update gradle config to ignore auto-generated file from sonar and JaCoCo

apps/openchallenges/challenge-service/build.gradle

@@ -100,13 +100,41 @@ jacocoTestReport {
   reports {
     xml.required = true
   }
+
+    afterEvaluate {
+    // A single star (*) selects files AND subdirectories.
+    // Exclude Java classes from the JaCoCo report. These files must be excluded from SonarCloud
+    // report separatedly (see SonarCloud config)
+    def autoGeneratedFiles = [
+      '**/api/*.*',
+      '**/configuration/EnumConverterConfiguration*.*',
+      '**/configuration/HomeController*.*',
+      '**/configuration/SpringDocConfiguration*.*',
+      '**/model/dto/**',
+      '**/RFC3339DateFormat.*'
+    ]
+    classDirectories.setFrom(files(classDirectories.files.collect {
+        fileTree(dir: it, exclude: autoGeneratedFiles
+        )
+    }))
+  }
 }
 
 sonar {
+    // A single star (*) only selects files, not subdirectories.
+  def autoGeneratedFiles = [
+    '**/api/*',
+    '**/configuration/EnumConverterConfiguration*.*',
+    '**/configuration/HomeController*.*',
+    '**/configuration/SpringDocConfiguration*.*',
+    '**/model/dto/**',
+    '**/RFC3339DateFormat.*'
+  ]
   properties {
     property("sonar.host.url", "https://sonarcloud.io")
     property("sonar.organization", "sage-bionetworks")
     property("sonar.projectKey", "${project.name}")
+    property("sonar.coverage.exclusions", autoGeneratedFiles.join(","))
     // Include the pull request number (ignored if not set)
     property("sonar.pullrequest.key", System.getenv('SONAR_PULL_REQUEST_NUMBER'))
   }

apps/openchallenges/image-service/build.gradle

@@ -164,7 +164,6 @@ sonar {
     property("sonar.organization", "sage-bionetworks")
     property("sonar.host.url", "https://sonarcloud.io")
     property("sonar.coverage.exclusions", autoGeneratedFiles.join(","))
-    // property("sonar.log.level", "DEBUG")
     // Include the pull request number (ignored if not set)
     property("sonar.pullrequest.key", System.getenv('SONAR_PULL_REQUEST_NUMBER'))
   }