diff --git a/THIRD-PARTY-LICENSES.txt b/THIRD-PARTY-LICENSES.txt
index 8f3fad24..693216ce 100644
--- a/THIRD-PARTY-LICENSES.txt
+++ b/THIRD-PARTY-LICENSES.txt
@@ -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:1.16.0-beta.1 - 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)
@@ -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:1.16.0-beta.1 - https://github.com/dockstore/dockstore-support)
+ (GNU General Public License (GPLv3)) tooltester (io.dockstore:tooltester:1.16.0-beta.1 - https://github.com/dockstore/dockstore-support)
+ (GNU General Public License (GPLv3)) topicgenerator (io.dockstore:topicgenerator:1.16.0-beta.1 - 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:1.16.0-beta.1 - 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/dockstore-support-reports/generated/src/main/resources/pom.xml b/dockstore-support-reports/generated/src/main/resources/pom.xml
new file mode 100644
index 00000000..bd7e5d04
--- /dev/null
+++ b/dockstore-support-reports/generated/src/main/resources/pom.xml
@@ -0,0 +1,88 @@
+
+
+
+ 4.0.0
+ io.dockstore
+ dockstore-support-reports
+ 1.16.0-beta.1
+
+
+ Apache Software License, Version 2.0
+ https://www.apache.org/licenses/LICENSE-2.0
+
+
+
+
+ io.dockstore
+ toolbackup
+ 1.16.0-beta.1
+ compile
+
+
+ io.dockstore
+ tooltester
+ 1.16.0-beta.1
+ compile
+
+
+ io.dockstore
+ metricsaggregator
+ 1.16.0-beta.1
+ compile
+
+
+ io.dockstore
+ topicgenerator
+ 1.16.0-beta.1
+ compile
+
+
+
+
+
+ true
+
+ artifacts.oicr.on.ca.ca-snapshots
+ https://artifacts.oicr.on.ca/artifactory/collab-snapshot
+
+
+
+ false
+
+ artifacts.oicr.on.ca
+ artifacts.oicr.on.ca
+ https://artifacts.oicr.on.ca/artifactory/collab-release
+
+
+ apache-releases
+ Apache Releases repository
+ https://repository.apache.org/content/repositories/releases/
+
+
+
+ true
+
+
+ false
+
+ artifactory.broadinstitute.org
+ artifactory.broadinstitute.org
+ https://broadinstitute.jfrog.io/artifactory/libs-release/
+
+
+
diff --git a/githubdelivery/dependency-reduced-pom.xml b/githubdelivery/dependency-reduced-pom.xml
new file mode 100644
index 00000000..48068fbc
--- /dev/null
+++ b/githubdelivery/dependency-reduced-pom.xml
@@ -0,0 +1,331 @@
+
+
+
+ dockstore-support
+ io.dockstore
+ ${revision}${changelist}
+
+ 4.0.0
+ githubdelivery
+ githubdelivery
+ ${revision}${changelist}
+ A command-line client for rerunning github release events
+ https://github.com/dockstore/dockstore-support
+
+
+ Apache Software License, Version 2.0
+ https://www.apache.org/licenses/LICENSE-2.0
+
+
+
+ ${github.url}
+ ${github.url}
+ ${github.url}
+
+
+ Dockstore
+ https://www.dockstore.org/
+
+
+
+
+
+ maven-jar-plugin
+ 3.0.2
+
+
+
+ true
+ true
+
+
+
+
+
+
+
+
+ maven-shade-plugin
+
+
+ githubDeliveryS3Client
+ package
+
+ shade
+
+
+
+
+
+ io.dockstore.githubdelivery.GithubDeliveryS3Client
+
+
+
+
+
+
+
+
+
+ *:*
+
+ META-INF/*.SF
+ META-INF/*.DSA
+ META-INF/*.RSA
+
+
+
+
+
+
+ maven-enforcer-plugin
+
+
+ maven-dependency-plugin
+
+
+ analyze
+
+ analyze-only
+
+
+ true
+ true
+ true
+
+
+
+
+
+ maven-compiler-plugin
+
+ 17
+
+
+
+ maven-checkstyle-plugin
+
+
+ compile
+
+ check
+
+
+ true
+
+
+
+
+ true
+ true
+
+
+
+ com.github.spotbugs
+ spotbugs-maven-plugin
+ 4.5.3.0
+
+
+ maven-surefire-plugin
+
+
+ test
+
+ test
+
+
+
+
+
+ maven-failsafe-plugin
+
+
+ integration-test
+
+ integration-test
+
+
+
+ verify
+
+ verify
+
+
+
+
+
+
+
+
+
+ artifacts.oicr.on.ca.ca-snapshots
+ https://artifacts.oicr.on.ca/artifactory/collab-snapshot
+
+
+
+ false
+
+ artifacts.oicr.on.ca
+ artifacts.oicr.on.ca
