[add] implement vulnerability checking and advisory fetching, enhance repo processing, and add utility functions

.gitignore

@@ -2,4 +2,10 @@ dist
 output.csv
 output/
 node_modules/
-cache
+cache
+failed-install.txt
+success copy.txt
+current-processing.log
+current.log
+left_subtract.txt
+processed.log

src/bundle/index.mjs

@@ -1,21 +1,25 @@
 import wp from 'webpack';
 import path from 'node:path'
 import {createRequire,builtinModules} from 'node:module'
+import { mkdirSync } from 'node:fs';
 
 /**
  * 
  * @param {string} l library name
  * @param {string} moduleLocation module location
  * @param {string} outputPath 
- * @returns 
+ * @returns the compressed file path
  */
 export function wpCompress(l, moduleLocation,outputPath = path.resolve('./output/')) {
+    const basePackage = path.basename(path.resolve(moduleLocation));
+    const finalOutputPath = path.resolve(outputPath, basePackage);
+    mkdirSync(finalOutputPath, { recursive: true });
     return new Promise((resolve, reject) => {
-
+    
     const libraryLocation = extractFunctionForModule(l, moduleLocation);
-    console.log(libraryLocation);
+    // console.log(libraryLocation);
     const outputFile = l + '.bundle.cjs';
-    console.log(`[WebPack] Compressing ${l} in ${moduleLocation} to ${path.join(outputPath, outputFile)}`);
+    console.log(`[WebPack] Compressing ${l} in ${moduleLocation} to ${path.join(finalOutputPath, outputFile)}`);
     const moduleFallbackMap = builtinModules.reduce((prev, current) => {
         prev[current] = false;
         return prev;
@@ -36,7 +40,7 @@ export function wpCompress(l, moduleLocation,outputPath = path.resolve('./output
             fallback:moduleFallbackMap
         },
         output: {
-            path: outputPath,
+            path: finalOutputPath,
             filename: outputFile,
             clean: false,
             iife: false,
@@ -52,7 +56,7 @@ export function wpCompress(l, moduleLocation,outputPath = path.resolve('./output
             // console.log(`[WebPack]`,stats?.toJson().errors);
             reject(err || stats);
         }else{
-            resolve(path.resolve(outputPath, outputFile));
+            resolve(path.resolve(finalOutputPath, outputFile));
         }
     });
 });

src/libcalls.mjs

@@ -82,7 +82,9 @@ export class LibraryTypesRecorder {
             return undefined;
         } else if(type.isNull()){
             return null;
-        } else if(type.isBigInt()){
+        } else if (type.isVoid()){
+            return undefined;
+        }else if(type.isBigInt()){
             return simpleFaker.number.bigInt();
         }else if (type.isString()) {
             

src/tsCalls.mjs

@@ -16,8 +16,14 @@ import {builtinModules} from 'node:module'
 export function getImportCallsAndArgumentTypes(importDecls, checker, mainFilePath, libraryTypesRecorder) {
     // const libraryTypesRecorder = new LibraryTypesRecorder(checker);
     for (const importStringDecl of importDecls) {
+
         // console.log(importStringDecl);
         const importDecl = importStringDecl.getFirstAncestor();
+        const packageName = importStringDecl.getLiteralValue();
+        if(isNodeModule(packageName)) {
+            // just skip node module scanning.
+            continue;
+        }
         if (importDecl === undefined) {
             console.error("Import declaration is undefined for", importStringDecl.getText());
             continue;

src_dataset/FILTER_LIST.mjs

@@ -41,7 +41,8 @@ const FILTER_LIST = [
     "https://github.com/foliojs-fork/linebreaker",
     "https://github.com/segmentio/analytics.js-video-plugins",
     "https://github.com/cucumber/cucumber-expressions-javascript",
-    "https://github.com/jakwings/node-temp-fs"
+    "https://github.com/jakwings/node-temp-fs",
+    "https://github.com/bower/bower/tree/master/packages/*"
 ];
 
