Updated idea extensions on new design.

Author: RamSaw

MetricsReloaded/utils/src/main/java/org/jetbrains/research/groups/ml_methods/utils/PSIUtil.java

@@ -1,13 +1,16 @@
 package org.jetbrains.research.groups.ml_methods.utils;
 
+import com.intellij.openapi.fileTypes.StdFileTypes;
+import com.intellij.openapi.project.Project;
+import com.intellij.openapi.roots.ProjectRootManager;
+import com.intellij.openapi.roots.TestSourcesFilter;
+import com.intellij.openapi.vfs.VirtualFile;
 import com.intellij.psi.*;
 import com.intellij.psi.util.PsiTreeUtil;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 
-import java.util.HashSet;
-import java.util.Optional;
-import java.util.Set;
+import java.util.*;
 
 import static com.sixrr.metrics.utils.MethodUtils.calculateSignature;
 
@@ -103,4 +106,29 @@ public static String getHumanReadableName(@Nullable PsiElement element) {
         }
         return "???";
     }
+
+    public static List<VirtualFile> getAllJavaFiles(Project project, boolean includeTestSources) {
+        List<VirtualFile> javaVirtualFiles = new ArrayList<>();
+        ProjectRootManager projectRootManager = ProjectRootManager.getInstance(project);
+        projectRootManager.getFileIndex().iterateContent(virtualFile -> {
+            if (isJavaFile(virtualFile)) {
+                if (includeTestSources && TestSourcesFilter.isTestSources(virtualFile, project)) {
+                    javaVirtualFiles.add(virtualFile);
+                }
+                if (!TestSourcesFilter.isTestSources(virtualFile, project)) {
+                    javaVirtualFiles.add(virtualFile);
+                }
+            }
+            return true;
+        });
+        return javaVirtualFiles;
+    }
+
+    public static int getNumberOfJavaFiles(Project project, boolean includeTestSources) {
+        return getAllJavaFiles(project, includeTestSources).size();
+    }
+
+    public static boolean isJavaFile(VirtualFile virtualFile) {
+        return virtualFile.getFileType().equals(StdFileTypes.JAVA);
+    }
 }

core/src/main/java/org/jetbrains/research/groups/ml_methods/algorithm/AlgorithmsRepository.java

@@ -4,6 +4,7 @@
 
 import java.util.Arrays;
 import java.util.List;
+import java.util.Optional;
 
 public class AlgorithmsRepository {
     private static final List<Algorithm> ALGORITHMS = Arrays.asList(
@@ -12,6 +13,10 @@ public class AlgorithmsRepository {
             new HAC()
     );
 
+    public static Optional<Algorithm> getAlgorithmByName(String algorithmName) {
+        return ALGORITHMS.stream().filter(algorithm -> algorithm.getDescriptionString().equals(algorithmName)).findAny();
+    }
+
     public enum AlgorithmType {
         ARI, CCDA, HAC
     }

features-extraction/src/main/java/org/jetbrains/research/groups/ml_methods/extraction/FeaturesExtractionApplicationStarter.java

@@ -89,7 +89,7 @@ public void main(String[] args) {
                     LOGGER.info(
                             refactoring.getMethod() + "->" +
                                     refactoring.getTargetClass() + System.lineSeparator() +
-                                    extractMethodDeclaration(refactoring.getMethod()))
+                                    extractMethodDeclaration(refactoring.getMethodOrThrow()))
             );
 
             List<FeatureVector> vectors;

features-extraction/src/main/java/org/jetbrains/research/groups/ml_methods/extraction/FormatterApplicationStarter.java

@@ -93,7 +93,7 @@ public void main(String[] args) {
                     LOGGER.info(
                             refactoring.getMethod() + "->" +
                                     refactoring.getTargetClass() + System.lineSeparator() +
-                                    extractMethodDeclaration(refactoring.getMethod()))
+                                    extractMethodDeclaration(refactoring.getMethodOrThrow()))
             );
             writer.write(refactorings, out);
         } catch (Throwable throwable) {

features-extraction/src/main/java/org/jetbrains/research/groups/ml_methods/extraction/MoveMethodFeaturesExtractor.java

@@ -49,13 +49,13 @@ private MoveMethodFeaturesExtractor() {}
         List<FeatureVector> vectors = new ArrayList<>();
         for (MoveMethodRefactoring refactoring : refactorings) {
             MethodInfo methodInfo =
-                repository.getMethodInfo(refactoring.getMethod()).orElseThrow(
+                repository.getMethodInfo(refactoring.getMethodOrThrow()).orElseThrow(
                     () -> new IllegalArgumentException(
                             "Refactoring of method which was not found in scope"
                     )
                 );
 
-            vectors.add(extractor.extract(methodInfo, refactoring.getTargetClass()));
+            vectors.add(extractor.extract(methodInfo, refactoring.getTargetClassOrThrow()));
         }
 
         return vectors;

features-extraction/src/main/java/org/jetbrains/research/groups/ml_methods/extraction/refactoring/RefactoringTextRepresentation.java

@@ -44,8 +44,8 @@ public RefactoringTextRepresentation(String sourceClassQualifiedName, String met
     }
 
     public RefactoringTextRepresentation(MoveMethodRefactoring refactoring) {
-        PsiMethod method = refactoring.getMethod();
-        PsiClass targetClass = refactoring.getTargetClass();
+        PsiMethod method = refactoring.getMethodOrThrow();
+        PsiClass targetClass = refactoring.getTargetClassOrThrow();
         if (method.getContainingClass() == null || method.getContainingClass().getQualifiedName() == null) {
             String errorMessage = "Refactorings without source qualified names are not supported. " +
                     "Problem during creating refactoring for method " + method.getName() + ".";

refactorings-generation/src/main/java/org/jetbrains/research/groups/ml_methods/generation/RefactoringsGenerationApplicationStarter.java

@@ -15,7 +15,7 @@
 import org.jetbrains.research.groups.ml_methods.generation.constraints.GenerationConstraintsFactory;
 import org.jetbrains.research.groups.ml_methods.generation.constraints.GenerationConstraintsFactory.GenerationConstraintType;
 import org.jetbrains.research.groups.ml_methods.refactoring.MoveMethodRefactoring;
-import org.jetbrains.research.groups.ml_methods.utils.PsiSearchUtil;
+import org.jetbrains.research.groups.ml_methods.utils.PSIUtil;
 
 import java.io.IOException;
 import java.nio.file.Path;
@@ -72,7 +72,7 @@ public void main(String[] args) {
                 System.err.println("Empty scope. Probably project cannot be open. Reload it with IDEA.");
                 APPLICATION.exit(true, true);
             }
-            int numberOfJavaFiles = PsiSearchUtil.getNumberOfJavaFiles(project, false);
+            int numberOfJavaFiles = PSIUtil.getNumberOfJavaFiles(project, false);
             int numberOfRefactoringsToGenerate = (int) (numberOfJavaFiles * 0.03);
             List<MoveMethodRefactoring> generatedRefactoring = RefactoringsGenerator.generate(GenerationConstraintsFactory.get(
                     GenerationConstraintType.ACCEPT_RELEVANT_PROPERTIES), numberOfRefactoringsToGenerate, scope);