From 415dc721fee79607ef7bf4af0fce82c7291a9936 Mon Sep 17 00:00:00 2001 From: prabhu <7842+prabhu@users.noreply.github.com> Date: Fri, 3 Jan 2025 12:16:57 +0000 Subject: [PATCH] uv workspace support (#1524) * Support for uv workspace Signed-off-by: Prabhu Subramanian --------- Signed-off-by: Prabhu Subramanian --- .github/workflows/snapshot-tests.yml | 16 ++- ci/Dockerfile | 2 +- ci/base-images/cdxgen/Dockerfile.python | 2 +- ci/base-images/sle/Dockerfile.lang | 2 +- lib/cli/index.js | 23 +++- lib/helpers/utils.js | 165 +++++++++++++++++++--- lib/helpers/utils.test.js | 22 ++- test/data/pyproject_uv-workspace.toml | 21 +++ test/data/uv-workspace.lock | 176 ++++++++++++++++++++++++ types/lib/cli/index.d.ts.map | 2 +- types/lib/helpers/utils.d.ts | 14 +- types/lib/helpers/utils.d.ts.map | 2 +- 12 files changed, 404 insertions(+), 43 deletions(-) create mode 100644 test/data/pyproject_uv-workspace.toml create mode 100644 test/data/uv-workspace.lock diff --git a/.github/workflows/snapshot-tests.yml b/.github/workflows/snapshot-tests.yml index e7c0ecbb7f..287a10647b 100644 --- a/.github/workflows/snapshot-tests.yml +++ b/.github/workflows/snapshot-tests.yml @@ -2,7 +2,16 @@ name: Test BOM Snapshots on: workflow_dispatch: - + push: + branches: + - master + - release/* + tags: + - 'v*' + pull_request: + paths-ignore: + - 'docs/**' + - '*.md' concurrency: group: "${{ github.workflow }}-${{ github.head_ref || github.run_id }}" @@ -26,7 +35,7 @@ jobs: run: | rm -rf original_snapshots new_snapshots src_repos cdxgen_tarball=$(pnpm pack | tail -1) - npm install -g "$cdxgen_tarball" + sudo npm install -g "$cdxgen_tarball" git clone https://github.com/appthreat/cdxgen-samples.git original_snapshots python3.12 -m venv .venv source .venv/bin/activate && pip install -r test/diff/requirements.txt @@ -35,7 +44,8 @@ jobs: run: | source .venv/bin/activate python test/diff/generate.py - + env: + ATOM_JAVA_HOME: /usr/lib/jvm/java-21-openjdk-amd64 - name: Upload shell scripts generated as artifact uses: actions/upload-artifact@v4 with: diff --git a/ci/Dockerfile b/ci/Dockerfile index 9e8e9bf9ba..cd21542abb 100644 --- a/ci/Dockerfile +++ b/ci/Dockerfile @@ -21,7 +21,7 @@ ARG SBT_VERSION=1.10.5 ARG MAVEN_VERSION=3.9.9 ARG GRADLE_VERSION=8.11 ARG GO_VERSION=1.23.3 -ARG NODE_VERSION=23.2.0 +ARG NODE_VERSION=23.5.0 ARG PYTHON_VERSION=3.12 ENV GOPATH=/opt/app-root/go \ diff --git a/ci/base-images/cdxgen/Dockerfile.python b/ci/base-images/cdxgen/Dockerfile.python index 8dba2881b6..fa58d00f78 100644 --- a/ci/base-images/cdxgen/Dockerfile.python +++ b/ci/base-images/cdxgen/Dockerfile.python @@ -11,7 +11,7 @@ LABEL maintainer="CycloneDX" \ org.opencontainers.image.description="Rolling image with cdxgen SBOM generator for Python 3.12 apps" \ org.opencontainers.docker.cmd="docker run --rm -v /tmp:/tmp -p 9090:9090 -v $(pwd):/app:rw -t ghcr.io/cyclonedx/cdxgen-python:v11 -r /app --server" -ARG NODE_VERSION=23.2.0 +ARG NODE_VERSION=23.5.0 ENV NVM_DIR="/root/.nvm" \ PYTHON_CMD=python3 \ diff --git a/ci/base-images/sle/Dockerfile.lang b/ci/base-images/sle/Dockerfile.lang index 5b5d34409b..03b58eb4cc 100644 --- a/ci/base-images/sle/Dockerfile.lang +++ b/ci/base-images/sle/Dockerfile.lang @@ -3,7 +3,7 @@ FROM registry.suse.com/bci/python:3.12 ARG JAVA_VERSION=23.0.1-tem ARG MAVEN_VERSION=3.9.9 ARG GCC_VERSION=13 -ARG NODE_VERSION=23.2.0 +ARG NODE_VERSION=23.5.0 ENV JAVA_VERSION=$JAVA_VERSION \ MAVEN_VERSION=$MAVEN_VERSION \ diff --git a/lib/cli/index.js b/lib/cli/index.js index 73a774fb56..258c108b4b 