Add file searching ability to CodeDirectory (#363)

Analyzing binary result from multiple tools shows we'll need this
functionality in multiple places, so we're adding it to the generally
available `CodeDirectory` type.

framework/codemodder-base/src/main/java/io/codemodder/CLI.java

@@ -377,10 +377,11 @@ public Integer call() throws IOException {
       }
 
       // create the loader
+      CodeDirectory codeDirectory = new DefaultCodeDirectory(projectPath);
       List<Path> sarifFiles =
           sarifs != null ? sarifs.stream().map(Path::of).collect(Collectors.toList()) : List.of();
       Map<String, List<RuleSarif>> pathSarifMap =
-          SarifParser.create().parseIntoMap(sarifFiles, projectPath);
+          SarifParser.create().parseIntoMap(sarifFiles, codeDirectory);
       List<ParameterArgument> codemodParameters =
           createFromParameterStrings(this.codemodParameters);
       CodemodLoader loader =

framework/codemodder-base/src/main/java/io/codemodder/CodeDirectory.java

@@ -1,10 +1,22 @@
 package io.codemodder;
 
+import java.io.IOException;
 import java.nio.file.Path;
+import java.util.Optional;
 
 /** Holds a code directory (e.g., a repository root). */
 public interface CodeDirectory {
 
   /** The filesystem directory path we are running against. */
   Path asPath();
+
+  /**
+   * Find a file with the given trailing path. This is useful for situations in which you only know
+   * the last part of the path for a file within the project.
+   */
+  Optional<Path> findFilesWithTrailingPath(final String path) throws IOException;
+
+  static CodeDirectory from(final Path projectDir) {
+    return new DefaultCodeDirectory(projectDir);
+  }
 }

framework/codemodder-base/src/main/java/io/codemodder/DefaultCodeDirectory.java

@@ -1,8 +1,15 @@
 package io.codemodder;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.FileVisitResult;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.SimpleFileVisitor;
+import java.nio.file.attribute.BasicFileAttributes;
 import java.util.Objects;
+import java.util.Optional;
+import java.util.concurrent.atomic.AtomicReference;
 
 final class DefaultCodeDirectory implements CodeDirectory {
 
@@ -26,4 +33,31 @@ final class DefaultCodeDirectory implements CodeDirectory {
   public Path asPath() {
     return repositoryDir;
   }
+
+  @Override
+  public Optional<Path> findFilesWithTrailingPath(final String path) throws IOException {
+    // find the files with the trailing path
+    AtomicReference<Path> found = new AtomicReference<>();
+
+    final String cleanPath =
+        path.trim()
+            .replace("\\\\", "\\")
+            .replace("//", "/")
+            .replace('\\', File.separatorChar)
+            .replace('/', File.separatorChar);
+
+    Files.walkFileTree(
+        repositoryDir,
+        new SimpleFileVisitor<>() {
+          @Override
+          public FileVisitResult visitFile(final Path file, final BasicFileAttributes attrs) {
+            if (file.toString().endsWith(cleanPath)) {
+              found.set(file);
+              return FileVisitResult.TERMINATE;
+            }
+            return FileVisitResult.CONTINUE;
+          }
+        });
+    return Optional.ofNullable(found.get());
+  }
 }

framework/codemodder-base/src/main/java/io/codemodder/DefaultSarifParser.java

@@ -30,10 +30,10 @@ private Optional<Map.Entry<String, RuleSarif>> tryToBuild(
       final String toolName,
       final String rule,
       final SarifSchema210 sarif,
-      final Path repositoryRoot,
+      final CodeDirectory codeDirectory,
       final List<RuleSarifFactory> factories) {
     for (final var factory : factories) {
-      final var maybeRuleSarif = factory.build(toolName, rule, sarif, repositoryRoot);
+      final var maybeRuleSarif = factory.build(toolName, rule, sarif, codeDirectory);
       if (maybeRuleSarif.isPresent()) {
         return Optional.of(Map.entry(toolName, maybeRuleSarif.get()));
       }
@@ -64,7 +64,7 @@ private String extractRuleId(final Result result, final Run run) {
   }
 
   private Stream<Map.Entry<String, RuleSarif>> fromSarif(
-      final Run run, final SarifSchema210 sarif, final Path repositoryRoot) {
+      final Run run, final SarifSchema210 sarif, final CodeDirectory codeDirectory) {
     // driver name
     final var toolName = run.getTool().getDriver().getName();
     final List<RuleSarifFactory> factories =
@@ -81,20 +81,21 @@ private Stream<Map.Entry<String, RuleSarif>> fromSarif(
             : Stream.<String>empty();
 
     return allResults.flatMap(
-        rule -> tryToBuild(toolName, rule, sarif, repositoryRoot, factories).stream());
+        rule -> tryToBuild(toolName, rule, sarif, codeDirectory, factories).stream());
   }
 
