Release 1.1.0 (#37)

* Start update

* Run npm run generate:server:edge

* Finalize update

* Update Overview in README

Author: tschaffter

.github/workflows/ci.yml

@@ -80,7 +80,7 @@ jobs:
       uses: docker/login-action@v1
       with:
         username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_PASSWORD }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
     - name: Build and push
       id: docker_build
       uses: docker/build-push-action@v2

.github/workflows/lock.yml

@@ -1,4 +1,4 @@
-name: 'Lock Threads'
+name: Lock threads
 
 on:
   schedule:

README.md

@@ -1,7 +1,7 @@
 # NLP Sandbox Date Annotator Example
 
 [![GitHub Release](https://img.shields.io/github/release/nlpsandbox/date-annotator-example-java.svg?include_prereleases&color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/nlpsandbox/date-annotator-example-java/releases)
-[![GitHub CI](https://img.shields.io/github/workflow/status/nlpsandbox/date-annotator-example-java/ci.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/nlpsandbox/date-annotator-example-java/actions)
+[![GitHub CI](https://img.shields.io/github/workflow/status/nlpsandbox/date-annotator-example-java/CI.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/nlpsandbox/date-annotator-example-java/actions)
 [![GitHub License](https://img.shields.io/github/license/nlpsandbox/date-annotator-example-java.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/nlpsandbox/date-annotator-example-java/blob/develop/LICENSE)
 [![Docker Pulls](https://img.shields.io/docker/pulls/nlpsandbox/date-annotator-example-java.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&label=pulls&logo=docker)](https://hub.docker.com/r/nlpsandbox/date-annotator-example-java)
 [![Discord](https://img.shields.io/discord/770484164393828373.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&label=Discord&logo=discord)](https://nlpsandbox.io/discord "Realtime support / chat with the community and the team")
@@ -12,14 +12,13 @@ Example implementation of the [NLP Sandbox Date Annotator]
 ## Overview
 
 This repository provides a Java-Spring implementation of the [NLP Sandbox Date
-Annotator]. The Date Annotator is one of the first NLP Tools that can be
-benchmarked on [nlpsandbox.io]. A Date Annotator takes as input a clinical note
-and outputs a list of predicted date annotations found in the clinical note.
+Annotator]. A Date Annotator takes as input a clinical note and outputs a list
+of predicted date annotations found in the clinical note.
 
 ### Specification
 
-- Date Annotator API version: 1.0.2
-- Tool version: 1.0.2
+- Date Annotator API version: 1.1.0
+- Tool version: 1.1.0
 - Docker image: [nlpsandbox/date-annotator-example-java]
 
 ## Model
@@ -52,7 +51,7 @@ Build and start the Date Annotator.
 
     cd server/
     mvn package
-    java -jar target/openapi-spring-1.0.0.jar
+    java -jar target/openapi-spring-1.1.0.jar
 
 ### Accessing the UI
 

docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.8"
 
 services:
   date-annotator:
-    image: nlpsandbox/date-annotator-example-java:1.0.2
+    image: nlpsandbox/date-annotator-example-java:1.1.0
     build:
       context: server
       dockerfile: Dockerfile

package.json

@@ -2,8 +2,13 @@
     "devDependencies": {
         "@openapitools/openapi-generator-cli": "2.2.6"
     },
+    "private": true,
     "scripts": {
         "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: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"
     }
 }

server/Dockerfile

@@ -1,7 +1,6 @@
 FROM python:3.9.4-slim-buster
 
 ENV APP_DIR=/opt/app
-ENV APP_VERSION="1.0.2"
 
 SHELL ["/bin/bash", "-euxo", "pipefail", "-c"]
 
@@ -21,8 +20,8 @@ RUN apt-get update -qq -y \
 WORKDIR ${APP_DIR}
 COPY src src/
 COPY pom.xml ./
-RUN mvn package \
-    && mv target/openapi-spring-${APP_VERSION}.jar target/app.jar
+RUN mvn clean package \
+    && mv target/openapi-spring-*.jar target/app.jar
 
 WORKDIR /
 COPY docker-entrypoint.sh .

server/pom.xml

@@ -4,7 +4,7 @@
     <artifactId>openapi-spring</artifactId>
     <packaging>jar</packaging>
     <name>openapi-spring</name>
-    <version>1.0.2</version>
+    <version>1.1.0</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>2.4.5</version>
+        <version>2.3.3.RELEASE</version>
     </parent>
     <build>
         <sourceDirectory>src/main/java</sourceDirectory>

