diff --git a/.circleci/config.yml b/.circleci/config.yml
index 1a12f497a..2fa0ae743 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -2,7 +2,7 @@ version: 2.1
parameters:
java-tag:
type: string
- default: "17.0.3"
+ default: "21.0.5"
run_against_develop_core:
type: boolean
default: false
@@ -17,14 +17,14 @@ executors:
machine_integration_test_exec:
machine: # run the steps with Ubuntu VM
- image: ubuntu-2204:2023.10.1
+ image: ubuntu-2204:2024.04.4
environment:
PGHOST: 127.0.0.1
resource_class: medium
toil_wes_test_executor:
machine: # run the steps with Ubuntu VM
- image: ubuntu-2204:2023.10.1
+ image: ubuntu-2204:2024.11.1
resource_class: medium
common_filters: &common_filters
@@ -52,7 +52,7 @@ common_jobs: &common_jobs
- integration-tests:
matrix:
parameters:
- testing_profile: [ "singularity-tests", "bitbucket-tests" ]
+ testing_profile: [ "singularity-tests", "bitbucket-tests", "toil-integration-tests" ]
<<: *common_filters
<<: *slack_context
requires:
@@ -198,7 +198,8 @@ jobs:
- run:
name: findDevelopSnapshot
command: |
- ./mvnw versions:update-properties -Dincludes=io.dockstore:* -DallowSnapshots
+ # grab the latest snapshot version that doesn't seem to correspond to a feature branch or similar
+ ./mvnw versions:update-properties -Dincludes="io.dockstore:*" -Dmaven.version.ignore=\.*-\.*-SNAPSHOT -DallowSnapshots
- run:
name: force update to latest snapshot versions, # review this step to see what versions were used, also see https://stackoverflow.com/questions/29020716/maven-what-does-u-update-snapshots-really-do
command: |
diff --git a/.github/collab-mvn-settings.xml b/.github/collab-mvn-settings.xml
deleted file mode 100644
index 711bbdc0d..000000000
--- a/.github/collab-mvn-settings.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-
-
-
- central
- dockstore-bot
- ${env.COLLAB_DEPLOY_TOKEN}
-
-
-
diff --git a/.github/snapshot-mvn-settings.xml b/.github/snapshot-mvn-settings.xml
deleted file mode 100644
index ce26d73be..000000000
--- a/.github/snapshot-mvn-settings.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-
-
-
- snapshots
- dockstore-snapshot-bot
- ${env.SNAPSHOT_DEPLOY_TOKEN}
-
-
-
diff --git a/.github/workflows/deploy_artifacts.yml b/.github/workflows/deploy_artifacts.yml
new file mode 100644
index 000000000..13390ac1b
--- /dev/null
+++ b/.github/workflows/deploy_artifacts.yml
@@ -0,0 +1,16 @@
+name: Deploy artifacts
+
+on:
+ push:
+ tags:
+ - '**'
+ branches-ignore:
+ - 'master'
+ - 'release/**'
+ - 'hotfix/**'
+ - 'dependabot/**'
+
+jobs:
+ build:
+ uses: dockstore/workflow-actions/.github/workflows/deploy_artifacts.yaml@main
+ secrets: inherit
diff --git a/.github/workflows/deploy_snapshot.yml b/.github/workflows/deploy_snapshot.yml
deleted file mode 100644
index e7faceaef..000000000
--- a/.github/workflows/deploy_snapshot.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: Deploy develop snapshot
-
-on:
- push:
- branches:
- - develop
-
- # Allows you to run this workflow manually from the Actions tab
- workflow_dispatch:
-
-jobs:
- build:
- runs-on: ubuntu-22.04
-
- steps:
- - uses: actions/checkout@v4
- # Step that does that actual cache save and restore
- - uses: actions/cache@v4
- with:
- path: ~/.m2/repository
- key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
- restore-keys: |
- ${{ runner.os }}-maven-
-
- - name: Set up JDK
- uses: actions/setup-java@v4
- with:
- java-version: '17.0.4+8'
- distribution: 'adopt'
- - name: install git secrets
- run: |
- wget --no-verbose -O git-secrets-1.3.0.tar.gz https://github.com/awslabs/git-secrets/archive/1.3.0.tar.gz
- tar -zxf git-secrets-1.3.0.tar.gz
- cd git-secrets-1.3.0
- sudo make install
-
- - name: Deploy with mvnw
- run: ./mvnw --batch-mode deploy -ntp -s .github/snapshot-mvn-settings.xml -DskipTests
- env:
- SNAPSHOT_DEPLOY_TOKEN: ${{ secrets.SNAPSHOT_DEPLOY_TOKEN }}
diff --git a/.github/workflows/deploy_tagged.yml b/.github/workflows/deploy_tagged.yml
deleted file mode 100644
index 614cd5d6b..000000000
--- a/.github/workflows/deploy_tagged.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-name: Tagged release deploy
-
-on:
- workflow_dispatch:
- inputs:
- changelist:
- description: 'patch and pre-release metadata'
- required: true
- default: '.0-alpha.1'
-
-
-jobs:
- call-reusable-tagged-release:
- uses: dockstore/workflow-actions/.github/workflows/deploy_tagged.yaml@main
- with:
- changelist: ${{ inputs.changelist }}
- secrets: inherit
diff --git a/.github/workflows/mvnw.yml b/.github/workflows/mvnw.yml
index 070f98bb3..30fa93b93 100644
--- a/.github/workflows/mvnw.yml
+++ b/.github/workflows/mvnw.yml
@@ -7,7 +7,7 @@ jobs:
runs-on: ubuntu-22.04
strategy:
matrix:
- java: [ '17.0.4+8' ]
+ java: [ '17.0.4+8', '21.0.5+11.0.LTS' ]
steps:
- name: install git secrets
diff --git a/THIRD-PARTY-LICENSES.txt b/THIRD-PARTY-LICENSES.txt
index 414a32e15..242de71cd 100644
--- a/THIRD-PARTY-LICENSES.txt
+++ b/THIRD-PARTY-LICENSES.txt
@@ -1,40 +1,40 @@
-Lists of 403 third-party dependencies.
+Lists of 406 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)
(Apache 2.0) annotation (org.typelevel:simulacrum-scalafix-annotations_2.13:0.5.4 - https://github.com/typelevel/simulacrum-scalafix)
- (Apache License 2.0) Annotations for Metrics (io.dropwizard.metrics:metrics-annotation:4.2.19 - https://metrics.dropwizard.io/metrics-annotation)
+ (Apache License 2.0) Annotations for Metrics (io.dropwizard.metrics:metrics-annotation:4.2.30 - https://metrics.dropwizard.io/metrics-annotation)
(The BSD License) ANTLR 4 Runtime (org.antlr:antlr4-runtime:4.10.1 - http://www.antlr.org/antlr4-runtime)
- (EPL 2.0) (GPL2 w/ CPE) aopalliance version 1.0 repackaged as a module (org.glassfish.hk2.external:aopalliance-repackaged:3.0.4 - https://github.com/eclipse-ee4j/glassfish-hk2/external/aopalliance-repackaged)
- (Apache-2.0) Apache Avro (org.apache.avro:avro:1.11.3 - https://avro.apache.org)
+ (EPL 2.0) (GPL2 w/ CPE) aopalliance version 1.0 repackaged as a module (org.glassfish.hk2.external:aopalliance-repackaged:3.0.6 - https://github.com/eclipse-ee4j/glassfish-hk2/external/aopalliance-repackaged)
+ (Apache-2.0) Apache Avro (org.apache.avro:avro:1.11.4 - https://avro.apache.org)
(Apache License, Version 2.0) Apache Commons BeanUtils (commons-beanutils:commons-beanutils:1.9.4 - https://commons.apache.org/proper/commons-beanutils/)
(Apache-2.0) Apache Commons Codec (commons-codec:commons-codec:1.17.1 - https://commons.apache.org/proper/commons-codec/)
(Apache License, Version 2.0) Apache Commons Collections (commons-collections:commons-collections:3.2.2 - http://commons.apache.org/collections/)
(Apache License, Version 2.0) Apache Commons Collections (org.apache.commons:commons-collections4:4.4 - https://commons.apache.org/proper/commons-collections/)
- (Apache-2.0) Apache Commons Compress (org.apache.commons:commons-compress:1.26.0 - https://commons.apache.org/proper/commons-compress/)
+ (Apache-2.0) Apache Commons Compress (org.apache.commons:commons-compress:1.26.2 - https://commons.apache.org/proper/commons-compress/)
(Apache-2.0) Apache Commons Configuration (org.apache.commons:commons-configuration2:2.10.1 - https://commons.apache.org/proper/commons-configuration/)
(Apache License, Version 2.0) Apache Commons CSV (org.apache.commons:commons-csv:1.5 - http://commons.apache.org/proper/commons-csv/)
(Apache License, Version 2.0) Apache Commons Exec (org.apache.commons:commons-exec:1.3 - http://commons.apache.org/proper/commons-exec/)
- (Apache-2.0) Apache Commons IO (commons-io:commons-io:2.15.1 - https://commons.apache.org/proper/commons-io/)
- (Apache-2.0) Apache Commons Lang (org.apache.commons:commons-lang3:3.14.0 - https://commons.apache.org/proper/commons-lang/)
- (Apache-2.0) Apache Commons Logging (commons-logging:commons-logging:1.3.0 - https://commons.apache.org/proper/commons-logging/)
+ (Apache-2.0) Apache Commons IO (commons-io:commons-io:2.18.0 - https://commons.apache.org/proper/commons-io/)
+ (Apache-2.0) Apache Commons Lang (org.apache.commons:commons-lang3:3.17.0 - https://commons.apache.org/proper/commons-lang/)
+ (Apache-2.0) Apache Commons Logging (commons-logging:commons-logging:1.3.4 - https://commons.apache.org/proper/commons-logging/)
(Apache License, Version 2.0) Apache Commons Net (commons-net:commons-net:3.9.0 - https://commons.apache.org/proper/commons-net/)
- (Apache-2.0) Apache Commons Text (org.apache.commons:commons-text:1.11.0 - https://commons.apache.org/proper/commons-text)
+ (Apache-2.0) Apache Commons Text (org.apache.commons:commons-text:1.13.0 - https://commons.apache.org/proper/commons-text)
(Apache License, Version 2.0) Apache Commons Validator (commons-validator:commons-validator:1.7 - http://commons.apache.org/proper/commons-validator/)
- (Apache License, Version 2.0) Apache Commons VFS (org.apache.commons:commons-vfs2:2.9.0 - http://commons.apache.org/proper/commons-vfs/)
+ (Apache-2.0) Apache Commons VFS (org.apache.commons:commons-vfs2:2.10.0 - https://commons.apache.org/proper/commons-vfs/)
(The Apache Software License, Version 2.0) Apache Groovy (org.codehaus.groovy:groovy:2.5.14 - https://groovy-lang.org)
(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-v2:1.41.8 - https://github.com/googleapis/google-http-java-client/google-http-client-apache-v2)
(Apache License, Version 2.0) Apache HttpAsyncClient (org.apache.httpcomponents:httpasyncclient:4.1.4 - http://hc.apache.org/httpcomponents-asyncclient)
(Apache License, Version 2.0) Apache HttpClient (org.apache.httpcomponents:httpclient:4.5.14 - http://hc.apache.org/httpcomponents-client-ga)
- (Apache License, Version 2.0) Apache HttpClient (org.apache.httpcomponents.client5:httpclient5:5.2.1 - https://hc.apache.org/httpcomponents-client-5.0.x/5.2.1/httpclient5/)
- (Apache License, Version 2.0) Apache HttpComponents Core HTTP/1.1 (org.apache.httpcomponents.core5:httpcore5:5.2.3 - https://hc.apache.org/httpcomponents-core-5.2.x/5.2.3/httpcore5/)
- (Apache License, Version 2.0) Apache HttpComponents Core HTTP/2 (org.apache.httpcomponents.core5:httpcore5-h2:5.2 - https://hc.apache.org/httpcomponents-core-5.2.x/5.2/httpcore5-h2/)
+ (Apache License, Version 2.0) Apache HttpClient (org.apache.httpcomponents.client5:httpclient5:5.4.1 - https://hc.apache.org/httpcomponents-client-5.4.x/5.4.1/httpclient5/)
+ (Apache License, Version 2.0) Apache HttpComponents Core HTTP/1.1 (org.apache.httpcomponents.core5:httpcore5:5.3.2 - https://hc.apache.org/httpcomponents-core-5.3.x/5.3.2/httpcore5/)
+ (Apache License, Version 2.0) Apache HttpComponents Core HTTP/2 (org.apache.httpcomponents.core5:httpcore5-h2:5.3.1 - https://hc.apache.org/httpcomponents-core-5.3.x/5.3.1/httpcore5-h2/)
(Apache License, Version 2.0) Apache HttpCore (org.apache.httpcomponents:httpcore:4.4.16 - http://hc.apache.org/httpcomponents-core-ga)
(Apache License, Version 2.0) Apache HttpCore NIO (org.apache.httpcomponents:httpcore-nio:4.4.16 - http://hc.apache.org/httpcomponents-core-ga)
- (Apache License, Version 2.0) Apache Log4j API (org.apache.logging.log4j:log4j-api:2.17.1 - https://logging.apache.org/log4j/2.x/log4j-api/)
+ (Apache-2.0) Apache Log4j API (org.apache.logging.log4j:log4j-api:2.23.1 - https://logging.apache.org/log4j/2.x/log4j/log4j-api/)
(MIT) argparse4j (net.sourceforge.argparse4j:argparse4j:0.9.0 - https://argparse4j.github.io)
(Apache License, Version 2.0) AssertJ fluent assertions (org.assertj:assertj-core:3.14.0 - http://assertj.org/assertj-core)
(Apache 2.0) async-http-client-backend (com.softwaremill.sttp:async-http-client-backend_2.13:1.7.2 - http://softwaremill.com/open-source)
@@ -87,8 +87,8 @@ Lists of 403 third-party dependencies.
