pylantir 0.0.9__tar.gz → 0.1.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- pylantir-0.1.1/.devcontainer/Dockerfile +12 -0
- pylantir-0.1.1/.devcontainer/devcontainer.json +44 -0
- pylantir-0.1.1/.github/dependabot.yml +22 -0
- pylantir-0.1.1/.github/template-sync.yml +21 -0
- pylantir-0.1.1/.github/workflows/CI.yml +21 -0
- pylantir-0.1.1/.github/workflows/publish.yml +33 -0
- pylantir-0.1.1/.github/workflows/schedule-update-actions.yml +25 -0
- pylantir-0.1.1/.github/workflows/semantic-pr-check.yml +17 -0
- pylantir-0.1.1/.github/workflows/sphinx.yml +18 -0
- pylantir-0.1.1/.github/workflows/template-sync.yml +12 -0
- pylantir-0.1.1/.gitignore +129 -0
- pylantir-0.1.1/.pre-commit-config.yaml +60 -0
- pylantir-0.1.1/.pypirc +10 -0
- pylantir-0.1.1/.vscode/launch.json +19 -0
- pylantir-0.1.1/.vscode/settings.json +29 -0
- pylantir-0.1.1/CODE_OF_CONDUCT.md +9 -0
- {pylantir-0.0.9 → pylantir-0.1.1}/PKG-INFO +16 -6
- {pylantir-0.0.9 → pylantir-0.1.1}/README.md +15 -5
- pylantir-0.1.1/SECURITY.md +41 -0
- pylantir-0.1.1/SUPPORT.md +25 -0
- pylantir-0.1.1/docs/Makefile +20 -0
- pylantir-0.1.1/docs/conf.py +67 -0
- pylantir-0.1.1/docs/devcontainer.md +16 -0
- pylantir-0.1.1/docs/developer.md +3 -0
- pylantir-0.1.1/docs/index.rst +20 -0
- pylantir-0.1.1/docs/make.bat +35 -0
- pylantir-0.1.1/docs/modules.rst +7 -0
- pylantir-0.1.1/docs/pre-commit-config.md +6 -0
- pylantir-0.1.1/docs/pylint.md +507 -0
- pylantir-0.1.1/docs/pyproject.md +9 -0
- pylantir-0.1.1/docs/python_package.hello_world.rst +21 -0
- pylantir-0.1.1/docs/python_package.rst +29 -0
- pylantir-0.1.1/docs/requirements.txt +3 -0
- pylantir-0.1.1/docs/vscode.md +1 -0
- pylantir-0.1.1/docs/workflows.md +4 -0
- pylantir-0.1.1/pylantir.png +0 -0
- {pylantir-0.0.9 → pylantir-0.1.1}/pyproject.toml +1 -1
- pylantir-0.1.1/src/README.md +1 -0
- {pylantir-0.0.9 → pylantir-0.1.1}/src/pylantir/__init__.py +1 -1
- {pylantir-0.0.9 → pylantir-0.1.1}/src/pylantir/cli/run.py +4 -1
- {pylantir-0.0.9 → pylantir-0.1.1}/src/pylantir/config/mwl_config.json +12 -2
- {pylantir-0.0.9 → pylantir-0.1.1}/src/pylantir/redcap_to_db.py +88 -18
- pylantir-0.1.1/tests/client.py +63 -0
- pylantir-0.1.1/tests/client2.py +46 -0
- pylantir-0.1.1/tests/conftest.py +30 -0
- pylantir-0.1.1/tests/mpps_tester.py +147 -0
- pylantir-0.1.1/tests/query_db.py +44 -0
- pylantir-0.1.1/tests/test_methods.py +32 -0
- pylantir-0.0.9/src/pylantir/.env +0 -2
- {pylantir-0.0.9 → pylantir-0.1.1}/LICENSE +0 -0
- {pylantir-0.0.9 → pylantir-0.1.1}/src/pylantir/cli/__init__.py +0 -0
- {pylantir-0.0.9 → pylantir-0.1.1}/src/pylantir/db_setup.py +0 -0
- {pylantir-0.0.9 → pylantir-0.1.1}/src/pylantir/models.py +0 -0
- {pylantir-0.0.9 → pylantir-0.1.1}/src/pylantir/mwl_server.py +0 -0
- {pylantir-0.0.9 → pylantir-0.1.1}/src/pylantir/populate_db.py +0 -0
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FROM mcr.microsoft.com/devcontainers/python:3
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RUN python -m pip install --upgrade pip \
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&& python -m pip install 'flit>=3.8.0'
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ENV FLIT_ROOT_INSTALL=1
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COPY pyproject.toml .
