diff --git a/.circleci/config.yml b/.circleci/config.yml index b8cbb892..e5e52b56 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: "17.0.11" orbs: build-tools: circleci/build-tools@2.7.0 executors: diff --git a/THIRD-PARTY-LICENSES.txt b/THIRD-PARTY-LICENSES.txt index 2035b320..ef3274ff 100644 --- a/THIRD-PARTY-LICENSES.txt +++ b/THIRD-PARTY-LICENSES.txt @@ -1,5 +1,5 @@ -Lists of 421 third-party dependencies. +Lists of 417 third-party dependencies. (The Apache Software License, Version 2.0) Adapter: RxJava 2 (com.squareup.retrofit2:adapter-rxjava2:2.9.0 - https://github.com/square/retrofit) (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/) @@ -27,10 +27,6 @@ Lists of 421 third-party dependencies. (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 Cache (org.apache.httpcomponents:httpclient-cache:4.5.2 - http://hc.apache.org/httpcomponents-client) - (Apache License, Version 2.0) Apache HttpClient Fluent API (org.apache.httpcomponents:fluent-hc:4.5.2 - http://hc.apache.org/httpcomponents-client) - (Apache License, Version 2.0) Apache HttpClient Mime (org.apache.httpcomponents:httpmime:4.5.2 - http://hc.apache.org/httpcomponents-client) - (Apache License, Version 2.0) Apache HttpClient OSGi bundle (org.apache.httpcomponents:httpclient-osgi:4.5.2 - http://hc.apache.org/httpcomponents-client) (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 HttpCore (org.apache.httpcomponents:httpcore:4.4.16 - http://hc.apache.org/httpcomponents-core-ga) @@ -80,8 +76,9 @@ Lists of 421 third-party dependencies. (Apache License, Version 2.0) AWS SDK for Java - Core (com.amazonaws:aws-java-sdk-core:1.11.83 - https://aws.amazon.com/sdkforjava) (Apache License 2.0) (The Apache Software License, Version 2.0) Bean Validation API (javax.validation:validation-api:2.0.1.Final - http://beanvalidation.org) (MIT) better-files (com.github.pathikrit:better-files_2.13:3.9.1 - https://github.com/pathikrit/better-files) + (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-jdk15on:1.60 - http://www.bouncycastle.org/java.html) - (Bouncy Castle Licence) Bouncy Castle Provider (org.bouncycastle:bcprov-jdk15on:1.69 - https://www.bouncycastle.org/java.html) + (Bouncy Castle Licence) Bouncy Castle Provider (org.bouncycastle:bcprov-jdk15on:1.60 - http://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) Caffeine cache (com.github.ben-manes.caffeine:caffeine:3.1.8 - https://github.com/ben-manes/caffeine) @@ -128,14 +125,14 @@ Lists of 421 third-party dependencies. (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) (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:3.3.0 - https://github.com/docker-java/docker-java) - (The Apache Software License, Version 2.0) docker-java-core (com.github.docker-java:docker-java-core:3.3.0 - https://github.com/docker-java/docker-java) - (The Apache Software License, Version 2.0) docker-java-transport (com.github.docker-java:docker-java-transport:3.3.0 - 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-httpclient5:3.3.0 - https://github.com/docker-java/docker-java) - (Apache Software License, Version 2.0) dockstore-common (io.dockstore:dockstore-common:1.16.0-alpha.3 - no url defined) - (Apache Software License, Version 2.0) dockstore-integration-testing (io.dockstore:dockstore-integration-testing:1.16.0-alpha.3 - no url defined) - (Apache Software License, Version 2.0) dockstore-language-plugin-parent (io.dockstore:dockstore-language-plugin-parent:1.16.0-alpha.3 - no url defined) - (Apache Software License, Version 2.0) dockstore-webservice (io.dockstore:dockstore-webservice:1.16.0-alpha.3 - 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 Software License, Version 2.0) dockstore-common (io.dockstore:dockstore-common:1.16.0-alpha.11 - no url defined) + (Apache Software License, Version 2.0) dockstore-integration-testing (io.dockstore:dockstore-integration-testing:1.16.0-alpha.11 - no url defined) + (Apache Software License, Version 2.0) dockstore-language-plugin-parent (io.dockstore:dockstore-language-plugin-parent:1.16.0-alpha.11 - no url defined) + (Apache Software License, Version 2.0) dockstore-webservice (io.dockstore:dockstore-webservice:1.16.0-alpha.11 - 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) @@ -288,7 +285,6 @@ Lists of 421 third-party dependencies. (Apache License, Version 2.0) jOOQ (org.jooq:jooq:3.19.7 - http://www.jooq.org/jooq) (The MIT License) JOpt Simple (net.sf.jopt-simple:jopt-simple:5.0.3 - http://pholser.github.io/jopt-simple) (Public Domain) JSON in Java (org.json:json:20231013 - https://github.com/douglascrockford/JSON-java) - (Revised BSD License) JSONLD Java :: Core (com.github.jsonld-java:jsonld-java:0.8.3 - http://github.com/jsonld-java/jsonld-java/jsonld-java/) (The MIT License) jsoup Java HTML Parser (org.jsoup:jsoup:1.10.2 - 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) JTokkit (com.knuddels:jtokkit:1.0.0 - https://github.com/knuddelsgmbh/jtokkit) @@ -356,7 +352,7 @@ Lists of 421 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-alpha.3 - no url defined) + (Apache Software License, Version 2.0) openapi-java-client (io.dockstore:openapi-java-client:1.16.0-alpha.11 - 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) @@ -398,11 +394,11 @@ Lists of 421 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-alpha.3 - no url defined) + (Apache Software License, Version 2.0) swagger-java-client (io.dockstore:swagger-java-client:1.16.0-alpha.11 - 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:2.0.2 - no url defined) + (Apache Software License, Version 2.0) swagger-java-zenodo-client (io.dockstore:swagger-java-zenodo-client:2.0.4 - 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) diff --git a/jira_automation/pom.xml b/jira_automation/pom.xml index 06453c31..144dfb9e 100644 --- a/jira_automation/pom.xml +++ b/jira_automation/pom.xml @@ -20,11 +20,6 @@ UTF-8 UTF-8 scm:git:git@github.com:dockstore/dockstore-support.git - - - 1.0 - .0-SNAPSHOT - diff --git a/metricsaggregator/src/main/java/io/dockstore/metricsaggregator/client/cli/TerraMetricsSubmitter.java b/metricsaggregator/src/main/java/io/dockstore/metricsaggregator/client/cli/TerraMetricsSubmitter.java index dcb41640..da6a61e0 100644 --- a/metricsaggregator/src/main/java/io/dockstore/metricsaggregator/client/cli/TerraMetricsSubmitter.java +++ b/metricsaggregator/src/main/java/io/dockstore/metricsaggregator/client/cli/TerraMetricsSubmitter.java @@ -478,7 +478,7 @@ static List getSourceUrlComponents(String sourceUrl) { private Optional getPrimaryDescriptorAbsolutePath(WorkflowsApi workflowsApi, MinimalWorkflowInfo workflow, String version) { Optional primaryDescriptorPath = Optional.empty(); try { - primaryDescriptorPath = Optional.of(workflowsApi.primaryDescriptor1(workflow.id(), version, workflow.descriptorType().toString()).getAbsolutePath()); + primaryDescriptorPath = Optional.of(workflowsApi.primaryDescriptor1(workflow.id(), workflow.descriptorType().toString(), version).getAbsolutePath()); } catch (ApiException e) { LOG.debug("Could not get primary descriptor path", e); } diff --git a/pom.xml b/pom.xml index c1838ad5..b89d66f2 100644 --- a/pom.xml +++ b/pom.xml @@ -38,7 +38,7 @@ scm:git:git@github.com:dockstore/dockstore-support.git UTF-8 - 1.16.0-alpha.3 + 1.16.0-alpha.11 3.0.0-M5 2.22.2 false diff --git a/topicgenerator/src/main/java/io/dockstore/topicgenerator/client/cli/TopicGeneratorClient.java b/topicgenerator/src/main/java/io/dockstore/topicgenerator/client/cli/TopicGeneratorClient.java index 367a044b..012e16c0 100644 --- a/topicgenerator/src/main/java/io/dockstore/topicgenerator/client/cli/TopicGeneratorClient.java +++ b/topicgenerator/src/main/java/io/dockstore/topicgenerator/client/cli/TopicGeneratorClient.java @@ -229,8 +229,9 @@ private void uploadTopics(TopicGeneratorConfig topicGeneratorConfig, String inpu // This command's input CSV headers are the generate-topic command's output headers final String trsId = entryWithAITopic.get(GenerateTopicsCommand.OutputCsvHeaders.trsId); final String aiTopic = entryWithAITopic.get(GenerateTopicsCommand.OutputCsvHeaders.aiTopic); + final String version = entryWithAITopic.get(OutputCsvHeaders.version); try { - extendedGa4GhApi.updateAITopic(new UpdateAITopicRequest().aiTopic(aiTopic), trsId); + extendedGa4GhApi.updateAITopic(new UpdateAITopicRequest().aiTopic(aiTopic), version, trsId); LOG.info("Uploaded AI topic for {}", trsId); } catch (ApiException exception) { LOG.error("Could not upload AI topic for {}", trsId);