(Bouncy Castle Licence) Bouncy Castle ASN.1 Extension and Utility APIs (org.bouncycastle:bcutil-jdk18on:1.78.1 - https://www.bouncycastle.org/java.html)
(Bouncy Castle Licence) Bouncy Castle PKIX, CMS, EAC, TSP, PKCS, OCSP, CMP, and CRMF APIs (org.bouncycastle:bcpkix-jdk18on:1.78.1 - https://www.bouncycastle.org/java.html)
(Bouncy Castle Licence) Bouncy Castle Provider (org.bouncycastle:bcprov-jdk18on:1.78.1 - https://www.bouncycastle.org/java.html)
- (Apache License, Version 2.0) Byte Buddy (without dependencies) (net.bytebuddy:byte-buddy:1.14.8 - https://bytebuddy.net/byte-buddy)
- (Apache License, Version 2.0) Byte Buddy agent (net.bytebuddy:byte-buddy-agent:1.14.8 - https://bytebuddy.net/byte-buddy-agent)
+ (Apache License, Version 2.0) Byte Buddy (without dependencies) (net.bytebuddy:byte-buddy:1.15.11 - https://bytebuddy.net/byte-buddy)
+ (Apache License, Version 2.0) Byte Buddy agent (net.bytebuddy:byte-buddy-agent:1.15.11 - https://bytebuddy.net/byte-buddy-agent)
(Apache License, Version 2.0) Caffeine cache (com.github.ben-manes.caffeine:caffeine:3.1.8 - https://github.com/ben-manes/caffeine)
(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)
@@ -97,7 +97,7 @@ Lists of 403 third-party dependencies.
(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_2.13:2.5.3 - https://typelevel.org/cats-effect/)
(ASF 2.0) cglib-nodep (cglib:cglib-nodep:3.2.9 - https://github.com/cglib/cglib/cglib-nodep)
- (The MIT License) Checker Qual (org.checkerframework:checker-qual:3.42.0 - https://checkerframework.org/)
+ (The MIT License) Checker Qual (org.checkerframework:checker-qual:3.48.4 - 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)
@@ -109,11 +109,12 @@ Lists of 403 third-party dependencies.
(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 MIT License (MIT)) ClassGraph (io.github.classgraph:classgraph:4.8.154 - https://github.com/classgraph/classgraph)
- (Apache License, Version 2.0) ClassMate (com.fasterxml:classmate:1.5.1 - https://github.com/FasterXML/java-classmate)
+ (Apache License, Version 2.0) ClassMate (com.fasterxml:classmate:1.7.0 - https://github.com/FasterXML/java-classmate)
(The Apache License, Version 2.0) com.helger:profiler (com.helger:profiler:1.1.1 - https://github.com/phax/profiler)
+ (BSD-2-Clause) commonmark-java core (org.commonmark:commonmark:0.24.0 - https://github.com/commonmark/commonmark-java/commonmark)
(The Apache Software License, Version 2.0) Commons Digester (commons-digester:commons-digester:2.1 - http://commons.apache.org/digester/)
(BSD-3-Clause) commons-compiler (org.codehaus.janino:commons-compiler:3.1.7 - http://janino-compiler.github.io/commons-compiler/)
- (Apache License 2.0) compiler (com.github.spullara.mustache.java:compiler:0.9.10 - http://github.com/spullara/mustache.java)
+ (Apache License 2.0) compiler (com.github.spullara.mustache.java:compiler:0.9.14 - http://github.com/spullara/mustache.java)
(Apache-2.0) config (com.typesafe:config:1.4.2 - https://github.com/lightbend/config)
(Apache 2) core (com.chuusai:shapeless_2.13:2.3.9 - https://github.com/milessabin/shapeless)
(MIT) core (com.github.julien-truffaut:monocle-core_2.13:2.1.0 - https://github.com/optics-dev/Monocle)
@@ -132,42 +133,42 @@ Lists of 403 third-party dependencies.
(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 License, Version 2.0) cwlavro-generated (io.cwl:cwlavro-generated:2.0.4.9 - no url defined)
- (Apache License, Version 2.0) cwlavro-tools (io.cwl:cwlavro-tools:2.0.4.9 - no url defined)
+ (Apache License, Version 2.0) cwlavro-generated (io.cwl:cwlavro-generated:2.1.0 - no url defined)
+ (Apache License, Version 2.0) cwlavro-tools (io.cwl:cwlavro-tools:2.1.0 - no url defined)
(The Apache Software License, Version 2.0) docker-java-api (com.github.docker-java:docker-java-api:3.3.6 - https://github.com/docker-java/docker-java)
(The Apache Software License, Version 2.0) docker-java-core (com.github.docker-java:docker-java-core:3.3.6 - https://github.com/docker-java/docker-java)
(The Apache Software License, Version 2.0) docker-java-transport (com.github.docker-java:docker-java-transport:3.3.6 - https://github.com/docker-java/docker-java)
(The Apache Software License, Version 2.0) docker-java-transport-httpclient5 (com.github.docker-java:docker-java-transport-httpclient5:3.3.6 - https://github.com/docker-java/docker-java)
- (Apache License 2.0) Dropwizard (io.dropwizard:dropwizard-core:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-core)
- (Apache License 2.0) Dropwizard Asset Bundle (io.dropwizard:dropwizard-assets:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-assets)
- (Apache License 2.0) Dropwizard Authentication (io.dropwizard:dropwizard-auth:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-auth)
- (Apache License 2.0) Dropwizard Configuration Support (io.dropwizard:dropwizard-configuration:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-configuration)
- (Apache License 2.0) Dropwizard Database Support (io.dropwizard:dropwizard-db:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-db)
- (Apache License 2.0) Dropwizard Health Checking Support (io.dropwizard:dropwizard-health:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-health)
- (Apache License 2.0) Dropwizard Hibernate Support (io.dropwizard:dropwizard-hibernate:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-hibernate)
- (Apache License 2.0) Dropwizard HTTP Client (io.dropwizard:dropwizard-client:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-client)
- (Apache License 2.0) Dropwizard Jackson Support (io.dropwizard:dropwizard-jackson:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-jackson)
- (Apache License 2.0) Dropwizard JDBI3 Support (io.dropwizard:dropwizard-jdbi3:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-jdbi3)
- (Apache License 2.0) Dropwizard Jersey Support (io.dropwizard:dropwizard-jersey:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-jersey)
- (Apache License 2.0) Dropwizard Jetty Support (io.dropwizard:dropwizard-jetty:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-jetty)
- (Apache License 2.0) Dropwizard Lifecycle Support (io.dropwizard:dropwizard-lifecycle:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-lifecycle)
- (Apache License 2.0) Dropwizard Logging Support (io.dropwizard:dropwizard-logging:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-logging)
- (Apache License 2.0) Dropwizard Metrics Support (io.dropwizard:dropwizard-metrics:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-metrics)
- (Apache License 2.0) Dropwizard Migrations (io.dropwizard:dropwizard-migrations:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-migrations)
- (Apache License 2.0) Dropwizard Multipart Form Support (io.dropwizard:dropwizard-forms:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-forms)
- (Apache License 2.0) Dropwizard Request Logging Support (io.dropwizard:dropwizard-request-logging:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-request-logging)
- (Apache License 2.0) Dropwizard Servlet Support (io.dropwizard:dropwizard-servlets:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-servlets)
- (Apache License 2.0) Dropwizard Test Helpers (io.dropwizard:dropwizard-testing:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-testing)
- (Apache License 2.0) Dropwizard Utility Classes (io.dropwizard:dropwizard-util:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-util)
- (Apache License 2.0) Dropwizard Validation Support (io.dropwizard:dropwizard-validation:4.0.2 - http://www.dropwizard.io/4.0.2/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-validation)
+ (Apache License 2.0) Dropwizard (io.dropwizard:dropwizard-core:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-core)
+ (Apache License 2.0) Dropwizard Asset Bundle (io.dropwizard:dropwizard-assets:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-assets)
+ (Apache License 2.0) Dropwizard Authentication (io.dropwizard:dropwizard-auth:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-auth)
+ (Apache License 2.0) Dropwizard Configuration Support (io.dropwizard:dropwizard-configuration:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-configuration)
+ (Apache License 2.0) Dropwizard Database Support (io.dropwizard:dropwizard-db:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-db)
+ (Apache License 2.0) Dropwizard Health Checking Support (io.dropwizard:dropwizard-health:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-health)
+ (Apache License 2.0) Dropwizard Hibernate Support (io.dropwizard:dropwizard-hibernate:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-hibernate)
+ (Apache License 2.0) Dropwizard HTTP Client (io.dropwizard:dropwizard-client:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-client)
+ (Apache License 2.0) Dropwizard Jackson Support (io.dropwizard:dropwizard-jackson:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-jackson)
+ (Apache License 2.0) Dropwizard JDBI3 Support (io.dropwizard:dropwizard-jdbi3:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-jdbi3)
+ (Apache License 2.0) Dropwizard Jersey Support (io.dropwizard:dropwizard-jersey:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-jersey)
+ (Apache License 2.0) Dropwizard Jetty Support (io.dropwizard:dropwizard-jetty:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-jetty)
+ (Apache License 2.0) Dropwizard Lifecycle Support (io.dropwizard:dropwizard-lifecycle:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-lifecycle)
+ (Apache License 2.0) Dropwizard Logging Support (io.dropwizard:dropwizard-logging:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-logging)
+ (Apache License 2.0) Dropwizard Metrics Support (io.dropwizard:dropwizard-metrics:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-metrics)
+ (Apache License 2.0) Dropwizard Migrations (io.dropwizard:dropwizard-migrations:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-migrations)
+ (Apache License 2.0) Dropwizard Multipart Form Support (io.dropwizard:dropwizard-forms:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-forms)
+ (Apache License 2.0) Dropwizard Request Logging Support (io.dropwizard:dropwizard-request-logging:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-request-logging)
+ (Apache License 2.0) Dropwizard Servlet Support (io.dropwizard:dropwizard-servlets:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-servlets)
+ (Apache License 2.0) Dropwizard Test Helpers (io.dropwizard:dropwizard-testing:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-testing)
+ (Apache License 2.0) Dropwizard Utility Classes (io.dropwizard:dropwizard-util:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-util)
+ (Apache License 2.0) Dropwizard Validation Support (io.dropwizard:dropwizard-validation:4.0.12 - http://www.dropwizard.io/4.0.12/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-validation)
(Apache 2) EasyMock (org.easymock:easymock:4.0.1 - http://easymock.org/easymock)
(The Apache Software License, Version 2.0) elasticsearch-core (org.elasticsearch:elasticsearch-core:7.10.2 - https://github.com/elastic/elasticsearch)
(The Apache Software License, Version 2.0) elasticsearch-x-content (org.elasticsearch:elasticsearch-x-content:7.10.2 - https://github.com/elastic/elasticsearch)
- (Apache 2.0) error-prone annotations (com.google.errorprone:error_prone_annotations:2.22.0 - https://errorprone.info/error_prone_annotations)
+ (Apache 2.0) error-prone annotations (com.google.errorprone:error_prone_annotations:2.36.0 - https://errorprone.info/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/)
- (The Apache Software License, Version 2.0) GeantyRef (io.leangen.geantyref:geantyref:1.3.14 - https://github.com/leangen/geantyref)
+ (The Apache Software License, Version 2.0) GeantyRef (io.leangen.geantyref:geantyref:2.0.0 - https://github.com/leangen/geantyref)
(Apache 2.0) genericExtras (io.circe:circe-generic-extras_2.13:0.14.1 - https://github.com/circe/circe-generic-extras)
(The MIT license) GitHub API for Java (org.kohsuke:github-api:1.322 - https://github-api.kohsuke.org/)
(The Apache Software License, Version 2.0) Gitlab Java API Wrapper (org.gitlab:java-gitlab-api:4.0.0 - http://nexus.sonatype.org/oss-repository-hosting.html/java-gitlab-api)
@@ -180,42 +181,42 @@ Lists of 403 third-party dependencies.