100644 --- a/lib/cli/index.js +++ b/lib/cli/index.js @@ -132,11 +132,11 @@ import { parsePkgJson, parsePkgLock, parsePnpmLock, - parsePoetrylockData, parsePom, parsePrivadoFile, parsePubLockData, parsePubYamlData, + parsePyLockData, parsePyProjectTomlFile, parseReqFile, parseSbtLock, @@ -1049,7 +1049,7 @@ function determinePackageType(pkg) { if ( pkg.purl.startsWith(cf) || purl.namespace?.includes(cf) || - purl.name.toLowerCase().includes(cf) + purl.name.toLowerCase().startsWith(cf) ) { return "framework"; } @@ -3023,7 +3023,7 @@ export async function createPythonBom(path, options) { )) && !uvLockFiles.length ) { - createUVLock(path); + createUVLock(path, options); uvLockFiles = getAllFiles( path, `${options.multiProject ? "**/" : ""}uv.lock`, @@ -3049,11 +3049,24 @@ export async function createPythonBom(path, options) { if (DEBUG_MODE) { console.log(`Parsing ${f}`); } - let retMap = await parsePoetrylockData(lockData, f); + let retMap = await parsePyLockData(lockData, f); + // Should we exit for workspace errors + if (retMap?.workspaceWarningShown) { + options.failOnError && process.exit(1); + } if (retMap.pkgList?.length) { pkgList = pkgList.concat(retMap.pkgList); pkgList = trimComponents(pkgList); } + // Retain the parent hierarchy + if (retMap?.parentComponent?.components?.length) { + if (!parentComponent.components) { + parentComponent.components = []; + } + parentComponent.components = parentComponent.components.concat( + retMap?.parentComponent?.components, + ); + } if (retMap.dependenciesList?.length) { dependencies = mergeDependencies( dependencies, @@ -3063,7 +3076,7 @@ export async function createPythonBom(path, options) { } // Retrieve the tree using virtualenv in deep mode and as a fallback // This is a slow operation - if (options.deep || !dependencies.length) { + if ((options.deep || !dependencies.length) && !f.endsWith("uv.lock")) { retMap = getPipFrozenTree(basePath, f, tempDir, parentComponent); if (retMap.pkgList?.length) { pkgList = pkgList.concat(retMap.pkgList); diff --git a/lib/helpers/utils.js b/lib/helpers/utils.js index 9bf18d34cf..6bfe310ce2 100644 --- a/lib/helpers/utils.js +++ b/lib/helpers/utils.js @@ -4272,6 +4272,8 @@ export function parsePyProjectTomlFile(tomlFile) { } let poetryMode = false; let uvMode = false; + let hatchMode = false; + const workspacePaths = []; let tomlData; const directDepsKeys = {}; const groupDepsKeys = {}; @@ -4293,6 +4295,18 @@ export function parsePyProjectTomlFile(tomlFile) { if (tomlData?.tool?.uv) { uvMode = true; } + if (tomlData?.["build-system"]?.["build-backend"]?.startsWith("hatchling.")) { + hatchMode = true; + } + if ( + uvMode && + tomlData.tool.uv.workspace && + Array.isArray(tomlData.tool.uv.workspace?.members) + ) { + for (const amember of tomlData.tool.uv.workspace.members) { + workspacePaths.push(amember.replace(/\/\*$/, "/**/pyproject.toml")); + } + } // uv and others if (tomlData?.project && Object.keys(tomlData.project).length) { handleBlock(pkg, tomlData.project); @@ -4332,13 +4346,13 @@ export function parsePyProjectTomlFile(tomlFile) { if (tomlData?.project?.dependencies) { for (const adep of tomlData.project.dependencies) { // Example: bcrypt>=4.2.0 - directDepsKeys[adep.split(" ")[0]] = true; + directDepsKeys[adep.split(/[\s<>=]/)[0]] = true; } } if (tomlData["dependency-groups"]) { for (const agroup of Object.keys(tomlData["dependency-groups"])) { tomlData["dependency-groups"][agroup].forEach((p) => { - const pname = p.split(/(==|<=|~=|>=|\[)/)[0].split(" ")[0]; + const