AUMCdb-MEDS 0.0.1__tar.gz

aumcdb_meds-0.0.1/.github/workflows/code-quality-main.yaml

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+# Same as `code-quality-pr.yaml` but triggered on commit to main branch
+# and runs on all files (instead of only the changed ones)
+
+name: Code Quality Main
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install packages
+        run: |
+          pip install .[dev]
+
+      - name: Run pre-commits
+        uses: pre-commit/action@v3.0.1

aumcdb_meds-0.0.1/.github/workflows/code-quality-pr.yaml

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+# This workflow finds which files were changed, prints them,
+# and runs `pre-commit` on those files.
+
+# Inspired by the sktime library:
+# https://github.com/alan-turing-institute/sktime/blob/main/.github/workflows/test.yml
+
+name: Code Quality PR
+
+on:
+  pull_request:
+    branches: [main, "release/*", "dev"]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install packages
+        run: |
+          pip install .[dev]
+
+      - name: Find modified files
+        id: file_changes
+        uses: trilom/file-changes-action@v1.2.4
+        with:
+          output: " "
+
+      - name: List modified files
+        run: echo '${{ steps.file_changes.outputs.files}}'
+
+      - name: Run pre-commits
+        uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --files ${{ steps.file_changes.outputs.files}}

aumcdb_meds-0.0.1/.github/workflows/python-build.yaml

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+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install pypa/build
+        run: >-
+          python3 -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: python3 -m build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/MEDS-transforms # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+      - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write # IMPORTANT: mandatory for sigstore
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Sign the dists with Sigstore
+        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release create
+          '${{ github.ref_name }}'
+          --repo '${{ github.repository }}'
+          --notes ""
+      - name: Upload artifact signatures to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        # Upload to GitHub Release using the `gh` CLI.
+        # `dist/` contains the built packages, and the
+        # sigstore-produced signatures and certificates.
+        run: >-
+          gh release upload
+          '${{ github.ref_name }}' dist/**
+          --repo '${{ github.repository }}'

aumcdb_meds-0.0.1/.github/workflows/tests.yaml

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+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, "release/*", "dev"]
+
+jobs:
+  run_tests_ubuntu:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+      fail-fast: false
+
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install packages
+        run: |
+          pip install -e .[tests]
+
+      #----------------------------------------------
+      #              run test suite
+      #----------------------------------------------
+      - name: Run tests
+        run: |
+          pytest src/ tests/ -v --cov=src --junitxml=junit.xml -s
+
+#      - name: Upload coverage to Codecov
+#        uses: codecov/codecov-action@v4.0.1
+#        with:
+#          token: ${{ secrets.CODECOV_TOKEN }}
+#      - name: Upload test results to Codecov
+#        if: ${{ !cancelled() }}
+#        uses: codecov/test-results-action@v1
+#        with:
+#          token: ${{ secrets.CODECOV_TOKEN }}