(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:2.10.1 - 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:1.41.8 - 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 InternalFutureFailureAccess and InternalFutures (com.google.guava:failureaccess:1.0.2 - 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:32.1.2-jre - https://github.com/google/guava)
- (BSD License 3) Hamcrest (org.hamcrest:hamcrest:2.2 - http://hamcrest.org/JavaHamcrest/)
+ (Apache License, Version 2.0) Guava: Google Core Libraries for Java (com.google.guava:guava:33.4.0-jre - https://github.com/google/guava)
+ (BSD-3-Clause) Hamcrest (org.hamcrest:hamcrest:3.0 - http://hamcrest.org/JavaHamcrest/)
(New BSD License) Hamcrest Core (org.hamcrest:hamcrest-core:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-core)
(GNU Library General Public License v2.1 or later) Hibernate Commons Annotations (org.hibernate.common:hibernate-commons-annotations:6.0.6.Final - http://hibernate.org)
(GNU Library General Public License v2.1 or later) Hibernate ORM - hibernate-core (org.hibernate.orm:hibernate-core:6.1.7.Final - https://hibernate.org/orm)
(Apache License 2.0) Hibernate Validator Engine (org.hibernate.validator:hibernate-validator:7.0.5.Final - http://hibernate.org/validator/hibernate-validator)
- (EPL 2.0) (GPL2 w/ CPE) HK2 API module (org.glassfish.hk2:hk2-api:3.0.4 - https://github.com/eclipse-ee4j/glassfish-hk2/hk2-api)
- (EPL 2.0) (GPL2 w/ CPE) HK2 Implementation Utilities (org.glassfish.hk2:hk2-utils:3.0.4 - https://github.com/eclipse-ee4j/glassfish-hk2/hk2-utils)
+ (EPL 2.0) (GPL2 w/ CPE) HK2 API module (org.glassfish.hk2:hk2-api:3.0.6 - https://github.com/eclipse-ee4j/glassfish-hk2/hk2-api)
+ (EPL 2.0) (GPL2 w/ CPE) HK2 Implementation Utilities (org.glassfish.hk2:hk2-utils:3.0.6 - https://github.com/eclipse-ee4j/glassfish-hk2/hk2-utils)
(The Apache Software License, Version 2.0) Hoverfly Java (io.specto:hoverfly-java:0.14.0 - https://github.com/SpectoLabs/hoverfly-java)
(The Apache Software License, Version 2.0) HPPC Collections (com.carrotsearch:hppc:0.8.1 - http://labs.carrotsearch.com/hppc.html/hppc)
(The Apache Software License, Version 2.0) IntelliJ IDEA Annotations (org.jetbrains:annotations:13.0 - http://www.jetbrains.org)
(Apache 2.0) io.grpc:grpc-context (io.grpc:grpc-context:1.27.2 - https://github.com/grpc/grpc-java)
(Eclipse Distribution License - v 1.0) istack common utility code runtime (com.sun.istack:istack-commons-runtime:4.0.1 - https://projects.eclipse.org/projects/ee4j/istack-commons/istack-commons-runtime)
- (Apache License, Version 2.0) J2ObjC Annotations (com.google.j2objc:j2objc-annotations:2.8 - https://github.com/google/j2objc/)
+ (Apache License, Version 2.0) J2ObjC Annotations (com.google.j2objc:j2objc-annotations:3.0.0 - https://github.com/google/j2objc/)
(The Apache Software License, Version 2.0) Jackson (org.codehaus.jackson:jackson-core-asl:1.9.13 - http://jackson.codehaus.org)
(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-jackson2:1.35.0 - https://github.com/googleapis/google-api-java-client/google-api-client-jackson2)
- (The Apache Software License, Version 2.0) Jackson dataformat: CBOR (com.fasterxml.jackson.dataformat:jackson-dataformat-cbor:2.15.2 - https://github.com/FasterXML/jackson-dataformats-binary)
- (The Apache Software License, Version 2.0) Jackson datatype: Guava (com.fasterxml.jackson.datatype:jackson-datatype-guava:2.15.2 - https://github.com/FasterXML/jackson-datatypes-collections)
- (The Apache Software License, Version 2.0) Jackson datatype: jdk8 (com.fasterxml.jackson.datatype:jackson-datatype-jdk8:2.15.2 - https://github.com/FasterXML/jackson-modules-java8/jackson-datatype-jdk8)
- (The Apache Software License, Version 2.0) Jackson datatype: JSR310 (com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.15.2 - https://github.com/FasterXML/jackson-modules-java8/jackson-datatype-jsr310)
+ (The Apache Software License, Version 2.0) Jackson dataformat: CBOR (com.fasterxml.jackson.dataformat:jackson-dataformat-cbor:2.18.2 - https://github.com/FasterXML/jackson-dataformats-binary)
+ (The Apache Software License, Version 2.0) Jackson datatype: Guava (com.fasterxml.jackson.datatype:jackson-datatype-guava:2.18.2 - https://github.com/FasterXML/jackson-datatypes-collections)
+ (The Apache Software License, Version 2.0) Jackson datatype: jdk8 (com.fasterxml.jackson.datatype:jackson-datatype-jdk8:2.18.2 - https://github.com/FasterXML/jackson-modules-java8/jackson-datatype-jdk8)
+ (The Apache Software License, Version 2.0) Jackson datatype: JSR310 (com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.18.2 - https://github.com/FasterXML/jackson-modules-java8/jackson-datatype-jsr310)
(The Apache Software License, Version 2.0) Jackson extensions to the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-jackson:1.29.2 - https://github.com/googleapis/google-http-java-client/google-http-client-jackson)
- (Apache License 2.0) Jackson Integration for Metrics (io.dropwizard.metrics:metrics-json:4.2.19 - https://metrics.dropwizard.io/metrics-json)
- (The Apache Software License, Version 2.0) Jackson Jakarta-RS: base (com.fasterxml.jackson.jakarta.rs:jackson-jakarta-rs-base:2.15.2 - https://github.com/FasterXML/jackson-jakarta-rs-providers/jackson-jakarta-rs-base)
- (The Apache Software License, Version 2.0) Jackson Jakarta-RS: JSON (com.fasterxml.jackson.jakarta.rs:jackson-jakarta-rs-json-provider:2.15.2 - https://github.com/FasterXML/jackson-jakarta-rs-providers/jackson-jakarta-rs-json-provider)
- (The Apache Software License, Version 2.0) Jackson module: Blackbird (com.fasterxml.jackson.module:jackson-module-blackbird:2.15.2 - https://github.com/FasterXML/jackson-modules-base)
- (The Apache Software License, Version 2.0) Jackson module: Jakarta XML Bind Annotations (jakarta.xml.bind) (com.fasterxml.jackson.module:jackson-module-jakarta-xmlbind-annotations:2.15.2 - https://github.com/FasterXML/jackson-modules-base)
- (The Apache Software License, Version 2.0) Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.15.2 - https://github.com/FasterXML/jackson)
- (The Apache Software License, Version 2.0) Jackson-core (com.fasterxml.jackson.core:jackson-core:2.15.2 - https://github.com/FasterXML/jackson-core)
- (The Apache Software License, Version 2.0) jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.15.2 - https://github.com/FasterXML/jackson)
- (The Apache Software License, Version 2.0) Jackson-dataformat-XML (com.fasterxml.jackson.dataformat:jackson-dataformat-xml:2.15.2 - https://github.com/FasterXML/jackson-dataformat-xml)
- (The Apache Software License, Version 2.0) Jackson-dataformat-YAML (com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.15.2 - https://github.com/FasterXML/jackson-dataformats-text)
- (The Apache Software License, Version 2.0) Jackson-datatype-Hibernate5-jakarta (com.fasterxml.jackson.datatype:jackson-datatype-hibernate5-jakarta:2.15.2 - https://github.com/FasterXML/jackson-datatype-hibernate)
- (The Apache Software License, Version 2.0) Jackson-JAXRS: base (com.fasterxml.jackson.jaxrs:jackson-jaxrs-base:2.15.2 - https://github.com/FasterXML/jackson-jaxrs-providers/jackson-jaxrs-base)
- (The Apache Software License, Version 2.0) Jackson-module-parameter-names (com.fasterxml.jackson.module:jackson-module-parameter-names:2.15.2 - https://github.com/FasterXML/jackson-modules-java8/jackson-module-parameter-names)
+ (Apache License 2.0) Jackson Integration for Metrics (io.dropwizard.metrics:metrics-json:4.2.30 - https://metrics.dropwizard.io/metrics-json)
+ (The Apache Software License, Version 2.0) Jackson Jakarta-RS: base (com.fasterxml.jackson.jakarta.rs:jackson-jakarta-rs-base:2.18.2 - https://github.com/FasterXML/jackson-jakarta-rs-providers/jackson-jakarta-rs-base)
+ (The Apache Software License, Version 2.0) Jackson Jakarta-RS: JSON (com.fasterxml.jackson.jakarta.rs:jackson-jakarta-rs-json-provider:2.18.2 - https://github.com/FasterXML/jackson-jakarta-rs-providers/jackson-jakarta-rs-json-provider)
+ (The Apache Software License, Version 2.0) Jackson module: Blackbird (com.fasterxml.jackson.module:jackson-module-blackbird:2.18.2 - https://github.com/FasterXML/jackson-modules-base)
+ (The Apache Software License, Version 2.0) Jackson module: Jakarta XML Bind Annotations (jakarta.xml.bind) (com.fasterxml.jackson.module:jackson-module-jakarta-xmlbind-annotations:2.18.2 - https://github.com/FasterXML/jackson-modules-base)
+ (The Apache Software License, Version 2.0) Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.18.2 - https://github.com/FasterXML/jackson)
+ (The Apache Software License, Version 2.0) Jackson-core (com.fasterxml.jackson.core:jackson-core:2.18.2 - https://github.com/FasterXML/jackson-core)
+ (The Apache Software License, Version 2.0) jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.18.2 - https://github.com/FasterXML/jackson)
+ (The Apache Software License, Version 2.0) Jackson-dataformat-XML (com.fasterxml.jackson.dataformat:jackson-dataformat-xml:2.18.2 - https://github.com/FasterXML/jackson-dataformat-xml)
+ (The Apache Software License, Version 2.0) Jackson-dataformat-YAML (com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.18.2 - https://github.com/FasterXML/jackson-dataformats-text)
+ (The Apache Software License, Version 2.0) Jackson-datatype-Hibernate5-jakarta (com.fasterxml.jackson.datatype:jackson-datatype-hibernate5-jakarta:2.18.2 - https://github.com/FasterXML/jackson-datatype-hibernate)
+ (The Apache Software License, Version 2.0) Jackson-JAXRS: base (com.fasterxml.jackson.jaxrs:jackson-jaxrs-base:2.18.2 - https://github.com/FasterXML/jackson-jaxrs-providers/jackson-jaxrs-base)
+ (The Apache Software License, Version 2.0) Jackson-module-parameter-names (com.fasterxml.jackson.module:jackson-module-parameter-names:2.18.2 - https://github.com/FasterXML/jackson-modules-java8/jackson-module-parameter-names)
(EDL 1.0) Jakarta Activation (com.sun.activation:jakarta.activation:2.0.1 - https://github.com/eclipse-ee4j/jaf/jakarta.activation)
(EDL 1.0) Jakarta Activation API (jakarta.activation:jakarta.activation-api:2.1.0 - https://github.com/eclipse-ee4j/jaf)
(EPL 2.0) (GPL2 w/ CPE) Jakarta Annotations API (jakarta.annotation:jakarta.annotation-api:2.1.1 - https://projects.eclipse.org/projects/ee4j.ca)
@@ -223,9 +224,9 @@ Lists of 403 third-party dependencies.
(The Apache Software License, Version 2.0) Jakarta Dependency Injection (jakarta.inject:jakarta.inject-api:2.0.1.MR - https://github.com/eclipse-ee4j/injection-api)
(Eclipse Public License v. 2.0) (GNU General Public License, version 2 with the GNU Classpath Exception) Jakarta Expression Language API (jakarta.el:jakarta.el-api:4.0.0 - https://projects.eclipse.org/projects/ee4j.el)
(Eclipse Public License v. 2.0) (GNU General Public License, version 2 with the GNU Classpath Exception) Jakarta Expression Language Implementation (org.glassfish:jakarta.el:4.0.2 - https://projects.eclipse.org/projects/ee4j.el)
- (Eclipse Distribution License v. 1.0) (Eclipse Public License v. 2.0) Jakarta Persistence API (jakarta.persistence:jakarta.persistence-api:3.0.0 - https://github.com/eclipse-ee4j/jpa-api)
+ (Eclipse Distribution License v. 1.0) (Eclipse Public License v. 2.0) Jakarta Persistence API (jakarta.persistence:jakarta.persistence-api:3.1.0 - https://github.com/eclipse-ee4j/jpa-api)
(EPL-2.0) (GPL-2.0-with-classpath-exception) Jakarta RESTful WS API (jakarta.ws.rs:jakarta.ws.rs-api:3.1.0 - https://github.com/eclipse-ee4j/jaxrs-api)
- (EPL 2.0) (GPL2 w/ CPE) Jakarta Servlet (jakarta.servlet:jakarta.servlet-api:5.0.0 - https://projects.eclipse.org/projects/ee4j.servlet)
+ (EPL 2.0) (GPL2 w/ CPE) Jakarta Servlet (jakarta.servlet:jakarta.servlet-api:6.1.0 - https://projects.eclipse.org/projects/ee4j.servlet)
(Eclipse Distribution License - v 1.0) Jakarta XML Binding API (jakarta.xml.bind:jakarta.xml.bind-api:3.0.1 - https://github.com/eclipse-ee4j/jaxb-api/jakarta.xml.bind-api)
(EPL 2.0) (GPL2 w/ CPE) jakarta.transaction API (jakarta.transaction:jakarta.transaction-api:2.0.0 - https://projects.eclipse.org/projects/ee4j.jta)
(BSD-3-Clause) janino (org.codehaus.janino:janino:3.1.7 - http://janino-compiler.github.io/janino/)
@@ -237,41 +238,41 @@ Lists of 403 third-party dependencies.
