Release 1.1.2 (#44)

* Update project files * Fix package.json * Run npm run generate:server:latest * Update tool info * Minor change * Update Dockerfile base image
nlpsandbox · Jun 2, 2021 · eb2cae0 · eb2cae0
1 parent a63cbea
commit eb2cae0
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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/workflows/ci.yml b/.github/workflows/ci.yml
@@ -6,40 +6,18 @@ on:
   push:
     branches:
       - main
-      - develop
     tags:
       - '*.*.*'
   pull_request:
 
 env:
-  docker_repository: nlpsandbox/date-annotator-example-java
+  docker_repository: docker.synapse.org/syn22277123/date-annotator-example-java
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Lint Dockerfiles
-      uses: docker://hadolint/hadolint:latest
-      with:
-        entrypoint: hadolint
-        args: server/Dockerfile
-
-  test:
-    needs: [lint]
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Validate docker-compose.yml
-      run: docker-compose -f docker-compose.yml config >/dev/null
-
-  docker:
-    needs: [test]
+  configure:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Prepare
-      id: prep
+    - name: Create configuration
       run: |
         DOCKER_IMAGE=${{ env.docker_repository }}
         VERSION=noop
@@ -60,46 +38,78 @@ jobs:
         fi
         TAGS="${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"
+          TAGS="$TAGS,${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}
+        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
+
+  docker:
+    needs: [lint]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - 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
@@ -17,8 +17,8 @@ of predicted date annotations found in the clinical note.
 
 ### Specification
 
-- Date Annotator API version: 1.1.1
-- Tool version: 1.1.1
+- Date Annotator API version: 1.1.2
+- Tool version: 1.1.2
 - Docker image: [nlpsandbox/date-annotator-example-java]
 
 ## Model

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -2,13 +2,13 @@ version: "3.8"
 
 services:
   date-annotator:
-    image: nlpsandbox/date-annotator-example-java:1.1.1
+    image: docker.synapse.org/syn22277123/date-annotator-example-java:1.1.2
     build:
       context: server
       dockerfile: Dockerfile
     container_name: date-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:
       - date-annotator
 
 networks:
-  nlp-sandbox:
-  nlp-sandbox-internal:
+  nlpsandbox:
+  nlpsandbox-internal:
     internal: true
diff --git a/package.json b/package.json
@@ -7,8 +7,8 @@
         "generate:server": "openapi-generator-cli generate -g spring -o server -i $npm_config_specification",
         "generate:server:latest": "openapi-generator-cli generate -g spring -o server -i https://nlpsandbox.github.io/nlpsandbox-schemas/date-annotator/latest/openapi.json",
         "generate:server:edge": "openapi-generator-cli generate -g spring -o server -i https://nlpsandbox.github.io/nlpsandbox-schemas/date-annotator/edge/openapi.json",
-        "install:dependencies": "npm ci && cd server && pip install -r requirements.txt",
-        "start:dev": "cd server && mvn clean package && java -jar target/openapi-spring-*.jar",
-        "start:prod": "docker-compose up --build"
+        "install:dependencies": "npm ci",
+        "start:dev": "cd server && mvn clean package && java -jar target/openapi-spring-1.1.2.jar",
+        "start:prod": "docker compose up --build"
     }
 }
diff --git a/server/Dockerfile b/server/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.9.4-slim-buster
+FROM debian:10.9-slim
 
 ENV APP_DIR=/opt/app
 

diff --git a/server/pom.xml b/server/pom.xml
@@ -4,7 +4,7 @@
     <artifactId>openapi-spring</artifactId>
     <packaging>jar</packaging>
     <name>openapi-spring</name>
-    <version>1.1.1</version>
+    <version>1.1.2</version>
     <properties>
         <java.version>1.8</java.version>
         <maven.compiler.source>${java.version}</maven.compiler.source>
@@ -14,7 +14,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.5.0</version>
+        <version>2.3.3.RELEASE</version>
     </parent>
     <build>
         <sourceDirectory>src/main/java</sourceDirectory>

diff --git a/server/src/main/java/org/openapitools/api/ToolApi.java b/server/src/main/java/org/openapitools/api/ToolApi.java
@@ -56,15 +56,15 @@ default Optional<NativeWebRequest> getRequest() {
     default ResponseEntity<Tool> getTool() {
         Tool tool = new Tool()
             .name("date-annotator-example-java")
-            .version("1.1.1")
+            .version("1.1.2")
             .license(License.APACHE_2_0)
             .repository("github:nlpsandbox/date-annotator-example-java")
             .description("Example implementation of the NLP Sandbox Date Annotator")
             .author("NLP Sandbox Team")
             .authorEmail("[email protected]")
             .url(URI.create("https://github.com/nlpsandbox/date-annotator-example-java"))
             .type("nlpsandbox:date-annotator")
-            .apiVersion("1.1.1");
+            .apiVersion("1.1.2");
         return new ResponseEntity<Tool>(tool, HttpStatus.OK);
     }
 

diff --git a/server/src/main/java/org/openapitools/configuration/OpenAPIDocumentationConfig.java b/server/src/main/java/org/openapitools/configuration/OpenAPIDocumentationConfig.java
@@ -17,7 +17,7 @@
 
 import javax.servlet.ServletContext;
 
