fix(dockerfile): analyze all FROM lines via batch analysis

src/main/java/io/github/guacsec/trustifyda/Provider.java

@@ -37,10 +37,16 @@ public abstract class Provider {
   public static class Content {
     public final byte[] buffer;
     public final String type;
+    public final boolean batch;
 
     public Content(byte[] buffer, String type) {
+      this(buffer, type, false);
+    }
+
+    public Content(byte[] buffer, String type, boolean batch) {
       this.buffer = buffer;
       this.type = type;
+      this.batch = batch;
     }
   }
 

src/main/java/io/github/guacsec/trustifyda/cli/App.java

@@ -33,6 +33,7 @@
 import io.github.guacsec.trustifyda.impl.ExhortApi;
 import io.github.guacsec.trustifyda.license.ProjectLicense;
 import io.github.guacsec.trustifyda.license.ProjectLicense.ProjectLicenseInfo;
+import io.github.guacsec.trustifyda.providers.DockerfileProvider;
 import io.github.guacsec.trustifyda.tools.Ecosystem;
 import java.io.IOException;
 import java.nio.file.Files;
@@ -219,6 +220,16 @@ private static Path validateFile(String filePath) {
   }
 
   private static CompletableFuture<String> executeCommand(CliArgs args) throws IOException {
+    if (isDockerfilePath(args.filePath)) {
+      if (args.command == Command.SBOM || args.command == Command.LICENSE) {
+        throw new IllegalArgumentException(
+            args.command
+                + " command is not supported for Dockerfiles/Containerfiles."
+                + " Use 'stack' or 'component' to analyze container images.");
+      }
+      Set<ImageRef> imageRefs = DockerfileProvider.parseImageRefs(args.filePath);
+      return executeImageAnalysis(imageRefs, args.outputFormat);
+    }
     return switch (args.command) {
       case STACK ->
           executeStackAnalysis(args.filePath.toAbsolutePath().toString(), args.outputFormat);
@@ -230,6 +241,10 @@ private static CompletableFuture<String> executeCommand(CliArgs args) throws IOE
     };
   }
 
+  private static boolean isDockerfilePath(Path filePath) {
+    return filePath != null && Ecosystem.isDockerfile(filePath.getFileName().toString());
+  }
+
   private static CompletableFuture<String> executeStackAnalysis(
       String filePath, OutputFormat outputFormat) throws IOException {
     Api api = new ExhortApi();
@@ -338,7 +353,11 @@ private static CompletableFuture<String> executeSbomGeneration(CliArgs args) thr
 
   private static String formatImageAnalysisResult(Map<ImageRef, AnalysisReport> analysisResults) {
     try {
-      return MAPPER.writeValueAsString(analysisResults);
+      Map<String, AnalysisReport> keyed = new LinkedHashMap<>();
+      for (Map.Entry<ImageRef, AnalysisReport> entry : analysisResults.entrySet()) {
+        keyed.put(entry.getKey().getImage().getFullName(), entry.getValue());
+      }
+      return MAPPER.writeValueAsString(keyed);
     } catch (JsonProcessingException e) {
       throw new RuntimeException("Failed to serialize image analysis results", e);
     }
@@ -349,7 +368,7 @@ private static Map<String, Map<String, SourceSummary>> extractImageSummary(
     Map<String, Map<String, SourceSummary>> imageSummaries = new HashMap<>();
 
     for (Map.Entry<ImageRef, AnalysisReport> entry : analysisResults.entrySet()) {
-      String imageKey = entry.getKey().toString();
+      String imageKey = entry.getKey().getImage().getFullName();
       Map<String, SourceSummary> imageSummary = extractSummary(entry.getValue());
       imageSummaries.put(imageKey, imageSummary);
     }