(The MIT License) Java SemVer (com.github.zafarkhaja:java-semver:0.9.0 - https://github.com/zafarkhaja/jsemver)
(The Apache Software License, Version 2.0) java-diff-utils (io.github.java-diff-utils:java-diff-utils:4.12 - https://github.com/java-diff-utils/java-diff-utils/java-diff-utils)
(CDDL/GPLv2+CE) JavaBeans Activation Framework API jar (javax.activation:javax.activation-api:1.2.0 - http://java.net/all/javax.activation-api/)
- (Apache License 2.0) (LGPL 2.1) (MPL 1.1) Javassist (org.javassist:javassist:3.29.2-GA - http://www.javassist.org/)
+ (Apache License 2.0) (LGPL 2.1) (MPL 1.1) Javassist (org.javassist:javassist:3.30.2-GA - https://www.javassist.org/)
(CDDL + GPLv2 with classpath exception) javax.annotation API (javax.annotation:javax.annotation-api:1.3.2 - http://jcp.org/en/jsr/detail?id=250)
(Eclipse Distribution License - v 1.0) JAXB Core (org.glassfish.jaxb:jaxb-core:3.0.2 - https://eclipse-ee4j.github.io/jaxb-ri/)
(Eclipse Distribution License - v 1.0) JAXB Runtime (org.glassfish.jaxb:jaxb-runtime:3.0.2 - https://eclipse-ee4j.github.io/jaxb-ri/)
(CDDL 1.1) (GPL2 w/ CPE) jaxb-api (javax.xml.bind:jaxb-api:2.3.1 - https://github.com/javaee/jaxb-spec/jaxb-api)
- (Apache License, version 2.0) JBoss Logging 3 (org.jboss.logging:jboss-logging:3.4.3.Final - http://www.jboss.org)
- (Apache License, Version 2.0) JCL 1.2 implemented over SLF4J (org.slf4j:jcl-over-slf4j:2.0.9 - http://www.slf4j.org)
+ (Apache License 2.0) JBoss Logging 3 (org.jboss.logging:jboss-logging:3.6.0.Final - http://www.jboss.org)
+ (Apache License, Version 2.0) JCL 1.2 implemented over SLF4J (org.slf4j:jcl-over-slf4j:2.0.16 - http://www.slf4j.org)
(Apache License, Version 2.0) jcommander (com.beust:jcommander:1.82 - https://jcommander.org)
- (Apache License 2.0) jdbi3 core (org.jdbi:jdbi3-core:3.41.2 - https://jdbi.org/jdbi3-parent/jdbi3-core/)
- (Apache License 2.0) jdbi3 guava (org.jdbi:jdbi3-guava:3.41.2 - https://jdbi.org/jdbi3-parent/jdbi3-guava/)
- (Apache License 2.0) jdbi3 sqlobject (org.jdbi:jdbi3-sqlobject:3.41.2 - https://jdbi.org/jdbi3-parent/jdbi3-sqlobject/)
- (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-connectors-apache5 (org.glassfish.jersey.connectors:jersey-apache5-connector:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-apache5-connector)
- (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-container-servlet (org.glassfish.jersey.containers:jersey-container-servlet:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-container-servlet)
- (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-container-servlet-core (org.glassfish.jersey.containers:jersey-container-servlet-core:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-container-servlet-core)
- (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:3.0.11 - 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:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/jersey-common)
- (Apache License, 2.0) (EPL 2.0) (Modified BSD) (The GNU General Public License (GPL), Version 2, With Classpath Exception) jersey-core-server (org.glassfish.jersey.core:jersey-server:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/jersey-server)
- (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-bean-validation (org.glassfish.jersey.ext:jersey-bean-validation:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-bean-validation)
- (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:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-entity-filtering)
- (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-metainf-services (org.glassfish.jersey.ext:jersey-metainf-services:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-metainf-services)
- (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-inject-hk2 (org.glassfish.jersey.inject:jersey-hk2:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-hk2)
- (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-jaxb (org.glassfish.jersey.media:jersey-media-jaxb:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-media-jaxb)
- (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:3.0.11 - 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:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-media-multipart)
- (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-test-framework-core (org.glassfish.jersey.test-framework:jersey-test-framework-core:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-test-framework-core)
- (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-test-framework-provider-inmemory (org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-inmemory:3.0.11 - https://projects.eclipse.org/projects/ee4j.jersey/project/project/jersey-test-framework-provider-inmemory)
- (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Http Utility (org.eclipse.jetty:jetty-http:11.0.16 - https://eclipse.dev/jetty/jetty-http)
- (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: IO Utility (org.eclipse.jetty:jetty-io:11.0.16 - https://eclipse.dev/jetty/jetty-io)
+ (Apache License 2.0) jdbi3 core (org.jdbi:jdbi3-core:3.47.0 - https://jdbi.org/jdbi3-parent/jdbi3-core/)
+ (Apache License 2.0) jdbi3 guava (org.jdbi:jdbi3-guava:3.47.0 - https://jdbi.org/jdbi3-parent/jdbi3-guava/)
+ (Apache License 2.0) jdbi3 sqlobject (org.jdbi:jdbi3-sqlobject:3.47.0 - https://jdbi.org/jdbi3-parent/jdbi3-sqlobject/)
+ (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-connectors-apache5 (org.glassfish.jersey.connectors:jersey-apache5-connector:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-apache5-connector)
+ (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-container-servlet (org.glassfish.jersey.containers:jersey-container-servlet:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-container-servlet)
+ (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-container-servlet-core (org.glassfish.jersey.containers:jersey-container-servlet-core:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-container-servlet-core)
+ (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:3.0.17 - 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:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/jersey-common)
+ (Apache License, 2.0) (EPL 2.0) (Modified BSD) (The GNU General Public License (GPL), Version 2, With Classpath Exception) jersey-core-server (org.glassfish.jersey.core:jersey-server:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/jersey-server)
+ (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-bean-validation (org.glassfish.jersey.ext:jersey-bean-validation:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-bean-validation)
+ (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:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-entity-filtering)
+ (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-metainf-services (org.glassfish.jersey.ext:jersey-metainf-services:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-metainf-services)
+ (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-inject-hk2 (org.glassfish.jersey.inject:jersey-hk2:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-hk2)
+ (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-jaxb (org.glassfish.jersey.media:jersey-media-jaxb:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-media-jaxb)
+ (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:3.0.17 - 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:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-media-multipart)
+ (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-test-framework-core (org.glassfish.jersey.test-framework:jersey-test-framework-core:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/jersey-test-framework-core)
+ (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-test-framework-provider-inmemory (org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-inmemory:3.0.17 - https://projects.eclipse.org/projects/ee4j.jersey/project/project/jersey-test-framework-provider-inmemory)
+ (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Http Utility (org.eclipse.jetty:jetty-http:11.0.24 - https://jetty.org/jetty-http)
+ (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: IO Utility (org.eclipse.jetty:jetty-io:11.0.24 - https://jetty.org/jetty-io)
(Apache Software License - Version 2.0) (Eclipse Public License - Version 1.0) Jetty :: Jakarta Servlet API and Schemas for JPMS and OSGi (org.eclipse.jetty.toolchain:jetty-jakarta-servlet-api:5.0.2 - https://eclipse.org/jetty/jetty-jakarta-servlet-api)
- (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Security (org.eclipse.jetty:jetty-security:11.0.16 - https://eclipse.dev/jetty/jetty-security)
- (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Server Core (org.eclipse.jetty:jetty-server:11.0.16 - https://eclipse.dev/jetty/jetty-server)
- (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Servlet Handling (org.eclipse.jetty:jetty-servlet:11.0.16 - https://eclipse.dev/jetty/jetty-servlet)
+ (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Security (org.eclipse.jetty:jetty-security:11.0.24 - https://jetty.org/jetty-security)
+ (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Server Core (org.eclipse.jetty:jetty-server:11.0.24 - https://jetty.org/jetty-server)
+ (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Servlet Handling (org.eclipse.jetty:jetty-servlet:11.0.24 - https://jetty.org/jetty-servlet)
(Apache Software License - Version 2.0) (Eclipse Public License - Version 1.0) Jetty :: SetUID Java (org.eclipse.jetty.toolchain.setuid:jetty-setuid-java:1.0.4 - https://eclipse.org/jetty/jetty-setuid-parent/jetty-setuid-java)
- (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Utilities (org.eclipse.jetty:jetty-util:11.0.16 - https://eclipse.dev/jetty/jetty-util)
- (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Utility Servlets and Filters (org.eclipse.jetty:jetty-servlets:11.0.16 - https://eclipse.dev/jetty/jetty-servlets)
+ (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Utilities (org.eclipse.jetty:jetty-util:11.0.24 - https://jetty.org/jetty-util)
+ (Apache Software License - Version 2.0) (Eclipse Public License - Version 2.0) Jetty :: Utility Servlets and Filters (org.eclipse.jetty:jetty-servlets:11.0.24 - https://jetty.org/jetty-servlets)
(Apache License, Version 2.0) JJWT :: API (io.jsonwebtoken:jjwt-api:0.11.5 - https://github.com/jwtk/jjwt/jjwt-api)
(Apache License, Version 2.0) JJWT :: Extensions :: Jackson (io.jsonwebtoken:jjwt-jackson:0.11.5 - https://github.com/jwtk/jjwt/jjwt-jackson)
(Apache License, Version 2.0) JJWT :: Impl (io.jsonwebtoken:jjwt-impl:0.11.5 - https://github.com/jwtk/jjwt/jjwt-impl)
@@ -279,41 +280,43 @@ Lists of 403 third-party dependencies.
(Apache License, Version 2.0) Joda-Time (joda-time:joda-time:2.12.5 - https://www.joda.org/joda-time/)
(Public Domain) JSON in Java (org.json:json:20231013 - https://github.com/douglascrockford/JSON-java)
(The Apache Software License, Version 2.0) JSON.simple (com.googlecode.json-simple:json-simple:1.1.1 - http://code.google.com/p/json-simple/)
+ (The MIT License) jsoup Java HTML Parser (org.jsoup:jsoup:1.19.1 - https://jsoup.org/)
(Apache License, Version 2.0) JSR 354 (Money and Currency API) (javax.money:money-api:1.1 - https://javamoney.github.io/)
- (MIT License) JUL to SLF4J bridge (org.slf4j:jul-to-slf4j:2.0.9 - http://www.slf4j.org)
+ (MIT License) JUL to SLF4J bridge (org.slf4j:jul-to-slf4j:2.0.16 - http://www.slf4j.org)
(Eclipse Public License 1.0) JUnit (junit:junit:4.13.2 - http://junit.org)
- (Eclipse Public License v2.0) JUnit Jupiter (Aggregator) (org.junit.jupiter:junit-jupiter:5.10.0 - https://junit.org/junit5/)
- (Eclipse Public License v2.0) JUnit Jupiter API (org.junit.jupiter:junit-jupiter-api:5.10.0 - https://junit.org/junit5/)
- (Eclipse Public License v2.0) JUnit Jupiter Engine (org.junit.jupiter:junit-jupiter-engine:5.10.0 - https://junit.org/junit5/)
- (Eclipse Public License v2.0) JUnit Jupiter Params (org.junit.jupiter:junit-jupiter-params:5.10.0 - https://junit.org/junit5/)
- (Eclipse Public License v2.0) JUnit Platform Commons (org.junit.platform:junit-platform-commons:1.10.0 - https://junit.org/junit5/)
- (Eclipse Public License v2.0) JUnit Platform Engine API (org.junit.platform:junit-platform-engine:1.10.0 - https://junit.org/junit5/)
- (Eclipse Public License v2.0) JUnit Vintage Engine (org.junit.vintage:junit-vintage-engine:5.10.0 - https://junit.org/junit5/)
- (Apache License 2.0) JVM Integration for Metrics (io.dropwizard.metrics:metrics-jvm:4.2.19 - https://metrics.dropwizard.io/metrics-jvm)
+ (Eclipse Public License v2.0) JUnit Jupiter (Aggregator) (org.junit.jupiter:junit-jupiter:5.11.4 - https://junit.org/junit5/)
+ (Eclipse Public License v2.0) JUnit Jupiter API (org.junit.jupiter:junit-jupiter-api:5.11.4 - https://junit.org/junit5/)
+ (Eclipse Public License v2.0) JUnit Jupiter Engine (org.junit.jupiter:junit-jupiter-engine:5.11.4 - https://junit.org/junit5/)
+ (Eclipse Public License v2.0) JUnit Jupiter Params (org.junit.jupiter:junit-jupiter-params:5.11.4 - https://junit.org/junit5/)
+ (Eclipse Public License v2.0) JUnit Platform Commons (org.junit.platform:junit-platform-commons:1.11.4 - https://junit.org/junit5/)
+ (Eclipse Public License v2.0) JUnit Platform Engine API (org.junit.platform:junit-platform-engine:1.11.4 - https://junit.org/junit5/)
+ (Eclipse Public License v2.0) JUnit Vintage Engine (org.junit.vintage:junit-vintage-engine:5.11.4 - https://junit.org/junit5/)
+ (Apache License 2.0) JVM Integration for Metrics (io.dropwizard.metrics:metrics-jvm:4.2.30 - https://metrics.dropwizard.io/metrics-jvm)
(The Apache License, Version 2.0) Kotlin Stdlib (org.jetbrains.kotlin:kotlin-stdlib:1.6.20 - https://kotlinlang.org/)
