Merge pull request #256 from CogStack/trainer-client

Pypi installable Client lib for common trainer functions

Author: tomolopolis

.github/workflows/ci.yml

@@ -3,10 +3,44 @@ name: ci-build
 on: [push]
 
 jobs:
-  # run tests / lint / etc. before building container image?
+  # Test and build client library
+  test-client:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.ref }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install requests pytest build
+
+      - name: Install client package in development mode
+        run: |
+          cd client
+          pip install -e .
+
+      - name: Run client tests
+        run: |
+          cd client
+          python -m pytest tests/ -v
+
+      - name: Build client package
+        run: |
+          cd client
+          python -m build
 
+  # Build and test webapp container
   build-and-push:
     runs-on: ubuntu-latest
+    needs: test-client
     steps:
       - name: Checkout main
         uses: actions/checkout@v4

.github/workflows/qa.yml

@@ -5,10 +5,50 @@ on:
     branches: [ main ]
 
 jobs:
-  # run tests / lint / etc. before building container image?
+  # Test and build client library
+  test-client:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v4
+        with:
+          ref: 'main'
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install requests pytest build
+
+      - name: Install client package in development mode
+        run: |
+          cd client
+          pip install -e .
+
+      - name: Run client tests
+        run: |
+          cd client
+          python -m pytest tests/ -v
+
+      - name: Build client package
+        run: |
+          cd client
+          python -m build
+
+      - name: Publish dev distribution to Test PyPI
+        uses: pypa/[email protected]
+        with:
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
 
+  # Build and test webapp container
   build-and-push:
     runs-on: ubuntu-latest
+    needs: test-client
     steps:
       - name: Checkout main
         uses: actions/checkout@v4

.github/workflows/release.yml

@@ -5,10 +5,53 @@ on:
     tags: ["v*.*.*"]
 
 jobs:
-  # run tests / lint / etc. before building container image?
+  # Test, build and publish client library
+  test-and-publish-client:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v4
+        with:
+          ref: "main"
+
+      - name: Release Tag
+        run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install requests pytest build twine
+
+      - name: Install client package in development mode
+        run: |
+          cd client
+          pip install -e .
+
+      - name: Run client tests
+        run: |
+          cd client
+          python -m pytest tests/ -v
+
+      - name: Build client package
+        run: |
+          cd client
+          python -m build
+
+      - name: Publish production distribution to PyPI
+        if: startsWith(github.ref, 'refs/tags') && ! github.event.release.prerelease
+        uses: pypa/[email protected]
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
 
+  # Build and test webapp container
   build-and-push:
     runs-on: ubuntu-latest
+    needs: test-and-publish-client
     steps:
       - name: Checkout main
         uses: actions/checkout@v4

client/README.md

@@ -0,0 +1,88 @@
+
+---
+
+# MedCATtrainer Client
+
+A Python client for interacting with a MedCATTrainer web application instance. This package allows you to manage datasets, concept databases, vocabularies, model packs, users, projects, and more via Python code or the command line.
+
+## Features
+
+- Manage datasets, concept databases, vocabularies, and model packs
+- Create and manage users and projects
+- Retrieve and upload project annotations
+- Command-line interface (CLI) for automation
+
+## Installation
+
+```sh
+pip install mctclient
+```
+
+Or, if installing from source:
+
+```sh
+cd client
+python -m build
+pip install dist/*.whl
+```
+
+## Python Usage
+
+```sh
+export MCTRAINER_USERNAME=<username>
+export MCTRAINER_PASSWORD=<password>
+```
+
+```python
+from mctclient import MedCATTrainerSession, MCTDataset, MCTConceptDB, MCTVocab, MCTModelPack, MCTMetaTask, MCTRelTask, MCTUser, MCTProject
+
+# Connect to your MedCATTrainer instance
+session = MedCATTrainerSession(server="http://localhost:8001")
+
+# List all projects
+projects = session.get_projects()
+for project in projects:
+    print(project)
+
+# Create a new dataset
+dataset = session.create_dataset(name="My Dataset", dataset_file="path/to/data.csv")
+
+# Create a new user
+user = session.create_user(username="newuser", password="password123")
+
+# Create a new project
+project = session.create_project(
+    name="My Project",
+    description="A new annotation project",
+    members=[user],
+    dataset=dataset
+)
+```
+
+### MedCATTrainerSession Methods
+
+- `create_project(name, description, members, dataset, cuis=[], cuis_file=None, concept_db=None, vocab=None, cdb_search_filter=None, modelpack=None, meta_tasks=[], rel_tasks=[])`
+- `create_dataset(name, dataset_file)`
+- `create_user(username, password)`
+- `create_medcat_model(cdb, vocab)`
+- `create_medcat_model_pack(model_pack)`
+- `get_users()`
+- `get_models()`
+- `get_model_packs()`
+- `get_meta_tasks()`
+- `get_rel_tasks()`
+- `get_projects()`
+- `get_datasets()`
+- `get_project_annos(projects)`
+
+Each method returns the corresponding object or a list of objects.
+
+## License
+
+This project is licensed under the Apache 2.0 License.
+
+## Contributing
+
+Pull requests are welcome! For major changes, please open an issue first to discuss what you would like to change.
+
+