cached location lookup data

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

@@ -366,10 +366,15 @@ public Integer call() throws IOException {
       log.debug("excluding paths: {}", pathExcludes);
 
       // get all files that match
+      log.debug("Listing source directories");
       List<SourceDirectory> sourceDirectories =
           sourceDirectoryLister.listJavaSourceDirectories(List.of(projectDirectory));
+
+      log.debug("Listing files");
       List<Path> filePaths = fileFinder.findFiles(projectPath, includesExcludes);
 
+      log.debug("Creating codemod regulator");
+
       // get codemod includes/excludes
       final CodemodRegulator regulator;
       if (codemodIncludes != null && codemodExcludes != null) {
@@ -386,10 +391,13 @@ public Integer call() throws IOException {
       }
 
       // create the loader
+      log.debug("Loading input files");
       CodeDirectory codeDirectory = new DefaultCodeDirectory(projectPath);
       List<Path> sarifFiles = convertToPaths(sarifs);
       List<Path> sonarIssuesJsonFiles = convertToPaths(sonarIssuesJsonFilePaths);
       List<Path> sonarHotspotJsonFiles = convertToPaths(sonarHotspotsJsonFilePaths);
+
+      log.debug("Parsing SARIFs");
       Map<String, List<RuleSarif>> pathSarifMap =
           SarifParser.create().parseIntoMap(sarifFiles, codeDirectory);
       List<ParameterArgument> codemodParameters =

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

@@ -2,6 +2,8 @@
 
 import com.google.inject.AbstractModule;
 import java.util.List;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /** A module that only configures if it is responsible for a codemod that's being loaded. */
 public abstract class CodemodCheckingAbstractModule extends AbstractModule {
@@ -19,10 +21,14 @@ protected CodemodCheckingAbstractModule(final List<Class<? extends CodeChanger>>
   @Override
   protected final void configure() {
     if (shouldActivate) {
+      log.info("Configuring module {}", this.getClass().getSimpleName());
       doConfigure();
+      log.info("Done configuration {}", this.getClass().getSimpleName());
     }
   }
 
   /** Do the configuration that you would normally do in the configure method. */
   protected abstract void doConfigure();
+
+  private static final Logger log = LoggerFactory.getLogger(CodemodCheckingAbstractModule.class);
 }

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

@@ -13,6 +13,8 @@
 import java.util.regex.Pattern;
 import javax.inject.Inject;
 import org.jetbrains.annotations.VisibleForTesting;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /** This type is responsible for loading codemods and the surrounding subsystem. */
 public final class CodemodLoader {
@@ -33,6 +35,8 @@ public CodemodLoader(
       final Path defectDojoFindingsJsonFile,
       final Path contrastVulnerabilitiesXmlFilePath) {
 
+    log.info("Loading providers");
+
     // get all the providers ready for dependency injection & codemod instantiation
     final List<CodemodProvider> providers =
         ServiceLoader.load(CodemodProvider.class).stream()
@@ -106,6 +110,7 @@ public CodemodLoader(
           wantsSarif.stream()
               .flatMap(toolName -> ruleSarifByTool.getOrDefault(toolName, List.of()).stream())
               .toList();
+      log.info("Loading modules from provider: {}", provider.getClass().getSimpleName());
       final Set<AbstractModule> modules =
           provider.getModules(
               repositoryDir,
@@ -125,7 +130,9 @@ public CodemodLoader(
     final List<CodemodIdPair> codemods = new ArrayList<>();
 
     // validate and instantiate the codemods
+    log.info("Instantiating codemods");
     final Injector injector = Guice.createInjector(allModules);
+    log.info("Codemods instantiated");
     final Set<String> codemodIds = new HashSet<>();
     for (final Class<? extends CodeChanger> type : orderedCodemodTypes) {
       final Codemod codemodAnnotation = type.getAnnotation(Codemod.class);
@@ -164,6 +171,8 @@ static boolean isValidCodemodId(final String codemodId) {
     return codemodIdPattern.matcher(codemodId).matches();
   }
 
