Release 1.1.2 (#53)

* Update project files * Run npm run generate:server:latest * Update tool info
nlpsandbox · Jun 2, 2021 · bfbed8a · bfbed8a
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -126,10 +126,10 @@ channel that best matches the topic of your request.
 
 <!-- Links -->
 
-[Code of Conduct]: https://github.com/nlpsandbox/date-annotator-example/blob/develop/.github/CODE_OF_CONDUCT.md
+[Code of Conduct]: CODE_OF_CONDUCT.md
 [upstream remote]: https://help.github.com/en/articles/configuring-a-remote-for-a-fork
 [reaction]: https://github.blog/2016-03-10-add-reactions-to-pull-requests-issues-and-comments/
-[docs site]: https://github.com/nlpsandbox/nlpsandbox-website-synapse
+[docs site]: https://nlpsandbox.io
 [Forking Workflow]: https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow
-[package.json]: package.json
+[package.json]: ../package.json
 [NLP Sandbox Discord server]: https://nlpsandbox.io/discord
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -5,38 +5,28 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
-    target-branch: "develop"
-    reviewers:
-      - "nlpsandbox/maintainers"
+    target-branch: "main"
 
   - package-ecosystem: "docker"
     directory: "/server"
     schedule:
       interval: "monthly"
-    target-branch: "develop"
-    reviewers:
-      - "nlpsandbox/maintainers"
+    target-branch: "main"
 
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "monthly"
-    target-branch: "develop"
-    reviewers:
-      - "nlpsandbox/maintainers"
+    target-branch: "main"
 
   - package-ecosystem: "npm"
     directory: "/"
     schedule:
       interval: "monthly"
-    target-branch: "develop"
-    reviewers:
-      - "nlpsandbox/maintainers"
+    target-branch: "main"
 
   - package-ecosystem: "pip"
     directory: "/server"
     schedule:
       interval: "monthly"
-    target-branch: "develop"
-    reviewers:
-      - "nlpsandbox/maintainers"
+    target-branch: "main"
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -6,31 +6,74 @@ on:
   push:
     branches:
       - main
-      - develop
     tags:
       - '*.*.*'
   pull_request:
 
 env:
-  docker_repository: nlpsandbox/physical-address-annotator-example
+  docker_repository: docker.synapse.org/syn22277123/physical-address-annotator-example
 
