Update Docker build CI and dependencies

.github/workflows/main.yml

@@ -10,77 +10,76 @@ jobs:
     runs-on: ubuntu-latest
 
     env:
-      PUBLIC_IMAGE: datastewardshipwizard/nanopub-submission-service
-      PRIVATE_IMAGE: ${{ secrets.PRIVATE_REGISTRY_URL }}/nanopub-submission-service
-      TAG_DEVELOP: develop
-      TAG_LATEST: latest
+      PUBLIC_IMAGE_PREFIX: 'datastewardshipwizard'
+      DOCKER_IMAGE_NAME: 'nanopub-submission-service'
+      DOCKER_META_CONTEXT: '.'
+      DOCKER_META_FILE: 'Dockerfile'
+      DOCKER_META_PLATFORMS: 'linux/amd64,linux/arm64'
 
     steps:
-    - uses: actions/checkout@v2
+    - name: '[setup] Check out repository'
+      uses: actions/checkout@v4
+      with:
+          fetch-depth: 0
 
-# (1) -> Build Docker image
-    - name: Update build info
-      run: |
-        ./scripts/build-info.sh
+    - name: '[setup] Set up QEMU'
+      uses: docker/setup-qemu-action@v3
 
-    - name: Docker build
-      run: |
-        docker build -t $PRIVATE_IMAGE:$GITHUB_SHA .
+    - name: '[setup] Set up Docker Buildx'
+      id: buildx
+      uses: docker/setup-buildx-action@v3
 
-# (2) -> Docker image tagging
-    - name: Docker login
-      if: github.event_name == 'push'
+    - name: '[setup ]Update build info'
       run: |
-        docker login -u "$DOCKER_HUB_USERNAME" -p "$DOCKER_HUB_PASSWORD"
-        docker login -u "$PRIVATE_REGISTRY_USERNAME" -p "$PRIVATE_REGISTRY_PASSWORD" "$PRIVATE_REGISTRY_URL"
-      env:
-        DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}
-        DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
-        PRIVATE_REGISTRY_URL: ${{ secrets.PRIVATE_REGISTRY_URL }}
-        PRIVATE_REGISTRY_USERNAME: ${{ secrets.PRIVATE_REGISTRY_USERNAME }}
-        PRIVATE_REGISTRY_PASSWORD: ${{ secrets.PRIVATE_REGISTRY_PASSWORD }}
+        ./scripts/build-info.sh
 
-    - name: Docker push - commit SHA (private)
-      if: github.event_name == 'push' && !startsWith(github.ref, 'refs/tags/')
-      run: |
-        docker push $PRIVATE_IMAGE:$GITHUB_SHA
+    - name: '[docker] Docker meta'
+      id: meta-test
+      uses: docker/metadata-action@v5
+      with:
+        images: |
+          ${{ env.PUBLIC_IMAGE_PREFIX }}/${{ env.DOCKER_IMAGE_NAME }}
+        tags: |
+          type=sha
 
-    - name: Docker tag and push - branch (private)
-      if: github.event_name == 'push' && startsWith(github.ref, 'refs/heads/') && !contains(github.ref, 'release')
-      run: |
-        GITHUB_BRANCH=`echo $GITHUB_REF | cut -d/ -f3- | sed 's#/#-#g'`
-        docker image tag $PRIVATE_IMAGE:$GITHUB_SHA $PRIVATE_IMAGE:$GITHUB_BRANCH
-        docker push $PRIVATE_IMAGE:$GITHUB_BRANCH
+    - name: '[docker] Docker build'
+      uses: docker/build-push-action@v4
+      with:
+        context: ${{ env.DOCKER_META_CONTEXT }}
+        file: ${{ env.DOCKER_META_FILE }}
+        platforms: ${{ env.DOCKER_META_PLATFORMS }}
+        push: false
+        tags: ${{ steps.meta-test.outputs.tags }}
+        labels: ${{ steps.meta-test.outputs.labels }}
 
-    - name: Docker tag and push - develop (public)
-      if: github.event_name == 'push' && github.ref == 'refs/heads/develop'
-      run: |
-        docker image tag $PRIVATE_IMAGE:$GITHUB_SHA $PUBLIC_IMAGE:$TAG_DEVELOP
-        docker push $PUBLIC_IMAGE:$TAG_DEVELOP
+    - name: '[docker-hub] Docker login'
+      if: github.event_name != 'pull_request' && github.actor != 'dependabot[bot]'
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKER_HUB_USERNAME }}
+        password: ${{ secrets.DOCKER_HUB_PASSWORD }}
 