src/main/java/io/github/guacsec/trustifyda/image/ImageRef.java

@@ -140,11 +140,26 @@ void checkImageDigest() {
     }
   }
 
+  private static final String DOCKER_HUB_LIBRARY_PREFIX = "docker.io/library/";
+
   // https://github.com/package-url/purl-spec/blob/master/PURL-TYPES.rst#oci
   public PackageURL getPackageURL() throws MalformedPackageURLException {
     TreeMap<String, String> qualifiers = new TreeMap<>();
     var repositoryUrl = this.image.getNameWithoutTag();
     var simpleName = this.image.getSimpleName();
+
+    // Normalize Docker Hub image references so all forms produce the same PURL:
+    //   node                    → docker.io/node
+    //   docker.io/library/node  → docker.io/node
+    if (repositoryUrl != null) {
+      var lower = repositoryUrl.toLowerCase();
+      if (lower.equals(simpleName.toLowerCase())) {
+        repositoryUrl = "docker.io/" + simpleName;
+      } else if (lower.startsWith(DOCKER_HUB_LIBRARY_PREFIX)) {
+        repositoryUrl = "docker.io/" + lower.substring(DOCKER_HUB_LIBRARY_PREFIX.length());
+      }
+    }
+
     if (repositoryUrl != null && !repositoryUrl.equalsIgnoreCase(simpleName)) {
       qualifiers.put(REPOSITORY_QUALIFIER, repositoryUrl.toLowerCase());
     }

src/main/java/io/github/guacsec/trustifyda/impl/ExhortApi.java

@@ -101,6 +101,7 @@ public final class ExhortApi implements Api {
   public static final String S_API_V5_LICENSES = "%s/api/v5/licenses/%s";
   public static final String S_API_V5_LICENSES_IDENTIFY = "%s/api/v5/licenses/identify";
   private static final String TRUSTIFY_DA_LICENSE_CHECK = "TRUSTIFY_DA_LICENSE_CHECK";
+  private static final String TRUSTIFY_DA_RECOMMEND = "TRUSTIFY_DA_RECOMMEND";
 
   private String endpoint;
 
@@ -296,10 +297,36 @@ public CompletableFuture<byte[]> stackAnalysisHtml(final String manifestFile) th
   public CompletableFuture<AnalysisReport> stackAnalysis(final String manifestFile)
       throws IOException {
     String exClientTraceId = commonHookBeginning(false);
+    var content = resolveStackContent(manifestFile);
+    var uri = resolveAnalysisUri(content);
+    var request = buildRequest(content, uri, MediaType.APPLICATION_JSON, "Stack Analysis");
+    if (content.batch) {
+      return this.client
+          .sendAsync(request, HttpResponse.BodyHandlers.ofString())
+          .thenApply(
+              response -> {
+                RequestManager.getInstance().addClientTraceIdToRequest(exClientTraceId);
+                if (debugLoggingIsNeeded()) {
+                  logExhortRequestId(response);
+                }
+                Map<String, AnalysisReport> reports = getBatchStackAnalysisReports(response);
+                commonHookAfterExhortResponse();
+                return reports.isEmpty()
+                    ? new AnalysisReport()
+                    : reports.values().iterator().next();
+              })
+          .exceptionally(
+              exception -> {
+                LOG.severe(
+                    String.format(
+                        "failed to invoke stackAnalysis (batch) for getting the json report,"
+                            + " received message= %s ",
+                        exception.getMessage()));
+                return new AnalysisReport();
+              });
+    }
     return this.client
-        .sendAsync(
-            this.buildStackRequest(manifestFile, MediaType.APPLICATION_JSON),
-            HttpResponse.BodyHandlers.ofString())
+        .sendAsync(request, HttpResponse.BodyHandlers.ofString())
         .thenApply(
             response ->
                 getAnalysisReportFromResponse(response, "StackAnalysis", "json", exClientTraceId))
@@ -361,15 +388,26 @@ public static boolean debugLoggingIsNeeded() {
     return Environment.getBoolean("TRUSTIFY_DA_DEBUG", false);
   }
 