aumcdb_meds-0.0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

aumcdb_meds-0.0.1/.pre-commit-config.yaml

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+default_language_version:
+  python: python3.12
+
+exclude: "docs/index.md|MIMIC-IV_Example/README.md|eICU_Example/README.md|AUMCdb_Example/README.md"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      # list of supported hooks: https://pre-commit.com/hooks.html
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-yaml
+      - id: debug-statements
+      - id: detect-private-key
+      - id: check-executables-have-shebangs
+      - id: check-toml
+      - id: check-case-conflict
+      - id: check-added-large-files
+        args: [--maxkb, "800"]
+
+  # python code formatting
+  - repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+      - id: black
+        args: [--line-length, "110"]
+
+  # python import sorting
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files", "-o", "wandb"]
+
+  - repo: https://github.com/PyCQA/autoflake
+    rev: v2.3.1
+    hooks:
+      - id: autoflake
+        args: [--in-place, --remove-all-unused-imports]
+
+  # python upgrading syntax to newer version
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.19.0
+    hooks:
+      - id: pyupgrade
+        args: [--py311-plus]
+
+  # python docstring formatting
+  #  - repo: https://github.com/myint/docformatter
+  #    rev: v1.7.5
+  #    hooks:
+  #      - id: docformatter
+  #        args: [--in-place, --wrap-summaries=110, --wrap-descriptions=110]
+
+  # python check (PEP8), programming errors and code complexity
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.1.1
+    hooks:
+      - id: flake8
+        args:
+          [
+            "--max-complexity=10",
+            "--extend-ignore",
+            "E402,E701,E251,E226,E302,W504,E704,E402,E401,C901,E203",
+            "--max-line-length=110",
+            "--exclude",
+            "logs/*,data/*",
+            "--per-file-ignores",
+            "__init__.py:F401",
+          ]
+
+  # yaml formatting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types: [yaml]
+        exclude: "environment.yaml"
+
+  # shell scripts linter
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+      - id: shellcheck
+
+  # md formatting
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.18
+    hooks:
+      - id: mdformat
+        args: ["--number"]
+        additional_dependencies:
+          - mdformat-gfm
+          - mdformat-tables
+          - mdformat_frontmatter
+          - mdformat-black
+          - mdformat-config
+          - mdformat-shfmt
+          - mdformat-mkdocs
+          - mdformat-toc
+          - mdformat-admon
+
+  # word spelling linter
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args:
+          - --skip=logs/**,data/**,*.ipynb,*.bib,env.yml,env_cpu.yml,*.svg,poetry.lock
+          - --ignore-words-list=ehr,crate
+
+  # jupyter notebook cell output clearing
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+
+  # jupyter notebook linting
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.8.7
+    hooks:
+      - id: nbqa-black
+        args: ["--line-length=110"]
+      - id: nbqa-isort
+        args: ["--profile=black"]
+      - id: nbqa-flake8
+        args:
+          [
+            "--extend-ignore=E203,E402,E501,F401,F841",
+            "--exclude=logs/*,data/*",
+          ]

aumcdb_meds-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Matthew McDermott
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

aumcdb_meds-0.0.1/PKG-INFO

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+Metadata-Version: 2.2
+Name: AUMCdb-MEDS
+Version: 0.0.1
+Summary: A template ETL pipeline to extract AUMCdb data into the MEDS format.
+Author-email: Patrick Rockenschaub <rockenschaub.patrick@gmail.com>
+Project-URL: Homepage, https://github.com/prockenschaub/AUMCdb_MEDS
+Project-URL: Issues, https://github.com/prockenschaub/AUMCdb_MEDS/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: meds-transforms>=0.1
+Requires-Dist: hydra-core
+Provides-Extra: dev
+Requires-Dist: pre-commit<4; extra == "dev"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Provides-Extra: local-parallelism
+Requires-Dist: hydra-joblib-launcher; extra == "local-parallelism"
+Provides-Extra: slurm-parallelism
+Requires-Dist: hydra-submitit-launcher; extra == "slurm-parallelism"
+
+# AUMCdb MEDS Extraction ETL
+
+This pipeline extracts the AUMCdb dataset into MEDS format. The AUMCdb dataset is a publicly available dataset from the
+Amsterdam University Medical Centers (AUMC) that contains clinical data from the hospital. You first need to request
+access [here](https://lifesciences.datastations.nl/dataset.xhtml?persistentId=doi:10.17026/dans-22u-f8vd).
+
+## Usage:
+
+```
+pip install AUMCdb_MEDS
+MEDS_extract-AUMCdb input_dir=$RAW_DATA_DIR output_dir=$MEDS_DIR
+```
+
+If you want, you can also use the `do_download` flag to download the data directly from the AUMCdb repository.
+You need to set the `AUMCDB_API_KEY` environment variable to your API key.
+Please get it from
+here: [AUMCdb API Key](https://lifesciences.datastations.nl/dataverseuser.xhtml?selectTab=dataRelatedToMe)
+
+```
+export AUMCDB_API_KEY=your_api_key
+MEDS_extract-AUMCdb input_dir=$RAW_DATA_DIR output_dir=$MEDS_DIR
+```
+
+This will download the dataset automatically for you.

