8000 Feature/core update ai topic hookup by denis-yuen · Pull Request #493 · dockstore/dockstore-support · GitHub
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Merged
merged 4 commits into from
Jun 11, 2024
Merged

Feature/core update ai topic hookup #493

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e01be50
update pom.xml
denis-yuen Jun 7, 2024
7f4ed05
update submit call
denis-yuen Jun 7, 2024
8b85fe5
try this
denis-yuen Jun 7, 2024
8605290
damnit parameter re-arrangement
denis-yuen Jun 10, 2024
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2 changes: 1 addition & 1 deletion .circleci/config.yml
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Expand Up @@ -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:
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32 changes: 14 additions & 18 deletions THIRD-PARTY-LICENSES.txt
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@@ -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/)
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
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5 changes: 0 additions & 5 deletions jira_automation/pom.xml
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Expand Up @@ -20,11 +20,6 @@
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<github.url>scm:git:git@github.com:dockstore/dockstore-support.git</github.url>

<!-- the following properties set sane defaults when no revision properties are set from the command-line -->
<revision>1.0</revision>
<changelist>.0-SNAPSHOT</changelist>

</properties>

<organization>
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2 changes: 1 addition & 1 deletion ...egator/src/main/java/io/dockstore/metricsaggregator/client/cli/TerraMetricsSubmitter.java
Original file line number Diff line number Diff line change
Expand Up @@ -478,7 +478,7 @@ static List<String> getSourceUrlComponents(String sourceUrl) {
private Optional<String> getPrimaryDescriptorAbsolutePath(WorkflowsApi workflowsApi, MinimalWorkflowInfo workflow, String version) {
Optional<String> primaryDescriptorPath = Optional.empty();
try {
primaryDescriptorPath = Optional.of(workflowsApi.primaryDescriptor1(workflow.id(), version, workflow.descriptorType().toString()).getAbsolutePath());
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Sigh @ swagger client parameter re-arrangement

primaryDescriptorPath = Optional.of(workflowsApi.primaryDescriptor1(workflow.id(), workflow.descriptorType().toString(), version).getAbsolutePath());
} catch (ApiException e) {
LOG.debug("Could not get primary descriptor path", e);
}
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2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -38,7 +38,7 @@

<github.url>scm:git:git@github.com:dockstore/dockstore-support.git</github.url>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<dockstore-core.version>1.16.0-alpha.3</dockstore-core.version>
<dockstore-core.version>1.16.0-alpha.11</dockstore-core.version>
<maven-surefire.version>3.0.0-M5</maven-surefire.version>
<maven-failsafe.version>2.22.2</maven-failsafe.version>
<skipTests>false</skipTests>
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3 changes: 2 additions & 1 deletion ...cgenerator/src/main/java/io/dockstore/topicgenerator/client/cli/TopicGeneratorClient.java
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Expand Up @@ -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);
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