   /**
    * Parse a list of SARIF files and organize the obtained {@link RuleSarif}s by tool name with a
    * map .
    */
+  @Override
   public Map<String, List<RuleSarif>> parseIntoMap(
-      final List<Path> sarifFiles, final Path repositoryRoot) {
+      final List<Path> sarifFiles, final CodeDirectory codeDirectory) {
     final var map = new HashMap<String, List<RuleSarif>>();
     sarifFiles.stream()
         .flatMap(f -> readSarifFile(f).stream())
         .flatMap(
-            sarif -> sarif.getRuns().stream().flatMap(run -> fromSarif(run, sarif, repositoryRoot)))
+            sarif -> sarif.getRuns().stream().flatMap(run -> fromSarif(run, sarif, codeDirectory)))
         .forEach(
             p ->
                 map.merge(

framework/codemodder-base/src/main/java/io/codemodder/RuleSarifFactory.java

@@ -1,13 +1,12 @@
 package io.codemodder;
 
 import com.contrastsecurity.sarif.SarifSchema210;
-import java.nio.file.Path;
 import java.util.Optional;
 
 /** Builds {@link RuleSarif}s. */
 public interface RuleSarifFactory {
 
   /** Builds {@link RuleSarif}s if it supports {@code toolName}. */
   Optional<RuleSarif> build(
-      String toolName, String rule, SarifSchema210 sarif, Path repositoryRoot);
+      String toolName, String rule, SarifSchema210 sarif, CodeDirectory codeDirectory);
 }

framework/codemodder-base/src/main/java/io/codemodder/SarifParser.java

@@ -14,7 +14,7 @@ public interface SarifParser {
    * Given a list of sarif {@link Path}s, organize them into a {@link Map} containing {@link
    * RuleSarif}s organized by tool name.
    */
-  Map<String, List<RuleSarif>> parseIntoMap(List<Path> sarifFiles, Path repositoryRoot);
+  Map<String, List<RuleSarif>> parseIntoMap(List<Path> sarifFiles, CodeDirectory codeDirectory);
 
   static SarifParser create() {
     return new DefaultSarifParser();

framework/codemodder-base/src/test/java/io/codemodder/DefaultCodeDirectoryTest.java

@@ -0,0 +1,68 @@
+package io.codemodder;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Optional;
+import java.util.stream.Stream;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.io.TempDir;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+
+final class DefaultCodeDirectoryTest {
+
+  private DefaultCodeDirectory codeDirectory;
+  private Path repoDir;
+
+  @BeforeEach
+  void setup(@TempDir final Path repoDir) throws IOException {
+    Path testFile1 = repoDir.resolve("my/other/test/file1.java");
+    Path srcFile1 = repoDir.resolve("src/main/file1.java");
+    Path srcFile2 = repoDir.resolve("src/main/file2.java");
+
+    Files.createDirectories(testFile1.getParent());
+    Files.createFile(testFile1);
+
+    Files.createDirectories(srcFile1.getParent());
+    Files.createFile(srcFile1);
+
+    Files.createDirectories(srcFile2.getParent());
+    Files.createFile(srcFile2);
+
+    Files.writeString(testFile1, "test file 1");
+    Files.writeString(srcFile1, "src file 1");
+    Files.writeString(srcFile2, "src file 2");
+
+    this.repoDir = repoDir;
+    codeDirectory = new DefaultCodeDirectory(repoDir);
+  }
+
+  @ParameterizedTest
+  @MethodSource("fileTests")
+  void it_finds_files(final String givenPath, final String expectedPath) throws IOException {
+    Optional<Path> filesWithTrailingPath = codeDirectory.findFilesWithTrailingPath(givenPath);
+
+    if (expectedPath == null) {
+      assertThat(filesWithTrailingPath).isEmpty();
+    } else {
+      assertThat(filesWithTrailingPath).isPresent();
+      Path expected = repoDir.resolve(expectedPath);
+      assertThat(filesWithTrailingPath.get()).isEqualTo(expected);
+    }
+  }
+
+  private static Stream<Arguments> fileTests() {
+    return Stream.of(
+        Arguments.of("file1.java", "my/other/test/file1.java"),
+        Arguments.of("main/file1.java", "src/main/file1.java"),
+        Arguments.of("main//file1.java", "src/main/file1.java"),
+        Arguments.of("main\\file1.java", "src/main/file1.java"),
+        Arguments.of("src\\\\main\\file1.java", "src/main/file1.java"),
+        Arguments.of("file2.java", "src/main/file2.java"),
+        Arguments.of("file3.java", null));
+  }
+}

framework/codemodder-testutils/src/main/java/io/codemodder/testutils/CodemodTestMixin.java

