fix(python): handle PEP 440 direct references and path dependencies in uv export

src/main/java/io/github/guacsec/trustifyda/providers/PythonPipProvider.java

@@ -95,7 +95,7 @@ public Content provideComponent() throws IOException {
 
   @Override
   protected Set<PackageURL> getIgnoredDependencies(String manifestContent) {
-    String[] lines = manifestContent.split(System.lineSeparator());
+    String[] lines = manifestContent.split("\\R");
     return Arrays.stream(lines)
         .filter(this::containsIgnorePattern)
         .map(PythonPipProvider::extractDepFull)

src/main/java/io/github/guacsec/trustifyda/providers/PythonUvProvider.java

@@ -193,6 +193,21 @@ UvDependencyData parseUvExport(String exportOutput) throws IOException {
       // Package line: name==version [; env-marker]
       if (!line.startsWith(" ") && !trimmed.startsWith("#")) {
         inViaBlock = false;
+
+        // PEP 440 direct references (name @ url) — skip, no pinned version available
+        if (isDirectReference(trimmed)) {
+          log.fine("Skipping PEP 440 direct reference: " + trimmed);
+          currentKey = null;
+          continue;
+        }
+
+        // Path dependencies (./local, ../local, /absolute, ~/home, C:\win) — skip
+        if (isPathDependency(trimmed)) {
+          log.fine("Skipping path dependency: " + trimmed);
+          currentKey = null;
+          continue;
+        }
+
         if (!trimmed.contains("==")) {
           throw new IOException("uv export: package '" + trimmed + "' has no pinned version");
         }
@@ -284,6 +299,22 @@ private static String parseEditableInstall(
     }
   }
 
+  private static final Pattern WINDOWS_DRIVE_PATH = Pattern.compile("^[a-zA-Z]:[/\\\\]");
+
+  /** Returns {@code true} if the line is a PEP 440 direct reference ({@code name @ url}). */
+  static boolean isDirectReference(String trimmedLine) {
+    return trimmedLine.contains(" @ ");
+  }
+
+  /** Returns {@code true} if the line is a local or absolute path dependency. */
+  static boolean isPathDependency(String trimmedLine) {
+    return trimmedLine.startsWith("./")
+        || trimmedLine.startsWith("../")
+        || trimmedLine.startsWith("/")
+        || trimmedLine.startsWith("~/")
+        || WINDOWS_DRIVE_PATH.matcher(trimmedLine).find();
+  }
+
   private static final Pattern BARE_PACKAGE_NAME = Pattern.compile("[A-Za-z0-9][A-Za-z0-9._-]*");
 
   private static void recordViaParent(

src/main/java/io/github/guacsec/trustifyda/utils/PythonControllerBase.java

@@ -35,6 +35,8 @@
 import java.util.List;
 import java.util.Map;
 import java.util.logging.Logger;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -112,10 +114,9 @@ public final List<Map<String, Object>> getDependencies(
 
   private void installingRequirementsOneByOne(String pathToRequirements) {
     try {
-      List<String> requirementsRows = Files.readAllLines(Path.of(pathToRequirements));
+      List<String> requirementsRows =
+          preprocessRequirementsLines(Files.readAllLines(Path.of(pathToRequirements)));
       requirementsRows.stream()
-          .filter((line) -> !line.trim().startsWith("#"))
-          .filter((line) -> !line.trim().isEmpty())
           .forEach(
               (dependency) -> {
                 String dependencyName = getDependencyName(dependency);
@@ -151,11 +152,7 @@ private List<Map<String, Object>> getDependenciesImpl(
     }
     List<String> linesOfRequirements;
     try {
-      linesOfRequirements =
-          Files.readAllLines(requirementsPath).stream()
-              .filter((line) -> !line.trim().startsWith("#") && !line.trim().isEmpty())
-              .map(String::trim)
-              .collect(Collectors.toList());
+      linesOfRequirements = preprocessRequirementsLines(Files.readAllLines(requirementsPath));
     } catch (IOException e) {
       log.warning(
           "Error while trying to read the requirements.txt file, will not be able to install"
@@ -377,6 +374,71 @@ protected String getDependencyNameShow(String pipShowOutput) {
     return versionToken.substring(0, endOfLine).trim();
   }
 
