Initial Commit

.cruft.json

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+{
+  "template": "https://github.com/monarch-initiative/cookiecutter-monarch-ingest.git",
+  "commit": "f8680f4f40af1832b99b0acf5b700eb904ff3d71",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "github_org_name": "monarch-initiative",
+      "project_name": "mic-ingest",
+      "project_description": "Ingest for Micronutrient Information Center using OntoGPT",
+      "__repo_name": "mic-ingest",
+      "__project_slug": "mic_ingest",
+      "__project_url": "https://github.com/monarch-initiative/mic-ingest",
+      "ingest_source": "lpi",
+      "ingest_type": "chemical_to_pathway",
+      "__ingest_name": "lpi_chemical_to_pathway",
+      "min_python_version": "3.10",
+      "full_name": "Corey Cox",
+      "email": "[email protected]",
+      "__author": "Corey Cox <[email protected]>",
+      "license": "BSD-3",
+      "_template": "https://github.com/monarch-initiative/cookiecutter-monarch-ingest.git",
+      "_commit": "f8680f4f40af1832b99b0acf5b700eb904ff3d71"
+    }
+  },
+  "directory": null
+}

.github/dependabot.yaml

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+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/create-release.yaml

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+### This workflow can be run manually from Actions tab in your repository by selecting the "Create Release" workflow.
+### When your project is ready for releases, you should:
+###   - Uncomment the `schedule` section to run this workflow automatically on a schedule.
+###     - As written, this workflow will run every Sunday at midnight UTC.
+###   - Remove the `draft: true` line from the `Create Release` step to publish the release immediately.
+# TODO: QC/Validation (ex. 0 rows)
+
+name: Create Release
+
+on:
+  workflow_dispatch:
+  # schedule:
+  #   - cron: '0 0 * * 0'
+
+jobs:
+  create-release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install Dependencies
+        run: poetry install --no-interaction
+
+      - name: Run Tests
+        run: make test
+
+      - name: Run Transform
+        run: |
+          make run
+          poetry run python scripts/generate-rdf.py
+
+      - name: Get Date for Release Tag
+        run: echo "DATE=$(date +%Y-%m-%d)" >> $GITHUB_ENV
+
+      # Further customization for this action is available. See:
+      # https://github.com/softprops/action-gh-release/?tab=readme-ov-file#-customizing
+      - name: Create Release
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: ${{ env.DATE }}
+          files: |
+            output/*
+          generate_release_notes: true
+          draft: true

.github/workflows/deploy-docs.yaml

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+name: Auto-Deploy Documentation
+
+on:
+  push:
+    branches: [main]
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install Dependencies
+        run: poetry install --with dev --no-interaction
+
+      - name: Build Documentation
+        run: make docs
+
+      - name: Deploy to gh-pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: site
+          target-folder: docs
+          clean: true

.github/workflows/test.yaml

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+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  test-backend:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+        os: [ubuntu-latest]
+        #os: [ ubuntu-latest, windows-latest ]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      #----------------------------------------------
+      #          install & configure poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+      #----------------------------------------------
+      #    install your root project, if required
+      #----------------------------------------------
+      - name: Install library
+        run: poetry install --no-interaction
+
+      #----------------------------------------------
+      #              run pytest
+      #----------------------------------------------
+      - name: Run tests
+        run: poetry run pytest tests
+

.github/workflows/update-docs.yaml

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+# This GitHub Action updates the documentation with information about the latest KG build/release.
+
+name: Update Documentation
+
+on:
+  workflow_dispatch:
+  workflow_run:
+    workflows: ["Create Release"]
+    types:
+      - completed
+
+jobs:
+  update-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install Dependencies
+        run: |
+          poetry install --with dev --no-interaction
+
+      - name: Build Documentation
+        run: |
+          poetry run python scripts/get-latest-report.py
+          make docs
+
+      - name: Deploy to gh-pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: site
+          target-folder: docs
+          clean: true

.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/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+*-env/
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# data input and ouptut
+data/
+output/
+test-output/
+
+#IDE stuff
+.idea/
+
+#MacOS DS Store
+.DS_STORE
+
+# Transform logs
+logs/

CONTRIBUTING.md

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+# Contribution Guidelines
+
+When contributing to this repository, please first discuss the changes you wish to make via an issue, email, or any other method, with the owners of this repository before issuing a pull request.
+
+## How to contribute
+
+### Reporting bugs or making feature requests
+
+To report a bug or suggest a new feature, please go to the [monarch-initiative/mic-ingest issue tracker](https://github.com/monarch-initiative/mic-ingest/issues), as we consolidate issues there.
+
+Please supply enough details to the developers to enable them to verify and troubleshoot your issue:
+
+* Provide a clear and descriptive title as well as a concise summary of the issue to identify the problem.
+* Describe the exact steps which reproduce the problem in as many details as possible.
+* Describe the behavior you observed after following the steps and point out what exactly is the problem with that behavior.
+* Explain which behavior you expected to see instead and why.
+* Provide screenshots of the expected or actual behaviour where applicable.
+
+
+### The development lifecycle
+
+1. Create a bug fix or feature development branch, based off the `main` branch of the upstream repo, and not your fork. Name the branch appropriately, briefly summarizing the bug fix or feature request. If none come to mind, you can include the issue number in the branch name. Some examples of branch names are, `bugfix/breaking-pipfile-error` or `feature/add-click-cli-layer`, or `bugfix/issue-414`
+2. Make sure your development branch has all the latest commits from the `main` branch.
+3. After completing work and testing locally, push the code to the appropriate branch on your fork or origin repository.
+4. Create a pull request from the bug/feature branch of your fork to the `main` branch of the upstream repository.
+
+**NOTE**: All the development must be done on a separate branch, either in your fork or in the origin repository. The `main` branch of the upstream repository should never be used for development.
+
+**ALSO NOTE**: github.com lets you create a pull request from the main branch, automating the steps above.
+
+> A code review (which happens with both the contributor and the reviewer present) is required for contributing.