Bumped to v0.4.1: upgraded Spring Boot and migrated Swagger SpringFox…

… to OpenAPI.

Dockerfile

@@ -1,9 +1,11 @@
 #Build jar file
-FROM openjdk:13-jdk-alpine as build-jar
-COPY . /
+FROM eclipse-temurin:latest as build-jar
+WORKDIR /app
+COPY . /app/
+RUN ./gradlew clean
 RUN ./gradlew build
 
 #Run jar file
-FROM openjdk:13-jdk-alpine
-COPY --from=build-jar build/libs/*.jar app.jar
+FROM eclipse-temurin:latest
+COPY --from=build-jar /app/build/libs/factoid-converters-0.4.1.jar app.jar
 ENTRYPOINT ["java","-Djava.security.egd=file:/dev/./urandom","-jar","/app.jar"]

README.md

@@ -20,7 +20,7 @@ java -jar build/libs/factoid-converters*.jar --server.port=8080
 RESTful API (Swagger docs):
 
 Once the app is built and running, 
-the auto-generated documentation is available at 
+the auto-generated OpenAPI/Swagger documentation is available at (ending with '/')
 `http://localhost:8080/convert/`
 
 ## Docker
@@ -33,7 +33,7 @@ docker run -it --rm --name factoid-converters -p <PORT>:8080 pathwaycommons/fact
 ```
 
 Optionally, a member of 'pathwaycommons' group can now push (upload) the latest Docker image there:
-
+(BTW: the latest Docker image is built automatically by Dockerhub on every git push to the master branch)
 ```commandline
 docker login
 docker push pathwaycommons/factoid-converters

build.gradle

@@ -12,8 +12,8 @@ buildscript {
     }
 }
 
-apply plugin: 'idea'
 apply plugin: 'java'
+apply plugin: 'idea'
 apply plugin: 'org.springframework.boot'
 apply plugin: 'io.spring.dependency-management'
 
@@ -30,14 +30,17 @@ repositories {
 dependencies {
     implementation 'org.springframework.boot:spring-boot-starter-actuator'
     implementation 'org.springframework.boot:spring-boot-starter-web'
-    runtimeOnly 'org.springframework.boot:spring-boot-devtools'
-    testImplementation 'org.springframework.boot:spring-boot-starter-test'
+    implementation "org.springframework.boot:spring-boot-configuration-processor"
+    implementation 'org.springdoc:springdoc-openapi-ui:1.7.0'
+
     implementation 'org.biopax.paxtools:sbgn-converter:5.3.0'
     implementation 'com.google.code.gson:gson:2.9.0'
     implementation 'org.apache.commons:commons-collections4:4.4'
-    implementation 'io.springfox:springfox-swagger2:2.7.0'
-    implementation 'io.springfox:springfox-swagger-ui:2.7.0'
 
+    runtimeOnly 'org.springframework.boot:spring-boot-devtools'
+    testImplementation 'org.springframework.boot:spring-boot-starter-test'
+
+    //java 9+ does not have Jax B Dependents
     implementation 'javax.xml.bind:jaxb-api:2.3.1'
     implementation 'com.sun.xml.bind:jaxb-core:2.3.0.1'
     implementation 'com.sun.xml.bind:jaxb-impl:2.3.6'
@@ -46,4 +49,4 @@ dependencies {
 
 sourceCompatibility = 8
 group = 'pathwaycommons'
-version =  '0.2.2'
+version =  '0.4.1'

src/main/java/factoid/web/Application.java

@@ -2,6 +2,7 @@
 
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.web.servlet.config.annotation.ResourceHandlerRegistry;
 import org.springframework.web.servlet.config.annotation.ViewControllerRegistry;
 import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
 
@@ -14,6 +15,15 @@ public void addViewControllers(ViewControllerRegistry registry) {
     registry.addRedirectViewController("/", "/swagger-ui.html");
   }
 