+ https://artifacts.oicr.on.ca/artifactory/collab-release
+
+
+ apache-releases
+ Apache Releases repository
+ https://repository.apache.org/content/repositories/releases/
+
+
+
+
+ org.junit.jupiter
+ junit-jupiter
+ 5.10.0
+ test
+
+
+ junit-jupiter-params
+ org.junit.jupiter
+
+
+ junit-jupiter-engine
+ org.junit.jupiter
+
+
+
+
+ org.junit.jupiter
+ junit-jupiter-api
+ 5.10.0
+ test
+
+
+ opentest4j
+ org.opentest4j
+
+
+ junit-platform-commons
+ org.junit.platform
+
+
+ apiguardian-api
+ org.apiguardian
+
+
+
+
+ io.dropwizard
+ dropwizard-testing
+ 4.0.2
+ test
+
+
+ javax.servlet-api
+ javax.servlet
+
+
+ dropwizard-configuration
+ io.dropwizard
+
+
+ dropwizard-core
+ io.dropwizard
+
+
+ dropwizard-jackson
+ io.dropwizard
+
+
+ dropwizard-jersey
+ io.dropwizard
+
+
+ dropwizard-jetty
+ io.dropwizard
+
+
+ dropwizard-lifecycle
+ io.dropwizard
+
+
+ dropwizard-logging
+ io.dropwizard
+
+
+ dropwizard-servlets
+ io.dropwizard
+
+
+ dropwizard-util
+ io.dropwizard
+
+
+ dropwizard-validation
+ io.dropwizard
+
+
+ metrics-annotation
+ io.dropwizard.metrics
+
+
+ jackson-datatype-guava
+ com.fasterxml.jackson.datatype
+
+
+ jackson-jakarta-rs-json-provider
+ com.fasterxml.jackson.jakarta.rs
+
+
+ jakarta.servlet-api
+ jakarta.servlet
+
+
+ argparse4j
+ net.sourceforge.argparse4j
+
+
+ jetty-io
+ org.eclipse.jetty
+
+
+ jetty-server
+ org.eclipse.jetty
+
+
+ jersey-container-servlet-core
+ org.glassfish.jersey.containers
+
+
+ jersey-apache5-connector
+ org.glassfish.jersey.connectors
+
+
+ httpclient5
+ org.apache.httpcomponents.client5
+
+
+ jersey-server
+ org.glassfish.jersey.core
+
+
+ jersey-test-framework-core
+ org.glassfish.jersey.test-framework
+
+
+ jersey-test-framework-provider-inmemory
+ org.glassfish.jersey.test-framework.providers
+
+
+
+
+
+
+ central
+ artifacts.oicr.on.ca-releases
+ https://artifacts.oicr.on.ca/artifactory/collab-release
+
+
+
+ UTF-8
+ UTF-8
+
+
diff --git a/jira_automation/dependency-reduced-pom.xml b/jira_automation/dependency-reduced-pom.xml
new file mode 100644
index 00000000..91a75259
--- /dev/null
+++ b/jira_automation/dependency-reduced-pom.xml
@@ -0,0 +1,70 @@
+
+
+
+ dockstore-support
+ io.dockstore
+ ${revision}${changelist}
+
+ 4.0.0
+ io.dockstore
+ jira_automation
+ jira_automation
+ ${revision}${changelist}
+ JIRA automation parent POM
+ https://github.com/dockstore/dockstore-support
+
+ Dockstore
+ https://www.dockstore.org/
+
+
+
+
+ maven-compiler-plugin
+ 3.10.1
+
+ 17
+ true
+ true
+
+
+
+ maven-shade-plugin
+
+
+ milestoneResolverId
+ package
+
+ shade
+
+
+
+
+
+ io.dockstore.jira.MilestoneResolver
+
+
+
+
+
+
+
+
+
+ *:*
+
+ META-INF/*.SF
+ META-INF/*.DSA
+ META-INF/*.RSA
+
+
+
+
+
+
+
+
+ scm:git:git@github.com:dockstore/dockstore-support.git
+ UTF-8
+ UTF-8
+
+
diff --git a/metricsaggregator/dependency-reduced-pom.xml b/metricsaggregator/dependency-reduced-pom.xml
new file mode 100644
index 00000000..2ff6e6c5
--- /dev/null
+++ b/metricsaggregator/dependency-reduced-pom.xml
@@ -0,0 +1,785 @@
+
+
+
+ dockstore-support
+ io.dockstore
+ ${revision}${changelist}
+
+ 4.0.0
+ metricsaggregator
+ metricsaggregator
+ ${revision}${changelist}
+ A service for aggregating metrics for entries on Dockstore
+ https://github.com/dockstore/dockstore-support
+
+
+ Apache Software License, Version 2.0
+ https://www.apache.org/licenses/LICENSE-2.0
+
+
+
+ ${github.url}
+ ${github.url}
+ ${github.url}
+
+
+ Dockstore
+ https://www.dockstore.org/
+
+
+
+
+
+ maven-jar-plugin
+ 3.0.2
+
+
+
+ true
+ true
+
+
+
+
+
+ maven-surefire-plugin
+
+
+ us-east-1
+ foobar
+ foobar
+
+
+
+
