModel): - """Executor secret configuration.""" - - name: Optional[str] = Field( - default=None, - description=( - "Name of a secret that will be mounted as volume to each executor. The same" - " name will be used for the secret and the volume" - ), - ) - mountPath: Optional[str] = Field( - default=None, - alias="mountPath", - description="The path where the secret will be mounted to executors", - ) - enabled: bool = Field( - default=False, description="Indicates whether the secret is enabled" - ) - - -class TaskmasterEnvProperties(BaseModel): - """Taskmaster environment properties model for the TESK.""" - - imageName: str = Field( - default=TeskConstants.taskmaster_image_name, - description="Taskmaster image name", - ) - imageVersion: str = Field( - default=TeskConstants.taskmaster_image_version, - description="Taskmaster image version", - ) - filerImageName: str = Field( - default=TeskConstants.filer_image_name, description="Filer image name" - ) - filerImageVersion: str = Field( - default=TeskConstants.filer_image_version, description="Filer image version" - ) - ftp: FtpConfig = Field(default=None, description="Test FTP account settings") - debug: bool = Field( - default=False, - description="If verbose (debug) mode of taskmaster is on (passes additional " - "flag to taskmaster and sets image pull policy to Always)", - ) - environment: Dict[str, str] = Field( - default={"key": "value"}, - description="Environment variables, that will be passed to taskmaster", - ) - serviceAccountName: str = Field( - default="default", description="Service Account name for taskmaster" - ) - debug: bool = Field( - default=False, - description="If verbose (debug) mode of taskmaster is on (passes additional " - "flag to taskmaster and sets image pull policy to Always)", - ) - executorSecret: Optional[ExecutorSecret] = Field( - default=None, - description="Executor secret configuration" - ) +from tesk.api.kubernetes.convert.taskmaster_env_properties import ( + TaskmasterEnvProperties, +) class SecretKeyRef(BaseModel): diff --git a/tesk/exceptions.py b/tesk/exceptions.py index add22fe0..155c228b 100644 --- a/tesk/exceptions.py +++ b/tesk/exceptions.py @@ -13,6 +13,7 @@ InternalServerError, NotFound, ) +from http import HTTPStatus class ConfigNotFoundError(FileNotFoundError): @@ -76,3 +77,7 @@ class ValidationError(Exception): class KubernetesError(ApiException): """Kubernetes error.""" + + def is_object_name_duplicated(self) -> bool: + """Check if object name is duplicated.""" + return self.status == HTTPStatus.CONFLICT diff --git a/tesk/utils.py b/tesk/utils.py index 8fef6e42..7b9ea2c2 100644 --- a/tesk/utils.py +++ b/tesk/utils.py @@ -2,7 +2,7 @@ import os from pathlib import Path -from typing import Optional +from typing import Any, List, Optional from foca import Foca from kubernetes.client.models import ( @@ -20,6 +20,7 @@ V1Volume, V1VolumeMount, ) +from pydantic import BaseModel from tesk.custom_config import ( Container, @@ -75,7 +76,6 @@ def get_taskmaster_template() -> V1Job: """ custom_conf = get_custom_config() try: - print(custom_conf.taskmaster_template) return job_to_v1job(custom_conf.taskmaster_template) except AttributeError: raise ConfigNotFoundError( @@ -189,3 +189,10 @@ def convert_job_metadata(job_metadata: JobMetadata) -> V1ObjectMeta: metadata=convert_job_metadata(job.metadata), spec=convert_job_spec(job.spec), ) + + +def pydantic_model_list_json(model_list: List[BaseModel]) -> List[dict[str, Any]]: + json_list = [] + for item in model_list: + json_list.append(item.json()) + return json_list From eb652f4a06d737448af8527abb320577a47170b1 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sat, 3 Aug 2024 22:13:39 +0530 Subject: [PATCH 06/22] make ruff happy --- tesk/api/ga4gh/tes/controllers.py | 3 - tesk/api/kubernetes/constants.py | 55 ++++++++++++++----- tesk/api/kubernetes/convert/__init__.py | 1 + tesk/api/kubernetes/convert/converter.py | 18 +++--- tesk/api/kubernetes/convert/data/__init__.py | 1 + tesk/api/kubernetes/convert/data/job.py | 23 ++++++-- tesk/api/kubernetes/convert/data/task.py | 20 ++++++- .../convert/executor_command_wrapper.py | 12 +++- tesk/api/kubernetes/convert/template.py | 12 +++- tesk/exceptions.py | 3 +- tesk/utils.py | 7 ++- 11 files changed, 115 insertions(+), 40 deletions(-) diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index 109e4092..e6c2e1d8 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/tesk/api/ga4gh/tes/controllers.py @@ -7,10 +7,7 @@ from tesk.api.ga4gh.tes.models import TesTask from tesk.api.ga4gh.tes.service_info.service_info import ServiceInfo from tesk.api.ga4gh.tes.task.create_task import CreateTesTask -from tesk.api.kubernetes.convert.converter import TesKubernetesConverter -from tesk.api.kubernetes.convert.template import KubernetesTemplateSupplier from tesk.exceptions import BadRequest, InternalServerError -from tesk.utils import get_custom_config # Get logger instance logger = logging.getLogger(__name__) diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py index 5ea8e81c..6163e571 100644 --- a/tesk/api/kubernetes/constants.py +++ b/tesk/api/kubernetes/constants.py @@ -6,6 +6,8 @@ class Constants(BaseModel): + """Constants related to job and tasks.""" + taskmaster_input: str = Field( default="JSON_INPUT", description="ENV var that serves as taskmaster script input (JSON format)", @@ -29,30 +31,47 @@ class Constants(BaseModel): ) job_name_taskm_rand_part_length: int = Field( default=4, - description="No of bytes of random part of task master's name (which end up encoded to hex)", + description=( + "No of bytes of random part of task master's name (which end up " + "encoded to hex)" + ), ) job_name_exec_no_length: int = Field( default=2, - description="No of digits reserved for executor number in executor's job name. Ends up padded with '0' for numbers < 10", + description=( + "No of digits reserved for executor number in executor's job name. Ends up " + "padded with '0' for numbers < 10", + ), ) job_name_filer_suf: str = Field( default="-outputs-filer", description="Output filer name suffix" ) ann_testask_name_key: str = Field( default="tes-task-name", - description="Key of the annotation, that stores name of TES task in both taskmaster's job and executor's jobs", + description=( + "Key of the annotation, that stores name of TES task in both taskmaster's " + "job and executor's jobs" + ), ) ann_json_input_key: str = Field( default="json-input", - description="Key of the annotation, that stores whole input TES task serialized to JSON", + description=( + "Key of the annotation, that stores whole input TES task serialized to " + "JSON", + ), ) label_testask_id_key: str = Field( default="taskmaster-name", - description="Key of the label, that stores taskmaster's name (==TES task generated ID) in executor jobs", + description=( + "Key of the label, that stores taskmaster's name (==TES task generated ID)" + " in executor jobs", + ), ) label_jobtype_key: str = Field( default="job-type", - description="Key of the label, that stores type of a job (taskmaster or executor)", + description=( + "Key of the label, that stores type of a job (taskmaster or executor)", + ), ) label_jobtype_value_taskm: str = Field( default="taskmaster", @@ -85,20 +104,30 @@ class Constants(BaseModel): ) absolute_path_message: str = Field( default="must be an absolute path", - description="Message for absolute path validation (to avoid message.properties)", + description=( + "Message for absolute path validation (to avoid message.properties)", + ), ) resource_disk_default: float = Field(0.1, description="Default resource disk value") completed_states: Set[str] = Field( default={"CANCELED", "COMPLETE", "EXECUTOR_ERROR", "SYSTEM_ERROR"}, - description="TES task states, indicating task is not running and cannot be cancelled", + description=( + "TES task states, indicating task is not running and cannot be cancelled", + ), ) ftp_secret_username_env: str = Field( default="TESK_FTP_USERNAME", - description="Name of taskmaster's ENV variable with username of FTP account used for storage", + description=( + "Name of taskmaster's ENV variable with username of FTP account used for " + "storage", + ), ) ftp_secret_password_env: str = Field( default="TESK_FTP_PASSWORD", - description="Name of taskmaster's ENV variable with password of FTP account used for storage", + description=( + "Name of taskmaster's ENV variable with password of FTP account used for " + "storage", + ), ) cancel_patch: str = Field( default='{"metadata":{"labels":{"task-status":"Cancelled"}}}', @@ -106,11 +135,9 @@ class Constants(BaseModel): ) -class PodPhase(BaseModel): - code: str = Field(default="Pending", description="The phase code of the pod") - - class K8sConstants(BaseModel): + """Constants related to Kubernetes.""" + k8s_batch_api_version: str = Field( default="batch/v1", description="Kubernetes Batch API version" ) diff --git a/tesk/api/kubernetes/convert/__init__.py b/tesk/api/kubernetes/convert/__init__.py index e69de29b..33ac4cc3 100644 --- a/tesk/api/kubernetes/convert/__init__.py +++ b/tesk/api/kubernetes/convert/__init__.py @@ -0,0 +1 @@ +"""Module for converting Kubernetes objects to Task objects.""" diff --git a/tesk/api/kubernetes/convert/converter.py b/tesk/api/kubernetes/convert/converter.py index fac4889b..a87273d5 100644 --- a/tesk/api/kubernetes/convert/converter.py +++ b/tesk/api/kubernetes/convert/converter.py @@ -23,7 +23,6 @@ from tesk.api.ga4gh.tes.models import TesExecutor, TesResources, TesTask from tesk.api.kubernetes.constants import Constants, K8sConstants from tesk.api.kubernetes.convert.data.job import Job -from tesk.api.kubernetes.convert.data.task import Task from tesk.api.kubernetes.convert.executor_command_wrapper import ExecutorCommandWrapper from tesk.api.kubernetes.convert.template import KubernetesTemplateSupplier from tesk.constants import TeskConstants @@ -121,16 +120,17 @@ def from_tes_task_to_k8s_config_map( task_master_config_map.metadata.annotations[ self.constants.ann_testask_name_key ] = task.name - # task_master_config_map.metadata.labels[self.constants.label_userid_key] = user["username"] + + # task_master_config_map.metadata.labels[self.constants.label_userid_key] + # = user["username"] if "tags" in task and "GROUP_NAME" in task.tags: task_master_config_map.metadata.labels[ self.constants.label_groupname_key ] = task.tags["GROUP_NAME"] # elif user["is_member"]: - # task_master_config_map.metadata.labels[self.constants.label_groupname_key] = user[ - # "any_group" - # ] + # task_master_config_map.metadata.labels[self.constants.label_groupname_key] + # = user["any_group"] executors_as_jobs = [ self.from_tes_executor_to_k8s_job( @@ -174,13 +174,16 @@ def decimal_to_float(obj): } except Exception as e: logger.info( - f"Compression of task {task_master_config_map.metadata.name} JSON configmap failed", + ( + f"Compression of task {task_master_config_map.metadata.name}" + f" JSON configmap failed" + ), e, ) return task_master_config_map - def from_tes_executor_to_k8s_job( + def from_tes_executor_to_k8s_job( # noqa: PLR0913 self, generated_task_id: str, tes_task_name: str, @@ -189,6 +192,7 @@ def from_tes_executor_to_k8s_job( resources: TesResources, # user: User ) -> V1Job: + """Create a Kubernetes job from a TES executor.""" # Get new template executor Job object job: V1Job = self.template_supplier.executor_template() diff --git a/tesk/api/kubernetes/convert/data/__init__.py b/tesk/api/kubernetes/convert/data/__init__.py index e69de29b..080fc38f 100644 --- a/tesk/api/kubernetes/convert/data/__init__.py +++ b/tesk/api/kubernetes/convert/data/__init__.py @@ -0,0 +1 @@ +"""Data structure module to handle k8s resources of TES.""" diff --git a/tesk/api/kubernetes/convert/data/job.py b/tesk/api/kubernetes/convert/data/job.py index 5df1c2ac..3fb13333 100644 --- a/tesk/api/kubernetes/convert/data/job.py +++ b/tesk/api/kubernetes/convert/data/job.py @@ -1,4 +1,8 @@ -"""A container for a single Kubernetes job object (can be both a taskmaster and an executor) and its list of worker pods (Kubernetes Pod objects).""" +"""A container for a single Kubernetes job object. + +Can be both a taskmaster and an executor, it list of worker pods (Kubernetes +Pod objects). +""" from typing import List, Optional @@ -6,7 +10,7 @@ class Job: - """A container for a single Kubernetes job object (can be both a taskmaster and an executor) and its list of worker pods (Kubernetes Pod objects)""" + """Class to list worker pods (Kubernetes Pod objects).""" def __init__(self, job: V1Job): """Initializes the Job with a Kubernetes job object.""" @@ -27,17 +31,26 @@ def has_pods(self) -> bool: return bool(self.pods) def get_first_pod(self) -> Optional[V1Pod]: - """Returns arbitrarily chosen pod from the list (currently the first one added) or None if the job has no pods.""" + """Returns arbitrarily chosen pod from the list. + + Currently the first one added or None if the job has no pods. + """ if not self.has_pods(): return None return self.pods[0] def get_pods(self) -> List[V1Pod]: - """Returns the list of job pods in the order of addition to the list or an empty list if no pods.""" + """Returns the list of job pods. + + Returns in the order of addition to the list or an empty list if no pods. + """ return self.pods def change_job_name(self, new_name: str): - """Changes the job name, as well as the names in its metadata and container specs.""" + """Changes the job name. + + Also the names in its metadata and container specs. + """ self.job.metadata.name = new_name self.job.spec.template.metadata.name = new_name if self.job.spec.template.spec.containers: diff --git a/tesk/api/kubernetes/convert/data/task.py b/tesk/api/kubernetes/convert/data/task.py index 67058769..ab49cf0a 100644 --- a/tesk/api/kubernetes/convert/data/task.py +++ b/tesk/api/kubernetes/convert/data/task.py @@ -14,11 +14,15 @@ class Task: - """Task is a composite that represents Kubernetes object's graph of a single TES task.""" + """Task is a composite. + + It represents Kubernetes object's graph of a single TES task. + """ def __init__( self, taskmaster: Optional[Job] = None, taskmaster_name: Optional[str] = None ): + """Initialize the Task.""" if taskmaster: self.taskmaster = taskmaster elif taskmaster_name: @@ -32,27 +36,34 @@ def __init__( self.constants = Constants() def add_executor(self, executor: Job): + """Add executor to the task.""" self.executors_by_name.setdefault(executor.get_job().metadata.name, executor) def set_output_filer(self, filer: Job): + """Set output filer for the task.""" self.output_filer = filer def get_taskmaster(self) -> Job: + """Get taskmaster job.""" return self.taskmaster def get_executors(self) -> List[Job]: + """Get executors.""" return sorted(self.executors_by_name.values(), key=self.extract_executor_number) def get_last_executor(self) -> Optional[Job]: + """Get last executor.""" if not self.executors_by_name: return None executors = self.get_executors() return executors[-1] if executors else None def get_output_filer(self) -> Optional[Job]: + """Get output filer.""" return self.output_filer def extract_executor_number(self, executor: Job) -> int: + """Extract executor number from the executor's name.""" taskmaster_name = self.taskmaster.get_job_name() prefix = taskmaster_name + self.constants.job_name_exec_prefix match = re.match(f"{re.escape(prefix)}(\d+)", executor.get_job_name()) @@ -61,5 +72,10 @@ def extract_executor_number(self, executor: Job) -> int: return float("inf") def get_executor_name(self, executor_index: int) -> str: + """Get executor name based on the taskmaster's job name and executor index.""" taskmaster_name = self.taskmaster.get_job_name() - return f"{taskmaster_name}{self.constants.job_name_exec_prefix}{str(executor_index).zfill(self.constants.job_name_exec_no_length)}" + return ( + f"{taskmaster_name}" + f"{self.constants.job_name_exec_prefix}" + f"{str(executor_index).zfill(self.constants.job_name_exec_no_length)}" + ) diff --git a/tesk/api/kubernetes/convert/executor_command_wrapper.py b/tesk/api/kubernetes/convert/executor_command_wrapper.py index 6fa088b0..5fde24c4 100644 --- a/tesk/api/kubernetes/convert/executor_command_wrapper.py +++ b/tesk/api/kubernetes/convert/executor_command_wrapper.py @@ -16,12 +16,16 @@ class ExecutorCommandWrapper: + """Wraps executor's command.""" + SPECIAL_CHARS = re.compile(r"[ !\"#$&'()*;<>?\[\\`{|~\t\n]") def __init__(self, executor: TesExecutor): + """Initialize the wrapper.""" self.executor = executor def get_commands_with_stream_redirects(self) -> List[str]: + """Get command with stream redirects.""" result = [] if ( @@ -38,10 +42,12 @@ def get_commands_with_stream_redirects(self) -> List[str]: for command_part in self.executor.command: if self.SPECIAL_CHARS.search(command_part): + # Replace single quotes with '"'"' if "'" in command_part: - command_part = command_part.replace("'", "'\"'\"'") - command_part = f"'{command_part}'" - command_parts.append(command_part) + replace_command_part = command_part.replace("'", "'\"'\"'") + # Quote the command part + quote_command_part = f"'{replace_command_part}'" + command_parts.append(quote_command_part) if self.executor.stdin: command_parts.append("<") diff --git a/tesk/api/kubernetes/convert/template.py b/tesk/api/kubernetes/convert/template.py index 45b7f1f4..6640e473 100644 --- a/tesk/api/kubernetes/convert/template.py +++ b/tesk/api/kubernetes/convert/template.py @@ -52,7 +52,10 @@ def task_master_template(self) -> V1Job: ) container = job.spec.template.spec.containers[0] - container.image = f"{self.taskmaster_env_properties.imageName}:{self.taskmaster_env_properties.imageVersion}" + container.image = ( + f"{self.taskmaster_env_properties.imageName}:" + f"{self.taskmaster_env_properties.imageVersion}" + ) container.args.extend( [ "-n", @@ -100,7 +103,8 @@ def task_master_template(self) -> V1Job: return job - def executor_template(self): + def executor_template(self) -> V1Job: + """Create a template for the executor job.""" container = V1Container(name="executor", resources=V1ResourceRequirements()) if self.taskmaster_env_properties.executorSecret is not None: @@ -125,7 +129,9 @@ def executor_template(self): kind=self.k8s_constants.k8s_batch_api_job_type, metadata=V1ObjectMeta( labels={ - self.constants.label_jobtype_key: self.constants.label_jobtype_value_exec + self.constants.label_jobtype_key: ( + self.constants.label_jobtype_value_exec + ) } ), spec=V1JobSpec( diff --git a/tesk/exceptions.py b/tesk/exceptions.py index 155c228b..a6af9a17 100644 --- a/tesk/exceptions.py +++ b/tesk/exceptions.py @@ -1,5 +1,7 @@ """App exceptions.""" +from http import HTTPStatus + from connexion.exceptions import ( BadRequestProblem, ExtraParameterProblem, @@ -13,7 +15,6 @@ InternalServerError, NotFound, ) -from http import HTTPStatus class ConfigNotFoundError(FileNotFoundError): diff --git a/tesk/utils.py b/tesk/utils.py index 7b9ea2c2..a4a887f8 100644 --- a/tesk/utils.py +++ b/tesk/utils.py @@ -79,7 +79,8 @@ def get_taskmaster_template() -> V1Job: return job_to_v1job(custom_conf.taskmaster_template) except AttributeError: raise ConfigNotFoundError( - "Custom configuration doesn't seem to have taskmaster_template in config file." + "Custom configuration doesn't seem to have taskmaster_template in config " + "file." ) from None @@ -94,7 +95,8 @@ def get_taskmaster_env_property() -> TaskmasterEnvProperties: return