diff --git a/k8s/welearn-datastack/values.yaml b/k8s/welearn-datastack/values.yaml
index b665a49..32f88fa 100644
--- a/k8s/welearn-datastack/values.yaml
+++ b/k8s/welearn-datastack/values.yaml
@@ -27,6 +27,7 @@ common:
RCLONE_CONFIG_DEST_ENV_AUTH: true
RCLONE_CONFIG_DEST_TYPE: azureblob
TEAM_EMAIL: welearn@learningplanetinstitute.org
+ TIKA_ADDRESS: http://tika:9998
embeddingModelFr: sentence-camembert-base
embeddingModelEn: all-minilm-l6-v2
modelsPathRoot: /models
diff --git a/poetry.lock b/poetry.lock
index 7cb4ff9..f097ba5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -14,103 +14,103 @@ files = [
[[package]]
name = "aiohttp"
-version = "3.12.13"
+version = "3.12.14"
description = "Async http client/server framework (asyncio)"
optional = false
python-versions = ">=3.9"
groups = ["main"]
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[package.dependencies]
aiohappyeyeballs = ">=2.5.0"
-aiosignal = ">=1.1.2"
+aiosignal = ">=1.4.0"
attrs = ">=17.3.0"
frozenlist = ">=1.1.1"
multidict = ">=4.5,<7.0"
@@ -138,14 +138,14 @@ typing-extensions = {version = ">=4.2", markers = "python_version < \"3.13\""}
[[package]]
name = "alembic"
-version = "1.16.2"
+version = "1.16.4"
description = "A database migration tool for SQLAlchemy."
optional = false
python-versions = ">=3.9"
groups = ["metrics"]
files = [
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]
[package.dependencies]
@@ -210,6 +210,48 @@ docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphi
tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
tests-mypy = ["mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\""]
+[[package]]
+name = "azure-core"
+version = "1.35.0"
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+
+[package.extras]
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[[package]]
name = "bandit"
version = "1.8.6"
@@ -526,14 +568,14 @@ files = [
[[package]]
name = "certifi"
-version = "2025.6.15"
+version = "2025.7.14"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
python-versions = ">=3.7"
groups = ["main", "metrics"]
files = [
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description = "Foreign Function Interface for Python calling C code."
optional = false
python-versions = ">=3.8"
-groups = ["metrics"]
-markers = "platform_python_implementation == \"CPython\" and sys_platform == \"win32\" or implementation_name == \"pypy\""
+groups = ["main", "metrics"]
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[package.dependencies]
pycparser = "*"
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test = ["PyYAML", "mock", "pytest"]
yaml = ["PyYAML"]
+[[package]]
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+description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
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+python-versions = "!=3.9.0,!=3.9.1,>=3.7"
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+sdist = ["build (>=1.0.0)"]
+ssh = ["bcrypt (>=3.1.5)"]
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+test-randomorder = ["pytest-randomly"]
+
[[package]]
name = "cymem"
version = "2.0.11"
@@ -863,14 +965,14 @@ files = [
[[package]]
name = "datasets"
-version = "3.6.0"
+version = "4.0.0"
description = "HuggingFace community-driven open-source library of datasets"
optional = false
python-versions = ">=3.9.0"
groups = ["main"]
files = [
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@@ -889,18 +991,17 @@ tqdm = ">=4.66.3"
xxhash = "*"
[package.extras]
-audio = ["librosa", "soundfile (>=0.12.1)", "soxr (>=0.4.0)"]
+audio = ["soundfile (>=0.12.1)", "torch (>=2.7.0)", "torchcodec (>=0.4.0)"]
benchmarks = ["tensorflow (==2.12.0)", "torch (==2.0.1)", "transformers (==4.30.1)"]
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jax = ["jax (>=0.3.14)", "jaxlib (>=0.3.14)"]
pdfs = ["pdfplumber (>=0.11.4)"]
quality = ["ruff (>=0.3.0)"]
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tensorflow = ["tensorflow (>=2.6.0)"]
tensorflow-gpu = ["tensorflow (>=2.6.0)"]
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torch = ["torch"]
vision = ["Pillow (>=9.4.0)"]
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- {file = "playwright-1.52.0-py3-none-macosx_11_0_universal2.whl", hash = "sha256:7223960b7dd7ddeec1ba378c302d1d09733b8dac438f492e9854c85d3ca7144f"},
- {file = "playwright-1.52.0-py3-none-manylinux1_x86_64.whl", hash = "sha256:d010124d24a321e0489a8c0d38a3971a7ca7656becea7656c9376bfea7f916d4"},
- {file = "playwright-1.52.0-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4173e453c43180acc60fd77ffe1ebee8d0efbfd9986c03267007b9c3845415af"},
- {file = "playwright-1.52.0-py3-none-win32.whl", hash = "sha256:cd0bdf92df99db6237a99f828e80a6a50db6180ef8d5352fc9495df2c92f9971"},
- {file = "playwright-1.52.0-py3-none-win_amd64.whl", hash = "sha256:dcbf75101eba3066b7521c6519de58721ea44379eb17a0dafa94f9f1b17f59e4"},