+  private static URI buildAnalysisUri(String template, String endpoint) {
+    String base = String.format(template, endpoint);
+    if (!Environment.getBoolean(TRUSTIFY_DA_RECOMMEND, true)) {
+      return URI.create(base + "?recommend=false");
+    }
+    return URI.create(base);
+  }
+
   @Override
   public CompletableFuture<AnalysisReport> componentAnalysis(
       final String manifest, final byte[] manifestContent) throws IOException {
     String exClientTraceId = commonHookBeginning(false);
     var manifestPath = Path.of(manifest);
     var provider = Ecosystem.getProvider(manifestPath);
-    var uri = URI.create(String.format(S_API_V_5_ANALYSIS, getEndpoint()));
     var content = provider.provideComponent();
     commonHookAfterProviderCreatedSbomAndBeforeExhort();
+    var uri = resolveAnalysisUri(content);
+    if (content.batch) {
+      return getBatchAnalysisReportForComponent(uri, content, exClientTraceId);
+    }
     return getAnalysisReportForComponent(uri, content, exClientTraceId);
   }
 
@@ -411,9 +449,12 @@ public CompletableFuture<AnalysisReport> componentAnalysis(String manifestFile)
     String exClientTraceId = commonHookBeginning(false);
     var manifestPath = Path.of(manifestFile);
     var provider = Ecosystem.getProvider(manifestPath);
-    var uri = URI.create(String.format(S_API_V_5_ANALYSIS, getEndpoint()));
     var content = provider.provideComponent();
     commonHookAfterProviderCreatedSbomAndBeforeExhort();
+    var uri = resolveAnalysisUri(content);
+    if (content.batch) {
+      return getBatchAnalysisReportForComponent(uri, content, exClientTraceId);
+    }
     return getAnalysisReportForComponent(uri, content, exClientTraceId);
   }
 
@@ -440,8 +481,48 @@ private CompletableFuture<AnalysisReport> getAnalysisReportForComponent(
             });
   }
 
+  /** Resolves the analysis URI based on whether the content is batch or single. */
+  private URI resolveAnalysisUri(Provider.Content content) {
+    if (content.batch) {
+      return buildAnalysisUri(S_API_V_5_BATCH_ANALYSIS, getEndpoint());
+    }
+    return buildAnalysisUri(S_API_V_5_ANALYSIS, getEndpoint());
+  }
+
+  /**
+   * Sends batch content to the batch-analysis endpoint and returns the first analysis report from
+   * the batch response map.
+   */
+  private CompletableFuture<AnalysisReport> getBatchAnalysisReportForComponent(
+      URI uri, Provider.Content content, String exClientTraceId) {
+    return this.client
+        .sendAsync(
+            this.buildRequest(content, uri, MediaType.APPLICATION_JSON, "Batch Component Analysis"),
+            HttpResponse.BodyHandlers.ofString())
+        .thenApply(
+            response -> {
+              RequestManager.getInstance().addClientTraceIdToRequest(exClientTraceId);
+              if (debugLoggingIsNeeded()) {
+                logExhortRequestId(response);
+              }
+              Map<String, AnalysisReport> reports = getBatchStackAnalysisReports(response);
+              commonHookAfterExhortResponse();
+              return reports.isEmpty() ? new AnalysisReport() : reports.values().iterator().next();
+            })
+        .exceptionally(
+            exception -> {
+              LOG.severe(
+                  String.format(
+                      "failed to invoke Batch Component Analysis for getting the json report,"
+                          + " received message= %s ",
+                      exception.getMessage()));
+              return new AnalysisReport();
+            });
+  }
+
   /**
-   * Build an HTTP request wrapper for sending to the Backend API for Stack Analysis only.
+   * Build an HTTP request wrapper for sending to the Backend API for Stack Analysis only. Uses the
+   * batch-analysis endpoint when the provider returns batch content.
    *
    * @param manifestFile the path for the manifest file
    * @param acceptType the type of requested content
@@ -450,13 +531,21 @@ private CompletableFuture<AnalysisReport> getAnalysisReportForComponent(
    */
   private HttpRequest buildStackRequest(final String manifestFile, final MediaType acceptType)
       throws IOException {
+    var content = resolveStackContent(manifestFile);
+    var uri = resolveAnalysisUri(content);
+    return buildRequest(content, uri, acceptType, "Stack Analysis");
+  }
+
+  /**
+   * Resolves the provider for the given manifest file and produces the stack content. Also tracks
+   * timing via {@link #commonHookAfterProviderCreatedSbomAndBeforeExhort()}.
+   */
+  private Provider.Content resolveStackContent(String manifestFile) throws IOException {
     var manifestPath = Path.of(manifestFile);
     var provider = Ecosystem.getProvider(manifestPath);
-    var uri = URI.create(String.format(S_API_V_5_ANALYSIS, getEndpoint()));
     var content = provider.provideStack();
     commonHookAfterProviderCreatedSbomAndBeforeExhort();
-
-    return buildRequest(content, uri, acceptType, "Stack Analysis");
+    return content;
   }
 
