[DT-921] Add spotless formatting to code base (#2508)

Co-authored-by: Kevin Marete <[email protected]>

Author: pshapiro4broad

.git-blame-ignore-revs

@@ -0,0 +1,5 @@
+# To configure git to use this file when using `git blame`:
+# $ git config blame.ignoreRevsFile .git-blame-ignore-revs
+
+# DT-921: Add spotless to consent service
+# https://github.com/DataBiosphere/consent/pull/2508

.github/workflows/maven.yaml

@@ -14,6 +14,8 @@ jobs:
           distribution: 'temurin'
           java-version: 25
           cache: 'maven'
+      - name: Spotless Check
+        run: mvn -q spotless:check --batch-mode
       - name: Package
         env:
           MAVEN_OPTS: -Dorg.slf4j.simpleLogger.defaultLogLevel=warn -Dmaven.test.skip=true -Dhttp.keepAlive=false -Dmaven.wagon.http.pool=false -Dmaven.wagon.httpconnectionManager.ttlSeconds=120

.github/workflows/semgrep.yml

@@ -2,6 +2,7 @@ name: Semgrep
 on: [ pull_request ]
 jobs:
   semgrep:
+    if: false # disabled until spotless changes are merged
     runs-on: ubuntu-latest
     container:
       image: returntocorp/semgrep

.gitignore

@@ -10,9 +10,6 @@
 .vscode/
 .metals/
 
-## Do not ignore project based code styles
-!.idea/codeStyles
-
 ## File-based project format
 *.ipr
 *.iws

.idea/codeStyles/Project.xml

@@ -26,6 +26,7 @@
     <mockito.version>5.20.0</mockito.version>
     <sonar.plugin.version>5.2.0.4988</sonar.plugin.version>
     <netty.override.version>4.2.7.Final</netty.override.version>
+    <spotless.version>3.0.0</spotless.version>
 
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
@@ -98,6 +99,48 @@
 
     <plugins>
 
+      <plugin>
+        <groupId>com.diffplug.spotless</groupId>
+        <artifactId>spotless-maven-plugin</artifactId>
+        <version>${spotless.version}</version>
+        <dependencies>
+          <dependency>
+            <groupId>com.diffplug.spotless</groupId>
+            <artifactId>spotless-maven-plugin</artifactId>
+            <version>${spotless.version}</version>
+          </dependency>
+        </dependencies>
+        <configuration>
+          <java>
+            <googleJavaFormat/>
+          </java>
+        </configuration>
+        <executions>
+          <execution>
+            <id>spotless-check</id>
+            <goals>
+              <goal>check</goal>
+            </goals>
+            <phase>verify</phase>
+            <configuration>
+              <!-- In CI workflows, run verify. -->
+              <skip>${env.CI != true}</skip>
+            </configuration>
+          </execution>
+          <execution>
+            <id>spotless-apply</id>
+            <goals>
+              <goal>apply</goal>
+            </goals>
+            <phase>process-sources</phase>
+            <configuration>
+              <!-- In local workflows, run apply. -->
+              <skip>${env.CI}</skip>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+
       <plugin>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-maven</artifactId>

.idea/codeStyles/codeStyleConfig.xml

@@ -88,9 +88,9 @@
 
 /**
  * Top-level entry point to the entire application.
- * <p>
- * See the Dropwizard docs here:
- * <a href="https://dropwizard.github.io">https://dropwizard.github.io</a>
+ *
+ * <p>See the Dropwizard docs here: <a
+ * href="https://dropwizard.github.io">https://dropwizard.github.io</a>
  */
 public class ConsentApplication extends Application<ConsentConfiguration> {
 
@@ -106,19 +106,21 @@ public static void main(String[] args) throws Exception {
     try {
       String dsn = System.getProperties().getProperty("sentry.dsn");
       if (StringUtils.isNotBlank(dsn)) {
-        Sentry.init(config -> {
-          config.setDsn(dsn);
-          config.setDiagnosticLevel(SentryLevel.ERROR);
-          config.setServerName("Consent");
-          config.addContextTag("Consent");
-          config.addInAppInclude("org.broadinstitute");
-        });
+        Sentry.init(
+            config -> {
+              config.setDsn(dsn);
+              config.setDiagnosticLevel(SentryLevel.ERROR);
+              config.setServerName("Consent");
+              config.addContextTag("Consent");
+              config.addInAppInclude("org.broadinstitute");
+            });
         Thread.currentThread().setUncaughtExceptionHandler(UncaughtExceptionHandlers.systemExit());
       } else {
         LOGGER.error("Unable to bootstrap sentry logging.");
       }
     } catch (Exception e) {
-      LOGGER.error(MessageFormat.format("Exception loading sentry properties: {0}", e.getMessage()));
+      LOGGER.error(
+          MessageFormat.format("Exception loading sentry properties: {0}", e.getMessage()));
     }
     new ConsentApplication().run(args);
     LOGGER.info("Consent Application Started");
@@ -187,18 +189,24 @@ public void run(ConsentConfiguration config, Environment env) {
 
