Emit inverse relationships

Fixes #413. Previously, "find references" and "find implementations"
didn't work as expected with Sourcegraph 5.0 due to
https://github.com/sourcegraph/sourcegraph/issues/50927.

This PR is a workaround until that issue gets fixed so that users can
index with scip-java and get the best possible navigation experience.

Author: olafurpg

scip-java/src/main/scala/com/sourcegraph/scip_java/commands/IndexSemanticdbCommand.scala

@@ -36,6 +36,10 @@ final case class IndexSemanticdbCommand(
     @Description(
       "Whether to infer the location of SemanticDB files based as produced by Bazel"
     ) bazel: Boolean = true,
+    @Description(
+      "Whether to emit parent->child relationships for 'Find references' and 'Find implementations'. " +
+        "This flag exists as a workaround for the issue https://github.com/sourcegraph/sourcegraph/issues/50927"
+    ) emitInverseRelationships: Boolean = true,
     @Description("URL to a PackageHub instance")
     @Hidden
     packagehub: Option[String] = None,
@@ -85,7 +89,8 @@ final case class IndexSemanticdbCommand(
         format,
         parallel,
         packages.map(_.toPackageInformation).asJava,
-        buildKind
+        buildKind,
+        emitInverseRelationships
       )
     ScipSemanticdb.run(options)
     postPackages(packages)

scip-semanticdb/src/main/java/com/sourcegraph/scip_semanticdb/BazelBuildTool.java

@@ -8,7 +8,6 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.PathMatcher;
-import java.sql.Array;
 import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
@@ -48,7 +47,8 @@ public void error(Throwable e) {
             ScipOutputFormat.TYPED_PROTOBUF,
             options.parallel,
             mavenPackages,
-            "");
+            "",
+            true);
     ScipSemanticdb.run(scipOptions);
     if (!scipOptions.reporter.hasErrors()) {
       System.out.println("done: " + scipOptions.output);

scip-semanticdb/src/main/java/com/sourcegraph/scip_semanticdb/ScipSemanticdb.java

@@ -65,7 +65,8 @@ private void run() throws IOException {
 
   private void runTyped(List<Path> files, PackageTable packages) {
     writer.emitTyped(typedMetadata());
-    filesStream(files).forEach(document -> processTypedDocument(document, packages));
+    InverseReferenceRelationships references = inverseReferenceRelationships(files);
+    filesStream(files).forEach(document -> processTypedDocument(document, packages, references));
   }
 
   private String typedSymbol(String symbol, Package pkg) {
@@ -82,7 +83,8 @@ public static boolean isDefinitionRole(Role role) {
     return role == Role.DEFINITION || role == Role.SYNTHETIC_DEFINITION;
   }
 
-  private void processTypedDocument(Path path, PackageTable packages) {
+  private void processTypedDocument(
+      Path path, PackageTable packages, InverseReferenceRelationships references) {
     for (ScipTextDocument doc : parseTextDocument(path).collect(Collectors.toList())) {
       if (doc.semanticdb.getOccurrencesCount() == 0) {
         continue;
@@ -130,6 +132,19 @@ private void processTypedDocument(Path path, PackageTable packages) {
         Scip.SymbolInformation.Builder scipInfo =
             Scip.SymbolInformation.newBuilder().setSymbol(typedSymbol(info.getSymbol(), pkg));
 
+        // TODO: this can be removed once https://github.com/sourcegraph/sourcegraph/issues/50927 is
+        // fixed.
+        ArrayList<String> inverseReferences = references.map.get(info.getSymbol());
+        if (inverseReferences != null) {
+          for (String inverseReference : inverseReferences) {
+            scipInfo.addRelationships(
+                Scip.Relationship.newBuilder()
+                    .setSymbol(inverseReference)
+                    .setIsImplementation(true)
+                    .setIsReference(true));
+          }
+        }
+
         for (int i = 0; i < info.getDefinitionRelationshipsCount(); i++) {
           String definitionSymbol = info.getDefinitionRelationships(i);
           if (definitionSymbol.isEmpty()) {
@@ -245,6 +260,50 @@ private Stream<Path> filesStream(List<Path> files) {
     return options.parallel ? files.parallelStream() : files.stream();
   }
 
