Merge branch 'hotfix-1.27.11'

Author: arteymix

gemma-core/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>gemma</artifactId>
         <groupId>gemma</groupId>
-        <version>1.27.10</version>
+        <version>1.27.11</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>gemma-core</artifactId>
@@ -14,22 +14,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-antrun-plugin</artifactId>
-                <version>1.7</version>
-                <configuration>
-                    <target>
-                        <taskdef name="schemaexport" classname="org.hibernate.tool.hbm2ddl.SchemaExportTask">
-                            <classpath>
-                                <path refid="maven.dependency.classpath"/>
-                            </classpath>
-                        </taskdef>
-                        <mkdir dir="target/schema"/>
-                        <schemaexport quiet="true" text="true" create="true" drop="false" delimiter=";"
-                                      output="${project.build.directory}/schema/gemma-ddl.sql"
-                                      config="${project.basedir}/src/main/resources/hibernate.cfg.xml">
-                            <fileset dir="src/main/resources" includes="**/*.hbm.xml"/>
-                        </schemaexport>
-                    </target>
-                </configuration>
+                <version>3.0.0</version>
                 <executions>
                     <execution>
                         <id>version-file</id>
@@ -46,12 +31,31 @@
                         </configuration>
                     </execution>
                     <execution>
+                        <id>schema-export</id>
                         <phase>generate-resources</phase>
                         <goals>
                             <goal>run</goal>
                         </goals>
+                        <configuration>
+                            <target>
+                                <taskdef name="schemaexport" classname="org.hibernate.tool.hbm2ddl.SchemaExportTask"/>
+                                <mkdir dir="${project.build.directory}/schema"/>
+                                <schemaexport quiet="true" text="true" create="true" drop="false" delimiter=";"
+                                         output="${project.build.directory}/schema/gemma-ddl.sql"
+                                         config="${project.basedir}/src/main/resources/hibernate.cfg.xml">
+                                    <fileset dir="${project.basedir}/src/main/resources" includes="**/*.hbm.xml"/>
+                                </schemaexport>
+                            </target>
+                        </configuration>
                     </execution>
                 </executions>
+                <dependencies>
+                    <dependency>
+                        <groupId>org.hibernate</groupId>
+                        <artifactId>hibernate-core</artifactId>
+                        <version>${hibernate.version}</version>
+                    </dependency>
+                </dependencies>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
@@ -120,7 +124,7 @@
                                     <pluginExecutionFilter>
                                         <groupId>org.apache.maven.plugins</groupId>
                                         <artifactId>maven-antrun-plugin</artifactId>
-                                        <versionRange>[1.7,)</versionRange>
+                                        <versionRange>[3.0.0,)</versionRange>
                                         <goals>
                                             <goal>run</goal>
                                         </goals>
@@ -150,7 +154,7 @@
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-dependency-plugin</artifactId>
-                        <version>3.2.0</version>
+                        <version>3.1.2</version>
                         <executions>
                             <execution>
                                 <phase>process-resources</phase>
@@ -167,14 +171,6 @@
                                             <outputDirectory>${project.build.directory}/schema</outputDirectory>
                                             <includes>**/*.sql</includes>
                                         </artifactItem>
-                                        <artifactItem>
-                                            <groupId>gemma</groupId>
-                                            <artifactId>gemma-model</artifactId>
-                                            <version>1.10.1</version>
-                                            <overWrite>true</overWrite>
-                                            <outputDirectory>${project.build.directory}/schema</outputDirectory>
-                                            <includes>**/*.sql</includes>
-                                        </artifactItem>
                                     </artifactItems>
                                 </configuration>
                             </execution>
@@ -264,7 +260,7 @@
             <version>1.7</version>
         </dependency>
 