 jobs:
+  configure:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Create configuration
+      run: |
+        DOCKER_IMAGE=${{ env.docker_repository }}
+        VERSION=noop
+        PUSH=false
+        if [ "${{ github.event_name }}" = "schedule" ]; then
+          VERSION=nightly
+          PUSH=true
+        elif [[ $GITHUB_REF == refs/tags/* ]]; then
+          VERSION=${GITHUB_REF#refs/tags/}
+        elif [[ $GITHUB_REF == refs/heads/* ]]; then
+          VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
+          if [ "${{ github.event.repository.default_branch }}" = "$VERSION" ]; then
+            VERSION=edge
+            PUSH=true
+          fi
+        elif [[ $GITHUB_REF == refs/pull/* ]]; then
+          VERSION=pr-${{ github.event.number }}
+        fi
+        TAGS="${DOCKER_IMAGE}:${VERSION}"
+        if [[ $VERSION =~ ^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
+          TAGS="$TAGS,${DOCKER_IMAGE}:latest"
+          PUSH=true
+        fi
+        printf "%s\n" \
+          "version=${VERSION}" \
+          "tags=${TAGS}" \
+          "created=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" \
+          "push=${PUSH}" | tee -a .github_env
+
+    - name: Upload .github_env
+      uses: actions/upload-artifact@v2
+      with:
+        name: GITHUB_ENV
+        path: .github_env
+
   lint:
+    needs: [configure]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+
     - name: Lint Dockerfiles
       uses: docker://hadolint/hadolint:latest
       with:
         entrypoint: hadolint
         args: server/Dockerfile
+
     - name: Validate docker-compose.yml
       run: |
         docker-compose -f docker-compose.yml config >/dev/null
+
     - name: Check that packages in requirements.txt files are in asc order
       run: |
         sort -f --check server/requirements.txt
         sort -f --check server/test-requirements.txt
+
     - name: Lint Python code with Flake8
       uses: docker://alpine/flake8:latest
       with:
@@ -44,15 +87,18 @@ jobs:
         python-version: [3.7, 3.8, 3.9]
     steps:
     - uses: actions/checkout@v2
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         cd server
         python -m pip install --upgrade pip
         pip install tox tox-gh-actions
+
     - name: Test with tox
       run: |
         cd server
@@ -63,68 +109,42 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - name: Prepare
-      id: prep
-      run: |
-        DOCKER_IMAGE=${{ env.docker_repository }}
-        VERSION=noop
-        PUSH=false
-        if [ "${{ github.event_name }}" = "schedule" ]; then
-          VERSION=nightly
-          PUSH=true
-        elif [[ $GITHUB_REF == refs/tags/* ]]; then
-          VERSION=${GITHUB_REF#refs/tags/}
-        elif [[ $GITHUB_REF == refs/heads/* ]]; then
-          VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
-          if [ "${{ github.event.repository.default_branch }}" = "$VERSION" ]; then
-            VERSION=edge
-            PUSH=true
-          fi
-        elif [[ $GITHUB_REF == refs/pull/* ]]; then
-          VERSION=pr-${{ github.event.number }}
-        fi
-        TAGS="${DOCKER_IMAGE}:${VERSION}"
-        if [[ $VERSION =~ ^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
-          MINOR=${VERSION%.*}
-          MAJOR=${MINOR%.*}
-          TAGS="$TAGS,${DOCKER_IMAGE}:${MINOR},${DOCKER_IMAGE}:${MAJOR},${DOCKER_IMAGE}:latest"
-          PUSH=true
-        # elif [ "${{ github.event_name }}" = "push" ]; then
-        #   TAGS="$TAGS,${DOCKER_IMAGE}:sha-${GITHUB_SHA::8}"
-        fi
-        echo ::set-output name=version::${VERSION}
-        echo ::set-output name=tags::${TAGS}
-        echo ::set-output name=created::$(date -u +'%Y-%m-%dT%H:%M:%SZ')
-        echo ::set-output name=push::${PUSH}
+
+    - name: Download .github_env
+      uses: actions/download-artifact@v2
+      with:
+        name: GITHUB_ENV
+        path: .
+
+    - name: Restore $GITHUB_ENV
+      run: cat .github_env >> $GITHUB_ENV
+
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v1
+
     - name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v1
-    - name: Login to DockerHub
-      if: steps.prep.outputs.push == 'true'
+
+    - name: Login to Synapse Docker Registry
+      if: env.push == 'true'
       uses: docker/login-action@v1
       with:
-        username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_TOKEN }}
+        registry: docker.synapse.org
+        username: ${{ secrets.SYNAPSE_USERNAME }}
+        password: ${{ secrets.SYNAPSE_TOKEN }}
+
     - name: Build and push
       id: docker_build
       uses: docker/build-push-action@v2
       with:
         context: server
         file: server/Dockerfile
         platforms: linux/amd64
-        push: ${{ steps.prep.outputs.push }}
-        tags: ${{ steps.prep.outputs.tags }}
+        push: ${{ env.push }}
+        tags: ${{ env.tags }}
         labels: |
-          org.opencontainers.image.created=${{ steps.prep.outputs.created }}
+          org.opencontainers.image.created=${{ env.created }}
           org.opencontainers.image.source=${{ github.repositoryUrl }}
-          org.opencontainers.image.version=${{ steps.prep.outputs.version }}
+          org.opencontainers.image.version=${{ env.version }}
           org.opencontainers.image.revision=${{ github.sha }}
           org.opencontainers.image.licenses=${{ github.event.repository.license.name }}
-    - name: Docker Hub Description
-      if: steps.prep.outputs.push == 'true'
-      uses: peter-evans/dockerhub-description@v2
-      with:
-        username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_PASSWORD }}
-        repository: ${{ env.docker_repository }}
diff --git a/README.md b/README.md
@@ -19,8 +19,8 @@ physical address annotations found in the clinical note.
 
