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theisurutheisuru
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Prepare for release of BioSamples 5.3.12
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Lines changed: 178 additions & 172 deletions

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‎agents/pom.xml‎

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@@ -9,7 +9,7 @@
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<parent>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>biosamples</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</parent>
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<modules>

‎agents/solr/pom.xml‎

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<parent>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>biosamples</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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<relativePath>../../</relativePath>
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</parent>
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<dependencies>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>properties</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>models-solr</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>messaging</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>utils-ols</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>

‎agents/uploadworkers/pom.xml‎

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<parent>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>biosamples</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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<relativePath>../../</relativePath>
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</parent>
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<dependencies>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>biosamples-spring-boot-starter</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>org.springframework.boot</groupId>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>properties</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>utils-webapp</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>messaging</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>models-mongo</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>

‎client/client/pom.xml‎

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<parent>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>biosamples</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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<relativePath>../../</relativePath>
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</parent>
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<dependencies>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>models-core</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>org.springframework.hateoas</groupId>

‎client/pom.xml‎

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<parent>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>biosamples</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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<relativePath>../</relativePath>
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</parent>
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‎client/starter/pom.xml‎

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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>biosamples-spring-boot-starter</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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<packaging>jar</packaging>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>client</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>org.springframework.boot</groupId>

‎commons/pom.xml‎

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<parent>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>biosamples</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</parent>
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<properties>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>models-mongo</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>uk.ac.ebi.biosamples</groupId>
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<artifactId>models-core</artifactId>
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<version>5.3.12-RC1</version>
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<version>5.3.12</version>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.core</groupId>

‎docker-agents.sh‎

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#!/bin/bash
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set -e
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docker-compose run --rm --service-ports biosamples-agents-solr java -jar agents-solr-5.3.12-RC1.jar
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docker-compose run --rm --service-ports biosamples-agents-solr java -jar agents-solr-5.3.12.jar
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echo "Successfully runned agents"

‎docker-compose.yml‎

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command:
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- java
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- -jar
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- webapps-core-5.3.12-RC1.war
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- webapps-core-5.3.12.war
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environment:
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- env=local
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#application properties
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command:
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- java
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- -jar
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- webapps-core-v2-5.3.12-RC1.jar
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- webapps-core-v2-5.3.12.jar
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environment:
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#application properties
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- biosamples.bulksubmisison.webin.superuser.validation=true
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command:
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- java
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- -jar
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- agents-solr-5.3.12-RC1.jar
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- agents-solr-5.3.12.jar
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environment:
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- SPRING_RABBITMQ_HOST=rabbitmq
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- SPRING_RABBITMQ_PUBLISHER-CONFIRMS=true
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command:
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- java
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- -jar
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- agents-uploadworkers-5.3.12-RC1.jar
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- agents-uploadworkers-5.3.12.jar
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environment:
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- SPRING_RABBITMQ_HOST=rabbitmq
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- SPRING_RABBITMQ_PUBLISHER-CONFIRMS=true
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command:
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- java
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- -jar
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- pipelines-ena-5.3.12-RC1.jar
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- pipelines-ena-5.3.12.jar
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environment:
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- BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
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- LOGGING_FILE=/logs/pipelines-ena.log
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command:
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- java
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- -jar
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- pipelines-ncbi-5.3.12-RC1.jar
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- pipelines-ncbi-5.3.12.jar
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environment:
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- BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
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- LOGGING_FILE=/logs/pipelines-ncbi.log
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command:
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- java
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- -jar
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- pipelines-accession-5.3.12-RC1.jar
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- pipelines-accession-5.3.12.jar
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environment:
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- BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
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- LOGGING_FILE=/logs/pipelines-accession.log
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command:
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- java
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- -jar
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- pipelines-copydown-5.3.12-RC1.jar
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- pipelines-copydown-5.3.12.jar
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environment:
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- BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
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- LOGGING_FILE=/logs/pipelines-copydown.log
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command:
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- java
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- -jar
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- pipelines-curation-5.3.12-RC1.jar
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- pipelines-curation-5.3.12.jar
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environment:
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- BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
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- LOGGING_FILE=/logs/pipelines-curation.log
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command:
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- java
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- -jar
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- pipelines-zooma-5.3.12-RC1.jar
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- pipelines-zooma-5.3.12.jar
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environment:
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- BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
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- LOGGING_FILE=/logs/pipelines-zooma.log
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command:
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- java
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- -jar
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- pipelines-reindex-5.3.12-RC1.jar
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- pipelines-reindex-5.3.12.jar
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environment:
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- BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
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- LOGGING_FILE=/logs/pipelines-reindex.log
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command:
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- java
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- -jar
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- pipelines-export-5.3.12-RC1.jar
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- pipelines-export-5.3.12.jar
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- --gzip
349349
- /export/export.json.gzip
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environment:
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command:
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- java
364364
- -jar
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- integration-5.3.12-RC1.jar
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- integration-5.3.12.jar
366366
environment:
367367
- BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
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- BIOSAMPLES_CLIENT_URI_V2=http://biosamples-webapps-core-v2:8080/biosamples/v2

‎docker-integration.big.sh‎

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for X in 1 2 3 4 5
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do
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#java -jar integration/target/integration-4.0.0-SNAPSHOT.jar --phase=$X $ARGS $@
14-
docker-compose run --rm --service-ports biosamples-integration java -jar integration-5.3.12-RC1.jar --phase=$X $ARGS $@
14+
docker-compose run --rm --service-ports biosamples-integration java -jar integration-5.3.12.jar --phase=$X $ARGS $@
1515
sleep 10 #solr is configured to commit every 5 seconds
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done

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