java 21 updates and license inventory

.github/workflows/codeql.yml

@@ -15,25 +15,44 @@ jobs:
       contents: read
       security-events: write
 
-    strategy:
-      fail-fast: false
-      matrix:
-        language: [ javascript ]
-
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v4
         with:
-          languages: ${{ matrix.language }}
+          languages: javascript
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v4
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v4
+        with:
+          category: javascript
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v4
+        with:
+          languages: java
+          queries: +security-and-quality
+
+      - uses: actions/cache@v5
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('./wdl-parsing/WDLParsingFunction/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-   
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v4
+        with:
+          working-directory: ./wdl-parsing/WDLParsingFunction
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v4
         with:
-          category: "/language:${{ matrix.language }}"
+          category: java
+          working-directory: ./wdl-parsing/WDLParsingFunction  

.github/workflows/maven.yml

@@ -18,7 +18,7 @@ jobs:
   testWithSAMCLI:
      runs-on: ubuntu-latest
      steps:
-     - uses: actions/checkout@v2
+     - uses: actions/checkout@v6
      - name: Set up Python
        uses: actions/setup-python@v2
        with:
@@ -27,6 +27,23 @@ jobs:
        run: |
          python -m pip install --upgrade pip
          pip install aws-sam-cli
+     - name: Set up JDK
+       uses: actions/setup-java@v5
+       with:
+         java-version: '21.0.10+7.0.LTS'
+         distribution: 'temurin'
+
+     - uses: actions/cache@v5
+       with:
+         path: ~/.m2/repository
+         key: ${{ runner.os }}-maven-${{ hashFiles('./wdl-parsing/WDLParsingFunction/pom.xml') }}
+         restore-keys: |
+           ${{ runner.os }}-maven-
+
+     - name: Test Java build 
+       working-directory: ./wdl-parsing/WDLParsingFunction
+       run: mvn -B -ntp clean install
+
      - name: Test wdl parsing with SAM CLI build and invoke
        working-directory: ./wdl-parsing
        run: | 

wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.dev.txt

@@ -0,0 +1,8 @@
+
+Lists of 6 third-party dependencies.
+     (Eclipse Public License v2.0) JUnit Jupiter API (org.junit.jupiter:junit-jupiter-api:5.7.2 - https://junit.org/junit5/)
+     (Eclipse Public License v2.0) JUnit Jupiter Engine (org.junit.jupiter:junit-jupiter-engine:5.7.2 - https://junit.org/junit5/)
+     (Eclipse Public License v2.0) JUnit Platform Commons (org.junit.platform:junit-platform-commons:1.7.2 - https://junit.org/junit5/)
+     (Eclipse Public License v2.0) JUnit Platform Engine API (org.junit.platform:junit-platform-engine:1.7.2 - https://junit.org/junit5/)
+     (The Apache License, Version 2.0) org.apiguardian:apiguardian-api (org.apiguardian:apiguardian-api:1.1.0 - https://github.com/apiguardian-team/apiguardian)
+     (The Apache License, Version 2.0) org.opentest4j:opentest4j (org.opentest4j:opentest4j:1.2.0 - https://github.com/ota4j-team/opentest4j)

wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.properties

@@ -0,0 +1,74 @@
+# Generated by org.codehaus.mojo.license.AddThirdPartyMojo
+#-------------------------------------------------------------------------------
+# Already used licenses in project :
+# - Apache 2
+# - Apache 2.0
+# - Apache 2.0 License
+# - Apache License 2.0
+# - Apache License, Version 2.0
+# - Apache License, version 2.0
+# - Apache Software License - Version 2.0
+# - Apache Software Licenses
+# - Apache-2.0
+# - BSD 3-clause
+# - BSD New
+# - BSD New license
+# - BSD-2-Clause
+# - CC0
+# - CDDL + GPLv2 with classpath exception
+# - CDDL 1.1
+# - CDDL+GPL License
+# - CDDL/GPLv2+CE
+# - Common Public License Version 1.0
+# - EDL 1.0
+# - Eclipse Distribution License - v 1.0
+# - Eclipse Public License - Version 1.0
+# - Eclipse Public License - v 1.0
+# - Eclipse Public License 1.0
+# - GNU Lesser General Public License
+# - GPL2 w/ CPE
+# - LGPL 2.1
+# - MIT
+# - MIT License
+# - MIT license
+# - MPL 1.1
+# - New BSD License
+# - The Apache License, Version 2.0
+# - The Apache Software License, Version 2.0
+# - The MIT License
+# - Three-clause BSD-style
+#-------------------------------------------------------------------------------
+# If there is a missing license file the command 'mvn clean install' will fail
+# (if the pom.xml license-maven-plugin tag failOnMissing is true) and a warning
+# message will list the artifact with the missing license. The artifact and the
+# appropriate license string can be added to this file (THIRD-PARTY-LICENSE.properties)
+# which should then allow 'mvn clean install' to proceed
+# When supplying the artifact name, replace colons with two hyphens
+#
+# Please fill the missing licenses for dependencies :
+#
+#Fri Apr 03 14:05:39 PDT 2020
+org.broadinstitute--wdl-draft2_2.13--85=WDL License https://github.com/openwdl/wdl/blob/master/LICENSE
+org.broadinstitute--cromwell-wdl-model-draft2_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+org.broadinstitute--cromwell-wdl-transforms-new-base_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+org.broadinstitute--wdl-biscayne_2.13--85=WDL License https://github.com/openwdl/wdl/blob/master/LICENSE
+org.broadinstitute--cromwell-wdl-model-draft3_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+org.broadinstitute--cromwell-wdl-transforms-draft2_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+org.broadinstitute--cromwell-wdl-transforms-shared_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+org.broadinstitute--cromwell-wdl-model-core_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+org.broadinstitute--cromwell-wdl-model-biscayne_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+com.readytalk--metrics3-statsd--4.2.0=The Apache Software License, Version 2.0
+org.broadinstitute--cromwell-common_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+org.broadinstitute--cromwell-wdl-transforms-draft3_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+org.broadinstitute--cromwell-wdl-transforms-biscayne_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+org.broadinstitute--language-factory-core_2.13--85=WDL License https://github.com/openwdl/wdl/blob/master/LICENSE
+org.broadinstitute--wdl-draft3_2.13--85=WDL License https://github.com/openwdl/wdl/blob/master/LICENSE
+org.broadinstitute--cromwell-core_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+org.broadinstitute--cromwell-wom_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+com.readytalk--metrics-statsd-common--4.2.0=WDL License https://github.com/openwdl/wdl/blob/master/LICENSE
+org.antlr--antlr-runtime--3.4=The BSD License (https://www.antlr.org/license.html)
+dom4j--dom4j--1.6.1=https://github.com/dom4j/dom4j/blob/master/LICENSE
+io.netty--netty-tcnative-classes--2.0.46.Final=https://github.com/netty/netty-tcnative/blob/main/LICENSE.txt
+org.w3id.cwl.sdk--cwljava--1.0.0=Apache License, Version 2.0
+org.broadinstitute--womtool_2.13--85=Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt
+