Merge pull request #3 from h2020charisma/develop

Promote the latest development changes to the stable branch

.github/workflows/docker-publish.yml

@@ -64,6 +64,7 @@ jobs:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           tags: |
             type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'develop') }}
+            type=raw,value=stable,enable=${{ github.ref == format('refs/heads/{0}', 'main') }}
             type=ref,event=branch
             type=ref,event=tag
             type=ref,event=pr

.github/workflows/test.yml

@@ -0,0 +1,65 @@
+---
+on:  # yamllint disable-line rule:truthy
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+  workflow_dispatch:
+
+env:
+  POETRY_VERSION: 1.7.1
+
+jobs:
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - '3.9'
+          - '3.10'
+          - '3.11'
+
+    steps:
+      - name: Checkout the repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Load the cached Poetry installation
+        id: cached-poetry
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: poetry-${{ env.POETRY_VERSION }}-0
+
+      - name: Install Poetry
+        if: steps.cached-poetry.outputs.cache-hit != 'true'
+        uses: snok/install-poetry@v1
+        with:
+          version: ${{ env.POETRY_VERSION }}
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - name: Load the cached dependencies
+        id: cached-deps
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: py${{ matrix.python-version }}-deps-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Install dependencies
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      - name: Perform package installation
+        run: poetry install --no-interaction
+
+      - name: Run tests
+        run: poetry run pytest

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "pynanomapper"]
-	path = pynanomapper
+	path = extern/pynanomapper
 	url = https://github.com/ideaconsult/pynanomapper.git
 [submodule "ramanchada2"]
-	path = ramanchada2
+	path = extern/ramanchada2
 	url = https://github.com/h2020charisma/ramanchada2.git

.python-version

@@ -1 +1 @@
-3.9
+3.11

Dockerfile

@@ -1,16 +1,16 @@
-FROM python:3.9-slim as requirements-stage
+FROM python:3.11-slim as requirements-stage
 
 WORKDIR /tmp
 
 RUN pip install poetry
 
 COPY ./pyproject.toml ./poetry.lock* /tmp/
-COPY ./pynanomapper /tmp/pynanomapper
-COPY ./ramanchada2 /tmp/ramanchada2
+COPY ./extern/pynanomapper /tmp/extern/pynanomapper
+COPY ./extern/ramanchada2 /tmp/extern/ramanchada2
 
-RUN poetry export -f requirements.txt --output requirements.txt --without-hashes
+RUN poetry export -f requirements.txt --output requirements.txt --without=dev --without-hashes
 
-FROM tiangolo/uvicorn-gunicorn-fastapi:python3.9-slim
+FROM tiangolo/uvicorn-gunicorn-fastapi:python3.11-slim
 
 LABEL maintainer="Luchesar ILIEV <luchesar.iliev@gmail.com>" \
       org.opencontainers.image.created=$BUILD_DATE \
@@ -24,15 +24,16 @@ LABEL maintainer="Luchesar ILIEV <luchesar.iliev@gmail.com>" \
       org.opencontainers.image.version="latest"
 
 COPY --from=requirements-stage /tmp/requirements.txt /app/requirements.txt
-COPY ./pynanomapper /tmp/pynanomapper
-COPY ./ramanchada2 /tmp/ramanchada2
+COPY ./extern/pynanomapper /tmp/extern/pynanomapper
+COPY ./extern/ramanchada2 /tmp/extern/ramanchada2
 
 RUN pip install --no-cache-dir --upgrade -r /app/requirements.txt
 
 RUN find /tmp -mindepth 1 -delete
 
-ENV RAMANCHADA_API_CONFIG="/app/app/config/config.yaml"
+COPY ./src/rcapi /app/rcapi
 
-COPY ./app /app/app
+RUN sed -i '/^upload_dir:/s|:.*|: "/var/uploads"|' /app/rcapi/config/config.yaml
 
-RUN sed -i '/^upload_dir:/s|:.*|: "/var/uploads"|' /app/app/config/config.yaml
+ENV RAMANCHADA_API_CONFIG="/app/rcapi/config/config.yaml"
+ENV MODULE_NAME="rcapi.main"

README.md

@@ -1,6 +1,48 @@
 # ramanchada-api
 
-## Dev notes
+A web API for the RamanChada 2 Raman spectroscopy harmonisation library, incorporating the AMBIT/eNanoMapper data model.
+
+## Developer notes
+
+### Installation
+
+[Install Poetry](https://python-poetry.org/docs/#installation), then run:
+```
+poetry install
+```
+
+### Run development server
+
+```
+poetry run dev
+```
+
+### Work in a shell with installed package and dependencies
+
+```
+poetry shell
+```
+
+Exit with `exit` or Ctrl-D.
+
+### Add dependency
+
+```
+poetry add <pkgname>
+```
+
+### Run tests
+
+```
+poetry run pytest
+```
+
+### Test Docker image
+
+```
+docker build -t ramanchada-api:latest .
+docker run -it --rm -p 127.0.0.1:8000:80 ramanchada-api
+```
 