-        <!-- Lucene (version is synced with baseCode -->
+        <!-- Lucene (version is synced with baseCode) -->
         <dependency>
             <groupId>org.apache.lucene</groupId>
             <artifactId>lucene-core</artifactId>
@@ -276,7 +272,7 @@
             <version>${lucene.version}</version>
         </dependency>
 
-        <!-- Jena -->
+        <!-- Jena (version is synced with baseCode) -->
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-core</artifactId>
@@ -375,7 +371,7 @@
             <version>1.7.4</version>
         </dependency>
         <!-- bit array -->
-        <!-- it can't be updated though because the binary format has changed and we store those in the database -->
+        <!-- it can't be updated though because the binary format has changed, and we store those in the database -->
         <dependency>
             <groupId>com.googlecode.javaewah</groupId>
             <artifactId>JavaEWAH</artifactId>

gemma-core/src/main/config/log4j.properties

@@ -10,7 +10,7 @@
 log4j.appender.stderr=org.apache.log4j.ConsoleAppender
 log4j.appender.stderr.target=System.err
 log4j.appender.stderr.layout=org.apache.log4j.PatternLayout
-log4j.appender.stderr.layout.ConversionPattern=[Gemma %d] %p [%t] %C.%M(%L) | %m%n
+log4j.appender.stderr.layout.ConversionPattern=%d %highlight{%p} %style{%pid}{magenta} [%t] %style{%C.%M(%L)}{cyan} | %m%n
 
 # Log to a file. Note that if File is a relative path, the output file goes wherever the application JVM was started from.
 # Define gemma.log.dir as a parameter to your JAVA_OPTS and make sure this is passed to java when you start it.
@@ -19,7 +19,7 @@ log4j.appender.file.File=${gemma.log.dir}/gemma.log
 log4j.appender.file.MaxFileSize=10000KB
 log4j.appender.file.MaxBackupIndex=10
 log4j.appender.file.layout=org.apache.log4j.PatternLayout
-log4j.appender.file.layout.ConversionPattern=[Gemma - %t (%d)] %p %C.%M(%L) | %m%nLso
+log4j.appender.file.layout.ConversionPattern=[Gemma - %t (%d)] %p %C.%M(%L) | %m%n
 
 # Log file for WARNING and higher level errors
 log4j.appender.warningFile=org.apache.log4j.DailyRollingFileAppender

gemma-core/src/main/java/ubic/gemma/core/analysis/expression/coexpression/links/AbstractMatrixRowPairAnalysis.java

@@ -21,7 +21,7 @@
 import cern.colt.bitvector.BitMatrix;
 import cern.colt.list.DoubleArrayList;
 import cern.colt.list.ObjectArrayList;
-import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.time.StopWatch;
 import org.apache.commons.logging.Log;

gemma-core/src/main/java/ubic/gemma/core/analysis/expression/diff/LinearModelAnalyzer.java

@@ -20,14 +20,17 @@
 
 import cern.colt.matrix.DoubleMatrix1D;
 import cern.colt.matrix.impl.DenseDoubleMatrix1D;
-import org.apache.commons.collections.Transformer;
-import org.apache.commons.collections.TransformerUtils;
+import org.apache.commons.collections4.Transformer;
+import org.apache.commons.collections4.TransformerUtils;
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.StopWatch;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.context.annotation.Scope;
+import org.springframework.core.task.AsyncTaskExecutor;
 import org.springframework.stereotype.Component;
 import ubic.basecode.dataStructure.matrix.DenseDoubleMatrix;
 import ubic.basecode.dataStructure.matrix.DoubleMatrix;
@@ -140,6 +143,9 @@ private static BioAssayDimension createBADMap( List<BioMaterial> columnsToUse )
         return reorderedDim;
     }
 
