Issue 10652 java formatter

pom.xml

@@ -41,6 +41,7 @@
 		<springfox.version>3.0.0</springfox.version>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+		<formatVersion>2.22.1</formatVersion>
 
 		<!-- Sonar -->
 		<sonar.projectKey>cBioPortal_cbioportal</sonar.projectKey>
@@ -550,6 +551,32 @@
                     </execution>
                 </executions>
             </plugin>
+
+            <!-- Format Code -->
+            <plugin>
+                <groupId>com.spotify.fmt</groupId>
+                <artifactId>fmt-maven-plugin</artifactId>
+                <version>${formatVersion}</version>
+                <configuration>
+	                <sourceDirectory>src/main/java</sourceDirectory>
+	                <testSourceDirectory>src/test/java</testSourceDirectory>
+	                <verbose>true</verbose>
+	                <filesNamePattern>.*\.java</filesNamePattern>
+	                <skip>false</skip>
+	                <skipSourceDirectory>false</skipSourceDirectory>
+	                <skipTestSourceDirectory>false</skipTestSourceDirectory>
+	                <skipSortingImports>false</skipSortingImports>
+	                <style>google</style>
+            	</configuration>
+                <executions>
+                    <execution>
+                        <goals>
+							<goal>check</goal>
+                            <goal>format</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
 	</build>
 

src/main/java/org/cbioportal/AsyncConfig.java

@@ -1,31 +1,25 @@
 package org.cbioportal;
 
+import java.util.concurrent.Executor;
 import org.springframework.beans.factory.annotation.Value;
-import org.springframework.core.env.Environment;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.scheduling.annotation.AsyncConfigurer;
+import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
 
-import java.lang.Runtime;
-import java.util.concurrent.Executor;
-
 @Configuration
 @EnableAsync
 public class AsyncConfig implements AsyncConfigurer {
-
-
-    @Value("${multithread.core_pool_size:#{T(java.lang.Runtime).getRuntime().availableProcessors()}}")
-    private int corePoolSize;
 
-    @Override
-    public Executor getAsyncExecutor() {
-        ThreadPoolTaskExecutor executor = new ThreadPoolTaskExecutor();
-        executor.setCorePoolSize(corePoolSize);
-        executor.setThreadNamePrefix("ThreadPoolTaskExecutor-");
-        executor.initialize();
-        return executor;
-    }
+  @Value("${multithread.core_pool_size:#{T(java.lang.Runtime).getRuntime().availableProcessors()}}")
+  private int corePoolSize;
 
+  @Override
+  public Executor getAsyncExecutor() {
+    ThreadPoolTaskExecutor executor = new ThreadPoolTaskExecutor();
+    executor.setCorePoolSize(corePoolSize);
+    executor.setThreadNamePrefix("ThreadPoolTaskExecutor-");
+    executor.initialize();
+    return executor;
+  }
 }

src/main/java/org/cbioportal/PortalApplication.java

@@ -7,18 +7,15 @@
 import org.springframework.context.annotation.PropertySource;
 import org.springframework.context.annotation.PropertySources;
 
-@SpringBootApplication(exclude = {
-    MongoAutoConfiguration.class,
-    MongoDataAutoConfiguration.class
-})
+@SpringBootApplication(exclude = {MongoAutoConfiguration.class, MongoDataAutoConfiguration.class})
 @PropertySources({
-    @PropertySource(ignoreResourceNotFound = true, value = "classpath:application.properties"),
-    @PropertySource(ignoreResourceNotFound = true, value = "classpath:security.properties"),
-    @PropertySource(ignoreResourceNotFound = true, value = "classpath:maven.properties"),
-    @PropertySource(ignoreResourceNotFound = true, value = "classpath:git.properties")
+  @PropertySource(ignoreResourceNotFound = true, value = "classpath:application.properties"),
+  @PropertySource(ignoreResourceNotFound = true, value = "classpath:security.properties"),
+  @PropertySource(ignoreResourceNotFound = true, value = "classpath:maven.properties"),
+  @PropertySource(ignoreResourceNotFound = true, value = "classpath:git.properties")
 })
 public class PortalApplication {
-    public static void main(String[] args) {
-        SpringApplication.run(PortalApplication.class, args);
-    }
+  public static void main(String[] args) {
+    SpringApplication.run(PortalApplication.class, args);
+  }
 }

src/main/java/org/cbioportal/WebAppConfig.java

@@ -1,7 +1,6 @@
 package org.cbioportal;
 
 import java.util.List;
-
 import org.cbioportal.web.util.InvolvedCancerStudyExtractorInterceptor;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
@@ -16,28 +15,29 @@
 // TODO Consider creating separate DispatcherServlets as in the original web.xml
 // See: https://stackoverflow.com/a/30686733/11651683
 @Configuration
-//@EnableAspectJAutoProxy // TODO no idea what this does; is this logging aspect still useful?
+// @EnableAspectJAutoProxy // TODO no idea what this does; is this logging aspect still useful?
 public class WebAppConfig implements WebMvcConfigurer {
 
-	private static final String SINGLE_PAGE_APP_ROOT = "forward:/";
+  private static final String SINGLE_PAGE_APP_ROOT = "forward:/";
 
-	@Value("${springdoc.swagger-ui.path:/swagger-ui.html}")
-	private String swaggerRedirectUrl;
+  @Value("${springdoc.swagger-ui.path:/swagger-ui.html}")
+  private String swaggerRedirectUrl;
 
