Merge branch 'hotfix-1.29.6'

gemma-cli/pom.xml

@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.29.5</version>
+ <version>1.29.6</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-cli</artifactId>

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

@@ -142,4 +142,5 @@ log4j.logger.org.hibernate=WARN
 log4j.logger.org.hibernate.cache.ReadWriteCache=ERROR
 # Avoid warnings about collection fail-safe cleanup.
 log4j.logger.org.hibernate.engine.loading.LoadContexts=ERROR
-log4j.logger.net.sf.ehcache.hibernate.strategy.AbstractReadWriteEhcacheAccessStrategy=ERROR
+log4j.logger.net.sf.ehcache.hibernate.strategy.AbstractReadWriteEhcacheAccessStrategy=ERROR
+log4j.logger.org.hibernate.cache.ehcache.internal.strategy.AbstractReadWriteEhcacheAccessStrategy=ERROR

gemma-cli/src/main/java/ubic/gemma/core/apps/DifferentialExpressionAnalysisCli.java

@@ -505,7 +505,7 @@ private Collection<ExperimentalFactor> guessFactors( ExpressionExperiment ee ) {
  */
  private Collection<DifferentialExpressionAnalysis> tryToRedoBasedOnOldAnalysis( ExpressionExperiment ee ) {
  Collection<DifferentialExpressionAnalysis> oldAnalyses = differentialExpressionAnalysisService
- .findByInvestigation( ee );
+ .findByExperiment( ee );
 
  if ( oldAnalyses.isEmpty() ) {
  throw new IllegalArgumentException( "There are no old analyses to redo" );

gemma-core/pom.xml

@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.29.5</version>
+ <version>1.29.6</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-core</artifactId>
@@ -64,9 +64,20 @@
  <dependency>
  <groupId>org.dom4j</groupId>
  <artifactId>dom4j</artifactId>
- <version>2.1.3</version>
+ <version>${dom4j.version}</version>
  <scope>runtime</scope>
  </dependency>
+ <!-- Hibernate's JBoss logging will hook into Log4j 1.2 API -->
+ <dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-core</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-1.2-api</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
  </dependencies>
  </plugin>
  <plugin>
@@ -78,6 +89,11 @@
  <goals>
  <goal>test-jar</goal>
  </goals>
+ <configuration>
+ <excludes>
+ <exclude>log4j-test.properties</exclude>
+ </excludes>
+ </configuration>
  </execution>
  </executions>
  </plugin>
@@ -112,8 +128,8 @@
  <version>1.5</version>
  <dependencies><!-- yes, this needs to be here. -->
  <dependency>
- <groupId>mysql</groupId>
- <artifactId>mysql-connector-java</artifactId>
+ <groupId>com.mysql</groupId>
+ <artifactId>mysql-connector-j</artifactId>
  <version>${mysql.version}</version>
  <scope>runtime</scope>
  </dependency>
@@ -282,6 +298,12 @@
  <groupId>ubc.chibi.compass-fork</groupId>
  <artifactId>compass-fork</artifactId>
  <version>1.2.0</version>
+ <exclusions>
+ <exclusion>
+ <groupId>commons-el</groupId>
+ <artifactId>commons-el</artifactId>
+ </exclusion>
+ </exclusions>
  </dependency>
 
  <!-- Apache Commons -->

gemma-core/src/main/java/ubic/gemma/core/analysis/expression/AnalysisUtilServiceImpl.java

@@ -73,15 +73,15 @@ public boolean deleteOldAnalyses( ExpressionExperiment expExp ) {
  }
 
  for ( DifferentialExpressionAnalysis diff : differentialExpressionAnalysisService
- .findByInvestigation( expExp ) ) {
+ .findByExperiment( expExp ) ) {
  try {
  differentialExpressionAnalysisService.remove( diff );
  } catch ( Exception e ) {
  AnalysisUtilServiceImpl.log.warn( "Could not remove analysis: " + diff + ": " + e.getMessage() );
  removedAll = false;
  }
  }
- for ( CoexpressionAnalysis coex : coexpressionAnalysisService.findByInvestigation( expExp ) ) {
+ for ( CoexpressionAnalysis coex : coexpressionAnalysisService.findByExperiment( expExp ) ) {
  try {
  coexpressionAnalysisService.remove( coex );
  } catch ( Exception e ) {

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

@@ -48,7 +48,7 @@ public class LinkAnalysisPersisterImpl implements LinkAnalysisPersister {
 
  @Override
  public boolean deleteAnalyses( BioAssaySet ee ) {
- Collection<CoexpressionAnalysis> oldAnalyses = coexpressionAnalysisService.findByInvestigation( ee );
+ Collection<CoexpressionAnalysis> oldAnalyses = coexpressionAnalysisService.findByExperiment( ee );
 
  if ( oldAnalyses.isEmpty() )
  return false;

