diff --git a/.github/collab-mvn-settings.xml b/.github/collab-mvn-settings.xml deleted file mode 100644 index 711bbdc0..00000000 --- a/.github/collab-mvn-settings.xml +++ /dev/null @@ -1,9 +0,0 @@ - - - - central - dockstore-bot - ${env.COLLAB_DEPLOY_TOKEN} - - - diff --git a/.github/workflows/deploy_artifacts.yml b/.github/workflows/deploy_artifacts.yml new file mode 100644 index 00000000..ba7a61a7 --- /dev/null +++ b/.github/workflows/deploy_artifacts.yml @@ -0,0 +1,20 @@ +name: Deploy artifacts + +on: + push: + tags: + - '**' + # Run for all branches except the following + branches-ignore: + - 'master' + - 'release/**' + - 'hotfix/**' + - 'dependabot/**' + +jobs: + deploy_artifacts: + uses: dockstore/workflow-actions/.github/workflows/deploy_artifacts.yaml@seab-6771/reusable-image-deploy + with: + createDockerImage: true + quayRepository: dockstore-support + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/deploy_tagged.yml b/.github/workflows/deploy_tagged.yml deleted file mode 100644 index ae800c1d..00000000 --- a/.github/workflows/deploy_tagged.yml +++ /dev/null @@ -1,19 +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: ${{ inputs.changelist }} - createDockerImage: true - dockerTagPrefix: 'quay.io/dockstore/dockstore-support' - secrets: inherit diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index 96751199..342cb0c9 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -32,33 +32,3 @@ jobs: run: ./mvnw -B clean install - name: code coverage run: bash <(curl -s https://codecov.io/bash) - - - if: github.ref == 'refs/heads/develop' - name: Set S3 folder name and quay tag name - run: | - S3_FOLDER=${GITHUB_REF##refs/tags/} - if [ $GITHUB_REF == $S3_FOLDER ]; then - # If this isn't a tag, it must be a branch - S3_FOLDER=${GITHUB_REF##refs/heads/} - fi - # QUAY_TAG differs from S3_FOLDER because it only contains the git ref with no short hash. It also replaces slashes with underscores. - echo "QUAY_TAG=${S3_FOLDER//\//_}" >> $GITHUB_ENV - echo "S3_FOLDER=${S3_FOLDER}-$(echo $GITHUB_SHA | cut -c -7)" >> $GITHUB_ENV - - # neat, quay itself uses manual github actions https://github.com/quay/quay/blob/master/.github/workflows/build-and-publish.yaml - - if: github.ref == 'refs/heads/develop' - name: Login to Quay.io - uses: docker/login-action@v3 - with: - registry: quay.io - username: ${{ secrets.QUAY_USER }} - password: ${{ secrets.QUAY_TOKEN }} - - - if: github.ref == 'refs/heads/develop' - name: Build and push - id: docker_build - uses: docker/build-push-action@v6 - with: - context: . - push: true - tags: quay.io/dockstore/dockstore-support:${{env.QUAY_TAG}} diff --git a/THIRD-PARTY-LICENSES.txt b/THIRD-PARTY-LICENSES.txt index 1ebbce43..ea28327e 100644 --- a/THIRD-PARTY-LICENSES.txt +++ b/THIRD-PARTY-LICENSES.txt @@ -10,15 +10,15 @@ Lists of 426 third-party dependencies. (Apache License 2.0) Annotations for Metrics (io.dropwizard.metrics:metrics-annotation:4.2.19 - 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) + (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-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) (The Apache Software License, Version 2.0) Apache Commons Configuration (org.apache.commons:commons-configuration2:2.10.1 - https://commons.apache.org/proper/commons-configuration/) (Apache-2.0) Apache Commons CSV (org.apache.commons:commons-csv:1.10.0 - https://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 IO (commons-io:commons-io:2.16.1 - 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 Text (org.apache.commons:commons-text:1.11.0 - https://commons.apache.org/proper/commons-text) @@ -134,17 +134,17 @@ Lists of 426 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-client (com.spotify:docker-client:8.16.0 - https://github.com/spotify/docker-client) (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 Software License, Version 2.0) dockstore-common (io.dockstore:dockstore-common:1.16.0-beta.8 - no url defined) - (Apache Software License, Version 2.0) dockstore-integration-testing (io.dockstore:dockstore-integration-testing:1.16.0-beta.8 - no url defined) - (Apache Software License, Version 2.0) dockstore-language-plugin-parent (io.dockstore:dockstore-language-plugin-parent:1.16.0-beta.8 - no url defined) - (Apache Software License, Version 2.0) dockstore-webservice (io.dockstore:dockstore-webservice:1.16.0-beta.8 - no url defined) + (Apache Software License, Version 2.0) dockstore-common (io.dockstore:dockstore-common:1.17.0-alpha.0 - no url defined) + (Apache Software License, Version 2.0) dockstore-integration-testing (io.dockstore:dockstore-integration-testing:1.17.0-alpha.0 - no url defined) + (Apache Software License, Version 2.0) dockstore-language-plugin-parent (io.dockstore:dockstore-language-plugin-parent:1.17.0-alpha.0 - no url defined) + (Apache Software License, Version 2.0) dockstore-webservice (io.dockstore:dockstore-webservice:1.17.0-alpha.0 - no url defined) (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) @@ -337,7 +337,7 @@ Lists of 426 third-party dependencies. (Apache License 2.0) Metrics Utility Jakarta Servlets (io.dropwizard.metrics:metrics-jakarta-servlets:4.2.19 - 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) - (Apache Software License, Version 2.0) metricsaggregator (io.dockstore:metricsaggregator:1.16.0-SNAPSHOT - https://github.com/dockstore/dockstore-support) + (Apache Software License, Version 2.0) metricsaggregator (io.dockstore:metricsaggregator:1.17.0-SNAPSHOT - https://github.com/dockstore/dockstore-support) (Eclipse Distribution License - v 1.0) MIME streaming extension (org.jvnet.mimepull:mimepull:1.9.15 - https://github.com/eclipse-ee4j/metro-mimepull) (The MIT License) mockito-core (org.mockito:mockito-core:3.12.4 - https://github.com/mockito/mockito) (The MIT License) mockito-inline (org.mockito:mockito-inline:3.12.4 - https://github.com/mockito/mockito) @@ -362,7 +362,7 @@ Lists of 426 third-party dependencies. (Apache License, Version 2.0) Objenesis (org.objenesis:objenesis:3.2 - http://objenesis.org/objenesis) (The Apache Software License, Version 2.0) okhttp (com.squareup.okhttp3:okhttp:4.10.0 - https://square.github.io/okhttp/) (The Apache Software License, Version 2.0) okio (com.squareup.okio:okio-jvm:3.0.0 - https://github.com/square/okio/) - (Apache Software License, Version 2.0) openapi-java-client (io.dockstore:openapi-java-client:1.16.0-beta.8 - no url defined) + (Apache Software License, Version 2.0) openapi-java-client (io.dockstore:openapi-java-client:1.17.0-alpha.0 - no url defined) (The Apache License, Version 2.0) OpenCensus (io.opencensus:opencensus-api:0.31.0 - https://github.com/census-instrumentation/opencensus-java) (Apache 2) opencsv (com.opencsv:opencsv:5.7.1 - http://opencsv.sf.net) (Apache 2.0) optics (io.circe:circe-optics_2.13:0.14.1 - https://github.com/circe/circe-optics) @@ -404,11 +404,11 @@ Lists of 426 third-party dependencies. (Apache License 2.0) swagger-core-jakarta (io.swagger.core.v3:swagger-core-jakarta:2.2.15 - https://github.com/swagger-api/swagger-core/modules/swagger-core-jakarta) (Apache License 2.0) swagger-integration-jakarta (io.swagger.core.v3:swagger-integration-jakarta:2.2.15 - https://github.com/swagger-api/swagger-core/modules/swagger-integration-jakarta) (Apache Software License, Version 2.0) swagger-java-bitbucket-client (io.dockstore:swagger-java-bitbucket-client:2.0.3 - no