Merge pull request #6 from ds-wizard/release/1.2.0

Release 1.2.0

.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

bin/np

@@ -61,4 +61,3 @@ fi
 
 >&2 echo "ERROR: Failed to find or download nanopub jar file."
 exit 1
-

nanopub_submitter/api.py

@@ -6,8 +6,8 @@
 
 from typing import Tuple
 
-from nanopub_submitter.config import cfg_parser
-from nanopub_submitter.consts import NICE_NAME, VERSION, BUILD_INFO,\
+from nanopub_submitter.config import cfg_parser, RequestConfig
+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
@@ -43,6 +43,12 @@ def _extract_content_type(header: str) -> Tuple[str, str]:
     return input_format, DEFAULT_ENCODING
 
 
+def _extract_servers(header: str) -> list[str]:
+    if header == '':
+        return []
+    return list(map(lambda x: x.strip(), header.split(',')))
+
+
 @app.get(path='/')
 async def get_info():
     return fastapi.responses.JSONResponse(
@@ -62,7 +68,11 @@ async def submit_nanopub(request: fastapi.Request):
     # (2) Extract data
     submission_id = str(uuid.uuid4())
     data = await request.body()
-    input_format, encoding = _extract_content_type(request.headers.get('Content-Type'))
+    input_format, encoding = _extract_content_type(request.headers.get('Content-Type', ''))
+    req_cfg = RequestConfig(
+        servers=_extract_servers(request.headers.get('X-NP-Servers', '')),
+        uri_replace=request.headers.get('X-URI-Replace', None)
+    )
     if input_format != 'application/trig':
         return fastapi.responses.Response(
             status_code=fastapi.status.HTTP_400_BAD_REQUEST,
@@ -73,6 +83,7 @@ async def submit_nanopub(request: fastapi.Request):
     try:
         result = process(
             cfg=cfg,
+            req_cfg=req_cfg,
             submission_id=submission_id,
             data=data.decode(encoding),
         )
@@ -85,16 +96,17 @@ async def submit_nanopub(request: fastapi.Request):
         LOG.error(f'[{submission_id}] Unexpected processing error: {str(e)}')
         return fastapi.responses.PlainTextResponse(
             status_code=fastapi.status.HTTP_500_INTERNAL_SERVER_ERROR,
-            content='Failed to process the nanopublication',
+            content=f'Failed to process the nanopublication: {str(e)}',
         )
     # (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/config.py

@@ -260,3 +260,10 @@ def config(self) -> SubmitterConfig:
 
 
 cfg_parser = SubmitterConfigParser()
+
+
+class RequestConfig:
+
+    def __init__(self, servers: list[str], uri_replace: Optional[str]):
+        self.servers = servers
+        self.uri_replace = uri_replace

nanopub_submitter/consts.py

@@ -1,6 +1,6 @@
 PACKAGE_NAME = 'nanopub_submitter'
 NICE_NAME = 'DSW Nanopublication Submission Service'
-PACKAGE_VERSION = '1.1.0'
+PACKAGE_VERSION = '1.2.0'
 ENV_CONFIG = 'SUBMISSION_CONFIG'
 LOGGER_NAME = 'DSW_SUBMITTER'
 

nanopub_submitter/nanopub.py

@@ -4,7 +4,7 @@
 
 from typing import Optional, Tuple
 
-from nanopub_submitter.config import SubmitterConfig
+from nanopub_submitter.config import SubmitterConfig, RequestConfig
 from nanopub_submitter.consts import DEFAULT_ENCODING, PACKAGE_NAME, PACKAGE_VERSION
 from nanopub_submitter.logger import LOG
 from nanopub_submitter.triple_store import store_to_triple_store
@@ -40,9 +40,11 @@ def __str__(self):
 
 class NanopubProcessingContext:
 
-    def __init__(self, submission_id: str, cfg: SubmitterConfig):
+    def __init__(self, submission_id: str, cfg: SubmitterConfig,
+                 req_cfg: RequestConfig):
         self.id = submission_id
         self.cfg = cfg
+        self.req_cfg = req_cfg
         self.uri = None
 
     def cleanup(self):
@@ -54,6 +56,20 @@ def cleanup(self):
             except Exception:
                 pass
 
