@appthreat/atom 0.7.5 → 0.8.0

package/index.js

@@ -1,19 +1,21 @@
 #!/usr/bin/env node
 
 const os = require("os");
-const fs = require("fs");
 const path = require("path");
 const { spawnSync } = require("child_process");
 const isWin = require("os").platform() === "win32";
 const LOG4J_CONFIG = path.join(__dirname, "plugins", "log4j2.xml");
 const ATOM_HOME = path.join(__dirname, "plugins", "atom-1.0.0");
-const APP_LIB_DIR = path.join(__dirname, "plugins", "atom-1.0.0", "lib");
+const APP_LIB_DIR = path.join(ATOM_HOME, "lib");
 const freeMemoryGB = Math.floor(os.freemem() / 1024 / 1024 / 1024);
 const JAVA_OPTS = `${
   process.env.JAVA_OPTS || ""
 } -Xms${freeMemoryGB}G -Xmx${freeMemoryGB}G`;
 const APP_MAIN_CLASS = "io.appthreat.atom.Atom";
-let APP_CLASSPATH = path.join(APP_LIB_DIR, "io.appthreat.atom-1.0.0.jar");
+let APP_CLASSPATH = path.join(
+  APP_LIB_DIR,
+  "io.appthreat.atom-1.0.0-classpath.jar"
+);
 let JAVACMD = "java";
 if (process.env.JAVA_HOME) {
   JAVACMD = path.join(
@@ -22,35 +24,8 @@ if (process.env.JAVA_HOME) {
     "java" + (isWin ? ".exe" : "")
   );
 }
-const getAllFiles = (dir, extn, files, result, regex) => {
-  regex = regex || new RegExp(`\\.jar$`);
-  files = files || fs.readdirSync(dir);
-  for (let i = 0; i < files.length; i++) {
-    let file = path.join(dir, files[i]);
-    if (fs.statSync(file).isDirectory()) {
-      // Ignore directories
-      const dirName = path.basename(file);
-      if (
-        dirName.startsWith(".") ||
-        IGNORE_DIRS.includes(dirName.toLowerCase())
-      ) {
-        continue;
-      }
-      try {
-        result = getAllFiles(file, extn, fs.readdirSync(file), result, regex);
-      } catch (error) {
-        continue;
-      }
-    } else {
-      if (regex.test(file) && !file.includes("io.appthreat.atom-1.0.0.jar")) {
-        result.push(file);
-      }
-    }
-  }
-  return result;
-};
 
-const atomLibs = getAllFiles(APP_LIB_DIR, ".jar", undefined, [APP_CLASSPATH]);
+const atomLibs = [APP_CLASSPATH];
 const argv = process.argv.slice(2);
 const args = [
   "-cp",
@@ -61,7 +36,8 @@ const args = [
 ];
 const env = {
   ...process.env,
-  JAVA_OPTS
+  JAVA_OPTS,
+  ATOM_HOME
 };
 const cwd = process.env.ATOM_CWD || process.cwd();
 spawnSync(JAVACMD, args, {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@appthreat/atom",
-  "version": "0.7.5",
+  "version": "0.8.0",
   "description": "Create atom (⚛) representation for your application, packages and libraries",
   "main": "index.js",
   "scripts": {

package/plugins/atom-1.0.0/bin/atom

@@ -360,7 +360,7 @@ declare -r lib_dir="$(realpath "${app_home}/../lib")"
 declare -a app_mainclass=(io.appthreat.atom.Atom)
 