 const FILTER_LIST_REGEX = FILTER_LIST.map(GlobToRegExp)

src_dataset/cache.mjs

@@ -9,9 +9,9 @@ import { resolve } from "node:path";
  * @param {()=>Promise<T>} asyncCallback 
  * @returns {Promise<T>}
  */
-export async function cacheFunctionOutput(fileName, asyncCallback, silent=false) {
+export async function cacheFunctionOutput(fileName, asyncCallback, silent=false,passthrough=false) {
     const fileLoc = resolve('../cache-repos', fileName);
-    if (existsSync(fileLoc)) {
+    if (!passthrough && existsSync(fileLoc)) {
         !silent && console.log("[cacher] Using cached ", fileLoc);
         const fileContents = (await readFile(fileLoc)).toString();
         return JSON.parse(fileContents);

src_dataset/index.mjs

@@ -30,9 +30,9 @@ const intermediateRepoList = await cacheFunctionOutput('repos.n2.json', async fu
 // const packageMap = new Map(packageList)
 
 console.log(`Total repos`,intermediateRepoList.length)
-const intermediateRepoListSmaller = intermediateRepoList.slice(0,10000);
+const intermediateRepoListSmaller = intermediateRepoList.slice(0,20000);
 
-const repoStatus = await processPromisesBatch(intermediateRepoListSmaller,20,cloneRepoAndCheck)
+const repoStatus = await processPromisesBatch(intermediateRepoListSmaller,40,cloneRepoAndCheck)
 
 const repoStatusString = csv.stringify(repoStatus);
 await fsp.writeFile('repostatus.csv', repoStatusString);

src_dataset/mine.mjs

@@ -43,6 +43,15 @@ export async function cloneRepoAndCheck([repoName, repoGitUrl, downloadCount]) {
     // console.log(repoName, packageJSONContents.license)
     if (!hasAnyActualDependencies(packageJSONContents, repoName)) {
         // console.log("[git] skipping", repoName, "has no dependencies");
+        await removeUnnecessaryClone(repoPath);
+        // console.log("Cleaned up ", repoPath);
+        return [repoName, null];
+    }
+
+    if(isLikelyTypescriptProject(packageJSONContents)) {
+        await removeUnnecessaryClone(repoPath);
+        // console.warn("[git] Ignoring ", repoName, "because it is a typescript project.");
+        // console.log("Cleaned up ", repoPath);
         return [repoName, null];
     }
 
@@ -58,15 +67,37 @@ export async function cloneRepoAndCheck([repoName, repoGitUrl, downloadCount]) {
         }
         const packageFile = resolve(repoPath, 'package.json')
         if (!existsSync(packageFile)){
-            console.warn("[git] Unexpected package.json not found in", repoName, "at", packageFile);
+            // console.warn("[git] Unexpected package.json not found in", repoName, "at", packageFile);
             return [repoName, null];}
 
         // finally, return the test script if it exists
         return [repoName, ((packageJSONContents?.scripts?.test))]
     }
-    else return [repoName, null]
+    else{
+        await removeUnnecessaryClone(repoPath);
+
+        return [repoName, null]
+    }
 }
 
+function isLikelyTypescriptProject(packageJSONContents) {
+    if (packageJSONContents.devDependencies !== undefined) {
+        if (Object.keys(packageJSONContents.devDependencies).some(e => e.startsWith('typescript'))) {
+            return true;
+        }
+        if (Object.keys(packageJSONContents.dependencies).some(e => e.startsWith('typescript'))) {
+            return true;
+        }
+    }
+    return false;
+}
+async function removeUnnecessaryClone(repoPath) {
+    if(existsSync(repoPath)){
+         console.log("[git] unnecessary clone, removing", repoPath) ;
+        //  while(true){}
+        await rm(repoPath, { recursive: true, force: true });
+    }
+}
 