+  @Override
+  public void addResourceHandlers(ResourceHandlerRegistry registry) {
+    registry.addResourceHandler("/webjars/**")
+        .addResourceLocations("classpath:/META-INF/resources/webjars/");
+
+    registry.addResourceHandler("swagger-ui.html")
+        .addResourceLocations("classpath:/META-INF/resources/");
+  }
+
   public static void main(String[] args) {
     SpringApplication.run(Application.class, args);
   }

src/main/java/factoid/web/Controller.java

@@ -5,8 +5,8 @@
 
 import factoid.converter.BiopaxToFactoid;
 import factoid.converter.FactoidToBiopax;
-import io.swagger.annotations.ApiOperation;
-import io.swagger.annotations.ApiParam;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.Parameter;
 import org.biopax.paxtools.io.SimpleIOHandler;
 import org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter;
 import org.biopax.paxtools.model.Model;
@@ -31,13 +31,13 @@
 @RequestMapping(value = "/v2", method = {RequestMethod.POST})
 public class Controller {
 
-  @ApiOperation(value = "json-to-biopax", notes = "Converts a Factoid model to BioPAX.")
+  @Operation(summary = "json-to-biopax", description = "Converts a Factoid model to BioPAX.")
   @RequestMapping(path = "/json-to-biopax",
     consumes = MediaType.APPLICATION_JSON_VALUE,
     produces = "application/vnd.biopax.rdf+xml"
   )
   public String jsonToBiopax(
-    @ApiParam("Factoid document content (JSON string)") @RequestBody String body) {
+    @Parameter(description = "Factoid document content (JSON string)") @RequestBody String body) {
     // Add templates to converter by the reader
     FactoidToBiopax converter = new FactoidToBiopax();
     try {
@@ -52,13 +52,13 @@ public String jsonToBiopax(
     return converter.convertToBiopax();
   }
 
-  @ApiOperation(value = "json-to-sbgn", notes = "Converts a Factoid model to SBGN-ML (via BioPAX).")
+  @Operation(summary = "json-to-sbgn", description = "Converts a Factoid model to SBGN-ML (via BioPAX).")
   @RequestMapping(path = "/json-to-sbgn",
     consumes = MediaType.APPLICATION_JSON_VALUE,
     produces = "application/xml"
   )
   public String jsonToSbgn(
-    @ApiParam("Factoid document (JSON string)") @RequestBody String body) {
+    @Parameter(description = "Factoid document (JSON string)") @RequestBody String body) {
     try {
       InputStream is = new ByteArrayInputStream(jsonToBiopax(body).getBytes(StandardCharsets.UTF_8));
       Model model = new SimpleIOHandler().convertFromOWL(is);
@@ -73,13 +73,13 @@ public String jsonToSbgn(
     }
   }
 
-  @ApiOperation(value = "biopax-to-sbgn", notes = "Converts a factoid BioPAX model to SBGN-ML (SBGN PD).")
+  @Operation(summary = "biopax-to-sbgn", description = "Converts a factoid BioPAX model to SBGN-ML (SBGN PD).")
   @RequestMapping(path = "/biopax-to-sbgn",
     consumes = "application/vnd.biopax.rdf+xml",
     produces = "application/xml"
   )
   public String biopaxToSbgn(
-    @ApiParam("A factoid (small) BioPAX RDF/XML model") @RequestBody String body) {
+    @Parameter(description = "A factoid (small) BioPAX RDF/XML model") @RequestBody String body) {
     try {
       InputStream is = new ByteArrayInputStream(body.getBytes(StandardCharsets.UTF_8));
       Model model = new SimpleIOHandler().convertFromOWL(is);
@@ -94,13 +94,13 @@ public String biopaxToSbgn(
     }
   }
 