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

@@ -37,7 +37,6 @@
 import ubic.gemma.model.expression.designElement.CompositeSequence;
 import ubic.gemma.model.expression.experiment.*;
 import ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService;
-import ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService;
 import ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService;
 import ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
@@ -76,7 +75,7 @@ public class DifferentialExpressionAnalyzerServiceImpl implements DifferentialEx
  @Override
  public int deleteAnalyses( ExpressionExperiment expressionExperiment ) {
  Collection<DifferentialExpressionAnalysis> diffAnalysis = differentialExpressionAnalysisService
- .findByInvestigation( expressionExperiment );
+ .findByExperiment( expressionExperiment );
 
  int result = 0;
  if ( diffAnalysis == null || diffAnalysis.isEmpty() ) {
@@ -361,7 +360,7 @@ private void deleteAnalysisFiles( DifferentialExpressionAnalysis analysis ) {
  private void deleteOldAnalyses( ExpressionExperiment expressionExperiment,
  DifferentialExpressionAnalysis newAnalysis, Collection<ExperimentalFactor> factors ) {
  Collection<DifferentialExpressionAnalysis> diffAnalyses = differentialExpressionAnalysisService
- .findByInvestigation( expressionExperiment );
+ .findByExperiment( expressionExperiment );
  int numDeleted = 0;
  if ( diffAnalyses == null || diffAnalyses.isEmpty() ) {
  DifferentialExpressionAnalyzerServiceImpl.log

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

@@ -743,8 +743,8 @@ private DifferentialExpressionAnalysis doAnalysis( BioAssaySet bioAssaySet,
  */
 
  // this used to be a Set, but a List is much faster.
- Map<String, List<DifferentialExpressionAnalysisResult>> resultLists = new HashMap<>();
- Map<String, List<Double>> pvaluesForQvalue = new HashMap<>();
+ Map<String, List<DifferentialExpressionAnalysisResult>> resultLists = new HashMap<>( properDesignMatrix.getTerms().size() );
+ Map<String, List<Double>> pvaluesForQvalue = new HashMap<>( properDesignMatrix.getTerms().size() );
 
  // We use the design matrix to ensure that we only consider terms that actually ended up in the model. 
  for ( String factorName : properDesignMatrix.getTerms() ) {
@@ -1332,7 +1332,7 @@ private Map<FactorValue, ExpressionDataDoubleMatrix> makeSubSets( DifferentialEx
  "You cannot analyze a factor and use it for subsetting at the same time." );
  }
 
- Map<FactorValue, List<BioMaterial>> subSetSamples = new HashMap<>();
+ Map<FactorValue, List<BioMaterial>> subSetSamples = new HashMap<>( subsetFactor.getFactorValues().size() );
  for ( FactorValue fv : subsetFactor.getFactorValues() ) {
  assert fv.getMeasurement() == null;
  subSetSamples.put( fv, new ArrayList<BioMaterial>() );

gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/PreprocessorServiceImpl.java

@@ -20,18 +20,15 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Component;
 
 import org.springframework.stereotype.Service;
 import ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService;
 import ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService;
-import ubic.gemma.core.analysis.preprocess.filter.NoRowsLeftAfterFilteringException;
 import ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper;
 import ubic.gemma.core.analysis.report.ExpressionExperimentReportService;
 import ubic.gemma.core.analysis.service.ExpressionDataFileService;
 import ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix;
 import ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis;
-import ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType;
 import ubic.gemma.model.common.auditAndSecurity.eventType.BatchCorrectionEvent;
 import ubic.gemma.model.common.quantitationtype.QuantitationType;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
@@ -251,7 +248,7 @@ private ExpressionExperiment processExceptForVectorCreate( ExpressionExperiment
  * Redo any old diff ex analyses
  */
  Collection<DifferentialExpressionAnalysis> oldAnalyses = differentialExpressionAnalysisService
- .findByInvestigation( ee );
+ .findByExperiment( ee );
 
  if ( !oldAnalyses.isEmpty() ) {
 

gemma-core/src/main/java/ubic/gemma/core/association/phenotype/PhenotypeAssoManagerServiceHelperImpl.java

@@ -470,7 +470,7 @@ private void updatePhenotypeAssociationPublication( PhenotypeAssociation phe,
  if ( toUpdate ) {
 
  for ( PhenotypeAssociationPublication associationPublication : phe.getPhenotypeAssociationPublications() ) {
- this.phenotypeAssociationService.removePhenotypePublication( associationPublication.getId() );
+ this.phenotypeAssociationService.removePhenotypePublication( associationPublication );
  }
 