+ maven-failsafe-plugin
+ ${maven-fire.version}
+
+
+ us-east-1
+ foobar
+ foobar
+
+
+
+
+
+
+
+ maven-shade-plugin
+
+
+ metricsAggregatorClient
+ package
+
+ shade
+
+
+
+
+
+ io.dockstore.metricsaggregator.client.cli.MetricsAggregatorClient
+
+
+
+
+
+
+
+
+
+ *:*
+
+ META-INF/*.SF
+ META-INF/*.DSA
+ META-INF/*.RSA
+ migrations.xml
+ migrations.*.xml
+
+
+
+
+
+
+ maven-enforcer-plugin
+
+
+ maven-dependency-plugin
+
+
+ analyze
+
+ analyze-only
+
+
+ true
+ true
+ true
+
+ org.apache.commons:commons-configuration2
+ org.slf4j:slf4j-api
+ software.amazon.awssdk:s3
+ org.glassfish.jersey.inject:jersey-hk2
+ javax.money:money-api
+ org.javamoney.moneta:moneta-core
+ ch.qos.logback:logback-classic
+ ch.qos.logback:logback-core
+ com.google.guava:guava
+ jakarta.validation:jakarta.validation-api
+ org.hibernate.validator:hibernate-validator
+ org.glassfish:jakarta.el
+ software.amazon.awssdk:auth
+ software.amazon.awssdk:aws-core
+ software.amazon.awssdk:sdk-core
+
+
+
+
+
+
+ maven-compiler-plugin
+
+ 17
+
+
+
+ maven-javadoc-plugin
+
+
+ site-deploy
+
+ aggregate
+ test-aggregate
+
+ false
+
+
+ false
+
+
+ maven-checkstyle-plugin
+
+
+ compile
+
+ check
+
+
+ true
+
+
+
+
+ true
+ true
+
+
+
+ com.github.spotbugs
+ spotbugs-maven-plugin
+ 4.5.3.0
+
+
+ maven-surefire-plugin
+ ${maven-surefire.version}
+
+
+ test
+
+ test
+
+
+
+
+
+ maven-failsafe-plugin
+ ${maven-failsafe.version}
+
+
+ integration-test
+
+ integration-test
+
+
+
+ verify
+
+ verify
+
+
+
+
+ ${skip-metricsaggregator-ITs}
+
+
+
+ org.codehaus.mojo
+ build-helper-maven-plugin
+
+
+ add_script
+ package
+
+ attach-artifact
+
+
+
+
+ scripts/format-dnastack-validation-data.sh
+ format-dnastack-validation-data.sh
+ dist
+
+
+
+
+
+
+
+
+
+
+
+ artifacts.oicr.on.ca.ca-snapshots
+ https://artifacts.oicr.on.ca/artifactory/collab-snapshot
+
+
+
+ false
+
+ artifacts.oicr.on.ca
+ artifacts.oicr.on.ca
+ https://artifacts.oicr.on.ca/artifactory/collab-release
+
+
+ apache-releases
+ Apache Releases repository
+ https://repository.apache.org/content/repositories/releases/
+
+
+
+
+ io.dockstore
+ dockstore-webservice
+ 1.16.0-beta.2
+ test
+
+
+ jackson-datatype-hibernate5-jakarta
+ com.fasterxml.jackson.datatype
+
+
+ jackson-dataformat-cbor
+ com.fasterxml.jackson.dataformat
+
+
+ google-api-services-oauth2
+ com.google.apis
+
+
+ logstash-logback-encoder
+ net.logstash.logback
+
+
+ dropwizard-logging
+ io.dropwizard
+
+
+ dropwizard-lifecycle
+ io.dropwizard
+
+
+ swagger-java-quay-client
+ io.dockstore
+
+
+ swagger-java-sam-client
+ io.dockstore
+
+
+ swagger-java-bitbucket-client
+ io.dockstore
+
+
+ swagger-java-discourse-client
+ io.dockstore
+
+
+ dockstore-language-plugin-parent
+ io.dockstore
+
+
+ swagger-java-zenodo-client
+ io.dockstore
+
+
+ commons-validator
+ commons-validator
+
+
+ swagger-models-jakarta
+ io.swagger.core.v3
+
+
+ dropwizard-core
+ io.dropwizard
+
+
+ dropwizard-hibernate
+ io.dropwizard
+
+
+ hibernate-core
+ org.hibernate.orm
+
+
+ dropwizard-assets
+ io.dropwizard
+
+
+ dropwizard-client
+ io.dropwizard
+
+
+ dropwizard-jersey
+ io.dropwizard
+
+
+ jersey-server
+ org.glassfish.jersey.core
+
+
+ dropwizard-auth
+ io.dropwizard
+
+
+ metrics-annotation
+ io.dropwizard.metrics
+
+
+ dropwizard-db
+ io.dropwizard
+
+
+ dropwizard-migrations
+ io.dropwizard
+
+
+ dropwizard-forms
+ io.dropwizard
+
+
+ httpasyncclient
+ org.apache.httpcomponents
+
+
+ httpclient5
+ org.apache.httpcomponents.client5
+
+
+ httpcore5
+ org.apache.httpcomponents.core5
+
+
+ jetty-servlets
+ org.eclipse.jetty
+
+
+ jetty-servlet
+ org.eclipse.jetty