 declare -r script_conf_file="${app_home}/../conf/application.ini"
-declare -r app_classpath="$lib_dir/io.appthreat.atom-1.0.0.jar:$lib_dir/org.scala-lang.scala3-library_3-3.3.0.jar:$lib_dir/com.github.pathikrit.better-files_3-3.9.2.jar:$lib_dir/com.github.scopt.scopt_3-4.1.0.jar:$lib_dir/org.apache.logging.log4j.log4j-core-2.19.0.jar:$lib_dir/org.apache.logging.log4j.log4j-slf4j2-impl-2.19.0.jar:$lib_dir/io.joern.c2cpg_3-1.1.1742.jar:$lib_dir/io.joern.dataflowengineoss_3-1.1.1742.jar:$lib_dir/io.joern.pysrc2cpg_3-1.1.1742.jar:$lib_dir/io.joern.javasrc2cpg_3-1.1.1742.jar:$lib_dir/io.joern.jssrc2cpg_3-1.1.1742.jar:$lib_dir/io.joern.jimple2cpg_3-1.1.1742.jar:$lib_dir/org.scala-lang.scala-library-2.13.10.jar:$lib_dir/org.apache.logging.log4j.log4j-api-2.19.0.jar:$lib_dir/org.slf4j.slf4j-api-2.0.7.jar:$lib_dir/io.joern.semanticcpg_3-1.1.1742.jar:$lib_dir/io.joern.x2cpg_3-1.1.1742.jar:$lib_dir/org.scala-lang.modules.scala-parallel-collections_3-1.0.4.jar:$lib_dir/com.diffplug.spotless.spotless-eclipse-cdt-10.5.0.jar:$lib_dir/org.jline.jline-3.23.0.jar:$lib_dir/org.antlr.antlr4-runtime-4.7.jar:$lib_dir/io.circe.circe-core_3-0.14.5.jar:$lib_dir/io.circe.circe-generic_3-0.14.5.jar:$lib_dir/io.circe.circe-parser_3-0.14.5.jar:$lib_dir/io.shiftleft.codepropertygraph_3-1.3.600.jar:$lib_dir/io.joern.javaparser-symbol-solver-core-3.24.3-SL3.jar:$lib_dir/org.gradle.gradle-tooling-api-7.6.1.jar:$lib_dir/org.projectlombok.lombok-1.18.28.jar:$lib_dir/org.scala-lang.modules.scala-parser-combinators_3-2.2.0.jar:$lib_dir/net.lingala.zip4j.zip4j-2.11.5.jar:$lib_dir/com.lihaoyi.upickle_3-2.0.0.jar:$lib_dir/com.fasterxml.jackson.core.jackson-databind-2.15.1.jar:$lib_dir/com.typesafe.config-1.4.2.jar:$lib_dir/com.michaelpollmeier.versionsort-1.0.11.jar:$lib_dir/org.soot-oss.soot-4.4.1.jar:$lib_dir/org.json4s.json4s-native_3-4.0.6.jar:$lib_dir/com.diffplug.spotless.spotless-eclipse-base-3.5.2.jar:$lib_dir/org.eclipse.platform.org.eclipse.core.filebuffers-3.7.200.jar:$lib_dir/io.circe.circe-numbers_3-0.14.5.jar:$lib_dir/org.typelevel.cats-core_3-2.9.0.jar:$lib_dir/io.circe.circe-jawn_3-0.14.5.jar:$lib_dir/io.shiftleft.codepropertygraph-protos_3-1.3.600.jar:$lib_dir/io.shiftleft.codepropertygraph-domain-classes_3-1.3.600.jar:$lib_dir/io.shiftleft.overflowdb-traversal_3-1.171.jar:$lib_dir/io.shiftleft.overflowdb-formats_3-1.171.jar:$lib_dir/io.joern.javaparser-core-3.24.3-SL3.jar:$lib_dir/org.javassist.javassist-3.29.0-GA.jar:$lib_dir/com.google.guava.guava-31.1-jre.jar:$lib_dir/com.lihaoyi.ujson_3-2.0.0.jar:$lib_dir/com.lihaoyi.upack_3-2.0.0.jar:$lib_dir/com.lihaoyi.upickle-implicits_3-2.0.0.jar:$lib_dir/com.fasterxml.jackson.core.jackson-annotations-2.15.1.jar:$lib_dir/com.fasterxml.jackson.core.jackson-core-2.15.1.jar:$lib_dir/commons-io.commons-io-2.7.jar:$lib_dir/org.smali.dexlib2-2.5.2.jar:$lib_dir/org.ow2.asm.asm-9.4.jar:$lib_dir/org.ow2.asm.asm-tree-9.4.jar:$lib_dir/org.ow2.asm.asm-util-9.4.jar:$lib_dir/org.ow2.asm.asm-commons-9.4.jar:$lib_dir/xmlpull.xmlpull-1.1.3.4d_b4_min.jar:$lib_dir/de.upb.cs.swt.axml-2.1.3.jar:$lib_dir/ca.mcgill.sable.polyglot-2006.jar:$lib_dir/de.upb.cs.swt.heros-1.2.3.jar:$lib_dir/ca.mcgill.sable.jasmin-3.0.3.jar:$lib_dir/javax.annotation.javax.annotation-api-1.3.2.jar:$lib_dir/javax.xml.bind.jaxb-api-2.4.0-b180830.0359.jar:$lib_dir/org.glassfish.jaxb.jaxb-runtime-2.4.0-b180830.0438.jar:$lib_dir/com.google.protobuf.protobuf-java-3.21.7.jar:$lib_dir/com.google.protobuf.protobuf-java-util-3.21.2.jar:$lib_dir/org.json4s.json4s-core_3-4.0.6.jar:$lib_dir/org.json4s.json4s-native-core_3-4.0.6.jar:$lib_dir/org.eclipse.platform.org.eclipse.core.resources-3.18.200.jar:$lib_dir/org.eclipse.platform.org.eclipse.core.runtime-3.26.100.jar:$lib_dir/org.eclipse.platform.org.eclipse.text-3.12.300.jar:$lib_dir/org.eclipse.platform.org.eclipse.core.filesystem-1.9.500.jar:$lib_dir/org.typelevel.cats-kernel_3-2.9.0.jar:$lib_dir/org.typelevel.jawn-parser_3-1.4.0.jar:$lib_dir/io.shiftleft.overflowdb-core-1.171.jar:$lib_dir/net.oneandone.reflections8.reflections8-0.11.7.jar:$lib_dir/com.massisframework.j-text-utils-0.3.4.jar:$lib_dir/com.github.tototoshi.scala-csv_3-1.3.10.jar:$lib_dir/org.scala-lang.modules.scala-xml_3-2.1.0.jar:$lib_dir/io.spray.spray-json_3-1.3.6.jar:$lib_dir/com.google.guava.failureaccess-1.0.1.jar:$lib_dir/com.google.guava.listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar:$lib_dir/com.google.code.findbugs.jsr305-3.0.2.jar:$lib_dir/org.checkerframework.checker-qual-3.12.0.jar:$lib_dir/com.google.errorprone.error_prone_annotations-2.11.0.jar:$lib_dir/com.google.j2objc.j2objc-annotations-1.3.jar:$lib_dir/com.lihaoyi.upickle-core_3-2.0.0.jar:$lib_dir/org.ow2.asm.asm-analysis-9.4.jar:$lib_dir/org.functionaljava.functionaljava-4.2.jar:$lib_dir/ca.mcgill.sable.java_cup-0.9.2.jar:$lib_dir/javax.activation.javax.activation-api-1.2.0.jar:$lib_dir/org.glassfish.jaxb.txw2-2.4.0-b180830.0438.jar:$lib_dir/com.sun.istack.istack-commons-runtime-3.0.7.jar:$lib_dir/org.jvnet.staxex.stax-ex-1.8.jar:$lib_dir/com.sun.xml.fastinfoset.FastInfoset-1.2.15.jar:$lib_dir/com.google.code.gson.gson-2.8.9.jar:$lib_dir/org.json4s.json4s-ast_3-4.0.6.jar:$lib_dir/org.json4s.json4s-scalap_3-4.0.6.jar:$lib_dir/com.thoughtworks.paranamer.paranamer-2.8.jar:$lib_dir/org.eclipse.platform.org.eclipse.osgi-3.18.300.jar:$lib_dir/org.eclipse.platform.org.eclipse.equinox.common-3.17.0.jar:$lib_dir/org.eclipse.platform.org.eclipse.core.jobs-3.13.200.jar:$lib_dir/org.eclipse.platform.org.eclipse.equinox.registry-3.11.200.jar:$lib_dir/org.eclipse.platform.org.eclipse.equinox.preferences-3.10.100.jar:$lib_dir/org.eclipse.platform.org.eclipse.core.contenttype-3.8.200.jar:$lib_dir/org.eclipse.platform.org.eclipse.equinox.app-1.6.200.jar:$lib_dir/org.eclipse.platform.org.eclipse.core.commands-3.10.300.jar:$lib_dir/net.sf.trove4j.core-3.1.0.jar:$lib_dir/org.msgpack.msgpack-core-0.9.1.jar:$lib_dir/com.h2database.h2-mvstore-1.4.200.jar:$lib_dir/commons-lang.commons-lang-2.6.jar:$lib_dir/au.com.bytecode.opencsv-2.4.jar:$lib_dir/com.lihaoyi.geny_3-0.7.1.jar:$lib_dir/org.osgi.org.osgi.service.prefs-1.1.2.jar:$lib_dir/org.osgi.osgi.annotation-8.0.1.jar"
+declare -r app_classpath="$lib_dir/io.appthreat.atom-1.0.0-classpath.jar"
 