-    - name: Docker tag and push - latest (public)
-      if: github.event_name == 'push' && github.ref == 'refs/heads/master'
-      run: |
-        docker image tag $PRIVATE_IMAGE:$GITHUB_SHA $PUBLIC_IMAGE:$TAG_LATEST
-        docker push $PUBLIC_IMAGE:$TAG_LATEST
+    - name: '[docker-hub] Docker meta'
+      id: meta-public
+      if: github.event_name != 'pull_request' && github.actor != 'dependabot[bot]'
+      uses: docker/metadata-action@v5
+      with:
+        images: |
+          ${{ env.PUBLIC_IMAGE_PREFIX }}/${{ env.DOCKER_IMAGE_NAME }}
+        tags: |
+          type=ref,event=branch
+          type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'main') }}
+          type=semver,pattern={{version}}
+          type=semver,pattern={{major}}.{{minor}}
+          type=semver,pattern={{major}},enable=${{ !startsWith(github.ref, 'refs/tags/v0.') }}
 
-    - name: Docker tag and push - version tag (public)
-      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
-      run: |
-        GITHUB_TAG=`echo $GITHUB_REF | cut -d/ -f3`
-        # Release vX.Y.Z
-        if [[ $GITHUB_TAG =~ ^v[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
-          IMAGE_TAG_MAJOR="$PUBLIC_IMAGE:"`echo $GITHUB_TAG | sed -E "s/v(.*)\..*\..*/\1/g"`
-          IMAGE_TAG_MINOR="$PUBLIC_IMAGE:"`echo $GITHUB_TAG | sed -E "s/v(.*)\..*/\1/g"`
-          IMAGE_TAG_PATCH="$PUBLIC_IMAGE:"`echo $GITHUB_TAG | sed -E "s/v//g"`
-          echo "Publishing release: $IMAGE_TAG_PATCH";
-          docker image tag $PRIVATE_IMAGE:$GITHUB_SHA $IMAGE_TAG_MAJOR && docker push $IMAGE_TAG_MAJOR;
-          docker image tag $PRIVATE_IMAGE:$GITHUB_SHA $IMAGE_TAG_MINOR && docker push $IMAGE_TAG_MINOR;
-          docker image tag $PRIVATE_IMAGE:$GITHUB_SHA $IMAGE_TAG_PATCH && docker push $IMAGE_TAG_PATCH;
-        fi
-        # Release candidate vX.Y.Z-rc.R
-        if [[ $GITHUB_TAG =~ ^v[0-9]+\.[0-9]+\.[0-9]+-rc\.[0-9]+$ ]]; then
-          IMAGE_TAG_RC="$PUBLIC_IMAGE:"`echo $GITHUB_TAG | sed -E "s/v//g"`
-          echo "Publishing release candidate: $IMAGE_TAG_RC";
-          docker image tag $PRIVATE_IMAGE:$GITHUB_SHA $IMAGE_TAG_RC && docker push $IMAGE_TAG_RC;
-        fi
+    - name: '[docker-hub] Docker build+push'
+      uses: docker/build-push-action@v4
+      if: github.event_name != 'pull_request' && steps.meta-public.outputs.tags != ''
+      with:
+        context: ${{ env.DOCKER_META_CONTEXT }}
+        file: ${{ env.DOCKER_META_FILE }}
+        platforms: ${{ env.DOCKER_META_PLATFORMS }}
+        push: true
+        tags: ${{ steps.meta-public.outputs.tags }}
+        labels: ${{ steps.meta-public.outputs.labels }}

Dockerfile

@@ -1,7 +1,7 @@
-FROM python:3.9-slim-buster
+FROM python:3.11-slim-bookworm
 
 RUN apt-get update && \
-  apt install -y --no-install-recommends bash default-jre && \
+  apt install -y --no-install-recommends bash default-jre build-essential gcc && \
   rm -rf /var/lib/apt/lists/*
 