+    @property
+    def target_servers(self) -> list[str]:
+        if len(self.req_cfg.servers) > 0:
+            return self.req_cfg.servers
+        return self.cfg.nanopub.target_servers
+
+    @property
+    def uri_replace(self) -> Optional[str]:
+        if self.req_cfg.uri_replace is None:
+            return self.cfg.nanopub.uri_replace
+        if '|' in self.req_cfg.uri_replace:
+            return self.req_cfg.uri_replace
+        return None
+
     @property
     def input_file(self) -> str:
         return f'{self.id}.trig'
@@ -100,23 +116,29 @@ def _split_nanopubs(nanopub_bundle: str) -> list[str]:
 def _publish_nanopub(nanopub_bundle: str, ctx: NanopubProcessingContext) -> list[str]:
     success = []
     nanopubs = _split_nanopubs(nanopub_bundle)
-    for server in ctx.cfg.nanopub.target_servers:
+    for server in ctx.target_servers:
         ctx.debug(f'Submitting to: {server}')
         ok = True
         for nanopub in nanopubs:
-            r = requests.post(
-                url=server,
-                data=nanopub,
-                headers={
-                    'Content-Type': f'application/trig; charset={DEFAULT_ENCODING}',
-                    'User-Agent': f'{PACKAGE_NAME}/{PACKAGE_VERSION}',
-                }
-            )
-            if not r.ok:
+            try:
+                r = requests.post(
+                    url=server,
+                    data=nanopub.encode(encoding=DEFAULT_ENCODING),
+                    headers={
+                        'Content-Type': f'application/trig; charset={DEFAULT_ENCODING}',
+                        'User-Agent': f'{PACKAGE_NAME}/{PACKAGE_VERSION}',
+                    },
+                    timeout=10,
+                )
+                if not r.ok:
+                    ok = False
+                    ctx.warn(f'Failed to publish nanopub via {server}')
+                    ctx.debug(f'status={r.status_code}')
+                    ctx.debug(r.text)
+                    break
+            except Exception as e:
                 ok = False
-                ctx.warn(f'Failed to publish nanopub via {server}')
-                ctx.debug(f'status={r.status_code}')
-                ctx.debug(r.text)
+                ctx.warn(f'Failed to publish nanopub via {server}: {str(e)}')
                 break
         if ok:
             ctx.info(f'Nanopub published via {server}')
@@ -173,10 +195,10 @@ def _run_np_sign(ctx: NanopubProcessingContext) -> str:
         ctx=ctx,
     )
     if exit_code != EXIT_SUCCESS:
-        LOG.warn(f'Failed to make TrustyURI ({exit_code}):\n{stdout}\n\n{stderr}')
+        LOG.warn(f'Failed to sign the nanopub ({exit_code}):\n{stdout}\n\n{stderr}')
         raise NanopubProcessingError(
             status_code=500,
-            message='Failed to make TrustyURI for nanopub.'
+            message='Failed to sign the nanopub.'
         )
     return ctx.signed_file
 
@@ -192,8 +214,13 @@ def _extract_np_uri(nanopub: str) -> Optional[str]:
     return last_this_prefix
 
 
-def process(cfg: SubmitterConfig, submission_id: str, data: str) -> NanopubSubmissionResult:
-    ctx = NanopubProcessingContext(submission_id=submission_id, cfg=cfg)
+def process(cfg: SubmitterConfig, req_cfg: RequestConfig,
+            submission_id: str, data: str) -> NanopubSubmissionResult:
+    ctx = NanopubProcessingContext(
+        submission_id=submission_id,
+        cfg=cfg,
+        req_cfg=req_cfg,
+    )
     ctx.debug('Preprocessing nanopublication as RDF')
     try:
         graph = rdflib.ConjunctiveGraph()
@@ -234,8 +261,8 @@ def process(cfg: SubmitterConfig, submission_id: str, data: str) -> NanopubSubmi
         ctx.cleanup()
         raise NanopubProcessingError(400, 'Failed to get nanopub URI')
 
-    if cfg.nanopub.uri_replace is not None:
-        old, new = cfg.nanopub.uri_replace.split('|', maxsplit=1)
+    if ctx.uri_replace is not None:
+        old, new = ctx.uri_replace.split('|', maxsplit=1)
         new_uri = nanopub_uri.replace(old, new)
         LOG.debug(f'Replacing {nanopub_uri} with {new_uri}')
         nanopub_uri = new_uri