+  private static final Logger log = LoggerFactory.getLogger(CodemodLoader.class);
+
   private static final Pattern codemodIdPattern =
       Pattern.compile("^([A-Za-z0-9]+):(([A-Za-z0-9]+)/)+([A-Za-z0-9\\-\\.]+)$");
 }

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

@@ -5,6 +5,7 @@
 import com.contrastsecurity.sarif.SarifSchema210;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import java.io.IOException;
+import java.io.InputStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.*;
@@ -17,10 +18,14 @@ final class DefaultSarifParser implements SarifParser {
 
   private Optional<SarifSchema210> readSarifFile(final Path sarifFile) {
     try {
-      return Optional.of(
-          new ObjectMapper().readValue(Files.newInputStream(sarifFile), SarifSchema210.class));
+      log.debug("Reading input file: {}", sarifFile);
+      InputStream stream = Files.newInputStream(sarifFile);
+      log.debug("Parsing to SARIF input files");
+      SarifSchema210 sarif = new ObjectMapper().readValue(stream, SarifSchema210.class);
+      log.debug("Parsed SARIF input files");
+      return Optional.of(sarif);
     } catch (final IOException e) {
-      LOG.error("Problem deserializing SARIF file: {}", sarifFile, e);
+      log.error("Problem deserializing SARIF file: {}", sarifFile, e);
       return Optional.empty();
     }
   }
@@ -33,14 +38,15 @@ private Optional<Map.Entry<String, RuleSarif>> tryToBuild(
       final CodeDirectory codeDirectory,
       final List<RuleSarifFactory> factories) {
     for (final var factory : factories) {
+      log.debug("Building SARIF: {}", factory.getClass().getSimpleName());
       final var maybeRuleSarif =
           factory.build(toolName, rule.ruleId, rule.messageText, sarif, codeDirectory);
       if (maybeRuleSarif.isPresent()) {
         return Optional.of(Map.entry(toolName, maybeRuleSarif.get()));
       }
     }
 
-    LOG.info("Found SARIF from unsupported tool: {}", toolName);
+    log.info("Found SARIF from unsupported tool: {}", toolName);
     return Optional.empty();
   }
 
@@ -60,7 +66,7 @@ private RuleDescriptor extractRuleId(final Result result, final Run run) {
       if (maybeRule.isPresent()) {
         return maybeRule.get();
       } else {
-        LOG.info("Could not find rule id for result.");
+        log.info("Could not find rule id for result.");
         return null;
       }
     }
@@ -72,10 +78,12 @@ private Stream<Map.Entry<String, RuleSarif>> fromSarif(
       final Run run, final SarifSchema210 sarif, final CodeDirectory codeDirectory) {
     // driver name
     final var toolName = run.getTool().getDriver().getName();
+    log.debug("Loading SARIF rule factories");
     final List<RuleSarifFactory> factories =
         ServiceLoader.load(RuleSarifFactory.class).stream()
             .map(ServiceLoader.Provider::get)
             .toList();
+    log.debug("Done loading SARIF rule factories");
     final var runResults = run.getResults();
     final var allResults =
         runResults != null
@@ -105,16 +113,18 @@ public Map<String, List<RuleSarif>> parseIntoMap(
         .flatMap(
             sarif -> sarif.getRuns().stream().flatMap(run -> fromSarif(run, sarif, codeDirectory)))
         .forEach(
-            p ->
-                map.merge(
-                    p.getKey(),
-                    new ArrayList<>(Collections.singletonList(p.getValue())),
-                    (l1, l2) -> {
-                      l1.add(l2.get(0));
-                      return l1;
-                    }));
+            p -> {
+              log.debug("Merging SARIF results");
+              map.merge(
+                  p.getKey(),
+                  new ArrayList<>(Collections.singletonList(p.getValue())),
+                  (l1, l2) -> {
+                    l1.add(l2.get(0));
+                    return l1;
+                  });
+            });
     return map;
   }
 
-  private static final Logger LOG = LoggerFactory.getLogger(DefaultSarifParser.class);
+  private static final Logger log = LoggerFactory.getLogger(DefaultSarifParser.class);
 }