+
+
+ jakarta.servlet-api
+ jakarta.servlet
+
+
+ jetty-server
+ org.eclipse.jetty
+
+
+ jetty-http
+ org.eclipse.jetty
+
+
+ dropwizard-jetty
+ io.dropwizard
+
+
+ dropwizard-jackson
+ io.dropwizard
+
+
+ swagger-annotations
+ io.swagger
+
+
+ java-jwt
+ com.auth0
+
+
+ swagger-jaxrs2-jakarta
+ io.swagger.core.v3
+
+
+ swagger-jaxrs2-servlet-initializer-jakarta
+ io.swagger.core.v3
+
+
+ okhttp
+ com.squareup.okhttp3
+
+
+ swagger-core
+ io.swagger
+
+
+ jackson-jakarta-rs-json-provider
+ com.fasterxml.jackson.jakarta.rs
+
+
+ google-http-client-jackson
+ com.google.http-client
+
+
+ cwlavro-tools
+ io.cwl
+
+
+ cwlavro-generated
+ io.cwl
+
+
+ json
+ org.json
+
+
+ elasticsearch
+ org.elasticsearch
+
+
+ elasticsearch-rest-client
+ org.elasticsearch.client
+
+
+ elasticsearch-rest-high-level-client
+ org.elasticsearch.client
+
+
+ elasticsearch-x-content
+ org.elasticsearch
+
+
+ elasticsearch-core
+ org.elasticsearch
+
+
+ groovy
+ org.codehaus.groovy
+
+
+ sqs
+ software.amazon.awssdk
+
+
+ cloudwatch
+ software.amazon.awssdk
+
+
+ github-api
+ org.kohsuke
+
+
+ jjwt-api
+ io.jsonwebtoken
+
+
+ jjwt-impl
+ io.jsonwebtoken
+
+
+ jjwt-jackson
+ io.jsonwebtoken
+
+
+ java-gitlab-api
+ org.gitlab
+
+
+ caffeine
+ com.github.ben-manes.caffeine
+
+
+ orcid-model-jakarta
+ org.orcid
+
+
+ jaxb-runtime
+ org.glassfish.jaxb
+
+
+ jakarta.persistence-api
+ jakarta.persistence
+
+
+ swagger-integration-jakarta
+ io.swagger.core.v3
+
+
+
+
+ io.dockstore
+ dockstore-integration-testing
+ 1.16.0-beta.2
+ tests
+ test
+
+
+ docker-java-transport-httpclient5
+ com.github.docker-java
+
+
+ docker-java-core
+ com.github.docker-java
+
+
+ docker-java-transport
+ com.github.docker-java
+
+
+ docker-java-api
+ com.github.docker-java
+
+
+ swagger-java-client
+ io.dockstore
+
+
+ dropwizard-jdbi3
+ io.dropwizard
+
+
+ joda-time
+ joda-time
+
+
+ httpclient5
+ org.apache.httpcomponents.client5
+
+
+ httpcore5
+ org.apache.httpcomponents.core5
+
+
+ github-api
+ org.kohsuke
+
+
+ jackson-dataformat-cbor
+ com.fasterxml.jackson.dataformat
+
+
+ caffeine
+ com.github.ben-manes.caffeine
+
+
+
+
+ org.junit.jupiter
+ junit-jupiter-api
+ 5.10.0
+ test
+
+
+ opentest4j
+ org.opentest4j
+
+
+ junit-platform-commons
+ org.junit.platform
+
+
+ apiguardian-api
+ org.apiguardian
+
+
+
+
+ io.dropwizard
+ dropwizard-testing
+ 4.0.2
+ test
+
+
+ javax.servlet-api
+ javax.servlet
+
+
+ dropwizard-configuration
+ io.dropwizard
+
+
+ dropwizard-servlets
+ io.dropwizard
+
+
+ dropwizard-util
+ io.dropwizard
+
+
+ dropwizard-validation
+ io.dropwizard
+
+
+ jackson-datatype-guava
+ com.fasterxml.jackson.datatype
+
+
+ argparse4j
+ net.sourceforge.argparse4j
+
+
+ jetty-io
+ org.eclipse.jetty
+
+
+ jersey-container-servlet-core
+ org.glassfish.jersey.containers
+
+
+ jersey-apache5-connector
+ org.glassfish.jersey.connectors
+
+
+ jersey-test-framework-core
+ org.glassfish.jersey.test-framework
+
+
+ jersey-test-framework-provider-inmemory
+ org.glassfish.jersey.test-framework.providers
+
+
+ dropwizard-core
+ io.dropwizard
+
+
+ dropwizard-jackson
+ io.dropwizard
+
+
+ dropwizard-jersey
+ io.dropwizard
+
+
+ dropwizard-jetty
+ io.dropwizard
+
+
+ dropwizard-lifecycle
+ io.dropwizard
+
+
+ dropwizard-logging
+ io.dropwizard
+
+
+ metrics-annotation
+ io.dropwizard.metrics
+
+
+ jackson-jakarta-rs-json-provider
+ com.fasterxml.jackson.jakarta.rs
+
+
+ jakarta.servlet-api
+ jakarta.servlet
+
+
+ jetty-server
+ org.eclipse.jetty
+
+
+ jersey-server
+ org.glassfish.jersey.core
+
+
+ httpclient5
+ org.apache.httpcomponents.client5
+
+