   @Override
@@ -539,7 +628,7 @@ <H, T> CompletableFuture<T> performBatchAnalysis(
       final String analysisName)
       throws IOException {
     String exClientTraceId = commonHookBeginning(false);
-    var uri = URI.create(String.format(S_API_V_5_BATCH_ANALYSIS, getEndpoint()));
+    var uri = buildAnalysisUri(S_API_V_5_BATCH_ANALYSIS, getEndpoint());
     var sboms = sbomsGenerator.get();
     var content =
         new Provider.Content(
@@ -601,27 +690,29 @@ public CompletableFuture<ComponentAnalysisResult> componentAnalysisWithLicense(
     String exClientTraceId = commonHookBeginning(false);
     var manifestPath = Path.of(manifestFile);
     var provider = Ecosystem.getProvider(manifestPath);
-    var uri = URI.create(String.format(S_API_V_5_ANALYSIS, getEndpoint()));
     var content = provider.provideComponent();
     String sbomJson = new String(content.buffer);
     commonHookAfterProviderCreatedSbomAndBeforeExhort();
-    return getAnalysisReportForComponent(uri, content, exClientTraceId)
-        .thenCompose(
-            report -> {
-              if (!isLicenseCheckEnabled()) {
-                return CompletableFuture.completedFuture(new ComponentAnalysisResult(report, null));
-              }
-              return LicenseCheck.runLicenseCheck(this, provider, manifestPath, sbomJson, report)
-                  .thenApply(summary -> new ComponentAnalysisResult(report, summary))
-                  .exceptionally(
-                      ex -> {
-                        LOG.warning(
-                            String.format(
-                                "License check failed, continuing without it: %s",
-                                ex.getMessage()));
-                        return new ComponentAnalysisResult(report, null);
-                      });
-            });
+    var uri = resolveAnalysisUri(content);
+    CompletableFuture<AnalysisReport> reportFuture =
+        content.batch
+            ? getBatchAnalysisReportForComponent(uri, content, exClientTraceId)
+            : getAnalysisReportForComponent(uri, content, exClientTraceId);
+    return reportFuture.thenCompose(
+        report -> {
+          if (!isLicenseCheckEnabled() || content.batch) {
+            return CompletableFuture.completedFuture(new ComponentAnalysisResult(report, null));
+          }
+          return LicenseCheck.runLicenseCheck(this, provider, manifestPath, sbomJson, report)
+              .thenApply(summary -> new ComponentAnalysisResult(report, summary))
+              .exceptionally(
+                  ex -> {
+                    LOG.warning(
+                        String.format(
+                            "License check failed, continuing without it: %s", ex.getMessage()));
+                    return new ComponentAnalysisResult(report, null);
+                  });
+        });
   }
 
   /**