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RUN touch README.md \
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&& mkdir -p src/python_package \
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&& python -m flit install --only-deps --deps develop \
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&& rm -r pyproject.toml README.md src
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// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
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// https://github.com/microsoft/vscode-dev-containers/tree/v0.222.0/containers/python-3-miniconda
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{
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"name": "Python Environment",
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"build": {
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"dockerfile": "Dockerfile",
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"context": ".."
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},
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"customizations": {
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"vscode": {
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"extensions": [
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"editorconfig.editorconfig",
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"github.vscode-pull-request-github",
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"ms-azuretools.vscode-docker",
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"ms-python.python",
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"ms-python.vscode-pylance",
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"ms-python.pylint",
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"ms-python.isort",
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"ms-python.flake8",
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"ms-python.black-formatter",
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"ms-vsliveshare.vsliveshare",
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"ryanluker.vscode-coverage-gutters",
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"bungcip.better-toml",
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"GitHub.copilot"
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],
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"settings": {
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"python.defaultInterpreterPath": "/usr/local/bin/python",
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"black-formatter.path": [
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"/usr/local/py-utils/bin/black"
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],
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"pylint.path": [
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"/usr/local/py-utils/bin/pylint"
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],
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"flake8.path": [
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"/usr/local/py-utils/bin/flake8"
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],
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"isort.path": [
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"/usr/local/py-utils/bin/isort"
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]
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}
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}
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},
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"onCreateCommand": "pre-commit install-hooks"
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}
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version: 2
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updates:
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- package-ecosystem: pip
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directory: "/"
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schedule:
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interval: daily
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time: "13:00"
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open-pull-requests-limit: 10
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reviewers:
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- dciborow
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allow:
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- dependency-type: indirect
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commit-message:
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prefix: "fix: "
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: daily
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commit-message:
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prefix: "fix: "
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files:
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- ".gitignore" # include
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- ".github"
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- ".vscode"
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- "tests/conftest.py"
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- ".flake8"
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- ".pre-commit-config.yml"
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- ".pypirc"
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- "docs"
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- "src/README.md"
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- "CODE_OF_CONDUCT.md"
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- "LICENSE"
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- "SECURITY.md"
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- "SUPPORT.md"
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- "pyproject.toml"
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- "!.github/workflows/template-sync.yml"
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- "!.github/template-sync.yml"
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- "!src/python_project"
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- "!tests/test_methods.py"
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name: Python CI
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on:
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push:
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branches: [ main ]
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pull_request:
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release:
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types: [created]
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validation:
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uses: microsoft/action-python/.github/workflows/validation.yml@0.6.4
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with:
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workdir: '.'
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publish:
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uses: microsoft/action-python/.github/workflows/publish.yml@0.6.4
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secrets:
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PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
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TEST_PYPI_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
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name: Publish Python Package
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on:
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tags:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install build tools
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run: |
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run: twine upload dist/*
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name: GitHub Actions Version Updater
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# Controls when the action will run.
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on:
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name: Deploy Sphinx documentation to Pages
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# Byte-compiled / optimized / DLL files
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# Distribution / packaging
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.Python
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build/
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MANIFEST
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.cache
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nosetests.xml
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coverage.xml
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# Translations
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ci:
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autoupdate_commit_msg: "chore: update pre-commit hooks"
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autofix_commit_msg: "style: pre-commit fixes"
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.1.0
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hooks:
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- id: check-added-large-files
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- id: check-case-conflict
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- id: check-merge-conflict
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- id: check-yaml
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- id: debug-statements
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- id: trailing-whitespace
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- repo: https://github.com/PyCQA/isort
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rev: 5.12.0
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hooks:
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args: ["-a", "from __future__ import annotations"]
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- repo: https://github.com/asottile/pyupgrade
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rev: v2.31.0
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hooks:
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- id: pyupgrade
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args: [--py37-plus]
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- repo: https://github.com/hadialqattan/pycln
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|
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rev: v1.2.5
|
|
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hooks:
|
|
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- id: pycln
|
|
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args: [--config=pyproject.toml]
|
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stages: [manual]
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- repo: https://github.com/codespell-project/codespell
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rev: v2.1.0
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hooks:
|
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- id: codespell
|
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|
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- repo: https://github.com/pre-commit/pygrep-hooks
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rev: v1.9.0
|
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hooks:
|
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- id: python-check-blanket-noqa
|
|
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- id: python-check-blanket-type-ignore
|
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- id: python-no-log-warn
|
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- id: python-no-eval
|
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- id: python-use-type-annotations
|
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- id: rst-backticks
|
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- id: rst-directive-colons
|
|
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- id: rst-inline-touching-normal
|
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|
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- repo: https://github.com/mgedmin/check-manifest
|
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rev: "0.47"
|
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hooks:
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- id: check-manifest
|
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stages: [manual]
|
pylantir-0.1.1/.pypirc
ADDED
|
@@ -0,0 +1,19 @@
|
|
|
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|
+
{
|
|
2
|
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"version": "0.1.0",
|
|
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|
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"configurations": [
|
|
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|
+
{
|
|
5
|
+
"name": "Python: Debug Tests",
|
|
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|
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"type": "python",
|
|
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|
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"request": "launch",
|
|
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|
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"program": "${file}",
|
|
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|
+
"purpose": [
|
|
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|
+
"debug-test"
|
|
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|
+
],
|
|
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|
+
"console": "integratedTerminal",
|
|
13
|
+
"justMyCode": false,
|
|
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|
+
"env": {
|
|
15
|
+
"PYTEST_ADDOPTS": "--no-cov -n0 --dist no"
|
|
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|
+
}
|
|
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|
+
}
|
|
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|
+
]
|
|
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|
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}
|
|
@@ -0,0 +1,29 @@
|
|
|
1
|
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{
|
|
2
|
+
"editor.formatOnSave": true,
|
|
3
|
+
"editor.formatOnPaste": true,
|
|
4
|
+
"files.trimTrailingWhitespace": true,
|
|
5
|
+
"files.autoSave": "onFocusChange",
|
|
6
|
+
"git.autofetch": true,
|
|
7
|
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"[jsonc]": {
|
|
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|
+
"editor.defaultFormatter": "vscode.json-language-features"
|
|
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|
+
},
|
|
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|
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"[python]": {
|
|
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|
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"editor.defaultFormatter": "ms-python.black-formatter"
|
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},
|
|
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|
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|
|
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|
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"python.formatting.provider": "black",
|
|
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|
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"python.testing.unittestEnabled": false,
|
|
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"python.testing.pytestEnabled": true,
|
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"pylint.args": [
|
|
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|
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"--rcfile=pyproject.toml"
|
|
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|
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|
|
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|
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"black-formatter.args": [
|
|
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|
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"--config=pyproject.toml"
|
|
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|
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],
|
|
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|
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"flake8.args": [
|
|
24
|
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"--toml-config=pyproject.toml"
|
|
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|
+
],
|
|
26
|
+
"isort.args": [
|
|
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|
+
"--settings-path=pyproject.toml"
|
|
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|
+
]
|
|
29
|
+
}
|
|
@@ -0,0 +1,9 @@
|
|
|
1
|
+
# Microsoft Open Source Code of Conduct
|
|
2
|
+
|
|
3
|
+
This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
|
|
4
|
+
|
|
5
|
+
Resources:
|
|
6
|
+
|
|
7
|
+
- [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/)
|
|
8
|
+
- [Microsoft Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/)
|
|
9
|
+
- Contact [opencode@microsoft.com](mailto:opencode@microsoft.com) with questions or concerns
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: pylantir
|
|
3
|
-
Version: 0.
|
|
3
|
+
Version: 0.1.1
|
|
4
4
|
Summary: Python - DICOM Modality WorkList
|
|
5
5
|
Author-email: Milton Camacho <miltoncamachoicc@gmail.com>
|
|
6
6
|
Requires-Python: >=3.11.1
|
|
@@ -82,12 +82,19 @@ pylantir start --ip 127.0.0.1 --port 4242 --AEtitle MWL_SERVER --pylantir_config
|
|
|
82
82
|
|
|
83
83
|
## Tests
|
|
84
84
|
|
|
85
|
-
|
|
85
|
+
If you want to run the tests make sure to clone the repository and run them from there.
|
|
86
|
+
|
|
87
|
+
Git clone the repository:
|
|
88
|
+
|
|
89
|
+
```bash
|
|
90
|
+
git clone https://github.com/miltoncamacho/pylantir
|
|
91
|
+
cd pylantir/tests
|
|
92
|
+
```
|
|
86
93
|
|
|
87
94
|
Query the worklist database to check that you have some entries using:
|
|
88
95
|
|
|
89
96
|
```bash
|
|
90
|
-
|
|
97
|
+
python query-db.py
|
|
91
98
|
```
|
|
92
99
|
|
|
93
100
|
Then, you can get a StudyUID from one of the entries to test the MPPS workflow. For example: 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
|
|
@@ -95,19 +102,19 @@ Then, you can get a StudyUID from one of the entries to test the MPPS workflow.