 function filterRepo(repoGitUrl) {
     return matchFilterList(repoGitUrl);

src_vuln/index.mjs

@@ -0,0 +1,65 @@
+import { cacheFunctionOutput } from "../src_dataset/cache.mjs";
+import { bifurcateArray, getGithubTokenFromEnvironment } from "./lib.mjs";
+import { checkForParentDep, findSlicedDeps } from "./slicedeps.mjs";
+import { basename } from "path";
+
+const githubToken = getGithubTokenFromEnvironment();
+
+const vulnTargets = await findSlicedDeps();
+const affects = [...vulnTargets].join(',');
+
+// console.log(query)
+
+const res = await cacheFunctionOutput('advisories.json', async () => {
+    const query = `?ecosystem=npm&affects=${affects}`;
+    const res = await fetch('https://api.github.com/advisories'+query,
+        {
+            headers:{
+                Authorization: `Bearer ${githubToken}`,
+            }
+        }
+    );
+    const x = await res.json();
+    return x;
+},true, false);
+
+const cveMap = res.map(e=>({
+        summary: e.summary,
+        source: e.source_code_location,
+        severity: e.severity,
+        repo_name: basename(e.source_code_location),
+        cve: e.cve_id,
+        identifiers: e.identifiers,
+        cvss: e.cvss,
+    }));
+
+const [fullMaps,emptyMap]= bifurcateArray(cveMap, (e)=>e.source)
+
+
+// const slicedReposSoFar = await findSlicedDepsSoFar();
+const depMap = new Map();
+for(const depo of fullMaps){
+    if(!depMap.has(depo.repo_name)) {
+        depMap.set(depo.repo_name, []);
+    }
+    depMap.get(depo.repo_name).push(depo);
+}
+const depKeys = ([...depMap.keys()])
+console.log(depKeys)
+const repoKeys = await checkForParentDep(depKeys);
+console.log(repoKeys);
+// for(const repo of slicedReposSoFar) {
+//     const deps = await getDepsOfRepo(repo);
+//     console.log(repo,deps);
+//     const depCVEs = fullMaps.filter(e=>(deps).includes(e.repo_name));
+//     depMap.set(repo, depCVEs);
+// }
+console.log(cveMap.length, "advisories found");
+console.log(fullMaps.length, "advisories found");
+console.log(emptyMap.length, "advisories found");
+// what is pending
+// see what's been sliced so far. Find their dependencies, link back to 
+
+
+
+

src_vuln/lib.mjs

@@ -0,0 +1,26 @@
+import assert from "assert";
+
+/**
+ * Bifurcate an array into two arrays based on a predicate function.
+ * @template T
+ * @param {T[]} arr 
+ * @param {(T)=>boolean} predicate 
+ * @returns {[T[], T[]]}
+ */
+export function bifurcateArray(arr, predicate) {
+    const truthy = [];
+    const falsy = [];
+    for (const item of arr) {
+        if (predicate(item)) {
+            truthy.push(item);
+        } else {
+            falsy.push(item);
+        }
+    }
+    return [truthy, falsy];
+}
+export function getGithubTokenFromEnvironment() {
+    assert(process.env.GITHUB_TOKEN, "No token :(");
+    const githubToken = process.env.GITHUB_TOKEN;
+    return githubToken;
+}