 # java_cmd is overrode in process_args when -java-home is used
 declare java_cmd=$(get_java_cmd)

package/plugins/atom-1.0.0/bin/atom.bat

@@ -40,7 +40,7 @@ rem "-J" is stripped, "-D" is left as is, and everything is appended to JAVA_OPT
 set _JAVA_PARAMS=
 set _APP_ARGS=
 
-set "APP_CLASSPATH=%APP_LIB_DIR%\io.appthreat.atom-1.0.0.jar;%APP_LIB_DIR%\org.scala-lang.scala3-library_3-3.3.0.jar;%APP_LIB_DIR%\com.github.pathikrit.better-files_3-3.9.2.jar;%APP_LIB_DIR%\com.github.scopt.scopt_3-4.1.0.jar;%APP_LIB_DIR%\org.apache.logging.log4j.log4j-core-2.19.0.jar;%APP_LIB_DIR%\org.apache.logging.log4j.log4j-slf4j2-impl-2.19.0.jar;%APP_LIB_DIR%\io.joern.c2cpg_3-1.1.1742.jar;%APP_LIB_DIR%\io.joern.dataflowengineoss_3-1.1.1742.jar;%APP_LIB_DIR%\io.joern.pysrc2cpg_3-1.1.1742.jar;%APP_LIB_DIR%\io.joern.javasrc2cpg_3-1.1.1742.jar;%APP_LIB_DIR%\io.joern.jssrc2cpg_3-1.1.1742.jar;%APP_LIB_DIR%\io.joern.jimple2cpg_3-1.1.1742.jar;%APP_LIB_DIR%\org.scala-lang.scala-library-2.13.10.jar;%APP_LIB_DIR%\org.apache.logging.log4j.log4j-api-2.19.0.jar;%APP_LIB_DIR%\org.slf4j.slf4j-api-2.0.7.jar;%APP_LIB_DIR%\io.joern.semanticcpg_3-1.1.1742.jar;%APP_LIB_DIR%\io.joern.x2cpg_3-1.1.1742.jar;%APP_LIB_DIR%\org.scala-lang.modules.scala-parallel-collections_3-1.0.4.jar;%APP_LIB_DIR%\com.diffplug.spotless.spotless-eclipse-cdt-10.5.0.jar;%APP_LIB_DIR%\org.jline.jline-3.23.0.jar;%APP_LIB_DIR%\org.antlr.antlr4-runtime-4.7.jar;%APP_LIB_DIR%\io.circe.circe-core_3-0.14.5.jar;%APP_LIB_DIR%\io.circe.circe-generic_3-0.14.5.jar;%APP_LIB_DIR%\io.circe.circe-parser_3-0.14.5.jar;%APP_LIB_DIR%\io.shiftleft.codepropertygraph_3-1.3.600.jar;%APP_LIB_DIR%\io.joern.javaparser-symbol-solver-core-3.24.3-SL3.jar;%APP_LIB_DIR%\org.gradle.gradle-tooling-api-7.6.1.jar;%APP_LIB_DIR%\org.projectlombok.lombok-1.18.28.jar;%APP_LIB_DIR%\org.scala-lang.modules.scala-parser-combinators_3-2.2.0.jar;%APP_LIB_DIR%\net.lingala.zip4j.zip4j-2.11.5.jar;%APP_LIB_DIR%\com.lihaoyi.upickle_3-2.0.0.jar;%APP_LIB_DIR%\com.fasterxml.jackson.core.jackson-databind-2.15.1.jar;%APP_LIB_DIR%\com.typesafe.config-1.4.2.jar;%APP_LIB_DIR%\com.michaelpollmeier.versionsort-1.0.11.jar;%APP_LIB_DIR%\org.soot-oss.soot-4.4.1.jar;%APP_LIB_DIR%\org.json4s.json4s-native_3-4.0.6.jar;%APP_LIB_DIR%\com.diffplug.spotless.spotless-eclipse-base-3.5.2.