pylantir 0.0.2__tar.gz → 0.0.2rc53.post1__tar.gz

pylantir-0.0.2rc53.post1/.devcontainer/Dockerfile

@@ -0,0 +1,12 @@
+FROM mcr.microsoft.com/devcontainers/python:3
+
+RUN python -m pip install --upgrade pip \
+    && python -m pip install 'flit>=3.8.0'
+
+ENV FLIT_ROOT_INSTALL=1
+
+COPY pyproject.toml .
+RUN touch README.md \
+    && mkdir -p src/python_package \
+    && python -m flit install --only-deps --deps develop \
+    && rm -r pyproject.toml README.md src

pylantir-0.0.2rc53.post1/.devcontainer/devcontainer.json

@@ -0,0 +1,44 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.222.0/containers/python-3-miniconda
+{
+	"name": "Python Environment",
+	"build": {
+		"dockerfile": "Dockerfile",
+		"context": ".."
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"editorconfig.editorconfig",
+				"github.vscode-pull-request-github",
+				"ms-azuretools.vscode-docker",
+				"ms-python.python",
+				"ms-python.vscode-pylance",
+				"ms-python.pylint",
+				"ms-python.isort",
+				"ms-python.flake8",
+				"ms-python.black-formatter",
+				"ms-vsliveshare.vsliveshare",
+				"ryanluker.vscode-coverage-gutters",
+				"bungcip.better-toml",
+				"GitHub.copilot"
+			],
+			"settings": {
+				"python.defaultInterpreterPath": "/usr/local/bin/python",
+				"black-formatter.path": [
+					"/usr/local/py-utils/bin/black"
+				],
+				"pylint.path": [
+					"/usr/local/py-utils/bin/pylint"
+				],
+				"flake8.path": [
+					"/usr/local/py-utils/bin/flake8"
+				],
+				"isort.path": [
+					"/usr/local/py-utils/bin/isort"
+				]
+			}
+		}
+	},
+	"onCreateCommand": "pre-commit install-hooks"
+}

pylantir-0.0.2rc53.post1/.github/dependabot.yml

@@ -0,0 +1,22 @@
+version: 2
+updates:
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: daily
+    time: "13:00"
+  open-pull-requests-limit: 10
+  reviewers:
+  - dciborow
+  allow:
+  - dependency-type: direct
+  - dependency-type: indirect
+  commit-message:
+    prefix: "fix: "
+- package-ecosystem: "github-actions"
+  directory: "/"
+  schedule:
+    interval: daily
+    time: "13:00"
+  commit-message:
+    prefix: "fix: "

pylantir-0.0.2rc53.post1/.github/template-sync.yml

@@ -0,0 +1,21 @@
+files:
+  - ".gitignore"  # include
+  - ".github"
+  - ".vscode"
+  - "tests/conftest.py"
+  - ".flake8"
+  - ".pre-commit-config.yml"
+  - ".pypirc"
+  - "docs"
+  - "src/README.md"
+  - "CODE_OF_CONDUCT.md"
+  - "LICENSE"
+  - "README.md"
+  - "SECURITY.md"
+  - "SUPPORT.md"
+  - "pyproject.toml"
+
+  - "!.github/workflows/template-sync.yml"
+  - "!.github/template-sync.yml"
+  - "!src/python_project"
+  - "!tests/test_methods.py"

pylantir-0.0.2rc53.post1/.github/workflows/CI.yml

@@ -0,0 +1,21 @@
+name: Python CI
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  release:
+    types: [created]    
+  workflow_dispatch:
+
+jobs:
+  validation:
+    uses: microsoft/action-python/.github/workflows/validation.yml@0.6.4
+    with:
+      workdir: '.'
+
+  publish:
+    uses: microsoft/action-python/.github/workflows/publish.yml@0.6.4
+    secrets:
+      PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      TEST_PYPI_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD  }}

pylantir-0.0.2rc53.post1/.github/workflows/publish.yml

@@ -0,0 +1,33 @@
+name: Publish Python Package
+
+on:
+  push:
+    tags:
+      - "v*"  # Only run on version tags like v1.2.3
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install build tools
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: twine upload dist/*

pylantir-0.0.2rc53.post1/.github/workflows/schedule-update-actions.yml

@@ -0,0 +1,25 @@
+name: GitHub Actions Version Updater
+
+# Controls when the action will run.
+on:
+  workflow_dispatch:
+  schedule:
+    # Automatically run on every Sunday
+    - cron:  '0 0 * * 0'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3.5.2
+        with:
+          # [Required] Access token with `workflow` scope.
+          token: ${{ secrets.PAT }}
+
+      - name: Run GitHub Actions Version Updater
+        uses: saadmk11/github-actions-version-updater@v0.7.4
+        with:
+          # [Required] Access token with `workflow` scope.
+          token: ${{ secrets.PAT }}
+          pull_request_title: "ci: Update GitHub Actions to Latest Version"