src_vuln/slicedeps.mjs

@@ -0,0 +1,97 @@
+import { readdir, opendir } from 'node:fs/promises'
+import path, { basename, dirname } from 'node:path';
+
+
+
+/**
+ * Finds all dependencies that are sliced by the slicer.
+ * this function will search find the list of dependencies that are sliced by the slicer.
+ * in the dist folder, theres a folder of repos. in that, there is a folder for each dependency.
+ * collate into a set and return it.
+ * Eg.
+ * dist/
+ *  └── align-text/
+ *     └── kind-of
+ *    └── longest
+ * 
+ * it will return kind-of and longest as sliced deps.
+ */
+export async function findSlicedDeps(){
+    /**
+     * @type {Set<string>}
+     */
+    const slicedDeps = new Set();
+    const distPath = path.resolve('dist');
+    
+    for await(const p of walk(distPath)) {
+        if(p.endsWith("package.json")) {slicedDeps.add(basename(dirname(p)))}
+        else continue;
+    }
+    return slicedDeps;
+}
+
+/**
+ * Given a list of deps, find the repos that have these
+ * @param {string[]} dependencies 
+ */
+export async function checkForParentDep(dependencies){
+    // dep -> main
+    const map = await getReverseDeps();
+    const reposet = dependencies.flatMap(dep => (map.get(dep)??[]));
+    const repos = new Set(reposet);
+    return repos;
+}
+
+// for a given dep, find the list of main repo that has this dep. return map.
+async function getReverseDeps() {
+    const x = new Map();
+    const distPath = path.resolve('dist');
+
+    for await(const p of walk(distPath)) {
+        if (p.endsWith("package.json")) {
+            const repo = basename(dirname(dirname(p)));
+            const depName = basename(dirname(p));
+
+            if (!x.has(depName)) {
+                x.set(depName, []);
+            }
+            x.get(depName).push(repo);
+            // console.log(p,repo, depName);
+        }
+        else continue;
+    }
+    return x;
+}
+
+export async function findSlicedDepsSoFar() {
+    // return all folder names in the output directory.
+    const distPath = path.resolve('output');
+    const dirEntries = await readdir(distPath, { withFileTypes: true });
+    const repos = dirEntries.filter(dirent => dirent.isDirectory()).map(dirent => dirent.name);
+    return repos;
+}
+/**
+ * 
+ * @param {string} repo 
+ */
+export async function getDepsOfRepo(repo){
+    const distPath = path.resolve('output', repo);
+    const dirEntry = await readdir(distPath, { withFileTypes: true });
+    const deps = dirEntry.filter(dirent => dirent.isFile()).map(dirent => dirent.name.replace('.bundle.cjs',''));
+    return deps;
+}
+
+/**
+ * FS walk primitive
+ * Ref: https://gist.github.com/lovasoa/8691344
+ * @param {string} dir 
+ * @returns {AsyncGenerator<string>}
+ */
+async function* walk(dir) {
+    for await (const d of await opendir(dir)) {
+        const entry = path.join(dir, d.name);
+        if (d.isDirectory()) yield* walk(entry);
+        else if (d.isFile()) yield entry;
+    }
+}
+// checkForParentDep('thenify', 'glob-parent', 'terser', 'url-parse').then(console.log).catch(console.error);