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.core.filebuffers-3.7.200.jar;%APP_LIB_DIR%\io.circe.circe-numbers_3-0.14.5.jar;%APP_LIB_DIR%\org.typelevel.cats-core_3-2.9.0.jar;%APP_LIB_DIR%\io.circe.circe-jawn_3-0.14.5.jar;%APP_LIB_DIR%\io.shiftleft.codepropertygraph-protos_3-1.3.600.jar;%APP_LIB_DIR%\io.shiftleft.codepropertygraph-domain-classes_3-1.3.600.jar;%APP_LIB_DIR%\io.shiftleft.overflowdb-traversal_3-1.171.jar;%APP_LIB_DIR%\io.shiftleft.overflowdb-formats_3-1.171.jar;%APP_LIB_DIR%\io.joern.javaparser-core-3.24.3-SL3.jar;%APP_LIB_DIR%\org.javassist.javassist-3.29.0-GA.jar;%APP_LIB_DIR%\com.google.guava.guava-31.1-jre.jar;%APP_LIB_DIR%\com.lihaoyi.ujson_3-2.0.0.jar;%APP_LIB_DIR%\com.lihaoyi.upack_3-2.0.0.jar;%APP_LIB_DIR%\com.lihaoyi.upickle-implicits_3-2.0.0.jar;%APP_LIB_DIR%\com.fasterxml.jackson.core.jackson-annotations-2.15.1.jar;%APP_LIB_DIR%\com.fasterxml.jackson.core.jackson-core-2.15.1.jar;%APP_LIB_DIR%\commons-io.commons-io-2.7.jar;%APP_LIB_DIR%\org.smali.dexlib2-2.5.2.jar;%APP_LIB_DIR%\org.ow2.asm.asm-9.4.jar;%APP_LIB_DIR%\org.ow2.asm.asm-tree-9.4.jar;%APP_LIB_DIR%\org.ow2.asm.asm-util-9.4.jar;%APP_LIB_DIR%\org.ow2.asm.asm-commons-9.4.jar;%APP_LIB_DIR%\xmlpull.xmlpull-1.1.3.4d_b4_min.jar;%APP_LIB_DIR%\de.upb.cs.swt.axml-2.1.3.jar;%APP_LIB_DIR%\ca.mcgill.sable.polyglot-2006.jar;%APP_LIB_DIR%\de.upb.cs.swt.heros-1.2.3.jar;%APP_LIB_DIR%\ca.mcgill.sable.jasmin-3.0.3.jar;%APP_LIB_DIR%\javax.annotation.javax.annotation-api-1.3.2.jar;%APP_LIB_DIR%\javax.xml.bind.jaxb-api-2.4.0-b180830.0359.jar;%APP_LIB_DIR%\org.glassfish.jaxb.jaxb-runtime-2.4.0-b180830.0438.jar;%APP_LIB_DIR%\com.google.protobuf.protobuf-java-3.21.7.jar;%APP_LIB_DIR%\com.google.protobuf.protobuf-java-util-3.21.2.jar;%APP_LIB_DIR%\org.json4s.json4s-core_3-4.0.6.jar;%APP_LIB_DIR%\org.json4s.json4s-native-core_3-4.0.6.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.core.resources-3.18.200.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.core.runtime-3.26.100.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.text-3.12.300.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.core.filesystem-1.9.500.jar;%APP_LIB_DIR%\org.typelevel.cats-kernel_3-2.9.0.jar;%APP_LIB_DIR%\org.typelevel.jawn-parser_3-1.4.0.jar;%APP_LIB_DIR%\io.shiftleft.overflowdb-core-1.171.jar;%APP_LIB_DIR%\net.oneandone.reflections8.reflections8-0.11.7.jar;%APP_LIB_DIR%\com.massisframework.j-text-utils-0.3.4.jar;%APP_LIB_DIR%\com.github.tototoshi.scala-csv_3-1.3.