- {file = "playwright-1.52.0-py3-none-win_arm64.whl", hash = "sha256:9d0085b8de513de5fb50669f8e6677f0252ef95a9a1d2d23ccee9638e71e65cb"},
-]
-
-[package.dependencies]
-greenlet = ">=3.1.1,<4.0.0"
-pyee = ">=13,<14"
-
[[package]]
name = "portalocker"
version = "2.10.1"
@@ -3393,12 +3549,12 @@ version = "2.22"
description = "C parser in Python"
optional = false
python-versions = ">=3.8"
-groups = ["metrics"]
-markers = "platform_python_implementation == \"CPython\" and sys_platform == \"win32\" or implementation_name == \"pypy\""
+groups = ["main", "metrics"]
files = [
{file = "pycparser-2.22-py3-none-any.whl", hash = "sha256:c3702b6d3dd8c7abc1afa565d7e63d53a1d0bd86cdc24edd75470f4de499cfcc"},
{file = "pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6"},
]
+markers = {main = "platform_python_implementation != \"PyPy\"", metrics = "platform_python_implementation == \"CPython\" and sys_platform == \"win32\" or implementation_name == \"pypy\""}
[[package]]
name = "pydantic"
@@ -3534,24 +3690,6 @@ files = [
[package.dependencies]
typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
-[[package]]
-name = "pyee"
-version = "13.0.0"
-description = "A rough port of Node.js's EventEmitter to Python with a few tricks of its own"
-optional = false
-python-versions = ">=3.8"
-groups = ["metrics"]
-files = [
- {file = "pyee-13.0.0-py3-none-any.whl", hash = "sha256:48195a3cddb3b1515ce0695ed76036b5ccc2ef3a9f963ff9f77aec0139845498"},
- {file = "pyee-13.0.0.tar.gz", hash = "sha256:b391e3c5a434d1f5118a25615001dbc8f669cf410ab67d04c4d4e07c55481c37"},
-]
-
-[package.dependencies]
-typing-extensions = "*"
-
-[package.extras]
-dev = ["black", "build", "flake8", "flake8-black", "isort", "jupyter-console", "mkdocs", "mkdocs-include-markdown-plugin", "mkdocstrings[python]", "mypy", "pytest", "pytest-asyncio ; python_version >= \"3.4\"", "pytest-trio ; python_version >= \"3.7\"", "sphinx", "toml", "tox", "trio", "trio ; python_version > \"3.6\"", "trio-typing ; python_version > \"3.6\"", "twine", "twisted", "validate-pyproject[all]"]
-
[[package]]
name = "pygments"
version = "2.19.2"
@@ -3567,26 +3705,6 @@ files = [
[package.extras]
windows-terminal = ["colorama (>=0.4.6)"]
-[[package]]
-name = "pypdf"
-version = "5.7.0"
-description = "A pure-python PDF library capable of splitting, merging, cropping, and transforming PDF files"
-optional = false
-python-versions = ">=3.8"
-groups = ["main"]
-files = [
- {file = "pypdf-5.7.0-py3-none-any.whl", hash = "sha256:203379453439f5b68b7a1cd43cdf4c5f7a02b84810cefa7f93a47b350aaaba48"},
- {file = "pypdf-5.7.0.tar.gz", hash = "sha256:68c92f2e1aae878bab1150e74447f31ab3848b1c0a6f8becae9f0b1904460b6f"},
-]
-
-[package.extras]
-crypto = ["cryptography"]
-cryptodome = ["PyCryptodome"]
-dev = ["black", "flit", "pip-tools", "pre-commit", "pytest-cov", "pytest-socket", "pytest-timeout", "pytest-xdist", "wheel"]
-docs = ["myst_parser", "sphinx", "sphinx_rtd_theme"]
-full = ["Pillow (>=8.0.0)", "cryptography"]
-image = ["Pillow (>=8.0.0)"]
-
[[package]]
name = "pyphen"
version = "0.17.2"
@@ -3706,28 +3824,32 @@ files = [
[[package]]
name = "pywin32"
-version = "310"
+version = "311"
description = "Python for Window Extensions"
optional = false
python-versions = "*"
groups = ["main", "metrics"]
files = [
- {file = "pywin32-310-cp310-cp310-win32.whl", hash = "sha256:6dd97011efc8bf51d6793a82292419eba2c71cf8e7250cfac03bba284454abc1"},
- {file = "pywin32-310-cp310-cp310-win_amd64.whl", hash = "sha256:c3e78706e4229b915a0821941a84e7ef420bf2b77e08c9dae3c76fd03fd2ae3d"},
- {file = "pywin32-310-cp310-cp310-win_arm64.whl", hash = "sha256:33babed0cf0c92a6f94cc6cc13546ab24ee13e3e800e61ed87609ab91e4c8213"},
- {file = "pywin32-310-cp311-cp311-win32.whl", hash = "sha256:1e765f9564e83011a63321bb9d27ec456a0ed90d3732c4b2e312b855365ed8bd"},
- {file = "pywin32-310-cp311-cp311-win_amd64.whl", hash = "sha256:126298077a9d7c95c53823934f000599f66ec9296b09167810eb24875f32689c"},
- {file = "pywin32-310-cp311-cp311-win_arm64.whl", hash = "sha256:19ec5fc9b1d51c4350be7bb00760ffce46e6c95eaf2f0b2f1150657b1a43c582"},
- {file = "pywin32-310-cp312-cp312-win32.whl", hash = "sha256:8a75a5cc3893e83a108c05d82198880704c44bbaee4d06e442e471d3c9ea4f3d"},
- {file = "pywin32-310-cp312-cp312-win_amd64.whl", hash = "sha256:bf5c397c9a9a19a6f62f3fb821fbf36cac08f03770056711f765ec1503972060"},
- {file = "pywin32-310-cp312-cp312-win_arm64.whl", hash = "sha256:2349cc906eae872d0663d4d6290d13b90621eaf78964bb1578632ff20e152966"},
- {file = "pywin32-310-cp313-cp313-win32.whl", hash = "sha256:5d241a659c496ada3253cd01cfaa779b048e90ce4b2b38cd44168ad555ce74ab"},
- {file = "pywin32-310-cp313-cp313-win_amd64.whl", hash = "sha256:667827eb3a90208ddbdcc9e860c81bde63a135710e21e4cb3348968e4bd5249e"},