success.txt

@@ -0,0 +1,204 @@
+glob-parent
+is-glob
+mime-types
+doctrine
+define-property
+jsonfile
+optionator
+http-errors
+type-check
+levn
+is-extendable
+esquery
+on-finished
+error-ex
+finalhandler
+content-disposition
+terser
+proxy-addr
+prop-types
+has-values
+has-value
+url-parse
+simple-swizzle
+compressible
+global-modules
+thenify
+mz
+clone-deep
+shallow-clone
+prettier-linter-helpers
+cors
+fd-slicer
+object.pick
+language-tags
+union-value
+object-copy
+static-extend
+memory-fs
+pinkie-promise
+hash.js
+pretty-error
+renderkid
+wbuf
+browserify-zlib
+hmac-drbg
+des.js
+dom-converter
+expand-tilde
+homedir-polyfill
+zip-stream
+crc32-stream
+one-time
+resolve-dir
+yargs-unparser
+# warning
+bplist-parser
+for-own
+md5
+is-relative
+is-absolute
+is-unc-path
+redis-parser
+recursive-readdir
+path-root
+lazy-cache
+# css-to-react-native
+parse-filepath
+request-progress
+jest-junit
+postcss-initial
+unixify
+cookie-parser
+saslprep
+window-size
+cookies
+keygrip
+contains-path
+fined
+object.defaults
+is-color-stop
+gonzales-pe
+bufferutil
+make-iterator
+glob-base
+uid-safe
+fancy-log
+object.map
+object.omit
+find-babel-config
+utf-8-validate
+mquery
+xlsx
+json-to-pretty-yaml
+easy-table
+named-placeholders
+is-dotfile
+parse-glob
+plugin-error
+is-equal-shallow
+original
+detective-typescript
+detective-es6
+json2mq
+create-error-class
+detective-cjs
+to-through
+resolve-options
+ansi-gray
+bcrypt
+mixin-object
+optimize-css-assets-webpack-plugin
+ordered-read-streams
+sync-fetch
+to-absolute-glob
+glogg
+unique-stream
+align-text
+gulplog
+blob
+center-align
+right-align
+wkx
+chai-as-promised
+json-pointer
+has-glob
+# promptly
+hot-shots
+semver-greatest-satisfied-range
+each-props
+is2
+levenary
+airbnb-prop-types
+remove-bom-stream
+remove-bom-buffer
+dotenv-defaults
+rework
+vizion
+array-sort
+default-compare
+pad-right
+passport-local
+console.table
+cli-tableau
+condense-newlines
+requireg
+object.reduce
+properties-reader
+array-initial
+default-resolution
+collection-map
+ansi-red
+broccoli-merge-trees
+eslint-plugin-react-native
+is-valid-path
+strip-hex-prefix
+uglify-es
+ansi-cyan
+method-override
+# readline2
+number-allocator
+has-gulplog
+ethjs-util
+unescape
+validate.io-integer
+stream-parser
+compute-gcd
+validate.io-integer-array
+compute-lcm
+set-getter
+passport-oauth2
+i18n-iso-countries
+sha1
+json-diff
+dreamopt
+highlight-es
+basic-auth-connect
+glob2base
+third-party-capital
+new-date
+webrtc-adapter
+xhr-request-promise
+contentful-resolve-response
+jest-sonar-reporter
+parse-author
+amd-name-resolver
+mocha-multi-reporters
+eslint-plugin-filenames
+apache-crypt
+semver-intersect
+fetch-ponyfill
+karma-mocha
+is-odd
+babel-plugin-ember-modules-api-polyfill
+csurf
+taketalk
+require-and-forget
+geojson-equality
+relative
+pkg-config
+rss-parser
+xml-but-prettier
+karma-spec-reporter
+speakeasy
+parsejson