pylantir-0.0.2rc53.post1/.github/workflows/semantic-pr-check.yml

@@ -0,0 +1,17 @@
+name: "Semantic PR Check"
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - edited
+      - synchronize
+
+jobs:
+  main:
+    name: Validate PR title
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v5.2.0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

pylantir-0.0.2rc53.post1/.github/workflows/sphinx.yml

@@ -0,0 +1,18 @@
+name: Deploy Sphinx documentation to Pages
+
+on:
+  push:
+    branches: [main] # branch to trigger deployment
+
+jobs:
+  pages:
+    runs-on: ubuntu-20.04
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+    - id: deployment
+      uses: sphinx-notes/pages@v3

pylantir-0.0.2rc53.post1/.github/workflows/template-sync.yml

@@ -0,0 +1,12 @@
+name: Template Sync
+on:
+  workflow_dispatch:
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3.5.2 # important!
+      - uses: euphoricsystems/action-sync-template-repository@v2.5.1
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          dry-run: true

pylantir-0.0.2rc53.post1/.gitignore

@@ -0,0 +1,129 @@
+# 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/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

pylantir-0.0.2rc53.post1/.pre-commit-config.yaml

@@ -0,0 +1,60 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["-a", "from __future__ import annotations"]
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.0
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus]
+
+  - repo: https://github.com/hadialqattan/pycln
+    rev: v1.2.5
+    hooks:
+      - id: pycln
+        args: [--config=pyproject.toml]
+        stages: [manual]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.1.0
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.9.0
+    hooks:
+      - id: python-check-blanket-noqa
+      - id: python-check-blanket-type-ignore
+      - id: python-no-log-warn
+      - id: python-no-eval
+      - id: python-use-type-annotations
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/mgedmin/check-manifest
+    rev: "0.47"
+    hooks:
+      - id: check-manifest
+        stages: [manual]

pylantir-0.0.2rc53.post1/.pypirc

@@ -0,0 +1,10 @@
+[distutils]
+index-servers =
+    pypi
+    testpypi
+
+[pypi]
+repository = https://upload.pypi.org/legacy/
+
+[testpypi]
+repository = https://test.pypi.org/legacy/

pylantir-0.0.2rc53.post1/.vscode/launch.json

@@ -0,0 +1,19 @@
+{
+    "version": "0.1.0",
+    "configurations": [
+        {
+            "name": "Python: Debug Tests",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": [
+                "debug-test"
+            ],
+            "console": "integratedTerminal",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--no-cov -n0 --dist no"
+            }
+        }
+    ]
+}

pylantir-0.0.2rc53.post1/.vscode/settings.json

@@ -0,0 +1,29 @@
+{
+    "editor.formatOnSave": true,
+    "editor.formatOnPaste": true,
+    "files.trimTrailingWhitespace": true,
+    "files.autoSave": "onFocusChange",
+    "git.autofetch": true,
+    "[jsonc]": {
+        "editor.defaultFormatter": "vscode.json-language-features"
+    },
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.black-formatter"
+    },
+    "python.defaultInterpreterPath": "/usr/local/bin/python",
+    "python.formatting.provider": "black",
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true,
+    "pylint.args": [
+        "--rcfile=pyproject.toml"
+    ],
+    "black-formatter.args": [
+        "--config=pyproject.toml"
+    ],
+    "flake8.args": [
+        "--toml-config=pyproject.toml"
+    ],
+    "isort.args": [
+        "--settings-path=pyproject.toml"
+    ]
+}

pylantir-0.0.2rc53.post1/CODE_OF_CONDUCT.md

@@ -0,0 +1,9 @@
+# Microsoft Open Source Code of Conduct
+
+This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
+
+Resources:
+
+- [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/)
+- [Microsoft Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/)
+- Contact [opencode@microsoft.com](mailto:opencode@microsoft.com) with questions or concerns

pylantir-0.0.2rc53.post1/LICENSE

@@ -0,0 +1,21 @@
+    MIT License
+
+    Copyright (c) Microsoft Corporation.
+
+    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

{pylantir-0.0.2 → pylantir-0.0.2rc53.post1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: pylantir
-Version: 0.0.2
+Version: 0.0.2rc53.post1
 Summary: Python - DICOM Modality WorkList
 Author-email: Milton Camacho <miltoncamachoicc@gmail.com>
 Requires-Python: >=3.11.1
@@ -13,10 +13,14 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+License-File: LICENSE
 Requires-Dist: pynetdicom
 Requires-Dist: sqlalchemy
 Requires-Dist: PyCap
 Requires-Dist: uuid
+Requires-Dist: coloredlogs
+Requires-Dist: python-dotenv
+Requires-Dist: pandas
 Requires-Dist: pyspark>=3.0.0 ; extra == "spark"
 Requires-Dist: bandit[toml]==1.7.5 ; extra == "test"
 Requires-Dist: black==23.3.0 ; extra == "test"
@@ -27,7 +31,7 @@ Requires-Dist: flake8-formatter_junit_xml ; extra == "test"
 Requires-Dist: flake8 ; extra == "test"
 Requires-Dist: flake8-pyproject ; extra == "test"
 Requires-Dist: pre-commit==3.3.1 ; extra == "test"
-Requires-Dist: pylint==2.17.4 ; extra == "test"
+Requires-Dist: pylint==3.3.6 ; extra == "test"
 Requires-Dist: pylint_junit ; extra == "test"
 Requires-Dist: pytest-cov==4.0.0 ; extra == "test"
 Requires-Dist: pytest-mock<3.10.1 ; extra == "test"
@@ -62,20 +66,35 @@ To get started simply install using:
 pip install pylantir
 ```
 
+You need to provide your REDCap API URL and API token before starting the server.
+Set up environmental variables before starting the server:
+
+```bash
+export REDCAP_API_URL=<your API url>
+export REDCAP_API_TOKEN=<your API token>
+```
+
 Start a server called with AEtitle MWL_SERVER.
 