 ### Specification
 
-- Physical Address Annotator API version: 1.1.1
-- Tool version: 1.1.1
+- Physical Address Annotator API version: 1.1.2
+- Tool version: 1.1.2
 - Docker image: [nlpsandbox/physical-address-annotator-example]
 
 ## Model

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -2,13 +2,13 @@ version: "3.8"
 
 services:
   physical-address-annotator:
-    image: nlpsandbox/physical-address-annotator-example:1.1.1
+    image: docker.synapse.org/syn22277123/physical-address-annotator-example:1.1.2
     build:
       context: server
       dockerfile: Dockerfile
     container_name: physical-address-annotator
     networks:
-      - nlp-sandbox-internal
+      - nlpsandbox-internal
 
   nginx:
     image: nginx:1.19.6-alpine
@@ -21,14 +21,14 @@ services:
       - ./nginx/nginx.conf:/etc/nginx/nginx.conf:ro
       - ./nginx/templates:/etc/nginx/templates:ro
     networks:
-      - nlp-sandbox
-      - nlp-sandbox-internal
+      - nlpsandbox
+      - nlpsandbox-internal
     ports:
       - "80:80"
     depends_on:
       - physical-address-annotator
 
 networks:
-  nlp-sandbox:
-  nlp-sandbox-internal:
+  nlpsandbox:
+  nlpsandbox-internal:
     internal: true
diff --git a/package-lock.json b/package-lock.json
diff --git a/server/openapi_server/controllers/tool_controller.py b/server/openapi_server/controllers/tool_controller.py
@@ -13,16 +13,16 @@ def get_tool():  # noqa: E501
     """
     tool = Tool(
         name="physical-address-annotator-example",
-        version="1.1.1",
+        version="1.1.2",
         license=License.APACHE_2_0,
         repository="github:nlpsandbox/physical-address-annotator-example",
         description="Example implementation of the NLP Sandbox Physical " +
                 "Address Annotator",
         author="NLP Sandbox Team",
-        author_email="[email protected]",
+        author_email="[email protected]",
         url="https://github.com/nlpsandbox/physical-address-annotator-example",
         type="nlpsandbox:physical-address-annotator",
-        api_version="1.1.1"
+        api_version="1.1.2"
     )
     return tool, 200
 

diff --git a/server/openapi_server/openapi/openapi.yaml b/server/openapi_server/openapi/openapi.yaml
@@ -27,7 +27,7 @@ info:
     name: Apache 2.0
     url: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE
   title: NLP Sandbox Physical Address Annotator API
-  version: 1.1.1
+  version: 1.1.2
   x-logo:
     url: https://nlpsandbox.github.io/nlpsandbox-schemas/logo.png
 servers:
@@ -411,7 +411,7 @@ components:
         authorEmail: [email protected]
         url: https://example.com
         type: nlpsandbox:date-annotator
-        apiVersion: 1.1.1
+        apiVersion: 1.1.2
       properties:
         name:
           description: The tool name
@@ -482,7 +482,7 @@ components:
           authorEmail: [email protected]
           url: https://example.com
           type: nlpsandbox:date-annotator
-          apiVersion: 1.1.1
+          apiVersion: 1.1.2
         - name: awesome-nlp-tool
           version: 1.0.6
           license: apache-2.0
@@ -492,7 +492,7 @@ components:
           authorEmail: [email protected]
           url: https://example.com
           type: nlpsandbox:date-annotator
-          apiVersion: 1.1.1
+          apiVersion: 1.1.2
       properties:
         tools:
           description: A list of tools