- {file = "pywin32-310-cp313-cp313-win_arm64.whl", hash = "sha256:e308f831de771482b7cf692a1f308f8fca701b2d8f9dde6cc440c7da17e47b33"},
- {file = "pywin32-310-cp38-cp38-win32.whl", hash = "sha256:0867beb8addefa2e3979d4084352e4ac6e991ca45373390775f7084cc0209b9c"},
- {file = "pywin32-310-cp38-cp38-win_amd64.whl", hash = "sha256:30f0a9b3138fb5e07eb4973b7077e1883f558e40c578c6925acc7a94c34eaa36"},
- {file = "pywin32-310-cp39-cp39-win32.whl", hash = "sha256:851c8d927af0d879221e616ae1f66145253537bbdd321a77e8ef701b443a9a1a"},
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+ {file = "pywin32-311-cp310-cp310-win32.whl", hash = "sha256:d03ff496d2a0cd4a5893504789d4a15399133fe82517455e78bad62efbb7f0a3"},
+ {file = "pywin32-311-cp310-cp310-win_amd64.whl", hash = "sha256:797c2772017851984b97180b0bebe4b620bb86328e8a884bb626156295a63b3b"},
+ {file = "pywin32-311-cp310-cp310-win_arm64.whl", hash = "sha256:0502d1facf1fed4839a9a51ccbcc63d952cf318f78ffc00a7e78528ac27d7a2b"},
+ {file = "pywin32-311-cp311-cp311-win32.whl", hash = "sha256:184eb5e436dea364dcd3d2316d577d625c0351bf237c4e9a5fabbcfa5a58b151"},
+ {file = "pywin32-311-cp311-cp311-win_amd64.whl", hash = "sha256:3ce80b34b22b17ccbd937a6e78e7225d80c52f5ab9940fe0506a1a16f3dab503"},
+ {file = "pywin32-311-cp311-cp311-win_arm64.whl", hash = "sha256:a733f1388e1a842abb67ffa8e7aad0e70ac519e09b0f6a784e65a136ec7cefd2"},
+ {file = "pywin32-311-cp312-cp312-win32.whl", hash = "sha256:750ec6e621af2b948540032557b10a2d43b0cee2ae9758c54154d711cc852d31"},
+ {file = "pywin32-311-cp312-cp312-win_amd64.whl", hash = "sha256:b8c095edad5c211ff31c05223658e71bf7116daa0ecf3ad85f3201ea3190d067"},
+ {file = "pywin32-311-cp312-cp312-win_arm64.whl", hash = "sha256:e286f46a9a39c4a18b319c28f59b61de793654af2f395c102b4f819e584b5852"},
+ {file = "pywin32-311-cp313-cp313-win32.whl", hash = "sha256:f95ba5a847cba10dd8c4d8fefa9f2a6cf283b8b88ed6178fa8a6c1ab16054d0d"},
+ {file = "pywin32-311-cp313-cp313-win_amd64.whl", hash = "sha256:718a38f7e5b058e76aee1c56ddd06908116d35147e133427e59a3983f703a20d"},
+ {file = "pywin32-311-cp313-cp313-win_arm64.whl", hash = "sha256:7b4075d959648406202d92a2310cb990fea19b535c7f4a78d3f5e10b926eeb8a"},
+ {file = "pywin32-311-cp314-cp314-win32.whl", hash = "sha256:b7a2c10b93f8986666d0c803ee19b5990885872a7de910fc460f9b0c2fbf92ee"},
+ {file = "pywin32-311-cp314-cp314-win_amd64.whl", hash = "sha256:3aca44c046bd2ed8c90de9cb8427f581c479e594e99b5c0bb19b29c10fd6cb87"},
+ {file = "pywin32-311-cp314-cp314-win_arm64.whl", hash = "sha256:a508e2d9025764a8270f93111a970e1d0fbfc33f4153b388bb649b7eec4f9b42"},
+ {file = "pywin32-311-cp38-cp38-win32.whl", hash = "sha256:6c6f2969607b5023b0d9ce2541f8d2cbb01c4f46bc87456017cf63b73f1e2d8c"},
+ {file = "pywin32-311-cp38-cp38-win_amd64.whl", hash = "sha256:c8015b09fb9a5e188f83b7b04de91ddca4658cee2ae6f3bc483f0b21a77ef6cd"},
+ {file = "pywin32-311-cp39-cp39-win32.whl", hash = "sha256:aba8f82d551a942cb20d4a83413ccbac30790b50efb89a75e4f586ac0bb8056b"},
+ {file = "pywin32-311-cp39-cp39-win_amd64.whl", hash = "sha256:e0c4cfb0621281fe40387df582097fd796e80430597cb9944f0ae70447bacd91"},
+ {file = "pywin32-311-cp39-cp39-win_arm64.whl", hash = "sha256:62ea666235135fee79bb154e695f3ff67370afefd71bd7fea7512fc70ef31e3d"},
]
markers = {main = "platform_system == \"Windows\"", metrics = "sys_platform == \"win32\""}
@@ -3888,39 +4010,39 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""}
[[package]]
name = "qdrant-client"
-version = "1.14.3"
+version = "1.12.2"
description = "Client library for the Qdrant vector search engine"
optional = false
python-versions = ">=3.9"
groups = ["main"]
files = [
- {file = "qdrant_client-1.14.3-py3-none-any.whl", hash = "sha256:66faaeae00f9b5326946851fe4ca4ddb1ad226490712e2f05142266f68dfc04d"},
- {file = "qdrant_client-1.14.3.tar.gz", hash = "sha256:bb899e3e065b79c04f5e47053d59176150c0a5dabc09d7f476c8ce8e52f4d281"},
+ {file = "qdrant_client-1.12.2-py3-none-any.whl", hash = "sha256:a0ae500a46a679ff3521ba3f1f1cf3d72b57090a768cec65fc317066bcbac1e6"},
+ {file = "qdrant_client-1.12.2.tar.gz", hash = "sha256:2777e09b3e89bb22bb490384d8b1fa8140f3915287884f18984f7031a346aba5"},
]
[package.dependencies]
grpcio = ">=1.41.0"
+grpcio-tools = ">=1.41.0"
httpx = {version = ">=0.20.0", extras = ["http2"]}
numpy = {version = ">=1.26", markers = "python_version == \"3.12\""}
portalocker = ">=2.7.0,<3.0.0"
-protobuf = ">=3.20.0"
-pydantic = ">=1.10.8,<2.0.dev0 || >2.2.0"
+pydantic = ">=1.10.8"
urllib3 = ">=1.26.14,<3"
[package.extras]
-fastembed = ["fastembed (>=0.7,<0.8)"]
-fastembed-gpu = ["fastembed-gpu (>=0.7,<0.8)"]
+fastembed = ["fastembed (==0.5.0)"]
+fastembed-gpu = ["fastembed-gpu (==0.5.0)"]
[[package]]
name = "refinedoc"
-version = "0.0.3"
+version = "1.0.1"
description = "Python library for post-extraction refinement of text that may be derived from PDF extraction."