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

@@ -24,7 +24,9 @@ public ExecutionStatus configure(final LoggerContext lc) {
     ca.setContext(lc);
     ca.setName(APPENDER_NAME);
     PatternLayoutEncoder patternLayoutEncoder = new PatternLayoutEncoder();
-    patternLayoutEncoder.setPattern("%m%n");
+    // add the timestamp
+    //    patternLayoutEncoder.setPattern("%m%n");
+    patternLayoutEncoder.setPattern("%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n");
     patternLayoutEncoder.setContext(lc);
     patternLayoutEncoder.setCharset(StandardCharsets.UTF_8);
     patternLayoutEncoder.start();

gradle/build-plugins/src/main/kotlin/io.codemodder.maven-publish.gradle.kts

@@ -26,7 +26,7 @@ signing {
         val signingPassword: String? by project
         useInMemoryPgpKeys(signingKey, signingPassword)
     }
-//    sign(extensions.getByType<PublishingExtension>().publications.getByName(publicationName))
+    sign(extensions.getByType<PublishingExtension>().publications.getByName(publicationName))
 }
 
 publishing {

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

@@ -1,58 +1,32 @@
 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.Path;
 import java.util.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /** A {@link RuleSarif} for AppScan results. */
 final class AppScanRuleSarif implements RuleSarif {
 
   private final SarifSchema210 sarif;
   private final String messageText;
   private final Map<Path, List<Result>> resultsCache;
-  private final List<String> locations;
-
-  /** A map of a AppScan SARIF "location" URIs mapped to their respective file paths. */
-  private final Map<Path, Set<Integer>> artifactLocationIndices;
+  private final AppScanSarifLocationData sarifLocationData;
 
   /**
    * 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.
    */
   AppScanRuleSarif(
-      final String messageText, final SarifSchema210 sarif, final CodeDirectory codeDirectory) {
+      final String messageText,
+      final SarifSchema210 sarif,
+      final AppScanSarifLocationData sarifLocationData) {
     this.sarif = Objects.requireNonNull(sarif);
     this.messageText = Objects.requireNonNull(messageText);
     this.resultsCache = new HashMap<>();
-    this.locations =
-        sarif.getRuns().get(0).getArtifacts().stream()
-            .map(Artifact::getLocation)
-            .map(ArtifactLocation::getUri)
-            .map(u -> u.substring(8)) // trim the file:/// of all results
-            .toList();
-    Map<Path, Set<Integer>> artifactLocationIndicesMap = new HashMap<>();
-
-    for (int i = 0; i < locations.size(); i++) {
-      final Integer index = i;
-      String path = locations.get(i);
-      path = path.replace('\\', '/');
-      // we have a real but partial path, now we have to find it in the repository
-      Optional<Path> existingRealPath;
-      try {
-        existingRealPath = codeDirectory.findFilesWithTrailingPath(path);
-      } catch (IOException e) {
-        throw new UncheckedIOException(e);
-      }
-
-      // add to the map if we found a matching file
-      existingRealPath.ifPresent(
-          p -> artifactLocationIndicesMap.computeIfAbsent(p, k -> new HashSet<>()).add(index));
-    }
-    this.artifactLocationIndices = Map.copyOf(artifactLocationIndicesMap);
+    this.sarifLocationData = Objects.requireNonNull(sarifLocationData);
   }
 
   @Override
@@ -71,6 +45,9 @@ public List<Region> getRegionsFromResultsByRule(final Path path) {
    */
   @Override
   public List<Result> getResultsByLocationPath(final Path path) {
+
+    Map<Path, Set<Integer>> artifactLocationIndices =
+        sarifLocationData.getArtifactLocationIndices();
     return resultsCache.computeIfAbsent(
         path,
         p ->
@@ -117,4 +94,6 @@ public String getRule() {
   }
 
   static final String toolName = "HCL AppScan Static Analyzer";
+
+  private static final Logger log = LoggerFactory.getLogger(AppScanRuleSarif.class);
 }

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

@@ -4,11 +4,18 @@
 import io.codemodder.CodeDirectory;
 import io.codemodder.RuleSarif;
 import io.codemodder.RuleSarifFactory;
-import java.util.Optional;
+import java.util.*;
 
 /** A factory for building {@link AppScanRuleSarif}s. */
 public final class AppScanRuleSarifFactory implements RuleSarifFactory {
 
+  /** A map of a AppScan SARIF "location" URIs mapped to their respective file paths. */
+  private final Map<SarifSchema210, AppScanSarifLocationData> sarifLocationDataCache;
+
+  public AppScanRuleSarifFactory() {
+    this.sarifLocationDataCache = new HashMap<>();
+  }
+
   @Override
   public Optional<RuleSarif> build(
       final String toolName,
@@ -17,7 +24,12 @@ public Optional<RuleSarif> build(
       final SarifSchema210 sarif,
       final CodeDirectory codeDirectory) {
     if (AppScanRuleSarif.toolName.equals(toolName)) {
-      return Optional.of(new AppScanRuleSarif(messageText, sarif, codeDirectory));
+      AppScanSarifLocationData sarifLocationData = sarifLocationDataCache.get(sarif);
+      if (sarifLocationData == null) {
+        sarifLocationData = new AppScanSarifLocationData(sarif, codeDirectory);
+        sarifLocationDataCache.put(sarif, sarifLocationData);
+      }
+      return Optional.of(new AppScanRuleSarif(messageText, sarif, sarifLocationData));
     }
     return Optional.empty();
   }

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

@@ -0,0 +1,55 @@
+package io.codemodder.providers.sarif.appscan;
+
+import com.contrastsecurity.sarif.Artifact;
+import com.contrastsecurity.sarif.ArtifactLocation;
+import com.contrastsecurity.sarif.SarifSchema210;
+import io.codemodder.CodeDirectory;
+import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.nio.file.Path;
+import java.util.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/** Holds the locations of the artifacts in the SARIF file. */
+final class AppScanSarifLocationData {
+
+  private final Map<Path, Set<Integer>> artifactLocationIndices;
+
+  AppScanSarifLocationData(final SarifSchema210 sarif, final CodeDirectory codeDirectory) {
+    log.debug("Cleaning locations");
+    List<String> locations =
+        sarif.getRuns().get(0).getArtifacts().stream()
+            .map(Artifact::getLocation)
+            .map(ArtifactLocation::getUri)
+            .map(u -> u.substring(8)) // trim the file:/// of all results
+            .toList();
+
+    Map<Path, Set<Integer>> artifactLocationIndicesMap = new HashMap<>();
+
+    log.info("Calculating locations in project dir");
+    for (int i = 0; i < locations.size(); i++) {
+      final Integer index = i;
+      String path = locations.get(i);
+      path = path.replace('\\', '/');
+      // we have a real but partial path, now we have to find it in the repository
+      Optional<Path> existingRealPath;
+      try {
+        existingRealPath = codeDirectory.findFilesWithTrailingPath(path);
+      } catch (IOException e) {
+        throw new UncheckedIOException(e);
+      }
+      // add to the map if we found a matching file
+      existingRealPath.ifPresent(
+          p -> artifactLocationIndicesMap.computeIfAbsent(p, k -> new HashSet<>()).add(index));
+    }
+    log.info("Done calculating locations");
+    this.artifactLocationIndices = Map.copyOf(artifactLocationIndicesMap);
+  }
+
+  Map<Path, Set<Integer>> getArtifactLocationIndices() {
+    return artifactLocationIndices;
+  }
+
+  private static final Logger log = LoggerFactory.getLogger(AppScanSarifLocationData.class);
+}

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

@@ -21,7 +21,7 @@
 final class AppScanModuleTest {
 
   @Codemod(
-      id = "appscan-test:java/finds-stuff",
+      id = "appscan:java/finds-stuff",
       importance = Importance.LOW,
       reviewGuidance = ReviewGuidance.MERGE_AFTER_CURSORY_REVIEW)
   static class AppScanSarifTestCodemod implements CodeChanger {