+  private static final Pattern INLINE_OPTION_PATTERN = Pattern.compile("\\s--");
+  private static final Pattern WINDOWS_DRIVE_PATH_PATTERN = Pattern.compile("^[a-zA-Z]:[/\\\\]");
+
+  /**
+   * Preprocesses raw requirements.txt lines by joining line continuations, stripping inline
+   * options, and filtering out pip option lines, URLs, local paths, and empty/comment lines.
+   */
+  public static List<String> preprocessRequirementsLines(List<String> rawLines) {
+    // Join line continuations (trailing backslash, possibly followed by whitespace)
+    List<String> joined = new ArrayList<>();
+    StringBuilder current = new StringBuilder();
+    for (String line : rawLines) {
+      String stripped = line.stripTrailing();
+      if (stripped.endsWith("\\")) {
+        current.append(stripped, 0, stripped.length() - 1);
+      } else {
+        current.append(line);
+        joined.add(current.toString());
+        current = new StringBuilder();
+      }
+    }
+    if (current.length() > 0) {
+      joined.add(current.toString());
+    }
+
+    List<String> result = new ArrayList<>();
+    for (String raw : joined) {
+      String line = raw.trim();
+      if (line.isEmpty() || line.startsWith("#")) {
+        continue;
+      }
+      // Filter out pip options (lines starting with -)
+      if (line.startsWith("-")) {
+        continue;
+      }
+      // Filter out local path requirements (./path, ../path, /abs/path, C:\path, C:/path)
+      if (line.startsWith("./")
+          || line.startsWith("../")
+          || line.startsWith("/")
+          || WINDOWS_DRIVE_PATH_PATTERN.matcher(line).find()) {
+        continue;
+      }
+      // Strip PEP 508 direct references (name @ url -> name) before URL check
+      int atIndex = line.indexOf(" @ ");
+      if (atIndex != -1) {
+        line = line.substring(0, atIndex).trim();
+      }
+      // Strip inline pip options (--hash=..., --config-settings=..., etc.)
+      Matcher optionMatcher = INLINE_OPTION_PATTERN.matcher(line);
+      if (optionMatcher.find()) {
+        line = line.substring(0, optionMatcher.start()).trim();
+      }
+      // Filter out bare URLs and VCS URLs — check the requirement part (before any marker)
+      // to avoid false positives from marker strings
+      String requirementPart = line.contains(";") ? line.substring(0, line.indexOf(";")) : line;
+      if (requirementPart.contains("://")) {
+        continue;
+      }
+      if (!line.isEmpty()) {
+        result.add(line);
+      }
+    }
+    return result;
+  }
+
   public static String getDependencyName(String dep) {
     int markerSeparator = dep.indexOf(";");
     String requirement = markerSeparator == -1 ? dep : dep.substring(0, markerSeparator);

src/test/java/io/github/guacsec/trustifyda/providers/Python_Uv_Provider_Test.java

@@ -392,6 +392,212 @@ void test_parseUvExport_via_skips_non_bare_package_names() throws IOException {
     assertThat(data.graph().values().stream().allMatch(p -> p.children().isEmpty())).isTrue();
   }
 
