Merge pull request #1 from FNNDSC/wip

WIP stuff and automatic testing in GitHub Actions

.dockerignore

@@ -2,6 +2,7 @@
 .gitignore
 .dockerignore
 .idea
+.venv
 Dockerfile
 docker-compose.yml
 README.md

.github/workflows/test.yml

@@ -0,0 +1,35 @@
+name: Test
+
+on:
+  push:
+    branches: [ master ]
+    paths:
+      - '.github/workflows/test.yml'
+      - '**.py'
+  pull_request:
+
+jobs:
+  test:
+    name: Tests
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Spin up ChRIS
+        uses: FNNDSC/miniChRIS-docker@master
+        with:
+          # for testing, we need to create plugin instances, but we don't need the plugins to actually run.
+          services: chris oxidicom graphql-engine
+      - name: Build
+        run: docker compose build test
+      - name: Test
+        id: test
+        continue-on-error: true  # we want to upload coverage, even on failure
+        run: docker compose run -T --use-aliases test
+      - name: Copy coverage.xml from container
+        run: docker cp "$(docker compose ps -a test -q | tail -n 1):/app/coverage.xml" coverage.xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -1 +1,4 @@
 .idea
+__pycache__
+/src/serie/version.txt
+/.test_data

Dockerfile

@@ -1,8 +1,11 @@
 FROM python:3.12.3-alpine
 
 WORKDIR /app
-COPY requirements.lock ./
-RUN PYTHONDONTWRITEBYTECODE=1 pip install --no-cache-dir -r requirements.lock
+ARG REQUIREMENTS_FILE=requirements.lock
+COPY ${REQUIREMENTS_FILE} ./requirements.txt
+RUN --mount=type=cache,sharing=locked,target=/root/.cache/pip \
+    sed -i' ' -e '/-e file:\./d' requirements.txt \
+    && env PYTHONDONTWRITEBYTECODE=1 pip install -r requirements.txt
 
 COPY src .
 CMD ["fastapi", "run", "main.py"]

README.md

@@ -42,10 +42,19 @@ docker compose --profile hasura up -d
 
 ### Testing
 
+Run unit tests on-the-metal:
+
 ```shell
 rye run pytest
 ```
 
+End-to-end tests require _SERIE_ to run in the same docker network as _CUBE_ and Hasura,
+so we need to run them with Docker Compose:
+
+```shell
+docker compose run test
+```
+
 ### Deployment
 
 See https://github.com/FNNDSC/charts

docker-compose.yml

@@ -1,6 +1,6 @@
-# Run SERIE in development mode in an existing miniChRIS network.
 
 services:
+  # Run SERIE in development mode in an existing miniChRIS network.
   dev:
     build:
       context: .
@@ -12,8 +12,33 @@ services:
     networks:
       minichris-local:
         aliases:
-          - poc.handler.chris
-
+          - dev.serie
+  # End-to-end testing
+  test:
+    build:
+      context: .
+      args:
+        REQUIREMENTS_FILE: requirements-dev.lock
+    command: pytest --color=yes --run-e2e --cov=serie --cov-report=xml
+    working_dir: /app
+    volumes:
+      # /app is a volume and the source code files are binded as subdirectories
+      # instead of directly mounting `.:/app` so that pytest and coverage can
+      # write temporary files to /app
+      - test:/app
+      - ./src/serie:/app/serie:ro
+      - ./tests:/app/tests:ro
+      - /var/run/docker.sock:/var/run/docker.sock
+    environment:
+      CHRIS_URL: http://chris:8000/api/v1/
+    networks:
+      minichris-local:
+        aliases:
+          - test.serie
+    profiles:
+      - test
 networks:
   minichris-local:
     external: true
+volumes:
+  test:

pyproject.toml

@@ -1,14 +1,17 @@
 [project]
 name = "serie"
-version = "0.1.0"
+version = "0.0.0"  # <-- version in pyproject.toml is ignored. Set the version in src/serie/version.txt
 description = "Specific Endpoints for Research Integration Events"
 authors = [
     { name = "FNNDSC", email = "[email protected]" }
 ]
 dependencies = [
     "fastapi>=0.111.1",
-    "aiochris~=0.5.0",
+    "aiochris~=0.8.0",
     "yarl>=1.9.4",
+    "asyncstdlib>=3.12.4",
+    "pydantic-settings>=2.3.4",
+    "requests>=2.32.3",
 ]
 readme = "README.md"
 requires-python = ">= 3.12"
@@ -19,8 +22,17 @@ build-backend = "hatchling.build"
 
 [tool.rye]
 managed = true
-dev-dependencies = []
-virtual = true
+dev-dependencies = [
+    "pytest>=8.3.2",
+    "pytest-asyncio>=0.23.8",
+    "asyncio>=3.4.3",
+    "aiohttp>=3.9.5",
+    "pydicom>=2.4.4",
+    "asyncer>=0.0.7",
+    "pynetdicom>=2.1.0",
+    "docker>=7.1.0",
+    "pytest-cov>=5.0.0",
+]
 