optional = false
python-versions = ">=3.9"
groups = ["main"]
files = [
- {file = "refinedoc-0.0.3-py3-none-any.whl", hash = "sha256:f3c5e835740ebfa1966b91b2d634615ecf877c2ff6db230c082ac54382607546"},
- {file = "refinedoc-0.0.3.tar.gz", hash = "sha256:c975f73db347a7e8f376bc47a0064e13281b5e502e2fe11c655d8dde13931182"},
+ {file = "refinedoc-1.0.1-py3-none-any.whl", hash = "sha256:a2840fefb110b33d84474ef3b5e3b3813a55fb7c8e42a70615f51acb1b3885c7"},
+ {file = "refinedoc-1.0.1.tar.gz", hash = "sha256:afad515bcbd13e9e7ba40d149d6b2a8a04c88323bc31eef2eddf3e3bbd6e921b"},
]
[[package]]
@@ -5572,4 +5694,4 @@ testing = ["coverage[toml]", "zope.event", "zope.testing"]
[metadata]
lock-version = "2.1"
python-versions = ">=3.12,<3.13"
-content-hash = "2209d1c3df8969624e0fbecbe4c0cbf522d111c555fef01e54f986a078fa9a5f"
+content-hash = "9d8f5dfb68575623759507b8b8450ccaaaa08b03cd5e390f97639800f4b2a3ae"
diff --git a/pyproject.toml b/pyproject.toml
index e666061..89bd269 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,9 +29,8 @@ requests = "^2.32.4"
wikipedia-api = "^0.8.1"
sentence-transformers = "^4.1.0"
spacy = "^3.8.7"
-pypdf = "^5.6.0"
-refinedoc = "^0.0.3"
-qdrant-client = "^1.14.2"
+refinedoc = "^1.0.0"
+qdrant-client = "1.12.2"
python-dotenv = "^1.1.0"
beautifulsoup4 = "^4.13.4"
pyphen = "^0.17.2"
@@ -46,6 +45,7 @@ psycopg2-binary = "^2.9.10"
brotli = "^1.1.0"
scikit-learn = "~=1.6.1"
optimum = {extras = ["onnxruntime"], version = "^1.26.1"}
+azure-storage-blob = "^12.26.0"
[tool.poetry.group.metrics.dependencies]
alembic = "^1.16.1"
diff --git a/sql/89920abb7ff8_populate_corpus_category.sql b/sql/89920abb7ff8_populate_corpus_category.sql
index 6ce5ef9..3557efe 100644
--- a/sql/89920abb7ff8_populate_corpus_category.sql
+++ b/sql/89920abb7ff8_populate_corpus_category.sql
@@ -4,7 +4,7 @@ INSERT
INTO
corpus_related.category(title)
VALUES
- ('Academic scientific publications')
+ ('academic scientific publications')
RETURNING id AS catid
)
UPDATE
diff --git a/sql/qty_document_in_qdrant b/sql/qty_document_in_qdrant
deleted file mode 100644
index 2977a4b..0000000
--- a/sql/qty_document_in_qdrant
+++ /dev/null
@@ -1,11 +0,0 @@
--- document_related.qty_document_in_qdrant source
-
-CREATE MATERIALIZED VIEW document_related.qty_document_in_qdrant
-TABLESPACE pg_default
-AS SELECT count(1) AS document_in_qdrant
- FROM ( SELECT ps.document_id,
- max(ps.operation_order) AS max_order
- FROM document_related.process_state ps
- WHERE ps.title = 'document_in_qdrant'::document_related.step
- GROUP BY ps.document_id) latest
-WITH NO DATA;
\ No newline at end of file
diff --git a/tests/document_collector_hub/plugins_test/test_hal.py b/tests/document_collector_hub/plugins_test/test_hal.py
index 2a254e1..a9eeb5a 100644
--- a/tests/document_collector_hub/plugins_test/test_hal.py
+++ b/tests/document_collector_hub/plugins_test/test_hal.py
@@ -125,12 +125,15 @@ def test__convert_json_dict_to_welearndoc(self):
doc0["abstract_s"][0].split(".")[0] + "...",
)
+ @patch("welearn_datastack.modules.pdf_extractor._send_pdf_to_tika")
@patch(
"welearn_datastack.plugins.rest_requesters.hal.HAL_URL_BASE",
"https://example.org/",
)
@patch("requests.Session.get")
- def test__convert_json_dict_to_welearndoc_mode_pdf(self, mock_get):
+ def test__convert_json_dict_to_welearndoc_mode_pdf(
+ self, mock_get, mock_send_pdf_to_tika
+ ):
class MockResponse:
def __init__(self, status_code):
self.content = (
@@ -144,6 +147,9 @@ def __init__(self, status_code):
def raise_for_status(self):
pass
+ mock_send_pdf_to_tika.return_value = {
+ "X-TIKA:content": "For primary vpiRNAs that are produced from the abundant
"
+ }
mock_get.side_effect = [MockResponse(200)]
os.environ["PDF_SIZE_PAGE_LIMIT"] = "100000"
doc0 = self.content_json["response"]["docs"][0]
diff --git a/tests/document_collector_hub/plugins_test/test_oapen.py b/tests/document_collector_hub/plugins_test/test_oapen.py