aumcdb_meds-0.0.1/README.md

@@ -0,0 +1,24 @@
+# AUMCdb MEDS Extraction ETL
+
+This pipeline extracts the AUMCdb dataset into MEDS format. The AUMCdb dataset is a publicly available dataset from the
+Amsterdam University Medical Centers (AUMC) that contains clinical data from the hospital. You first need to request
+access [here](https://lifesciences.datastations.nl/dataset.xhtml?persistentId=doi:10.17026/dans-22u-f8vd).
+
+## Usage:
+
+```
+pip install AUMCdb_MEDS
+MEDS_extract-AUMCdb input_dir=$RAW_DATA_DIR output_dir=$MEDS_DIR
+```
+
+If you want, you can also use the `do_download` flag to download the data directly from the AUMCdb repository.
+You need to set the `AUMCDB_API_KEY` environment variable to your API key.
+Please get it from
+here: [AUMCdb API Key](https://lifesciences.datastations.nl/dataverseuser.xhtml?selectTab=dataRelatedToMe)
+
+```
+export AUMCDB_API_KEY=your_api_key
+MEDS_extract-AUMCdb input_dir=$RAW_DATA_DIR output_dir=$MEDS_DIR
+```
+
+This will download the dataset automatically for you.

aumcdb_meds-0.0.1/pyproject.toml

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+[build-system]
+requires = ["setuptools>=64", "setuptools-scm>=8.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "AUMCdb-MEDS"
+dynamic = ["version"]
+authors = [
+  { name="Patrick Rockenschaub", email="rockenschaub.patrick@gmail.com" },
+]
+description = "A template ETL pipeline to extract AUMCdb data into the MEDS format."
+readme = "README.md"
+requires-python = ">=3.11"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+  "meds-transforms>=0.1", "hydra-core"
+]
+
+[tool.setuptools_scm]
+
+[project.optional-dependencies]
+dev = ["pre-commit<4"]
+tests = ["pytest", "pytest-cov"]
+local_parallelism = ["hydra-joblib-launcher"]
+slurm_parallelism = ["hydra-submitit-launcher"]
+
+[project.scripts]
+MEDS_extract-AUMCdb = "AUMCdb_MEDS.__main__:main"
+
+[project.urls]
+Homepage = "https://github.com/prockenschaub/AUMCdb_MEDS"
+Issues = "https://github.com/prockenschaub/AUMCdb_MEDS/issues"

aumcdb_meds-0.0.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

aumcdb_meds-0.0.1/src/AUMCdb_MEDS/__init__.py

@@ -0,0 +1,38 @@
+from importlib.metadata import PackageNotFoundError, version
+from importlib.resources import files
+
+from omegaconf import OmegaConf
+
+__package_name__ = "AUMCdb_MEDS"
+try:
+    __version__ = version(__package_name__)
+except PackageNotFoundError:  # pragma: no cover
+    __version__ = "unknown"
+
+MAIN_CFG = files(__package_name__).joinpath("configs/main.yaml")
+EVENT_CFG = files(__package_name__).joinpath("configs/event_configs.yaml")
+ETL_CFG = files(__package_name__).joinpath("configs/ETL.yaml")
+RUNNER_CFG = files(__package_name__).joinpath("configs/runner.yaml")
+PRE_MEDS_PY = files(__package_name__).joinpath("pre_MEDS.py")
+PRE_MEDS_CFG = files(__package_name__).joinpath("configs/pre_MEDS.yaml")
+DATASET_CFG = files(__package_name__).joinpath("dataset.yaml")
+
+dataset_info = OmegaConf.load(DATASET_CFG)
+
+HAS_PRE_MEDS = PRE_MEDS_PY.exists()
+
+event_config = OmegaConf.load(EVENT_CFG)
+
+__all__ = [
+    "event_config",
+    "EVENT_CFG",
+    "ETL_CFG",
+    "HAS_PRE_MEDS",
+    "PRE_MEDS_CFG",
+    "MAIN_CFG",
+    "RUNNER_CFG",
+    "DATASET_CFG",
+    "dataset_info",
+    "__package_name__",
+    "__version__",
+]