Move to next version of the software 5.3.9-SNAPSHOT

EBIBioSamples · Dec 18, 2024 · 4887a63 · 4887a63
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commit 4887a63
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Showing 51 changed files with 341 additions and 341 deletions.
diff --git a/agents/pom.xml b/agents/pom.xml
@@ -9,7 +9,7 @@
 	<parent>
 		<groupId>uk.ac.ebi.biosamples</groupId>
 		<artifactId>biosamples</artifactId>
-		<version>5.3.8-SNAPSHOT</version>
+		<version>5.3.9-SNAPSHOT</version>
 	</parent>
 
 	<modules>

diff --git a/agents/solr/pom.xml b/agents/solr/pom.xml
@@ -7,30 +7,30 @@
 	<parent>
 		<groupId>uk.ac.ebi.biosamples</groupId>
 		<artifactId>biosamples</artifactId>
-		<version>5.3.8-SNAPSHOT</version>
+		<version>5.3.9-SNAPSHOT</version>
 		<relativePath>../../</relativePath>
 	</parent>
 
 	<dependencies>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>properties</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>models-solr</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>messaging</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>utils-ols</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 
 		<dependency>

diff --git a/agents/uploadworkers/pom.xml b/agents/uploadworkers/pom.xml
@@ -7,15 +7,15 @@
 	<parent>
 		<groupId>uk.ac.ebi.biosamples</groupId>
 		<artifactId>biosamples</artifactId>
-		<version>5.3.8-SNAPSHOT</version>
+		<version>5.3.9-SNAPSHOT</version>
 		<relativePath>../../</relativePath>
 	</parent>
 
 	<dependencies>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>biosamples-spring-boot-starter</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
@@ -33,22 +33,22 @@
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>properties</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>utils-webapp</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>messaging</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>models-mongo</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>

diff --git a/client/client/pom.xml b/client/client/pom.xml
@@ -21,15 +21,15 @@
 	<parent>
 		<groupId>uk.ac.ebi.biosamples</groupId>
 		<artifactId>biosamples</artifactId>
-		<version>5.3.8-SNAPSHOT</version>
+		<version>5.3.9-SNAPSHOT</version>
 		<relativePath>../../</relativePath>
 	</parent>
 
 	<dependencies>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>models-core</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.springframework.hateoas</groupId>

diff --git a/client/pom.xml b/client/pom.xml
@@ -14,7 +14,7 @@
 	<parent>
 		<groupId>uk.ac.ebi.biosamples</groupId>
 		<artifactId>biosamples</artifactId>
-		<version>5.3.8-SNAPSHOT</version>
+		<version>5.3.9-SNAPSHOT</version>
 		<relativePath>../</relativePath>
 	</parent>
 

diff --git a/client/starter/pom.xml b/client/starter/pom.xml
@@ -4,7 +4,7 @@
 
 	<groupId>uk.ac.ebi.biosamples</groupId>
 	<artifactId>biosamples-spring-boot-starter</artifactId>
-	<version>5.3.8-SNAPSHOT</version>
+	<version>5.3.9-SNAPSHOT</version>
 
 	<packaging>jar</packaging>
 
@@ -17,7 +17,7 @@
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>client</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.springframework.boot</groupId>

diff --git a/commons/pom.xml b/commons/pom.xml
@@ -7,7 +7,7 @@
 <parent>
 	<groupId>uk.ac.ebi.biosamples</groupId>
 	<artifactId>biosamples</artifactId>
-	<version>5.3.8-SNAPSHOT</version>
+	<version>5.3.9-SNAPSHOT</version>
 </parent>
 
 	<properties>
@@ -24,12 +24,12 @@
 	<dependency>
 	<groupId>uk.ac.ebi.biosamples</groupId>
 	<artifactId>models-mongo</artifactId>
-	<version>5.3.8-SNAPSHOT</version>
+	<version>5.3.9-SNAPSHOT</version>
 	</dependency>
 	<dependency>
 	<groupId>uk.ac.ebi.biosamples</groupId>
 	<artifactId>models-core</artifactId>
-	<version>5.3.8-SNAPSHOT</version>
+	<version>5.3.9-SNAPSHOT</version>
 	</dependency>
 	<dependency>
 	<groupId>com.fasterxml.jackson.core</groupId>

diff --git a/docker-agents.sh b/docker-agents.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
 set -e
 