+
+
+ cloud.localstack
+ localstack-utils
+ 0.2.23
+ test
+
+
+ aws-java-sdk-kinesis
+ com.amazonaws
+
+
+ aws-java-sdk-simpleworkflow
+ com.amazonaws
+
+
+ aws-java-sdk-dynamodb
+ com.amazonaws
+
+
+ aws-java-sdk-s3
+ com.amazonaws
+
+
+ ion-java
+ com.amazon.ion
+
+
+ lombok
+ org.projectlombok
+
+
+ log4j-core
+ org.apache.logging.log4j
+
+
+ kinesis
+ software.amazon.awssdk
+
+
+
+
+ uk.org.webcompere
+ system-stubs-jupiter
+ 2.0.1
+ test
+
+
+ mockito-inline
+ org.mockito
+
+
+
+
+ uk.org.webcompere
+ system-stubs-core
+ 2.0.1
+ test
+
+
+ mockito-inline
+ org.mockito
+
+
+
+
+
+
+ central
+ artifacts.oicr.on.ca-releases
+ https://artifacts.oicr.on.ca/artifactory/collab-release
+
+
+
+ UTF-8
+ UTF-8
+
+
diff --git a/toolbackup/dependency-reduced-pom.xml b/toolbackup/dependency-reduced-pom.xml
new file mode 100644
index 00000000..071e4b15
--- /dev/null
+++ b/toolbackup/dependency-reduced-pom.xml
@@ -0,0 +1,356 @@
+
+
+
+ dockstore-support
+ io.dockstore
+ ${revision}${changelist}
+
+ 4.0.0
+ toolbackup
+ toolbackup
+ ${revision}${changelist}
+ A program back-up of all resources on Dockstore or any GA4GH tool-registry-api to S3
+ https://github.com/dockstore/dockstore-support
+
+
+ GNU General Public License (GPLv3)
+ https://www.gnu.org/licenses/gpl-3.0.html
+
+
+
+ ${github.url}
+ ${github.url}
+ ${github.url}
+
+
+ Dockstore
+ https://www.dockstore.org/
+
+
+
+
+
+ maven-jar-plugin
+ 3.0.2
+
+
+
+ true
+ true
+ true
+
+
+
+
+
+
+
+
+ maven-shade-plugin
+
+
+ client
+ package
+
+ shade
+
+
+
+
+
+ io.dockstore.toolbackup.client.cli.Client
+
+
+
+ client
+
+
+
+ downloader
+ package
+
+ shade
+
+
+
+
+
+ io.dockstore.toolbackup.client.cli.Downloader
+
+
+
+ downloader
+
+
+
+
+
+
+ *:*
+
+ META-INF/*.SF
+ META-INF/*.DSA
+ META-INF/*.RSA
+
+
+
+
+
+
+ maven-enforcer-plugin
+
+
+ enforce
+
+ enforce
+
+
+
+
+
+ Best Practice is to always define plugin versions!
+
+
+ No Snapshots Allowed!
+ false
+
+ io.dockstore:*
+
+
+
+
+
+
+
+
+
+ maven-dependency-plugin
+
+
+ analyze
+
+ analyze-only
+
+
+ true
+ true
+ true
+
+ org.glassfish.hk2:hk2-api
+ javax.xml.bind:jaxb-api
+
+
+
+
+
+
+ maven-compiler-plugin
+
+
+ maven-javadoc-plugin
+
+
+ site-deploy
+
+ aggregate
+ test-aggregate
+
+ false
+
+
+ false
+
+
+ maven-checkstyle-plugin
+
+
+ compile
+
+ check
+
+
+ true
+
+
+
+
+ true
+ true
+
+
+
+ com.github.spotbugs
+ spotbugs-maven-plugin
+
+
+ org.codehaus.mojo
+ cobertura-maven-plugin
+
+
+ net.sourceforge.cobertura
+ cobertura
+ 2.1.1
+
+
+
+
+
+ xml
+ html
+
+ true
+
+
+ io/dockstore/client/Bridge.class
+ io/dockstore/client/Bridge.*
+ io/swagger/client/**/*.class
+ io/swagger/quay/client/**/*.class
+ **/*$*
+
+
+ io.dockstore.client.Bridge
+
+
+
+
+
+ maven-surefire-plugin
+ 2.19.1
+
+ -Djava.security.manager=allow
+ @{argLine}
+
+
+
+ maven-failsafe-plugin
+
+
+ integration-test
+
+ integration-test
+
+
+
+ verify
+
+ verify
+
+
+
+
+ ${skip-toolbackup-ITs}
+ -Djava.security.manager=allow
+ @{argLine}
+
+
+
+ org.eluder.coveralls
+ coveralls-maven-plugin
+
+
+
+
+
+ apache-releases
+ Apache Releases repository
+ https://repository.apache.org/content/repositories/releases/
+
+
+ eclipse-egit-github
+ Eclipse egit github repository
+ https://repo.eclipse.org/content/repositories/egit-releases
+
+
+
+ false
+
+ jcenter
+ bintray
+ https://jcenter.bintray.com
+
+
+
+
+ junit
+ junit
+ 4.13.2
+ test
+
+
+ hamcrest-core
+ org.hamcrest
+
+
+
+
+ uk.org.webcompere
+ system-stubs-core
+ 2.0.1
+ test
+
+
+ mockito-inline
+ org.mockito
+
+
+
+
+ uk.org.webcompere
+ system-stubs-jupiter
+ 2.0.1
+ test
+
+