index fe1fdd3..8a9587d 100644
--- a/tests/document_collector_hub/plugins_test/test_oapen.py
+++ b/tests/document_collector_hub/plugins_test/test_oapen.py
@@ -80,8 +80,9 @@ def test_get_oapen_url_from_handle_id(self):
"https://library.oapen.org/handle/20.500.12657/12345",
)
+ @patch("welearn_datastack.modules.pdf_extractor._send_pdf_to_tika")
@patch("welearn_datastack.plugins.rest_requesters.oapen.get_new_https_session")
- def test_get_pdf_content(self, mock_get_new_https_session):
+ def test_get_pdf_content(self, mock_get_new_https_session, mock_send_pdf_to_tika):
class MockResponse:
def __init__(self, status_code):
self.content = (
@@ -96,6 +97,9 @@ def raise_for_status(self):
pass
os.environ["PDF_SIZE_PAGE_LIMIT"] = "100000"
+ mock_send_pdf_to_tika.return_value = {
+ "X-TIKA:content": "For primary vpiRNAs that are produced from the abundant
"
+ }
mock_response = MockResponse(200)
mock_get_new_https_session.return_value.get.return_value = mock_response
diff --git a/tests/document_collector_hub/plugins_test/test_open_alex.py b/tests/document_collector_hub/plugins_test/test_open_alex.py
index b965b82..1d24ddb 100644
--- a/tests/document_collector_hub/plugins_test/test_open_alex.py
+++ b/tests/document_collector_hub/plugins_test/test_open_alex.py
@@ -72,8 +72,9 @@ def test__generate_api_query_params(self):
tested_query,
)
+ @patch("welearn_datastack.modules.pdf_extractor._send_pdf_to_tika")
@patch("welearn_datastack.plugins.rest_requesters.open_alex.get_new_https_session")
- def test__get_pdf_content(self, http_session_mock):
+ def test__get_pdf_content(self, http_session_mock, mock_send_pdf_to_tika):
mock_session = Mock()
http_session_mock.return_value = mock_session
@@ -81,7 +82,9 @@ def test__get_pdf_content(self, http_session_mock):
mock_session.get.return_value = MockResponse(
status_code=200, content=self.pdf.read_bytes()
)
-
+ mock_send_pdf_to_tika.return_value = {
+ "X-TIKA:content": "2.2. Measurements of Fiber Parameters Small pieces were extracted from various positions on the strip. and mechanical properties to provide additional information regarding these areas of study and growth conditions.
"
+ }
tested_result = self.openalexColector._get_pdf_content("https://example.org/1")
self.assertTrue(
tested_result.startswith(
diff --git a/tests/document_collector_hub/test_pdf_extractor.py b/tests/document_collector_hub/test_pdf_extractor.py
index e05e0a3..3a2ae36 100644
--- a/tests/document_collector_hub/test_pdf_extractor.py
+++ b/tests/document_collector_hub/test_pdf_extractor.py
@@ -1,24 +1,16 @@
+import io
import unittest
-from pathlib import Path
+from unittest.mock import MagicMock, patch
-from pypdf import PdfReader
-
-from welearn_datastack.data.enumerations import DeletePart
from welearn_datastack.modules import pdf_extractor
+from welearn_datastack.modules.pdf_extractor import (
+ _parse_tika_content,
+ _send_pdf_to_tika,
+ extract_txt_from_pdf_with_tika,
+)
class TestPDFExtractor(unittest.TestCase):
- def setUp(self):
- resources_fp = (
- Path(__file__).parent / "resources" / "file_plugin_input" / "hal_pdf.pdf"
- )
-
- self.reader = PdfReader(resources_fp)
-
- def test_extract_txt_from_pdf(self):
- pdf_content = pdf_extractor.extract_txt_from_pdf(self.reader)
- self.assertEqual(len(pdf_content), len(self.reader.pages))
-
def test_replace_ligatures(self):
text = "first flight"
cleaned_text = pdf_extractor.replace_ligatures(text)
@@ -34,12 +26,67 @@ def test_remove_hyphens(self):
cleaned_text = pdf_extractor.remove_hyphens(text)
self.assertEqual(cleaned_text, "wellknown\n")
- def test_check_page_size_positive(self):
- ret = pdf_extractor.large_pages_size_flag(self.reader, 10000)
- self.assertEqual(len(ret[0]), len(self.reader.pages))
- self.assertTrue(ret[1])
+ @patch("welearn_datastack.modules.pdf_extractor.get_new_https_session")
+ def test_send_pdf_to_tika(self, mock_get_session):