+  /** Verifies that PEP 440 direct references (name @ url) are skipped without throwing. */
+  @Test
+  void test_parseUvExport_skips_direct_references() throws IOException {
+    Path pyprojectPath = Path.of(UV_FIXTURE, "pyproject.toml");
+    var provider = new PythonUvProvider(pyprojectPath);
+
+    String exportOutput =
+        "# This file was autogenerated by uv\n"
+            + "certifi @ git+https://github.com/certifi/python-certifi.git@abcdef1234567890\n"
+            + "    # via requests\n"
+            + "anyio==3.6.2\n"
+            + "    # via test-project\n";
+
+    // Given/When
+    var data = provider.parseUvExport(exportOutput);
+
+    // Then — direct reference is skipped, not in graph
+    assertThat(data.graph()).doesNotContainKey("certifi");
+    // anyio after the skipped line is still parsed correctly
+    assertThat(data.graph()).containsKey("anyio");
+    assertThat(data.graph().get("anyio").version()).isEqualTo("3.6.2");
+    assertThat(data.directDeps()).contains("anyio");
+  }
+
+  /** Verifies that path dependencies (./local-package) are skipped without throwing. */
+  @Test
+  void test_parseUvExport_skips_path_dependencies() throws IOException {
+    Path pyprojectPath = Path.of(UV_FIXTURE, "pyproject.toml");
+    var provider = new PythonUvProvider(pyprojectPath);
+
+    String exportOutput =
+        "# This file was autogenerated by uv\n"
+            + "./local-package\n"
+            + "    # via test-project\n"
+            + "../sibling-package\n"
+            + "    # via test-project\n"
+            + "/absolute/path/package\n"
+            + "    # via test-project\n"
+            + "~/home-relative/package\n"
+            + "    # via test-project\n"
+            + "C:\\Users\\dev\\my-package\n"
+            + "    # via test-project\n"
+            + "anyio==3.6.2\n"
+            + "    # via test-project\n";
+
+    // Given/When
+    var data = provider.parseUvExport(exportOutput);
+
+    // Then — all path dependency forms are skipped
+    assertThat(data.graph()).doesNotContainKey("./local-package");
+    assertThat(data.graph()).doesNotContainKey("../sibling-package");
+    assertThat(data.graph()).doesNotContainKey("/absolute/path/package");
+    assertThat(data.graph()).doesNotContainKey("~/home-relative/package");
+    assertThat(data.graph()).doesNotContainKey("c:\\users\\dev\\my-package");
+    // anyio is still parsed correctly
+    assertThat(data.graph()).containsKey("anyio");
+    assertThat(data.directDeps()).contains("anyio");
+  }
+
+  /**
+   * Verifies that # via comments after a skipped path dependency do not corrupt the graph by
+   * attaching to the previous package.
+   */
+  @Test
+  void test_parseUvExport_via_after_skipped_path_dep_does_not_corrupt_graph() throws IOException {
+    Path pyprojectPath = Path.of(UV_FIXTURE, "pyproject.toml");
+    var provider = new PythonUvProvider(pyprojectPath);
+
+    // Given — anyio is parsed first, then a path dependency is skipped. The "# via requests"
+    // after the skipped path dep should NOT make anyio a child of requests.
+    String exportOutput =
+        "# This file was autogenerated by uv\n"
+            + "anyio==3.6.2\n"
+            + "    # via test-project\n"
+            + "./local-package\n"
+            + "    # via requests\n"
+            + "requests==2.25.1\n"
+            + "    # via test-project\n";
+
+    // When
+    var data = provider.parseUvExport(exportOutput);
+
+    // Then — requests should NOT have anyio as a child (that would be a corruption)
+    assertThat(data.graph().get("requests").children()).doesNotContain("anyio");
+    // Both anyio and requests are direct deps
+    assertThat(data.directDeps()).containsExactlyInAnyOrder("anyio", "requests");
+  }
+
+  /**
+   * Verifies that # via comments after skipped direct references do not create incorrect
+   * parent-child relationships with the previous package.
+   */
+  @Test
+  void test_parseUvExport_via_after_skipped_does_not_corrupt_graph() throws IOException {
+    Path pyprojectPath = Path.of(UV_FIXTURE, "pyproject.toml");
+    var provider = new PythonUvProvider(pyprojectPath);
+
+    // anyio is parsed first, then a direct reference is skipped. The "# via requests" after
+    // the skipped package should NOT make anyio a child of requests.
+    String exportOutput =
+        "# This file was autogenerated by uv\n"
+            + "anyio==3.6.2\n"
+            + "    # via test-project\n"
+            + "certifi @ git+https://github.com/certifi/python-certifi.git@abcdef\n"
+            + "    # via requests\n"
+            + "requests==2.25.1\n"
+            + "    # via test-project\n";
+
