information-resource-registry 0.0.0__tar.gz

information_resource_registry-0.0.0/.cruft.json

@@ -0,0 +1,27 @@
+{
+  "template": "https://github.com/linkml/linkml-project-cookiecutter",
+  "commit": "d9b85bbbdcc49163416a3e3e18e23fe2ecce501b",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "information-resource-registry",
+      "__project_slug": "information_resource_registry",
+      "github_org": "biolink",
+      "__source_path": "src/information_resource_registry/schema/information_resource_registry.yaml",
+      "project_description": "The information resource registry is a listing of data sources present in the NCATS Data Translator system.  Each information resource has an identifier, a short description, and an URL to more information about that resource.",
+      "full_name": "Sierra Moxon",
+      "email": "smoxon@lbl.gov",
+      "__author": "Sierra Moxon <smoxon@lbl.gov>",
+      "license": "Apache Software License 2.0",
+      "main_schema_class": "InformationResourceContainer",
+      "create_python_classes": "No",
+      "use_schemasheets": "No",
+      "google_sheet_id": "1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ",
+      "google_sheet_tabs": "personinfo enums",
+      "__google_sheet_module": "personinfo_enums",
+      "github_token_for_pypi_deployment": "PYPI_PASSWORD",
+      "_template": "https://github.com/linkml/linkml-project-cookiecutter"
+    }
+  },
+  "directory": null
+}

information_resource_registry-0.0.0/.env.public

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+# This file is public in git. No sensitive info allowed.
+
+###### schema definition variables, used by makefile
+
+LINKML_SCHEMA_NAME="information_resource_registry"
+LINKML_SCHEMA_AUTHOR="Sierra Moxon <smoxon@lbl.gov>"
+LINKML_SCHEMA_DESCRIPTION="The information resource registry is a listing of data sources present in the NCATS Data Translator system.  Each information resource has an identifier, a short description, and an URL to more information about that resource."
+LINKML_SCHEMA_SOURCE_PATH="src/information_resource_registry/schema/information_resource_registry.yaml"
+LINKML_SCHEMA_GOOGLE_SHEET_ID="1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ"
+LINKML_SCHEMA_GOOGLE_SHEET_TABS="personinfo enums"
+
+###### linkml generator variables, used by makefile
+
+## gen-project configuration file
+LINKML_GENERATORS_CONFIG_YAML= --config-file config.yaml
+
+## pass args if gendoc ignores config.yaml (i.e. --no-mergeimports)
+LINKML_GENERATORS_DOC_ARGS=
+
+## pass args to workaround genowl rdfs config bug (linkml#1453)
+##   (i.e. --no-type-objects --no-metaclasses --metadata-profile rdfs)
+LINKML_GENERATORS_OWL_ARGS=
+
+## pass args to trigger experimental java/typescript generation
+LINKML_GENERATORS_JAVA_ARGS=
+LINKML_GENERATORS_TYPESCRIPT_ARGS=
+

information_resource_registry-0.0.0/.github/workflows/pr-auto-standardize.yaml

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+name: Auto-standardize catalog on PR
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+    paths:
+      - 'infores_catalog.yaml'
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  standardize:
+    # Skip forks
+    if: ${{ github.event.pull_request.head.repo.full_name == github.repository }}
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout PR branch
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.pull_request.head.ref }}
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Run standardization
+        run: make standardize-data
+
+      - name: Check for changes
+        id: git-check
+        run: |
+          if git diff --quiet -- infores_catalog.yaml; then
+            echo "changed=false" >> "$GITHUB_OUTPUT"
+          else
+            echo "changed=true" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Commit and push if changed
+        if: steps.git-check.outputs.changed == 'true'
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git add infores_catalog.yaml
+          git commit -m "Auto-standardize infores_catalog.yaml"
+          git push

information_resource_registry-0.0.0/.github/workflows/pr-verify-pull-request.yaml

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+# This is a basic workflow to help you get started with Actions
+
+name: Verify Pull Request
+
+# Controls when the action will run.
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+  workflow_dispatch:
+    types: trigger-verify-pull-request
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: [ "3.10", "3.11", "3.12" ]
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v5
+        name: setup python environment
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --all-extras 
+
+      - name: Run tests, codespell, and yamllint
+        run: |
+          make test_pr
+
+      - name: Validate YAML file
+        run: yamllint -c .yamllint-config src/information_resource_registry/schema/information_resource_registry.yaml
+
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1
+        with:
+          ignore_words_list: amination,ehr,mor,nin,brite,mirgate,BRITE
+          skip: SEMMEDDB*,semmed*,.idea,.venv,.git,*.pdf,*.svg,context.*,registry.md
+

information_resource_registry-0.0.0/.github/workflows/push-main-regenerate-artifacts.yaml

