Track workspaces for transitive dependencies for uv monorepos

.github/workflows/repotests.yml

@@ -431,8 +431,6 @@ jobs:
       - name: repotests bionomia
         run: |
           bin/cdxgen.js -r -t ruby repotests/bionomia -o bomresults/bom-bionomia.json --fail-on-error
-          CDXGEN_DEBUG_MODE=debug bin/cdxgen.js -r -t ruby3.3.6 repotests/bionomia -o bomresults/bom-bionomia-deep.json --deep --fail-on-error
-          CDXGEN_DEBUG_MODE=debug bin/cdxgen.js -r -p -t ruby3.3.6 repotests/bionomia -o bomresults/bom-bionomia-research.json --profile research --fail-on-error
         shell: bash
       - name: repotests bazel-examples
         run: |

lib/helpers/utils.js

@@ -2613,7 +2613,19 @@ export async function parsePnpmLock(
               if (!depsWorkspaceRefs[dref]) {
                 depsWorkspaceRefs[dref] = [];
               }
-              depsWorkspaceRefs[dref].push(wref);
+              if (!depsWorkspaceRefs[dref].includes(wref)) {
+                depsWorkspaceRefs[dref].push(wref);
+              }
+              if (dependenciesMap[dref]) {
+                for (const l2ref of dependenciesMap[dref]) {
+                  if (!depsWorkspaceRefs[l2ref]) {
+                    depsWorkspaceRefs[l2ref] = [];
+                  }
+                  if (!depsWorkspaceRefs[l2ref].includes(wref)) {
+                    depsWorkspaceRefs[l2ref].push(wref);
+                  }
+                }
+              }
             }
           }
           const thePkg = {
@@ -2693,7 +2705,7 @@ export async function parsePnpmLock(
     }
     if (depsWorkspaceRefs[apkg["bom-ref"]]?.length) {
       const wsprops = apkg.properties.filter(
-        (p) => p.name === "interal:workspaceRef",
+        (p) => p.name === "internal:workspaceRef",
       );
       if (!wsprops.length) {
         for (const wref of depsWorkspaceRefs[apkg["bom-ref"]]) {
@@ -4647,6 +4659,7 @@ export async function parsePyLockData(lockData, lockFile, pyProjectFile) {
   const dependenciesList = [];
   const depsMap = {};
   const existingPkgMap = {};
+  const pkgBomRefMap = {};
   let directDepsKeys = {};
   let groupDepsKeys = {};
   let parentComponent;
@@ -4901,6 +4914,7 @@ export async function parsePyLockData(lockData, lockFile, pyProjectFile) {
     }
     // This would help the lookup
     existingPkgMap[pkg.name.toLowerCase()] = pkg["bom-ref"];
+    pkgBomRefMap[pkg["bom-ref"]] = pkg;
     pkgList.push(pkg);
     if (!depsMap[pkg["bom-ref"]]) {
       depsMap[pkg["bom-ref"]] = new Set();
@@ -4922,6 +4936,24 @@ export async function parsePyLockData(lockData, lockFile, pyProjectFile) {
           const nameStr =
             apkgDep.name || apkgDep.split(/(==|<=|~=|>=)/)[0].split(" ")[0];
           depsMap[pkg["bom-ref"]].add(existingPkgMap[nameStr] || nameStr);
+          // Propagate the workspace properties to the child components
+          if (
+            existingPkgMap[nameStr] &&
+            pkgBomRefMap[existingPkgMap[nameStr]]
+          ) {
+            const dependentPkg = pkgBomRefMap[existingPkgMap[nameStr]];
+            dependentPkg.properties = dependentPkg.properties || [];
+            const addedValue = {};
+            for (const pprop of pkg.properties) {
+              if (
+                pprop.name.startsWith("internal:workspace") &&
+                !addedValue[pprop.value]
+              ) {
+                dependentPkg.properties.push(pprop);
+                addedValue[pprop.value] = true;
+              }
+            }
+          }
         }
       } else if (Object.keys(apkg.dependencies).length) {
         for (const apkgDep of Object.keys(apkg.dependencies)) {
@@ -4933,15 +4965,38 @@ export async function parsePyLockData(lockData, lockFile, pyProjectFile) {
   pkgList = await getPyMetadata(pkgList, false);
   for (const key of Object.keys(depsMap)) {
     const dependsOnList = new Set();
+    const parentPkg = pkgBomRefMap[key];
     for (const adep of Array.from(depsMap[key])) {
+      let depRef;
       if (adep.startsWith("pkg:")) {
-        dependsOnList.add(adep);
+        depRef = adep;
       } else if (existingPkgMap[adep]) {
-        dependsOnList.add(existingPkgMap[adep]);
+        depRef = existingPkgMap[adep];
       } else if (existingPkgMap[`py${adep}`]) {
-        dependsOnList.add(existingPkgMap[`py${adep}`]);
+        depRef = existingPkgMap[`py${adep}`];
       } else if (existingPkgMap[adep.replace(/-/g, "_")]) {
-        dependsOnList.add(existingPkgMap[adep.replace(/-/g, "_")]);
+        depRef = existingPkgMap[adep.replace(/-/g, "_")];
+      }
+      if (depRef) {
+        dependsOnList.add(depRef);
+        // We need to propagate the workspace properties from the parent
+        const dependentPkg = pkgBomRefMap[depRef];
+        dependentPkg.properties = dependentPkg.properties || [];
+        const addedValue = {};
+        for (const p of dependentPkg.properties) {
+          if (p.name.startsWith("internal:workspace")) {
+            addedValue[p.value] = true;
+          }
+        }
+        for (const pprop of parentPkg.properties) {
+          if (
+            pprop.name.startsWith("internal:workspace") &&
+            !addedValue[pprop.value]
+          ) {
+            dependentPkg.properties.push(pprop);
+            addedValue[pprop.value] = true;
+          }
+        }
       }
     }
     dependenciesList.push({