|
|
|
95
102
|
Take this and run a create action to mark the worklist Procedure Step Status as IN_PROGRESS
|
|
96
103
|
|
|
97
104
|
```bash
|
|
98
|
-
|
|
105
|
+
python test-mpps.py --AEtitle MWL_SERVER --mpps_action create --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
|
|
99
106
|
```
|
|
100
107
|
|
|
101
108
|
You can verify that this in fact modified your database re-running:
|
|
102
109
|
|
|
103
110
|
```bash
|
|
104
|
-
|
|
111
|
+
python query-db.py
|
|
105
112
|
```
|
|
106
113
|
|
|
107
114
|
Finally, you can also simulate the pocedure completion efectively updating the Procedure Step Status to COMPLETED or DISCONTINUED:
|
|
108
115
|
|
|
109
116
|
```bash
|
|
110
|
-
|
|
117
|
+
python test-mpps.py --AEtitle MWL_SERVER --mpps_action set --mpps_status COMPLETED --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632 --sop_uid 1.2.840.10008.3.1.2.3.4.187176383255263644225774937658729238426
|
|
111
118
|
```
|
|
112
119
|
|
|
113
120
|
## Usage
|
|
@@ -137,6 +144,8 @@ usage: pylantir [-h] [--AEtitle AETITLE] [--ip IP] [--port PORT] [--pylantir_con
|
|
|
137
144
|
- **site**: Site ID:string
|
|
138
145
|
- **protocol**: `{"site": "protocol_name", "mapping": "HIS/RIS mapping"}`
|
|
139
146
|
- **redcap2wl**: Dictionary of REDCap fields to worklist fields mapping e.g., `{"redcap_field": "worklist_field"}`
|
|
147
|
+
- **db_update_interval**: How often to reload the database e
|
|
148
|
+
- **operation_interval**: What is the time range in a day in which the database will be updated e.g., `{"start_time":[hours,minutes],"end_time":[hours,minutes]}`
|
|
140
149
|
- **--mpps_action {create,set}**: Action to perform for MPPS either create or set
|
|
141
150
|
- **--mpps_status {COMPLETED,DISCONTINUED}**: Status to set for MPPS either COMPLETED or DISCONTINUED
|
|
142
151
|
- **--callingAEtitle CALLINGAETITLE**: Calling AE Title for MPPS, it helps when the MWL is limited to only accept certain AE titles
|
|
@@ -152,6 +161,7 @@ As a default pylantir will try to read a JSON structured file with the following
|
|
|
152
161
|
"db_path": "/path/to/worklist.db",
|
|
153
162
|
"db_echo": "False",
|
|
154
163
|
"db_update_interval": 60,
|
|
164
|
+
"operation_interval": {"start_time": [0,0],"end_time": [23,59]},
|
|
155
165
|
"allowed_aet": [],
|
|
156
166
|
"site": "792",
|
|
157
167
|
"redcap2wl": {
|
|
@@ -35,12 +35,19 @@ pylantir start --ip 127.0.0.1 --port 4242 --AEtitle MWL_SERVER --pylantir_config
|
|
|
35
35
|
|
|
36
36
|
## Tests
|
|
37
37
|
|
|
38
|
-
|
|
38
|
+
If you want to run the tests make sure to clone the repository and run them from there.
|
|
39
|
+
|
|
40
|
+
Git clone the repository:
|
|
41
|
+
|
|
42
|
+
```bash
|
|
43
|
+
git clone https://github.com/miltoncamacho/pylantir
|
|
44
|
+
cd pylantir/tests
|
|
45
|
+
```
|
|
39
46
|
|
|
40
47
|
Query the worklist database to check that you have some entries using:
|
|
41
48
|
|
|
42
49
|
```bash
|
|
43
|
-
|
|
50
|
+
python query-db.py
|
|
44
51
|
```
|
|
45
52
|
|
|
46
53
|
Then, you can get a StudyUID from one of the entries to test the MPPS workflow. For example: 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
|
|
@@ -48,19 +55,19 @@ Then, you can get a StudyUID from one of the entries to test the MPPS workflow.