@@ -115,11 +115,12 @@ private void verifyCodemod(
     Path sonarJson = testResourceDir.resolve("sonar-issues.json");
 
     // Check for any sarif files and build the RuleSarif map
+    CodeDirectory codeDir = CodeDirectory.from(tmpDir);
     List<Path> allSarifs = new ArrayList<>();
     Files.newDirectoryStream(testResourceDir, "*.sarif")
         .iterator()
         .forEachRemaining(allSarifs::add);
-    Map<String, List<RuleSarif>> map = SarifParser.create().parseIntoMap(allSarifs, tmpDir);
+    Map<String, List<RuleSarif>> map = SarifParser.create().parseIntoMap(allSarifs, codeDir);
 
     // Check for any a defectdojo
     Path defectDojo = testResourceDir.resolve("defectdojo.json");

framework/codemodder-testutils/src/main/java/io/codemodder/testutils/RawFileCodemodTest.java

@@ -127,8 +127,9 @@ private void verifyCodemod(
           files.filter(file -> file.getFileName().toString().endsWith(".sarif")).toList();
     }
 
+    final CodeDirectory codeDirectory = CodeDirectory.from(tmpDir);
     final Map<String, List<RuleSarif>> map =
-        SarifParser.create().parseIntoMap(allSarifFiles, tmpDir);
+        SarifParser.create().parseIntoMap(allSarifFiles, codeDirectory);
 
     // grab all the .before and .after files in the dir
     final List<Path> allBeforeFiles;

plugins/codemodder-plugin-appscan/src/main/java/io/codemodder/providers/sarif/appscan/AppScanRuleSarif.java

@@ -1,24 +1,19 @@
 package io.codemodder.providers.sarif.appscan;
 
 import com.contrastsecurity.sarif.*;
+import io.codemodder.CodeDirectory;
 import io.codemodder.RuleSarif;
 import java.io.IOException;
 import java.io.UncheckedIOException;
-import java.nio.file.FileVisitResult;
-import java.nio.file.Files;
 import java.nio.file.Path;
-import java.nio.file.SimpleFileVisitor;
-import java.nio.file.attribute.BasicFileAttributes;
 import java.util.*;
-import java.util.concurrent.atomic.AtomicReference;
 
 /** A {@link RuleSarif} for AppScan results. */
 final class AppScanRuleSarif implements RuleSarif {
 
   private final SarifSchema210 sarif;
   private final String ruleId;
   private final Map<Path, List<Result>> resultsCache;
-  private final Path repositoryRoot;
   private final List<String> locations;
 
   /** A map of a AppScan SARIF "location" URIs mapped to their respective file paths. */
@@ -28,11 +23,10 @@ final class AppScanRuleSarif implements RuleSarif {
    * Creates an {@link AppScanRuleSarif} that has already done the work of mapping AppScan SARIF
    * locations, which are strange combinations of class name and file path, into predictable paths.
    */
-  public AppScanRuleSarif(
-      final String ruleId, final SarifSchema210 sarif, final Path repositoryRoot) {
+  AppScanRuleSarif(
+      final String ruleId, final SarifSchema210 sarif, final CodeDirectory codeDirectory) {
     this.sarif = Objects.requireNonNull(sarif);
     this.ruleId = Objects.requireNonNull(ruleId);
-    this.repositoryRoot = repositoryRoot;
     this.resultsCache = new HashMap<>();
     this.locations =
         sarif.getRuns().get(0).getArtifacts().stream()
@@ -49,7 +43,7 @@ public AppScanRuleSarif(
       // we have a real but partial path, now we have to find it in the repository
       Optional<Path> existingRealPath;
       try {
-        existingRealPath = findFileWithTrailingPath(path);
+        existingRealPath = codeDirectory.findFilesWithTrailingPath(path);
       } catch (IOException e) {
         throw new UncheckedIOException(e);
       }
@@ -61,24 +55,6 @@ public AppScanRuleSarif(
     this.artifactLocationIndices = Map.copyOf(artifactLocationIndicesMap);
   }
 
-  private Optional<Path> findFileWithTrailingPath(final String path) throws IOException {
-    // find the files with the trailing path
-    AtomicReference<Path> found = new AtomicReference<>();
-    Files.walkFileTree(
-        repositoryRoot,
-        new SimpleFileVisitor<>() {
-          @Override
-          public FileVisitResult visitFile(final Path file, final BasicFileAttributes attrs) {
-            if (file.toString().endsWith(path)) {
-              found.set(file);
-              return FileVisitResult.TERMINATE;
-            }
-            return FileVisitResult.CONTINUE;
-          }
-        });
-    return Optional.ofNullable(found.get());
-  }
-
   @Override
   public List<Region> getRegionsFromResultsByRule(final Path path) {
     List<Result> resultsByLocationPath = getResultsByLocationPath(path);

plugins/codemodder-plugin-appscan/src/main/java/io/codemodder/providers/sarif/appscan/AppScanRuleSarifFactory.java