 [tool.hatch.metadata]
 allow-direct-references = true

requirements-dev.lock

@@ -9,19 +9,26 @@
 #   generate-hashes: false
 #   universal: false
 
-aiochris==0.5.0
+-e file:.
+aiochris==0.8.0
+    # via serie
 aiohttp==3.9.5
     # via aiochris
 aiosignal==1.3.1
     # via aiohttp
 annotated-types==0.7.0
     # via pydantic
 anyio==4.4.0
+    # via asyncer
     # via httpx
     # via starlette
     # via watchfiles
 async-property==0.2.2
     # via aiochris
+asyncer==0.0.7
+asyncio==3.4.3
+asyncstdlib==3.12.4
+    # via serie
 attrs==23.2.0
     # via aiohttp
 beartype==0.19.0rc0
@@ -32,14 +39,21 @@ casefy==0.1.7
 certifi==2024.7.4
     # via httpcore
     # via httpx
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
 click==8.1.7
     # via typer
     # via uvicorn
+coverage==7.6.0
+    # via pytest-cov
 dnspython==2.6.1
     # via email-validator
+docker==7.1.0
 email-validator==2.2.0
     # via fastapi
 fastapi==0.111.1
+    # via serie
 fastapi-cli==0.0.4
     # via fastapi
 frozenlist==1.4.1
@@ -58,7 +72,10 @@ idna==3.7
     # via anyio
     # via email-validator
     # via httpx
+    # via requests
     # via yarl
+iniconfig==2.0.0
+    # via pytest
 jinja2==3.1.4
     # via fastapi
     # via pyserde
@@ -73,22 +90,41 @@ multidict==6.0.5
     # via yarl
 mypy-extensions==1.0.0
     # via typing-inspect
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
 plum-dispatch==2.2.2
     # via pyserde
 pydantic==2.8.2
     # via fastapi
+    # via pydantic-settings
 pydantic-core==2.20.1
     # via pydantic
+pydantic-settings==2.3.4
+    # via serie
+pydicom==2.4.4
+    # via pynetdicom
 pygments==2.18.0
     # via rich
+pynetdicom==2.1.0
 pyserde==0.19.3
     # via aiochris
+pytest==8.3.2
+    # via pytest-asyncio
+    # via pytest-cov
+pytest-asyncio==0.23.8
+pytest-cov==5.0.0
 python-dotenv==1.0.1
+    # via pydantic-settings
     # via uvicorn
 python-multipart==0.0.9
     # via fastapi
 pyyaml==6.0.1
     # via uvicorn
+requests==2.32.3
+    # via docker
+    # via serie
 rich==13.7.1
     # via typer
 shellingham==1.5.4
@@ -109,6 +145,9 @@ typing-extensions==4.12.2
     # via typing-inspect
 typing-inspect==0.9.0
     # via pyserde
+urllib3==2.2.2
+    # via docker
+    # via requests
 uvicorn==0.30.1
     # via fastapi
 uvloop==0.19.0
@@ -120,3 +159,4 @@ websockets==12.0
 yarl==1.9.4
     # via aiochris
     # via aiohttp
+    # via serie

requirements.lock

@@ -9,7 +9,9 @@
 #   generate-hashes: false
 #   universal: false
 
-aiochris==0.5.0
+-e file:.
+aiochris==0.8.0
+    # via serie
 aiohttp==3.9.5
     # via aiochris
 aiosignal==1.3.1
@@ -22,6 +24,8 @@ anyio==4.4.0
     # via watchfiles
 async-property==0.2.2
     # via aiochris
+asyncstdlib==3.12.4
+    # via serie
 attrs==23.2.0
     # via aiohttp
 beartype==0.19.0rc0
@@ -32,6 +36,9 @@ casefy==0.1.7
 certifi==2024.7.4
     # via httpcore
     # via httpx
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
 click==8.1.7
     # via typer
     # via uvicorn
@@ -40,6 +47,7 @@ dnspython==2.6.1
 email-validator==2.2.0
     # via fastapi
 fastapi==0.111.1
+    # via serie
 fastapi-cli==0.0.4
     # via fastapi
 frozenlist==1.4.1
@@ -58,6 +66,7 @@ idna==3.7
     # via anyio
     # via email-validator
     # via httpx
+    # via requests
     # via yarl
 jinja2==3.1.4
     # via fastapi
@@ -77,18 +86,24 @@ plum-dispatch==2.2.2
     # via pyserde
 pydantic==2.8.2
     # via fastapi
+    # via pydantic-settings
 pydantic-core==2.20.1
     # via pydantic
+pydantic-settings==2.3.4
+    # via serie
 pygments==2.18.0
     # via rich
 pyserde==0.19.3
     # via aiochris
 python-dotenv==1.0.1
+    # via pydantic-settings
     # via uvicorn
 python-multipart==0.0.9
     # via fastapi
 pyyaml==6.0.1
     # via uvicorn
+requests==2.32.3
+    # via serie
 rich==13.7.1
     # via typer
 shellingham==1.5.4
@@ -109,6 +124,8 @@ typing-extensions==4.12.2
     # via typing-inspect
 typing-inspect==0.9.0
     # via pyserde
+urllib3==2.2.2
+    # via requests
 uvicorn==0.30.1
     # via fastapi
 uvloop==0.19.0
@@ -120,3 +137,4 @@ websockets==12.0
 yarl==1.9.4
     # via aiochris
     # via aiohttp
+    # via serie