custom_conf.taskmaster_env_properties except AttributeError: raise ConfigNotFoundError( - "Custom configuration doesn't seem to have taskmaster_env_properties in config file." + "Custom configuration doesn't seem to have taskmaster_env_properties in " + "config file." ) from None @@ -192,6 +194,7 @@ def convert_job_metadata(job_metadata: JobMetadata) -> V1ObjectMeta: def pydantic_model_list_json(model_list: List[BaseModel]) -> List[dict[str, Any]]: + """Convert a list of pydantic models to a list of JSON objects.""" json_list = [] for item in model_list: json_list.append(item.json()) From 89e2dfbf409efa6991b823b394aee3cd611d81ab Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sat, 3 Aug 2024 22:15:53 +0530 Subject: [PATCH 07/22] make typos happy --- tesk/api/ga4gh/tes/controllers.py | 7 +++---- tesk/api/kubernetes/client_wrapper.py | 3 --- tesk/api/kubernetes/convert/template.py | 2 +- tesk/constants.py | 2 +- 4 files changed, 5 insertions(+), 9 deletions(-) diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index e6c2e1d8..1fdbba22 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/tesk/api/ga4gh/tes/controllers.py @@ -38,12 +38,11 @@ def CreateTask(**kwargs) -> dict: # type: ignore try: request_body = kwargs.get("body") if request_body is None: - logger("Nothing recieved in request body.") - raise BadRequest("No request body recieved.") + logger("Nothing received in request body.") + raise BadRequest("No request body received.") tes_task = TesTask(**request_body) namespace = "tesk" - task_creater = CreateTesTask(tes_task, namespace) - task_creater.response() + CreateTesTask(tes_task, namespace).response() except Exception as e: raise InternalServerError from e diff --git a/tesk/api/kubernetes/client_wrapper.py b/tesk/api/kubernetes/client_wrapper.py index 0d387ad5..01d25e56 100644 --- a/tesk/api/kubernetes/client_wrapper.py +++ b/tesk/api/kubernetes/client_wrapper.py @@ -22,9 +22,6 @@ def __init__(self, namespace=TeskConstants.tesk_namespace): Args: namespace: Namespace to use for Kubernetes. """ - # NOTE: WE might want to provide config files to load_kube_config - # we can have env variable define this or it can be passed from - # custom in FOCA config. Latter is prefered. config.load_kube_config() self.batch_api = client.BatchV1Api() self.core_api = client.CoreV1Api() diff --git a/tesk/api/kubernetes/convert/template.py b/tesk/api/kubernetes/convert/template.py index 6640e473..8940c75c 100644 --- a/tesk/api/kubernetes/convert/template.py +++ b/tesk/api/kubernetes/convert/template.py @@ -1,4 +1,4 @@ -"""Create tamplates for kubernetes objects.""" +"""Create template for kubernetes objects.""" import logging import uuid diff --git a/tesk/constants.py b/tesk/constants.py index 6ffaafae..f545cd89 100644 --- a/tesk/constants.py +++ b/tesk/constants.py @@ -22,7 +22,7 @@ class TeskConstants: taskmaster_service_account_name: str = os.getenv( "TESK_API_TASKMASTER_SERVICE_ACCOUNT_NAME", "taskmaster" ) - taskmaster_environement_executor_backoff_limit: str = os.getenv( + taskmaster_environment_executor_backoff_limit: str = os.getenv( "ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT", "2" ) filer_environment_filer_backoff_limit: str = os.getenv( From f9b630b4e10bd457a9e71ba38cd8745000bbccab Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sun, 4 Aug 2024 09:51:26 +0530 Subject: [PATCH 08/22] make mypy happy --- tesk/api/ga4gh/tes/controllers.py | 7 +- tesk/api/ga4gh/tes/models.py | 2 +- tesk/api/ga4gh/tes/task/create_task.py | 28 +++--- tesk/api/kubernetes/client_wrapper.py | 65 ++++++++---- tesk/api/kubernetes/constants.py | 51 ++++------ tesk/api/kubernetes/convert/converter.py | 98 +++++++++++++------ tesk/api/kubernetes/convert/data/job.py | 23 +++-- tesk/api/kubernetes/convert/data/task.py | 23 ++++- .../convert/executor_command_wrapper.py | 5 +- .../convert/taskmaster_env_properties.py | 5 - tesk/api/kubernetes/convert/template.py | 34 ++++++- tesk/utils.py | 4 +- 12 files changed, 222 insertions(+), 123 deletions(-) diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index 1fdbba22..4be42c30 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/tesk/api/ga4gh/tes/controllers.py @@ -28,21 +28,20 @@ def CancelTask(id, *args, **kwargs) -> dict: # type: ignore # POST /tasks @log_traffic -def CreateTask(**kwargs) -> dict: # type: ignore +def CreateTask(**kwargs) -> dict[str, str]: # type: ignore """Create task. Args: - *args: Variable length argument list. **kwargs: Arbitrary keyword arguments. """ try: request_body = kwargs.get("body") if request_body is None: - logger("Nothing received in request body.") + logger.error("Nothing received in request body.") raise BadRequest("No request body received.") tes_task = TesTask(**request_body) namespace = "tesk" - CreateTesTask(tes_task, namespace).response() + return CreateTesTask(tes_task, namespace).response() except Exception as e: raise InternalServerError from e diff --git a/tesk/api/ga4gh/tes/models.py b/tesk/api/ga4gh/tes/models.py index c442e1e0..54bb6bac 100644 --- a/tesk/api/ga4gh/tes/models.py +++ b/tesk/api/ga4gh/tes/models.py @@ -275,7 +275,7 @@ class TesResources(BaseModel): example={"VmSize": "Standard_D64_v3"}, ) backend_parameters_strict: Optional[bool] = Field( - False, + default=False, description="If set to true, backends should fail the task if any " "backend_parameters\nkey/values are unsupported, otherwise, backends should " "attempt to run the task", diff --git a/tesk/api/ga4gh/tes/task/create_task.py b/tesk/api/ga4gh/tes/task/create_task.py index 3fb29b38..abb21098 100644 --- a/tesk/api/ga4gh/tes/task/create_task.py +++ b/tesk/api/ga4gh/tes/task/create_task.py @@ -2,7 +2,7 @@ import logging -from tesk.api.ga4gh.tes.models import TesTask +from tesk.api.ga4gh.tes.models import TesResources, TesTask from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper from tesk.api.kubernetes.constants import Constants from tesk.api.kubernetes.convert.converter import TesKubernetesConverter @@ -30,7 +30,7 @@ def __init__(self, task: TesTask, namespace=TeskConstants.tesk_namespace): self.tes_kubernetes_converter = TesKubernetesConverter(self.namespace) self.constants = Constants() - def create_task(self): + def create_task(self) -> dict[str, str]: """Create TES task.""" attempts_no = 0 while attempts_no < self.constants.job_create_attempts_no: @@ -38,10 +38,11 @@ def create_task(self): attempts_no += 1 resources = self.task.resources - if resources and resources.ram_gb: - minimum_ram_gb = self.kubernetes_client_wrapper.minimum_ram_gb() - if resources.ram_gb < minimum_ram_gb: - self.task.resources.ram_gb = minimum_ram_gb + minimum_ram_gb = self.kubernetes_client_wrapper.minimum_ram_gb() + if not self.task.resources: + self.task.resources = TesResources(cpu_cores=int(minimum_ram_gb)) + if resources and resources.ram_gb and resources.ram_gb < minimum_ram_gb: + self.task.resources.ram_gb = minimum_ram_gb task_master_job = ( self.tes_kubernetes_converter.from_tes_task_to_k8s_job( @@ -54,16 +55,20 @@ def create_task(self): self.tes_kubernetes_converter.from_tes_task_to_k8s_config_map( self.task, task_master_job, - # user + # self.user ) ) + + # Create ConfigMap and Job _ = self.kubernetes_client_wrapper.create_config_map( task_master_config_map ) created_job = self.kubernetes_client_wrapper.create_job(task_master_job) - print(task_master_config_map) - print(task_master_job) - return created_job.metadata.name + + assert created_job.metadata is not None + assert created_job.metadata.name is not None + + return {"id": created_job.metadata.name} except KubernetesError as e: if ( @@ -75,7 +80,8 @@ def create_task(self): except Exception as exc: logging.error("ERROR: In createTask", exc_info=True) raise exc + return {} # Dummy return to silence mypy - def response(self) -> dict: + def response(self) -> dict[str, str]: """Create response.""" return self.create_task() diff --git a/tesk/api/kubernetes/client_wrapper.py b/tesk/api/kubernetes/client_wrapper.py index 01d25e56..de138cc9 100644 --- a/tesk/api/kubernetes/client_wrapper.py +++ b/tesk/api/kubernetes/client_wrapper.py @@ -4,9 +4,16 @@ from typing import Optional from kubernetes import client, config -from kubernetes.client import V1ConfigMap, V1Job, V1LimitRangeList +from kubernetes.client import ( + V1ConfigMap, + V1Job, + V1LabelSelector, + V1LimitRangeList, + V1PodList, +) from kubernetes.utils.quantity import parse_quantity # type: ignore +from tesk.api.kubernetes.constants import Constants from tesk.constants import TeskConstants from tesk.exceptions import KubernetesError, NotFound @@ -26,6 +33,7 @@ def __init__(self, namespace=TeskConstants.tesk_namespace): self.batch_api = client.BatchV1Api() self.core_api = client.CoreV1Api() self.namespace = namespace + self.constant = Constants() def create_job(self, job: V1Job) -> V1Job: """Create a job in the Kubernetes cluster. @@ -73,9 +81,11 @@ def read_taskmaster_job(self, task_id: str) -> V1Job: name=task_id, namespace=self.namespace ) if ( - # TODO: Put all these string in constants.py - "job-type" in job.metadata.labels - and job.metadata.labels["job-type"] == "taskmaster" + job.metadata + and job.metadata.labels + and self.constant.label_jobtype_key in job.metadata.labels + and job.metadata.labels[self.constant.label_jobtype_key] + == self.constant.label_jobtype_value_taskm ): return job except KubernetesError as e: @@ -103,13 +113,14 @@ def list_limits(self, label_selector=None, limit=None) -> V1LimitRangeList: """List limit ranges in the Kubernetes cluster. Args: - label_selector: Label selector to filter limit ranges. - limit: Maximum number of limit ranges to return. + label_selector: Label selector to filter limit ranges. + limit: Maximum number of limit ranges to return. """ try: - return self.core_api.list_namespaced_limit_range( + limits: V1LimitRangeList = self.core_api.list_namespaced_limit_range( namespace=self.namespace, label_selector=label_selector, limit=limit ) + return limits except KubernetesError as e: logger.error(f"Exception when listing limits: {e}") raise @@ -118,17 +129,18 @@ def minimum_ram_gb(self) -> float: """Get the minimum amount of RAM in the cluster. Returns: - Minimum amount of RAM in the cluster in GB. + Minimum amount of RAM in the cluster in GB. """ try: min_ram = 0 limits = self.list_limits().items for limit in limits: - for item in limit.spec.limits: - if "memory" in item.min: - mem_quantity = item.min["memory"] - mem_bytes = self.quantity_to_bytes(mem_quantity) - min_ram = max(min_ram, mem_bytes) + if limit.spec: + for item in limit.spec.limits: + if item.min and "memory" in item.min: + mem_quantity = item.min["memory"] + mem_bytes = self.quantity_to_bytes(mem_quantity) + min_ram = max(min_ram, mem_bytes) return min_ram / (1024**3) except (ValueError, TypeError) as e: logger.error(f"Error in minimum_ram_gb: {e}") @@ -139,21 +151,32 @@ def minimum_ram_gb(self) -> float: def quantity_to_bytes(self, quantity: str) -> int: """Convert quantity(resource) to bytes.""" - return parse_quantity(quantity) + parsed_quantity: int = parse_quantity(quantity) + return parsed_quantity - def list_single_job_pods(self, job: V1Job): + def list_single_job_pods(self, job: V1Job) -> V1PodList: """List pods associated with a single job. Args: job: Job object to list pods for. """ - label_selector = ",".join( - f"{k}={v}" for k, v in job.spec.selector.match_labels.items() - ) try: - return self.core_api.list_namespaced_pod( - namespace=self.namespace, label_selector=label_selector - ) + if ( + job.spec + and job.spec.selector + and isinstance(job.spec.selector, V1LabelSelector) + and job.spec.selector.match_labels + ): + label_selector = ",".join( + f"{k}={v}" for k, v in job.spec.selector.match_labels.items() + ) + namespaced_pods: V1PodList = self.core_api.list_namespaced_pod( + namespace=self.namespace, label_selector=label_selector + ) + return namespaced_pods + else: + logger.error("Job spec, selector, or match_labels is None or invalid") + return V1PodList(items=[]) except KubernetesError as e: logger.error(f"Exception when listing pods: {e}") raise diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py index 6163e571..82f8d867 100644 --- a/tesk/api/kubernetes/constants.py +++ b/tesk/api/kubernetes/constants.py @@ -16,7 +16,7 @@ class Constants(BaseModel): default="executors", description="Key in JSON taskmaster input, which holds list of executors", ) - volume_name: str = Field("PVC", description="Volume name") + volume_name: str = Field(default="PVC", description="Volume name") job_create_attempts_no: int = Field( default=5, description="Number of attempts of job creation in case of name collision", @@ -38,10 +38,8 @@ class Constants(BaseModel): ) job_name_exec_no_length: int = Field( default=2, - description=( - "No of digits reserved for executor number in executor's job name. Ends up " - "padded with '0' for numbers < 10", - ), + description="No of digits reserved for executor number in executor's job name." + " Ends up padded with '0' for numbers < 10", ) job_name_filer_suf: str = Field( default="-outputs-filer", description="Output filer name suffix" @@ -55,23 +53,18 @@ class Constants(BaseModel): ) ann_json_input_key: str = Field( default="json-input", - description=( - "Key of the annotation, that stores whole input TES task serialized to " - "JSON", - ), + description="Key of the annotation, that stores whole input TES task serialized" + " to JSON", ) label_testask_id_key: str = Field( default="taskmaster-name", - description=( - "Key of the label, that stores taskmaster's name (==TES task generated ID)" - " in executor jobs", - ), + description="Key of the label, that stores taskmaster's name (==TES task " + "generated ID) in executor jobs", ) label_jobtype_key: str = Field( default="job-type", - description=( - "Key of the label, that stores type of a job (taskmaster or executor)", - ), + description="Key of the label, that stores type of a job (taskmaster or " + "executor)", ) label_jobtype_value_taskm: str = Field( default="taskmaster", @@ -104,30 +97,26 @@ class Constants(BaseModel): ) absolute_path_message: str = Field( default="must be an absolute path", - description=( - "Message for absolute path validation (to avoid message.properties)", - ), + description="Message for absolute path validation (to avoid " + "message.properties)", + ) + resource_disk_default: float = Field( + default=0.1, description="Default resource disk value" ) - resource_disk_default: float = Field(0.1, description="Default resource disk value") completed_states: Set[str] = Field( default={"CANCELED", "COMPLETE", "EXECUTOR_ERROR", "SYSTEM_ERROR"}, - description=( - "TES task states, indicating task is not running and cannot be cancelled", - ), + description="TES task states, indicating task is not running and cannot be " + "cancelled", ) ftp_secret_username_env: str = Field( default="TESK_FTP_USERNAME", - description=( - "Name of taskmaster's ENV variable with username of FTP account used for " - "storage", - ), + description="Name of taskmaster's ENV variable with username of FTP account " + "used for storage", ) ftp_secret_password_env: str = Field( default="TESK_FTP_PASSWORD", - description=( - "Name of taskmaster's ENV variable with password of FTP account used for " - "storage", - ), + description="Name of taskmaster's ENV variable with password of FTP account " + "used for storage", ) cancel_patch: str = Field( default='{"metadata":{"labels":{"task-status":"Cancelled"}}}', diff --git a/tesk/api/kubernetes/convert/converter.py b/tesk/api/kubernetes/convert/converter.py index a87273d5..79085636 100644 --- a/tesk/api/kubernetes/convert/converter.py +++ b/tesk/api/kubernetes/convert/converter.py @@ -6,14 +6,17 @@ import logging from decimal import Decimal from io import BytesIO -from typing import Any +from typing import Any, Optional from kubernetes.client import ( V1ConfigMap, V1ConfigMapVolumeSource, V1Container, V1EnvVar, + V1JobSpec, V1ObjectMeta, + V1PodSpec, + V1PodTemplateSpec, V1ResourceRequirements, V1Volume, ) @@ -48,56 +51,62 @@ def __init__(self, namespace=TeskConstants.tesk_namespace): self.k8s_constants = K8sConstants() self.namespace = namespace - # TODO: Add user to the method when auth implemented in FOCA def from_tes_task_to_k8s_job(self, task: TesTask): """Convert TES task to Kubernetes job.""" - taskmsater_job: V1Job = KubernetesTemplateSupplier( + taskmaster_job: V1Job = KubernetesTemplateSupplier( self.namespace ).task_master_template() - if taskmsater_job.metadata is None: - taskmsater_job.metadata = V1ObjectMeta() + if taskmaster_job.metadata is None: + taskmaster_job.metadata = V1ObjectMeta() - if taskmsater_job.metadata.annotations is None: - taskmsater_job.metadata.annotations = {} + if taskmaster_job.metadata.annotations is None: + taskmaster_job.metadata.annotations = {} - if taskmsater_job.metadata.labels is None: - taskmsater_job.metadata.labels = {} + if taskmaster_job.metadata.labels is None: + taskmaster_job.metadata.labels = {} - # taskmsater_job.metadata.name = task.name - - taskmsater_job.metadata.annotations[self.constants.ann_testask_name_key] = ( - task.name - ) - # taskmsater_job.metadata.labels[self.constants.label_userid_key] = user[ + # taskmaster_job.metadata.name = task.name + if task.name: + taskmaster_job.metadata.annotations[self.constants.ann_testask_name_key] = ( + task.name + ) + # taskmaster_job.metadata.labels[self.constants.label_userid_key] = user[ # "username" # ] # if task.tags and "GROUP_NAME" in task.tags: - # taskmsater_job.metadata.labels[self.constants.label_userid_key] = task[ + # taskmaster_job.metadata.labels[self.constants.label_userid_key] = task[ # "tags" # ]["GROUP_NAME"] # elif user["is_member"]: - # taskmsater_job.metadata.labels[self.constants.label_groupname_key] = user[ + # taskmaster_job.metadata.labels[self.constants.label_groupname_key] = user[ # "any_group" # ] try: - taskmsater_job.metadata.annotations[self.constants.ann_json_input_key] = ( + taskmaster_job.metadata.annotations[self.constants.ann_json_input_key] = ( task.json() ) except Exception as ex: logger.info( - f"Serializing task {taskmsater_job.metadata.name} to JSON failed", ex + f"Serializing task {taskmaster_job.metadata.name} to JSON failed", ex ) volume = V1Volume( name="jsoninput", - config_map=V1ConfigMapVolumeSource(name=taskmsater_job.metadata.name), + config_map=V1ConfigMapVolumeSource(name=taskmaster_job.metadata.name), ) - taskmsater_job.spec.template.spec.volumes.append(volume) - return taskmsater_job + if taskmaster_job.spec is None: + taskmaster_job.spec = V1JobSpec(template=V1PodTemplateSpec()) + if taskmaster_job.spec.template.spec is None: + taskmaster_job.spec.template.spec = V1PodSpec(containers=[]) + if taskmaster_job.spec.template.spec.volumes is None: + taskmaster_job.spec.template.spec.volumes = [] + + taskmaster_job.spec.template.spec.volumes.append(volume) + return taskmaster_job def from_tes_task_to_k8s_config_map( self, @@ -106,10 +115,14 @@ def from_tes_task_to_k8s_config_map( # user, ) -> V1ConfigMap: """Create a Kubernetes ConfigMap from a TES task.""" + if job.metadata is None: + job.metadata = V1ObjectMeta() + task_master_config_map = V1ConfigMap( metadata=V1ObjectMeta(name=job.metadata.name) ) + assert task_master_config_map.metadata is not None task_master_config_map.metadata.labels = ( task_master_config_map.metadata.labels or {} ) @@ -117,14 +130,15 @@ def from_tes_task_to_k8s_config_map( task_master_config_map.metadata.annotations or {} ) - task_master_config_map.metadata.annotations[ - self.constants.ann_testask_name_key - ] = task.name + if task.name: + task_master_config_map.metadata.annotations[ + self.constants.ann_testask_name_key + ] = task.name # task_master_config_map.metadata.labels[self.constants.label_userid_key] # = user["username"] - if "tags" in task and "GROUP_NAME" in task.tags: + if task.tags and "GROUP_NAME" in task.tags: task_master_config_map.metadata.labels[ self.constants.label_groupname_key ] = task.tags["GROUP_NAME"] @@ -132,6 +146,9 @@ def from_tes_task_to_k8s_config_map( # task_master_config_map.metadata.labels[self.constants.label_groupname_key] # = user["any_group"] + assert task_master_config_map.metadata.name is not None + assert task.resources is not None + executors_as_jobs = [ self.from_tes_executor_to_k8s_job( task_master_config_map.metadata.name, @@ -145,10 +162,14 @@ def from_tes_task_to_k8s_config_map( ] task_master_input: dict[str, Any] = { - "inputs": pydantic_model_list_json(task.inputs) or [], - "outputs": pydantic_model_list_json(task.outputs) or [], + "inputs": pydantic_model_list_json(task.inputs) if task.inputs else [], + "outputs": pydantic_model_list_json(task.outputs) if task.outputs else [], "volumes": task.volumes or [], - "resources": {"disk_gb": float(task.resources.disk_gb) or 10.0}, + "resources": { + "disk_gb": float(task.resources.disk_gb) + if task.resources.disk_gb + else 10.0 + }, } task_master_input[self.constants.taskmaster_input_exec_key] = [ exec_job.to_dict() for exec_job in executors_as_jobs @@ -186,7 +207,7 @@ def decimal_to_float(obj): def from_tes_executor_to_k8s_job( # noqa: PLR0913 self, generated_task_id: str, - tes_task_name: str, + tes_task_name: Optional[str], executor: TesExecutor, executor_index: int, resources: TesResources, @@ -197,11 +218,15 @@ def from_tes_executor_to_k8s_job( # noqa: PLR0913 job: V1Job = self.template_supplier.executor_template() # Set executors name based on taskmaster's job name + # TODO: Fix me ASAP Job(job).change_job_name( # Task(job, generated_task_id).get_executor_name(executor_index) "newname" ) + if job.metadata is None: + job.metadata = V1ObjectMeta() + # Put arbitrary labels and annotations job.metadata.labels = job.metadata.labels or {} job.metadata.labels[self.constants.label_testask_id_key] = generated_task_id @@ -209,7 +234,15 @@ def from_tes_executor_to_k8s_job( # noqa: PLR0913 # job.metadata.labels[self.constants.label_userid_key] = user.username job.metadata.annotations = job.metadata.annotations or {} - job.metadata.annotations[self.constants.ann_testask_name_key] = tes_task_name + if tes_task_name: + job.metadata.annotations[self.constants.ann_testask_name_key] = ( + tes_task_name + ) + + if job.spec is None: + job.spec = V1JobSpec(template=V1PodTemplateSpec()) + if job.spec.template.spec is None: + job.spec.template.spec = V1PodSpec(containers=[]) container: V1Container = job.spec.template.spec.containers[0] @@ -235,9 +268,10 @@ def from_tes_executor_to_k8s_job( # noqa: PLR0913 container.env = [] container.working_dir = executor.workdir - container.resources = V1ResourceRequirements(requests={}) + assert container.resources.requests is not None + if resources.cpu_cores: container.resources.requests["cpu"] = parse_quantity( str(resources.cpu_cores) diff --git a/tesk/api/kubernetes/convert/data/job.py b/tesk/api/kubernetes/convert/data/job.py index 3fb13333..8a30907a 100644 --- a/tesk/api/kubernetes/convert/data/job.py +++ b/tesk/api/kubernetes/convert/data/job.py @@ -6,7 +6,7 @@ from typing import List, Optional -from kubernetes.client import V1Job, V1Pod +from kubernetes.client import V1Job, V1ObjectMeta, V1Pod class Job: @@ -51,11 +51,22 @@ def change_job_name(self, new_name: str): Also the names in its metadata and container specs. """ - self.job.metadata.name = new_name - self.job.spec.template.metadata.name = new_name - if self.job.spec.template.spec.containers: - self.job.spec.template.spec.containers[0].name = new_name + if self.job.metadata is None: + self.job.metadata = V1ObjectMeta(name=new_name) + else: + self.job.metadata.name = new_name + + if ( + self.job is not None + and self.job.spec is not None + and self.job.spec.template is not None + and self.job.spec.template.metadata is not None + ): + self.job.spec.template.metadata.name = new_name + + if self.job.spec.template.spec and self.job.spec.template.spec.containers: + self.job.spec.template.spec.containers[0].name = new_name def get_job_name(self) -> Optional[str]: """Returns the job name.""" - return self.job.metadata.name + return self.job.metadata.name if self.job.metadata else None diff --git a/tesk/api/kubernetes/convert/data/task.py b/tesk/api/kubernetes/convert/data/task.py index ab49cf0a..49fc5de0 100644 --- a/tesk/api/kubernetes/convert/data/task.py +++ b/tesk/api/kubernetes/convert/data/task.py @@ -34,10 +34,17 @@ def __init__( self.executors_by_name: Dict[str, Job] = {} self.output_filer: Optional[Job] = None self.constants = Constants() + self.MAX_INT = 2**31 - 1 - def add_executor(self, executor: Job): + def add_executor(self, executor: Job) -> None: """Add executor to the task.""" - self.executors_by_name.setdefault(executor.get_job().metadata.name, executor) + metadata = executor.get_job().metadata + assert metadata is not None + + name = metadata.name + assert name is not None + + self.executors_by_name.setdefault(name, executor) def set_output_filer(self, filer: Job): """Set output filer for the task.""" @@ -65,11 +72,19 @@ def get_output_filer(self) -> Optional[Job]: def extract_executor_number(self, executor: Job) -> int: """Extract executor number from the executor's name.""" taskmaster_name = self.taskmaster.get_job_name() + assert taskmaster_name is not None + prefix = taskmaster_name + self.constants.job_name_exec_prefix - match = re.match(f"{re.escape(prefix)}(\d+)", executor.get_job_name()) + exec_name = executor.get_job_name() + + if not exec_name: + return self.MAX_INT + + match = re.match(f"{re.escape(prefix)}(\d+)", exec_name) if match: return int(match.group(1)) - return float("inf") + + return self.MAX_INT def get_executor_name(self, executor_index: int) -> str: """Get executor name based on the taskmaster's job name and executor index.""" diff --git a/tesk/api/kubernetes/convert/executor_command_wrapper.py b/tesk/api/kubernetes/convert/executor_command_wrapper.py index 5fde24c4..08e515f7 100644 --- a/tesk/api/kubernetes/convert/executor_command_wrapper.py +++ b/tesk/api/kubernetes/convert/executor_command_wrapper.py @@ -41,13 +41,14 @@ def get_commands_with_stream_redirects(self) -> List[str]: command_parts = [] for command_part in self.executor.command: + command = "" if self.SPECIAL_CHARS.search(command_part): # Replace single quotes with '"'"' if "'" in command_part: replace_command_part = command_part.replace("'", "'\"'\"'") # Quote the command part - quote_command_part = f"'{replace_command_part}'" - command_parts.append(quote_command_part) + command = f"'{replace_command_part}'" + command_parts.append(command) if self.executor.stdin: command_parts.append("<") diff --git a/tesk/api/kubernetes/convert/taskmaster_env_properties.py b/tesk/api/kubernetes/convert/taskmaster_env_properties.py index d0f7ef7d..79d7df5a 100644 --- a/tesk/api/kubernetes/convert/taskmaster_env_properties.py +++ b/tesk/api/kubernetes/convert/taskmaster_env_properties.py @@ -69,11 +69,6 @@ class TaskmasterEnvProperties(BaseModel): serviceAccountName: str = Field( default="default", description="Service Account name for taskmaster" ) - debug: bool = Field( - default=False, - description="If verbose (debug) mode of taskmaster is on (passes additional " - "flag to taskmaster and sets image pull policy to Always)", - ) executorSecret: Optional[ExecutorSecret] = Field( default=None, description="Executor secret configuration" ) diff --git a/tesk/api/kubernetes/convert/template.py b/tesk/api/kubernetes/convert/template.py index 8940c75c..6457686c 100644 --- a/tesk/api/kubernetes/convert/template.py +++ b/tesk/api/kubernetes/convert/template.py @@ -2,6 +2,7 @@ import logging import uuid +from typing import Iterable from kubernetes.client import ( V1Container, @@ -41,12 +42,18 @@ def __init__(self, namespace=TeskConstants.tesk_namespace, security_context=None def get_task_master_name(self) -> str: """Generate a unique name for the taskmaster job.""" - return self.constants.job_name_taskm_prefix + str(uuid.uuid4()) + name: str = self.constants.job_name_taskm_prefix + str(uuid.uuid4()) + return name def task_master_template(self) -> V1Job: """Create a template for the taskmaster job.""" job: V1Job = self.taskmaster_template + if job.spec is None: + job.spec = V1JobSpec(template=V1PodTemplateSpec()) + if job.spec.template.spec is None: + job.spec.template.spec = V1PodSpec(containers=[]) + job.spec.template.spec.service_account_name = ( self.taskmaster_env_properties.serviceAccountName ) @@ -56,6 +63,9 @@ def task_master_template(self) -> V1Job: f"{self.taskmaster_env_properties.imageName}:" f"{self.taskmaster_env_properties.imageVersion}" ) + + assert isinstance(container.args, Iterable) + container.args.extend( [ "-n", @@ -71,12 +81,19 @@ def task_master_template(self) -> V1Job: container.args.append("-d") container.image_pull_policy = "Always" + if job.metadata is None: + job.metadata = V1ObjectMeta(labels={}) + + assert job.metadata.labels is not None + job.metadata.labels[self.constants.label_jobtype_key] = ( self.constants.label_jobtype_value_taskm ) task_master_name = self.get_task_master_name() job.metadata.name = task_master_name + assert isinstance(container.env, Iterable) + container.env.extend( [ V1EnvVar(name=key.upper().replace(".", "_"), value=value) @@ -97,6 +114,8 @@ def task_master_template(self) -> V1Job: if self.taskmaster_env_properties.ftp.enabled: for env in container.env: if env.name in ftp_secrets: + assert env.value_from is not None + assert env.value_from.secret_key_ref is not None env.value_from.secret_key_ref.name = ( self.taskmaster_env_properties.ftp.secretName ) @@ -111,8 +130,10 @@ def executor_template(self) -> V1Job: container.volume_mounts = [ V1VolumeMount( read_only=True, - name=self.taskmaster_env_properties.executorSecret.name, - mount_path=self.taskmaster_env_properties.executorSecret.mountPath, + name=str(self.taskmaster_env_properties.executorSecret.name), + mount_path=str( + self.taskmaster_env_properties.executorSecret.mountPath + ), ) ] @@ -140,9 +161,14 @@ def executor_template(self) -> V1Job: ) if self.taskmaster_env_properties.executorSecret is not None: + if job.spec is None: + job.spec = V1JobSpec(template=V1PodTemplateSpec()) + if job.spec.template.spec is None: + job.spec.template.spec = V1PodSpec(containers=[]) + job.spec.template.spec.volumes = [ V1Volume( - name=self.taskmaster_env_properties.executorSecret.name, + name=str(self.taskmaster_env_properties.executorSecret.name), secret=V1SecretVolumeSource( secret_name=self.taskmaster_env_properties.executorSecret.name ), diff --git a/tesk/utils.py b/tesk/utils.py index a4a887f8..b8ea88e6 100644 --- a/tesk/utils.py +++ b/tesk/utils.py @@ -2,7 +2,7 @@ import os from pathlib import Path -from typing import Any, List, Optional +from typing import Any, List, Optional, Sequence from foca import Foca from kubernetes.client.models import ( @@ -193,7 +193,7 @@ def convert_job_metadata(job_metadata: JobMetadata) -> V1ObjectMeta: ) -def pydantic_model_list_json(model_list: List[BaseModel]) -> List[dict[str, Any]]: +def pydantic_model_list_json(model_list: Sequence[BaseModel]) -> List[dict[str, Any]]: """Convert a list of pydantic models to a list of JSON objects.""" json_list = [] for item in model_list: From 5f449265bc2e6aeecbeceae523bac9e5d9eb8591 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sun, 4 Aug 2024 10:37:37 +0530 Subject: [PATCH 09/22] make bandit happy --- pyproject.toml | 5 +++-- tesk/custom_config.py | 2 +- tesk/utils.py | 15 ++++++++++----- 3 files changed, 14 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 49795030..05534c30 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,9 +4,10 @@ requires = ["poetry-core"] [tool.bandit] skips = [ + "B101", # Use of asserts is discouraged as it is removed during byte generation, we don't need that! + "B108", # Insecure usage of temp file/directory, false positive. "B321", # FTP-related functions are being called. - "B402", # A FTP-related module is being imported. - "B108" # Insecure usage of temp file/directory, false positive. + "B402" # A FTP-related module is being imported. ] [tool.poetry] diff --git a/tesk/custom_config.py b/tesk/custom_config.py index 78a285db..55f14298 100644 --- a/tesk/custom_config.py +++ b/tesk/custom_config.py @@ -43,7 +43,7 @@ class DownwardAPIItem(BaseModel): """Downward API item configuration.""" path: str - fieldRef: Dict[str, str] + fieldRef: str class Volume(BaseModel): diff --git a/tesk/utils.py b/tesk/utils.py index b8ea88e6..6262dcc6 100644 --- a/tesk/utils.py +++ b/tesk/utils.py @@ -2,17 +2,18 @@ import os from pathlib import Path -from typing import Any, List, Optional, Sequence +from typing import List, Optional, Sequence from foca import Foca from kubernetes.client.models import ( V1Container, - V1DownwardAPIProjection, V1DownwardAPIVolumeFile, + V1DownwardAPIVolumeSource, V1EnvVar, V1EnvVarSource, V1Job, V1JobSpec, + V1ObjectFieldSelector, V1ObjectMeta, V1PodSpec, V1PodTemplateSpec, @@ -126,14 +127,18 @@ def convert_downward_api_item( downward_api_item: DownwardAPIItem, ) -> V1DownwardAPIVolumeFile: return V1DownwardAPIVolumeFile( - path=downward_api_item.path, field_ref=downward_api_item.fieldRef + path=downward_api_item.path, + field_ref=V1ObjectFieldSelector( + # TODO: Check if this is correct. + field_path=downward_api_item.fieldRef + ), ) def convert_volume(volume: Volume) -> V1Volume: if volume.downwardAPI: return V1Volume( name=volume.name, - downward_api=V1DownwardAPIProjection( + downward_api=V1DownwardAPIVolumeSource( items=[ convert_downward_api_item(item) for item in volume.downwardAPI["items"] @@ -193,7 +198,7 @@ def convert_job_metadata(job_metadata: JobMetadata) -> V1ObjectMeta: ) -def pydantic_model_list_json(model_list: Sequence[BaseModel]) -> List[dict[str, Any]]: +def pydantic_model_list_json(model_list: Sequence[BaseModel]) -> List[str]: """Convert a list of pydantic models to a list of JSON objects.""" json_list = [] for item in model_list: From ad17a00b91f95ac5bb0f80c442639ade2752d4d9 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sun, 4 Aug 2024 11:57:08 +0530 Subject: [PATCH 10/22] fix config --- compressed_data | 1 + encoded_data.txt | 1 + tesk/custom_config.py | 2 +- tesk/utils.py | 6 +----- 4 files changed, 4 insertions(+), 6 deletions(-) create mode 100644 compressed_data create mode 100644 encoded_data.txt diff --git a/compressed_data b/compressed_data new file mode 100644 index 00000000..134cf15e --- /dev/null +++ b/compressed_data @@ -0,0 +1 @@ +{"inputs": ["{\"name\": null, \"description\": null, \"url\": \"s3://my-object-store/file1\", \"path\": \"/data/file1\", \"type\": \"FILE\", \"content\": null, \"streamable\": null}"], "outputs": ["{\"name\": null, \"description\": null, \"url\": \"s3://my-object-store/outfile-1\", \"path\": \"/data/outfile\", \"path_prefix\": null, \"type\": \"FILE\"}"], "volumes": ["/vol/A/"], "resources": {"disk_gb": 40.0}, "executors": [{"api_version": "batch/v1", "kind": "Job", "metadata": {"annotations": {"tes-task-name": "string"}, "creation_timestamp": null, "deletion_grace_period_seconds": null, "deletion_timestamp": null, "finalizers": null, "generate_name": null, "generation": null, "labels": {"job-type": "executor", "taskmaster-name": "task-fef96900-6da7-4672-a1ec-14bf3d720c8f", "executor-no": "0"}, "managed_fields": null, "name": "newname", "namespace": null, "owner_references": null, "resource_version": null, "self_link": null, "uid": null}, "spec": {"active_deadline_seconds": null, "backoff_limit": null, "backoff_limit_per_index": null, "completion_mode": null, "completions": null, "manual_selector": null, "max_failed_indexes": null, "parallelism": null, "pod_failure_policy": null, "pod_replacement_policy": null, "selector": null, "suspend": null, "template": {"metadata": {"annotations": null, "creation_timestamp": null, "deletion_grace_period_seconds": null, "deletion_timestamp": null, "finalizers": null, "generate_name": null, "generation": null, "labels": null, "managed_fields": null, "name": "newname", "namespace": null, "owner_references": null, "resource_version": null, "self_link": null, "uid": null}, "spec": {"active_deadline_seconds": null, "affinity": null, "automount_service_account_token": null, "containers": [{"args": null, "command": ["/bin/sh", "-c", " < /data/file1 > /tmp/stdout.log 2> /tmp/stderr.log"], "env": [{"name": "BLASTDB", "value": "/data/GRC38", "value_from": null}, {"name": "HMMERDB", "value": "/data/hmmer", "value_from": null}], "env_from": null, "image": null, "image_pull_policy": null, "lifecycle": null, "liveness_probe": null, "name": "newname", "ports": null, "readiness_probe": null, "resize_policy": null, "resources": {"claims": null, "limits": null, "requests": {"cpu": 4.0, "memory": 8589934592.0}}, "restart_policy": null, "security_context": null, "startup_probe": null, "stdin": null, "stdin_once": null, 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"volumes": null}}, "ttl_seconds_after_finished": null}, "status": null}]} \ No newline at end of file diff --git a/encoded_data.txt b/encoded_data.txt new file mode 100644 index 00000000..33aa3d46 --- /dev/null +++ b/encoded_data.txt @@ -0,0 +1 @@ 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diff --git a/tesk/custom_config.py b/tesk/custom_config.py index 55f14298..78a285db 100644 --- a/tesk/custom_config.py +++ b/tesk/custom_config.py @@ -43,7 +43,7 @@ class DownwardAPIItem(BaseModel): """Downward API item configuration.""" path: str - fieldRef: str + fieldRef: Dict[str, str] class Volume(BaseModel): diff --git a/tesk/utils.py b/tesk/utils.py index 6262dcc6..2e504656 100644 --- a/tesk/utils.py +++ b/tesk/utils.py @@ -13,7 +13,6 @@ V1EnvVarSource, V1Job, V1JobSpec, - V1ObjectFieldSelector, V1ObjectMeta, V1PodSpec, V1PodTemplateSpec, @@ -128,10 +127,7 @@ def convert_downward_api_item( ) -> V1DownwardAPIVolumeFile: return V1DownwardAPIVolumeFile( path=downward_api_item.path, - field_ref=V1ObjectFieldSelector( - # TODO: Check if this is correct. - field_path=downward_api_item.fieldRef - ), + field_ref=downward_api_item.fieldRef, ) def convert_volume(volume: Volume) -> V1Volume: From 2b7a25196fdc4b9c6ee2431be250c9e75cd39697 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sun, 4 Aug 2024 12:06:21 +0530 Subject: [PATCH 11/22] minor --- tesk/utils.