+ mockito-inline
+ org.mockito
+
+
+
+
+
+
+
+ org.codehaus.mojo
+ cobertura-maven-plugin
+
+
+
+ xml
+ html
+
+ true
+
+
+ io/dockstore/client/Bridge.class
+ io/dockstore/client/Bridge.*
+ io/swagger/client/**/*.class
+ io/swagger/quay/client/**/*.class
+ **/*$*
+
+
+ io.dockstore.client.Bridge
+
+
+
+
+
+
+
+
+
+ io.cwl
+ cwlavro-tools
+
+
+ io.cwl
+ cwlavro-generated
+
+
+
+
+ 1.11.83
+ 1.7.22
+ UTF-8
+ UTF-8
+
+
diff --git a/tooltester/dependency-reduced-pom.xml b/tooltester/dependency-reduced-pom.xml
new file mode 100644
index 00000000..d125463f
--- /dev/null
+++ b/tooltester/dependency-reduced-pom.xml
@@ -0,0 +1,288 @@
+
+
+
+ dockstore-support
+ io.dockstore
+ ${revision}${changelist}
+
+ 4.0.0
+ tooltester
+ tooltester
+ ${revision}${changelist}
+ A service for testing verified tools on Dockstore
+ https://github.com/dockstore/dockstore-support
+
+
+ GNU General Public License (GPLv3)
+ https://www.gnu.org/licenses/gpl-3.0.html
+
+
+
+ ${github.url}
+ ${github.url}
+ ${github.url}
+
+
+ Dockstore
+ https://www.dockstore.org/
+
+
+
+
+ maven-shade-plugin
+
+
+ client
+ package
+
+ shade
+
+
+
+
+
+ io.dockstore.tooltester.client.cli.Client
+
+
+
+
+
+
+
+
+
+ *:*
+
+ META-INF/*.SF
+ META-INF/*.DSA
+ META-INF/*.RSA
+
+
+
+
+
+
+ maven-enforcer-plugin
+
+
+ enforce
+
+ enforce
+
+
+
+
+
+ Best Practice is to always define plugin versions!
+
+
+ No Snapshots Allowed!
+ false
+
+ io.dockstore:*
+
+
+
+
+
+
+
+
+
+ maven-dependency-plugin
+
+
+ analyze
+
+ analyze-only
+
+
+ true
+ true
+ true
+
+ org.glassfish.jersey.inject:jersey-hk2
+
+
+
+
+
+
+ maven-compiler-plugin
+
+ 17
+
+
+
+ maven-javadoc-plugin
+
+
+ site-deploy
+
+ aggregate
+ test-aggregate
+
+ false
+
+
+ false
+
+
+ maven-checkstyle-plugin
+
+
+ com.github.spotbugs
+ spotbugs-maven-plugin
+
+
+ maven-surefire-plugin
+ ${maven-surefire.version}
+
+
+ test
+
+ test
+
+
+
+
+ -Djava.security.manager=allow
+ @{argLine}
+
+
+
+ maven-failsafe-plugin
+ ${maven-failsafe.version}
+
+
+ integration-test
+
+ integration-test
+
+
+
+ verify
+
+ verify
+
+
+
+
+ ${skip-tooltester-ITs}
+ -Djava.security.manager=allow
+ @{argLine}
+
+
+
+
+
+
+ artifacts.oicr.on.ca
+ artifacts.oicr.on.ca
+ https://artifacts.oicr.on.ca/artifactory/collab-release
+
+
+ apache-releases
+ Apache Releases repository
+ https://repository.apache.org/content/repositories/releases/
+
+
+ eclipse-egit-github
+ Eclipse egit github repository
+ https://repo.eclipse.org/content/repositories/egit-releases
+
+
+
+
+ org.hamcrest
+ hamcrest-all
+ 1.3
+ test
+
+
+ uk.org.webcompere
+ system-stubs-jupiter
+ 2.0.1
+ test
+
+
+ mockito-inline
+ org.mockito
+
+
+
+
+ uk.org.webcompere
+ system-stubs-core
+ 2.0.1
+ test
+
+
+ mockito-inline
+ org.mockito
+
+
+
+
+ org.junit.jupiter
+ junit-jupiter-api
+ 5.10.0
+ test
+
+
+ opentest4j
+ org.opentest4j
+
+
+ junit-platform-commons
+ org.junit.platform
+
+
+ apiguardian-api
+ org.apiguardian
+
+
+
+
+
+
+
+ io.cwl
+ cwlavro-tools
+
+
+ httpclient-osgi
+ org.apache.httpcomponents
+
+
+ httpcore-osgi
+ org.apache.httpcomponents
+
+
+
+
+ io.cwl
+ cwlavro-generated
+
+
+ httpclient-osgi
+ org.apache.httpcomponents
+
+
+ httpcore-osgi
+ org.apache.httpcomponents
+
+
+
+
+ xml-apis
+ xml-apis
+ 1.4.01
+
+
+
+
+ UTF-8
+ UTF-8
+
+
diff --git a/topicgenerator/dependency-reduced-pom.xml b/topicgenerator/dependency-reduced-pom.xml
new file mode 100644
index 00000000..153511b8
--- /dev/null
+++ b/topicgenerator/dependency-reduced-pom.xml
@@ -0,0 +1,677 @@
+
+
+
+ dockstore-support
+ io.dockstore
+ ${revision}${changelist}
+
+ 4.0.0
+ topicgenerator