test_src/build-package.cjs

@@ -0,0 +1,198 @@
+const {writeFile} = require('fs/promises');
+
+const libs = `glob-parent
+is-glob
+mime-types
+doctrine
+define-property
+jsonfile
+optionator
+http-errors
+type-check
+levn
+is-extendable
+esquery
+on-finished
+error-ex
+finalhandler
+content-disposition
+terser
+proxy-addr
+prop-types
+has-values
+has-value
+url-parse
+simple-swizzle
+compressible
+global-modules
+thenify
+mz
+clone-deep
+shallow-clone
+prettier-linter-helpers
+cors
+fd-slicer
+object.pick
+language-tags
+union-value
+object-copy
+static-extend
+memory-fs
+pinkie-promise
+hash.js
+pretty-error
+renderkid
+wbuf
+browserify-zlib
+hmac-drbg
+des.js
+dom-converter
+expand-tilde
+homedir-polyfill
+zip-stream
+crc32-stream
+one-time
+resolve-dir
+yargs-unparser
+warning
+bplist-parser
+for-own
+md5
+is-relative
+is-absolute
+is-unc-path
+redis-parser
+recursive-readdir
+path-root
+lazy-cache
+css-to-react-native
+parse-filepath
+request-progress
+jest-junit
+postcss-initial
+unixify
+cookie-parser
+saslprep
+window-size
+cookies
+keygrip
+contains-path
+fined
+object.defaults
+is-color-stop
+gonzales-pe
+bufferutil
+make-iterator
+glob-base
+uid-safe
+fancy-log
+object.map
+object.omit
+find-babel-config
+utf-8-validate
+mquery
+xlsx
+json-to-pretty-yaml
+easy-table
+named-placeholders
+is-dotfile
+parse-glob
+plugin-error
+is-equal-shallow
+original
+detective-typescript
+detective-es6
+json2mq
+create-error-class
+detective-cjs
+to-through
+resolve-options
+ansi-gray
+bcrypt
+mixin-object
+optimize-css-assets-webpack-plugin
+ordered-read-streams
+sync-fetch
+to-absolute-glob
+glogg
+unique-stream
+align-text
+gulplog
+blob
+center-align
+right-align
+wkx
+chai-as-promised
+json-pointer
+has-glob
+promptly
+hot-shots
+semver-greatest-satisfied-range
+each-props
+is2
+levenary
+airbnb-prop-types
+remove-bom-stream
+remove-bom-buffer
+dotenv-defaults
+rework
+vizion
+array-sort
+default-compare
+pad-right
+passport-local
+console.table
+cli-tableau
+condense-newlines
+requireg
+object.reduce
+properties-reader
+array-initial
+default-resolution
+collection-map
+ansi-red
+broccoli-merge-trees
+eslint-plugin-react-native
+is-valid-path
+strip-hex-prefix
+uglify-es
+ansi-cyan
+method-override
+readline2
+number-allocator
+has-gulplog
+ethjs-util
+unescape
+validate.io-integer
+stream-parser
+compute-gcd
+validate.io-integer-array
+compute-lcm
+set-getter
+passport-oauth2
+i18n-iso-countries
+sha1
+json-diff
+dreamopt
+highlight-es
+basic-auth-connect
+glob2base
+third-party-capital
+new-date
+webrtc-adapter
+xhr-request-promise
+contentful-resolve-response
+jest-sonar-reporter
+parse-author
+amd-name-resolver
+mocha-multi-reporters
+eslint-plugin-filenames
+apache-crypt`;
+const libsArray = libs.split('\n').map(e => e.trim());
+
+const newPackageJson = {
+    dependencies: Object.fromEntries(libsArray.map(lib => [lib, "latest"])),
+}
+
+console.log(JSON.stringify(newPackageJson, null, 2));
+writeFile('vulncheck.package.json', JSON.stringify(newPackageJson, null, 2));

test_src/check_diff.cjs

@@ -0,0 +1,45 @@
+// diff the two csv files, and perform a left subtract and right subtract.
+const fsp = require('fs/promises')
+
+async function main(){
+    const file1 = 'success.txt';
+    const file2String = `mime-types
+http-errors
+source-map-support
+compressible
+global-modules
+thenify
+mz
+memory-fs
+pinkie-promise
+pretty-error
+renderkid
+hpack.js
+wbuf
+expand-tilde
+homedir-polyfill
+basic-auth
+for-own
+is-unc-path
+recursive-readdir
+path-root
+cookies
+bufferutil
+utf-8-validate
+easy-table
+is-dotfile`;
+    const file1String = await fsp.readFile(file1, 'utf8');
+    const f1Elements = file1String.split('\n').filter(Boolean);
+    const f2Elements = file2String.split('\n').filter(Boolean);
+    const leftSubtract = f1Elements.filter(x => !f2Elements.includes(x));
+    // const rightSubtract = f2Elements.filter(x => !f1Elements.includes(x));
+    console.log('Left Subtract:f1, not in f2');
+    const leftSubtractString = leftSubtract.join('\n')
+    await fsp.writeFile('left_subtract.txt', leftSubtractString, 'utf8');
+    // console.log('Right Subtract: done, but not in main list', rightSubtract);
+}
+
+
+main().catch(err => {
+    console.error('Error:', err);
+});