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/tesk/utils.py b/tesk/utils.py index 2e504656..c5878323 100644 --- a/tesk/utils.py +++ b/tesk/utils.py @@ -13,6 +13,7 @@ V1EnvVarSource, V1Job, V1JobSpec, + V1ObjectFieldSelector, V1ObjectMeta, V1PodSpec, V1PodTemplateSpec, @@ -125,9 +126,18 @@ def convert_env_var_source( def convert_downward_api_item( downward_api_item: DownwardAPIItem, ) -> V1DownwardAPIVolumeFile: + field_ref = None + if downward_api_item.fieldRef: + field_path = downward_api_item.fieldRef.get("fieldPath") + if field_path: + field_ref = V1ObjectFieldSelector( + api_version=downward_api_item.fieldRef.get("apiVersion"), + field_path=field_path, + ) + return V1DownwardAPIVolumeFile( path=downward_api_item.path, - field_ref=downward_api_item.fieldRef, + field_ref=field_ref, ) def convert_volume(volume: Volume) -> V1Volume: From da720a7ee7ca0eaa0e9fd77c1016b64e7726238d Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 7 Aug 2024 22:50:57 +0530 Subject: [PATCH 12/22] chore: WIP list task --- tesk/api/ga4gh/tes/controllers.py | 25 ++- tesk/api/ga4gh/tes/models.py | 8 + tesk/api/ga4gh/tes/task/create_task.py | 15 +- tesk/api/ga4gh/tes/task/get_task.py | 140 ++++++++++++ tesk/api/ga4gh/tes/task/task_request.py | 23 ++ tesk/api/kubernetes/client_wrapper.py | 99 ++++++++- tesk/api/kubernetes/constants.py | 10 + tesk/api/kubernetes/convert/converter.py | 207 +++++++++++++++++- .../kubernetes/convert/data/build_strategy.py | 58 +++++ tesk/api/kubernetes/convert/data/job.py | 9 + .../convert/data/single_task_strategy.py | 56 +++++ .../kubernetes/convert/data/task_builder.py | 72 ++++++ .../convert/data/task_list_strategy.py | 72 ++++++ tesk/app.py | 2 +- tesk/utils.py | 20 ++ 15 files changed, 794 insertions(+), 22 deletions(-) create mode 100644 tesk/api/ga4gh/tes/task/get_task.py create mode 100644 tesk/api/ga4gh/tes/task/task_request.py create mode 100644 tesk/api/kubernetes/convert/data/build_strategy.py create mode 100644 tesk/api/kubernetes/convert/data/single_task_strategy.py create mode 100644 tesk/api/kubernetes/convert/data/task_builder.py create mode 100644 tesk/api/kubernetes/convert/data/task_list_strategy.py diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index 4be42c30..0d9e682b 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/tesk/api/ga4gh/tes/controllers.py @@ -1,13 +1,16 @@ """Controllers for GA4GH TES API endpoints.""" import logging - +import json from foca.utils.logging import log_traffic # type: ignore from tesk.api.ga4gh.tes.models import TesTask from tesk.api.ga4gh.tes.service_info.service_info import ServiceInfo from tesk.api.ga4gh.tes.task.create_task import CreateTesTask from tesk.exceptions import BadRequest, InternalServerError +from tesk.api.ga4gh.tes.task.get_task import GetTesTask +from tesk.api.ga4gh.tes.models import TaskView +from tesk.utils import enum_to_string # Get logger instance logger = logging.getLogger(__name__) @@ -28,7 +31,7 @@ def CancelTask(id, *args, **kwargs) -> dict: # type: ignore # POST /tasks @log_traffic -def CreateTask(**kwargs) -> dict[str, str]: # type: ignore +def CreateTask(**kwargs) -> dict: """Create task. Args: @@ -40,15 +43,15 @@ def CreateTask(**kwargs) -> dict[str, str]: # type: ignore logger.error("Nothing received in request body.") raise BadRequest("No request body received.") tes_task = TesTask(**request_body) - namespace = "tesk" - return CreateTesTask(tes_task, namespace).response() + response = CreateTesTask(tes_task).response() + return response except Exception as e: raise InternalServerError from e # GET /tasks/service-info @log_traffic -def GetServiceInfo() -> dict: # type: ignore +def GetServiceInfo() -> dict: """Get service info.""" service_info = ServiceInfo() return service_info.response() @@ -56,14 +59,22 @@ def GetServiceInfo() -> dict: # type: ignore # GET /tasks @log_traffic -def ListTasks(*args, **kwargs) -> dict: # type: ignore +def ListTasks(*args, **kwargs): """List all available tasks. Args: *args: Variable length argument list. **kwargs: Arbitrary keyword arguments. """ - pass + get_tes_task = GetTesTask() + view = TaskView(kwargs.get("view")) + name_prefix = kwargs.get("name_prefix") + page_size = kwargs.get("page_size") + page_token = kwargs.get("page_token") + response = get_tes_task.list_tasks( + view=view, name_prefix=name_prefix, page_size=page_size, page_token=page_token + ) + return json.loads(response.json()) # GET /tasks diff --git a/tesk/api/ga4gh/tes/models.py b/tesk/api/ga4gh/tes/models.py index 54bb6bac..a479d7ca 100644 --- a/tesk/api/ga4gh/tes/models.py +++ b/tesk/api/ga4gh/tes/models.py @@ -568,3 +568,11 @@ class TesListTasksResponse(BaseModel): description="Token used to return the next page of results. This value can be " "used\nin the `page_token` field of the next ListTasks request.", ) + + +class TaskView(str, Enum): + """View of task for API response.""" + + MINIMAL = "MINIMAL" + BASIC = "BASIC" + FULL = "FULL" diff --git a/tesk/api/ga4gh/tes/task/create_task.py b/tesk/api/ga4gh/tes/task/create_task.py index abb21098..e3e69363 100644 --- a/tesk/api/ga4gh/tes/task/create_task.py +++ b/tesk/api/ga4gh/tes/task/create_task.py @@ -2,17 +2,21 @@ import logging +from pydantic import BaseModel + from tesk.api.ga4gh.tes.models import TesResources, TesTask from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper from tesk.api.kubernetes.constants import Constants from tesk.api.kubernetes.convert.converter import TesKubernetesConverter from tesk.constants import TeskConstants from tesk.exceptions import KubernetesError +from tesk.api.ga4gh.tes.task.task_request import TesTaskRequest +from tesk.api.ga4gh.tes.models import TesCreateTaskResponse logger = logging.getLogger(__name__) -class CreateTesTask: +class CreateTesTask(TesTaskRequest): """Create TES task.""" # TODO: Add user to the class when auth implemented in FOCA @@ -25,12 +29,12 @@ def __init__(self, task: TesTask, namespace=TeskConstants.tesk_namespace): """ self.task = task # self.user = user - self.kubernetes_client_wrapper = KubernetesClientWrapper() self.namespace = namespace + self.kubernetes_client_wrapper = KubernetesClientWrapper() self.tes_kubernetes_converter = TesKubernetesConverter(self.namespace) self.constants = Constants() - def create_task(self) -> dict[str, str]: + def create_task(self) -> TesCreateTaskResponse: """Create TES task.""" attempts_no = 0 while attempts_no < self.constants.job_create_attempts_no: @@ -68,7 +72,7 @@ def create_task(self) -> dict[str, str]: assert created_job.metadata is not None assert created_job.metadata.name is not None - return {"id": created_job.metadata.name} + return TesCreateTaskResponse(id=created_job.metadata.name) except KubernetesError as e: if ( @@ -82,6 +86,5 @@ def create_task(self) -> dict[str, str]: raise exc return {} # Dummy return to silence mypy - def response(self) -> dict[str, str]: - """Create response.""" + def handle_request(self) -> BaseModel: return self.create_task() diff --git a/tesk/api/ga4gh/tes/task/get_task.py b/tesk/api/ga4gh/tes/task/get_task.py new file mode 100644 index 00000000..6c639951 --- /dev/null +++ b/tesk/api/ga4gh/tes/task/get_task.py @@ -0,0 +1,140 @@ +from typing import List +from kubernetes.client.models import V1JobList +from pydantic import BaseModel +from tesk.api.ga4gh.tes.models import TaskView, TesListTasksResponse, TesTask +from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper +from tesk.api.kubernetes.convert.converter import TesKubernetesConverter +from tesk.api.kubernetes.convert.data.task import Task +from tesk.api.kubernetes.convert.data.task_builder import TaskBuilder + +from tesk.api.ga4gh.tes.models import TesListTasksResponse, TesTask +from tesk.api.ga4gh.tes.task.task_request import TesTaskRequest +from tesk.constants import TeskConstants + + +class GetTesTaskInterface: + def __init__(self, namespace=TeskConstants.tesk_namespace): + self.kubernetes_client_wrapper = KubernetesClientWrapper(namespace=namespace) + self.tes_kubernetes_converter = TesKubernetesConverter() + + def get_task( + self, + task_id: str, + view: TaskView, + # user: User + ) -> TesTask: + task_master_job = self.kubernetes_client_wrapper.read_taskmaster_job(task_id) + executor_jobs = self.kubernetes_client_wrapper.list_single_task_executor_jobs( + task_master_job.metadata.name + ) + task_master_pods = self.kubernetes_client_wrapper.list_single_job_pods( + task_master_job + ) + task_builder = ( + TaskBuilder.new_single_task() + .add_job(task_master_job) + .add_job_list(executor_jobs.items) + .add_pod_list(task_master_pods.items) + ) + + for executor_job in executor_jobs.items: + executor_job_pods = self.kubernetes_client_wrapper.list_single_job_pods( + executor_job + ) + task_builder.add_pod_list(executor_job_pods.items) + + output_filer_job = ( + self.kubernetes_client_wrapper.get_single_task_output_filer_job( + task_master_job.metadata.name + ) + ) + if output_filer_job: + task_builder.add_job(output_filer_job) + + return self._get_task(task_builder.get_task(), view, False) + + def _get_task(self, task_objects: Task, view: TaskView, is_list: bool) -> TesTask: + if view == TaskView.MINIMAL: + return self.tes_kubernetes_converter.from_k8s_jobs_to_tes_task_minimal( + task_objects, is_list + ) + + task = self.tes_kubernetes_converter.from_k8s_jobs_to_tes_task_basic( + task_objects, view == TaskView.BASIC + ) + + if view == TaskView.BASIC: + return task + + for i, executor_job in enumerate(task_objects.get_executors()): + if executor_job.has_pods(): + executor_log = task.logs[0].logs[i] + if view == TaskView.FULL: + executor_pod_log = self.kubernetes_client_wrapper.read_pod_log( + executor_job.get_first_pod().metadata.name + ) + if executor_pod_log is not None: + executor_log.stdout = executor_pod_log + + if task_objects.taskmaster.has_pods(): + task_master_pod_log = self.kubernetes_client_wrapper.read_pod_log( + task_objects.get_taskmaster().get_first_pod().metadata.name + ) + if task_master_pod_log is not None: + task.logs[0].system_logs.append(task_master_pod_log) + + return task + + def list_tasks( + self, + name_prefix: str, + page_size: int, + page_token: str, + view: TaskView, + # user: User, + ) -> TesListTasksResponse: + taskmaster_jobs: V1JobList = ( + self.kubernetes_client_wrapper.list_all_taskmaster_jobs_for_user( + page_token, + page_size, + # user + ) + ) + executor_jobs = self.kubernetes_client_wrapper.list_all_task_executor_jobs() + filer_jobs = self.kubernetes_client_wrapper.list_all_filer_jobs() + job_pods = self.kubernetes_client_wrapper.list_all_job_pods() + task_list_builder = ( + TaskBuilder.new_task_list() + .add_job_list(taskmaster_jobs.items) + .add_job_list(executor_jobs.items) + .add_job_list(filer_jobs.items) + .add_pod_list(job_pods.items) + ) + + tasks: List[TesTask] = [ + self._get_task(task, view, True) + for task in task_list_builder.get_task_list() + ] + + response = TesListTasksResponse( + tasks=tasks, next_page_token=taskmaster_jobs.metadata._continue + ) + + return response + + +class GetTesTask(TesTaskRequest, GetTesTaskInterface): + def handle_request( + self, + name_prefix: str, + page_size: int, + page_token: str, + view: TaskView, + # user: User, + ) -> BaseModel: + return self.list_tasks( + name_prefix=name_prefix, + page_size=page_size, + page_token=page_token, + view=view, + ) diff --git a/tesk/api/ga4gh/tes/task/task_request.py b/tesk/api/ga4gh/tes/task/task_request.py new file mode 100644 index 00000000..e955d97d --- /dev/null +++ b/tesk/api/ga4gh/tes/task/task_request.py @@ -0,0 +1,23 @@ +import logging +from abc import ABC, abstractmethod +import json +from pydantic import BaseModel + + +logger = logging.getLogger(__name__) + + +class TesTaskRequest(ABC): + @abstractmethod + def handle_request(self) -> BaseModel: + """Business logic for the request.""" + pass + + def response(self) -> dict: + """Get response for the request.""" + response: BaseModel = self.handle_request() + try: + return json.load(json.dumps(response)) + except (TypeError, ValueError) as e: + logger.info(e) + return response.dict() diff --git a/tesk/api/kubernetes/client_wrapper.py b/tesk/api/kubernetes/client_wrapper.py index de138cc9..1e35cdbf 100644 --- a/tesk/api/kubernetes/client_wrapper.py +++ b/tesk/api/kubernetes/client_wrapper.py @@ -7,6 +7,7 @@ from kubernetes.client import ( V1ConfigMap, V1Job, + V1JobList, V1LabelSelector, V1LimitRangeList, V1PodList, @@ -94,16 +95,21 @@ def read_taskmaster_job(self, task_id: str) -> V1Job: raise raise Exception(f"Task {task_id} not found") - def list_jobs(self, label_selector=None, limit=None): + def list_jobs(self, page_token: str = None, label_selector=None, limit=None): """List jobs in the Kubernetes cluster. Args: + page_token: pageToken supplied by user (from previous result; points to + next page of results) label_selector: Label selector to filter jobs. limit: Maximum number of jobs to return. """ try: return self.batch_api.list_namespaced_job( - namespace=self.namespace, label_selector=label_selector, limit=limit + namespace=self.namespace, + label_selector=label_selector, + limit=limit, + _continue=page_token, ) except KubernetesError as e: logger.error(f"Exception when listing jobs: {e}") @@ -154,6 +160,84 @@ def quantity_to_bytes(self, quantity: str) -> int: parsed_quantity: int = parse_quantity(quantity) return parsed_quantity + def list_all_taskmaster_jobs_for_user( + self, + page_token: str, + items_per_page: int, + # user: str + ) -> V1JobList: + """Gets all Taskmaster job objects, a User is allowed to see. + + Args: + page_token: pageToken supplied by user (from previous result; points to + next page of results) + items_per_page: Value submitted by user, limiting number of results. + user: User identifier. + + Returns: + Job list of Taskmaster jobs that user is allowed to see. + """ + # TODO: Implement this method when auth is implemented in FOCA. + label_selector = f"{self.constant.label_jobtype_key}={self.constant.label_jobtype_value_taskm}" + # if user.get_label_selector(): + # label_selector += f",{user.get_label_selector()}" + + result = self.list_jobs(page_token, label_selector, items_per_page) + + # if user.is_member_in_non_managed_groups(): + # filtered_job_list = [ + # job for job in result.items + # if user.is_group_manager( + # job.metadata.labels.get(self.constant.label_groupname_key) + # ) or user.get_username() + # == job.metadata.labels.get(self.constant.label_userid_key) + # ] + # result.items = filtered_job_list + + return result + + def list_single_task_executor_jobs(self, task_id: str) -> V1JobList: + """List single task executor job.""" + label_selector = (self.constant.label_testask_id_key + "=" + task_id,) + return self.list_jobs(label_selector=label_selector) + + def get_single_task_output_filer_job(self, task_id: str) -> Optional[V1Job]: + """Get single task output filer job.""" + try: + job: V1Job = self.batch_api.read_namespaced_job( + name=task_id + self.constant.job_name_filer_suf, + namespace=self.namespace, + ) + return job + except KubernetesError as e: + if e.status != NotFound.code: + logger.error(f"Exception when reading output filer job: {e}") + raise + return None + + def list_all_taskmaster_jobs(self) -> V1JobList: + """List all taskmaster jobs in the Kubernetes cluster.""" + label_selector = ( + self.constant.label_jobtype_key + + "=" + + self.constant.label_jobtype_value_taskm + ) + return self.list_jobs(label_selector=label_selector) + + def list_all_task_executor_jobs(self) -> V1JobList: + """List all executor jobs in the Kubernetes cluster.""" + label_selector = ( + self.constant.label_jobtype_key + + "=" + + self.constant.label_jobtype_value_exec + ) + return self.list_jobs(label_selector=label_selector) + + def list_all_filer_jobs(self) -> V1JobList: + """List all output filer jobs in the Kubernetes cluster.""" + label_selector = "!" + self.constant.label_jobtype_key + return self.list_jobs(label_selector=label_selector) + def list_single_job_pods(self, job: V1Job) -> V1PodList: """List pods associated with a single job. @@ -181,6 +265,17 @@ def list_single_job_pods(self, job: V1Job) -> V1PodList: logger.error(f"Exception when listing pods: {e}") raise + def list_all_job_pods(self): + """List all job pods.""" + label_selector = "job-name" + try: + return self.core_api.list_namespaced_pod( + namespace=self.namespace, label_selector=label_selector + ) + except KubernetesError as e: + logger.error(f"Couldn't list job of {self.namespace} namespace.") + raise + def read_pod_log(self, pod_name: str) -> Optional[str]: """Read logs from a pod. diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py index 82f8d867..f21631a7 100644 --- a/tesk/api/kubernetes/constants.py +++ b/tesk/api/kubernetes/constants.py @@ -1,5 +1,6 @@ """Constants for Kubernetes API.""" +from enum import Enum from typing import Set from pydantic import BaseModel, Field @@ -146,3 +147,12 @@ class K8sConstants(BaseModel): resource_mem_one_gb: int = Field( default=1073741824, description="One Gibibyte (Gi) in bytes" ) + + class PodPhase(Enum): + """Pod state.""" + + PENDING = "Pending" + + def get_code(self) -> str: + """Return the pod state.""" + return self.value diff --git a/tesk/api/kubernetes/convert/converter.py b/tesk/api/kubernetes/convert/converter.py index 79085636..79fa778d 100644 --- a/tesk/api/kubernetes/convert/converter.py +++ b/tesk/api/kubernetes/convert/converter.py @@ -19,11 +19,21 @@ V1PodTemplateSpec, V1ResourceRequirements, V1Volume, + V1JobStatus, + V1ObjectMeta, ) from kubernetes.client.models import V1Job from kubernetes.utils.quantity import parse_quantity # type: ignore -from tesk.api.ga4gh.tes.models import TesExecutor, TesResources, TesTask +from tesk.api.ga4gh.tes.models import ( + TesExecutor, + TesResources, + TesTask, + TesExecutorLog, + TesState, + TesTaskLog, + TesExecutorLog, +) from tesk.api.kubernetes.constants import Constants, K8sConstants from tesk.api.kubernetes.convert.data.job import Job from tesk.api.kubernetes.convert.executor_command_wrapper import ExecutorCommandWrapper @@ -31,6 +41,10 @@ from tesk.constants import TeskConstants from tesk.custom_config import TaskmasterEnvProperties from tesk.utils import get_taskmaster_env_property, pydantic_model_list_json +from tesk.api.kubernetes.convert.data.task import Task +from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper +from tesk.api.kubernetes.convert.data.job import JobStatus +from tesk.utils import time_formatter, decimal_to_float logger = logging.getLogger(__name__) @@ -50,6 +64,7 @@ def __init__(self, namespace=TeskConstants.tesk_namespace): self.constants = Constants() self.k8s_constants = K8sConstants() self.namespace = namespace + self.kubernetes_client_wrapper = KubernetesClientWrapper(namespace=namespace) def from_tes_task_to_k8s_job(self, task: TesTask): """Convert TES task to Kubernetes job.""" @@ -175,11 +190,6 @@ def from_tes_task_to_k8s_config_map( exec_job.to_dict() for exec_job in executors_as_jobs ] - def decimal_to_float(obj): - if isinstance(obj, Decimal): - return float(obj) - raise TypeError - taskmaster_input_as_json = json.loads( json.dumps(task_master_input, default=decimal_to_float) ) @@ -283,3 +293,188 @@ def from_tes_executor_to_k8s_job( # noqa: PLR0913 ) return job + + def is_job_in_status(tested_object: V1JobStatus, test_objective: JobStatus) -> bool: + no_of_pods_in_state = None + if test_objective == JobStatus.ACTIVE: + no_of_pods_in_state = tested_object.active + elif test_objective == JobStatus.SUCCEEDED: + no_of_pods_in_state = tested_object.succeeded + elif test_objective == JobStatus.FAILED: + if tested_object.succeeded is not None and tested_object.succeeded > 0: + return False + no_of_pods_in_state = tested_object.failed + + return no_of_pods_in_state is not None and no_of_pods_in_state > 0 + + def extract_state_from_k8s_jobs(self, taskmaster_with_executors: Task) -> TesState: + # task_master_job: V1Job = taskmaster_with_executors.get_taskmaster().get_job() + # last_executor: Optional[Job] = taskmaster_with_executors.get_last_executor() + # output_filer: Optional[Job] = taskmaster_with_executors.get_output_filer() + # task_master_cancelled = ( + # task_master_job.metadata.labels.get(self.constants.label_taskstate_key) + # == self.constants.label_taskstate_value_canc + # ) + # task_master_running = self.is_job_in_status( + # tested_object=task_master_job.status, + # test_objective=JobStatus.ACTIVE + # ) + # print(task_master_running) + # task_master_completed = self.is_job_in_status( + # task_master_job.status, JobStatus.SUCCEEDED + # ) + # print(task_master_completed) + # executor_present = last_executor is not None + # last_executor_failed = executor_present and self.is_job_in_status( + # last_executor.get_job().status, JobStatus.FAILED + # ) + # print(last_executor_failed) + # last_executor_completed = executor_present and self.is_job_in_status( + # last_executor.get_job().status, JobStatus.SUCCEEDED + # ) + # print(last_executor_completed) + # output_filer_failed = output_filer is not None and self.is_job_in_status( + # output_filer.get_job().status, JobStatus.FAILED + # ) + # print(output_filer_failed) + # pending = self.k8s_constants.PodPhase.PENDING + # task_master_pending = any( + # pod.status.phase == pending + # for pod in taskmaster_with_executors.get_taskmaster().get_pods() + # ) + # last_executor_pending = executor_present and any( + # pod.status.phase == pending for pod in last_executor.get_pods() + # ) + + # if task_master_cancelled: + # return TesState.CANCELED + # if task_master_completed and output_filer_failed: + # return TesState.SYSTEM_ERROR + # if task_master_completed and last_executor_completed: + # return TesState.COMPLETE + # if task_master_completed and last_executor_failed: + # return TesState.EXECUTOR_ERROR + # if task_master_pending: + # return TesState.QUEUED + # if task_master_running and not executor_present: + # return TesState.INITIALIZING + # if last_executor_pending: + # return TesState.QUEUED + # if task_master_running: + # return TesState.RUNNING + return TesState.SYSTEM_ERROR + + def extract_executor_log_from_k8s_job_and_pod( + self, executor: Job + ) -> TesExecutorLog: + """Extracts TesExecutorLog from executor job and pod objects. + + Does not contain stdout (which needs access to pod log). + """ + log = TesExecutorLog() + executor_job: V1Job = executor.get_job() + start_time = getattr(executor_job.status, "start_time", None) + log.start_time = time_formatter(start_time) + + end_time = getattr(executor_job.status, "completion_time", None) + log.end_time = time_formatter(end_time) + + log.stdout = "" + + if executor.has_pods(): + first_pod_status = getattr(executor.get_first_pod(), "status", None) + exit_code = None + + if first_pod_status: + container_statuses = getattr(first_pod_status, "container_statuses", []) + if container_statuses: + container_status = container_statuses[0] + container_state = getattr(container_status, "state", None) + if container_state: + terminated = getattr(container_state, "terminated", None) + if terminated: + exit_code = getattr(terminated, "exit_code", None) + + log.exit_code = exit_code + + return log + + def from_k8s_jobs_to_tes_task_minimal( + self, taskmaster_with_executors: Task, is_list: bool + ) -> TesTask: + """Convert Kubernetes jobs to TES task.""" + + executors = taskmaster_with_executors.get_executors() + task = TesTask( + # FIXME: I don't think this is it :'( + executors=[ + TesExecutor( + image=executor.image or None, command=executor.command or None + ) + for executor in executors + ] + ) + metadata: V1ObjectMeta = ( + taskmaster_with_executors.get_taskmaster().get_job().metadata + ) + task.id = metadata.name + task.state = self.extract_state_from_k8s_jobs(taskmaster_with_executors) + if not is_list: + # FIXME: This is a hack, we need to get the real values + log = TesTaskLog(logs=TesExecutorLog(exit_code=0)) + task.logs.append(log) + metadata = taskmaster_with_executors.taskmaster.job["metadata"]["labels"] + log.metadata["USER_ID"] = metadata[self.constants.label_userid_key] + if self.constants.label_groupname_key in metadata: + log.metadata["GROUP_NAME"] = metadata[ + self.constants.label_groupname_key + ] + return task + + def from_k8s_jobs_to_tes_task_basic( + self, taskmaster_with_executors: Task, nullify_input_content: bool + ) -> TesTask: + task = TesTask() + task_master_job: V1Job = taskmaster_with_executors.taskmaster.job + task_master_job_metadata: V1ObjectMeta = task_master_job.metadata + input_json = (task_master_job_metadata.annotations or {}).get( + self.constants.ann_json_input_key, "" + ) + try: + task = TesTask.parse_raw(input_json) + if nullify_input_content and task.inputs: + for input_item in task.inputs: + input_item["content"] = None + except json.JSONDecodeError as ex: + print( + f"Deserializing task {task_master_job_metadata['name']} from JSON failed; {ex}" + ) + + task.id = task_master_job_metadata["name"] + task.state = self.extract_state_from_k8s_jobs(taskmaster_with_executors) + task.creation_time = time_formatter( + task_master_job_metadata["creation_timestamp"] + ) + log = TesTaskLog() + task.logs.append(log) + log.metadata["USER_ID"] = task_master_job_metadata["labels"][ + self.constants.label_userid_key + ] + if self.constants.label_groupname_key in task_master_job_metadata["labels"]: + log["GROUP_NAME"] = task_master_job_metadata["labels"][ + self.constants.label_groupname_key + ] + log.start_time = ( + time_formatter(task_master_job.status.start_time) + if task_master_job.status.start_time + else None + ) + log.end_time = ( + time_formatter(task_master_job.status.completion_time) + if task_master_job.status.completion_time + else None + ) + for executor_job in taskmaster_with_executors.get_executors(): + executor_log = self.extract_executor_log_from_k8s_job_and_pod(executor_job) + task.logs.append(executor_log) + return task diff --git a/tesk/api/kubernetes/convert/data/build_strategy.py b/tesk/api/kubernetes/convert/data/build_strategy.py new file mode 100644 index 00000000..e6fa97f6 --- /dev/null +++ b/tesk/api/kubernetes/convert/data/build_strategy.py @@ -0,0 +1,58 @@ +"""Part of the toolset aimed at building Kubernetes object structure of a task or tasks. + +Gradually adding to it objects returned by calls to Kubernetes API (jobs and pods). +Implementing classes are responsible of creating, +storing and maintaining the actual `Task` object or `Task` object's list. +""" + +from abc import ABC, abstractmethod +from typing import List, Optional + +from tesk.api.kubernetes.convert.data.job import Job +from tesk.api.kubernetes.convert.data.task import Task + + +class BuildStrategy(ABC): + """Part of the toolset aimed at building Kubernetes object structure of a task/s. + + Gradually adding to it objects returned by calls to Kubernetes API (jobs and pods). + Implementing classes are responsible of creating, + storing and maintaining the actual `Task` object or `Task` object's list. + """ + + @abstractmethod + def add_task_master_job(self, taskmaster_job: Job): + """Add taskmaster job. + + Method should optionally filter and place the passed taskmaster's job object + in the resulting structure. + """ + pass + + @abstractmethod + def add_executor_job(self, executor_job: Job): + """Add executor job. + + Method should optionally filter and place the passed executor's job object + in the resulting structure (and match it to appropriate taskmaster). + """ + pass + + @abstractmethod + def add_output_filer_job(self, filer_job: Job): + """Add output filer job. + + Method should optionally filter and place the passed output filer's job object + in the resulting structure (and match it to appropriate taskmaster). + """ + pass + + @abstractmethod + def get_task(self) -> Optional[Task]: + """Return the single task object.""" + pass + + @abstractmethod + def get_task_list(self) -> List[Task]: + """Return the list of task objects.""" + pass diff --git a/tesk/api/kubernetes/convert/data/job.py b/tesk/api/kubernetes/convert/data/job.py index 8a30907a..e6d66ee3 100644 --- a/tesk/api/kubernetes/convert/data/job.py +++ b/tesk/api/kubernetes/convert/data/job.py @@ -5,6 +5,7 @@ """ from typing import List, Optional +from enum import Enum from kubernetes.client import V1Job, V1ObjectMeta, V1Pod @@ -70,3 +71,11 @@ def change_job_name(self, new_name: str): def get_job_name(self) -> Optional[str]: """Returns the job name.""" return self.job.metadata.name if self.job.metadata else None + + +class JobStatus(Enum): + """State of job.""" + + ACTIVE = "Active" + SUCCEEDED = "Succeeded" + FAILED = "Failed" diff --git a/tesk/api/kubernetes/convert/data/single_task_strategy.py b/tesk/api/kubernetes/convert/data/single_task_strategy.py new file mode 100644 index 00000000..ddd02abc --- /dev/null +++ b/tesk/api/kubernetes/convert/data/single_task_strategy.py @@ -0,0 +1,56 @@ +"""Tool aimed at building Kubernetes object structure of a single task. + +Job objects passed to its methods must be prefiltered and belong to a single task +(the class does not perform job objects filtering itself). +Pods must be added, when all jobs have already been added. +Thus, correct order of calls: +- Taskmaster TaskBuilder#addJobList(List) or TaskBuilder#addJob(V1Job) +- Executors and outputFiler TaskBuilder#addJobList(List) or TaskBuilder#addJob(V1Job) +- Pods by TaskBuilder#addPodList(List) +""" + +from typing import List, Optional + +from tesk.api.kubernetes.convert.data.build_strategy import BuildStrategy +from tesk.api.kubernetes.convert.data.job import Job +from tesk.api.kubernetes.convert.data.task import Task + + +class SingleTaskStrategy(BuildStrategy): + """Tool aimed at building Kubernetes object structure of a single task. + + Job objects passed to its methods must be prefiltered and belong to a single task + (the class does not perform job objects filtering itself). + Pods must be added, when all jobs have already been added. + Thus, correct order of calls: + - Taskmaster TaskBuilder#addJobList(List) or TaskBuilder#addJob(V1Job) + - Executors and outputFiler TaskBuilder#addJobList(List) or + TaskBuilder#addJob(V1Job) + - Pods by TaskBuilder#addPodList(List) + """ + + def __init__(self): + """Initialise SingleTaskStrategy.""" + self.task = None + + def add_task_master_job(self, taskmaster_job: Job): + """Add taskmaster job.""" + self.task = Task(taskmaster_job) + + def add_executor_job(self, executor_job: Job): + """Add executor job.""" + if self.task: + self.task.add_executor(executor_job) + + def add_output_filer_job(self, filer_job: Job): + """Add output filer job.""" + if self.task: + self.task.set_output_filer(filer_job) + + def get_task(self) -> Optional[Task]: + """Get task.""" + return self.task + + def get_task_list(self) -> List[Task]: + """Get single task as list.""" + return [self.task] if self.task else [] diff --git a/tesk/api/kubernetes/convert/data/task_builder.py b/tesk/api/kubernetes/convert/data/task_builder.py new file mode 100644 index 00000000..07f890a7 --- /dev/null +++ b/tesk/api/kubernetes/convert/data/task_builder.py @@ -0,0 +1,72 @@ +"""Module aimed at building Kubernetes object structure of a task or a list of tasks,. + +Gradually adding to it objects returned by calls to Kubernetes API (jobs and pods). +This class takes care of matching jobs with corresponding pods and holds a flat +collection (mapped by name) of resulting Job objects (can be both taskmasters and +executors belonging to the same or different task).Accepts a BuildStrategy BuildStrategy +, which implementing classes are responsible of creating, storing and maintaining the +actual {@link Task} object or {@link Task} object's list by implementing +BuildStrategy#addTaskMasterJob(Job) and BuildStrategy#addExecutorJob(Job). +""" + +from kubernetes.client import V1Job, V1Pod + +from tesk.api.kubernetes.constants import Constants +from tesk.api.kubernetes.convert.data.build_strategy import BuildStrategy +from tesk.api.kubernetes.convert.data.job import Job +from tesk.api.kubernetes.convert.data.single_task_strategy import SingleTaskStrategy +from tesk.api.kubernetes.convert.data.task_list_strategy import TaskListStrategy + + +class TaskBuilder: + @staticmethod + def new_single_task(): + return TaskBuilder(SingleTaskStrategy()) + + @staticmethod + def new_task_list(): + return TaskBuilder(TaskListStrategy()) + + def __init__(self, build_strategy: BuildStrategy): + self.build_strategy = build_strategy + self.all_jobs_by_name = {} + self.constants = Constants() + + def add_job(self, job: V1Job): + wrapped_job = Job(job) + job_type = job.metadata.labels.get(self.constants.label_jobtype_key) + if job_type == self.constants.label_jobtype_value_taskm: + self.build_strategy.add_task_master_job(wrapped_job) + elif job_type == self.constants.label_jobtype_value_exec: + self.build_strategy.add_executor_job(wrapped_job) + else: + self.build_strategy.add_output_filer_job(wrapped_job) + self.all_jobs_by_name[job.metadata.name] = wrapped_job + return self + + def add_job_list(self, jobs: list[V1Job]): + for job in jobs: + self.add_job(job) + return self + + def add_pod_list(self, pods: list[V1Pod]): + for pod in pods: + self.add_pod(pod) + return self + + def add_pod(self, pod: V1Pod): + for job in self.all_jobs_by_name.values(): + selectors = job.job.spec.selector.match_labels + labels = pod.metadata.labels + if all(item in labels.items() for item in selectors.items()): + job.add_pod(pod) + break + + def get_task(self): + return self.build_strategy.get_task() + + def get_task_list(self): + return self.build_strategy.get_task_list() + + def get_all_jobs_by_name(self): + return self.all_jobs_by_name diff --git a/tesk/api/kubernetes/convert/data/task_list_strategy.py b/tesk/api/kubernetes/convert/data/task_list_strategy.py new file mode 100644 index 00000000..ed4c9840 --- /dev/null +++ b/tesk/api/kubernetes/convert/data/task_list_strategy.py @@ -0,0 +1,72 @@ +"""Module aimed at building Kubernetes object structure of a list of tasks. + +Accomplised by passing to it results of Kubernetes batch method calls. +All taskmaster jobs with unique names passed to it will get stored. +Only those executor jobs that match already stored taskmaster jobs will be stored +(filtering done by taskmaster's name and corresponding executor's label). +Pods must be added, when all jobs have already been added. +Thus, correct order of calls: +- Taskmasters by TaskBuilder#addJobList(List) +- Executors and outputFilers by TaskBuilder#addJobList(List) +- Pods by TaskBuilder#addPodList(List) +""" + +from typing import Dict, List, Optional + +from tesk.api.kubernetes.constants import Constants +from tesk.api.kubernetes.convert.data.build_strategy import BuildStrategy +from tesk.api.kubernetes.convert.data.job import Job +from tesk.api.kubernetes.convert.data.task import Task + + +class TaskListStrategy(BuildStrategy): + """Class for building Kubernetes object structure of a list of tasks. + + Accomplised by passing to it results of Kubernetes batch method calls. + All taskmaster jobs with unique names passed to it will get stored. + Only those executor jobs that match already stored taskmaster jobs will be stored + (filtering done by taskmaster's name and corresponding executor's label). + Pods must be added, when all jobs have already been added. + Thus, correct order of calls: + - Taskmasters by TaskBuilder#addJobList(List) + - Executors and outputFilers by TaskBuilder#addJobList(List) + - Pods by TaskBuilder#addPodList(List) + """ + + def __init__(self): + """Intialize TaskListStrategy.""" + self.tasks_by_id: Dict[str, Task] = {} + self.constants = Constants() + + def add_task_master_job(self, taskmaster_job: Job): + """Add taskmater job.""" + task_name = taskmaster_job.get_job().metadata.name + if task_name not in self.tasks_by_id: + self.tasks_by_id[task_name] = Task(taskmaster_job) + + def add_executor_job(self, executor_job: Job): + """Add executor Job.""" + taskmaster_name = executor_job.get_job().metadata.labels.get( + self.constants.label_testask_id_key + ) + if taskmaster_name in self.tasks_by_id: + self.tasks_by_id[taskmaster_name].add_executor(executor_job) + + def add_output_filer_job(self, filer_job: Job): + """Add output filer job.""" + output_filer_suffix = filer_job.get_job_name().find( + self.constants.job_name_filer_suf + ) + if output_filer_suffix == -1: + return + taskmaster_name = filer_job.get_job_name()[:output_filer_suffix] + if taskmaster_name in self.tasks_by_id: + self.tasks_by_id[taskmaster_name].set_output_filer(filer_job) + + def get_task(self) -> Optional[Task]: + """Get task.""" + raise NotImplementedError("This method is not supported for TaskListStrategy") + + def get_task_list(self) -> List[Task]: + """Get list of tasks.""" + return list(self.tasks_by_id.values()) diff --git a/tesk/app.py b/tesk/app.py index 1dd4883a..7f3df49e 100644 --- a/tesk/app.py +++ b/tesk/app.py @@ -46,7 +46,7 @@ def init_app() -> FlaskApp: def main() -> None: """Run FOCA application.""" app = init_app() - app.run(port=app.port) + app.run(port=8081) if __name__ == "__main__": diff --git a/tesk/utils.py b/tesk/utils.py index c5878323..98321076 100644 --- a/tesk/utils.py +++ b/tesk/utils.py @@ -1,8 +1,11 @@ """Utility functions for the TESK package.""" +import datetime import os from pathlib import Path +from enum import Enum from typing import List, Optional, Sequence +from decimal import Decimal from foca import Foca from kubernetes.client.models import ( @@ -210,3 +213,20 @@ def pydantic_model_list_json(model_list: Sequence[BaseModel]) -> List[str]: for item in model_list: json_list.append(item.json()) return json_list + + +def time_formatter(time: Optional[str]) -> Optional[str]: + """Set start time in RFC 3339 format.""" + rfc_time = time.strftime("%Y-%m-%dT%H:%M:%SZ") if time else None + return rfc_time + + +def decimal_to_float(obj): + if isinstance(obj, Decimal): + return float(obj) + raise TypeError + + +def enum_to_string(enum): + if isinstance(enum, Enum): + return str(enum.name) From 38f2b4665ae739ef9a350198ecc9d99d404947b9 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Thu, 8 Aug 2024 12:21:40 +0530 Subject: [PATCH 13/22] chore: clean up a bit --- deployment/config.yaml | 6 +- tesk/api/ga4gh/tes/controllers.py | 3 - tesk/api/ga4gh/tes/task/create_task.py | 40 ++-- tesk/api/ga4gh/tes/task/get_task.py | 41 ++-- tesk/api/ga4gh/tes/task/task_request.py | 16 +- tesk/api/kubernetes/client_wrapper.py | 4 +- tesk/api/kubernetes/constants.py | 8 + tesk/api/kubernetes/convert/converter.py | 226 ++++++++++-------- .../kubernetes/convert/data/build_strategy.py | 2 +- tesk/api/kubernetes/convert/data/job.py | 5 +- .../convert/data/single_task_strategy.py | 2 +- .../kubernetes/convert/data/task_builder.py | 2 +- .../convert/data/task_list_strategy.py | 2 +- .../convert/taskmaster_env_properties.py | 4 +- tesk/api/kubernetes/convert/template.py | 54 +++-- tesk/constants.py | 9 +- tesk/custom_config.py | 52 ++-- tesk/utils.py | 62 +++-- 18 files changed, 302 insertions(+), 236 deletions(-) diff --git a/deployment/config.yaml b/deployment/config.yaml index 8057b463..d9ab80d5 100644 --- a/deployment/config.yaml +++ b/deployment/config.yaml @@ -125,17 +125,17 @@ custom: # Taskmaster image name imageName: docker.io/elixircloud/tesk-core-taskmaster # Taskmaster image version - imageVersion: latest + imageVersion: v0.10.2 # Filer image name filerImageName: docker.io/elixircloud/tesk-core-filer # Filer image version - filerImageVersion: latest + filerImageVersion: v0.10.2 # Test FTP account settings ftp: # Name of the secret with FTP account credentials secretName: account-secret # If FTP account enabled (based on non-emptiness of secretName) - enabled: false + enabled: true # If verbose (debug) mode of taskmaster is on (passes additional flag to taskmaster and sets image pull policy to Always) debug: false # Environment variables, that will be passed to taskmaster diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index 0d9e682b..8a95857d 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/tesk/api/ga4gh/tes/controllers.py @@ -39,9 +39,6 @@ def CreateTask(**kwargs) -> dict: """ try: request_body = kwargs.get("body") - if request_body is None: - logger.error("Nothing received in request body.") - raise BadRequest("No request body received.") tes_task = TesTask(**request_body) response = CreateTesTask(tes_task).response() return response diff --git a/tesk/api/ga4gh/tes/task/create_task.py b/tesk/api/ga4gh/tes/task/create_task.py index e3e69363..5540cf7b 100644 --- a/tesk/api/ga4gh/tes/task/create_task.py +++ b/tesk/api/ga4gh/tes/task/create_task.py @@ -4,14 +4,9 @@ from pydantic import BaseModel -from tesk.api.ga4gh.tes.models import TesResources, TesTask -from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper -from tesk.api.kubernetes.constants import Constants -from tesk.api.kubernetes.convert.converter import TesKubernetesConverter -from tesk.constants import TeskConstants -from tesk.exceptions import KubernetesError +from tesk.api.ga4gh.tes.models import TesCreateTaskResponse, TesResources, TesTask from tesk.api.ga4gh.tes.task.task_request import TesTaskRequest -from tesk.api.ga4gh.tes.models import TesCreateTaskResponse +from tesk.exceptions import KubernetesError logger = logging.getLogger(__name__) @@ -20,19 +15,19 @@ class CreateTesTask(TesTaskRequest): """Create TES task.""" # TODO: Add user to the class when auth implemented in FOCA - def __init__(self, task: TesTask, namespace=TeskConstants.tesk_namespace): + def __init__( + self, + task: TesTask, + # user: User + ): """Initialize the CreateTask class. Args: task: TES task to create. - namespace: Kubernetes namespace where the task is created. """ + super().