(The Apache License, Version 2.0) Kotlin Stdlib Common (org.jetbrains.kotlin:kotlin-stdlib-common:1.6.20 - https://kotlinlang.org/)
(The Apache License, Version 2.0) Kotlin Stdlib Jdk7 (org.jetbrains.kotlin:kotlin-stdlib-jdk7:1.5.31 - https://kotlinlang.org/)
(The Apache License, Version 2.0) Kotlin Stdlib Jdk8 (org.jetbrains.kotlin:kotlin-stdlib-jdk8:1.5.31 - https://kotlinlang.org/)
(The Apache Software License, Version 2.0) lang-mustache (org.elasticsearch.plugin:lang-mustache-client:7.10.2 - https://github.com/elastic/elasticsearch)
(WDL License https://github.com/openwdl/wdl/blob/master/LICENSE) language-factory-core (org.broadinstitute:language-factory-core_2.13:85 - no url defined)
- (Apache License, Version 2.0) Liquibase (org.liquibase:liquibase-core:4.23.0 - http://www.liquibase.com)
- (MIT License) liquibase-slf4j (com.mattbertolini:liquibase-slf4j:5.0.0 - https://github.com/mattbertolini/liquibase-slf4j)
- (Apache Software Licenses) Log4j Implemented Over SLF4J (org.slf4j:log4j-over-slf4j:2.0.9 - http://www.slf4j.org)
- (Eclipse Public License - v 1.0) (GNU Lesser General Public License) Logback Access Module (ch.qos.logback:logback-access:1.4.12 - http://logback.qos.ch/logback-access)
- (Eclipse Public License - v 1.0) (GNU Lesser General Public License) Logback Classic Module (ch.qos.logback:logback-classic:1.4.12 - http://logback.qos.ch/logback-classic)
- (Eclipse Public License - v 1.0) (GNU Lesser General Public License) Logback Core Module (ch.qos.logback:logback-core:1.4.12 - http://logback.qos.ch/logback-core)
+ (Apache License, Version 2.0) Liquibase (org.liquibase:liquibase-core:4.30.0 - http://www.liquibase.com)
+ (MIT License) liquibase-slf4j (com.mattbertolini:liquibase-slf4j:5.1.0 - https://github.com/mattbertolini/liquibase-slf4j)
+ (Apache Software Licenses) Log4j Implemented Over SLF4J (org.slf4j:log4j-over-slf4j:2.0.16 - http://www.slf4j.org)
+ (Eclipse Public License - v 1.0) (GNU Lesser General Public License) Logback Access Common Module (ch.qos.logback.access:logback-access-common:2.0.5 - http://logback.qos.ch/logback-access-common)
+ (Eclipse Public License - v 1.0) (GNU Lesser General Public License) Logback Access Jetty 11 Module (ch.qos.logback.access:logback-access-jetty11:2.0.5 - http://logback.qos.ch/logback-access-jetty11)
+ (Eclipse Public License - v 1.0) (GNU Lesser General Public License) Logback Classic Module (ch.qos.logback:logback-classic:1.5.16 - http://logback.qos.ch/logback-classic)
+ (Eclipse Public License - v 1.0) (GNU Lesser General Public License) Logback Core Module (ch.qos.logback:logback-core:1.5.16 - http://logback.qos.ch/logback-core)
(Apache License, Version 2.0) (MIT License) Logstash Logback Encoder (net.logstash.logback:logstash-logback-encoder:4.11 - https://github.com/logstash/logstash-logback-encoder)
(Apache License, Version 2.0) Lucene Core (org.apache.lucene:lucene-core:8.7.0 - https://lucene.apache.org/lucene-parent/lucene-core)
- (Apache License 2.0) Metrics Core (io.dropwizard.metrics:metrics-core:4.2.19 - https://metrics.dropwizard.io/metrics-core)
- (Apache License 2.0) Metrics Health Checks (io.dropwizard.metrics:metrics-healthchecks:4.2.19 - https://metrics.dropwizard.io/metrics-healthchecks)
- (Apache License 2.0) Metrics Integration for Apache HttpClient 5.x (io.dropwizard.metrics:metrics-httpclient5:4.2.19 - https://metrics.dropwizard.io/metrics-httpclient5)
- (Apache License 2.0) Metrics Integration for Caffeine 2.x (io.dropwizard.metrics:metrics-caffeine:4.2.19 - https://metrics.dropwizard.io/metrics-caffeine)
- (Apache License 2.0) Metrics Integration for JDBI3 (io.dropwizard.metrics:metrics-jdbi3:4.2.19 - https://metrics.dropwizard.io/metrics-jdbi3)
- (Apache License 2.0) Metrics Integration for Jersey 3.x (io.dropwizard.metrics:metrics-jersey3:4.2.19 - https://metrics.dropwizard.io/metrics-jersey3)
- (Apache License 2.0) Metrics Integration for Jetty 11.x and higher (io.dropwizard.metrics:metrics-jetty11:4.2.19 - https://metrics.dropwizard.io/metrics-jetty11)
- (Apache License 2.0) Metrics Integration for Logback (io.dropwizard.metrics:metrics-logback:4.2.19 - https://metrics.dropwizard.io/metrics-logback)
- (Apache License 2.0) Metrics Integration with JMX (io.dropwizard.metrics:metrics-jmx:4.2.19 - https://metrics.dropwizard.io/metrics-jmx)
- (Apache License 2.0) Metrics Utility Jakarta Servlets (io.dropwizard.metrics:metrics-jakarta-servlets:4.2.19 - https://metrics.dropwizard.io/metrics-jakarta-servlets)
+ (Apache License 2.0) Metrics Core (io.dropwizard.metrics:metrics-core:4.2.30 - https://metrics.dropwizard.io/metrics-core)
+ (Apache License 2.0) Metrics Health Checks (io.dropwizard.metrics:metrics-healthchecks:4.2.30 - https://metrics.dropwizard.io/metrics-healthchecks)
+ (Apache License 2.0) Metrics Integration for Apache HttpClient 5.x (io.dropwizard.metrics:metrics-httpclient5:4.2.30 - https://metrics.dropwizard.io/metrics-httpclient5)
+ (Apache License 2.0) Metrics Integration for Caffeine 2.x (io.dropwizard.metrics:metrics-caffeine:4.2.30 - https://metrics.dropwizard.io/metrics-caffeine)
+ (Apache License 2.0) Metrics Integration for JDBI3 (io.dropwizard.metrics:metrics-jdbi3:4.2.30 - https://metrics.dropwizard.io/metrics-jdbi3)
+ (Apache License 2.0) Metrics Integration for Jersey 3.x (io.dropwizard.metrics:metrics-jersey3:4.2.30 - https://metrics.dropwizard.io/metrics-jersey3)
+ (Apache License 2.0) Metrics Integration for Jetty 11.x and higher (io.dropwizard.metrics:metrics-jetty11:4.2.30 - https://metrics.dropwizard.io/metrics-jetty11)
+ (Apache License 2.0) Metrics Integration for Logback (io.dropwizard.metrics:metrics-logback:4.2.30 - https://metrics.dropwizard.io/metrics-logback)
+ (Apache License 2.0) Metrics Integration with JMX (io.dropwizard.metrics:metrics-jmx:4.2.30 - https://metrics.dropwizard.io/metrics-jmx)
+ (Apache License 2.0) Metrics Utility Jakarta Servlets (io.dropwizard.metrics:metrics-jakarta-servlets:4.2.30 - https://metrics.dropwizard.io/metrics-jakarta-servlets)
(The Apache Software License, Version 2.0) metrics3-statsd (com.readytalk:metrics3-statsd:4.2.0 - no url defined)
(Apache 2) metrics4-scala (nl.grons:metrics4-scala_2.13:4.2.8 - https://github.com/erikvanoosten/metrics-scala)
(Eclipse Distribution License - v 1.0) MIME streaming extension (org.jvnet.mimepull:mimepull:1.9.15 - https://github.com/eclipse-ee4j/metro-mimepull)
@@ -342,7 +345,7 @@ Lists of 403 third-party dependencies.
(The Apache Software License, Version 2.0) okio (com.squareup.okio:okio-jvm:3.0.0 - https://github.com/square/okio/)
(The Apache License, Version 2.0) OpenCensus (io.opencensus:opencensus-api:0.31.0 - https://github.com/census-instrumentation/opencensus-java)
(The Apache License, Version 2.0) OpenCensus (io.opencensus:opencensus-contrib-http-util:0.31.0 - https://github.com/census-instrumentation/opencensus-java)
- (Apache 2) opencsv (com.opencsv:opencsv:5.7.1 - http://opencsv.sf.net)
+ (Apache 2) opencsv (com.opencsv:opencsv:5.9 - http://opencsv.sf.net)
(Apache 2.0) optics (io.circe:circe-optics_2.13:0.14.1 - https://github.com/circe/circe-optics)
(MIT License) ORCID - Model (org.orcid:orcid-model-jakarta:3.3.0 - https://github.com/ORCID/orcid-model)
(The Apache License, Version 2.0) org.apiguardian:apiguardian-api (org.apiguardian:apiguardian-api:1.1.2 - https://github.com/apiguardian-team/apiguardian)
@@ -375,14 +378,14 @@ Lists of 403 third-party dependencies.
(MIT) Sentry SDK (io.sentry:sentry:5.7.4 - https://github.com/getsentry/sentry-java)
(MIT) Sentry SDK (io.sentry:sentry-logback:5.7.4 - https://github.com/getsentry/sentry-java)
(The Apache Software License, Version 2.0) server (org.elasticsearch:elasticsearch:7.10.2 - https://github.com/elastic/elasticsearch)
- (EPL 2.0) (GPL2 w/ CPE) ServiceLocator Default Implementation (org.glassfish.hk2:hk2-locator:3.0.4 - https://github.com/eclipse-ee4j/glassfish-hk2/hk2-locator)
- (MIT License) SLF4J API Module (org.slf4j:slf4j-api:2.0.9 - http://www.slf4j.org)
- (Apache License, Version 2.0) SnakeYAML (org.yaml:snakeyaml:2.0 - https://bitbucket.org/snakeyaml/snakeyaml)
+ (EPL 2.0) (GPL2 w/ CPE) ServiceLocator Default Implementation (org.glassfish.hk2:hk2-locator:3.0.6 - https://github.com/eclipse-ee4j/glassfish-hk2/hk2-locator)
+ (MIT License) SLF4J API Module (org.slf4j:slf4j-api:2.0.16 - http://www.slf4j.org)
+ (Apache License, Version 2.0) SnakeYAML (org.yaml:snakeyaml:2.3 - https://bitbucket.org/snakeyaml/snakeyaml)
(MIT) sourcecode_2.13 (com.lihaoyi:sourcecode_2.13:0.2.8 - https://github.com/lihaoyi/sourcecode)
- (GNU LESSER GENERAL PUBLIC LICENSE, Version 2.1) SpotBugs Annotations (com.github.spotbugs:spotbugs-annotations:4.7.3 - https://spotbugs.github.io/)
+ (GNU LESSER GENERAL PUBLIC LICENSE, Version 2.1) SpotBugs Annotations (com.github.spotbugs:spotbugs-annotations:4.8.6 - https://spotbugs.github.io/)
(Apache 2) spray-json (io.spray:spray-json_2.13:1.3.6 - https://github.com/spray/spray-json)
(Apache-2.0) ssl-config-core (com.typesafe:ssl-config-core_2.13:0.3.8 - https://github.com/lightbend/ssl-config)
- (The BSD License) Stax2 API (org.codehaus.woodstox:stax2-api:4.2.1 - http://github.com/FasterXML/stax2-api)
+ (The BSD 2-Clause License) Stax2 API (org.codehaus.woodstox:stax2-api:4.2.2 - http://github.com/FasterXML/stax2-api)
(Apache License 2.0) swagger-annotations (io.swagger:swagger-annotations:1.6.8 - https://github.com/swagger-api/swagger-core/modules/swagger-annotations)
(Apache License 2.0) swagger-annotations-jakarta (io.swagger.core.v3:swagger-annotations-jakarta:2.2.15 - https://github.com/swagger-api/swagger-core/modules/swagger-annotations-jakarta)
(Apache License 2.0) swagger-core (io.swagger:swagger-core:1.6.8 - https://github.com/swagger-api/swagger-core/modules/swagger-core)
@@ -393,11 +396,11 @@ Lists of 403 third-party dependencies.
(Apache License 2.0) swagger-models (io.swagger:swagger-models:1.6.8 - https://github.com/swagger-api/swagger-core/modules/swagger-models)
(Apache License 2.0) swagger-models-jakarta (io.swagger.core.v3:swagger-models-jakarta:2.2.15 - https://github.com/swagger-api/swagger-core/modules/swagger-models-jakarta)
(Common Public License Version 1.0) System Rules (com.github.stefanbirkner:system-rules:1.19.0 - http://stefanbirkner.github.io/system-rules/)
- (MIT License) System Stubs Core (uk.org.webcompere:system-stubs-core:2.0.1 - https://github.com/webcompere/system-stubs/system-stubs-core/)
- (MIT License) System Stubs Jupiter (uk.org.webcompere:system-stubs-jupiter:2.0.1 - https://github.com/webcompere/system-stubs/system-stubs-jupiter/)
- (Apache License 2.0) Throttling Appender (io.dropwizard.logback:logback-throttling-appender:1.4.0 - https://github.com/dropwizard/logback-throttling-appender/)
- (Apache License, Version 2.0) tomcat-jdbc (org.apache.tomcat:tomcat-jdbc:10.1.13 - https://tomcat.apache.org/)
- (Apache License, Version 2.0) tomcat-juli (org.apache.tomcat:tomcat-juli:10.1.13 - https://tomcat.apache.org/)
+ (MIT License) System Stubs Core (uk.org.webcompere:system-stubs-core:2.1.7 - https://github.com/webcompere/system-stubs/system-stubs-core/)
+ (MIT License) System Stubs Jupiter (uk.org.webcompere:system-stubs-jupiter:2.1.7 - https://github.com/webcompere/system-stubs/system-stubs-jupiter/)
+ (Apache License 2.0) Throttling Appender (io.dropwizard.logback:logback-throttling-appender:1.4.2 - https://github.com/dropwizard/logback-throttling-appender/)
+ (Apache License, Version 2.0) tomcat-jdbc (org.apache.tomcat:tomcat-jdbc:10.1.34 - https://tomcat.apache.org/)
+ (Apache License, Version 2.0) tomcat-juli (org.apache.tomcat:tomcat-juli:10.1.34 - https://tomcat.apache.org/)
(Eclipse Distribution License - v 1.0) TXW2 Runtime (org.glassfish.jaxb:txw2:3.0.2 - https://eclipse-ee4j.github.io/jaxb-ri/)
(WDL License https://github.com/openwdl/wdl/blob/master/LICENSE) wdl-biscayne (org.broadinstitute:wdl-biscayne_2.13:85 - 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)
diff --git a/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml b/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml
index 90ee7b489..cb6cebbc1 100644
--- a/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml
+++ b/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml
@@ -19,7 +19,7 @@
4.0.0
io.dockstore
dockstore-cli-integration-testing
- 1.16.0
+ 1.17.0
Apache Software License, Version 2.0
@@ -30,13 +30,13 @@
io.dockstore
dockstore-client
- 1.16.0
+ 1.17.0
compile
io.dockstore
dockstore-integration-testing
- 1.16.0
+ 1.17.0
tests
compile
@@ -49,13 +49,19 @@
io.dockstore
dockstore-common
- 1.16.0
+ 1.17.0
compile
+
+
+ com.auth0
+ java-jwt
+
+
io.dockstore
dockstore-webservice
- 1.16.0
+ 1.17.0
compile
@@ -67,19 +73,19 @@
io.dockstore
openapi-java-client
- 1.16.0
+ 1.17.0
compile
io.dropwizard
dropwizard-jdbi3
- 4.0.2
+ 4.0.12
compile
commons-io
commons-io
- 2.15.1
+ 2.18.0
compile
@@ -91,21 +97,21 @@
ch.qos.logback
logback-classic
- 1.4.12
+ 1.5.16
runtime
true
ch.qos.logback
logback-core
- 1.4.12
+ 1.5.16
runtime
true
com.fasterxml.jackson.dataformat
jackson-dataformat-cbor
- 2.15.2
+ 2.18.2
compile
diff --git a/dockstore-cli-integration-testing/pom.xml b/dockstore-cli-integration-testing/pom.xml
index 75c2ee41a..7f89e2d85 100644
--- a/dockstore-cli-integration-testing/pom.xml
+++ b/dockstore-cli-integration-testing/pom.xml
@@ -71,6 +71,12 @@
io.dockstore
dockstore-common
${dockstore-core.version}
+
+
+ com.auth0
+ java-jwt
+
+
io.dockstore
@@ -268,6 +274,8 @@
--add-opens java.base/java.base=ALL-UNNAMED
--add-opens java.base/java.lang.reflect=ALL-UNNAMED
--add-opens java.base/sun.nio.fs=ALL-UNNAMED
+
+ -Djava.security.manager=allow
-da:org.hibernate...
diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/ClientIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/ClientIT.java
index 3abb4d790..6d39bef34 100644
--- a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/ClientIT.java
+++ b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/ClientIT.java
@@ -405,7 +405,6 @@ void touchOnAllHelpMessages() throws IOException {
checkCommandForHelp(new String[] { WORKFLOW, LAUNCH }, false);
checkCommandForHelp(new String[] { WORKFLOW, VERSION_TAG }, false);
checkCommandForHelp(new String[] { WORKFLOW, UPDATE_WORKFLOW }, false);
- checkCommandForHelp(new String[] { WORKFLOW, "restub" }, false);
checkCommandForHelp(new String[] { WORKFLOW, DOWNLOAD }, true);
checkCommandForHelp(new String[] { WORKFLOW, LIST }, true);
@@ -425,7 +424,6 @@ void touchOnAllHelpMessages() throws IOException {
checkCommandForHelp(new String[] { WORKFLOW, VERSION_TAG }, true);
checkCommandForHelp(new String[] { WORKFLOW, UPDATE_WORKFLOW }, true);
checkCommandForHelp(new String[] { WORKFLOW, MANUAL_PUBLISH }, true);
- checkCommandForHelp(new String[] { WORKFLOW, "restub" }, true);
checkCommandForHelp(new String[] { WORKFLOW, STAR }, true);
checkCommandForHelp(new String[] { WORKFLOW, TEST_PARAMETER }, true);
checkCommandForHelp(new String[] { WORKFLOW, VERIFY }, true);
diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/GeneralWorkflowIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/GeneralWorkflowIT.java
index 5e6dbb8b3..567725883 100644
--- a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/GeneralWorkflowIT.java
+++ b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/GeneralWorkflowIT.java
@@ -185,38 +185,7 @@ void testRefreshAndPublishInvalid() throws Exception {
- /**
- * This tests that a restub will work on an unpublished, full workflow
- */
- @Test
- void testRestub() {
- // Refresh and then restub
- refreshByOrganizationReplacement(USER_2_USERNAME, Set.of(SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow"));
- Client.main(new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, REFRESH, ENTRY,
- SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow", SCRIPT_FLAG });
- Client.main(new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, "restub", ENTRY,
- SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow", SCRIPT_FLAG });
- final long count = testingPostgres.runSelectStatement("select count(*) from workflowversion", long.class);
- assertEquals(0, count, "there should be 0 workflow versions, there are " + count);
- }
-
- /**
- * This tests that a restub will not work on an published, full workflow
- */
- @Test
- void testRestubError() throws Exception {
- // Refresh and then restub
- refreshByOrganizationReplacement(USER_2_USERNAME, Set.of(SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow"));
- Client.main(new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, REFRESH, ENTRY,
- SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow", SCRIPT_FLAG });
- Client.main(new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, PUBLISH, ENTRY,
- SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow", SCRIPT_FLAG });
-
- int exitCode = catchSystemExit(() -> Client.main(new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, "restub", ENTRY,
- SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow", SCRIPT_FLAG }));
- assertEquals(Client.CLIENT_ERROR, exitCode);
- }
/**
* Tests updating workflow descriptor type when a workflow is FULL and when it is a STUB
@@ -314,10 +283,16 @@ void testRefreshRelatedConcepts() throws Exception {
// check that invalid
final long count4 = testingPostgres.runSelectStatement("select count(*) from workflowversion where valid='f'", long.class);
assertTrue(4 <= count4, "there should be at least 4 invalid versions, there are " + count4);
+ }
+
+ /**
+ * This test tests a bunch of different assumptions for how refresh should work for workflows
+ */
+ @Test
+ void testRefreshRelatedConceptsWdl() throws Exception {
+ // refresh all
+ refreshByOrganizationReplacement(USER_2_USERNAME, Set.of(SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow"));
- // Restub
- Client.main(new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, "restub", ENTRY,
- SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow", SCRIPT_FLAG });
// Update workflow to WDL
Client.main(
@@ -344,7 +319,7 @@ void testRefreshRelatedConcepts() throws Exception {
// should now not be able to publish
int exitCode = catchSystemExit(() -> Client.main(new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, PUBLISH, ENTRY,
- SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow", SCRIPT_FLAG }));
+ SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/hello-dockstore-workflow", SCRIPT_FLAG }));
assertEquals(Client.API_ERROR, exitCode);
}
@@ -458,25 +433,6 @@ void testGitLab() {
"select count(*) from workflow where actualdefaultversion = 'test' and author is null and email is null and description is null",
long.class);
assertEquals(0, count7, "The given workflow should now have contact info and description");
-
- // restub
- Client.main(new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, "restub", ENTRY,
- SourceControlEnum.GITLAB_COM + "/dockstore.test.user2/dockstore-workflow-example", SCRIPT_FLAG });
- final long count8 = testingPostgres.runSelectStatement(
- "select count(*) from workflow where mode='STUB' and sourcecontrol = '" + SourceControlEnum.GITLAB_COM
- + "' and organization = 'dockstore.test.user2' and repository = 'dockstore-workflow-example'", long.class);
- assertEquals(1, count8, "The workflow should now be a stub");
-
- // Convert to WDL workflow
- Client.main(
- new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, UPDATE_WORKFLOW, ENTRY,
- SourceControlEnum.GITLAB_COM + "/dockstore.test.user2/dockstore-workflow-example", "--descriptor-type", DescriptorTypeEnum.WDL.toString(),
- SCRIPT_FLAG });
-
- // Should now be a WDL workflow
- final long count9 = testingPostgres.runSelectStatement("select count(*) from workflow where descriptortype='wdl'", long.class);
- assertEquals(1, count9, "there should be no 1 wdl workflow" + count9);
-
}
@@ -543,28 +499,6 @@ void testTestParameterFile() {
"test.wdl.json", SCRIPT_FLAG });
final long count4 = testingPostgres.runSelectStatement("select count(*) from sourcefile where type='CWL_TEST_JSON'", long.class);
assertEquals(2, count4, "there should be two sourcefiles that are cwl test parameter files, there are " + count4);
-
- // Restub
- Client.main(new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, "restub", ENTRY,
- SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/parameter_test_workflow", SCRIPT_FLAG });
-
- // Change to WDL
- Client.main(
- new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, UPDATE_WORKFLOW, ENTRY,
- SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/parameter_test_workflow", "--descriptor-type", DescriptorTypeEnum.WDL.toString(),
- "--workflow-path", "Dockstore.wdl", SCRIPT_FLAG });
-
- // Should be no sourcefiles
- final long count5 = testingPostgres.runSelectStatement("select count(*) from sourcefile where type like '%_TEST_JSON'", long.class);
- assertEquals(0, count5, "there should be no source files that are test parameter files, there are " + count5);
-
- // Update version wdltest with test parameters
- Client.main(
- new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt"), WORKFLOW, TEST_PARAMETER, ENTRY,
- SourceControlEnum.GITHUB_COM + "/DockstoreTestUser2/parameter_test_workflow", VERSION, "wdltest", "--add",
- "test.wdl.json", SCRIPT_FLAG });
- final long count6 = testingPostgres.runSelectStatement("select count(*) from sourcefile where type='WDL_TEST_JSON'", long.class);
- assertEquals(1, count6, "there should be one sourcefile that is a wdl test parameter file, there are " + count6);
}
diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/GitHubAppToolIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/GitHubAppToolIT.java
index 08deb1047..7dae488c9 100644
--- a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/GitHubAppToolIT.java
+++ b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/GitHubAppToolIT.java
@@ -200,13 +200,6 @@ void versionTag() throws Exception {
assertTrue(systemErrRule.getText().contains("Command not supported for GitHub App entries"));
}
- @Test
- void restub() throws Exception {
- int exitCode = catchSystemExit(() -> Client.main(new String[]{WORKFLOW, "restub", ENTRY, ENTRY_PATH, CONFIG, ResourceHelpers.resourceFilePath("config_file2.txt")}));
- assertEquals(Client.COMMAND_ERROR, exitCode);
- assertTrue(systemErrRule.getOutput().getText().contains("Command not supported for GitHub App entries"), "looked like: " + systemErrRule.getOutput().getText());
- }
-
private void publishWorkflow() {
final ApiClient webClient = getWebClient(USER_2_USERNAME, testingPostgres);
final WorkflowsApi workflowApi = new WorkflowsApi(webClient);
diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java
index ae27f0a2a..e94603a9a 100644
--- a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java
+++ b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/MockedIT.java
@@ -75,6 +75,7 @@
@RunWith(PowerMockRunner.class)
@PrepareForTest({ Client.class, ToolClient.class, UsersApi.class })
@Category({ConfidentialTest.class, ToolTest.class })
+@Ignore("leave this till later, will likely need Mockito/Powermock specific-work for Java 21")
public class MockedIT {
@Rule
diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/WDLWorkflowIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/WDLWorkflowIT.java
index 214933c64..5b8f60947 100644
--- a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/WDLWorkflowIT.java
+++ b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/WDLWorkflowIT.java
@@ -97,7 +97,7 @@ void testRunningCheckerWDLWorkflow() throws IOException {
workflowApi.publish1(refresh.getId(), publishRequest);
// get test json
- String testVersion = "1.3.0";
+ String testVersion = "1.4.0";
// Also test that files can be gotten by owner even though it's hidden
List workflowVersions = refresh.getWorkflowVersions();
workflowVersions.stream().filter(v -> v.getName().equals(testVersion)).forEach(v -> v.setHidden(true));
diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/common/CLICommonTestUtilities.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/common/CLICommonTestUtilities.java
index 444dbc8e5..ab09c08e4 100644
--- a/dockstore-cli-integration-testing/src/test/java/io/dockstore/common/CLICommonTestUtilities.java
+++ b/dockstore-cli-integration-testing/src/test/java/io/dockstore/common/CLICommonTestUtilities.java
@@ -100,7 +100,7 @@ public static void dropAndCreateWithTestData(DropwizardTestSupport migrationList = Arrays
.asList("1.3.0.generated", "1.3.1.consistency", "test", "1.4.0", "1.5.0", "test_1.5.0", "1.6.0", "1.7.0",
- "1.8.0", "1.9.0", "1.10.0", "1.11.0", "1.12.0", "1.13.0", "1.14.0", "1.15.0", "1.16.0");
+ "1.8.0", "1.9.0", "1.10.0", "1.11.0", "1.12.0", "1.13.0", "1.14.0", "1.15.0", "1.16.0", "1.17.0");
CommonTestUtilities.runMigration(migrationList, application, dropwizardConfigurationFile);
}
@@ -201,7 +201,7 @@ private static void cleanStatePrivate1(DropwizardTestSupport4.0.0
io.dockstore
dockstore-cli-reports
- 1.16.0
+ 1.17.0
Apache Software License, Version 2.0
@@ -30,25 +30,31 @@
io.dockstore