+  private static class InverseReferenceRelationships {
+    public final Map<String, ArrayList<String>> map;
+
+    private InverseReferenceRelationships(Map<String, ArrayList<String>> map) {
+      this.map = map;
+    }
+  }
+
+  private InverseReferenceRelationships inverseReferenceRelationships(List<Path> files) {
+    if (!options.emitInverseRelationships) {
+        return new InverseReferenceRelationships(Collections.emptyMap());
+    }
+    return new InverseReferenceRelationships(
+        filesStream(files)
+            .flatMap(this::parseTextDocument)
+            .flatMap(this::referenceRelationships)
+            .collect(
+                Collectors.groupingBy(
+                    SymbolRelationship::getTo,
+                    Collectors.mapping(
+                        SymbolRelationship::getFrom, Collectors.toCollection(ArrayList::new)))));
+  }
+
+  private Stream<SymbolRelationship> referenceRelationships(ScipTextDocument document) {
+    ArrayList<SymbolRelationship> relationships = new ArrayList<>();
+    for (int i = 0; i < document.semanticdb.getSymbolsCount(); i++) {
+      SymbolInformation info = document.semanticdb.getSymbols(i);
+      if (!supportsReferenceRelationship(info)) {
+        continue;
+      }
+      if (info.getSymbol().isEmpty() || SemanticdbSymbols.isLocal(info.getSymbol())) {
+        continue;
+      }
+      for (int j = 0; j < info.getOverriddenSymbolsCount(); j++) {
+        String overriddenSymbol = info.getOverriddenSymbols(j);
+        if (SemanticdbSymbols.isLocal(overriddenSymbol)) {
+          continue;
+        }
+        relationships.add(new SymbolRelationship(info.getSymbol(), overriddenSymbol));
+      }
+    }
+    return relationships.stream();
+  }
+
   private Set<String> exportSymbols(List<Path> files) {
     return filesStream(files)
         .flatMap(this::parseTextDocument)

scip-semanticdb/src/main/java/com/sourcegraph/scip_semanticdb/ScipSemanticdbOptions.java

@@ -17,6 +17,7 @@ public class ScipSemanticdbOptions {
   public final boolean parallel;
   public final List<MavenPackage> packages;
   public final String buildKind;
+  public final boolean emitInverseRelationships;
 
   public ScipSemanticdbOptions(
       List<Path> targetroots,
@@ -28,7 +29,8 @@ public ScipSemanticdbOptions(
       ScipOutputFormat format,
       boolean parallel,
       List<MavenPackage> packages,
-      String buildKind) {
+      String buildKind,
+      boolean emitInverseRelationships) {
     this.targetroots = targetroots;
     this.output = output;
     this.sourceroot = sourceroot;
@@ -39,5 +41,6 @@ public ScipSemanticdbOptions(
     this.parallel = parallel;
     this.packages = packages;
     this.buildKind = buildKind;
+    this.emitInverseRelationships = emitInverseRelationships;
   }
 }

scip-semanticdb/src/main/java/com/sourcegraph/scip_semanticdb/SymbolRelationship.java

@@ -0,0 +1,19 @@
+package com.sourcegraph.scip_semanticdb;
+
+public class SymbolRelationship {
+  public final String from;
+  public final String to;
+
+  public SymbolRelationship(String from, String to) {
+    this.from = from;
+    this.to = to;
+  }
+
+  public String getFrom() {
+    return from;
+  }
+
+  public String getTo() {
+    return to;
+  }
+}

tests/snapshots/src/main/generated/ByteParser.scala

@@ -107,6 +107,9 @@ abstract class ByteParser[J] extends upickle.core.BufferingByteParser{
   protected[this] def close(): Unit
 //                    ^^^^^ definition semanticdb maven maven/com.lihaoyi/ujson_2.13 1.4.0 ujson/ByteParser#close().
 //                          documentation ```scala\ndef close(): Unit\n```
+//                          relationship is_reference is_implementation ujson/ByteArrayParser#close().
+//                          relationship is_reference is_implementation ujson/ByteBufferParser#close().
+//                          relationship is_reference is_implementation ujson/InputStreamParser#close().
 //                             ^^^^ reference semanticdb maven maven/org.scala-lang/scala-library 2.13.10 scala/Unit#
 
   /**

tests/snapshots/src/main/generated/CharParser.scala

@@ -107,6 +107,8 @@ abstract class CharParser[J] extends upickle.core.BufferingCharParser{
   protected[this] def close(): Unit
 //                    ^^^^^ definition semanticdb maven maven/com.lihaoyi/ujson_2.13 1.4.0 ujson/CharParser#close().
 //                          documentation ```scala\ndef close(): Unit\n```
+//                          relationship is_reference is_implementation ujson/CharSequenceParser#close().
+//                          relationship is_reference is_implementation ujson/StringParser#close().
 //                             ^^^^ reference semanticdb maven maven/org.scala-lang/scala-library 2.13.10 scala/Unit#
 
   /**

tests/snapshots/src/main/generated/com/airbnb/epoxy/AsyncEpoxyDiffer.java

@@ -60,6 +60,7 @@ interface ResultCallback {
     void onResult(@NonNull DiffResult result);
 //       ^^^^^^^^ definition semanticdb maven . . com/airbnb/epoxy/AsyncEpoxyDiffer#ResultCallback#onResult().
 //                documentation ```java\npublic abstract void onResult(DiffResult result)\n```
+//                relationship is_reference is_implementation com/airbnb/epoxy/EpoxyControllerAdapter#onResult().
 //                 ^^^^^^^ reference semanticdb maven maven/androidx.annotation/annotation 1.1.0 androidx/annotation/NonNull#
 //                         ^^^^^^^^^^ reference semanticdb maven . . com/airbnb/epoxy/DiffResult#
 //                                    ^^^^^^ definition local 0