__init__() self.task = task # self.user = user - self.namespace = namespace - self.kubernetes_client_wrapper = KubernetesClientWrapper() - self.tes_kubernetes_converter = TesKubernetesConverter(self.namespace) - self.constants = Constants() def create_task(self) -> TesCreateTaskResponse: """Create TES task.""" @@ -43,31 +38,32 @@ def create_task(self) -> TesCreateTaskResponse: resources = self.task.resources minimum_ram_gb = self.kubernetes_client_wrapper.minimum_ram_gb() + if not self.task.resources: self.task.resources = TesResources(cpu_cores=int(minimum_ram_gb)) if resources and resources.ram_gb and resources.ram_gb < minimum_ram_gb: self.task.resources.ram_gb = minimum_ram_gb - task_master_job = ( - self.tes_kubernetes_converter.from_tes_task_to_k8s_job( - self.task, - # self.user - ) + taskmaster_job = self.tes_kubernetes_converter.from_tes_task_to_k8s_job( + self.task, + # self.user ) - task_master_config_map = ( + print(taskmaster_job) + taskmaster_config_map = ( self.tes_kubernetes_converter.from_tes_task_to_k8s_config_map( self.task, - task_master_job, + taskmaster_job, # self.user ) ) + print(taskmaster_config_map) # Create ConfigMap and Job _ = self.kubernetes_client_wrapper.create_config_map( - task_master_config_map + taskmaster_config_map ) - created_job = self.kubernetes_client_wrapper.create_job(task_master_job) + created_job = self.kubernetes_client_wrapper.create_job(taskmaster_job) assert created_job.metadata is not None assert created_job.metadata.name is not None diff --git a/tesk/api/ga4gh/tes/task/get_task.py b/tesk/api/ga4gh/tes/task/get_task.py index 6c639951..e4d56204 100644 --- a/tesk/api/ga4gh/tes/task/get_task.py +++ b/tesk/api/ga4gh/tes/task/get_task.py @@ -1,21 +1,22 @@ +"""Module for getting task.""" + from typing import List + from kubernetes.client.models import V1JobList from pydantic import BaseModel + from tesk.api.ga4gh.tes.models import TaskView, TesListTasksResponse, TesTask -from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper -from tesk.api.kubernetes.convert.converter import TesKubernetesConverter +from tesk.api.ga4gh.tes.task.task_request import TesTaskRequest from tesk.api.kubernetes.convert.data.task import Task from tesk.api.kubernetes.convert.data.task_builder import TaskBuilder -from tesk.api.ga4gh.tes.models import TesListTasksResponse, TesTask -from tesk.api.ga4gh.tes.task.task_request import TesTaskRequest -from tesk.constants import TeskConstants +class GetTesTaskInterface(TesTaskRequest): + """Base class for listing task request.""" -class GetTesTaskInterface: - def __init__(self, namespace=TeskConstants.tesk_namespace): - self.kubernetes_client_wrapper = KubernetesClientWrapper(namespace=namespace) - self.tes_kubernetes_converter = TesKubernetesConverter() + def __init__(self): + """Initialise base class for listing task.""" + super().__init__() def get_task( self, @@ -23,18 +24,18 @@ def get_task( view: TaskView, # user: User ) -> TesTask: - task_master_job = self.kubernetes_client_wrapper.read_taskmaster_job(task_id) + taskmaster_job = self.kubernetes_client_wrapper.read_taskmaster_job(task_id) executor_jobs = self.kubernetes_client_wrapper.list_single_task_executor_jobs( - task_master_job.metadata.name + taskmaster_job.metadata.name ) - task_master_pods = self.kubernetes_client_wrapper.list_single_job_pods( - task_master_job + taskmaster_pods = self.kubernetes_client_wrapper.list_single_job_pods( + taskmaster_job ) task_builder = ( TaskBuilder.new_single_task() - .add_job(task_master_job) + .add_job(taskmaster_job) .add_job_list(executor_jobs.items) - .add_pod_list(task_master_pods.items) + .add_pod_list(taskmaster_pods.items) ) for executor_job in executor_jobs.items: @@ -45,7 +46,7 @@ def get_task( output_filer_job = ( self.kubernetes_client_wrapper.get_single_task_output_filer_job( - task_master_job.metadata.name + taskmaster_job.metadata.name ) ) if output_filer_job: @@ -77,11 +78,11 @@ def _get_task(self, task_objects: Task, view: TaskView, is_list: bool) -> TesTas executor_log.stdout = executor_pod_log if task_objects.taskmaster.has_pods(): - task_master_pod_log = self.kubernetes_client_wrapper.read_pod_log( + taskmaster_pod_log = self.kubernetes_client_wrapper.read_pod_log( task_objects.get_taskmaster().get_first_pod().metadata.name ) - if task_master_pod_log is not None: - task.logs[0].system_logs.append(task_master_pod_log) + if taskmaster_pod_log is not None: + task.logs[0].system_logs.append(taskmaster_pod_log) return task @@ -123,7 +124,7 @@ def list_tasks( return response -class GetTesTask(TesTaskRequest, GetTesTaskInterface): +class GetTesTask(GetTesTaskInterface): def handle_request( self, name_prefix: str, diff --git a/tesk/api/ga4gh/tes/task/task_request.py b/tesk/api/ga4gh/tes/task/task_request.py index e955d97d..23a6b538 100644 --- a/tesk/api/ga4gh/tes/task/task_request.py +++ b/tesk/api/ga4gh/tes/task/task_request.py @@ -1,13 +1,27 @@ +"""Base class for tesk request.""" + +import json import logging from abc import ABC, abstractmethod -import json + from pydantic import BaseModel +from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper +from tesk.api.kubernetes.constants import Constants +from tesk.api.kubernetes.convert.converter import TesKubernetesConverter logger = logging.getLogger(__name__) class TesTaskRequest(ABC): + """Base class for tesk request ecapsulating common methods and members.""" + + def __init__(self): + """Initialise base class for tesk request.""" + self.kubernetes_client_wrapper = KubernetesClientWrapper() + self.tes_kubernetes_converter = TesKubernetesConverter() + self.constants = Constants() + @abstractmethod def handle_request(self) -> BaseModel: """Business logic for the request.""" diff --git a/tesk/api/kubernetes/client_wrapper.py b/tesk/api/kubernetes/client_wrapper.py index 1e35cdbf..515abbfa 100644 --- a/tesk/api/kubernetes/client_wrapper.py +++ b/tesk/api/kubernetes/client_wrapper.py @@ -24,7 +24,7 @@ class KubernetesClientWrapper: """Kubernetes client wrapper class.""" - def __init__(self, namespace=TeskConstants.tesk_namespace): + def __init__(self): """Initialize the Kubernetes client wrapper. Args: @@ -33,7 +33,7 @@ def __init__(self, namespace=TeskConstants.tesk_namespace): config.load_kube_config() self.batch_api = client.BatchV1Api() self.core_api = client.CoreV1Api() - self.namespace = namespace + self.namespace = TeskConstants.tesk_namespace self.constant = Constants() def create_job(self, job: V1Job) -> V1Job: diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py index f21631a7..4386b34c 100644 --- a/tesk/api/kubernetes/constants.py +++ b/tesk/api/kubernetes/constants.py @@ -123,6 +123,14 @@ class Constants(BaseModel): default='{"metadata":{"labels":{"task-status":"Cancelled"}}}', description="Patch object passed to job API, when cancelling task", ) + executor_backoff_limit: str = Field( + default="EXECUTOR_BACKOFF_LIMIT", + description="Set a number of retries of a job execution.", + ) + filer_backoff_limit: str = Field( + default="FILER_BACKOFF_LIMIT", + description="Set a number of retries of a filer job execution.", + ) class K8sConstants(BaseModel): diff --git a/tesk/api/kubernetes/convert/converter.py b/tesk/api/kubernetes/convert/converter.py index 79fa778d..f297acf0 100644 --- a/tesk/api/kubernetes/convert/converter.py +++ b/tesk/api/kubernetes/convert/converter.py @@ -14,37 +14,38 @@ V1Container, V1EnvVar, V1JobSpec, + V1JobStatus, V1ObjectMeta, V1PodSpec, V1PodTemplateSpec, V1ResourceRequirements, V1Volume, - V1JobStatus, - V1ObjectMeta, ) from kubernetes.client.models import V1Job from kubernetes.utils.quantity import parse_quantity # type: ignore from tesk.api.ga4gh.tes.models import ( TesExecutor, - TesResources, - TesTask, TesExecutorLog, + TesResources, TesState, + TesTask, TesTaskLog, - TesExecutorLog, ) +from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper from tesk.api.kubernetes.constants import Constants, K8sConstants -from tesk.api.kubernetes.convert.data.job import Job +from tesk.api.kubernetes.convert.data.job import Job, JobStatus +from tesk.api.kubernetes.convert.data.task import Task from tesk.api.kubernetes.convert.executor_command_wrapper import ExecutorCommandWrapper from tesk.api.kubernetes.convert.template import KubernetesTemplateSupplier -from tesk.constants import TeskConstants from tesk.custom_config import TaskmasterEnvProperties -from tesk.utils import get_taskmaster_env_property, pydantic_model_list_json -from tesk.api.kubernetes.convert.data.task import Task -from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper -from tesk.api.kubernetes.convert.data.job import JobStatus -from tesk.utils import time_formatter, decimal_to_float +from tesk.utils import ( + decimal_to_float, + enum_to_string, + get_taskmaster_env_property, + pydantic_model_list_json, + time_formatter, +) logger = logging.getLogger(__name__) @@ -52,25 +53,21 @@ class TesKubernetesConverter: """Convert TES requests to Kubernetes resources.""" - def __init__(self, namespace=TeskConstants.tesk_namespace): + def __init__(self): """Initialize the converter.""" self.taskmaster_env_properties: TaskmasterEnvProperties = ( get_taskmaster_env_property() ) - self.template_supplier = KubernetesTemplateSupplier( - namespace=namespace - # security_context=security_context - ) + self.template_supplier = KubernetesTemplateSupplier() self.constants = Constants() self.k8s_constants = K8sConstants() - self.namespace = namespace - self.kubernetes_client_wrapper = KubernetesClientWrapper(namespace=namespace) + self.kubernetes_client_wrapper = KubernetesClientWrapper() def from_tes_task_to_k8s_job(self, task: TesTask): """Convert TES task to Kubernetes job.""" - taskmaster_job: V1Job = KubernetesTemplateSupplier( - self.namespace - ).task_master_template() + taskmaster_job: V1Job = ( + self.template_supplier.get_taskmaster_template_with_value_from_config() + ) if taskmaster_job.metadata is None: taskmaster_job.metadata = V1ObjectMeta() @@ -99,9 +96,15 @@ def from_tes_task_to_k8s_job(self, task: TesTask): # "any_group" # ] + # Convert Pydantic model to dictionary + task_dict = task.dict() + + # Serialize to JSON with indentation + json_input = json.dumps(task_dict, indent=2, default=enum_to_string) + try: taskmaster_job.metadata.annotations[self.constants.ann_json_input_key] = ( - task.json() + json_input ) except Exception as ex: logger.info( @@ -126,57 +129,63 @@ def from_tes_task_to_k8s_job(self, task: TesTask): def from_tes_task_to_k8s_config_map( self, task: TesTask, - job: V1Job, + taskmaster_job: V1Job, # user, ) -> V1ConfigMap: """Create a Kubernetes ConfigMap from a TES task.""" - if job.metadata is None: - job.metadata = V1ObjectMeta() - - task_master_config_map = V1ConfigMap( - metadata=V1ObjectMeta(name=job.metadata.name) + assert taskmaster_job.metadata is not None, ( + "Taskmaster job metadata should have already been set while create" + " taskmaster!" ) - assert task_master_config_map.metadata is not None - task_master_config_map.metadata.labels = ( - task_master_config_map.metadata.labels or {} - ) - task_master_config_map.metadata.annotations = ( - task_master_config_map.metadata.annotations or {} + taskmaster_config_map = V1ConfigMap( + metadata=V1ObjectMeta(name=taskmaster_job.metadata.name) ) - if task.name: - task_master_config_map.metadata.annotations[ - self.constants.ann_testask_name_key - ] = task.name + assert ( + taskmaster_config_map.metadata is not None + ), "Taskmaster metadata is should have already been set!" + + if taskmaster_config_map.metadata.labels is None: + taskmaster_config_map.metadata.labels = {} + + if taskmaster_config_map.metadata.annotations is None: + taskmaster_config_map.metadata.annotations = {} + + # FIXME: Figure out what to do if task.name is none. + task_name = task.name or "String" + + taskmaster_config_map.metadata.annotations[ + self.constants.ann_testask_name_key + ] = task_name - # task_master_config_map.metadata.labels[self.constants.label_userid_key] + # taskmaster_config_map.metadata.labels[self.constants.label_userid_key] # = user["username"] if task.tags and "GROUP_NAME" in task.tags: - task_master_config_map.metadata.labels[ + taskmaster_config_map.metadata.labels[ self.constants.label_groupname_key ] = task.tags["GROUP_NAME"] # elif user["is_member"]: - # task_master_config_map.metadata.labels[self.constants.label_groupname_key] + # taskmaster_config_map.metadata.labels[self.constants.label_groupname_key] # = user["any_group"] - assert task_master_config_map.metadata.name is not None + assert taskmaster_config_map.metadata.name is not None assert task.resources is not None executors_as_jobs = [ self.from_tes_executor_to_k8s_job( - task_master_config_map.metadata.name, - task.name, - executor, - idx, - task.resources, - # user, + generated_task_id=taskmaster_config_map.metadata.name, + tes_task_name=task_name, + executor=executor, + executor_index=idx, + resources=task.resources, + # user=user, ) for idx, executor in enumerate(task.executors) ] - task_master_input: dict[str, Any] = { + taskmaster_input: dict[str, Any] = { "inputs": pydantic_model_list_json(task.inputs) if task.inputs else [], "outputs": pydantic_model_list_json(task.outputs) if task.outputs else [], "volumes": task.volumes or [], @@ -186,19 +195,20 @@ def from_tes_task_to_k8s_config_map( else 10.0 }, } - task_master_input[self.constants.taskmaster_input_exec_key] = [ + taskmaster_input[self.constants.taskmaster_input_exec_key] = [ exec_job.to_dict() for exec_job in executors_as_jobs ] taskmaster_input_as_json = json.loads( - json.dumps(task_master_input, default=decimal_to_float) + json.dumps(taskmaster_input, default=decimal_to_float) ) + try: with BytesIO() as obj: with gzip.GzipFile(fileobj=obj, mode="wb") as gzip_file: json_data = json.dumps(taskmaster_input_as_json) gzip_file.write(json_data.encode("utf-8")) - task_master_config_map.binary_data = { + taskmaster_config_map.binary_data = { f"{self.constants.taskmaster_input}.gz": base64.b64encode( obj.getvalue() ).decode("utf-8") @@ -206,13 +216,13 @@ def from_tes_task_to_k8s_config_map( except Exception as e: logger.info( ( - f"Compression of task {task_master_config_map.metadata.name}" + f"Compression of task {taskmaster_config_map.metadata.name}" f" JSON configmap failed" ), e, ) - return task_master_config_map + return taskmaster_config_map def from_tes_executor_to_k8s_job( # noqa: PLR0913 self, @@ -225,36 +235,42 @@ def from_tes_executor_to_k8s_job( # noqa: PLR0913 ) -> V1Job: """Create a Kubernetes job from a TES executor.""" # Get new template executor Job object - job: V1Job = self.template_supplier.executor_template() + executor_job: V1Job = ( + self.template_supplier.get_executor_template_with_value_from_config() + ) # Set executors name based on taskmaster's job name - # TODO: Fix me ASAP - Job(job).change_job_name( - # Task(job, generated_task_id).get_executor_name(executor_index) - "newname" - ) + Job(executor_job).change_job_name(new_name=generated_task_id) - if job.metadata is None: - job.metadata = V1ObjectMeta() + if executor_job.metadata is None: + executor_job.metadata = V1ObjectMeta() # Put arbitrary labels and annotations - job.metadata.labels = job.metadata.labels or {} - job.metadata.labels[self.constants.label_testask_id_key] = generated_task_id - job.metadata.labels[self.constants.label_execno_key] = str(executor_index) + executor_job.metadata.labels = executor_job.metadata.labels or {} + executor_job.metadata.labels[self.constants.label_testask_id_key] = ( + generated_task_id + ) + executor_job.metadata.labels[self.constants.label_execno_key] = str( + executor_index + ) # job.metadata.labels[self.constants.label_userid_key] = user.username - job.metadata.annotations = job.metadata.annotations or {} + if executor_job.metadata is None: + executor_job.metadata = V1ObjectMeta() + if executor_job.metadata.annotations is None: + executor_job.metadata.annotations = {} + if tes_task_name: - job.metadata.annotations[self.constants.ann_testask_name_key] = ( + executor_job.metadata.annotations[self.constants.ann_testask_name_key] = ( tes_task_name ) - if job.spec is None: - job.spec = V1JobSpec(template=V1PodTemplateSpec()) - if job.spec.template.spec is None: - job.spec.template.spec = V1PodSpec(containers=[]) + if executor_job.spec is None: + executor_job.spec = V1JobSpec(template=V1PodTemplateSpec()) + if executor_job.spec.template.spec is None: + executor_job.spec.template.spec = V1PodSpec(containers=[]) - container: V1Container = job.spec.template.spec.containers[0] + container: V1Container = executor_job.spec.template.spec.containers[0] # TODO: Not sure what to do with this # Convert potential TRS URI into docker image @@ -264,7 +280,7 @@ def from_tes_executor_to_k8s_job( # noqa: PLR0913 if not container.command: container.command = [] - # Map executor's command to job container's command + for command in ExecutorCommandWrapper( executor ).get_commands_with_stream_redirects(): @@ -292,7 +308,7 @@ def from_tes_executor_to_k8s_job( # noqa: PLR0913 f"{resources.ram_gb:.6f}Gi" ) - return job + return executor_job def is_job_in_status(tested_object: V1JobStatus, test_objective: JobStatus) -> bool: no_of_pods_in_state = None @@ -308,22 +324,22 @@ def is_job_in_status(tested_object: V1JobStatus, test_objective: JobStatus) -> b return no_of_pods_in_state is not None and no_of_pods_in_state > 0 def extract_state_from_k8s_jobs(self, taskmaster_with_executors: Task) -> TesState: - # task_master_job: V1Job = taskmaster_with_executors.get_taskmaster().get_job() + # taskmaster_job: V1Job = taskmaster_with_executors.get_taskmaster().get_job() # last_executor: Optional[Job] = taskmaster_with_executors.get_last_executor() # output_filer: Optional[Job] = taskmaster_with_executors.get_output_filer() - # task_master_cancelled = ( - # task_master_job.metadata.labels.get(self.constants.label_taskstate_key) + # taskmaster_cancelled = ( + # taskmaster_job.metadata.labels.get(self.constants.label_taskstate_key) # == self.constants.label_taskstate_value_canc # ) - # task_master_running = self.is_job_in_status( - # tested_object=task_master_job.status, + # taskmaster_running = self.is_job_in_status( + # tested_object=taskmaster_job.status, # test_objective=JobStatus.ACTIVE # ) - # print(task_master_running) - # task_master_completed = self.is_job_in_status( - # task_master_job.status, JobStatus.SUCCEEDED + # print(taskmaster_running) + # taskmaster_completed = self.is_job_in_status( + # taskmaster_job.status, JobStatus.SUCCEEDED # ) - # print(task_master_completed) + # print(taskmaster_completed) # executor_present = last_executor is not None # last_executor_failed = executor_present and self.is_job_in_status( # last_executor.get_job().status, JobStatus.FAILED @@ -338,7 +354,7 @@ def extract_state_from_k8s_jobs(self, taskmaster_with_executors: Task) -> TesSta # ) # print(output_filer_failed) # pending = self.k8s_constants.PodPhase.PENDING - # task_master_pending = any( + # taskmaster_pending = any( # pod.status.phase == pending # for pod in taskmaster_with_executors.get_taskmaster().get_pods() # ) @@ -346,21 +362,21 @@ def extract_state_from_k8s_jobs(self, taskmaster_with_executors: Task) -> TesSta # pod.status.phase == pending for pod in last_executor.get_pods() # ) - # if task_master_cancelled: + # if taskmaster_cancelled: # return TesState.CANCELED - # if task_master_completed and output_filer_failed: + # if taskmaster_completed and output_filer_failed: # return TesState.SYSTEM_ERROR - # if task_master_completed and last_executor_completed: + # if taskmaster_completed and last_executor_completed: # return TesState.COMPLETE - # if task_master_completed and last_executor_failed: + # if taskmaster_completed and last_executor_failed: # return TesState.EXECUTOR_ERROR - # if task_master_pending: + # if taskmaster_pending: # return TesState.QUEUED - # if task_master_running and not executor_present: + # if taskmaster_running and not executor_present: # return TesState.INITIALIZING # if last_executor_pending: # return TesState.QUEUED - # if task_master_running: + # if taskmaster_running: # return TesState.RUNNING return TesState.SYSTEM_ERROR @@ -435,9 +451,9 @@ def from_k8s_jobs_to_tes_task_basic( self, taskmaster_with_executors: Task, nullify_input_content: bool ) -> TesTask: task = TesTask() - task_master_job: V1Job = taskmaster_with_executors.taskmaster.job - task_master_job_metadata: V1ObjectMeta = task_master_job.metadata - input_json = (task_master_job_metadata.annotations or {}).get( + taskmaster_job: V1Job = taskmaster_with_executors.taskmaster.job + taskmaster_job_metadata: V1ObjectMeta = taskmaster_job.metadata + input_json = (taskmaster_job_metadata.annotations or {}).get( self.constants.ann_json_input_key, "" ) try: @@ -447,31 +463,31 @@ def from_k8s_jobs_to_tes_task_basic( input_item["content"] = None except json.JSONDecodeError as ex: print( - f"Deserializing task {task_master_job_metadata['name']} from JSON failed; {ex}" + f"Deserializing task {taskmaster_job_metadata['name']} from JSON failed; {ex}" ) - task.id = task_master_job_metadata["name"] + task.id = taskmaster_job_metadata["name"] task.state = self.extract_state_from_k8s_jobs(taskmaster_with_executors) task.creation_time = time_formatter( - task_master_job_metadata["creation_timestamp"] + taskmaster_job_metadata["creation_timestamp"] ) log = TesTaskLog() task.logs.append(log) - log.metadata["USER_ID"] = task_master_job_metadata["labels"][ + log.metadata["USER_ID"] = taskmaster_job_metadata["labels"][ self.constants.label_userid_key ] - if self.constants.label_groupname_key in task_master_job_metadata["labels"]: - log["GROUP_NAME"] = task_master_job_metadata["labels"][ + if self.constants.label_groupname_key in taskmaster_job_metadata["labels"]: + log["GROUP_NAME"] = taskmaster_job_metadata["labels"][ self.constants.label_groupname_key ] log.start_time = ( - time_formatter(task_master_job.status.start_time) - if task_master_job.status.start_time + time_formatter(taskmaster_job.status.start_time) + if taskmaster_job.status.start_time else None ) log.end_time = ( - time_formatter(task_master_job.status.completion_time) - if task_master_job.status.completion_time + time_formatter(taskmaster_job.status.completion_time) + if taskmaster_job.status.completion_time else None ) for executor_job in taskmaster_with_executors.get_executors(): diff --git a/tesk/api/kubernetes/convert/data/build_strategy.py b/tesk/api/kubernetes/convert/data/build_strategy.py index e6fa97f6..9bf24606 100644 --- a/tesk/api/kubernetes/convert/data/build_strategy.py +++ b/tesk/api/kubernetes/convert/data/build_strategy.py @@ -21,7 +21,7 @@ class BuildStrategy(ABC): """ @abstractmethod - def add_task_master_job(self, taskmaster_job: Job): + def add_taskmaster_job(self, taskmaster_job: Job): """Add taskmaster job. Method should optionally filter and place the passed taskmaster's job object diff --git a/tesk/api/kubernetes/convert/data/job.py b/tesk/api/kubernetes/convert/data/job.py index e6d66ee3..73251dd0 100644 --- a/tesk/api/kubernetes/convert/data/job.py +++ b/tesk/api/kubernetes/convert/data/job.py @@ -4,8 +4,8 @@ Pod objects). """ -from typing import List, Optional from enum import Enum +from typing import List, Optional from kubernetes.client import V1Job, V1ObjectMeta, V1Pod @@ -23,8 +23,7 @@ def get_job(self) -> V1Job: return self.job def add_pod(self, pod: V1Pod): - """Adds a single pod to the list (without any duplication checks).""" - # TODO: This doesn't take care of duplication, use set on id or name + """Adds a single pod to the list.""" self.pods.append(pod) def has_pods(self) -> bool: diff --git a/tesk/api/kubernetes/convert/data/single_task_strategy.py b/tesk/api/kubernetes/convert/data/single_task_strategy.py index ddd02abc..dd84b3e9 100644 --- a/tesk/api/kubernetes/convert/data/single_task_strategy.py +++ b/tesk/api/kubernetes/convert/data/single_task_strategy.py @@ -33,7 +33,7 @@ def __init__(self): """Initialise SingleTaskStrategy.""" self.task = None - def add_task_master_job(self, taskmaster_job: Job): + def add_taskmaster_job(self, taskmaster_job: Job): """Add taskmaster job.""" self.task = Task(taskmaster_job) diff --git a/tesk/api/kubernetes/convert/data/task_builder.py b/tesk/api/kubernetes/convert/data/task_builder.py index 07f890a7..0882c187 100644 --- a/tesk/api/kubernetes/convert/data/task_builder.py +++ b/tesk/api/kubernetes/convert/data/task_builder.py @@ -36,7 +36,7 @@ def add_job(self, job: V1Job): wrapped_job = Job(job) job_type = job.metadata.labels.get(self.constants.label_jobtype_key) if job_type == self.constants.label_jobtype_value_taskm: - self.build_strategy.add_task_master_job(wrapped_job) + self.build_strategy.add_taskmaster_job(wrapped_job) elif job_type == self.constants.label_jobtype_value_exec: self.build_strategy.add_executor_job(wrapped_job) else: diff --git a/tesk/api/kubernetes/convert/data/task_list_strategy.py b/tesk/api/kubernetes/convert/data/task_list_strategy.py index ed4c9840..7f8a14cd 100644 --- a/tesk/api/kubernetes/convert/data/task_list_strategy.py +++ b/tesk/api/kubernetes/convert/data/task_list_strategy.py @@ -38,7 +38,7 @@ def __init__(self): self.tasks_by_id: Dict[str, Task] = {} self.constants = Constants() - def add_task_master_job(self, taskmaster_job: Job): + def add_taskmaster_job(self, taskmaster_job: Job): """Add taskmater job.""" task_name = taskmaster_job.get_job().metadata.name if task_name not in self.tasks_by_id: diff --git a/tesk/api/kubernetes/convert/taskmaster_env_properties.py b/tesk/api/kubernetes/convert/taskmaster_env_properties.py index 79d7df5a..3ba0e306 100644 --- a/tesk/api/kubernetes/convert/taskmaster_env_properties.py +++ b/tesk/api/kubernetes/convert/taskmaster_env_properties.py @@ -62,8 +62,8 @@ class TaskmasterEnvProperties(BaseModel): description="If verbose (debug) mode of taskmaster is on (passes additional " "flag to taskmaster and sets image pull policy to Always)", ) - environment: Dict[str, str] = Field( - default={"key": "value"}, + environment: Optional[Dict[str, str]] = Field( + default=None, description="Environment variables, that will be passed to taskmaster", ) serviceAccountName: str = Field( diff --git a/tesk/api/kubernetes/convert/template.py b/tesk/api/kubernetes/convert/template.py index 6457686c..296c3a17 100644 --- a/tesk/api/kubernetes/convert/template.py +++ b/tesk/api/kubernetes/convert/template.py @@ -29,7 +29,10 @@ class KubernetesTemplateSupplier: """Templates for tasmaster's and executor's job object..""" - def __init__(self, namespace=TeskConstants.tesk_namespace, security_context=None): + def __init__( + self, + # security_context=None + ): """Initialize the converter.""" self.taskmaster_template: V1Job = get_taskmaster_template() self.taskmaster_env_properties: TaskmasterEnvProperties = ( @@ -37,15 +40,16 @@ def __init__(self, namespace=TeskConstants.tesk_namespace, security_context=None ) self.constants = Constants() self.k8s_constants = K8sConstants() - self.namespace = namespace - self.security_context = security_context + self.tesk_constants = TeskConstants() + self.namespace = self.tesk_constants.tesk_namespace + # self.security_context = security_context - def get_task_master_name(self) -> str: + def get_taskmaster_name(self) -> str: """Generate a unique name for the taskmaster job.""" name: str = self.constants.job_name_taskm_prefix + str(uuid.uuid4()) return name - def task_master_template(self) -> V1Job: + def get_taskmaster_template_with_value_from_config(self) -> V1Job: """Create a template for the taskmaster job.""" job: V1Job = self.taskmaster_template @@ -84,21 +88,36 @@ def task_master_template(self) -> V1Job: if job.metadata is None: job.metadata = V1ObjectMeta(labels={}) - assert job.metadata.labels is not None + if job.metadata.labels is None: + job.metadata.labels = V1ObjectMeta() job.metadata.labels[self.constants.label_jobtype_key] = ( self.constants.label_jobtype_value_taskm ) - task_master_name = self.get_task_master_name() - job.metadata.name = task_master_name + taskmaster_name = self.get_taskmaster_name() + job.metadata.name = taskmaster_name + container.name = taskmaster_name assert isinstance(container.env, Iterable) + if container.env is None: + container.env = V1EnvVar() + + if self.taskmaster_env_properties: + container.env.extend( + [ + V1EnvVar(name=key.upper().replace(".", "_"), value=value) + for key, value in self.taskmaster_env_properties.environment.items() + ] + ) + + # Set backoff env variables for `filer` and `executor` + backoff_limits = { + self.constants.filer_backoff_limit: self.tesk_constants.filer_backoff_limit, + self.constants.executor_backoff_limit: self.tesk_constants.executor_backoff_limit, + } container.env.extend( - [ - V1EnvVar(name=key.upper().replace(".", "_"), value=value) - for key, value in self.taskmaster_env_properties.environment.items() - ] + [V1EnvVar(name=key, value=value) for key, value in backoff_limits.items()] ) ftp_secrets = [ @@ -122,9 +141,12 @@ def task_master_template(self) -> V1Job: return job - def executor_template(self) -> V1Job: + def get_executor_template_with_value_from_config(self) -> V1Job: """Create a template for the executor job.""" - container = V1Container(name="executor", resources=V1ResourceRequirements()) + container = V1Container( + name=self.constants.label_jobtype_value_exec, + resources=V1ResourceRequirements(), + ) if self.taskmaster_env_properties.executorSecret is not None: container.volume_mounts = [ @@ -142,8 +164,8 @@ def executor_template(self) -> V1Job: restart_policy=self.k8s_constants.job_restart_policy, ) - if self.security_context: - pod_spec.security_context = self.security_context + # if self.security_context: + # pod_spec.security_context = self.security_context job = V1Job( api_version=self.k8s_constants.k8s_batch_api_version, diff --git a/tesk/constants.py b/tesk/constants.py index f545cd89..dcdd5a91 100644 --- a/tesk/constants.py +++ b/tesk/constants.py @@ -23,8 +23,11 @@ class TeskConstants: "TESK_API_TASKMASTER_SERVICE_ACCOUNT_NAME", "taskmaster" ) taskmaster_environment_executor_backoff_limit: str = os.getenv( - "ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT", "2" + "ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT", "6" ) - filer_environment_filer_backoff_limit: str = os.getenv( - "TESK_API_TASKMASTER_ENVIRONMENT_FILER_BACKOFF_LIMIT", "2" + filer_backoff_limit: str = os.getenv("FILER_BACKOFF_LIMIT", "2") + executor_backoff_limit: str = os.getenv("EXECUTOR_BACKOFF_LIMIT", "2") + # TODO: IDK what to do with this + tesk_api_taskmaster_environment_filer_backoff_limit: str = os.getenv( + "TESK_API_TASKMASTER_ENVIRONMENT_FILER_BACKOFF_LIMIT", "6" ) diff --git a/tesk/custom_config.py b/tesk/custom_config.py index 78a285db..961a2258 100644 --- a/tesk/custom_config.py +++ b/tesk/custom_config.py @@ -10,7 +10,7 @@ ) -class SecretKeyRef(BaseModel): +class PydanticK8sSecretKeyRef(BaseModel): """Reference to a secret key.""" name: str @@ -18,20 +18,20 @@ class SecretKeyRef(BaseModel): optional: Optional[bool] = Field(False, description="If the reference is optional") -class EnvVarSource(BaseModel): +class PydanticK8sEnvVarSource(BaseModel): """Source for an environment variable.""" - secretKeyRef: Optional[SecretKeyRef] = None + secretKeyRef: Optional[PydanticK8sSecretKeyRef] = None -class EnvVar(BaseModel): +class PydanticK8sEnvVar(BaseModel): """Environment variable.""" name: str - valueFrom: Optional[EnvVarSource] = None + valueFrom: Optional[PydanticK8sEnvVarSource] = None -class VolumeMount(BaseModel): +class PydanticK8sVolumeMount(BaseModel): """Volume mount configuration.""" name: str @@ -39,72 +39,72 @@ class VolumeMount(BaseModel): readOnly: bool -class DownwardAPIItem(BaseModel): +class PydanticK8sDownwardAPIItem(BaseModel): """Downward API item configuration.""" path: str fieldRef: Dict[str, str] -class Volume(BaseModel): +class PydanticK8sVolume(BaseModel): """Volume configuration.""" name: str - downwardAPI: Optional[Dict[str, List[DownwardAPIItem]]] = None + downwardAPI: Optional[Dict[str, List[PydanticK8sDownwardAPIItem]]] = None -class Container(BaseModel): +class PydanticK8sContainer(BaseModel): """Container configuration.""" name: str image: str args: List[str] - env: List[EnvVar] - volumeMounts: List[VolumeMount] + env: List[PydanticK8sEnvVar] + volumeMounts: List[PydanticK8sVolumeMount] -class PodSpec(BaseModel): +class PydanticK8sPodSpec(BaseModel): """Pod specification.""" serviceAccountName: str - containers: List[Container] - volumes: List[Volume] + containers: List[PydanticK8sContainer] + volumes: List[PydanticK8sVolume] restartPolicy: str -class PodMetadata(BaseModel): +class PydanticK8sPodMetadata(BaseModel): """Pod metadata.""" name: str -class PodTemplate(BaseModel): +class PydanticK8sPodTemplate(BaseModel): """Pod template configuration.""" - metadata: PodMetadata - spec: PodSpec + metadata: PydanticK8sPodMetadata + spec: PydanticK8sPodSpec -class JobSpec(BaseModel): +class PydanticK8sJobSpec(BaseModel): """Job specification.""" - template: PodTemplate + template: PydanticK8sPodTemplate -class JobMetadata(BaseModel): +class PydanticK8sJobMetadata(BaseModel): """Job metadata.""" name: str labels: Dict[str, str] -class Job(BaseModel): +class PydanticK8sJob(BaseModel): """Kubernetes Job configuration.""" apiVersion: str kind: str - metadata: JobMetadata - spec: JobSpec + metadata: PydanticK8sJobMetadata + spec: PydanticK8sJobSpec class CustomConfig(BaseModel): @@ -112,5 +112,5 @@ class CustomConfig(BaseModel): # Define custom configuration fields here service_info: Service - taskmaster_template: Job # This is Pydantic model for V1Job + taskmaster_template: PydanticK8sJob # This is Pydantic model for V1Job taskmaster_env_properties: TaskmasterEnvProperties diff --git a/tesk/utils.py b/tesk/utils.py index 98321076..2221dad3 100644 --- a/tesk/utils.py +++ b/tesk/utils.py @@ -1,11 +1,10 @@ """Utility functions for the TESK package.""" -import datetime import os -from pathlib import Path +from decimal import Decimal from enum import Enum +from pathlib import Path from typing import List, Optional, Sequence -from decimal import Decimal from foca import Foca from kubernetes.client.models import ( @@ -27,19 +26,19 @@ from pydantic import BaseModel from tesk.custom_config import ( - Container, CustomConfig, - DownwardAPIItem, - EnvVar, - EnvVarSource, - Job, - JobMetadata, - JobSpec, - PodSpec, - PodTemplate, + PydanticK8sContainer, + PydanticK8sDownwardAPIItem, + PydanticK8sEnvVar, + PydanticK8sEnvVarSource, + PydanticK8sJob, + PydanticK8sJobMetadata, + PydanticK8sJobSpec, + PydanticK8sPodSpec, + PydanticK8sPodTemplate, + PydanticK8sVolume, + PydanticK8sVolumeMount, TaskmasterEnvProperties, - Volume, - VolumeMount, ) from tesk.exceptions import ConfigNotFoundError @@ -80,7 +79,7 @@ def get_taskmaster_template() -> V1Job: """ custom_conf = get_custom_config() try: - return job_to_v1job(custom_conf.taskmaster_template) + return pydantic_k8s_job_to_v1job(custom_conf.taskmaster_template) except AttributeError: raise ConfigNotFoundError( "Custom configuration doesn't seem to have taskmaster_template in config " @@ -104,15 +103,18 @@ def get_taskmaster_env_property() -> TaskmasterEnvProperties: ) from None -def job_to_v1job(job: Job) -> V1Job: +def pydantic_k8s_job_to_v1job(job: PydanticK8sJob) -> V1Job: """Convert a pydantic job model to a V1Job object. + FOCA validates config via pydantic models and kubernetes + client's models aren't written using pydantic. + Returns: The V1Job object. """ def convert_env_var_source( - env_var_source: Optional[EnvVarSource], + env_var_source: Optional[PydanticK8sEnvVarSource], ) -> Optional[V1EnvVarSource]: if env_var_source is None: return None @@ -127,7 +129,7 @@ def convert_env_var_source( return None def convert_downward_api_item( - downward_api_item: DownwardAPIItem, + downward_api_item: PydanticK8sDownwardAPIItem, ) -> V1DownwardAPIVolumeFile: field_ref = None if downward_api_item.fieldRef: @@ -143,7 +145,7 @@ def convert_downward_api_item( field_ref=field_ref, ) - def convert_volume(volume: Volume) -> V1Volume: + def convert_volume(volume: PydanticK8sVolume) -> V1Volume: if volume.downwardAPI: return V1Volume( name=volume.name, @@ -156,19 +158,19 @@ def convert_volume(volume: Volume) -> V1Volume: ) return V1Volume(name=volume.name) - def convert_env_var(env_var: EnvVar) -> V1EnvVar: + def convert_env_var(env_var: PydanticK8sEnvVar) -> V1EnvVar: return