-	@Override
-	public void addResourceHandlers(ResourceHandlerRegistry registry) {
-		registry.addResourceHandler("/images/**").addResourceLocations("classpath:/webapp/images/");
-		registry.addResourceHandler("/reactapp/**").addResourceLocations("classpath:/reactapp/");
-		registry.addResourceHandler("/js/**").addResourceLocations("classpath:/js/");
-	}
+  @Override
+  public void addResourceHandlers(ResourceHandlerRegistry registry) {
+    registry.addResourceHandler("/images/**").addResourceLocations("classpath:/webapp/images/");
+    registry.addResourceHandler("/reactapp/**").addResourceLocations("classpath:/reactapp/");
+    registry.addResourceHandler("/js/**").addResourceLocations("classpath:/js/");
+  }
 
-	@Override
-	public void addViewControllers(ViewControllerRegistry registry) {
-		registry.addRedirectViewController("/api", swaggerRedirectUrl);
-		registry.addRedirectViewController("/installations", "https://installationmap.netlify.app/");
-		registry.addRedirectViewController("/tutorials", "https://docs.cbioportal.org/user-guide/overview/#tutorial-slides");
-		registry.addRedirectViewController("/oql", "https://docs.cbioportal.org/user-guide/oql/");
-        registry.addRedirectViewController("/faq", "https://docs.cbioportal.org/user-guide/faq/");
+  @Override
+  public void addViewControllers(ViewControllerRegistry registry) {
+    registry.addRedirectViewController("/api", swaggerRedirectUrl);
+    registry.addRedirectViewController("/installations", "https://installationmap.netlify.app/");
+    registry.addRedirectViewController(
+        "/tutorials", "https://docs.cbioportal.org/user-guide/overview/#tutorial-slides");
+    registry.addRedirectViewController("/oql", "https://docs.cbioportal.org/user-guide/oql/");
+    registry.addRedirectViewController("/faq", "https://docs.cbioportal.org/user-guide/faq/");
 
 		List<String> endpoints = List.of(
 			"/results/*",
@@ -63,23 +63,22 @@ public void addViewControllers(ViewControllerRegistry registry) {
             "/news**"
 		);
 
-		endpoints.forEach( route -> registry.addViewController(route).setViewName(SINGLE_PAGE_APP_ROOT));
-	}
-
-	@Bean
-	public HandlerInterceptor involvedCancerStudyExtractorInterceptor() {
-		return new InvolvedCancerStudyExtractorInterceptor();
-	}
+    endpoints.forEach(route -> registry.addViewController(route).setViewName(SINGLE_PAGE_APP_ROOT));
+  }
 
-	@Override
-	public void addInterceptors(InterceptorRegistry registry) {
-		registry.addInterceptor(involvedCancerStudyExtractorInterceptor());
-	}
+  @Bean
+  public HandlerInterceptor involvedCancerStudyExtractorInterceptor() {
+    return new InvolvedCancerStudyExtractorInterceptor();
+  }
 
-	@Override
-	public void configurePathMatch(PathMatchConfigurer configurer) {
-		// Adds support for trailing slash Matches
-		configurer.setUseTrailingSlashMatch(true);
-	}
+  @Override
+  public void addInterceptors(InterceptorRegistry registry) {
+    registry.addInterceptor(involvedCancerStudyExtractorInterceptor());
+  }
 
+  @Override
+  public void configurePathMatch(PathMatchConfigurer configurer) {
+    // Adds support for trailing slash Matches
+    configurer.setUseTrailingSlashMatch(true);
+  }
 }

src/main/java/org/cbioportal/documentation/ExternalPageController.java

@@ -1,12 +1,5 @@
 package org.cbioportal.documentation;
 
-import org.springframework.stereotype.Controller;
-import org.springframework.transaction.annotation.Transactional;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.ResponseBody;
-
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
@@ -15,35 +8,45 @@
 import java.net.URLDecoder;
 import java.util.Collections;
 import java.util.Map;
+import org.springframework.stereotype.Controller;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.ResponseBody;
 
 // Retrieve the content of an external page
 // Make it auto-scannable
 @Controller
 public class ExternalPageController {
 
-    // service name: getexternalpage.json
-    // available via GET method
-    // sourceURL is required
-    @Transactional
-    @RequestMapping(value = "/api/getexternalpage.json", method = {RequestMethod.GET})
-    public @ResponseBody Map<String, String> getExternalPage(@RequestParam(required = true) String sourceURL) throws IOException {
-        String decodedString, pageText = "";
-
-        // decode the sourceURL and open a connection
-        sourceURL = URLDecoder.decode(sourceURL, "UTF-8");
-        URL url = new URL(sourceURL);
-        URLConnection connection = url.openConnection();
-
-        // create a reader
-        BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream(), "UTF-8"));
-
-        // read
-        while ((decodedString = in.readLine()) != null) {
-            pageText += decodedString + "\n";
-        }
-        in.close();
-
-        // turn the pageText into a singletonMap for json and return
-        return Collections.singletonMap("response", pageText);
+  // service name: getexternalpage.json
+  // available via GET method
+  // sourceURL is required
+  @Transactional
+  @RequestMapping(
+      value = "/api/getexternalpage.json",
+      method = {RequestMethod.GET})
+  public @ResponseBody Map<String, String> getExternalPage(
+      @RequestParam(required = true) String sourceURL) throws IOException {
+    String decodedString, pageText = "";
+
+    // decode the sourceURL and open a connection
+    sourceURL = URLDecoder.decode(sourceURL, "UTF-8");
+    URL url = new URL(sourceURL);
+    URLConnection connection = url.openConnection();
+
+    // create a reader
+    BufferedReader in =
+        new BufferedReader(new InputStreamReader(connection.getInputStream(), "UTF-8"));
+
+    // read
+    while ((decodedString = in.readLine()) != null) {
+      pageText += decodedString + "\n";
     }
-}
+    in.close();
+
+    // turn the pageText into a singletonMap for json and return
+    return Collections.singletonMap("response", pageText);
+  }
+}