From df8a18c8a1bf195178821d3d74f0925091b37500 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 8 Jun 2026 17:27:59 -0400 Subject: [PATCH 01/11] upgrades --- wdl-parsing/WDLParsingFunction/pom.xml | 28 ++++++++++++++++---------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/wdl-parsing/WDLParsingFunction/pom.xml b/wdl-parsing/WDLParsingFunction/pom.xml index dad9696..3df826b 100644 --- a/wdl-parsing/WDLParsingFunction/pom.xml +++ b/wdl-parsing/WDLParsingFunction/pom.xml @@ -26,10 +26,11 @@ https://repo.maven.apache.org/maven2 default + artifactory.broadinstitute.org artifactory.broadinstitute.org - https://broadinstitute.jfrog.io/artifactory/libs-release/ + https://us-central1-maven.pkg.dev/dsp-artifact-registry/libs-release/ true @@ -44,7 +45,7 @@ artifacts.oicr.on.ca artifacts.oicr.on.ca - https://artifacts.oicr.on.ca/artifactory/collab-release + https://artifacts.oicr.on.ca/artifactory/collab-release @@ -62,12 +63,14 @@ org.scala-lang scala-library - 2.12.12 + 2.13.9 + org.broadinstitute - womtool_2.12 - 65 + womtool_2.13 + 85 + compile org.junit.jupiter @@ -258,9 +261,9 @@ - com.coveo + com.spotify.fmt fmt-maven-plugin - 2.10 + 2.29 @@ -272,7 +275,10 @@ net.alchim31.maven scala-maven-plugin - 4.5.3 + 4.8.1 + + 2.13.12 + scala-compile @@ -309,10 +315,10 @@ org.apache.maven.plugins maven-compiler-plugin - 3.8.1 + 3.15.0 - 11 - 11 + 21 + 21 From 0abf05ba1d75de2450c4a200db5f16cb8c735f5b Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 8 Jun 2026 17:31:15 -0400 Subject: [PATCH 02/11] add build --- .github/workflows/maven.yml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index 460aa33..0ac08b3 100644 --- a/.github/workflows/maven.yml +++ b/.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 +27,15 @@ 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' + - name: Test Java build + working-directory: ./wdl-parsing + run: mvn clean install + - name: Test wdl parsing with SAM CLI build and invoke working-directory: ./wdl-parsing run: | From 9d411a9d989fa692beb8a53dec788012011753ee Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 8 Jun 2026 17:33:35 -0400 Subject: [PATCH 03/11] working directory --- .github/workflows/maven.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index 0ac08b3..91b30da 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -33,7 +33,7 @@ jobs: java-version: '21.0.10+7.0.LTS' distribution: 'temurin' - name: Test Java build - working-directory: ./wdl-parsing + working-directory: ./wdl-parsing/WDLParsingFunction run: mvn clean install - name: Test wdl parsing with SAM CLI build and invoke From a1104a3a19c5e6bcfe81d32ebf2753039510fdb3 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 8 Jun 2026 17:37:07 -0400 Subject: [PATCH 04/11] codeql upgrades --- .github/workflows/codeql.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index d5b6f52..80231da 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -18,22 +18,22 @@ jobs: strategy: fail-fast: false matrix: - language: [ javascript ] + language: [ javascript, java ] 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@v3 with: languages: ${{ matrix.language }} queries: +security-and-quality - name: Autobuild - uses: github/codeql-action/autobuild@v2 + uses: github/codeql-action/autobuild@v3 - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v2 + uses: github/codeql-action/analyze@v3 with: category: "/language:${{ matrix.language }}" From 70ff29561a480b3789b74c928a534fac3c40be3c Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 8 Jun 2026 17:40:33 -0400 Subject: [PATCH 05/11] add directory for codeql --- .github/workflows/codeql.yml | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 80231da..ef4f909 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -15,11 +15,6 @@ jobs: contents: read security-events: write - strategy: - fail-fast: false - matrix: - language: [ javascript, java ] - steps: - name: Checkout uses: actions/checkout@v6 @@ -27,13 +22,29 @@ jobs: - name: Initialize CodeQL uses: github/codeql-action/init@v3 with: - languages: ${{ matrix.language }} + languages: javascript + queries: +security-and-quality + + - name: Autobuild + uses: github/codeql-action/autobuild@v3 + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v3 + with: + category: javascript + + - name: Initialize CodeQL + uses: github/codeql-action/init@v3 + with: + languages: java queries: +security-and-quality - name: Autobuild uses: github/codeql-action/autobuild@v3 + working-directory: ./wdl-parsing/WDLParsingFunction - name: Perform CodeQL Analysis uses: github/codeql-action/analyze@v3 + working-directory: ./wdl-parsing/WDLParsingFunction with: - category: "/language:${{ matrix.language }}" + category: java From bfee59a76e9bfdea20f53bf3284209b61d742a26 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 8 Jun 2026 17:44:32 -0400 Subject: [PATCH 06/11] working directory? --- .github/workflows/codeql.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index ef4f909..9a60bcc 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -20,31 +20,31 @@ jobs: uses: actions/checkout@v6 - name: Initialize CodeQL - uses: github/codeql-action/init@v3 + uses: github/codeql-action/init@v4 with: languages: javascript queries: +security-and-quality - name: Autobuild - uses: github/codeql-action/autobuild@v3 + uses: github/codeql-action/autobuild@v4 - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v3 + uses: github/codeql-action/analyze@v4 with: category: javascript - name: Initialize CodeQL - uses: github/codeql-action/init@v3 + uses: github/codeql-action/init@v4 with: languages: java queries: +security-and-quality - name: Autobuild - uses: github/codeql-action/autobuild@v3 + uses: github/codeql-action/autobuild@v4 working-directory: ./wdl-parsing/WDLParsingFunction - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v3 + uses: github/codeql-action/analyze@v4 working-directory: ./wdl-parsing/WDLParsingFunction with: category: java From 40dc3d2b4a2526ce580f866a74453730073f4a58 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Mon, 8 Jun 2026 17:45:59 -0400 Subject: [PATCH 07/11] try with --- .github/workflows/codeql.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 9a60bcc..a8615b6 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -41,10 +41,11 @@ jobs: - name: Autobuild uses: github/codeql-action/autobuild@v4 - working-directory: ./wdl-parsing/WDLParsingFunction + with: + working-directory: ./wdl-parsing/WDLParsingFunction - name: Perform CodeQL Analysis uses: github/codeql-action/analyze@v4 - working-directory: ./wdl-parsing/WDLParsingFunction with: category: java + working-directory: ./wdl-parsing/WDLParsingFunction From 5d2494dcfd21ad30d5eb28b7f681cdd3c64897bf Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 9 Jun 2026 10:55:54 -0400 Subject: [PATCH 08/11] add cache, fix test for compliant new wdl --- .github/workflows/codeql.yml | 7 +++++++ .github/workflows/maven.yml | 10 +++++++++- .../src/test/java/io/dockstore/wdlparser/AppTest.java | 10 +++++----- 3 files changed, 21 insertions(+), 6 deletions(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index a8615b6..a582654 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -39,6 +39,13 @@ jobs: 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: diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index 91b30da..bfe81f8 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -31,7 +31,15 @@ jobs: uses: actions/setup-java@v5 with: java-version: '21.0.10+7.0.LTS' - distribution: 'temurin' + 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 clean install diff --git a/wdl-parsing/WDLParsingFunction/src/test/java/io/dockstore/wdlparser/AppTest.java b/wdl-parsing/WDLParsingFunction/src/test/java/io/dockstore/wdlparser/AppTest.java index b60d7a2..8987a1d 100644 --- a/wdl-parsing/WDLParsingFunction/src/test/java/io/dockstore/wdlparser/AppTest.java +++ b/wdl-parsing/WDLParsingFunction/src/test/java/io/dockstore/wdlparser/AppTest.java @@ -65,9 +65,9 @@ public void successfulResponse() throws IOException { @Test public void successfulResponseOfComplexWorkflow() throws IOException { LanguageParsingRequest request = new LanguageParsingRequest(); - request.setBranch("dockstore-test"); - request.setUri("https://github.com/dockstore-testing/gatk-sv-clinical.git"); - request.setDescriptorRelativePathInGit("GATKSVPipelineClinical.wdl"); + request.setBranch("v1.1"); + request.setUri("https://github.com/dockstore-testing/gatk-sv.git"); + request.setDescriptorRelativePathInGit("wdl/GATKSVPipelineSingleSample.wdl"); App app = new App(); APIGatewayProxyRequestEvent requestEvent = new APIGatewayProxyRequestEvent(); ObjectMapper objectMapper = new ObjectMapper(); @@ -87,9 +87,9 @@ public void successfulResponseOfComplexWorkflow() throws IOException { assertTrue(response.getClonedRepositoryAbsolutePath().contains("/tmp")); assertNotNull(response.getSecondaryFilePaths()); assertFalse( - response.getSecondaryFilePaths().contains("GATKSVPipelineClinical.wdl"), + response.getSecondaryFilePaths().contains("wdl/GATKSVPipelineSingleSample.wdl"), "Main descriptor isn't a secondary file path"); - final long expectedNumberOfFiles = 76; + final long expectedNumberOfFiles = 95; assertEquals(expectedNumberOfFiles, response.getSecondaryFilePaths().size()); System.out.println(response.getClonedRepositoryAbsolutePath()); } From 51c53973169d11d55053ddcdebca64fc9ca069ef Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 9 Jun 2026 11:14:47 -0400 Subject: [PATCH 09/11] upgrade spotbugs and exclude generated --- .github/workflows/maven.yml | 2 +- wdl-parsing/WDLParsingFunction/ignore.xml | 25 ++++++++++------------- wdl-parsing/WDLParsingFunction/pom.xml | 2 +- 3 files changed, 13 insertions(+), 16 deletions(-) diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index bfe81f8..e4de33e 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -42,7 +42,7 @@ jobs: - name: Test Java build working-directory: ./wdl-parsing/WDLParsingFunction - run: mvn clean install + run: mvn -B -ntp clean install - name: Test wdl parsing with SAM CLI build and invoke working-directory: ./wdl-parsing diff --git a/wdl-parsing/WDLParsingFunction/ignore.xml b/wdl-parsing/WDLParsingFunction/ignore.xml index d9492e9..6f84cfa 100644 --- a/wdl-parsing/WDLParsingFunction/ignore.xml +++ b/wdl-parsing/WDLParsingFunction/ignore.xml @@ -1,16 +1,13 @@ - - - - - - - - - - - - - - + + + + + + + + diff --git a/wdl-parsing/WDLParsingFunction/pom.xml b/wdl-parsing/WDLParsingFunction/pom.xml index 3df826b..fe55d9a 100644 --- a/wdl-parsing/WDLParsingFunction/pom.xml +++ b/wdl-parsing/WDLParsingFunction/pom.xml @@ -221,7 +221,7 @@ com.github.spotbugs spotbugs-maven-plugin - 4.0.4 + 4.9.8.3 ${project.basedir}/ignore.xml From 15170bb080803a9654432d8eb2193a0fb949a3ec Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 9 Jun 2026 11:25:32 -0400 Subject: [PATCH 10/11] update test and runtime --- wdl-parsing/template.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-parsing/template.yaml b/wdl-parsing/template.yaml index 8ba7a95..c4bcabd 100644 --- a/wdl-parsing/template.yaml +++ b/wdl-parsing/template.yaml @@ -16,7 +16,7 @@ Resources: Properties: CodeUri: WDLParsingFunction Handler: io.dockstore.wdlparser.App::handleRequest - Runtime: java11 + Runtime: java21 MemorySize: 512 Environment: # More info about Env Vars: https://github.com/awslabs/serverless-application-model/blob/master/versions/2016-10-31.md#environment-object Variables: From d54e060c2b89537a541effcd7b49c33a6324efe4 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Tue, 9 Jun 2026 13:38:27 -0400 Subject: [PATCH 11/11] add licensing information --- .../THIRD-PARTY-LICENSES.dev.txt | 8 + .../THIRD-PARTY-LICENSES.properties | 74 +++++++ .../THIRD-PARTY-LICENSES.txt | 193 ++++++++++++++++++ wdl-parsing/WDLParsingFunction/pom.xml | 44 +++- 4 files changed, 314 insertions(+), 5 deletions(-) create mode 100644 wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.dev.txt create mode 100644 wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.properties create mode 100644 wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.txt diff --git a/wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.dev.txt b/wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.dev.txt new file mode 100644 index 0000000..c963dd1 --- /dev/null +++ b/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) diff --git a/wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.properties b/wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.properties new file mode 100644 index 0000000..3b078d8 --- /dev/null +++ b/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 + diff --git a/wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.txt b/wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.txt new file mode 100644 index 0000000..3772c59 --- /dev/null +++ b/wdl-parsing/WDLParsingFunction/THIRD-PARTY-LICENSES.txt @@ -0,0 +1,193 @@ + +Lists of 191 third-party dependencies. + (Apache License, Version 2.0) akka-actor (com.typesafe.akka:akka-actor_2.13:2.5.32 - https://akka.io/) + (Apache License, Version 2.0) akka-protobuf (com.typesafe.akka:akka-protobuf_2.13:2.5.32 - https://akka.io/) + (Apache License, Version 2.0) akka-slf4j (com.typesafe.akka:akka-slf4j_2.13:2.5.32 - https://akka.io/) + (Apache License, Version 2.0) akka-stream (com.typesafe.akka:akka-stream_2.13:2.5.32 - https://akka.io/) + (MIT) Alleycats core (org.typelevel:alleycats-core_2.13:2.7.0 - https://github.com/typelevel/cats) + (MIT license) Animal Sniffer Annotations (org.codehaus.mojo:animal-sniffer-annotations:1.21 - https://www.mojohaus.org/animal-sniffer/animal-sniffer-annotations) + (Apache License, Version 2.0) Apache Commons Codec (commons-codec:commons-codec:1.15 - https://commons.apache.org/proper/commons-codec/) + (Apache License, Version 2.0) Apache Commons IO (commons-io:commons-io:2.11.0 - https://commons.apache.org/proper/commons-io/) + (Apache License, Version 2.0) Apache Commons Lang (org.apache.commons:commons-lang3:3.12.0 - https://commons.apache.org/proper/commons-lang/) + (Apache License, Version 2.0) Apache Commons Text (org.apache.commons:commons-text:1.10.0 - https://commons.apache.org/proper/commons-text) + (The Apache Software License, Version 2.0) Apache HTTP transport v2 for the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-apache-v2:1.41.2 - https://github.com/googleapis/google-http-java-client/google-http-client-apache-v2) + (Apache License, Version 2.0) Apache HttpClient (org.apache.httpcomponents:httpclient:4.5.13 - http://hc.apache.org/httpcomponents-client) + (Apache License, Version 2.0) Apache HttpCore (org.apache.httpcomponents:httpcore:4.4.15 - http://hc.apache.org/httpcomponents-core-ga) + (BSD) API Common (com.google.api:api-common:2.1.4 - https://github.com/googleapis/api-common-java) + (Apache 2.0) async-http-client-backend (com.softwaremill.sttp:async-http-client-backend_2.13:1.7.2 - http://softwaremill.com/open-source) + (Apache 2.0) async-http-client-backend-cats (com.softwaremill.sttp:async-http-client-backend-cats_2.13:1.7.2 - http://softwaremill.com/open-source) + (Apache License 2.0) Asynchronous Http Client (org.asynchttpclient:async-http-client:2.10.3 - http://github.com/AsyncHttpClient/async-http-client/async-http-client) + (Apache License 2.0) Asynchronous Http Client Netty Utils (org.asynchttpclient:async-http-client-netty-utils:2.10.3 - http://github.com/AsyncHttpClient/async-http-client/async-http-client-netty-utils) + (Apache 2.0) AutoValue Annotations (com.google.auto.value:auto-value-annotations:1.9 - https://github.com/google/auto/tree/master/value) + (Apache License, Version 2.0) AWS Lambda Java Core Library (com.amazonaws:aws-lambda-java-core:1.2.1 - https://aws.amazon.com/lambda/) + (Apache License, Version 2.0) AWS Lambda Java Events Library (com.amazonaws:aws-lambda-java-events:3.9.0 - https://aws.amazon.com/lambda/) + (MIT) better-files (com.github.pathikrit:better-files_2.13:3.9.1 - https://github.com/pathikrit/better-files) + (Bouncy Castle Licence) Bouncy Castle PKIX, CMS, EAC, TSP, PKCS, OCSP, CMP, and CRMF APIs (org.bouncycastle:bcpkix-jdk15on:1.67 - http://www.bouncycastle.org/java.html) + (Bouncy Castle Licence) Bouncy Castle Provider (org.bouncycastle:bcprov-jdk15on:1.67 - http://www.bouncycastle.org/java.html) + (Apache 2.0) cats (com.softwaremill.sttp:cats_2.13:1.7.2 - http://softwaremill.com/open-source) + (MIT) Cats core (org.typelevel:cats-core_2.13:2.7.0 - https://github.com/typelevel/cats) + (MIT) Cats Free (org.typelevel:cats-free_2.13:2.1.1 - https://github.com/typelevel/cats) + (MIT) Cats kernel (org.typelevel:cats-kernel_2.13:2.7.0 - https://github.com/typelevel/cats) + (MIT) Cats macros (org.typelevel:cats-macros_2.13:2.1.1 - https://github.com/typelevel/cats) + (Apache-2.0) cats-effect (org.typelevel:cats-effect_2.13:2.0.0 - https://typelevel.org/cats-effect/) + (The MIT License) Checker Qual (org.checkerframework:checker-qual:3.12.0 - https://checkerframework.org) + (Apache 2.0) Circe core (io.circe:circe-core_2.13:0.14.1 - https://github.com/circe/circe) + (Apache 2.0) Circe generic (io.circe:circe-generic_2.13:0.14.1 - https://github.com/circe/circe) + (Apache 2.0) Circe jawn (io.circe:circe-jawn_2.13:0.14.1 - https://github.com/circe/circe) + (Apache 2.0) Circe literal (io.circe:circe-literal_2.13:0.14.1 - https://github.com/circe/circe) + (Apache 2.0) Circe numbers (io.circe:circe-numbers_2.13:0.14.1 - https://github.com/circe/circe) + (Apache 2.0) Circe parser (io.circe:circe-parser_2.13:0.14.1 - https://github.com/circe/circe) + (Apache 2.0) Circe refined (io.circe:circe-refined_2.13:0.14.1 - https://github.com/circe/circe) + (Apache 2.0) Circe shapes (io.circe:circe-shapes_2.13:0.14.1 - https://github.com/circe/circe) + (Apache-2.0) circe-config (io.circe:circe-config_2.13:0.8.0 - https://github.com/circe/circe-config) + (Apache 2.0) circe-yaml (io.circe:circe-yaml_2.13:0.14.1 - https://github.com/circe/circe-yaml) + (The Apache Software License, Version 2.0) Cloud Resource Manager API v1-rev20220109-1.32.1 (com.google.apis:google-api-services-cloudresourcemanager:v1-rev20220109-1.32.1 - http://nexus.sonatype.org/oss-repository-hosting.html/google-api-services-cloudresourcemanager) + (BSD-3-Clause) commons-compiler (org.codehaus.janino:commons-compiler:3.1.7 - http://janino-compiler.github.io/commons-compiler/) + (Apache License, Version 2.0) config (com.typesafe:config:1.3.3 - https://github.com/lightbend/config) + (Apache 2) core (com.chuusai:shapeless_2.13:2.3.7 - https://github.com/milessabin/shapeless) + (MIT) core (com.github.julien-truffaut:monocle-core_2.13:2.1.0 - https://github.com/optics-dev/Monocle) + (Apache 2.0) core (com.softwaremill.sttp:core_2.13:1.7.2 - http://softwaremill.com/open-source) + (Apache 2) core (org.typelevel:kittens_2.13:2.3.2 - https://github.com/typelevel/kittens) + (Three-clause BSD-style) core (org.typelevel:simulacrum_2.13:1.0.1 - http://github.com/mpilquist/simulacrum) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-common (org.broadinstitute:cromwell-common_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-core (org.broadinstitute:cromwell-core_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-model-biscayne (org.broadinstitute:cromwell-wdl-model-biscayne_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-model-core (org.broadinstitute:cromwell-wdl-model-core_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-model-draft2 (org.broadinstitute:cromwell-wdl-model-draft2_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-model-draft3 (org.broadinstitute:cromwell-wdl-model-draft3_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-transforms-biscayne (org.broadinstitute:cromwell-wdl-transforms-biscayne_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-transforms-draft2 (org.broadinstitute:cromwell-wdl-transforms-draft2_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-transforms-draft3 (org.broadinstitute:cromwell-wdl-transforms-draft3_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-transforms-new-base (org.broadinstitute:cromwell-wdl-transforms-new-base_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-transforms-shared (org.broadinstitute:cromwell-wdl-transforms-shared_2.13:85 - no url defined) + (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wom (org.broadinstitute:cromwell-wom_2.13:85 - no url defined) + (Apache 2.0) error-prone annotations (com.google.errorprone:error_prone_annotations:2.7.1 - http://nexus.sonatype.org/oss-repository-hosting.html/error_prone_parent/error_prone_annotations) + (MIT) fansi_2.13 (com.lihaoyi:fansi_2.13:0.3.1 - https://github.com/lihaoyi/Fansi) + (MIT) ficus (com.iheart:ficus_2.13:1.5.2 - http://iheartradio.github.io/ficus) + (The Apache Software License, Version 2.0) FindBugs-jsr305 (com.google.code.findbugs:jsr305:3.0.2 - http://findbugs.sourceforge.net/) + (BSD) GAX (Google Api eXtensions) for Java (com.google.api:gax:2.12.2 - https://github.com/googleapis/gax-java) + (BSD) GAX (Google Api eXtensions) for Java (com.google.api:gax-grpc:2.12.2 - https://github.com/googleapis/gax-java) + (BSD) GAX (Google Api eXtensions) for Java (com.google.api:gax-httpjson:0.97.2 - https://github.com/googleapis/gax-java) + (Apache 2.0) genericExtras (io.circe:circe-generic-extras_2.13:0.14.1 - https://github.com/circe/circe-generic-extras) + (Apache 2.0) Google Android Annotations Library (com.google.android:annotations:4.1.1.4 - http://source.android.com/) + (The Apache Software License, Version 2.0) Google APIs Client Library for Java (com.google.api-client:google-api-client:1.33.2 - https://github.com/googleapis/google-api-java-client/google-api-client) + (The Apache Software License, Version 2.0) Google App Engine extensions to the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-appengine:1.41.4 - https://github.com/googleapis/google-http-java-client/google-http-client-appengine) + (BSD New license) Google Auth Library for Java - Credentials (com.google.auth:google-auth-library-credentials:1.5.3 - https://github.com/googleapis/google-auth-library-java/google-auth-library-credentials) + (BSD New license) Google Auth Library for Java - OAuth2 HTTP (com.google.auth:google-auth-library-oauth2-http:1.5.3 - https://github.com/googleapis/google-auth-library-java/google-auth-library-oauth2-http) + (Apache-2.0) Google Cloud Core (com.google.cloud:google-cloud-core:2.5.6 - https://github.com/googleapis/java-core) + (Apache-2.0) Google Cloud Core HTTP (com.google.cloud:google-cloud-core-http:2.5.6 - https://github.com/googleapis/java-core) + (Apache-2.0) Google Cloud Monitoring (com.google.cloud:google-cloud-monitoring:3.2.5 - https://github.com/googleapis/java-monitoring) + (Apache-2.0) Google Cloud Resource Manager (com.google.cloud:google-cloud-resourcemanager:1.2.5 - https://github.com/googleapis/java-resourcemanager) + (The Apache Software License, Version 2.0) Google HTTP Client Library for Java (com.google.http-client:google-http-client:1.41.3 - https://github.com/googleapis/google-http-java-client/google-http-client) + (The Apache Software License, Version 2.0) Google OAuth Client Library for Java (com.google.oauth-client:google-oauth-client:1.33.0 - https://github.com/googleapis/google-oauth-java-client/google-oauth-client) + (The Apache