  Collection<PhenotypeAssociationPublication> phenotypeAssociationPublications = new HashSet<>();

gemma-core/src/main/java/ubic/gemma/core/association/phenotype/PhenotypeAssociationManagerServiceImpl.java

@@ -1419,6 +1419,11 @@ private ValidateEvidenceValueObject determineSameGeneAndPhenotypeAnnotated(
  OntologyTerm ontologyTerm = this.ontologyService
  .getTerm( phenotypeAlreadyPresent.getValueUri() );
 
+ if ( ontologyTerm == null ) {
+ log.warn( String.format( "Unexpected null term for value URI %s from the ontology service.", phenotypeAlreadyPresent.getValueUri() ) );
+ continue;
+ }
+
  for ( OntologyTerm ot : ontologyTerm.getParents( true ) ) {
  parentOrChildTerm.add( ot.getUri() );
  }

gemma-core/src/main/java/ubic/gemma/core/expression/experiment/service/ExpressionExperimentSearchServiceImpl.java

@@ -240,11 +240,13 @@ public List<SearchResultDisplayObject> getAllTaxonExperimentGroup( Long taxonId
  expressionExperimentSetService.thaw( set );
  if ( set.getTaxon().getId().equals( taxonId ) ) {
  ExpressionExperimentSetValueObject eevo = expressionExperimentSetService.loadValueObject( set );
- newSRDO = new SearchResultDisplayObject( eevo );
- newSRDO.setUserOwned( securityService.isPrivate( set ) );
- ( ( ExpressionExperimentSetValueObject ) newSRDO.getResultValueObject() )
- .setIsPublic( securityService.isPublic( set ) );
- setResults.add( newSRDO );
+ if ( eevo != null ) {
+ newSRDO = new SearchResultDisplayObject( eevo );
+ newSRDO.setUserOwned( securityService.isPrivate( set ) );
+ ( ( ExpressionExperimentSetValueObject ) newSRDO.getResultValueObject() )
+ .setIsPublic( securityService.isPublic( set ) );
+ setResults.add( newSRDO );
+ }
  }
  }
 

gemma-core/src/main/java/ubic/gemma/core/ontology/OntologyService.java

@@ -14,7 +14,6 @@
  */
 package ubic.gemma.core.ontology;
 
-import org.springframework.beans.factory.InitializingBean;
 import ubic.basecode.ontology.model.OntologyIndividual;
 import ubic.basecode.ontology.model.OntologyResource;
 import ubic.basecode.ontology.model.OntologyTerm;
@@ -28,6 +27,7 @@
 import ubic.gemma.model.genome.Taxon;
 import ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject;
 
+import javax.annotation.Nullable;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
@@ -36,7 +36,7 @@
  * @author Paul
  */
 @SuppressWarnings("unused") // Possible external use
-public interface OntologyService extends InitializingBean {
+public interface OntologyService {
 
  /**
  * Will add the give vocab characteristic to the expression experiment.
@@ -147,6 +147,7 @@ Collection<CharacteristicValueObject> findExperimentsCharacteristicTags( String
  * @param uri uri
  * @return the OntologyResource
  */
+ @Nullable
  OntologyResource getResource( String uri );
 
  SequenceOntologyService getSequenceOntologyService();
@@ -155,6 +156,7 @@ Collection<CharacteristicValueObject> findExperimentsCharacteristicTags( String
  * @param uri uri
  * @return the OntologyTerm for the specified URI.
  */
+ @Nullable
  OntologyTerm getTerm( String uri );
 
  /**

gemma-core/src/main/java/ubic/gemma/core/ontology/OntologyServiceImpl.java

@@ -37,6 +37,8 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.compass.core.util.concurrent.ConcurrentHashSet;
+import org.springframework.beans.factory.DisposableBean;
+import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.core.io.Resource;
@@ -92,7 +94,7 @@
  * @author pavlidis
  */
 @Service
-public class OntologyServiceImpl implements OntologyService {
+public class OntologyServiceImpl implements OntologyService, InitializingBean, DisposableBean {
  /**
  * Throttle how many ontology terms we retrieve. We search the ontologies in a favored order, so we can stop when we
  * find "enough stuff".
@@ -187,6 +189,16 @@ public void afterPropertiesSet() {
 