dockstore-webservice
- 1.16.0
+ 1.17.0
compile
io.dockstore
dockstore-common
- 1.16.0
+ 1.17.0
compile
+
+
+ com.auth0
+ java-jwt
+
+
io.dockstore
dockstore-client
- 1.16.0
+ 1.17.0
compile
io.dockstore
dockstore-cli-integration-testing
- 1.16.0
+ 1.17.0
compile
diff --git a/dockstore-cli-reports/pom.xml b/dockstore-cli-reports/pom.xml
index 94ceb07e4..4bbb08bc9 100644
--- a/dockstore-cli-reports/pom.xml
+++ b/dockstore-cli-reports/pom.xml
@@ -35,6 +35,12 @@
io.dockstore
dockstore-common
${dockstore-core.version}
+
+
+ com.auth0
+ java-jwt
+
+
io.dockstore
diff --git a/dockstore-client/generated/src/main/resources/pom.xml b/dockstore-client/generated/src/main/resources/pom.xml
index 36e5ed221..a001b39ea 100644
--- a/dockstore-client/generated/src/main/resources/pom.xml
+++ b/dockstore-client/generated/src/main/resources/pom.xml
@@ -19,7 +19,7 @@
4.0.0
io.dockstore
dockstore-client
- 1.16.0
+ 1.17.0
Apache Software License, Version 2.0
@@ -30,7 +30,7 @@
org.glassfish.jersey.inject
jersey-hk2
- 3.0.11
+ 3.0.17
compile
@@ -66,31 +66,35 @@
io.dockstore
dockstore-common
- 1.16.0
+ 1.17.0
compile
org.postgresql
postgresql
+
+ com.auth0
+ java-jwt
+
io.dockstore
openapi-java-client
- 1.16.0
+ 1.17.0
compile
io.dockstore
openapi-java-wes-client
- 1.16.0
+ 1.17.0
compile
io.dockstore
dockstore-file-plugin-parent
- 1.16.0
+ 1.17.0
compile
@@ -102,7 +106,7 @@
org.apache.commons
commons-lang3
- 3.14.0
+ 3.17.0
compile
@@ -114,7 +118,7 @@
com.google.guava
guava
- 32.1.2-jre
+ 33.4.0-jre
compile
@@ -126,7 +130,7 @@
commons-io
commons-io
- 2.15.1
+ 2.18.0
compile
@@ -138,31 +142,31 @@
org.apache.commons
commons-text
- 1.11.0
+ 1.13.0
compile
com.fasterxml.jackson.core
jackson-databind
- 2.15.2
+ 2.18.2
compile
com.fasterxml.jackson.jaxrs
jackson-jaxrs-base
- 2.15.2
+ 2.18.2
compile
com.fasterxml.jackson.core
jackson-core
- 2.15.2
+ 2.18.2
compile
io.cwl
cwlavro-tools
- 2.0.4.9
+ 2.1.0
compile
@@ -178,7 +182,7 @@
io.cwl
cwlavro-generated
- 2.0.4.9
+ 2.1.0
compile
@@ -218,20 +222,20 @@
org.slf4j
slf4j-api
- 2.0.9
+ 2.0.16
compile
ch.qos.logback
logback-classic
- 1.4.12
+ 1.5.16
compile
true
org.yaml
snakeyaml
- 2.0
+ 2.3
compile
@@ -273,7 +277,7 @@
org.apache.commons
commons-vfs2
- 2.9.0
+ 2.10.0
compile
@@ -301,13 +305,13 @@
org.apache.httpcomponents.client5
httpclient5
- 5.2.1
+ 5.4.1
compile
com.github.spotbugs
spotbugs-annotations
- 4.7.3
+ 4.8.6
compile
@@ -355,7 +359,7 @@
org.glassfish.jersey.media
jersey-media-multipart
- 3.0.11
+ 3.0.17
compile
diff --git a/dockstore-client/pom.xml b/dockstore-client/pom.xml
index b7cbec466..eae138644 100644
--- a/dockstore-client/pom.xml
+++ b/dockstore-client/pom.xml
@@ -73,6 +73,10 @@
org.postgresql
postgresql
+
+ com.auth0
+ java-jwt
+
@@ -131,6 +135,8 @@
commons-io
commons-io
+
+ 2.18.0
org.apache.commons
@@ -271,7 +277,7 @@
org.apache.commons
commons-vfs2
- 2.9.0
+ 2.10.0
commons-httpclient
@@ -529,6 +535,8 @@
--add-opens java.base/java.io=ALL-UNNAMED
--add-opens java.base/java.util=ALL-UNNAMED
--add-opens java.base/java.base=ALL-UNNAMED
+
+ -Djava.security.manager=allow
${skipITs}
${excludeGroups}
diff --git a/dockstore-client/src/main/java/io/dockstore/client/cli/nested/AbstractEntryClient.java b/dockstore-client/src/main/java/io/dockstore/client/cli/nested/AbstractEntryClient.java
index b63587c58..649e07960 100644
--- a/dockstore-client/src/main/java/io/dockstore/client/cli/nested/AbstractEntryClient.java
+++ b/dockstore-client/src/main/java/io/dockstore/client/cli/nested/AbstractEntryClient.java
@@ -221,7 +221,7 @@ boolean getIgnoreChecksums() {
public CWL getCwlUtil() {
// TODO: may be reactivated if we find a different way to read CWL into Java
// String cwlrunner = CWLRunnerFactory.getCWLRunner();
- return new CWL(false, Utilities.parseConfig(getConfigFile()));
+ return new CWL(Utilities.parseConfig(getConfigFile()));
}
public abstract String getConfigFile();
diff --git a/dockstore-client/src/main/java/io/dockstore/client/cli/nested/WorkflowClient.java b/dockstore-client/src/main/java/io/dockstore/client/cli/nested/WorkflowClient.java
index c24c86d20..994752702 100644
--- a/dockstore-client/src/main/java/io/dockstore/client/cli/nested/WorkflowClient.java
+++ b/dockstore-client/src/main/java/io/dockstore/client/cli/nested/WorkflowClient.java
@@ -110,7 +110,8 @@ public class WorkflowClient extends AbstractEntryClient {
public static final String LAUNCH_COMMAND_NAME = LAUNCH;
public static final String GITHUB_APP_COMMAND_ERROR = "Command not supported for GitHub App entries";
public static final String UPDATE_WORKFLOW = "update_workflow";
- public static final String RESTUB = "restub";
+
+
protected static final Logger LOG = LoggerFactory.getLogger(WorkflowClient.class);
protected final WorkflowsApi workflowsApi;
protected final UsersApi usersApi;
@@ -281,8 +282,6 @@ protected void printClientSpecificHelp() {
out("");
out(" " + VERSION_TAG + " : updates an existing version tag of a workflow");
out("");
- out(" restub : converts a full, unpublished workflow back to a stub");
- out("");
}
@Override
@@ -907,7 +906,7 @@ protected void handleList() {
protected List getClientSpecificCommands() {
List possibleCommands = new ArrayList<>();
- possibleCommands.addAll(Arrays.asList(UPDATE_WORKFLOW, VERSION_TAG, RESTUB));
+ possibleCommands.addAll(Arrays.asList(UPDATE_WORKFLOW, VERSION_TAG));
return possibleCommands;
}
@@ -922,9 +921,6 @@ public boolean processEntrySpecificCommands(List args, String activeComm
case VERSION_TAG:
versionTag(args);
break;
- case RESTUB:
- restub(args);
- break;
default:
return false;
}
@@ -1041,7 +1037,7 @@ private void updateWorkflow(List args) {
workflow.setDescriptorType(Workflow.DescriptorTypeEnum.fromValue(descriptorType.toUpperCase()));
} else if (!descriptorType.equalsIgnoreCase(workflow.getDescriptorType().getValue())) {
errorMessage(
- "You cannot change the descriptor type of a FULL workflow. Revert it to a STUB if you wish to change descriptor type.",
+ "You cannot change the descriptor type of a FULL workflow.",
Client.CLIENT_ERROR);
}
@@ -1164,47 +1160,6 @@ protected void versionTag(List args) {
}
}
- private void restub(List args) {
- if (args.isEmpty() || args.contains(HELP) || args.contains("-h")) {
- restubHelp();
- } else {
- try {
- final String entry = reqVal(args, ENTRY);
- Workflow workflow = findAndGetDockstoreWorkflowByPath(entry, null, false, true);
- if (this.isAppTool) {
- errorMessage(GITHUB_APP_COMMAND_ERROR, COMMAND_ERROR);
- }
-
- if (workflow.isIsPublished()) {
- errorMessage("Cannot restub a published workflow. Please unpublish if you wish to restub.", Client.CLIENT_ERROR);
- }
-
- if (workflow.getMode() == Workflow.ModeEnum.STUB) {
- errorMessage("The given workflow is already a stub.", Client.CLIENT_ERROR);
- }
-
- workflowsApi.restub(workflow.getId());
- out("The workflow " + workflow.getPath() + " has been converted back to a stub.");
- } catch (ApiException ex) {
- exceptionMessage(ex, "", Client.API_ERROR);
- }
- }
- }
-
- private void restubHelp() {
- printHelpHeader();
- out("Usage: dockstore workflow restub " + HELP);
- out(" dockstore workflow restub [parameters]");
- out("");
- out("Description:");
- out(" Converts a full, unpublished workflow back to a stub.");
- out("");
- out("Required Parameters:");
- out(" " + ENTRY + " Complete workflow path in Dockstore (ex. quay.io/collaboratory/seqware-bwa-workflow)");
- out("");
- printHelpFooter();
- }
-
public SourceFile getDescriptorFromServer(String entry, DescriptorLanguage descriptorType) throws ApiException {
String[] parts = entry.split(":");
diff --git a/dockstore-client/src/main/java/io/dockstore/common/ToilOnlyTest.java b/dockstore-client/src/main/java/io/dockstore/common/ToilOnlyTest.java
new file mode 100644
index 000000000..495f5c07d
--- /dev/null
+++ b/dockstore-client/src/main/java/io/dockstore/common/ToilOnlyTest.java
@@ -0,0 +1,10 @@
+package io.dockstore.common;
+
+public interface ToilOnlyTest {
+
+ String NAME = "io.dockstore.common.ToilOnlyTest";
+
+ default String getName() {
+ return NAME;
+ }
+}
diff --git a/dockstore-client/src/main/java/io/github/collaboratory/cwl/CWLClient.java b/dockstore-client/src/main/java/io/github/collaboratory/cwl/CWLClient.java
index a71380899..8c5a454b2 100644
--- a/dockstore-client/src/main/java/io/github/collaboratory/cwl/CWLClient.java
+++ b/dockstore-client/src/main/java/io/github/collaboratory/cwl/CWLClient.java
@@ -177,7 +177,7 @@ public File provisionInputFiles() {
Class cwlClassTarget = getCWLClassTarget();
// Load CWL from JSON to object
- CWL cwlUtil = new CWL(false, config);
+ CWL cwlUtil = new CWL(config);
// This won't work since I am using zip files, it is expecting files to be unzipped
final String imageDescriptorContent = cwlUtil.parseCWL(localPrimaryDescriptorFile.getAbsolutePath()).getLeft();
Object cwlObject = null;
diff --git a/dockstore-client/src/main/java/io/github/collaboratory/cwl/cwlrunner/ToilWrapper.java b/dockstore-client/src/main/java/io/github/collaboratory/cwl/cwlrunner/ToilWrapper.java
index 3dc47b7e5..b993442ce 100644
--- a/dockstore-client/src/main/java/io/github/collaboratory/cwl/cwlrunner/ToilWrapper.java
+++ b/dockstore-client/src/main/java/io/github/collaboratory/cwl/cwlrunner/ToilWrapper.java
@@ -22,6 +22,8 @@
import io.dockstore.client.cli.ArgumentUtility;
import io.dockstore.client.cli.Client;
import io.dockstore.openapi.client.api.MetadataApi;
+import java.nio.file.Path;
+import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
@@ -35,9 +37,9 @@ public void checkForCWLDependencies(MetadataApi metadataApi) {
final ImmutablePair pair1 = io.cwl.avro.Utilities
.executeCommand(Joiner.on(" ").join(Arrays.asList(s1)), false, com.google.common.base.Optional.absent(),
com.google.common.base.Optional.absent());
- final String toilVersion = pair1.getValue().trim();
+ final String toilVersion = pair1.getKey().trim();
- final String expectedToilVersion = "3.15.0";
+ final String expectedToilVersion = "7.0.0";
if (!toilVersion.equals(expectedToilVersion)) {
ArgumentUtility.errorMessage("toil version is " + toilVersion + " , Dockstore is tested with " + expectedToilVersion
+ "\nOverride and run with `" + SCRIPT_FLAG + "`", Client.COMMAND_ERROR);
@@ -49,9 +51,15 @@ public List getExecutionCommand(String outputDir, String tmpDir, String
//TODO: this doesn't quite work yet, seeing "toil.batchSystems.abstractBatchSystem.InsufficientSystemResources: Requesting more disk
// than either physically available, or enforced by --maxDisk. Requested: 537944653824, Available: 134853001216" on trivial
// workflows like md5sum
+
+ //try normalizing paths
+ Path currentRelativePath = Path.of("");
+ Path tmpPath = Paths.get(currentRelativePath.toAbsolutePath().toString(), tmpDir);
+ tmpPath = tmpPath.normalize();
+
ArrayList command = new ArrayList<>(
- Arrays.asList("toil-cwl-runner", "--logError", "--outdir", outputDir, "--tmpdir-prefix", tmpDir, "--tmp-outdir-prefix",
- workingDir, cwlFile));
+ Arrays.asList("toil-cwl-runner", "--bypass-file-store", "--logError", "--outdir", outputDir, "--tmpdir-prefix", tmpPath.toString(), "--tmp-outdir-prefix",
+ workingDir, cwlFile));
jsonSettings.ifPresent(command::add);
return command;
}
diff --git a/dockstore-client/src/test/java/io/dockstore/client/cli/YamlValidatorTest.java b/dockstore-client/src/test/java/io/dockstore/client/cli/YamlValidatorTest.java
index 1217ec963..2b35b7a3f 100644