-  @ApiOperation(value = "biopax-to-json", notes = "Converts a BioPAX model to Factoid JSON.")
+  @Operation(summary = "biopax-to-json", description = "Converts a BioPAX model to Factoid JSON.")
   @RequestMapping(path = "/biopax-to-json",
     consumes = "application/vnd.biopax.rdf+xml",
     produces = "application/json"
   )
   public String biopaxToFactoid(
-		  @ApiParam("A BioPAX RDF/XML model") @RequestBody String body) {
+		  @Parameter(description = "A BioPAX RDF/XML model") @RequestBody String body) {
 	  BiopaxToFactoid converter = new BiopaxToFactoid();
 	  try {
 		  InputStream is = new ByteArrayInputStream(body.getBytes(StandardCharsets.UTF_8));
@@ -113,13 +113,13 @@ public String biopaxToFactoid(
 	  }
   }
 
-  @ApiOperation(value = "biopax-url-to-json", notes = "Converts a BioPAX model to Factoid JSON.")
+  @Operation(summary = "biopax-url-to-json", description = "Converts a BioPAX model to Factoid JSON.")
   @RequestMapping(path = "/biopax-url-to-json",
     consumes = "text/plain",
     produces = "application/json"
   )
   public String biopaxUrlToFactoid(
-		  @ApiParam("URL of a TAR-GZ compressed BioPAX RDF/XML file") @RequestBody String url) {
+		  @Parameter(description = "URL of a TAR-GZ compressed BioPAX RDF/XML file") @RequestBody String url) {
 	  BiopaxToFactoid converter = new BiopaxToFactoid();
 	  try {
 		  String body = getContentFromUrl(url);

src/main/java/factoid/web/OpenApiConfig.java

@@ -0,0 +1,42 @@
+package factoid.web;
+
+import io.swagger.v3.oas.models.OpenAPI;
+import io.swagger.v3.oas.models.info.Contact;
+import io.swagger.v3.oas.models.info.Info;
+import io.swagger.v3.oas.models.info.License;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class OpenApiConfig {
+
+  @Bean
+  public OpenAPI customOpenAPI() {
+    return new OpenAPI()
+      .info(apiInfo());
+  }
+
+  private Info apiInfo() {
+    return new Info()
+      .title("Factoid data converters")
+      .description("A RESTful web service, built with Spring Boot and Paxtools java libraries, that converts " +
+          "Factoid documents to BioPAX or SBGN formats.")
+      .version("2")
+      .contact(apiContact())
+      .license(apiLicence());
+  }
+
+  private License apiLicence() {
+    return new License()
+      .name("MIT Licence")
+      .url("https://opensource.org/licenses/mit-license.php");
+  }
+
+  private Contact apiContact() {
+    return new Contact()
+      .name("Pathway Commons")
+      .email("[email protected]")
+      .url("https://www.pathwaycommons.org");
+  }
+
+}

src/main/resources/config/application.properties

@@ -5,3 +5,10 @@ server.servlet.context-path = /convert
 # * - enables all actuator endpoints
 management.endpoints.web.exposure.include=health
 #management.endpoints.web.exposure.exclude=
+
+# OpenAPI/Swagger3 (feature and /v3/api-docs endpoint)
+springdoc.api-docs.enabled=true
+springdoc.swagger-ui.enabled=true
+#springdoc.packagesToScan=?
+#springdoc.pathsToMatch=?
+

src/test/java/factoid/web/ControllerT.java

@@ -1,15 +1,13 @@
 package factoid.web;
 
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.web.client.TestRestTemplate;
 import org.springframework.context.annotation.Import;
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.MediaType;
-import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import java.io.IOException;
 import java.nio.file.Files;
@@ -18,7 +16,6 @@
 import static org.junit.jupiter.api.Assertions.*;
 
 
-@ExtendWith(SpringExtension.class)
 @Import(Application.class)
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
 public class ControllerT {
@@ -73,7 +70,7 @@ public void testBiopaxToFactoid() throws IOException {
   }
 
   @Test
-  public void testBiopaxUrlToFactoid() throws IOException {
+  public void testBiopaxUrlToFactoid() {
     String url = "https://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.psp.BIOPAX.owl.gz";
     HttpHeaders headers = new HttpHeaders();
     headers.set("Content-Type", "text/plain");