+ # Mock de la session HTTP
+ mock_session = MagicMock()
+ mock_response = MagicMock()
+ mock_response.json.return_value = {
+ "X-TIKA:content": "Mock Content"
+ }
+ mock_response.raise_for_status.return_value = None
+ mock_session.put.return_value = mock_response
+ mock_get_session.return_value.__enter__.return_value = mock_session
+
+ # Appel de la méthode
+ pdf_content = io.BytesIO(b"Mock PDF content")
+ tika_base_url = "http://mock-tika-url"
+ result = _send_pdf_to_tika(pdf_content, tika_base_url)
+
+ # Assertions
+ mock_session.put.assert_called_once_with(
+ url=f"{tika_base_url}/tika",
+ files={"file": pdf_content},
+ headers={
+ "Accept": "application/json",
+ "Content-type": "application/octet-stream",
+ "X-Tika-PDFOcrStrategy": "no_ocr",
+ },
+ )
+ self.assertEqual(result, {"X-TIKA:content": "Mock Content"})
- def test_check_page_size_negative(self):
- ret = pdf_extractor.large_pages_size_flag(self.reader, 100000)
- self.assertEqual(len(ret[0]), len(self.reader.pages))
- self.assertFalse(ret[1])
+ def test_parse_tika_content(self):
+ tika_content = {
+ "X-TIKA:content": """
+
+ Page 1 content
+ Page 2 content
+
+ """
+ }
+
+ result = _parse_tika_content(tika_content)
+
+ expected_result = [["Page 1 content"], ["Page 2 content"]]
+ self.assertEqual(result, expected_result)
+
+ @patch("welearn_datastack.modules.pdf_extractor._send_pdf_to_tika")
+ @patch("welearn_datastack.modules.pdf_extractor._parse_tika_content")
+ def test_extract_txt_from_pdf_with_tika(
+ self, mock_parse_tika_content, mock_send_pdf_to_tika
+ ):
+ pdf_content = io.BytesIO(b"%PDF-1.4 simulated content")
+ tika_base_url = "http://localhost:9998"
+
+ mock_send_pdf_to_tika.return_value = {
+ "X-TIKA:content": "Page 1 content
"
+ }
+ mock_parse_tika_content.return_value = [["Page 1 content"]]
+
+ result = extract_txt_from_pdf_with_tika(pdf_content, tika_base_url)
+
+ self.assertEqual(result, [["Page 1 content"]])
+ mock_send_pdf_to_tika.assert_called_once_with(pdf_content, tika_base_url)
+ mock_parse_tika_content.assert_called_once_with(
+ mock_send_pdf_to_tika.return_value
+ )
diff --git a/welearn_datastack/modules/pdf_extractor.py b/welearn_datastack/modules/pdf_extractor.py
index 39737dc..52dc46c 100644
--- a/welearn_datastack/modules/pdf_extractor.py
+++ b/welearn_datastack/modules/pdf_extractor.py
@@ -1,49 +1,69 @@
+import io
import logging
-from typing import List, Tuple
+import re
+from typing import List
-from pypdf import PdfReader
+from bs4 import BeautifulSoup
from refinedoc.refined_document import RefinedDocument
+from welearn_datastack.utils_.http_client_utils import get_new_https_session
+
logger = logging.getLogger(__name__)
-def large_pages_size_flag(reader: PdfReader, limit: int) -> Tuple[List[int], bool]:
+def _send_pdf_to_tika(pdf_content: io.BytesIO, tika_base_url: str) -> dict:
+ """
+ Send a PDF document to Tika micro service and return the content as a dictionary
+ :param pdf_content: the PDF document content as a byte stream
+ :param tika_base_url: the base URL of the Tika micro service
+ :return: the content returned by Tika micro service as a dictionary (JSON)
+ """
+ tika_base_url = re.sub(r"\/$", "", tika_base_url)
+ pdf_process_addr = f"{tika_base_url}/tika"
+ local_headers = {
+ "Accept": "application/json",
+ "Content-type": "application/octet-stream",
+ "X-Tika-PDFOcrStrategy": "no_ocr",
+ }
+
+ with get_new_https_session() as http_session:
+ resp = http_session.put(
+ url=pdf_process_addr,
+ files={"file": pdf_content},
+ headers=local_headers,
+ )
+ resp.raise_for_status()
+ tika_content = resp.json()
+ return tika_content
+
+
+def _parse_tika_content(tika_content: dict) -> list[list[str]]:
"""
- Check the size of a PDF document page
- :param limit: In byte, limit the pdf need to not exceed
- :param reader: The PDF document already opened. Each page gonna be processed.