 ```bash
-pylantir start --ip 127.0.0.1 --port 4242 --AEtitle MWL_SERVER
+pylantir start --ip 127.0.0.1 --port 4242 --AEtitle MWL_SERVER --pylantir_config Path/to/your/config.json
 ```
 
 ## Tests
 
-Once your modality worklist server is running you can test it running the following:
+If you want to run the tests make sure to clone the repository and run them from there.
+
+Git clone the repository:
+
+```bash
+git clone https://github.com/miltoncamacho/pylantir
+cd pylantir/tests
+```
 
 Query the worklist database to check that you have some entries using:
 
 ```bash
-pylantir query-db
+python query-db.py
 ```
 
 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
@@ -83,19 +102,19 @@ Then, you can get a StudyUID from one of the entries to test the MPPS workflow.
 Take this and run a create action to mark the worklist Procedure Step Status as IN_PROGRESS
 
 ```bash
-pylantir test-mpps --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
+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
 ```
 
 You can verify that this in fact modified your database re-running:
 
 ```bash
-pylantir query-db
+python query-db.py
 ```
 
 Finally, you can also simulate the pocedure completion efectively updating the Procedure Step Status to COMPLETED or DISCONTINUED:
 
 ```bash
-pylantir test-mpps --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
+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
 ```
 
 ## Usage
@@ -122,10 +141,11 @@ usage: pylantir [-h] [--AEtitle AETITLE] [--ip IP] [--port PORT] [--pylantir_con
 - **--port PORT**: Port for the server
 - **--pylantir_config PYLANTIR_CONFIG**: Path to the configuration JSON file containing pylantir configs:
   - **allowed_aet**: List of allowed AE titles e.g. `["MRI_SCANNER", "MRI_SCANNER_2"]`
-  - **mri_visit_session_mapping**: Mapping of MRI visit to session e.g., `{"T1": "1", "T2": "2"}`
   - **site**: Site ID:string
-  - **protocol**: `{"site": "protocol_name"}`
+  - **protocol**: `{"site": "protocol_name", "mapping": "HIS/RIS mapping"}`
   - **redcap2wl**: Dictionary of REDCap fields to worklist fields mapping e.g., `{"redcap_field": "worklist_field"}`
+  - **db_update_interval**: How often to reload the database e
+  - **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]}`
 - **--mpps_action {create,set}**: Action to perform for MPPS either create or set
 - **--mpps_status {COMPLETED,DISCONTINUED}**: Status to set for MPPS either COMPLETED or DISCONTINUED
 - **--callingAEtitle CALLINGAETITLE**: Calling AE Title for MPPS, it helps when the MWL is limited to only accept certain AE titles
@@ -141,21 +161,19 @@ As a default pylantir will try to read a JSON structured file with the following
   "db_path": "/path/to/worklist.db",
   "db_echo": "False",
   "db_update_interval": 60,
+  "operation_interval": {"start_time": [0,0],"end_time": [23,59]},
   "allowed_aet": [],
-  "mri_visit_session_mapping": {
-    "t1_arm_1": "1",
-    "t2_arm_1": "2",
-    "t3_arm_1": "3"
-  },
   "site": "792",
   "redcap2wl": {
     "study_id": "study_id",
+    "instrument": "redcap_repeat_instrument",
+    "session_id" : "mri_instance",
     "family_id": "family_id",
     "youth_dob_y": "youth_dob_y",
     "t1_date": "t1_date",
     "demo_sex": "demo_sex",
-    "scheduled_date": "scheduled_start_date",
-    "scheduled_time": "scheduled_start_time",
+    "scheduled_date": "mri_date",
+    "scheduled_time": "mri_time",
     "mri_wt_lbs": "patient_weight_lb",
     "referring_physician": "referring_physician_name",
     "performing_physician": "performing_physician",
@@ -163,7 +181,8 @@ As a default pylantir will try to read a JSON structured file with the following
     "status": "performed_procedure_step_status"
   },
   "protocol": {
-    "792": "BRAIN_MRI_3T"
+    "792": "BRAIN_MRI_3T",
+    "mapping": "GEHC"
   }
 }
 ```