 WORKDIR /app

nanopub_submitter/api.py

@@ -7,7 +7,7 @@
 from typing import Tuple
 
 from nanopub_submitter.config import cfg_parser, RequestConfig
-from nanopub_submitter.consts import NICE_NAME, VERSION, BUILD_INFO,\
+from nanopub_submitter.consts import NICE_NAME, VERSION, BUILD_INFO, \
     ENV_CONFIG, DEFAULT_CONFIG, DEFAULT_ENCODING
 from nanopub_submitter.logger import LOG, init_default_logging, init_config_logging
 from nanopub_submitter.mailer import Mailer
@@ -101,11 +101,12 @@ async def submit_nanopub(request: fastapi.Request):
     # (4) Mail
     Mailer.get().notice(nanopub_uri=result.location)
     # (5) Return
+    headers = dict()
+    if result.location is not None:
+        headers['Location'] = result.location
     return fastapi.responses.Response(
         status_code=fastapi.status.HTTP_201_CREATED,
-        headers={
-            'Location': result.location,
-        },
+        headers=headers,
         content=str(result),
     )
 

nanopub_submitter/triple_store.py

@@ -6,7 +6,7 @@
 from typing import List
 
 from nanopub_submitter.config import SubmitterConfig
-from nanopub_submitter.consts import COMMENT_INSTRUCTION_DELIMITER,\
+from nanopub_submitter.consts import COMMENT_INSTRUCTION_DELIMITER, \
     COMMENT_POST_QUERY_PREFIX, COMMENT_PRE_QUERY_PREFIX
 
 
@@ -22,6 +22,17 @@ def create_graph(class_name: str) -> rdflib.Graph:
     return GRAPH_CLASSES.get(class_name, rdflib.Graph)()
 
 
+def _n3(node: rdflib.term.Node) -> str:
+    if isinstance(node, rdflib.URIRef):
+        return node.n3()
+    elif isinstance(node, rdflib.Literal):
+        return node.n3()
+    elif isinstance(node, rdflib.BNode):
+        return node.n3()
+    else:
+        raise ValueError(f'Unknown node type: {type(node)}')
+
+
 class QueryBuilder:
 
     def __init__(self):
@@ -89,7 +100,7 @@ def basic_query_builder(cfg: SubmitterConfig, data: str, input_format: str) -> s
     g = create_graph(cfg.triple_store.graph_class)
     g.parse(data=data, format=input_format)
     triples = [
-        f'{s.n3()} {p.n3()} {o.n3()} .' for s, p, o in g
+        f'{_n3(s)} {_n3(p)} {_n3(o)} .' for s, p, o in g
     ]
     if cfg.triple_store.graph_named is True and cfg.triple_store.graph_type:
         t = rdflib.URIRef(cfg.triple_store.graph_type)
@@ -115,7 +126,7 @@ def multi_graph_query_builder(cfg: SubmitterConfig, data: str, input_format: str
     qb.insert_multigraph_start()
     for ctx in cg.contexts():
         triples = [
-            f'{s.n3()} {p.n3()} {o.n3()} .'
+            f'{_n3(s)} {_n3(p)} {_n3(o)} .'
             for s, p, o in cg.triples((None, None, None), context=ctx)
         ]
         qb.insert_multigraph(triples=triples, graph_node=ctx.identifier)

requirements.txt

@@ -1,35 +1,27 @@
-asgiref==3.4.1
-certifi==2021.5.30
-charset-normalizer==2.0.6
-click==8.0.1
-colorama==0.4.4
-fastapi==0.68.1
-flake8==3.9.2
-h11==0.12.0
-httptools==0.2.0
-idna==3.2
-isodate==0.6.0
-mccabe==0.6.1
-mypy==0.910
-mypy-extensions==0.4.3
-pycodestyle==2.7.0
-pydantic==1.8.2
-pyflakes==2.3.1
-pyparsing==2.4.7
-python-dotenv==0.19.0
-PyYAML==5.4.1
-rdflib==6.0.1
-requests==2.26.0
+annotated-types==0.6.0
+anyio==4.2.0
+certifi==2023.11.17
+charset-normalizer==3.3.2
+click==8.1.7
+fastapi==0.109.0
+h11==0.14.0
+httptools==0.6.1
+idna==3.6
+isodate==0.6.1
+pydantic==2.5.3
+pydantic_core==2.14.6
+pyparsing==3.1.1
+python-dotenv==1.0.0
+PyYAML==6.0.1
+rdflib==7.0.0
+requests==2.31.0
 six==1.16.0
-SPARQLWrapper==1.8.5
-starlette==0.14.2
-toml==0.10.2
-types-aiofiles==0.1.9
-types-orjson==3.6.0
-types-PyYAML==5.4.10
-types-ujson==0.1.1
-typing-extensions==3.10.0.2
-urllib3==1.26.7
-uvicorn==0.15.0
-watchgod==0.7
-websockets==10.0
+sniffio==1.3.0
+SPARQLWrapper==2.0.0
+starlette==0.35.1
+typing_extensions==4.9.0
+urllib3==2.1.0
+uvicorn==0.26.0
+uvloop==0.19.0
+watchfiles==0.21.0
+websockets==12.0