@@ -1,19 +1,22 @@
 package io.codemodder.providers.sarif.appscan;
 
 import com.contrastsecurity.sarif.SarifSchema210;
+import io.codemodder.CodeDirectory;
 import io.codemodder.RuleSarif;
 import io.codemodder.RuleSarifFactory;
-import java.nio.file.Path;
 import java.util.Optional;
 
 /** A factory for building {@link AppScanRuleSarif}s. */
 public final class AppScanRuleSarifFactory implements RuleSarifFactory {
 
   @Override
   public Optional<RuleSarif> build(
-      String toolName, String rule, SarifSchema210 sarif, Path repositoryRoot) {
+      final String toolName,
+      final String rule,
+      final SarifSchema210 sarif,
+      final CodeDirectory codeDirectory) {
     if (AppScanRuleSarif.toolName.equals(toolName)) {
-      return Optional.of(new AppScanRuleSarif(rule, sarif, repositoryRoot));
+      return Optional.of(new AppScanRuleSarif(rule, sarif, codeDirectory));
     }
     return Optional.empty();
   }

plugins/codemodder-plugin-appscan/src/test/java/io/codemodder/providers/sarif/appscan/AppScanModuleTest.java

@@ -85,7 +85,8 @@ void it_works_with_appscan_sarif(@TempDir final Path repoDir) throws IOException
         new ObjectMapper().readValue(AppScanModuleTest.emptySarif, SarifSchema210.class);
     AppScanRuleSarifFactory ruleSarifFactory = new AppScanRuleSarifFactory();
     Optional<RuleSarif> ruleSarif =
-        ruleSarifFactory.build("HCL AppScan Static Analyzer", "SA2813462719", rawSarif, repoDir);
+        ruleSarifFactory.build(
+            "HCL AppScan Static Analyzer", "SA2813462719", rawSarif, CodeDirectory.from(repoDir));
     assertThat(ruleSarif.isPresent(), is(true));
     AppScanModule module =
         new AppScanModule(List.of(AppScanSarifTestCodemod.class), List.of(ruleSarif.get()));

plugins/codemodder-plugin-appscan/src/test/java/io/codemodder/providers/sarif/appscan/AppScanRuleSarifFactoryTest.java

@@ -6,6 +6,7 @@
 import com.contrastsecurity.sarif.Result;
 import com.contrastsecurity.sarif.SarifSchema210;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import io.codemodder.CodeDirectory;
 import io.codemodder.RuleSarif;
 import java.io.File;
 import java.io.IOException;
@@ -42,7 +43,7 @@ void it_parses_sarif_and_maps_java_locations(@TempDir final Path tmpDir) throws
                 new File("src/test/resources/webgoat_2023_8_binary.sarif"), SarifSchema210.class);
     Optional<RuleSarif> sarifRef =
         appScanRuleSarifFactory.build(
-            "HCL AppScan Static Analyzer", "SA2813462719", rawSarif, tmpDir);
+            "HCL AppScan Static Analyzer", "SA2813462719", rawSarif, CodeDirectory.from(tmpDir));
     assertThat(sarifRef.isPresent()).isTrue();
     RuleSarif ruleSarif = sarifRef.get();
 

plugins/codemodder-plugin-codeql/src/main/java/io/codemodder/providers/sarif/codeql/CodeQLRuleSarif.java

@@ -4,6 +4,7 @@
 import com.contrastsecurity.sarif.Result;
 import com.contrastsecurity.sarif.Run;
 import com.contrastsecurity.sarif.SarifSchema210;
+import io.codemodder.CodeDirectory;
 import io.codemodder.RuleSarif;
 import java.io.IOException;
 import java.nio.file.Files;
@@ -25,10 +26,10 @@ public final class CodeQLRuleSarif implements RuleSarif {
   private final Path repositoryRoot;
 
   public CodeQLRuleSarif(
-      final String ruleId, final SarifSchema210 sarif, final Path repositoryRoot) {
+      final String ruleId, final SarifSchema210 sarif, final CodeDirectory codeDirectory) {
     this.sarif = Objects.requireNonNull(sarif);
     this.ruleId = Objects.requireNonNull(ruleId);
-    this.repositoryRoot = repositoryRoot;
+    this.repositoryRoot = codeDirectory.asPath();
     this.resultsCache = new HashMap<>();
   }