+    @Autowired
+    private AsyncTaskExecutor taskExecutor;
+
     /**
      * Determine if any factor should be treated as the intercept term.
      */
@@ -1432,9 +1438,8 @@ private Map<String, LinearModelSummary> runAnalysis( final DoubleMatrix<Composit
     private Future<?> runAnalysisFuture( final DesignMatrix designMatrix, final DoubleMatrix<String, String> data,
             final Map<String, LinearModelSummary> rawResults, final DoubleMatrix1D librarySize,
             final DifferentialExpressionAnalysisConfig config ) {
-        ExecutorService service = Executors.newSingleThreadExecutor();
 
-        Future<?> f = service.submit( new Runnable() {
+        Future<?> f = taskExecutor.submit( new Runnable() {
             @Override
             public void run() {
                 StopWatch timer = new StopWatch();
@@ -1476,7 +1481,6 @@ public void run() {
             }
         } );
 
-        service.shutdown();
         return f;
     }
 }

gemma-core/src/main/java/ubic/gemma/core/analysis/service/ArrayDesignAnnotationServiceImpl.java

@@ -18,8 +18,8 @@
  */
 package ubic.gemma.core.analysis.service;
 
-import org.apache.commons.collections.Transformer;
-import org.apache.commons.collections.iterators.TransformIterator;
+import org.apache.commons.collections4.Transformer;
+import org.apache.commons.collections4.iterators.TransformIterator;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;

gemma-core/src/main/java/ubic/gemma/core/apps/ExperimentalDesignImportCli.java

@@ -57,8 +57,7 @@ protected void buildOptions( Options options ) {
 
         Option expOption = Option.builder( "e" ).required().hasArg().argName( "Expression experiment name" )
                 .desc(
-                        "Expression experiment short name. Most tools recognize comma-delimited values given on the command line, "
-                                + "and if this option is omitted, the tool will be applied to all expression experiments." )
+                        "Expression experiment short name" )
                 .longOpt( "experiment" ).build();
 
         options.addOption( expOption );

gemma-core/src/main/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLI.java

@@ -21,6 +21,8 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.springframework.core.task.AsyncTaskExecutor;
+import org.springframework.core.task.TaskExecutor;
 import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
 import ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader;
 import ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser;
@@ -64,8 +66,9 @@ protected void buildOptions( Options options ) {
     @Override
     protected void doWork() throws Exception {
         TaxonService taxonService = this.getBean( TaxonService.class );
+        AsyncTaskExecutor taskExecutor = this.getBean( AsyncTaskExecutor.class );
 
-        NCBIGene2GOAssociationLoader gene2GOAssLoader = new NCBIGene2GOAssociationLoader();
+        NCBIGene2GOAssociationLoader gene2GOAssLoader = new NCBIGene2GOAssociationLoader( taskExecutor );
 
         gene2GOAssLoader.setPersisterHelper( this.getPersisterHelper() );
 

gemma-core/src/main/java/ubic/gemma/core/apps/NcbiGeneLoaderCLI.java

@@ -22,6 +22,8 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.lang3.StringUtils;
+import org.springframework.core.task.AsyncTaskExecutor;
+import org.springframework.core.task.TaskExecutor;
 import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
 import ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader;
 import ubic.gemma.core.util.AbstractCLI;
@@ -98,7 +100,7 @@ protected boolean requireLogin() {
 
     @Override
     protected void doWork() throws Exception {
-        loader = new NcbiGeneLoader();
+        loader = new NcbiGeneLoader( this.getBean( AsyncTaskExecutor.class ) );
         TaxonService taxonService = this.getBean( TaxonService.class );
         loader.setTaxonService( taxonService );
         loader.setPersisterHelper( this.getPersisterHelper() );

gemma-core/src/main/java/ubic/gemma/core/externalDb/GoldenPathSequenceAnalysis.java

@@ -18,7 +18,7 @@
  */
 package ubic.gemma.core.externalDb;
 
-import org.apache.commons.collections.map.LRUMap;
+import org.apache.commons.collections4.map.LRUMap;
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.dao.DataAccessException;
 import org.springframework.jdbc.core.ResultSetExtractor;