Option to remove the atom file

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

.github/workflows/nodejstests.yml

@@ -49,12 +49,12 @@ jobs:
           sudo npm install -g .
           curl -L https://github.com/joernio/astgen/releases/latest/download/astgen-linux -o /usr/local/bin/astgen
           chmod +x /usr/local/bin/astgen
-          atom -l java -o $GITHUB_WORKSPACE/repotests/shiftleft-java-example/app.atom $GITHUB_WORKSPACE/repotests/shiftleft-java-example
-          atom -l js -o $GITHUB_WORKSPACE/repotests/juice-shop/app.atom $GITHUB_WORKSPACE/repotests/juice-shop
-          atom -l js -o $GITHUB_WORKSPACE/repotests/shiftleft-ts-example/app.atom $GITHUB_WORKSPACE/repotests/shiftleft-ts-example
-          atom -l python -o $GITHUB_WORKSPACE/repotests/DjanGoat/app.atom $GITHUB_WORKSPACE/repotests/DjanGoat
-          atom parsedeps -l python -o $GITHUB_WORKSPACE/repotests/DjanGoat/app.atom $GITHUB_WORKSPACE/repotests/DjanGoat
-          atom -l c -o $GITHUB_WORKSPACE/repotests/libexpat/app.atom $GITHUB_WORKSPACE/repotests/libexpat
+          atom -l java --remove-atom -o $GITHUB_WORKSPACE/repotests/shiftleft-java-example/app.atom $GITHUB_WORKSPACE/repotests/shiftleft-java-example
+          atom -l js --remove-atom -o $GITHUB_WORKSPACE/repotests/juice-shop/app.atom $GITHUB_WORKSPACE/repotests/juice-shop
+          atom -l js --remove-atom -o $GITHUB_WORKSPACE/repotests/shiftleft-ts-example/app.atom $GITHUB_WORKSPACE/repotests/shiftleft-ts-example
+          atom -l python --remove-atom -o $GITHUB_WORKSPACE/repotests/DjanGoat/app.atom $GITHUB_WORKSPACE/repotests/DjanGoat
+          atom parsedeps -l python --remove-atom -o $GITHUB_WORKSPACE/repotests/DjanGoat/app.atom $GITHUB_WORKSPACE/repotests/DjanGoat
+          atom -l c --remove-atom -o $GITHUB_WORKSPACE/repotests/libexpat/app.atom $GITHUB_WORKSPACE/repotests/libexpat
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   nodejs-testing-windows:
@@ -110,15 +110,15 @@ jobs:
       - name: test
         shell: pwsh
         run: |
-          atom -l java -o $env:GITHUB_WORKSPACE\\repotests\\shiftleft-java-example\\app.atom $env:GITHUB_WORKSPACE\\repotests\\shiftleft-java-example
-          atom -l python -o $env:GITHUB_WORKSPACE\\repotests\\DjanGoat\\app.atom $env:GITHUB_WORKSPACE\\repotests\\DjanGoat
-          atom parsedeps -l python -o $env:GITHUB_WORKSPACE\\repotests\\DjanGoat\\app.atom $env:GITHUB_WORKSPACE\\repotests\\DjanGoat
+          atom -l java --remove-atom -o $env:GITHUB_WORKSPACE\\repotests\\shiftleft-java-example\\app.atom $env:GITHUB_WORKSPACE\\repotests\\shiftleft-java-example
+          atom -l python --remove-atom -o $env:GITHUB_WORKSPACE\\repotests\\DjanGoat\\app.atom $env:GITHUB_WORKSPACE\\repotests\\DjanGoat
+          atom parsedeps --remove-atom -l python -o $env:GITHUB_WORKSPACE\\repotests\\DjanGoat\\app.atom $env:GITHUB_WORKSPACE\\repotests\\DjanGoat
           atom -l c -o $env:GITHUB_WORKSPACE\\repotests\\libexpat\\app.atom $env:GITHUB_WORKSPACE\\repotests\\libexpat
       - name: test2
         shell: cmd
         run: |
-          atom -l js -o %GITHUB_WORKSPACE%\\repotests\\juice-shop\\app.atom %GITHUB_WORKSPACE%\\repotests\\juice-shop
+          atom -l js --remove-atom -o %GITHUB_WORKSPACE%\\repotests\\juice-shop\\app.atom %GITHUB_WORKSPACE%\\repotests\\juice-shop
       - name: test3
         shell: cmd
         run: |
-          atom -l js -o %GITHUB_WORKSPACE%\\repotests\\shiftleft-ts-example\\app.atom %GITHUB_WORKSPACE%\\repotests\\shiftleft-ts-example
+          atom -l js --remove-atom -o %GITHUB_WORKSPACE%\\repotests\\shiftleft-ts-example\\app.atom %GITHUB_WORKSPACE%\\repotests\\shiftleft-ts-example