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+name: Regenerate Information Resource Registry Artifacts
+
+# Controls when the action will run. Triggers the workflow on push
+# event but only for the master branch, and specifically on the information_resource_registry.yaml
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: '0 7 * * 1'  # at 07:00 UTC every Monday
+  workflow_dispatch:
+    types: trigger-build-artifacts
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Setup Python Environment
+        uses: actions/setup-python@v5
+        with:
+          # Version range or exact version of a Python version to use, using SemVer's version range syntax.
+          python-version: '3.11'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Setup build environment
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential git wget curl
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Generate Information Resource Registry Artifacts
+        run: |
+          make gen-project
+          make test_pr
+          make sankey
+          make gendoc
+          if [ $? -eq 0 ]; then
+            git config --local user.email "action@github.com"
+            git config --local user.name "GitHub Action"
+            git add project/*
+            git add src/*
+            git add infores_catalog.yaml
+            git commit -m "Regenerate artifacts from infores_catalog.yaml"
+            git push
+          else
+            echo "'make' gen-project failed to finish successfully"
+          fi

information_resource_registry-0.0.0/.github/workflows/release-deploy-docs.yaml

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+---
+name: Auto-deployment of Information Resource Registry Documentation
+
+on:
+  release:
+    types: [created]
+  workflow_dispatch:
+    types: trigger-deploy-docs
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # otherwise, you will fail to push refs to dest repo
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --extra docs
+
+      - name: Build documentation.
+        run: |
+          mkdir -p docs
+          touch docs/.nojekyll
+          make gendoc
+          ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true
+          make mkd-gh-deploy
+      
+

information_resource_registry-0.0.0/.github/workflows/release-pypi-publish.yaml

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+---
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+  workflow_dispatch:
+    types: trigger-pypi-publish
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Build source and wheel archives
+        run: uv build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.2.2
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

information_resource_registry-0.0.0/.github/workflows/release-upload-artifacts.yaml

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+---
+name: Upload Release Artifacts
+
+on:
+  release:
+    types: [created]
+  workflow_dispatch:
+
+jobs:
+  upload-artifacts:
+    name: Create and upload release artifacts
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Install jq
+        run: sudo apt-get install -y jq
+
+      - name: Generate release artifacts
+        run: make create_release_extras
+
+      - name: Upload to GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: release-output/*
+
+      - name: Upload release artifacts (for debugging)
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-artifacts
+          path: release-output/

information_resource_registry-0.0.0/.github/workflows/weekly-url-check.yaml

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+name: Check Infores Catalog Links and Regenerate Artifacts
+on:
+  schedule:
+    - cron: '0 7 * * 1'  # at 07:00 UTC every Monday
+  workflow_dispatch:
+    types: trigger-url-check
+
+
+jobs:
+  check-external-links:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3.1.0
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --all-extras 
+
+      - name: Run URL validation
+        run: |
+          make check_urls
+      
+          

information_resource_registry-0.0.0/.gitignore

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+/docs/
+/project/docs/
+/tmp/
+
+# 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
+.idea
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# uv
+.python-version
+uv.lock
+.uv/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+release-output
+
+.DS_Store
+src/docs/registry.md
+src/docs/resources/*
+

information_resource_registry-0.0.0/.linkmllint.yaml

@@ -0,0 +1,10 @@
+extends: recommended
+rules:
+  standard_naming:
+    level: disabled
+  canonical_prefixes:
+    level: disabled
+  #no_invalid_slot_usage:
+  #  level: disabled
+  recommended:
+    level: disabled

information_resource_registry-0.0.0/.yamllint-config

@@ -0,0 +1,38 @@
+---
+
+yaml-files:
+- '*.yaml'
+- '*.yml'
+- '.yamllint'
+
+rules:
+    anchors: enable
+    braces: enable
+    brackets: enable
+    colons: enable
+    commas: enable
+    comments:
+        level: warning
+    comments-indentation: disable
+    document-end: disable
+    document-start:
+        level: warning
+    empty-lines: enable
+    empty-values: disable
+    float-values: disable
+    hyphens: enable
+    indentation: enable
+    key-duplicates: enable
+    key-ordering: disable
+    line-length:
+        level: warning
+        max: 200
+        allow-non-breakable-words: true
+        allow-non-breakable-inline-mappings: false
+    new-line-at-end-of-file: enable
+    new-lines: enable
+    octal-values: disable
+    quoted-strings: disable
+    trailing-spaces: disable
+    truthy:
+        level: warning

information_resource_registry-0.0.0/CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to make participation in our project and
+our community a harassment-free experience for everyone, regardless of age,
+body size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by [contacting the project team](contact.md). All complaints will be
+reviewed and investigated and will result in a response that is deemed
+necessary and appropriate to the circumstances. The project team is obligated
+to maintain confidentiality with regard to the reporter of an incident. Further
+details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This code of conduct has been derived from the excellent code of conduct of the
+[ATOM project](https://github.com/atom/atom/blob/master/CODE_OF_CONDUCT.md)
+which in turn is adapted from the [Contributor Covenant][homepage], version
+1.4, available at [https://contributor-covenant.org/version/1/4][version]
+
+[homepage]: https://contributor-covenant.org
+[version]: https://contributor-covenant.org/version/1/4/