EA-109160 - assert: StubProcessingHelperBase.handleNonPsiStubs

accept that some view providers may be different than during indexing
and use JavaSourceFilterScope to access Java stubs to avoid querying those view providers at all

java/java-tests/testSrc/com/intellij/java/index/IndexTest.groovy

@@ -71,6 +71,7 @@ import com.intellij.util.indexing.*
 import com.intellij.util.indexing.impl.MapIndexStorage
 import com.intellij.util.indexing.impl.MapReduceIndex
 import com.intellij.util.io.*
+import com.siyeh.ig.JavaOverridingMethodUtil
 import groovy.transform.CompileStatic
 import org.jetbrains.annotations.NotNull
 
@@ -797,4 +798,15 @@ class IndexTest extends JavaCodeInsightFixtureTestCase {
       assert files?.length == 1
     }).assertTiming()
   }
+
+  void "test class file in src content isn't returned from index"() {
+    def runnable = JavaPsiFacade.getInstance(project).findClass(Runnable.name, GlobalSearchScope.allScope(project))
+    def thread = JavaPsiFacade.getInstance(project).findClass(Thread.name, GlobalSearchScope.allScope(project))
+    def srcRoot = myFixture.tempDirFixture.getFile("")
+    WriteCommandAction.runWriteCommandAction(project) { VfsUtil.copy(this, thread.containingFile.virtualFile, srcRoot) }
+
+    def projectScope = GlobalSearchScope.projectScope(project)
+    assert !JavaOverridingMethodUtil.getOverridingMethodsIfCheapEnough(runnable.methods[0], projectScope, { true }).findFirst().present
+    assert StubIndex.instance.getElements(JavaStubIndexKeys.METHODS, 'run', project, projectScope, PsiMethod).empty 
+  }
 }

platform/indexing-impl/src/com/intellij/psi/stubs/StubProcessingHelperBase.java

@@ -18,6 +18,7 @@ package com.intellij.psi.stubs;
 import com.intellij.openapi.diagnostic.Logger;
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.vfs.VirtualFile;
+import com.intellij.psi.PsiBinaryFile;
 import com.intellij.psi.PsiElement;
 import com.intellij.psi.PsiFile;
 import com.intellij.psi.PsiManager;
@@ -107,6 +108,13 @@ public abstract class StubProcessingHelperBase {
       return true;
     }
 
+    if (psiFile instanceof PsiBinaryFile) {
+      // a file can be indexed as containing stubs, 
+      // but then in a specific project FileViewProviderFactory can decide not to create stub-aware PSI 
+      // because the file isn't in expected location
+      return true; 
+    }
+
     ObjectStubTree objectStubTree = StubTreeLoader.getInstance().readFromVFile(psiFile.getProject(), file);
     if (objectStubTree == null) {
       LOG.error("Stub index points to a file without indexed stubs: " + psiFile.getFileType());

plugins/InspectionGadgets/InspectionGadgetsAnalysis/src/com/siyeh/ig/JavaOverridingMethodUtil.java

@@ -19,6 +19,7 @@ import com.intellij.openapi.progress.ProgressManager;
 import com.intellij.openapi.project.Project;
 import com.intellij.psi.*;
 import com.intellij.psi.impl.java.stubs.index.JavaStubIndexKeys;
+import com.intellij.psi.impl.search.JavaSourceFilterScope;
 import com.intellij.psi.search.GlobalSearchScope;
 import com.intellij.psi.search.GlobalSearchScopeUtil;
 import com.intellij.psi.search.SearchScope;
@@ -60,7 +61,7 @@ public class JavaOverridingMethodUtil {
     if (!StubIndex.getInstance().processElements(JavaStubIndexKeys.METHODS,
                                                 name,
                                                 project,
-                                                effectiveSearchScope,
+                                                new JavaSourceFilterScope(effectiveSearchScope),
                                                 PsiMethod.class,
                                             m -> {
                                               ProgressManager.checkCanceled();