pname = p.split(/(==|<=|~=|>=)/)[0].split(" ")[0]; if (!groupDepsKeys[pname]) { groupDepsKeys[pname] = []; } @@ -4379,20 +4393,21 @@ export function parsePyProjectTomlFile(tomlFile) { parentComponent: pkg, poetryMode, uvMode, + hatchMode, + workspacePaths, directDepsKeys, groupDepsKeys, }; } /** - * Method to parse poetry.lock like data. - * TODO: Rewrite to use toml library. + * Method to parse python lock files such as poetry.lock, pdm.lock, uv.lock. * * @param {Object} lockData JSON data from poetry.lock, pdm.lock, or uv.lock file * @param {string} lockFile Lock file name for evidence * @param {string} pyProjectFile pyproject.toml file */ -export async function parsePoetrylockData(lockData, lockFile, pyProjectFile) { +export async function parsePyLockData(lockData, lockFile, pyProjectFile) { let pkgList = []; const rootList = []; const dependenciesList = []; @@ -4401,21 +4416,69 @@ export async function parsePoetrylockData(lockData, lockFile, pyProjectFile) { let directDepsKeys = {}; let groupDepsKeys = {}; let parentComponent; + let workspacePaths; + let workspaceWarningShown = false; + // Keep track of any workspace components to be added to the parent component + const workspaceComponentMap = {}; + const pkgParentMap = {}; if (!lockData) { return { pkgList, dependenciesList }; } if (!pyProjectFile && lockFile) { // See if there is a pyproject.toml in the same directory pyProjectFile = join(dirname(lockFile), "pyproject.toml"); - if (existsSync(pyProjectFile)) { - const pyProjMap = parsePyProjectTomlFile(pyProjectFile); - directDepsKeys = pyProjMap.directDepsKeys; - groupDepsKeys = pyProjMap.groupDepsKeys; - parentComponent = pyProjMap.parentComponent; - if (DEBUG_MODE) { - console.log( - `Parsing ${pyProjectFile} for dependencies and groups information.`, - ); + } + if (pyProjectFile && existsSync(pyProjectFile)) { + if (DEBUG_MODE) { + console.log( + `Parsing ${pyProjectFile} for dependencies and groups information.`, + ); + } + const pyProjMap = parsePyProjectTomlFile(pyProjectFile); + directDepsKeys = pyProjMap.directDepsKeys; + groupDepsKeys = pyProjMap.groupDepsKeys; + parentComponent = pyProjMap.parentComponent; + workspacePaths = pyProjMap.workspacePaths; + if (workspacePaths?.length) { + // Parent component is going to have children + parentComponent.components = []; + for (const awpath of workspacePaths) { + const wpyprojfiles = getAllFiles(dirname(lockFile), awpath); + if (!wpyprojfiles?.length) { + if (!workspaceWarningShown) { + console.log( + `Unable to collect pyproject.toml files for the workspace pattern ${awpath}. Ensure cdxgen is run from the root directory containing the application source code.`, + ); + console.log( + "The dependency tree in the generated SBOM will be flattened and therefore incorrect.", + ); + workspaceWarningShown = true; + } + continue; + } + for (const awpyproj of wpyprojfiles) { + if (DEBUG_MODE) { + console.log( + `Parsing workspace ${awpyproj} to improve the dependency tree.`, + ); + } + // Nested workspace is not supported + const wcompMap = parsePyProjectTomlFile(awpyproj); + if (wcompMap?.parentComponent) { + workspaceComponentMap[wcompMap.parentComponent.name] = + wcompMap.parentComponent; + } + const wparentComponentRef = wcompMap.parentComponent["bom-ref"]; + // Track the parents of workspace direct dependencies + if (wcompMap?.directDepsKeys) { + for (const wdd of Object.keys(wcompMap?.directDepsKeys)) { + if (!pkgParentMap[wdd]) { + pkgParentMap[wdd] = []; + } + pkgParentMap[wdd].push(wparentComponentRef); + } + } + } } } } @@ -4429,6 +4492,24 @@ export async function parsePoetrylockData(lockData, lockFile, pyProjectFile) { console.log("Error while parsing the lock data as toml", err); } } + // Check for workspaces + if (lockTomlObj?.manifest?.members) { + const workspaceMembers = lockTomlObj.manifest.members; + for (const amember of workspaceMembers) { + if (amember === parentComponent.name) { + continue; + } + if (workspaceComponentMap[amember]) { + parentComponent.components.push(workspaceComponentMap[amember]); + } else { + if (!workspaceWarningShown) { + console.log( + `Unable to identify the metadata for the workspace ${amember}. Check if the path specified in ${pyProjectFile} is valid.`, + ); + } + } + } + } for (const apkg of lockTomlObj.package || []) { // This avoids validation errors with uv.lock if (parentComponent?.name && parentComponent.name === apkg.name) { @@ -4452,6 +4533,26 @@ export async function parsePoetrylockData(lockData, lockFile, pyProjectFile) { value: apkg["python-versions"], }); } + if (apkg?.source) { + if (!apkg?.source?.registry?.startsWith("https://pypi.org/")) { + pkg.properties.push({ + name: "cdx:pypi:registry", + value: apkg.source.registry, + }); + } + if (apkg?.source?.virtual) { + pkg.properties.push({ + name: "cdx:pypi:virtual_path", + value: apkg.source.virtual, + }); + } + if (apkg?.source?.editable) { + pkg.properties.push({ + name: "cdx:pypi:virtual_path", + value: apkg.source.editable, + }); + } + } const purlString = new PackageURL( "pypi", "", @@ -4513,7 +4614,10 @@ export async function parsePoetrylockData(lockData, lockFile, pyProjectFile) { }); } } - if (directDepsKeys[pkg.name]) { + if ( + directDepsKeys[pkg.name] || + !Object.keys(workspaceComponentMap).length + ) { rootList.push(pkg); } // This would help the lookup @@ -4522,6 +4626,15 @@ export async function parsePoetrylockData(lockData, lockFile, pyProjectFile) { if (!depsMap[pkg["bom-ref"]]) { depsMap[pkg["bom-ref"]] = new Set(); } + // Track the workspace tree + if (pkgParentMap[pkg.name]) { + for (const pkgParentRef of pkgParentMap[pkg.name]) { + if (!depsMap[pkgParentRef]) { + depsMap[pkgParentRef] = new Set(); + } + depsMap[pkgParentRef].add(pkg["bom-ref"]); + } + } if (apkg.dependencies) { if (Array.isArray(apkg.dependencies)) { // pdm.lock files @@ -4558,9 +4671,11 @@ export async function parsePoetrylockData(lockData, lockFile, pyProjectFile) { }); } return { + parentComponent, pkgList, rootList, dependenciesList, + workspaceWarningShown, }; } @@ -10983,7 +11098,10 @@ export function executeAtom(src, args) { const env = { ...process.env, }; - + // Atom requires Java >= 21 + if (process.env?.ATOM_JAVA_HOME) { + env.JAVA_HOME = process.env.ATOM_JAVA_HOME; + } if (isWin) { env.PATH = `${env.PATH || env.Path}${_delimiter}${join( dirNameStr, @@ -11183,11 +11301,22 @@ function get_python_command_from_env(env) { /** * Create uv.lock file with uv sync command. * - * @param {string} basePath + * @param {string} basePath Path + * @param {Object} options CLI options */ -export function createUVLock(basePath) { +export function createUVLock(basePath, options) { const python_cmd = get_python_command_from_env(process.env); let uvSyncArgs = ["-m", "uv", "sync"]; + // Do not update the lock file in pre-build mode + if (options?.lifecycle?.includes("pre-build")) { + uvSyncArgs.push("--frozen"); + } else if (options?.recurse) { + uvSyncArgs = uvSyncArgs.concat(["--all-groups", "--all-packages"]); + } + // Install everything and do not remove