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-05-11T19:27:30.163340-07:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 @Configuration
 @EnableSwagger2
 public class OpenAPIDocumentationConfig {
@@ -29,7 +29,7 @@ ApiInfo apiInfo() {
             .license("Apache 2.0")
             .licenseUrl("https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE")
             .termsOfServiceUrl("https://nlpsandbox.io")
-            .version("1.1.0")
+            .version("1.1.2")
             .contact(new Contact("","", "[email protected]"))
             .build();
     }

diff --git a/server/src/main/java/org/openapitools/model/Error.java b/server/src/main/java/org/openapitools/model/Error.java
@@ -13,7 +13,7 @@
  * Problem details (tools.ietf.org/html/rfc7807)
  */
 @ApiModel(description = "Problem details (tools.ietf.org/html/rfc7807)")
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-02-25T15:53:35.186246-08:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 public class Error   {
   @JsonProperty("title")
   private String title;

diff --git a/server/src/main/java/org/openapitools/model/HealthCheck.java b/server/src/main/java/org/openapitools/model/HealthCheck.java
@@ -14,7 +14,7 @@
  * Represents the health of a service
  */
 @ApiModel(description = "Represents the health of a service")
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-02-25T15:53:35.186246-08:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 public class HealthCheck   {
   /**
    * Indicates whether the service status is acceptable or not

diff --git a/server/src/main/java/org/openapitools/model/Note.java b/server/src/main/java/org/openapitools/model/Note.java
@@ -13,7 +13,7 @@
  * A clinical note
  */
 @ApiModel(description = "A clinical note")
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-03-19T19:33:58.212495-07:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 public class Note   {
   @JsonProperty("identifier")
   private String identifier;

diff --git a/server/src/main/java/org/openapitools/model/TextAnnotation.java b/server/src/main/java/org/openapitools/model/TextAnnotation.java
@@ -13,7 +13,7 @@
  * An annotation in a text
  */
 @ApiModel(description = "An annotation in a text")
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-02-25T15:53:35.186246-08:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 public class TextAnnotation   {
   @JsonProperty("start")
   private Integer start;

diff --git a/server/src/main/java/org/openapitools/model/TextDateAnnotation.java b/server/src/main/java/org/openapitools/model/TextDateAnnotation.java
@@ -15,7 +15,7 @@
  * A date annotation in a text
  */
 @ApiModel(description = "A date annotation in a text")
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-02-25T15:53:35.186246-08:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 public class TextDateAnnotation   {
   @JsonProperty("start")
   private Integer start;

diff --git a/server/src/main/java/org/openapitools/model/TextDateAnnotationAllOf.java b/server/src/main/java/org/openapitools/model/TextDateAnnotationAllOf.java
@@ -12,7 +12,7 @@
 /**
  * TextDateAnnotationAllOf
  */
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-02-25T15:53:35.186246-08:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 public class TextDateAnnotationAllOf   {
   @JsonProperty("dateFormat")
   private String dateFormat;

diff --git a/server/src/main/java/org/openapitools/model/TextDateAnnotationRequest.java b/server/src/main/java/org/openapitools/model/TextDateAnnotationRequest.java
@@ -14,7 +14,7 @@
  * A request to annotate dates in a clinical note
  */
 @ApiModel(description = "A request to annotate dates in a clinical note")
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-02-25T15:53:35.186246-08:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 public class TextDateAnnotationRequest   {
   @JsonProperty("note")
   private Note note;

diff --git a/server/src/main/java/org/openapitools/model/TextDateAnnotationResponse.java b/server/src/main/java/org/openapitools/model/TextDateAnnotationResponse.java
@@ -16,7 +16,7 @@
  * The response to a dates annotation request
  */
 @ApiModel(description = "The response to a dates annotation request")
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-02-25T15:53:35.186246-08:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 public class TextDateAnnotationResponse   {
   @JsonProperty("textDateAnnotations")
   @Valid

diff --git a/server/src/main/java/org/openapitools/model/Tool.java b/server/src/main/java/org/openapitools/model/Tool.java
@@ -15,7 +15,7 @@
  * Information about an NLP tool
  */
 @ApiModel(description = "Information about an NLP tool")
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-03-19T19:33:58.212495-07:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 public class Tool   {
   @JsonProperty("name")
   private String name;

diff --git a/server/src/main/java/org/openapitools/model/ToolDependencies.java b/server/src/main/java/org/openapitools/model/ToolDependencies.java
@@ -16,7 +16,7 @@
  * A list of tool dependencies
  */
 @ApiModel(description = "A list of tool dependencies")
-@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-05-11T19:27:30.163340-07:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-06-02T14:41:13.852686-07:00[America/Los_Angeles]")
 public class ToolDependencies   {
   @JsonProperty("tools")
   @Valid