- :return: List of sizes for each page (index in the list equal index in pdf) and if one of this exceed limit
+ Parse the content returned by Tika micro service
+ :param tika_content: the content returned by Tika micro service
+ :return: the parsed content as a list of list of strings (one list per page
"""
- logger.info(f"Size limit for each page : {limit}")
- ret = []
- number_of_pages = len(reader.pages)
- logger.info(f"Test size of {number_of_pages} pages")
- flag = False
- for i in range(number_of_pages):
- page = reader.pages[i]
- page_size = len(page.get_contents().get_data()) # type: ignore
- ret.append(page_size)
- if page_size > limit:
- flag = True
+ htmlx = tika_content.get("X-TIKA:content")
+ soup = BeautifulSoup(htmlx, features="html.parser")
+ pages = soup.find_all("div", {"class": "page"})
+ res = [p.split("\n") for p in [page.get_text() for page in pages]]
- return ret, flag
+ return res
-def extract_txt_from_pdf(
- reader: PdfReader, remove_headers: bool = True, remove_footers: bool = True
+def extract_txt_from_pdf_with_tika(
+ pdf_content: io.BytesIO, tika_base_url: str
) -> List[List[str]]:
"""
Extract the text from a PDF document and return it as a list of strings for each page of the document and a list of
- strings for each page for a filtered document and the reference document (extracted with PyPDF)
+ strings for each page for a filtered document and the reference document (extracted with tika micro service)
- :param reader: the PDF reader object
- :return: a tuple containing the extracted & filtered text
+ :param pdf_content: the PDF document content as a byte stream
+ :param tika_base_url: the base URL of the Tika micro service
+ :return: Matrix of strings (list of list of strings) for each page of the document
"""
- pdf_content: List[List[str]] = []
- for page in reader.pages:
- text = page.extract_text().split("\n")
- page_content = [t.strip() for t in text if t.strip()]
- pdf_content.append(page_content)
+ tika_content = _send_pdf_to_tika(pdf_content, tika_base_url)
+ pdf_content = _parse_tika_content(tika_content)
refined_pdf_content = RefinedDocument(content=pdf_content)
diff --git a/welearn_datastack/plugins/rest_requesters/hal.py b/welearn_datastack/plugins/rest_requesters/hal.py
index f89fdd7..c09c8bf 100644
--- a/welearn_datastack/plugins/rest_requesters/hal.py
+++ b/welearn_datastack/plugins/rest_requesters/hal.py
@@ -5,23 +5,24 @@
from itertools import batched
from typing import Any, Iterable, List, Tuple
-from pypdf import PdfReader
from urllib3 import Retry
from welearn_datastack.constants import AUTHORIZED_LICENSES, HAL_URL_BASE
from welearn_datastack.data.scraped_welearn_document import ScrapedWeLearnDocument
-from welearn_datastack.exceptions import NoContent, PDFPagesSizeExceedLimit
+from welearn_datastack.exceptions import NoContent
from welearn_datastack.modules.pdf_extractor import (
delete_accents,
delete_non_printable_character,
- extract_txt_from_pdf,
- large_pages_size_flag,
+ extract_txt_from_pdf_with_tika,
remove_hyphens,
replace_ligatures,
)
from welearn_datastack.plugins.interface import IPluginRESTCollector
from welearn_datastack.utils_.http_client_utils import get_new_https_session
-from welearn_datastack.utils_.scraping_utils import get_url_without_hal_like_versionning
+from welearn_datastack.utils_.scraping_utils import (
+ get_url_without_hal_like_versionning,
+ remove_extra_whitespace,
+)
logger = logging.getLogger(__name__)
@@ -82,6 +83,7 @@ def __init__(self) -> None:
self._quantity_rows_retruned = "10000" # 30 by default, 10000 max
self.licenses = AUTHORIZED_LICENSES_WITHOUT_VERSION + LOCAL_LICENSES
self.pdf_size_page_limit: int = int(os.getenv("PDF_SIZE_PAGE_LIMIT", 100000))
+ self.tika_address = os.getenv("TIKA_ADDRESS", "http://localhost:9998")
@staticmethod
def _convert_hal_date_to_ts(hal_dt: str) -> float | None:
@@ -241,37 +243,28 @@ def _get_pdf_content(self, url: str) -> str:
response = client.get(url, headers=HEADERS)
response.raise_for_status()
- pdf_file = io.BytesIO(response.content)
-
- reader = PdfReader(pdf_file)
-
- sizes, size_flag = large_pages_size_flag(
- reader=reader, limit=self.pdf_size_page_limit
- )
-
- if size_flag:
- raise PDFPagesSizeExceedLimit(
- f"Limit is {self.pdf_size_page_limit} and pages are {sizes}"
+ with io.BytesIO(response.content) as pdf_file:
+ pdf_content = extract_txt_from_pdf_with_tika(
+ pdf_content=pdf_file, tika_base_url=self.tika_address
)
- pdf_content = extract_txt_from_pdf(reader=reader)
-
- # Delete non printable characters
- pdf_content = [
- [delete_non_printable_character(word) for word in page]
- for page in pdf_content
- ]
+ # Delete non printable characters
+ pdf_content = [
+ [delete_non_printable_character(word) for word in page]
+ for page in pdf_content
+ ]
- pages = []
- for content in pdf_content:
- page_text = " ".join(content)
- page_text = replace_ligatures(page_text)
- page_text = remove_hyphens(page_text)
- page_text = delete_accents(page_text)
+ pages = []
+ for content in pdf_content:
+ page_text = " ".join(content)
+ page_text = replace_ligatures(page_text)
+ page_text = remove_hyphens(page_text)
+ page_text = delete_accents(page_text)
- pages.append(page_text)
+ pages.append(page_text)
+ ret = remove_extra_whitespace(" ".join(pages))
- return " ".join(pages)
+ return ret
def _get_jsons(self, hal_ids: List[str]) -> List[dict]:
http = get_new_https_session()