10.jar;%APP_LIB_DIR%\org.scala-lang.modules.scala-xml_3-2.1.0.jar;%APP_LIB_DIR%\io.spray.spray-json_3-1.3.6.jar;%APP_LIB_DIR%\com.google.guava.failureaccess-1.0.1.jar;%APP_LIB_DIR%\com.google.guava.listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar;%APP_LIB_DIR%\com.google.code.findbugs.jsr305-3.0.2.jar;%APP_LIB_DIR%\org.checkerframework.checker-qual-3.12.0.jar;%APP_LIB_DIR%\com.google.errorprone.error_prone_annotations-2.11.0.jar;%APP_LIB_DIR%\com.google.j2objc.j2objc-annotations-1.3.jar;%APP_LIB_DIR%\com.lihaoyi.upickle-core_3-2.0.0.jar;%APP_LIB_DIR%\org.ow2.asm.asm-analysis-9.4.jar;%APP_LIB_DIR%\org.functionaljava.functionaljava-4.2.jar;%APP_LIB_DIR%\ca.mcgill.sable.java_cup-0.9.2.jar;%APP_LIB_DIR%\javax.activation.javax.activation-api-1.2.0.jar;%APP_LIB_DIR%\org.glassfish.jaxb.txw2-2.4.0-b180830.0438.jar;%APP_LIB_DIR%\com.sun.istack.istack-commons-runtime-3.0.7.jar;%APP_LIB_DIR%\org.jvnet.staxex.stax-ex-1.8.jar;%APP_LIB_DIR%\com.sun.xml.fastinfoset.FastInfoset-1.2.15.jar;%APP_LIB_DIR%\com.google.code.gson.gson-2.8.9.jar;%APP_LIB_DIR%\org.json4s.json4s-ast_3-4.0.6.jar;%APP_LIB_DIR%\org.json4s.json4s-scalap_3-4.0.6.jar;%APP_LIB_DIR%\com.thoughtworks.paranamer.paranamer-2.8.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.osgi-3.18.300.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.equinox.common-3.17.0.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.core.jobs-3.13.200.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.equinox.registry-3.11.200.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.equinox.preferences-3.10.100.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.core.contenttype-3.8.200.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.equinox.app-1.6.200.jar;%APP_LIB_DIR%\org.eclipse.platform.org.eclipse.core.commands-3.10.300.jar;%APP_LIB_DIR%\net.sf.trove4j.core-3.1.0.jar;%APP_LIB_DIR%\org.msgpack.msgpack-core-0.9.1.jar;%APP_LIB_DIR%\com.h2database.h2-mvstore-1.4.200.jar;%APP_LIB_DIR%\commons-lang.commons-lang-2.6.jar;%APP_LIB_DIR%\au.com.bytecode.opencsv-2.4.jar;%APP_LIB_DIR%\com.lihaoyi.geny_3-0.7.1.jar;%APP_LIB_DIR%\org.osgi.org.osgi.service.prefs-1.1.2.jar;%APP_LIB_DIR%\org.osgi.osgi.annotation-8.0.1.jar"
+set "APP_CLASSPATH=%APP_LIB_DIR%\io.appthreat.atom-1.0.0-classpath.jar"
 set "APP_MAIN_CLASS=io.appthreat.atom.Atom"
 set "SCRIPT_CONF_FILE=%APP_HOME%\conf\application.ini"