+ topicgenerator
+ ${revision}${changelist}
+ A service for generating topics using AI for public entries on Dockstore
+ https://github.com/dockstore/dockstore-support
+
+
+ GNU General Public License (GPLv3)
+ https://www.gnu.org/licenses/gpl-3.0.html
+
+
+
+ ${github.url}
+ ${github.url}
+ ${github.url}
+
+
+ Dockstore
+ https://www.dockstore.org/
+
+
+
+
+ maven-shade-plugin
+
+
+ topicGeneratorClient
+ package
+
+ shade
+
+
+
+
+
+ io.dockstore.topicgenerator.client.cli.TopicGeneratorClient
+
+
+
+
+
+
+
+
+
+ *:*
+
+ META-INF/*.SF
+ META-INF/*.DSA
+ META-INF/*.RSA
+ migrations.xml
+ migrations.*.xml
+
+
+
+
+
+
+ maven-enforcer-plugin
+
+
+ maven-dependency-plugin
+
+
+ analyze
+
+ analyze-only
+
+
+ true
+ true
+ true
+
+ org.glassfish.jersey.inject:jersey-hk2
+ ch.qos.logback:logback-classic
+
+
+
+
+
+
+ maven-compiler-plugin
+
+ 17
+
+
+
+ maven-javadoc-plugin
+
+
+ site-deploy
+
+ aggregate
+ test-aggregate
+
+ false
+
+
+ false
+
+
+ maven-checkstyle-plugin
+
+
+ compile
+
+ check
+
+
+ true
+
+
+
+
+ true
+ true
+
+
+
+ com.github.spotbugs
+ spotbugs-maven-plugin
+
+
+ maven-surefire-plugin
+ ${maven-surefire.version}
+
+
+ test
+
+ test
+
+
+
+
+
+ maven-failsafe-plugin
+ ${maven-failsafe.version}
+
+
+ integration-test
+
+ integration-test
+
+
+
+ verify
+
+ verify
+
+
+
+
+ ${skip-topicgenerator-ITs}
+
+
+
+
+
+
+
+ artifacts.oicr.on.ca.ca-snapshots
+ https://artifacts.oicr.on.ca/artifactory/collab-snapshot
+
+
+
+ false
+
+ artifacts.oicr.on.ca
+ artifacts.oicr.on.ca
+ https://artifacts.oicr.on.ca/artifactory/collab-release
+
+
+ apache-releases
+ Apache Releases repository
+ https://repository.apache.org/content/repositories/releases/
+
+
+
+
+ io.dockstore
+ dockstore-webservice
+ 1.16.0-beta.2
+ test
+
+
+ validation-api
+ javax.validation
+
+
+ classgraph
+ io.github.classgraph
+
+
+ jackson-datatype-hibernate5-jakarta
+ com.fasterxml.jackson.datatype
+
+
+ jackson-dataformat-cbor
+ com.fasterxml.jackson.dataformat
+
+
+ google-api-services-oauth2
+ com.google.apis
+
+
+ logstash-logback-encoder
+ net.logstash.logback
+
+
+ dropwizard-logging
+ io.dropwizard
+
+
+ dropwizard-lifecycle
+ io.dropwizard
+
+
+ swagger-java-quay-client
+ io.dockstore
+
+
+ swagger-java-sam-client
+ io.dockstore
+
+
+ swagger-java-bitbucket-client
+ io.dockstore
+
+
+ swagger-java-discourse-client
+ io.dockstore
+
+
+ dockstore-language-plugin-parent
+ io.dockstore
+
+
+ swagger-java-zenodo-client
+ io.dockstore
+
+
+ commons-validator
+ commons-validator
+
+
+ swagger-models-jakarta
+ io.swagger.core.v3
+
+
+ dropwizard-core
+ io.dropwizard
+
+
+ dropwizard-hibernate
+ io.dropwizard
+
+
+ hibernate-core
+ org.hibernate.orm
+
+
+ dropwizard-assets
+ io.dropwizard
+
+
+ dropwizard-client
+ io.dropwizard
+
+
+ dropwizard-jersey
+ io.dropwizard
+
+
+ jersey-server
+ org.glassfish.jersey.core
+
+
+ dropwizard-auth
+ io.dropwizard
+
+
+ metrics-annotation
+ io.dropwizard.metrics
+
+
+ dropwizard-db
+ io.dropwizard
+
+
+ dropwizard-migrations
+ io.dropwizard
+
+
+ dropwizard-forms
+ io.dropwizard
+
+
+ httpasyncclient
+ org.apache.httpcomponents
+
+
+ httpclient5
+ org.apache.httpcomponents.client5
+
+
+ httpcore5
+ org.apache.httpcomponents.core5
+
+
+ jetty-servlets
+ org.eclipse.jetty
+
+
+ jetty-servlet
+ org.eclipse.jetty
+
+
+ jakarta.servlet-api
+ jakarta.servlet
+
+
+ jetty-server
+ org.eclipse.jetty
+
+
+ jetty-http
+ org.eclipse.jetty
+
+
+ dropwizard-jetty
+ io.dropwizard
+
+
+ dropwizard-jackson
+ io.dropwizard
+
+
+ swagger-annotations
+ io.swagger
+
+
+ java-jwt
+ com.auth0
+
+
+ swagger-jaxrs2-jakarta
