Merge branch 'hotfix-1.31.6'

PavlidisLab · May 16, 2024 · b088226 · b088226
2 parents 2e7681b + 58403aa
commit b088226
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Showing 167 changed files with 2,746 additions and 1,336 deletions.
diff --git a/.idea/runConfigurations/Gemma_CLI.xml b/.idea/runConfigurations/Gemma_CLI.xml
diff --git a/.idea/runConfigurations/Gemma_Web.xml b/.idea/runConfigurations/Gemma_Web.xml
diff --git a/.idea/runConfigurations/Generate_testdb.xml b/.idea/runConfigurations/Generate_testdb.xml
diff --git a/.jenkins/Jenkinsfile b/.jenkins/Jenkinsfile
@@ -61,11 +61,10 @@ pipeline {
  stage('Build') {
  steps {
  setBuildStatus "Build", "Build #${env.BUILD_NUMBER} has started...", 'PENDING'
- sh 'mvn -B package -DskipTests'
+ sh 'mvn -B compile'
  }
  post {
  success {
- archiveArtifacts artifacts: '**/target/*.jar, **/target/*.war', fingerprint: true
  setBuildStatus "Build", "Build #${env.BUILD_NUMBER} succeeded.", 'SUCCESS'
  }
  unsuccessful {
@@ -90,6 +89,21 @@ pipeline {
  }
  }
  }
+ stage('Package') {
+ steps {
+ setBuildStatus "Package", "Package for build #${env.BUILD_NUMBER} have started...", 'PENDING'
+ sh 'mvn -B package -DskipTests'
+ }
+ post {
+ success {
+ archiveArtifacts artifacts: '**/target/*.jar, **/target/*.war', fingerprint: true
+ setBuildStatus "Package", "Package for build #${env.BUILD_NUMBER} have passed.", 'SUCCESS'
+ }
+ unsuccessful {
+ setBuildStatus "Package", "Package for build #${env.BUILD_NUMBER} failed.", 'FAILURE'
+ }
+ }
+ }
  stage('Run integration tests and perform deployment in parallel') {
  when {
  anyOf {

diff --git a/gemma-cli/pom.xml b/gemma-cli/pom.xml
@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.31.5</version>
+ <version>1.31.6</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-cli</artifactId>
@@ -29,7 +29,7 @@
  </program>
  </programs>
  <!-- this allows Log4j 2 to lookup for Log4j 1.2 configuration -->
- <extraJvmArguments>-Dlog4j1.compatibility=true -Djava.util.logging.manager=org.apache.logging.log4j.jul.LogManager -Djava.awt.headless=true</extraJvmArguments>
+ <extraJvmArguments>${jvmOptions}</extraJvmArguments>
  <!-- Gemma CLI extensions can be dropped in that folder -->
  <endorsedDir>contrib</endorsedDir>
  </configuration>

diff --git a/gemma-cli/src/main/config/log4j-dev.properties b/gemma-cli/src/main/config/log4j-dev.properties
@@ -59,4 +59,7 @@ log4j.logger.org.hibernate.cache.ehcache.internal.strategy.AbstractReadWriteEhca
 
 # Hibernate Search
 # This is necessary to see progress in IndexGemmaCLI command
-log4j.logger.org.hibernate.search.impl.SimpleIndexingProgressMonitor=INFO
+log4j.logger.org.hibernate.search.impl.SimpleIndexingProgressMonitor=INFO
+
+# Jena
+log4j.logger.com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler=ERROR
diff --git a/gemma-cli/src/main/config/log4j.properties b/gemma-cli/src/main/config/log4j.properties
@@ -123,4 +123,7 @@ log4j.logger.org.hibernate.cache.ehcache.internal.strategy.AbstractReadWriteEhca
 
 # Hibernate Search
 # This is necessary to see progress in IndexGemmaCLI command
-log4j.logger.org.hibernate.search.impl.SimpleIndexingProgressMonitor=INFO
+log4j.logger.org.hibernate.search.impl.SimpleIndexingProgressMonitor=INFO
+
+# Jena
+log4j.logger.com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler=ERROR
diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/GemmaCLI.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/GemmaCLI.java
@@ -143,11 +143,6 @@ public static void main( String[] args ) {
 
  loggingConfigurer.apply();
 
- /*
- * Guarantee that the security settings are uniform throughout the application (all threads).
- */
- SecurityContextHolder.setStrategyName( SecurityContextHolder.MODE_INHERITABLETHREADLOCAL );
-
  List<String> profiles = new ArrayList<>();
  profiles.add( "cli" );
 

diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLI.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLI.java
@@ -26,6 +26,8 @@
 import ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader;
 import ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser;
 import ubic.gemma.core.loader.util.fetcher.HttpFetcher;
+import ubic.gemma.core.ontology.OntologyUtils;
+import ubic.gemma.core.ontology.providers.GeneOntologyService;
 import ubic.gemma.core.util.AbstractAuthenticatedCLI;
 import ubic.gemma.core.util.AbstractCLI;
 import ubic.gemma.model.common.description.ExternalDatabase;
@@ -79,7 +81,6 @@ protected void buildOptions( Options options ) {
  @Override
  protected void doWork() throws Exception {
  NCBIGene2GOAssociationLoader gene2GOAssLoader = new NCBIGene2GOAssociationLoader();
-
  gene2GOAssLoader.setPersisterHelper( persisterHelper );
 
  Collection<Taxon> taxa = taxonService.loadAll();

diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/UpdateEE2CCli.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/UpdateEE2CCli.java
@@ -30,7 +30,7 @@ protected void processOptions( CommandLine commandLine ) throws ParseException {
 
  @Override
  protected void doWork() throws Exception {
- tableMaintenanceUtil.updateExpressionExperiment2CharacteristicEntries( truncate );
+ tableMaintenanceUtil.updateExpressionExperiment2CharacteristicEntries( null, truncate );
  }
 
  @Nullable

diff --git a/gemma-core/pom.xml b/gemma-core/pom.xml
@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.31.5</version>
+ <version>1.31.6</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-core</artifactId>
@@ -279,7 +279,7 @@
  <dependency>
  <groupId>org.apache.commons</groupId>
  <artifactId>commons-csv</artifactId>
- <version>1.10.0</version>
+ <version>1.11.0</version>
  </dependency>
  <dependency>
  <groupId>org.apache.commons</groupId>