url defined) - (Apache Software License, Version 2.0) swagger-java-client (io.dockstore:swagger-java-client:1.16.0-beta.8 - no url defined) + (Apache Software License, Version 2.0) swagger-java-client (io.dockstore:swagger-java-client:1.17.0-alpha.0 - no url defined) (Apache Software License, Version 2.0) swagger-java-discourse-client (io.dockstore:swagger-java-discourse-client:2.0.1 - no url defined) (Apache Software License, Version 2.0) swagger-java-quay-client (io.dockstore:swagger-java-quay-client:2.0.2 - no url defined) (Apache Software License, Version 2.0) swagger-java-sam-client (io.dockstore:swagger-java-sam-client:2.0.2 - no url defined) - (Apache Software License, Version 2.0) swagger-java-zenodo-client (io.dockstore:swagger-java-zenodo-client:2.1.3 - no url defined) + (Apache Software License, Version 2.0) swagger-java-zenodo-client (io.dockstore:swagger-java-zenodo-client:2.1.4 - no url defined) (Apache License 2.0) swagger-jaxrs2-jakarta (io.swagger.core.v3:swagger-jaxrs2-jakarta:2.2.15 - https://github.com/swagger-api/swagger-core/modules/swagger-jaxrs2-jakarta) (Apache License 2.0) swagger-jaxrs2-servlet-initializer-jakarta (io.swagger.core.v3:swagger-jaxrs2-servlet-initializer-jakarta:2.2.15 - https://github.com/swagger-api/swagger-core/modules/swagger-jaxrs2-servlet-initializer-jakarta) (Apache License 2.0) swagger-models (io.swagger:swagger-models:1.6.8 - https://github.com/swagger-api/swagger-core/modules/swagger-models) @@ -418,11 +418,11 @@ Lists of 426 third-party dependencies. (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/) - (GNU General Public License (GPLv3)) toolbackup (io.dockstore:toolbackup:1.16.0-SNAPSHOT - https://github.com/dockstore/dockstore-support) - (GNU General Public License (GPLv3)) tooltester (io.dockstore:tooltester:1.16.0-SNAPSHOT - https://github.com/dockstore/dockstore-support) - (GNU General Public License (GPLv3)) topicgenerator (io.dockstore:topicgenerator:1.16.0-SNAPSHOT - https://github.com/dockstore/dockstore-support) + (GNU General Public License (GPLv3)) toolbackup (io.dockstore:toolbackup:1.17.0-SNAPSHOT - https://github.com/dockstore/dockstore-support) + (GNU General Public License (GPLv3)) tooltester (io.dockstore:tooltester:1.17.0-SNAPSHOT - https://github.com/dockstore/dockstore-support) + (GNU General Public License (GPLv3)) topicgenerator (io.dockstore:topicgenerator:1.17.0-SNAPSHOT - https://github.com/dockstore/dockstore-support) (Eclipse Distribution License - v 1.0) TXW2 Runtime (org.glassfish.jaxb:txw2:3.0.2 - https://eclipse-ee4j.github.io/jaxb-ri/) - (GNU General Public License (GPLv3)) utils (io.dockstore:utils:1.16.0-SNAPSHOT - https://github.com/dockstore/dockstore-support) + (GNU General Public License (GPLv3)) utils (io.dockstore:utils:1.17.0-SNAPSHOT - https://github.com/dockstore/dockstore-support) (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) (WDL License https://github.com/openwdl/wdl/blob/master/LICENSE) wdl-draft3 (org.broadinstitute:wdl-draft3_2.13:85 - no url defined) diff --git a/pom.xml b/pom.xml index 35291061..a4e78ae4 100644 --- a/pom.xml +++ b/pom.xml @@ -33,12 +33,12 @@ --> - 1.16 + 1.17 .0-SNAPSHOT scm:git:git@github.com:dockstore/dockstore-support.git UTF-8 - 1.16.0-beta.8 + 1.17.0-alpha.0 3.0.0-M5 2.22.2 false @@ -119,6 +119,11 @@ artifacts.oicr.on.ca-releases https://artifacts.oicr.on.ca/artifactory/collab-release + + snapshots + artifacts.oicr.on.ca-snapshots + https://artifacts.oicr.on.ca/artifactory/collab-snapshot + diff --git a/toolbackup/pom.xml b/toolbackup/pom.xml index 87cb6e33..78b30f8b 100644 --- a/toolbackup/pom.xml +++ b/toolbackup/pom.xml @@ -204,7 +204,7 @@ commons-io commons-io - 2.15.1 + 2.16.1