V1EnvVar( name=env_var.name, value_from=convert_env_var_source(env_var.valueFrom) ) - def convert_volume_mount(volume_mount: VolumeMount) -> V1VolumeMount: + def convert_volume_mount(volume_mount: PydanticK8sVolumeMount) -> V1VolumeMount: return V1VolumeMount( name=volume_mount.name, mount_path=volume_mount.mountPath, read_only=volume_mount.readOnly, ) - def convert_container(container: Container) -> V1Container: + def convert_container(container: PydanticK8sContainer) -> V1Container: return V1Container( name=container.name, image=container.image, @@ -177,7 +179,7 @@ def convert_container(container: Container) -> V1Container: volume_mounts=[convert_volume_mount(vm) for vm in container.volumeMounts], ) - def convert_pod_spec(pod_spec: PodSpec) -> V1PodSpec: + def convert_pod_spec(pod_spec: PydanticK8sPodSpec) -> V1PodSpec: return V1PodSpec( service_account_name=pod_spec.serviceAccountName, containers=[ @@ -187,16 +189,16 @@ def convert_pod_spec(pod_spec: PodSpec) -> V1PodSpec: restart_policy=pod_spec.restartPolicy, ) - def convert_pod_template(pod_template: PodTemplate) -> V1PodTemplateSpec: + def convert_pod_template(pod_template: PydanticK8sPodTemplate) -> V1PodTemplateSpec: return V1PodTemplateSpec( metadata=V1ObjectMeta(name=pod_template.metadata.name), spec=convert_pod_spec(pod_template.spec), ) - def convert_job_spec(job_spec: JobSpec) -> V1JobSpec: + def convert_job_spec(job_spec: PydanticK8sJobSpec) -> V1JobSpec: return V1JobSpec(template=convert_pod_template(job_spec.template)) - def convert_job_metadata(job_metadata: JobMetadata) -> V1ObjectMeta: + def convert_job_metadata(job_metadata: PydanticK8sJobMetadata) -> V1ObjectMeta: return V1ObjectMeta(name=job_metadata.name, labels=job_metadata.labels) return V1Job( @@ -222,11 +224,19 @@ def time_formatter(time: Optional[str]) -> Optional[str]: def decimal_to_float(obj): + """Convert decimal to float. + + Can be used to make Decimal serializable. + """ if isinstance(obj, Decimal): return float(obj) raise TypeError def enum_to_string(enum): + """Converts enum to string. + + Can be used to make Enums serializable. + """ if isinstance(enum, Enum): return str(enum.name) From 0cd3110a20e72fec1d57cce6805b95715aed0e1f Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sat, 17 Aug 2024 11:36:15 +0530 Subject: [PATCH 14/22] fix error --- deployment/config.yaml | 5 +++-- tesk/api/kubernetes/convert/converter.py | 14 +++++++++++--- tesk/utils.py | 7 ++++--- 3 files changed, 18 insertions(+), 8 deletions(-) diff --git a/deployment/config.yaml b/deployment/config.yaml index d9ab80d5..eb26b398 100644 --- a/deployment/config.yaml +++ b/deployment/config.yaml @@ -85,7 +85,8 @@ custom: metadata: name: taskmaster spec: - serviceAccountName: default + serviceAccount: taskmaster + serviceAccountName: taskmaster containers: - name: taskmaster image: docker.io/elixircloud/tesk-core-taskmaster:v0.10.2 @@ -142,7 +143,7 @@ custom: environment: key: value # Service Account name for taskmaster - serviceAccountName: default + serviceAccountName: taskmaster # Logging configuration diff --git a/tesk/api/kubernetes/convert/converter.py b/tesk/api/kubernetes/convert/converter.py index f297acf0..e800ee3e 100644 --- a/tesk/api/kubernetes/convert/converter.py +++ b/tesk/api/kubernetes/convert/converter.py @@ -43,7 +43,7 @@ decimal_to_float, enum_to_string, get_taskmaster_env_property, - pydantic_model_list_json, + pydantic_model_list_dict, time_formatter, ) @@ -185,9 +185,14 @@ def from_tes_task_to_k8s_config_map( for idx, executor in enumerate(task.executors) ] + print("nice") + print(task) + print(task.volumes) + print("nice") + taskmaster_input: dict[str, Any] = { - "inputs": pydantic_model_list_json(task.inputs) if task.inputs else [], - "outputs": pydantic_model_list_json(task.outputs) if task.outputs else [], + "inputs": pydantic_model_list_dict(task.inputs) if task.inputs else [], + "outputs": pydantic_model_list_dict(task.outputs) if task.outputs else [], "volumes": task.volumes or [], "resources": { "disk_gb": float(task.resources.disk_gb) @@ -195,13 +200,16 @@ def from_tes_task_to_k8s_config_map( else 10.0 }, } + print(taskmaster_input) taskmaster_input[self.constants.taskmaster_input_exec_key] = [ exec_job.to_dict() for exec_job in executors_as_jobs ] + print(taskmaster_input) taskmaster_input_as_json = json.loads( json.dumps(taskmaster_input, default=decimal_to_float) ) + print(taskmaster_input_as_json) try: with BytesIO() as obj: diff --git a/tesk/utils.py b/tesk/utils.py index 2221dad3..aca6b399 100644 --- a/tesk/utils.py +++ b/tesk/utils.py @@ -5,6 +5,7 @@ from enum import Enum from pathlib import Path from typing import List, Optional, Sequence +import json from foca import Foca from kubernetes.client.models import ( @@ -209,11 +210,11 @@ def convert_job_metadata(job_metadata: PydanticK8sJobMetadata) -> V1ObjectMeta: ) -def pydantic_model_list_json(model_list: Sequence[BaseModel]) -> List[str]: - """Convert a list of pydantic models to a list of JSON objects.""" +def pydantic_model_list_dict(model_list: Sequence[BaseModel]) -> List[str]: + """Convert a list of pydantic models to a list of dictionaries.""" json_list = [] for item in model_list: - json_list.append(item.json()) + json_list.append(json.loads(item.json())) return json_list From aaad8fb276e196adbcbc07c0e227a5766114dc74 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 21 Aug 2024 17:15:18 +0530 Subject: [PATCH 15/22] fix: add fixed image and add image to containers --- deployment/config.yaml | 2 +- tesk/api/kubernetes/convert/converter.py | 13 ++++++++++--- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/deployment/config.yaml b/deployment/config.yaml index eb26b398..02577fee 100644 --- a/deployment/config.yaml +++ b/deployment/config.yaml @@ -126,7 +126,7 @@ custom: # Taskmaster image name imageName: docker.io/elixircloud/tesk-core-taskmaster # Taskmaster image version - imageVersion: v0.10.2 + imageVersion: fix-null-volumes # Filer image name filerImageName: docker.io/elixircloud/tesk-core-filer # Filer image version diff --git a/tesk/api/kubernetes/convert/converter.py b/tesk/api/kubernetes/convert/converter.py index e800ee3e..29d56616 100644 --- a/tesk/api/kubernetes/convert/converter.py +++ b/tesk/api/kubernetes/convert/converter.py @@ -282,9 +282,7 @@ def from_tes_executor_to_k8s_job( # noqa: PLR0913 # TODO: Not sure what to do with this # Convert potential TRS URI into docker image - # container.image = self.trs_client.get_docker_image_for_tool_version_uri( - # executor.image - # ) + container.image = executor.image if not container.command: container.command = [] @@ -316,6 +314,15 @@ def from_tes_executor_to_k8s_job( # noqa: PLR0913 f"{resources.ram_gb:.6f}Gi" ) + # # Workaround + # # Check if volumes is None and set it to an empty list if it is + # if ( + # executor_job.spec + # and executor_job.spec.spec + # and executor_job.spec.spec.volumes is None + # ): + # executor_job.spec.spec.volumes = [] + return executor_job def is_job_in_status(tested_object: V1JobStatus, test_objective: JobStatus) -> bool: From 46bbe2a719870af0a05a05e2625003eb093289a3 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Thu, 22 Aug 2024 13:26:33 +0530 Subject: [PATCH 16/22] fix: missing commands --- .../convert/executor_command_wrapper.py | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/tesk/api/kubernetes/convert/executor_command_wrapper.py b/tesk/api/kubernetes/convert/executor_command_wrapper.py index 08e515f7..642d6b63 100644 --- a/tesk/api/kubernetes/convert/executor_command_wrapper.py +++ b/tesk/api/kubernetes/convert/executor_command_wrapper.py @@ -9,7 +9,6 @@ params """ -import re from typing import List from tesk.api.ga4gh.tes.models import TesExecutor @@ -18,8 +17,6 @@ class ExecutorCommandWrapper: """Wraps executor's command.""" - SPECIAL_CHARS = re.compile(r"[ !\"#$&'()*;<>?\[\\`{|~\t\n]") - def __init__(self, executor: TesExecutor): """Initialize the wrapper.""" self.executor = executor @@ -38,17 +35,7 @@ def get_commands_with_stream_redirects(self) -> List[str]: result.append("/bin/sh") result.append("-c") - command_parts = [] - - for command_part in self.executor.command: - command = "" - if self.SPECIAL_CHARS.search(command_part): - # Replace single quotes with '"'"' - if "'" in command_part: - replace_command_part = command_part.replace("'", "'\"'\"'") - # Quote the command part - command = f"'{replace_command_part}'" - command_parts.append(command) + command_parts = [" ".join(self.executor.command)] if self.executor.stdin: command_parts.append("<") @@ -64,4 +51,4 @@ def get_commands_with_stream_redirects(self) -> List[str]: result.append(" ".join(command_parts)) - return result + return result \ No newline at end of file From 099c5289e60fce17c1da2be0cac6616091058f98 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Thu, 22 Aug 2024 13:33:43 +0530 Subject: [PATCH 17/22] fix: missing name of exec --- tesk/api/kubernetes/convert/converter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tesk/api/kubernetes/convert/converter.py b/tesk/api/kubernetes/convert/converter.py index 29d56616..0bae9a19 100644 --- a/tesk/api/kubernetes/convert/converter.py +++ b/tesk/api/kubernetes/convert/converter.py @@ -248,7 +248,7 @@ def from_tes_executor_to_k8s_job( # noqa: PLR0913 ) # Set executors name based on taskmaster's job name - Job(executor_job).change_job_name(new_name=generated_task_id) + Job(executor_job).change_job_name(Task(taskmaster_name=generated_task_id).get_executor_name(executor_index)) if executor_job.metadata is None: executor_job.metadata = V1ObjectMeta() From d96b6ae14cdbf7ee6335cbe8d99b3fc5f321a486 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Mon, 26 Aug 2024 14:09:38 +0530 Subject: [PATCH 18/22] fix: update the image --- deployment/config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/config.yaml b/deployment/config.yaml index 02577fee..b53ebb02 100644 --- a/deployment/config.yaml +++ b/deployment/config.yaml @@ -126,7 +126,7 @@ custom: # Taskmaster image name imageName: docker.io/elixircloud/tesk-core-taskmaster # Taskmaster image version - imageVersion: fix-null-volumes + imageVersion: fix-null-volumes3 # Filer image name filerImageName: docker.io/elixircloud/tesk-core-filer # Filer image version From d545d245dd47057fa68f99fc577685ce0904482e Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 28 Aug 2024 14:56:04 +0530 Subject: [PATCH 19/22] fix minor --- deployment/config.yaml | 2 +- tesk/api/ga4gh/tes/task/create_task.py | 36 ++++++++++++++----- .../convert/executor_command_wrapper.py | 2 +- tesk/api/kubernetes/convert/template.py | 2 ++ ...ask_execution_service.117cd92.openapi.yaml | 9 ++--- 5 files changed, 37 insertions(+), 14 deletions(-) diff --git a/deployment/config.yaml b/deployment/config.yaml index b53ebb02..2889a1b2 100644 --- a/deployment/config.yaml +++ b/deployment/config.yaml @@ -126,7 +126,7 @@ custom: # Taskmaster image name imageName: docker.io/elixircloud/tesk-core-taskmaster # Taskmaster image version - imageVersion: fix-null-volumes3 + imageVersion: fix-null-volumes5 # Filer image name filerImageName: docker.io/elixircloud/tesk-core-filer # Filer image version diff --git a/tesk/api/ga4gh/tes/task/create_task.py b/tesk/api/ga4gh/tes/task/create_task.py index 5540cf7b..3da339c1 100644 --- a/tesk/api/ga4gh/tes/task/create_task.py +++ b/tesk/api/ga4gh/tes/task/create_task.py @@ -7,7 +7,8 @@ from tesk.api.ga4gh.tes.models import TesCreateTaskResponse, TesResources, TesTask from tesk.api.ga4gh.tes.task.task_request import TesTaskRequest from tesk.exceptions import KubernetesError - +import os +from datetime import datetime logger = logging.getLogger(__name__) @@ -36,7 +37,8 @@ def create_task(self) -> TesCreateTaskResponse: try: attempts_no += 1 resources = self.task.resources - + limits = self.kubernetes_client_wrapper.list_limits() + print("limits", limits) minimum_ram_gb = self.kubernetes_client_wrapper.minimum_ram_gb() if not self.task.resources: @@ -49,7 +51,6 @@ def create_task(self) -> TesCreateTaskResponse: # self.user ) - print(taskmaster_job) taskmaster_config_map = ( self.tes_kubernetes_converter.from_tes_task_to_k8s_config_map( self.task, @@ -57,14 +58,33 @@ def create_task(self) -> TesCreateTaskResponse: # self.user ) ) - print(taskmaster_config_map) - # Create ConfigMap and Job - _ = self.kubernetes_client_wrapper.create_config_map( - taskmaster_config_map - ) + configmap = self.kubernetes_client_wrapper.create_config_map(taskmaster_config_map) created_job = self.kubernetes_client_wrapper.create_job(taskmaster_job) + os.makedirs("/tmp/tesk", exist_ok=True) + output_log_path = f"/tmp/tesk/output-at-{datetime.now().strftime('%H:%M:%S')}.log" + with open(output_log_path, "w") as f: + f.write("*********************************\n") + f.write(f"Manifest consumed to create taskmaster job as {type(taskmaster_job)}\n") + f.write(str(taskmaster_job) + "\n") + f.write("*********************************\n") + + f.write("*********************************\n") + f.write(f"Manifest consumed to create config map as {type(taskmaster_config_map)}\n") + f.write(str(taskmaster_config_map) + "\n") + f.write("*********************************\n") + + # Create ConfigMap and Job + f.write("*********************************\n") + f.write(f"Created ConfigMap as {type(configmap)}\n") + f.write(str(configmap) + "\n") + f.write("*********************************\n") + + f.write("*********************************\n") + f.write(f"Created taskmaster job as {type(created_job)}\n") + f.write(str(created_job) + "\n") + f.write("*********************************\n") assert created_job.metadata is not None assert created_job.metadata.name is not None diff --git a/tesk/api/kubernetes/convert/executor_command_wrapper.py b/tesk/api/kubernetes/convert/executor_command_wrapper.py index 642d6b63..ebda5921 100644 --- a/tesk/api/kubernetes/convert/executor_command_wrapper.py +++ b/tesk/api/kubernetes/convert/executor_command_wrapper.py @@ -51,4 +51,4 @@ def get_commands_with_stream_redirects(self) -> List[str]: result.append(" ".join(command_parts)) - return result \ No newline at end of file + return result diff --git a/tesk/api/kubernetes/convert/template.py b/tesk/api/kubernetes/convert/template.py index 296c3a17..b367c3c4 100644 --- a/tesk/api/kubernetes/convert/template.py +++ b/tesk/api/kubernetes/convert/template.py @@ -197,4 +197,6 @@ def get_executor_template_with_value_from_config(self) -> V1Job: ) ] + job.spec.template.spec.containers[0].restart_policy = "Never" + return job diff --git a/tesk/api/specs/task_execution_service.117cd92.openapi.yaml b/tesk/api/specs/task_execution_service.117cd92.openapi.yaml index fb2a8755..3d958827 100644 --- a/tesk/api/specs/task_execution_service.117cd92.openapi.yaml +++ b/tesk/api/specs/task_execution_service.117cd92.openapi.yaml @@ -582,7 +582,7 @@ components: type: integer description: Requested number of CPUs format: int32 - example: 4 + example: 1 preemptible: type: boolean description: |- @@ -595,12 +595,12 @@ components: type: number description: Requested RAM required in gigabytes (GB) format: double - example: 8 + example: 1 disk_gb: type: number description: Requested disk size in gigabytes (GB) format: double - example: 40 + example: 2 zones: type: array description: |- @@ -610,7 +610,8 @@ components: priority queue to which the job is assigned. items: type: string - example: us-west-1 + example: + - us-west-1 backend_parameters: type: object additionalProperties: From 9d1b89c3812096b47aca7d1ecd372ae42ed0b86f Mon Sep 17 00:00:00 2001 From: "alvaro.gonzalez" Date: Wed, 28 Aug 2024 13:06:37 +0300 Subject: [PATCH 20/22] change image for taskmaster --- deployment/config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/deployment/config.yaml b/deployment/config.yaml index 2889a1b2..1f578966 100644 --- a/deployment/config.yaml +++ b/deployment/config.yaml @@ -89,7 +89,7 @@ custom: serviceAccountName: taskmaster containers: - name: taskmaster - image: docker.io/elixircloud/tesk-core-taskmaster:v0.10.2 + image: docker.io/lvarin/tesk-core-taskmaster:testing args: - -f - /jsoninput/JSON_INPUT.gz @@ -124,9 +124,9 @@ custom: # Taskmaster environment properties taskmaster_env_properties: # Taskmaster image name - imageName: docker.io/elixircloud/tesk-core-taskmaster + imageName: docker.io/lvarin/tesk-core-taskmaster # Taskmaster image version - imageVersion: fix-null-volumes5 + imageVersion: testing # Filer image name filerImageName: docker.io/elixircloud/tesk-core-filer # Filer image version From e2adc6f1e73926d2c94717f80f7729662d839986 Mon Sep 17 00:00:00 2001 From: "alvaro.gonzalez" Date: Thu, 29 Aug 2024 11:01:20 +0300 Subject: [PATCH 21/22] fix: When restartPolicy or resouces.limits are missing --- tesk/services/taskmaster.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/tesk/services/taskmaster.py b/tesk/services/taskmaster.py index a89a8d4c..a5ca08b4 100755 --- a/tesk/services/taskmaster.py +++ b/tesk/services/taskmaster.py @@ -30,6 +30,18 @@ def run_executor(executor, namespace, pvc=None): {'backoffLimit': int(os.environ['EXECUTOR_BACKOFF_LIMIT'])} ) + if 'restartPolicy' not in spec.keys() and \ + 'restart_policy' in spec.keys(): + spec['restartPolicy'] = spec['restart_policy'] + + for container in spec['containers']: + if 'limits' not in container['resources'].keys(): + container['resources']['limits'] = None + if container['resources']['limits'] is None and \ + ('requests' in container['resources'].keys() and \ + container['resources']['requests'] is not None): + container['resources']['limits'] = container['resources']['requests'] + if pvc is not None: mounts = spec['containers'][0].setdefault('volumeMounts', []) mounts.extend(pvc.volume_mounts) From 104aa05c3292221a5fe6ca0f07b8fe9fd4781604 Mon Sep 17 00:00:00 2001 From: "alvaro.gonzalez" Date: Thu, 29 Aug 2024 11:52:45 +0300 Subject: [PATCH 22/22] fix: Code is using tabs, instead of 4 spaces --- tesk/services/taskmaster.py | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/tesk/services/taskmaster.py b/tesk/services/taskmaster.py index a5ca08b4..a0dcacb2 100755 --- a/tesk/services/taskmaster.py +++ b/tesk/services/taskmaster.py @@ -28,19 +28,19 @@ def run_executor(executor, namespace, pvc=None): if os.environ.get('EXECUTOR_BACKOFF_LIMIT') is not None: executor['spec'].update( {'backoffLimit': int(os.environ['EXECUTOR_BACKOFF_LIMIT'])} - ) - - if 'restartPolicy' not in spec.keys() and \ - 'restart_policy' in spec.keys(): - spec['restartPolicy'] = spec['restart_policy'] - - for container in spec['containers']: - if 'limits' not in container['resources'].keys(): - container['resources']['limits'] = None - if container['resources']['limits'] is None and \ - ('requests' in container['resources'].keys() and \ - container['resources']['requests'] is not None): - container['resources']['limits'] = container['resources']['requests'] + ) + + if 'restartPolicy' not in spec.keys() and \ + 'restart_policy' in spec.keys(): + spec['restartPolicy'] = spec['restart_policy'] + + for container in spec['containers']: + if 'limits' not in container['resources'].keys(): + container['resources']['limits'] = None + if container['resources']['limits'] is None and \ + ('requests' in container['resources'].keys() and \ + container['resources']['requests'] is not None): + container['resources']['limits'] = container['resources']['requests'] if pvc is not None: mounts = spec['containers'][0].setdefault('volumeMounts', [])