  }
 
+ @Override
+ public void destroy() throws Exception {
+ String doLoad = Configuration.getString( "load.ontologies" );
+ if ( StringUtils.isBlank( doLoad ) || Configuration.getBoolean( "load.ontologies" ) ) {
+ for ( AbstractOntologyService serv : this.ontologyServices ) {
+ serv.cancelInitializationThread();
+ }
+ }
+ }
+
  private void countOccurrences( Collection<CharacteristicValueObject> searchResults,
  Map<String, CharacteristicValueObject> previouslyUsedInSystem ) {
  StopWatch watch = new StopWatch();
@@ -298,6 +310,9 @@ public Collection<OntologyIndividual> findIndividuals( String givenSearch ) thro
  Collection<OntologyIndividual> results = new HashSet<>();
 
  for ( AbstractOntologyService ontology : ontologyServices ) {
+ if ( !ontology.isOntologyLoaded() ) {
+ continue;
+ }
  Collection<OntologyIndividual> found = ontology.findIndividuals( query );
  if ( found != null )
  results.addAll( found );
@@ -317,6 +332,9 @@ public Collection<Characteristic> findTermAsCharacteristic( String search ) thro
  }
 
  for ( AbstractOntologyService ontology : ontologyServices ) {
+ if ( !ontology.isOntologyLoaded() ) {
+ continue;
+ }
  Collection<OntologyTerm> found = ontology.findTerm( query );
  if ( found != null )
  results.addAll( this.convert( new HashSet<>( found ) ) );
@@ -549,6 +567,9 @@ public UberonOntologyService getUberonService() {
  @Override
  public OntologyResource getResource( String uri ) {
  for ( AbstractOntologyService ontology : ontologyServices ) {
+ if ( !ontology.isOntologyLoaded() ) {
+ continue;
+ }
  OntologyResource resource = ontology.getResource( uri );
  if ( resource != null )
  return resource;
@@ -564,6 +585,9 @@ public SequenceOntologyService getSequenceOntologyService() {
  @Override
  public OntologyTerm getTerm( String uri ) {
  for ( AbstractOntologyService ontology : ontologyServices ) {
+ if ( !ontology.isOntologyLoaded() ) {
+ continue;
+ }
  OntologyTerm term = ontology.getTerm( uri );
  if ( term != null )
  return term;
@@ -889,6 +913,9 @@ private Collection<CharacteristicValueObject> findCharacteristicsFromOntology( S
 
  // search all Ontology
  for ( AbstractOntologyService ontologyService : ontologyServicesToUse ) {
+ if ( !ontologyService.isOntologyLoaded() ) {
+ continue;
+ }
 
  Collection<OntologyTerm> ontologyTerms = ontologyService.findTerm( searchQuery );
 

gemma-core/src/main/java/ubic/gemma/core/search/SearchService.java

@@ -21,6 +21,7 @@
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import java.util.Collection;
 import java.util.List;
 import java.util.Set;

gemma-core/src/main/java/ubic/gemma/core/search/SearchServiceImpl.java

@@ -412,7 +412,7 @@ private void accreteResultsOthers( LinkedHashSet<SearchResult<?>> results, Searc
  results.addAll( gen );
  }
 
- if ( settings.getUseGo() ) {
+ if ( settings.hasResultType( Gene.class ) && settings.getUseGo() ) {
  try {
  // FIXME: add support for OR, but there's a bug in baseCode that prevents this https://github.com/PavlidisLab/baseCode/issues/22
  String query = settings.getQuery().replaceAll( "\\s+OR\\s+", "" );
@@ -639,10 +639,7 @@ private Collection<SearchResult<ArrayDesign>> arrayDesignSearch( SearchSettings
  }
  // FIXME: this should not be necessary, the AD is eagerly fetched in the model definition (see https://github.com/PavlidisLab/Gemma/issues/483)
  Hibernate.initialize( cs.getArrayDesign() );
- SearchResult<ArrayDesign> sr = new SearchResult<>( cs.getArrayDesign(), "ArrayDesign associated to probes obtained by a Compass search." );
- // indirect hit penalty
- sr.setScore( INDIRECT_HIT_PENALTY * r.getScore() );
- results.add( sr );
+ results.add( SearchResult.from( ArrayDesign.class, cs.getArrayDesign(), INDIRECT_HIT_PENALTY * r.getScore(), null, "ArrayDesign associated to probes obtained by a Compass search." ) );
  }
 
  watch.stop();
@@ -1043,7 +1040,7 @@ private Collection<SearchResult<CompositeSequence>> compositeSequenceSearch( Sea
  */
  private <T extends Identifiable> Collection<SearchResult<T>> dbHitsToSearchResult( Collection<T> entities, @Nullable String matchText, String source ) {
  StopWatch watch = StopWatch.createStarted();
- List<SearchResult<T>> results = new ArrayList<>();
+ List<SearchResult<T>> results = new ArrayList<>( entities.size() );
  for ( T e : entities ) {
  if ( e == null ) {
  if ( log.isDebugEnabled() )