.github/workflows/pr.yml

@@ -41,33 +41,33 @@ jobs:
           java-version: '21'
       - run: |
           sbt stage astGenDlTask
-          ./atom.sh -o /tmp/java.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh -o /tmp/juice.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh -o /tmp/ts.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh -o /tmp/py.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh -o /tmp/py2.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh -o /tmp/c.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/java.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/juice.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/ts.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/py.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/py2.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/c.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml
 
-          ./atom.sh data-flow -o /tmp/java2.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/java.slices.json
-          # ./atom.sh data-flow -o /tmp/juice2.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/juice.slices.json
-          ./atom.sh data-flow -o /tmp/ts2.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/ts.slices.json
-          ./atom.sh data-flow -o /tmp/py2.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py.slices.json
-          ./atom.sh data-flow --sink-filter ".*print.*" -o /tmp/c2.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/c.slices.json
+          ./atom.sh data-flow --remove-atom -o /tmp/java2.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/java.slices.json
+          # ./atom.sh data-flow --remove-atom -o /tmp/juice2.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/juice.slices.json
+          ./atom.sh data-flow --remove-atom -o /tmp/ts2.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/ts.slices.json
+          ./atom.sh data-flow --remove-atom -o /tmp/py2.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py.slices.json
+          ./atom.sh data-flow --sink-filter ".*print.*" --remove-atom -o /tmp/c2.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/c.slices.json
           ls -lh /tmp/*.atom /tmp/*.json
 
-          ./atom.sh usages -o /tmp/java3.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/java.usages.json
-          ./atom.sh usages -o /tmp/juice3.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/juice.usages.json
-          ./atom.sh usages -o /tmp/ts3.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/ts.usages.json
-          ./atom.sh usages -o /tmp/py3.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py.usages.json
-          ./atom.sh usages -o /tmp/py4.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py4.usages.json
-          ./atom.sh usages -o /tmp/c3.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/c.usages.json
+          ./atom.sh usages --remove-atom -o /tmp/java3.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/java.usages.json
+          ./atom.sh usages --remove-atom -o /tmp/juice3.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/juice.usages.json
+          ./atom.sh usages --remove-atom -o /tmp/ts3.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/ts.usages.json
+          ./atom.sh usages --remove-atom -o /tmp/py3.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py.usages.json
+          ./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
           ls -lh /tmp/*.atom /tmp/*.json
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - run: |
           npm install -g @cyclonedx/cdxgen --omit=optional
           cdxgen -t python --deep -o $GITHUB_WORKSPACE/repotests/django-DefectDojo/bom.json $GITHUB_WORKSPACE/repotests/django-DefectDojo
-          ./atom.sh reachables -o /tmp/django-DefectDojo.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/django-DefectDojo.reachables.json
+          ./atom.sh reachables --remove-atom -o /tmp/django-DefectDojo.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/django-DefectDojo.reachables.json
         env:
           JAVA_TOOL_OPTIONS: "-Dfile.encoding=UTF-8"
         if: runner.os != 'Windows'

.github/workflows/repotests.yml

@@ -105,41 +105,41 @@ jobs:
           node-version: '20.x'
       - run: |
           sbt stage astGenDlTask
-          ./atom.sh -o /tmp/java.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh -o /tmp/juice.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh -o /tmp/ts.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh -o /tmp/py.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh parsedeps -o /tmp/py.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh -o /tmp/py2.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml
-          ./atom.sh -o /tmp/c.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/java.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/juice.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/ts.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/py.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh parsedeps --remove-atom -o /tmp/py.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/py2.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml
+          ./atom.sh --remove-atom -o /tmp/c.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml
 