--- a/dockstore-client/src/test/java/io/dockstore/client/cli/YamlValidatorTest.java
+++ b/dockstore-client/src/test/java/io/dockstore/client/cli/YamlValidatorTest.java
@@ -90,7 +90,7 @@ void relativePrimaryPathYml() {
YamlVerifyUtility.dockstoreValidate(relativePathDockstoreYmlDirectory);
fail("Invalid YAML not caught");
} catch (YamlVerifyUtility.ValidateYamlException ex) {
- assertTrue(ex.getMessage().contains("the path must be an absolute path to be valid"));
+ assertTrue(ex.getMessage().contains("must be an absolute path to be valid"));
}
}
@@ -103,7 +103,7 @@ void relativeTestDescriptorPathYml() {
YamlVerifyUtility.dockstoreValidate(relativePathDockstoreYmlDirectory);
fail("Invalid YAML not caught");
} catch (YamlVerifyUtility.ValidateYamlException ex) {
- assertTrue(ex.getMessage().contains("the path must be an absolute path to be valid"));
+ assertTrue(ex.getMessage().contains("must be an absolute path to be valid"));
}
}
@@ -269,7 +269,7 @@ void invalidSubclass() {
// The below part of the error message is generated by this line,
// https://github.com/dockstore/dockstore-cli/blob/5aac6e6d221b7618bc9769a95834f73f37f75aaf/dockstore-client/src/main/java/io/dockstore/client/cli/YamlVerifyUtility.java#L188
+ "Property \"workflows[0].subclass\" must be a supported descriptor language (\"CWL\", \"WDL\", "
- + "\"GALAXY\", or \"NFL\") (current value: \"INVALID_SUBCLASS\")";
+ + "\"GALAXY\", \"SMK\", or \"NFL\") (current value: \"INVALID_SUBCLASS\")";
assertEquals(errorMsg, ex.getMessage());
}
}
diff --git a/dockstore-client/src/test/java/io/github/collaboratory/cwl/ToilLauncherIT.java b/dockstore-client/src/test/java/io/github/collaboratory/cwl/ToilLauncherIT.java
index 5f996f75e..7c28118b3 100644
--- a/dockstore-client/src/test/java/io/github/collaboratory/cwl/ToilLauncherIT.java
+++ b/dockstore-client/src/test/java/io/github/collaboratory/cwl/ToilLauncherIT.java
@@ -15,14 +15,16 @@
*/
package io.github.collaboratory.cwl;
+import io.dockstore.common.ToilOnlyTest;
import org.apache.commons.io.FileUtils;
-import org.junit.Ignore;
+import org.junit.experimental.categories.Category;
+import org.junit.jupiter.api.Tag;
/**
* @author dyuen
*/
-@Ignore
-// @Category(ToilOnlyTest.class)
+@Tag(ToilOnlyTest.NAME)
+@Category(ToilOnlyTest.class)
public class ToilLauncherIT extends LauncherIT {
public String getConfigFile() {
diff --git a/dockstore-client/src/test/resources/testDirectory3/mutect.cwl b/dockstore-client/src/test/resources/testDirectory3/mutect.cwl
index 116b98239..d791ef89c 100644
--- a/dockstore-client/src/test/resources/testDirectory3/mutect.cwl
+++ b/dockstore-client/src/test/resources/testDirectory3/mutect.cwl
@@ -10,7 +10,7 @@ doc: "Mutect 1.1.5"
hints:
- class: DockerRequirement
- dockerPull: quay.io/jeltje/mutect
+ dockerPull: quay.io/dockstore-testing/mutect
requirements:
- class: InlineJavascriptRequirement
diff --git a/dockstore-file-plugin-parent/generated/src/main/resources/pom.xml b/dockstore-file-plugin-parent/generated/src/main/resources/pom.xml
index a2ee737d2..429ebcfa9 100644
--- a/dockstore-file-plugin-parent/generated/src/main/resources/pom.xml
+++ b/dockstore-file-plugin-parent/generated/src/main/resources/pom.xml
@@ -19,7 +19,7 @@
4.0.0
io.dockstore
dockstore-file-plugin-parent
- 1.16.0
+ 1.17.0
Apache Software License, Version 2.0
@@ -36,7 +36,7 @@
org.apache.commons
commons-lang3
- 3.14.0
+ 3.17.0
compile
diff --git a/keysmap.list b/keysmap.list
index 7915ec3e4..b499519c9 100644
--- a/keysmap.list
+++ b/keysmap.list
@@ -1,34 +1,24 @@
io.swagger.core.v3:swagger-annotations:jar:2.1.7 = noSig
-com.fasterxml.jackson.datatype:jackson-datatype-joda:pom:2.12.1 = badSig
-com.fasterxml.jackson.core:jackson-databind:pom:2.12.1 = badSig
-com.fasterxml.jackson.core:jackson-annotations:pom:2.12.1 = badSig
-com.fasterxml.jackson.core:jackson-core:pom:2.12.1 = badSig
-com.fasterxml.jackson.dataformat:jackson-dataformat-xml:pom:2.12.1 = badSig
-com.fasterxml.jackson.datatype:jackson-datatype-joda:pom:2.13.4 = badSig
-com.fasterxml.jackson.core:jackson-databind:pom:2.13.4 = badSig
-com.fasterxml.jackson.core:jackson-annotations:pom:2.13.4 = badSig
-com.fasterxml.jackson.core:jackson-core:pom:2.13.4 = badSig
-com.fasterxml.jackson.dataformat:jackson-dataformat-xml:pom:2.13.4 = badSig
-com.fasterxml.jackson.datatype:jackson-datatype-joda:pom:2.13.4.2 = badSig
-com.fasterxml.jackson.core:jackson-databind:pom:2.13.4.2 = badSig
-com.fasterxml.jackson.core:jackson-annotations:pom:2.13.4.2 = badSig
-com.fasterxml.jackson.core:jackson-core:pom:2.13.4.2 = badSig
-com.fasterxml.jackson.dataformat:jackson-dataformat-xml:pom:2.13.4.2 = badSig
-com.fasterxml.jackson.datatype:jackson-datatype-joda:pom:2.13.5 = badSig
-com.fasterxml.jackson.core:jackson-databind:pom:2.13.5 = badSig
-com.fasterxml.jackson.core:jackson-annotations:pom:2.13.5 = badSig
-com.fasterxml.jackson.core:jackson-core:pom:2.13.5 = badSig
-com.fasterxml.jackson.dataformat:jackson-dataformat-xml:pom:2.13.5 = badSig
-com.fasterxml.jackson.datatype:jackson-datatype-joda:pom:2.14.2 = badSig
-com.fasterxml.jackson.core:jackson-databind:pom:2.14.2 = badSig
-com.fasterxml.jackson.core:jackson-annotations:pom:2.14.2 = badSig
-com.fasterxml.jackson.core:jackson-core:pom:2.14.2 = badSig
-com.fasterxml.jackson.dataformat:jackson-dataformat-xml:pom:2.14.2 = badSig
com.fasterxml.jackson.datatype:jackson-datatype-joda:pom:2.15.2 = badSig
com.fasterxml.jackson.core:jackson-databind:pom:2.15.2 = badSig
com.fasterxml.jackson.core:jackson-annotations:pom:2.15.2 = badSig
com.fasterxml.jackson.core:jackson-core:pom:2.15.2 = badSig
com.fasterxml.jackson.dataformat:jackson-dataformat-xml:pom:2.15.2 = badSig
+com.fasterxml.jackson.datatype:jackson-datatype-joda:pom:2.17.2 = badSig
+com.fasterxml.jackson.core:jackson-databind:pom:2.17.2 = badSig
+com.fasterxml.jackson.core:jackson-annotations:pom:2.17.2 = badSig
+com.fasterxml.jackson.core:jackson-core:pom:2.17.2 = badSig
+com.fasterxml.jackson.dataformat:jackson-dataformat-xml:pom:2.17.2 = badSig
+com.fasterxml.jackson.datatype:jackson-datatype-joda:pom:2.18.1 = badSig
+com.fasterxml.jackson.core:jackson-databind:pom:2.18.1 = badSig
+com.fasterxml.jackson.core:jackson-annotations:pom:2.18.1 = badSig
+com.fasterxml.jackson.core:jackson-core:pom:2.18.1 = badSig
+com.fasterxml.jackson.dataformat:jackson-dataformat-xml:pom:2.18.1 = badSig
+com.fasterxml.jackson.datatype:jackson-datatype-joda:pom:2.18.2 = badSig
+com.fasterxml.jackson.core:jackson-databind:pom:2.18.2 = badSig
+com.fasterxml.jackson.core:jackson-annotations:pom:2.18.2 = badSig
+com.fasterxml.jackson.core:jackson-core:pom:2.18.2 = badSig
+com.fasterxml.jackson.dataformat:jackson-dataformat-xml:pom:2.18.2 = badSig
org.broadinstitute:wdl-draft3_2.13:pom:84 = badSig
org.broadinstitute:wdl-biscayne_2.13:pom:84 = badSig
@@ -71,6 +61,8 @@ org.broadinstitute:cromwell-wdl-transforms-draft2_2.13:jar:84 = badSig
org.kohsuke:github-api:pom:1.322 = badSig
org.kohsuke:github-api:pom:1.313 = badSig
org.kohsuke:github-api:pom:1.123 = badSig
+com.auth0:java-jwt:pom:3.8.1 = noKey
+com.auth0:java-jwt:jar:3.8.1 = noKey
com.spotify:docker-client:pom:8.16.0 = badSig
org.eclipse.jetty.toolchain:jetty-servlet-api:pom:4.0.6 = badSig
org.eclipse.jetty.toolchain:jetty-jakarta-servlet-api:pom:5.0.2 = badSig
diff --git a/openapi-java-wes-client/generated/src/main/resources/pom.xml b/openapi-java-wes-client/generated/src/main/resources/pom.xml
index fe8ba92e6..88743998c 100644
--- a/openapi-java-wes-client/generated/src/main/resources/pom.xml
+++ b/openapi-java-wes-client/generated/src/main/resources/pom.xml
@@ -19,7 +19,7 @@
4.0.0
io.dockstore
openapi-java-wes-client
- 1.16.0
+ 1.17.0
Apache Software License, Version 2.0
@@ -36,19 +36,19 @@
org.glassfish.jersey.core
jersey-client
- 3.0.11
+ 3.0.17
compile
org.glassfish.jersey.media
jersey-media-multipart
- 3.0.11
+ 3.0.17
compile
org.glassfish.jersey.media
jersey-media-json-jackson
- 3.0.11
+ 3.0.17
compile
@@ -60,25 +60,25 @@
com.fasterxml.jackson.core
jackson-core
- 2.15.2
+ 2.18.2
compile
com.fasterxml.jackson.core
jackson-annotations
- 2.15.2
+ 2.18.2
compile
com.fasterxml.jackson.core
jackson-databind
- 2.15.2
+ 2.18.2
compile
org.glassfish.jersey.core
jersey-common
- 3.0.11
+ 3.0.17
compile
@@ -90,7 +90,7 @@
com.fasterxml.jackson.datatype
jackson-datatype-jsr310
- 2.15.2
+ 2.18.2
compile
diff --git a/pom.xml b/pom.xml
index bb695961d..9834f759f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -33,12 +33,12 @@
-->
- 1.16
+ 1.17
.0-SNAPSHOT
scm:git:git@github.com:dockstore/dockstore-cli.git
UTF-8
- 1.16.0
+ 1.17.0
2.22.2
2.22.2
false
@@ -53,7 +53,7 @@
${project.basedir}/target/jacoco.xml,${project.basedir}/target/jacoco-it.xml,${project.basedir}/../dockstore-cli-reports/target/site/jacoco-aggregate/jacoco.xml
- 2.0.4.9
+ 2.1.0
@@ -84,7 +84,7 @@
false
-
+
broad-dependencies.oicr.on.ca
broad-dependencies.oicr.on.ca
https://artifacts.oicr.on.ca/artifactory/broad-dependencies
@@ -200,28 +200,24 @@
-
-
- org.apache.commons
- commons-compress
- 1.26.0
-
-
- org.apache.commons
- commons-text
- 1.11.0
-
commons-io
commons-io
- 2.15.1
+
+ 2.18.0
+
+
+ commons-logging
+ commons-logging
+
+ 1.3.4
org.apache.commons
- commons-lang3
- 3.14.0
+ commons-vfs2
+
+ 2.10.0
-
@@ -232,7 +228,7 @@
org.jacoco
jacoco-maven-plugin
- 0.8.11
+ 0.8.12
com.googlecode.maven-download-plugin
@@ -366,6 +362,10 @@
random
1
+
+ -Djava.security.manager=allow
+ @{argLine}
+
@@ -378,6 +378,10 @@
random
1
+
+ -Djava.security.manager=allow
+ @{argLine}
+
@@ -446,7 +450,7 @@
org.codehaus.mojo
versions-maven-plugin
- 2.10.0
+ 2.18.0
org.codehaus.mojo
@@ -456,7 +460,7 @@
org.simplify4u.plugins
pgpverify-maven-plugin
- 1.17.0
+ 1.18.2
org.codehaus.mojo
diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh
index 579ee9307..1747c22ef 100755
--- a/scripts/install-tests.sh
+++ b/scripts/install-tests.sh
@@ -12,9 +12,17 @@ if [ "${TESTING_PROFILE}" = "unit-tests" ] || [ "${TESTING_PROFILE}" == "automat
fi
if [ "${TESTING_PROFILE}" = "toil-integration-tests" ]; then
- pip3 install --user toil[cwl]==3.15.0
+ pip3 install --user toil[cwl]==7.0.0
else
- pip3 install --user -r https://raw.githubusercontent.com/dockstore/dockstore/develop/dockstore-webservice/src/main/resources/requirements/1.15.0/requirements3.txt
+ sudo apt-get update
+ # https://stackoverflow.com/questions/44331836/apt-get-install-tzdata-noninteractive needed by cwltool
+ DEBIAN_FRONTEND=noninteractive sudo apt-get -qq --yes --force-yes install tzdata pipx curl
+ curl -o requirements.txt "https://dockstore.org/api/metadata/runner_dependencies?client_version=1.16.0&python_version=3"
+ pipx install cwltool==3.1.20240708091337
+ pipx install schema_salad==8.7.20240718183047
+ pipx install cwlref-runner
+ pipx runpip cwltool install -r requirements.txt # this ensures that your version of cwltool and its dependencies matches what we test with
+ pipx ensurepath
fi
if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then
diff --git a/support/generated/src/main/resources/pom.xml b/support/generated/src/main/resources/pom.xml
index 01c1a4ca2..f57af30f0 100644
--- a/support/generated/src/main/resources/pom.xml
+++ b/support/generated/src/main/resources/pom.xml
@@ -19,7 +19,7 @@
4.0.0
io.dockstore
support
- 1.16.0
+ 1.17.0
Apache Software License, Version 2.0
@@ -72,7 +72,7 @@
com.google.guava
guava
- 32.1.2-jre
+ 33.4.0-jre
compile