+ io.swagger.core.v3
+
+
+ swagger-jaxrs2-servlet-initializer-jakarta
+ io.swagger.core.v3
+
+
+ swagger-core
+ io.swagger
+
+
+ jackson-jakarta-rs-json-provider
+ com.fasterxml.jackson.jakarta.rs
+
+
+ google-http-client-jackson
+ com.google.http-client
+
+
+ cwlavro-tools
+ io.cwl
+
+
+ cwlavro-generated
+ io.cwl
+
+
+ json
+ org.json
+
+
+ elasticsearch
+ org.elasticsearch
+
+
+ elasticsearch-rest-client
+ org.elasticsearch.client
+
+
+ elasticsearch-rest-high-level-client
+ org.elasticsearch.client
+
+
+ elasticsearch-x-content
+ org.elasticsearch
+
+
+ elasticsearch-core
+ org.elasticsearch
+
+
+ groovy
+ org.codehaus.groovy
+
+
+ sqs
+ software.amazon.awssdk
+
+
+ cloudwatch
+ software.amazon.awssdk
+
+
+ github-api
+ org.kohsuke
+
+
+ jjwt-api
+ io.jsonwebtoken
+
+
+ jjwt-impl
+ io.jsonwebtoken
+
+
+ jjwt-jackson
+ io.jsonwebtoken
+
+
+ java-gitlab-api
+ org.gitlab
+
+
+ caffeine
+ com.github.ben-manes.caffeine
+
+
+ orcid-model-jakarta
+ org.orcid
+
+
+ jaxb-runtime
+ org.glassfish.jaxb
+
+
+ jakarta.persistence-api
+ jakarta.persistence
+
+
+ swagger-integration-jakarta
+ io.swagger.core.v3
+
+
+
+
+ io.dockstore
+ dockstore-integration-testing
+ 1.16.0-beta.2
+ tests
+ test
+
+
+ docker-java-transport-httpclient5
+ com.github.docker-java
+
+
+ docker-java-core
+ com.github.docker-java
+
+
+ docker-java-transport
+ com.github.docker-java
+
+
+ docker-java-api
+ com.github.docker-java
+
+
+ swagger-java-client
+ io.dockstore
+
+
+ dropwizard-jdbi3
+ io.dropwizard
+
+
+ joda-time
+ joda-time
+
+
+ httpclient5
+ org.apache.httpcomponents.client5
+
+
+ httpcore5
+ org.apache.httpcomponents.core5
+
+
+ github-api
+ org.kohsuke
+
+
+ jackson-dataformat-cbor
+ com.fasterxml.jackson.dataformat
+
+
+ caffeine
+ com.github.ben-manes.caffeine
+
+
+
+
+ org.junit.jupiter
+ junit-jupiter-api
+ 5.10.0
+ test
+
+
+ opentest4j
+ org.opentest4j
+
+
+ junit-platform-commons
+ org.junit.platform
+
+
+ apiguardian-api
+ org.apiguardian
+
+
+
+
+ io.dropwizard
+ dropwizard-testing
+ 4.0.2
+ test
+
+
+ javax.servlet-api
+ javax.servlet
+
+
+ dropwizard-configuration
+ io.dropwizard
+
+
+ dropwizard-servlets
+ io.dropwizard
+
+
+ dropwizard-util
+ io.dropwizard
+
+
+ dropwizard-validation
+ io.dropwizard
+
+
+ jackson-datatype-guava
+ com.fasterxml.jackson.datatype
+
+
+ argparse4j
+ net.sourceforge.argparse4j
+
+
+ jetty-io
+ org.eclipse.jetty
+
+
+ jersey-container-servlet-core
+ org.glassfish.jersey.containers
+
+
+ jersey-apache5-connector
+ org.glassfish.jersey.connectors
+
+
+ jersey-test-framework-core
+ org.glassfish.jersey.test-framework
+
+
+ jersey-test-framework-provider-inmemory
+ org.glassfish.jersey.test-framework.providers
+
+
+ dropwizard-core
+ io.dropwizard
+
+
+ dropwizard-jackson
+ io.dropwizard
+
+
+ dropwizard-jersey
+ io.dropwizard
+
+
+ dropwizard-jetty
+ io.dropwizard
+
+
+ dropwizard-lifecycle
+ io.dropwizard
+
+
+ dropwizard-logging
+ io.dropwizard
+
+
+ metrics-annotation
+ io.dropwizard.metrics
+
+
+ jackson-jakarta-rs-json-provider
+ com.fasterxml.jackson.jakarta.rs
+
+
+ jakarta.servlet-api
+ jakarta.servlet
+
+
+ jetty-server
+ org.eclipse.jetty
+
+
+ jersey-server
+ org.glassfish.jersey.core
+
+
+ httpclient5
+ org.apache.httpcomponents.client5
+
+
+
+
+ uk.org.webcompere
+ system-stubs-jupiter
+ 2.0.1
+ test
+
+
+ mockito-inline
+ org.mockito
+
+
+
+
+ uk.org.webcompere
+ system-stubs-core
+ 2.0.1
+ test
+
+
+ mockito-inline
+ org.mockito
+
+
+
+
+
+
+ central
+ artifacts.oicr.on.ca-releases
+ https://artifacts.oicr.on.ca/artifactory/collab-release
+
+
+
+ 0.18.2
+ UTF-8
+ UTF-8
+
+