anything extraneous + if (options?.deep) { + uvSyncArgs = uvSyncArgs.concat(["--all-extras", "--inexact"]); + } if (process?.env?.UV_INSTALL_ARGS) { const addArgs = process.env.UV_INSTALL_ARGS.split(" "); uvSyncArgs = uvSyncArgs.concat(addArgs); diff --git a/lib/helpers/utils.test.js b/lib/helpers/utils.test.js index 5021764035..54a8470628 100644 --- a/lib/helpers/utils.test.js +++ b/lib/helpers/utils.test.js @@ -75,11 +75,11 @@ import { parsePkgJson, parsePkgLock, parsePnpmLock, - parsePoetrylockData, parsePom, parsePrivadoFile, parsePubLockData, parsePubYamlData, + parsePyLockData, parsePyProjectTomlFile, parsePyRequiresDist, parseReqFile, @@ -4735,38 +4735,46 @@ test("parse pyproject.toml with custom poetry source", () => { expect(Object.keys(retMap.directDepsKeys).length).toEqual(6); }); -test("parse poetry.lock", async () => { - let retMap = await parsePoetrylockData( +test("parse python lock files", async () => { + let retMap = await parsePyLockData( readFileSync("./test/data/poetry.lock", { encoding: "utf-8" }), "./test/data/poetry.lock", ); expect(retMap.pkgList.length).toEqual(32); expect(retMap.pkgList[2].scope).toEqual("optional"); expect(retMap.dependenciesList.length).toEqual(32); - retMap = await parsePoetrylockData( + retMap = await parsePyLockData( readFileSync("./test/data/poetry1.lock", { encoding: "utf-8" }), "./test/data/poetry1.lock", ); expect(retMap.pkgList.length).toEqual(68); expect(retMap.dependenciesList.length).toEqual(68); - retMap = await parsePoetrylockData( + retMap = await parsePyLockData( readFileSync("./test/data/poetry-cpggen.lock", { encoding: "utf-8" }), "./test/data/poetry-cpggen.lock", ); expect(retMap.pkgList.length).toEqual(69); expect(retMap.dependenciesList.length).toEqual(69); - retMap = await parsePoetrylockData( + retMap = await parsePyLockData( readFileSync("./test/data/pdm.lock", { encoding: "utf-8" }), "./test/data/pdm.lock", ); expect(retMap.pkgList.length).toEqual(39); expect(retMap.dependenciesList.length).toEqual(37); - retMap = await parsePoetrylockData( + retMap = await parsePyLockData( readFileSync("./test/data/uv.lock", { encoding: "utf-8" }), "./test/data/uv.lock", ); expect(retMap.pkgList.length).toEqual(63); expect(retMap.dependenciesList.length).toEqual(63); + retMap = await parsePyLockData( + readFileSync("./test/data/uv-workspace.lock", { encoding: "utf-8" }), + "./test/data/uv-workspace.lock", + "./test/data/pyproject_uv-workspace.toml", + ); + expect(retMap.pkgList.length).toEqual(9); + expect(retMap.rootList.length).toEqual(9); + expect(retMap.dependenciesList.length).toEqual(9); }, 120000); test("parse wheel metadata", () => { diff --git a/test/data/pyproject_uv-workspace.toml b/test/data/pyproject_uv-workspace.toml new file mode 100644 index 0000000000..5701405776 --- /dev/null +++ b/test/data/pyproject_uv-workspace.toml @@ -0,0 +1,21 @@ +[project] +name = "my-app" +version = "0.1.0" +description = "An example of uv workspace" +readme = "README.md" +requires-python = ">=3.9" +dependencies = [ + "my-lib", +] + +[dependency-groups] +dev = [ + "ruff >= 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undefined; + workspaceWarningShown?: undefined; } | { + parentComponent: any; pkgList: any[]; rootList: { name: any; @@ -416,6 +418,7 @@ export function parsePoetrylockData(lockData: any, lockFile: string, pyProjectFi ref: string; dependsOn: any[]; }[]; + workspaceWarningShown: boolean; }>; /** * Method to parse requirements.txt data. 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