Export individual representations

Signed-off-by: Prabhu Subramanian <prabhu@appthreat.com>

.github/workflows/repotests.yml

@@ -135,7 +135,7 @@ jobs:
           ./atom.sh usages --remove-atom -o /tmp/py4.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py4.usages.json
           ./atom.sh usages --remove-atom -o /tmp/c3.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/c.usages.json
 
-          ./atom.sh --remove-atom -o /tmp/java-sec-code.atom -l java $GITHUB_WORKSPACE/repotests/java-sec-code -Dlog4j.configurationFile=log4j2.xml --export-atom --export-dir gml_exports
+          ./atom.sh --remove-atom -o /tmp/java-sec-code.atom -l java $GITHUB_WORKSPACE/repotests/java-sec-code -Dlog4j.configurationFile=log4j2.xml -x --export-dir gml_exports
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           JAVA_TOOL_OPTIONS: "-Dfile.encoding=UTF-8"
@@ -150,9 +150,3 @@ jobs:
         if: runner.os != 'Windows'
         env:
           JAVA_TOOL_OPTIONS: "-Dfile.encoding=UTF-8"
-      - run: |
-          cdxgen -t js -o $GITHUB_WORKSPACE/repotests/juice-shop/bom.json $GITHUB_WORKSPACE/repotests/juice-shop
-          ./atom.sh reachables --remove-atom -o /tmp/juice-shop.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/juice-shop.reachables.json
-        env:
-          JAVA_TOOL_OPTIONS: "-Dfile.encoding=UTF-8"
-        if: runner.os != 'Windows'

README.md

@@ -59,7 +59,7 @@ Usage: atom [parsedeps|data-flow|usages|reachables] [options] [input]
   -l, --language <value>   source language
   --with-data-deps         generate the atom with data-dependencies - defaults to `false`
   --remove-atom            do not persist the atom file - defaults to `false`
-  --export-atom            export the atom file with data-dependencies to graphml - defaults to `false`
+  -x, --export-atom        export the atom file with data-dependencies to graphml - defaults to `false`
   --export-dir <value>     export directory. Default: atom-exports
   --file-filter <value>    the name of the source file to generate slices from. Uses regex.
   --method-name-filter <value>
@@ -140,6 +140,8 @@ The resulting graphml files could be imported into [Neo4j](https://neo4j.com/lab
 atom -o app.atom -l java --export-atom --export-format dot --export-dir <export dir> <path to application>
 ```
 
+In dot format, individual representations such as ast, cdg, and cfg would also get exported.
+
 To also compute and include data-dependency graph (DDG) information in the exported files, pass `--with-data-deps`
 
 ```shell

build.sbt

@@ -1,9 +1,9 @@
 name                     := "atom"
 ThisBuild / organization := "io.appthreat"
-ThisBuild / version      := "1.7.5"
+ThisBuild / version      := "1.8.0"
 ThisBuild / scalaVersion := "3.3.1"
 
-val chenVersion      = "1.0.10"
+val chenVersion      = "1.1.1"
 
 lazy val atom = Projects.atom
 

codemeta.json

@@ -0,0 +1,45 @@
+{
+  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+  "@type": "SoftwareSourceCode",
+  "license": "https://spdx.org/licenses/Apache-2.0",
+  "codeRepository": "git+https://github.com/AppThreat/atom.git",
+  "contIntegration": "https://github.com/AppThreat/atom/actions",
+  "downloadUrl": "https://github.com/AppThreat/atom",
+  "issueTracker": "https://github.com/AppThreat/atom/issues",
+  "name": "atom",
+  "version": "1.8.0",
+  "description": ".",
+  "applicationCategory": "code-analysis",
+  "keywords": [
+    "static-analysis",
+    "code-analysis",
+    "dependency-analysis",
+    "code-hierarchy-analysis",
+    "static-slicer",
+    "reachability-analysis"
+  ],
+  "programmingLanguage": [
+    "Scala 3",
+    "Node.js"
+  ],
+  "runtimePlatform": [
+    "JVM"
+  ],
+  "operatingSystem": [
+    "Linux",
+    "Windows",
+    "MacOS"
+  ],
+  "softwareRequirements": [
+    "Java >= 21",
+    "Node.js >= 16"
+  ],
+  "author": [
+    {
+      "@type": "Person",
+      "givenName": "Team",
+      "familyName": "AppThreat",
+      "email": "cloud@appthreat.com"
+    }
+  ]
+}

src/main/scala/io/appthreat/atom/Atom.scala

@@ -44,12 +44,13 @@ object Atom:
     val DEFAULT_ATOM_OUT_FILE: String =
         if Properties.isWin || Charset.defaultCharset() != Charset.forName("UTF-8") then "app.atom"
         else "app.⚛"
-    val DEFAULT_SLICE_OUT_FILE        = "slices.json"
-    val DEFAULT_SLICE_DEPTH           = 7
-    val DEFAULT_MAX_DEFS: Int         = 2000
-    val FRAMEWORK_INPUT_TAG: String   = "framework-input"
-    val FRAMEWORK_OUTPUT_TAG: String  = "framework-output"
-    val DEFAULT_EXPORT_DIR: String    = "atom-exports"
+    val DEFAULT_SLICE_OUT_FILE       = "slices.json"
+    val DEFAULT_SLICE_DEPTH          = 7
+    val DEFAULT_MAX_DEFS: Int        = 2000
+    val FRAMEWORK_INPUT_TAG: String  = "framework-input"
+    val FRAMEWORK_OUTPUT_TAG: String = "framework-output"
+    val DEFAULT_EXPORT_DIR: String   = "atom-exports"
+    // Possible values: graphml, dot
     val DEFAULT_EXPORT_FORMAT: String = "graphml"
     // Possible values: no-delombok, default, types-only, run-delombok
     private val DEFAULT_DELOMBOK_MODE: String =
@@ -126,7 +127,7 @@ object Atom:
                     case config: AtomConfig => config.withRemoveAtom(true)
                     case _                  => c
             )
-        opt[Unit]("export-atom")
+        opt[Unit]('x', "export-atom")
             .text("export the atom file with data-dependencies to graphml - defaults to `false`")
             .action((_, c) =>
                 c match
@@ -323,9 +324,14 @@ object Atom:
                               _.name.startsWith("lambda")
                             ).gml(x.exportDir)
                         case _ =>
+                            // Export all representations
                             ag.method.internal.filterNot(_.name.startsWith("<")).filterNot(
                               _.name.startsWith("lambda")
                             ).dot(x.exportDir)
+                            // Export individual representations
+                            ag.method.internal.filterNot(_.name.startsWith("<")).filterNot(
+                              _.name.startsWith("lambda")
+                            ).exportAllRepr(x.exportDir)
                 case _: DataFlowConfig =>
                     val dataFlowSlice = sliceCpg(ag).collect { case x: DataFlowSlice => x }
                     val atomDataFlowSliceJson =

wrapper/nodejs/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@appthreat/atom",
-  "version": "1.7.5",
+  "version": "1.8.0",
   "description": "Create atom (⚛) representation for your application, packages and libraries",
   "exports": "./index.js",
   "type": "module",