-          ./atom.sh data-flow -o /tmp/java2.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/java.slices.json
-          # ./atom.sh data-flow -o /tmp/juice2.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/juice.slices.json
-          ./atom.sh data-flow -o /tmp/ts2.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/ts.slices.json
-          ./atom.sh data-flow -o /tmp/py2.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py.slices.json
-          ./atom.sh data-flow --sink-filter ".*print.*" -o /tmp/c2.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/c.slices.json
+          ./atom.sh data-flow --remove-atom -o /tmp/java2.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/java.slices.json
+          # ./atom.sh data-flow --remove-atom -o /tmp/juice2.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/juice.slices.json
+          ./atom.sh data-flow --remove-atom -o /tmp/ts2.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/ts.slices.json
+          ./atom.sh data-flow --remove-atom -o /tmp/py2.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py.slices.json
+          ./atom.sh data-flow --sink-filter ".*print.*" --remove-atom -o /tmp/c2.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/c.slices.json
 
-          ./atom.sh usages -o /tmp/java3.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/java.usages.json
-          # ./atom.sh usages -o /tmp/juice3.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/juice.usages.json
-          ./atom.sh usages -o /tmp/ts3.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/ts.usages.json
-          ./atom.sh usages -o /tmp/py3.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py.usages.json
-          ./atom.sh usages -o /tmp/py4.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py4.usages.json
-          ./atom.sh usages -o /tmp/c3.atom -l c $GITHUB_WORKSPACE/repotests/libexpat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/c.usages.json
+          ./atom.sh usages --remove-atom -o /tmp/java3.atom -l java $GITHUB_WORKSPACE/repotests/shiftleft-java-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/java.usages.json
+          # ./atom.sh usages --remove-atom -o /tmp/juice3.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/juice.usages.json
+          ./atom.sh usages --remove-atom -o /tmp/ts3.atom -l js $GITHUB_WORKSPACE/repotests/shiftleft-ts-example -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/ts.usages.json
+          ./atom.sh usages --remove-atom -o /tmp/py3.atom -l python $GITHUB_WORKSPACE/repotests/DjanGoat -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/py.usages.json
+          ./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
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           JAVA_TOOL_OPTIONS: "-Dfile.encoding=UTF-8"
       - run: |
           npm install -g @cyclonedx/cdxgen --omit=optional
           cdxgen -t java --deep -o $GITHUB_WORKSPACE/repotests/java-sec-code/bom.json $GITHUB_WORKSPACE/repotests/java-sec-code
-          ./atom.sh reachables -o /tmp/java-sec-code.atom -l java $GITHUB_WORKSPACE/repotests/java-sec-code -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/java-sec-code.reachables.json
+          ./atom.sh reachables --remove-atom -o /tmp/java-sec-code.atom -l java $GITHUB_WORKSPACE/repotests/java-sec-code -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/java-sec-code.reachables.json
           cdxgen -t python --deep -o $GITHUB_WORKSPACE/repotests/django-DefectDojo/bom.json $GITHUB_WORKSPACE/repotests/django-DefectDojo
-          ./atom.sh reachables -o /tmp/django-DefectDojo.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/django-DefectDojo.reachables.json
+          ./atom.sh reachables --remove-atom -o /tmp/django-DefectDojo.atom -l python $GITHUB_WORKSPACE/repotests/django-DefectDojo -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/django-DefectDojo.reachables.json
         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 -o /tmp/juice-shop.atom -l js $GITHUB_WORKSPACE/repotests/juice-shop -Dlog4j.configurationFile=log4j2.xml --slice-outfile /tmp/juice-shop.reachables.json
+          ./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'

build.sbt

@@ -1,6 +1,6 @@
 name                     := "atom"
 ThisBuild / organization := "io.appthreat"
-ThisBuild / version      := "1.6.4"
+ThisBuild / version      := "1.6.5"
 ThisBuild / scalaVersion := "3.3.1"
 
 val chenVersion      = "1.0.0"