+    // Given/When
+    var data = provider.parseUvExport(exportOutput);
+
+    // Then — requests should NOT have anyio as a child (that would be a corruption)
+    assertThat(data.graph().get("requests").children()).doesNotContain("anyio");
+    // certifi is skipped
+    assertThat(data.graph()).doesNotContainKey("certifi");
+    // Both anyio and requests are direct deps
+    assertThat(data.directDeps()).containsExactlyInAnyOrder("anyio", "requests");
+  }
+
+  /**
+   * Verifies that parseUvExport correctly handles a fixture file containing both direct references
+   * and path dependencies mixed with normal packages.
+   */
+  @Test
+  void test_parseUvExport_with_direct_refs_fixture() throws IOException {
+    Path exportPath = Path.of(UV_FIXTURE, "uv_export_direct_refs.txt");
+    Path pyprojectPath = Path.of(UV_FIXTURE, "pyproject.toml");
+    var provider = new PythonUvProvider(pyprojectPath);
+    String exportOutput = Files.readString(exportPath);
+
+    // Given/When
+    var data = provider.parseUvExport(exportOutput);
+
+    // Then — direct reference and path dependency are skipped
+    assertThat(data.graph()).doesNotContainKey("certifi");
+    assertThat(data.graph()).doesNotContainKey("./local-package");
+
+    // Normal packages are parsed correctly
+    assertThat(data.graph()).containsKeys("anyio", "flask", "requests", "idna", "sniffio");
+    assertThat(data.graph().get("anyio").version()).isEqualTo("3.6.2");
+    assertThat(data.graph().get("flask").version()).isEqualTo("2.0.3");
+    assertThat(data.graph().get("requests").version()).isEqualTo("2.25.1");
+
+    // Direct deps are correctly identified
+    assertThat(data.directDeps()).containsExactlyInAnyOrder("anyio", "flask", "requests");
+
+    // charset-normalizer is a child of requests (not corrupted by the skipped certifi)
+    assertThat(data.graph().get("requests").children()).contains("charset-normalizer");
+  }
+
+  /**
+   * Verifies that provideStack succeeds with export output containing direct references and path
+   * dependencies.
+   */
+  @Test
+  void test_provideStack_with_direct_refs() throws IOException {
+    Path pyprojectPath = Path.of(UV_FIXTURE, "pyproject.toml");
+    String exportOutput = Files.readString(Path.of(UV_FIXTURE, "uv_export_direct_refs.txt"));
+
+    System.setProperty(PythonUvProvider.PROP_TRUSTIFY_DA_UV_EXPORT, exportOutput);
+    try {
+      var provider = new PythonUvProvider(pyprojectPath);
+      var content = provider.provideStack();
+      assertThat(content.type).isEqualTo(Api.CYCLONEDX_MEDIA_TYPE);
+      String sbomJson = new String(content.buffer);
+      assertThat(sbomJson).contains("CycloneDX");
+      // Skipped packages should not appear
+      assertThat(sbomJson).doesNotContain("pkg:pypi/certifi@");
+      // Normal packages should appear
+      assertThat(sbomJson).contains("pkg:pypi/anyio@3.6.2");
+      assertThat(sbomJson).contains("pkg:pypi/flask@2.0.3");
+      assertThat(sbomJson).contains("pkg:pypi/requests@2.25.1");
+    } catch (RuntimeException | NoClassDefFoundError e) {
+      Assumptions.assumeTrue(false, "Skipping: SBOM serialization unavailable - " + e.getMessage());
+    } finally {
+      System.clearProperty(PythonUvProvider.PROP_TRUSTIFY_DA_UV_EXPORT);
+    }
+  }
+
+  /**
+   * Verifies that provideComponent succeeds with export output containing direct references and
+   * path dependencies.
+   */
+  @Test
+  void test_provideComponent_with_direct_refs() throws IOException {
+    Path pyprojectPath = Path.of(UV_FIXTURE, "pyproject.toml");
+    String exportOutput = Files.readString(Path.of(UV_FIXTURE, "uv_export_direct_refs.txt"));
+
+    System.setProperty(PythonUvProvider.PROP_TRUSTIFY_DA_UV_EXPORT, exportOutput);
+    try {
+      var provider = new PythonUvProvider(pyprojectPath);
+      var content = provider.provideComponent();
+      assertThat(content.type).isEqualTo(Api.CYCLONEDX_MEDIA_TYPE);
+      String sbomJson = new String(content.buffer);
+      assertThat(sbomJson).contains("CycloneDX");
+      assertThat(sbomJson).doesNotContain("pkg:pypi/certifi@");
+      assertThat(sbomJson).contains("pkg:pypi/anyio@3.6.2");
+      assertThat(sbomJson).contains("pkg:pypi/flask@2.0.3");
+      assertThat(sbomJson).contains("pkg:pypi/requests@2.25.1");
+    } catch (RuntimeException | NoClassDefFoundError e) {
+      Assumptions.assumeTrue(false, "Skipping: SBOM serialization unavailable - " + e.getMessage());
+    } finally {
+      System.clearProperty(PythonUvProvider.PROP_TRUSTIFY_DA_UV_EXPORT);
+    }
+  }
+
   @Test
   void test_parseUvExport_throws_on_unpinned_version() {
     Path pyprojectPath = Path.of(UV_FIXTURE, "pyproject.toml");