 ### Submodule update
 
@@ -11,7 +53,7 @@ git commit -am "Pull the latest commit for the submodules"
 git push
 ```
 
-### Run interminal
+### Run development server (old)
+```
+uvicorn src.rcapi.main:app --reload
 ```
-uvicorn app.main:app --reload
-```

docker-compose.yml

@@ -1,23 +1,68 @@
 networks:
+  ramanchada_api_prod:
+    name: ramanchada-api-prod
   ramanchada_api_dev:
     name: ramanchada-api-dev
 
 volumes:
+  uploads-prod:
+    driver: zfs
+    name: ${ZFSROOT}/ramanchada-api-uploads-prod
   uploads-dev:
     driver: zfs
     name: ${ZFSROOT}/ramanchada-api-uploads-dev
 
 services:
 
-  develop:
+  prod:
+    image: ghcr.io/h2020charisma/ramanchada-api:stable
+    container_name: ramanchada-api-prod
+    hostname: ramanchada-api-prod
+    restart: unless-stopped
+    labels:
+      traefik.enable: 'true'
+      traefik.http.routers.ramanchada-api-prod.entrypoints: tcp80v4*,tcp443v4*,tcp80v6*,tcp443v6*
+      traefik.http.routers.ramanchada-api-prod.rule: Host(`api.ramanchada.ideaconsult.net`)
+      traefik.http.routers.ramanchada-api-prod.middlewares: ramanchada-api-prod-cors
+      traefik.http.middlewares.ramanchada-api-prod-cors.headers.accessControlAllowCredentials: 'true'
+      traefik.http.middlewares.ramanchada-api-prod-cors.headers.accessControlAllowHeaders: >-
+        Authorization,
+        Cache-Control,
+        Content-Type,
+        DNT,
+        If-Modified-Since,
+        Keep-Alive,
+        User-Agent,
+        X-CustomHeader,
+        X-Requested-With
+      traefik.http.middlewares.ramanchada-api-prod-cors.headers.accessControlAllowMethods: >-
+        GET,
+        OPTIONS,
+        POST
+      traefik.http.middlewares.ramanchada-api-prod-cors.headers.accessControlAllowOriginList: >-
+        https://enanomapper.adma.ai,
+        https://enm-dev.adma.ai,
+        https://enm-experimental.adma.ai,
+        https://h5web-comp.vercel.app,
+        https://search.charisma.ideaconsult.net
+      traefik.http.middlewares.ramanchada-api-prod-cors.headers.accessControlMaxAge: 1728000
+      traefik.http.middlewares.ramanchada-api-prod-cors.headers.addVaryHeader: 'true'
+      com.centurylinklabs.watchtower.enable: 'true'
+      com.centurylinklabs.watchtower.scope: frequent
+    networks:
+      - ramanchada_api_prod
+    volumes:
+      - uploads-prod:/var/uploads
+
+  dev:
     image: ghcr.io/h2020charisma/ramanchada-api:develop
     container_name: ramanchada-api-dev
     hostname: ramanchada-api-dev
     restart: unless-stopped
     labels:
       traefik.enable: 'true'
       traefik.http.routers.ramanchada-api-dev.entrypoints: tcp80v4*,tcp443v4*,tcp80v6*,tcp443v6*
-      traefik.http.routers.ramanchada-api-dev.rule: Host(`api.ramanchada.ideaconsult.net`)
+      traefik.http.routers.ramanchada-api-dev.rule: Host(`api-dev.ramanchada.ideaconsult.net`)
       traefik.http.routers.ramanchada-api-dev.middlewares: ramanchada-api-dev-cors
       traefik.http.middlewares.ramanchada-api-dev-cors.headers.accessControlAllowCredentials: 'true'
       traefik.http.middlewares.ramanchada-api-dev-cors.headers.accessControlAllowHeaders: >-
@@ -35,10 +80,11 @@ services:
         OPTIONS,
         POST
       traefik.http.middlewares.ramanchada-api-dev-cors.headers.accessControlAllowOriginList: >-
-        https://search-dev.data.enanomapper.net,
-        https://search-experimental.data.enanomapper.net,
-        https://search.charisma.ideaconsult.net,
-        https://search.data.enanomapper.net
+        https://enanomapper.adma.ai,
+        https://enm-dev.adma.ai,
+        https://enm-experimental.adma.ai,
+        https://h5web-comp.vercel.app,
+        https://search.charisma.ideaconsult.net
       traefik.http.middlewares.ramanchada-api-dev-cors.headers.accessControlMaxAge: 1728000
       traefik.http.middlewares.ramanchada-api-dev-cors.headers.addVaryHeader: 'true'
       com.centurylinklabs.watchtower.enable: 'true'