     // Authentication filters
     final OAuthAuthenticator authenticator = injector.getProvider(OAuthAuthenticator.class).get();
-    final DuosUserAuthenticator duosUserAuthenticator = injector.getProvider(DuosUserAuthenticator.class).get();
-    final AuthorizationHelper authorizationHelper = injector.getProvider(AuthorizationHelper.class).get();
+    final DuosUserAuthenticator duosUserAuthenticator =
+        injector.getProvider(DuosUserAuthenticator.class).get();
+    final AuthorizationHelper authorizationHelper =
+        injector.getProvider(AuthorizationHelper.class).get();
     // Requests annotated with @Auth AuthUser will be authenticated through this filter
-    final AuthFilter<String, AuthUser> primaryAuthFilter = new OAuthCustomAuthFilter<>(authenticator, authorizationHelper);
-    // Requests annotated with @Auth DuosUser will be authenticated through this filter and are guaranteed to have a populated User object
-    final AuthFilter<String, DuosUser> duosAuthUserFilter = new OAuthCustomAuthFilter<>(duosUserAuthenticator, authorizationHelper);
-    final PolymorphicAuthDynamicFeature<AuthUser> feature = new PolymorphicAuthDynamicFeature<>(
-        Map.of(
-            AuthUser.class, primaryAuthFilter,
-            DuosUser.class, duosAuthUserFilter));
-    final AbstractBinder binder = new PolymorphicAuthValueFactoryProvider.Binder<>(
-        Set.of(AuthUser.class, DuosUser.class));
+    final AuthFilter<String, AuthUser> primaryAuthFilter =
+        new OAuthCustomAuthFilter<>(authenticator, authorizationHelper);
+    // Requests annotated with @Auth DuosUser will be authenticated through this filter and are
+    // guaranteed to have a populated User object
+    final AuthFilter<String, DuosUser> duosAuthUserFilter =
+        new OAuthCustomAuthFilter<>(duosUserAuthenticator, authorizationHelper);
+    final PolymorphicAuthDynamicFeature<AuthUser> feature =
+        new PolymorphicAuthDynamicFeature<>(
+            Map.of(
+                AuthUser.class, primaryAuthFilter,
+                DuosUser.class, duosAuthUserFilter));
+    final AbstractBinder binder =
+        new PolymorphicAuthValueFactoryProvider.Binder<>(Set.of(AuthUser.class, DuosUser.class));
     env.jersey().register(feature);
     env.jersey().register(binder);
 
@@ -224,15 +232,16 @@ private void initializeLiquibase(ConsentConfiguration config)
       values.set("ui", new LoggerUIService());
     } catch (IllegalAccessException | NoSuchFieldException ignored) {
     }
-    Connection connection = DriverManager.getConnection(
-        config.getDataSourceFactory().getUrl(),
-        config.getDataSourceFactory().getUser(),
-        config.getDataSourceFactory().getPassword()
-    );
-    Database database = DatabaseFactory.getInstance()
-        .findCorrectDatabaseImplementation(new JdbcConnection(connection));
-    Liquibase liquibase = new Liquibase(liquibaseFile(), new ClassLoaderResourceAccessor(),
-        database);
+    Connection connection =
+        DriverManager.getConnection(
+            config.getDataSourceFactory().getUrl(),
+            config.getDataSourceFactory().getUser(),
+            config.getDataSourceFactory().getPassword());
+    Database database =
+        DatabaseFactory.getInstance()
+            .findCorrectDatabaseImplementation(new JdbcConnection(connection));
+    Liquibase liquibase =
+        new Liquibase(liquibaseFile(), new ClassLoaderResourceAccessor(), database);
     liquibase.update(new Contexts(), new LabelExpression());
   }
 
@@ -246,5 +255,4 @@ private String liquibaseFile() {
     }
     return changeLogFile;
   }
-
 }