|
|
|
48
55
|
Take this and run a create action to mark the worklist Procedure Step Status as IN_PROGRESS
|
|
49
56
|
|
|
50
57
|
```bash
|
|
51
|
-
|
|
58
|
+
python test-mpps.py --AEtitle MWL_SERVER --mpps_action create --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
|
|
52
59
|
```
|
|
53
60
|
|
|
54
61
|
You can verify that this in fact modified your database re-running:
|
|
55
62
|
|
|
56
63
|
```bash
|
|
57
|
-
|
|
64
|
+
python query-db.py
|
|
58
65
|
```
|
|
59
66
|
|
|
60
67
|
Finally, you can also simulate the pocedure completion efectively updating the Procedure Step Status to COMPLETED or DISCONTINUED:
|
|
61
68
|
|
|
62
69
|
```bash
|
|
63
|
-
|
|
70
|
+
python test-mpps.py --AEtitle MWL_SERVER --mpps_action set --mpps_status COMPLETED --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632 --sop_uid 1.2.840.10008.3.1.2.3.4.187176383255263644225774937658729238426
|
|
64
71
|
```
|
|
65
72
|
|
|
66
73
|
## Usage
|
|
@@ -90,6 +97,8 @@ usage: pylantir [-h] [--AEtitle AETITLE] [--ip IP] [--port PORT] [--pylantir_con
|
|
|
90
97
|
- **site**: Site ID:string
|
|
91
98
|
- **protocol**: `{"site": "protocol_name", "mapping": "HIS/RIS mapping"}`
|
|
92
99
|
- **redcap2wl**: Dictionary of REDCap fields to worklist fields mapping e.g., `{"redcap_field": "worklist_field"}`
|
|
100
|
+
- **db_update_interval**: How often to reload the database e
|
|
101
|
+
- **operation_interval**: What is the time range in a day in which the database will be updated e.g., `{"start_time":[hours,minutes],"end_time":[hours,minutes]}`
|
|
93
102
|
- **--mpps_action {create,set}**: Action to perform for MPPS either create or set
|
|
94
103
|
- **--mpps_status {COMPLETED,DISCONTINUED}**: Status to set for MPPS either COMPLETED or DISCONTINUED
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<!-- BEGIN MICROSOFT SECURITY.MD V0.0.5 BLOCK -->
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## Security
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Microsoft takes the security of our software products and services seriously, which includes all source code repositories managed through our GitHub organizations, which include [Microsoft](https://github.com/Microsoft), [Azure](https://github.com/Azure), [DotNet](https://github.com/dotnet), [AspNet](https://github.com/aspnet), [Xamarin](https://github.com/xamarin), and [our GitHub organizations](https://opensource.microsoft.com/).
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If you believe you have found a security vulnerability in any Microsoft-owned repository that meets [Microsoft's definition of a security vulnerability](https://docs.microsoft.com/en-us/previous-versions/tn-archive/cc751383(v=technet.10)), please report it to us as described below.
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## Reporting Security Issues
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**Please do not report security vulnerabilities through public GitHub issues.**
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Instead, please report them to the Microsoft Security Response Center (MSRC) at [https://msrc.microsoft.com/create-report](https://msrc.microsoft.com/create-report).
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If you prefer to submit without logging in, send email to [secure@microsoft.com](mailto:secure@microsoft.com). If possible, encrypt your message with our PGP key; please download it from the [Microsoft Security Response Center PGP Key page](https://www.microsoft.com/en-us/msrc/pgp-key-msrc).
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You should receive a response within 24 hours. If for some reason you do not, please follow up via email to ensure we received your original message. Additional information can be found at [microsoft.com/msrc](https://www.microsoft.com/msrc).
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Please include the requested information listed below (as much as you can provide) to help us better understand the nature and scope of the possible issue:
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* Type of issue (e.g. buffer overflow, SQL injection, cross-site scripting, etc.)
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* Full paths of source file(s) related to the manifestation of the issue
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* The location of the affected source code (tag/branch/commit or direct URL)
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* Any special configuration required to reproduce the issue
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* Step-by-step instructions to reproduce the issue
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* Proof-of-concept or exploit code (if possible)
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* Impact of the issue, including how an attacker might exploit the issue
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This information will help us triage your report more quickly.
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If you are reporting for a bug bounty, more complete reports can contribute to a higher bounty award. Please visit our [Microsoft Bug Bounty Program](https://microsoft.com/msrc/bounty) page for more details about our active programs.
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## Preferred Languages
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We prefer all communications to be in English.
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## Policy
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Microsoft follows the principle of [Coordinated Vulnerability Disclosure](https://www.microsoft.com/en-us/msrc/cvd).
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<!-- END MICROSOFT SECURITY.MD BLOCK -->
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