Software License, Version 2.0) Graph Core (org.scala-graph:graph-core_2.13:1.13.1 - http://scala-graph.org) + (Apache 2.0) Gson (com.google.code.gson:gson:2.8.5 - https://github.com/google/gson/gson) + (The Apache Software License, Version 2.0) GSON extensions to the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-gson:1.41.3 - https://github.com/googleapis/google-http-java-client/google-http-client-gson) + (The Apache Software License, Version 2.0) Guava InternalFutureFailureAccess and InternalFutures (com.google.guava:failureaccess:1.0.1 - https://github.com/google/guava/failureaccess) + (The Apache Software License, Version 2.0) Guava ListenableFuture only (com.google.guava:listenablefuture:9999.0-empty-to-avoid-conflict-with-guava - https://github.com/google/guava/listenablefuture) + (Apache License, Version 2.0) Guava: Google Core Libraries for Java (com.google.guava:guava:31.0.1-jre - https://github.com/google/guava) + (Apache 2.0) io.grpc:grpc-alts (io.grpc:grpc-alts:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-api (io.grpc:grpc-api:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-auth (io.grpc:grpc-auth:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-context (io.grpc:grpc-context:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-core (io.grpc:grpc-core:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-grpclb (io.grpc:grpc-grpclb:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-netty-shaded (io.grpc:grpc-netty-shaded:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-protobuf (io.grpc:grpc-protobuf:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-protobuf-lite (io.grpc:grpc-protobuf-lite:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-services (io.grpc:grpc-services:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-stub (io.grpc:grpc-stub:1.44.1 - https://github.com/grpc/grpc-java) + (Apache 2.0) io.grpc:grpc-xds (io.grpc:grpc-xds:1.44.1 - https://github.com/grpc/grpc-java) + (The Apache Software License, Version 2.0) J2ObjC Annotations (com.google.j2objc:j2objc-annotations:1.3 - https://github.com/google/j2objc/) + (The Apache Software License, Version 2.0) Jackson 2 extensions to the Google APIs Client Library for Java (com.google.api-client:google-api-client-jackson2:1.33.2 - https://github.com/googleapis/google-api-java-client/google-api-client-jackson2) + (The Apache Software License, Version 2.0) Jackson 2 extensions to the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-jackson2:1.41.4 - https://github.com/googleapis/google-http-java-client/google-http-client-jackson2) + (The Apache Software License, Version 2.0) Jackson datatype: JSR310 (com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.12.3 - https://github.com/FasterXML/jackson-modules-java8/jackson-datatype-jsr310) + (The Apache Software License, Version 2.0) Jackson module: JAXB Annotations (com.fasterxml.jackson.module:jackson-module-jaxb-annotations:2.12.2 - https://github.com/FasterXML/jackson-modules-base) + (The Apache Software License, Version 2.0) Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.12.3 - http://github.com/FasterXML/jackson) + (The Apache Software License, Version 2.0) Jackson-core (com.fasterxml.jackson.core:jackson-core:2.12.7 - https://github.com/FasterXML/jackson-core) + (The Apache Software License, Version 2.0) jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.12.7.1 - http://github.com/FasterXML/jackson) + (EPL 2.0) (GPL2 w/ CPE) Jakarta Annotations API (jakarta.annotation:jakarta.annotation-api:1.3.5 - https://projects.eclipse.org/projects/ee4j.ca) + (EPL 2.0) (GPL2 w/ CPE) jakarta.ws.rs-api (jakarta.ws.rs:jakarta.ws.rs-api:2.1.6 - https://github.com/eclipse-ee4j/jaxrs-api) + (Eclipse Distribution License - v 1.0) jakarta.xml.bind-api (jakarta.xml.bind:jakarta.xml.bind-api:2.3.2 - https://github.com/eclipse-ee4j/jaxb-api/jakarta.xml.bind-api) + (BSD-3-Clause) janino (org.codehaus.janino:janino:3.1.7 - http://janino-compiler.github.io/janino/) + (The Apache Software License, Version 2.0) Java 6 (and higher) Extensions to the Google API Client Library for Java. (com.google.api-client:google-api-client-java6:1.33.2 - https://github.com/googleapis/google-api-java-client/google-api-client-java6) + (The Apache Software License, Version 2.0) Java 6 (and higher) extensions to the Google OAuth Client Library for Java. (com.google.oauth-client:google-oauth-client-java6:1.33.0 - https://github.com/googleapis/google-oauth-java-client/google-oauth-client-java6) + (Apache-2.0) (LGPL-2.1-or-later) Java Native Access (net.java.dev.jna:jna:5.9.0 - https://github.com/java-native-access/jna) + (EDL 1.0) JavaBeans Activation Framework API jar (jakarta.activation:jakarta.activation-api:1.2.1 - https://github.com/eclipse-ee4j/jaf/jakarta.activation-api) + (Apache 2) JavaEWAH (com.googlecode.javaewah:JavaEWAH:1.1.13 - https://github.com/lemire/javaewah) + (EPL 2.0) (GPL2 w/ CPE) javax.inject:1 as OSGi bundle (org.glassfish.hk2.external:jakarta.inject:2.6.1 - https://github.com/eclipse-ee4j/glassfish-hk2/external/jakarta.inject) + (Apache License, Version 2.0) JCL 1.2 implemented over SLF4J (org.slf4j:jcl-over-slf4j:1.7.32 - http://www.slf4j.org) + (Apache License, 2.0) (BSD 2-Clause) (EDL 1.0) (EPL 2.0) (GPL2 w/ CPE) (MIT license) (Modified BSD) (Public Domain) (W3C license) (jQuery license) jersey-core-client (org.glassfish.jersey.core:jersey-client:2.34 - https://projects.eclipse.org/projects/ee4j.jersey/jersey-client) + (Apache License, 2.0) (EPL 2.0) (Public Domain) (The GNU General Public License (GPL), Version 2, With Classpath Exception) jersey-core-common (org.glassfish.jersey.core:jersey-common:2.34 - https://projects.eclipse.org/projects/ee4j.jersey/jersey-common) + (Apache License, 2.0) (BSD 2-Clause) (EDL 1.0) (EPL 2.0) (GPL2 w/ CPE) (MIT license) (Modified BSD) (Public Domain) (W3C license) (jQuery license) jersey-ext-entity-filtering (org.glassfish.jersey.ext:jersey-entity-filtering:2.34 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-entity-filtering) + (Apache License, 2.0) (EPL 2.0) (The GNU General Public License (GPL), Version 2, With Classpath Exception) jersey-media-json-jackson (org.glassfish.jersey.media:jersey-media-json-jackson:2.34 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-media-json-jackson) + (Apache License, 2.0) (BSD 2-Clause) (EDL 1.0) (EPL 2.0) (GPL2 w/ CPE) (MIT license) (Modified BSD) (Public Domain) (W3C license) (jQuery license) jersey-media-multipart (org.glassfish.jersey.media:jersey-media-multipart:2.34 - 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no url defined) + (WDL License https://github.com/openwdl/wdl/blob/master/LICENSE) wdl-draft2 (org.broadinstitute:wdl-draft2_2.13:85 - no url defined) + (WDL License https://github.com/openwdl/wdl/blob/master/LICENSE) wdl-draft3 (org.broadinstitute:wdl-draft3_2.13:85 - no url defined) + (Unknown license) womtool (org.broadinstitute:womtool_2.13:85 - no url defined) diff --git a/wdl-parsing/WDLParsingFunction/pom.xml b/wdl-parsing/WDLParsingFunction/pom.xml index fe55d9a..b77cac3 100644 --- a/wdl-parsing/WDLParsingFunction/pom.xml +++ b/wdl-parsing/WDLParsingFunction/pom.xml @@ -116,11 +116,11 @@ ${jersey-version} - - jakarta.ws.rs - jakarta.ws.rs-api - 2.1.6 - + + jakarta.ws.rs + jakarta.ws.rs-api + 2.1.6 + com.google.code.findbugs @@ -174,6 +174,40 @@ maven-failsafe-plugin ${maven-plugin-version} + + org.codehaus.mojo + license-maven-plugin + 2.7.1 + + ${project.basedir} + THIRD-PARTY-LICENSES.properties + true + true + ^io\.dockstore + + + + distribution + + add-third-party + + + THIRD-PARTY-LICENSES.txt + test,system + + + + dev + + add-third-party + + + THIRD-PARTY-LICENSES.dev.txt + test + + + + org.apache.maven.plugins maven-dependency-plugin