-docker-compose run --rm --service-ports biosamples-agents-solr java -jar agents-solr-5.3.8-SNAPSHOT.jar
+docker-compose run --rm --service-ports biosamples-agents-solr java -jar agents-solr-5.3.9-SNAPSHOT.jar
 echo "Successfully runned agents"
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -18,7 +18,7 @@ services:
     command:
     - java
     - -jar
-    - webapps-core-5.3.8-SNAPSHOT.war
+    - webapps-core-5.3.9-SNAPSHOT.war
     environment:
     - env=local
     #application properties
@@ -111,7 +111,7 @@ services:
     command:
       - java
       - -jar
-      - webapps-core-v2-5.3.8-SNAPSHOT.jar
+      - webapps-core-v2-5.3.9-SNAPSHOT.jar
     environment:
       #application properties
       - biosamples.bulksubmisison.webin.superuser.validation=true
@@ -193,7 +193,7 @@ services:
     command:
     - java
     - -jar
-    - agents-solr-5.3.8-SNAPSHOT.jar
+    - agents-solr-5.3.9-SNAPSHOT.jar
     environment:
     - SPRING_RABBITMQ_HOST=rabbitmq
     - SPRING_RABBITMQ_PUBLISHER-CONFIRMS=true
@@ -218,7 +218,7 @@ services:
     command:
       - java
       - -jar
-      - agents-uploadworkers-5.3.8-SNAPSHOT.jar
+      - agents-uploadworkers-5.3.9-SNAPSHOT.jar
     environment:
       #AAP certificate
       - jwt.certificate=public.explore.der
@@ -247,7 +247,7 @@ services:
     command:
     - java
     - -jar
-    - pipelines-ena-5.3.8-SNAPSHOT.jar
+    - pipelines-ena-5.3.9-SNAPSHOT.jar
     environment:
     - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
     - LOGGING_FILE=/logs/pipelines-ena.log
@@ -262,7 +262,7 @@ services:
     command:
     - java
     - -jar
-    - pipelines-ncbi-5.3.8-SNAPSHOT.jar
+    - pipelines-ncbi-5.3.9-SNAPSHOT.jar
     environment:
     - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
     - LOGGING_FILE=/logs/pipelines-ncbi.log
@@ -277,7 +277,7 @@ services:
     command:
     - java
     - -jar
-    - pipelines-accession-5.3.8-SNAPSHOT.jar
+    - pipelines-accession-5.3.9-SNAPSHOT.jar
     environment:
     - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
     - LOGGING_FILE=/logs/pipelines-accession.log
@@ -292,7 +292,7 @@ services:
     command:
     - java
     - -jar
-    - pipelines-copydown-5.3.8-SNAPSHOT.jar
+    - pipelines-copydown-5.3.9-SNAPSHOT.jar
     environment:
     - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
     - LOGGING_FILE=/logs/pipelines-copydown.log
@@ -307,7 +307,7 @@ services:
     command:
     - java
     - -jar
-    - pipelines-curation-5.3.8-SNAPSHOT.jar
+    - pipelines-curation-5.3.9-SNAPSHOT.jar
     environment:
     - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
     - LOGGING_FILE=/logs/pipelines-curation.log
@@ -324,7 +324,7 @@ services:
     command:
     - java
     - -jar
-    - pipelines-zooma-5.3.8-SNAPSHOT.jar
+    - pipelines-zooma-5.3.9-SNAPSHOT.jar
     environment:
     - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
     - LOGGING_FILE=/logs/pipelines-zooma.log
@@ -341,7 +341,7 @@ services:
     command:
     - java
     - -jar
-    - pipelines-reindex-5.3.8-SNAPSHOT.jar
+    - pipelines-reindex-5.3.9-SNAPSHOT.jar
     environment:
     - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
     - LOGGING_FILE=/logs/pipelines-reindex.log
@@ -359,7 +359,7 @@ services:
     command:
     - java
     - -jar
-    - pipelines-export-5.3.8-SNAPSHOT.jar
+    - pipelines-export-5.3.9-SNAPSHOT.jar
     - --gzip
     - /export/export.json.gzip
     environment:
@@ -377,7 +377,7 @@ services:
     command:
     - java
     - -jar
-    - integration-5.3.8-SNAPSHOT.jar
+    - integration-5.3.9-SNAPSHOT.jar
     environment:
     - BIOSAMPLES_CLIENT_URI=http://biosamples-webapps-core:8080/biosamples
     - BIOSAMPLES_CLIENT_URI_V2=http://biosamples-webapps-core-v2:8080/biosamples/v2