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("1.0.2")
+            .version("1.1.0")
             .license(License.APACHE_2_0)
             .repository("github:nlpsandbox/date-annotator-example-java")
             .description("Example implementation of the NLP Sandbox Date Annotator")
             .author("The NLP Sandbox Team")
             .authorEmail("thomas.schaffter@sagebionetworks.org")
             .url(URI.create("https://github.com/nlpsandbox/date-annotator-example-java"))
             .type("nlpsandbox:date-annotator")
-            .apiVersion("1.0.2");
+            .apiVersion("1.1.0");
         return new ResponseEntity<Tool>(tool, HttpStatus.OK);
     }
 
@@ -88,7 +88,7 @@ default ResponseEntity<Tool> getTool() {
     )
     default ResponseEntity<ToolDependencies> getToolDependencies() {
         ToolDependencies dependencies = new ToolDependencies()
-            .toolDependencies(new ArrayList<Tool>());
+            .tools(new ArrayList<Tool>());
         return new ResponseEntity<ToolDependencies>(dependencies, HttpStatus.OK);
     }
 

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 = "2021-03-19T19:33:58.212495-07:00[America/Los_Angeles]")
+@javax.annotation.Generated(value = "org.openapitools.codegen.languages.SpringCodegen", date = "2021-05-11T19:27:30.163340-07:00[America/Los_Angeles]")
 @Configuration
 @EnableSwagger2
 public class OpenAPIDocumentationConfig {
@@ -29,8 +29,8 @@ ApiInfo apiInfo() {
             .license("Apache 2.0")
             .licenseUrl("https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE")
             .termsOfServiceUrl("https://nlpsandbox.io")
-            .version("1.0.2")
-            .contact(new Contact("","", "thomas.schaffter@sagebionetworks.org"))
+            .version("1.1.0")
+            .contact(new Contact("","", "team@nlpsandbox.io"))
             .build();
     }
 

server/src/main/java/org/openapitools/model/ToolDependencies.java

@@ -16,37 +16,37 @@
  * A list of tool dependencies
  */
 @ApiModel(description = "A list of tool dependencies")
-@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 = "2021-05-11T19:27:30.163340-07:00[America/Los_Angeles]")
 public class ToolDependencies   {
-  @JsonProperty("toolDependencies")
+  @JsonProperty("tools")
   @Valid
-  private List<Tool> toolDependencies = new ArrayList<>();
+  private List<Tool> tools = new ArrayList<>();
 
-  public ToolDependencies toolDependencies(List<Tool> toolDependencies) {
-    this.toolDependencies = toolDependencies;
+  public ToolDependencies tools(List<Tool> tools) {
+    this.tools = tools;
     return this;
   }
 
-  public ToolDependencies addToolDependenciesItem(Tool toolDependenciesItem) {
-    this.toolDependencies.add(toolDependenciesItem);
+  public ToolDependencies addToolsItem(Tool toolsItem) {
+    this.tools.add(toolsItem);
     return this;
   }
 
   /**
    * A list of tools
-   * @return toolDependencies
+   * @return tools
   */
   @ApiModelProperty(required = true, value = "A list of tools")
   @NotNull
 
   @Valid
 
-  public List<Tool> getToolDependencies() {
-    return toolDependencies;
+  public List<Tool> getTools() {
+    return tools;
   }
 
-  public void setToolDependencies(List<Tool> toolDependencies) {
-    this.toolDependencies = toolDependencies;
+  public void setTools(List<Tool> tools) {
+    this.tools = tools;
   }
 
 
@@ -59,20 +59,20 @@ public boolean equals(Object o) {
       return false;
     }
     ToolDependencies toolDependencies = (ToolDependencies) o;
-    return Objects.equals(this.toolDependencies, toolDependencies.toolDependencies);
+    return Objects.equals(this.tools, toolDependencies.tools);
   }
 
   @Override
   public int hashCode() {
-    return Objects.hash(toolDependencies);
+    return Objects.hash(tools);
   }
 
   @Override
   public String toString() {
     StringBuilder sb = new StringBuilder();
     sb.append("class ToolDependencies {\n");
 
-    sb.append("    toolDependencies: ").append(toIndentedString(toolDependencies)).append("\n");
+    sb.append("    tools: ").append(toIndentedString(tools)).append("\n");
     sb.append("}");
     return sb.toString();
   }