diff --git a/welearn_datastack/plugins/rest_requesters/oapen.py b/welearn_datastack/plugins/rest_requesters/oapen.py
index 9371272..03e1d42 100644
--- a/welearn_datastack/plugins/rest_requesters/oapen.py
+++ b/welearn_datastack/plugins/rest_requesters/oapen.py
@@ -9,13 +9,11 @@
from typing import Dict, Iterable, List, Tuple
from lingua import Language
-from pypdf import PdfReader
from welearn_datastack.constants import AUTHORIZED_LICENSES, HEADERS
from welearn_datastack.data.scraped_welearn_document import ScrapedWeLearnDocument
from welearn_datastack.exceptions import (
NoDescriptionFoundError,
- PDFPagesSizeExceedLimit,
TooMuchLanguages,
UnauthorizedLicense,
WrongLangFormat,
@@ -23,19 +21,14 @@
from welearn_datastack.modules.pdf_extractor import (
delete_accents,
delete_non_printable_character,
- extract_txt_from_pdf,
- large_pages_size_flag,
+ extract_txt_from_pdf_with_tika,
remove_hyphens,
replace_ligatures,
)
from welearn_datastack.plugins.interface import IPluginRESTCollector
from welearn_datastack.utils_.http_client_utils import get_new_https_session
from welearn_datastack.utils_.scraping_utils import remove_extra_whitespace
-from welearn_datastack.utils_.text_stat_utils import (
- get_language_detector,
- predict_duration,
- predict_readability,
-)
+from welearn_datastack.utils_.text_stat_utils import get_language_detector
logger = logging.getLogger(__name__)
@@ -67,6 +60,7 @@ def __init__(self) -> None:
self.corpus_name = self.related_corpus
self.corpus_fix = True
self.pdf_size_page_limit: int = int(os.getenv("PDF_SIZE_PAGE_LIMIT", 100000))
+ self.tika_address = os.getenv("TIKA_ADDRESS", "http://localhost:9998")
@staticmethod
def _extract_oapen_ids(urls: Iterable[str]) -> List[str]:
@@ -84,32 +78,26 @@ def _get_pdf_content(self, url: str) -> str:
response = client.get(url, headers=HEADERS)
response.raise_for_status()
- pdf_file = io.BytesIO(response.content)
-
- reader = PdfReader(pdf_file)
- sizes, size_flag = large_pages_size_flag(
- reader=reader, limit=self.pdf_size_page_limit
- )
+ with io.BytesIO(response.content) as pdf_file:
+ pdf_content = extract_txt_from_pdf_with_tika(
+ pdf_content=pdf_file, tika_base_url=self.tika_address
+ )
- if size_flag:
- raise PDFPagesSizeExceedLimit()
- pdf_content = extract_txt_from_pdf(reader=reader)
-
- # Delete non printable characters
- pdf_content = [
- [delete_non_printable_character(word) for word in page]
- for page in pdf_content
- ]
-
- pages = []
- for content in pdf_content:
- page_text = " ".join(content)
- page_text = replace_ligatures(page_text)
- page_text = remove_hyphens(page_text)
- page_text = delete_accents(page_text)
-
- pages.append(page_text)
- ret = remove_extra_whitespace(" ".join(pages))
+ # Delete non printable characters
+ pdf_content = [
+ [delete_non_printable_character(word) for word in page]
+ for page in pdf_content
+ ]
+
+ pages = []
+ for content in pdf_content:
+ page_text = " ".join(content)
+ page_text = replace_ligatures(page_text)
+ page_text = remove_hyphens(page_text)
+ page_text = delete_accents(page_text)
+
+ pages.append(page_text)
+ ret = remove_extra_whitespace(" ".join(pages))
return ret
diff --git a/welearn_datastack/plugins/rest_requesters/open_alex.py b/welearn_datastack/plugins/rest_requesters/open_alex.py
index 635ed64..a6da383 100644
--- a/welearn_datastack/plugins/rest_requesters/open_alex.py
+++ b/welearn_datastack/plugins/rest_requesters/open_alex.py
@@ -5,8 +5,6 @@
from itertools import batched
from typing import Any, Dict, List, Tuple
-from pypdf import PdfReader
-
from welearn_datastack.constants import (
AUTHORIZED_LICENSES,
HEADERS,
@@ -19,25 +17,19 @@
from welearn_datastack.exceptions import (
ClosedAccessContent,
PDFFileSizeExceedLimit,
- PDFPagesSizeExceedLimit,
UnauthorizedLicense,
UnauthorizedPublisher,
)
from welearn_datastack.modules.pdf_extractor import (
delete_accents,
delete_non_printable_character,
- extract_txt_from_pdf,
- large_pages_size_flag,
+ extract_txt_from_pdf_with_tika,
remove_hyphens,
replace_ligatures,
)
from welearn_datastack.plugins.interface import IPluginRESTCollector
from welearn_datastack.utils_.http_client_utils import get_new_https_session
from welearn_datastack.utils_.scraping_utils import remove_extra_whitespace
-from welearn_datastack.utils_.text_stat_utils import (
- predict_duration,
- predict_readability,
-)
logger = logging.getLogger(__name__)
@@ -50,6 +42,7 @@ def __init__(self) -> None:
self.corpus_fix = True
self.pdf_size_page_limit: int = int(os.getenv("PDF_SIZE_PAGE_LIMIT", 100000))
self.pdf_size_file_limit: int = int(os.getenv("PDF_SIZE_FILE_LIMIT", 2000000))
+ self.tika_address = os.getenv("TIKA_ADDRESS", "http://localhost:9998")
team_email = os.getenv("TEAM_EMAIL")
if not isinstance(team_email, str):
@@ -98,16 +91,10 @@ def _get_pdf_content(self, url: str, file_size_limit: int | None = None) -> str:
response.raise_for_status()
with io.BytesIO(response.content) as pdf_file:
- reader = PdfReader(pdf_file)
- sizes, size_flag = large_pages_size_flag(
- reader=reader, limit=self.pdf_size_page_limit
+ pdf_content = extract_txt_from_pdf_with_tika(
+ pdf_content=pdf_file, tika_base_url=self.tika_address
)
- if size_flag:
- raise PDFPagesSizeExceedLimit(f"PDF page is too heavy {sizes}")
-
- pdf_content = extract_txt_from_pdf(reader=reader)
-
# Delete non printable characters
pdf_content = [
[delete_non_printable_character(word) for word in page]