diff --git a/docker-integration.big.sh b/docker-integration.big.sh
@@ -11,7 +11,7 @@ ARGS=--spring.profiles.active=big
 for X in 1 2 3 4 5
 do
   #java -jar integration/target/integration-4.0.0-SNAPSHOT.jar --phase=$X $ARGS $@
-  docker-compose run --rm --service-ports biosamples-integration java -jar integration-5.3.8-SNAPSHOT.jar --phase=$X $ARGS $@
+  docker-compose run --rm --service-ports biosamples-integration java -jar integration-5.3.9-SNAPSHOT.jar --phase=$X $ARGS $@
   sleep 10 #solr is configured to commit every 5 seconds
 
 done

diff --git a/docker-integration.sh b/docker-integration.sh
@@ -1,25 +1,25 @@
-#!/bin/bash
-set -e
-
-./docker-webapp.sh --clean
-
-
-docker-compose up -d biosamples-agents-solr
-docker-compose up -d biosamples-agents-upload-workers
-
-#ARGS=--spring.profiles.active=big
-for X in 1 2 3 4 5 6
-do
-  echo "============================================================================================================"
-  echo "=================================== STARTING INTEGRATION TESTS PHASE-"$X "====================================="
-  echo "============================================================================================================"
-  #java -jar integration/target/integration-4.0.0-SNAPSHOT.jar --phase=$X $ARGS $@
-  docker-compose run --rm --service-ports biosamples-integration java -jar integration-5.3.8-SNAPSHOT.jar --phase=$X $ARGS $@
-  sleep 10 #solr is configured to commit every 5 seconds
-
-done
-
-#leave the agent up at the end
-docker-compose up -d biosamples-agents-solr
-
-echo "Successfully completed"
+#!/bin/bash
+set -e
+
+./docker-webapp.sh --clean
+
+
+docker-compose up -d biosamples-agents-solr
+docker-compose up -d biosamples-agents-upload-workers
+
+#ARGS=--spring.profiles.active=big
+for X in 1 2 3 4 5 6
+do
+  echo "============================================================================================================"
+  echo "=================================== STARTING INTEGRATION TESTS PHASE-"$X "====================================="
+  echo "============================================================================================================"
+  #java -jar integration/target/integration-4.0.0-SNAPSHOT.jar --phase=$X $ARGS $@
+  docker-compose run --rm --service-ports biosamples-integration java -jar integration-5.3.9-SNAPSHOT.jar --phase=$X $ARGS $@
+  sleep 10 #solr is configured to commit every 5 seconds
+
+done
+
+#leave the agent up at the end
+docker-compose up -d biosamples-agents-solr
+
+echo "Successfully completed"
diff --git a/docker-test.sh b/docker-test.sh
@@ -5,7 +5,7 @@ docker-compose up -d biosamples-agents-solr
 
 for X in "$@"
 do
-  docker-compose run --rm --service-ports biosamples-integration java -jar integration-5.3.8-SNAPSHOT.jar --phase=$X $ARGS $@
+  docker-compose run --rm --service-ports biosamples-integration java -jar integration-5.3.9-SNAPSHOT.jar --phase=$X $ARGS $@
   sleep 30 #solr is configured to commit every 5 seconds
 
 done

diff --git a/integration/pom.xml b/integration/pom.xml
@@ -6,36 +6,36 @@
 	<parent>
 		<groupId>uk.ac.ebi.biosamples</groupId>
 		<artifactId>biosamples</artifactId>
-		<version>5.3.8-SNAPSHOT</version>
+		<version>5.3.9-SNAPSHOT</version>
 		<relativePath>../</relativePath>
 	</parent>
 
 	<dependencies>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>biosamples-spring-boot-starter</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>models-sitemap</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>models-jsonld</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>properties</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>models-neo4j</artifactId>
-			<version>5.3.8-SNAPSHOT</version>
+			<version>5.3.9-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>