Merge branch 'hotfix-1.29.15'

gemma-cli/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>gemma</artifactId>
         <groupId>gemma</groupId>
-        <version>1.29.14</version>
+        <version>1.29.15</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>gemma-cli</artifactId>

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

@@ -14,19 +14,18 @@
  */
 package ubic.gemma.core.apps;
 
-import java.util.Arrays;
-import java.util.List;
-
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.lang3.StringUtils;
-
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
 import ubic.gemma.model.expression.experiment.BioAssaySet;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
 
+import java.util.Arrays;
+import java.util.List;
+
 /**
  * Delete one or more experiments from the system.
  *
@@ -83,13 +82,13 @@ protected void doWork() throws Exception {
                     continue;
                 }
 
-                if ( !ads.getExpressionExperiments( a ).isEmpty() ) {
+                if ( ads.getExpressionExperimentsCount( a ) > 0 ) {
                     log.info( "Platform still has experiments that must be deleted first: " + p );
                     addErrorObject( p, "Experiments still exist for platform" );
                     continue;
                 }
 
-                if ( !ads.getSwitchedExperimentIds( a ).isEmpty() ) {
+                if ( ads.getSwitchedExpressionExperimentCount( a ) > 0 ) {
                     log.info( "Platform still has experiments (switched to anther platform) that must be deleted first: " + p );
                     addErrorObject( p, "Experiments  (switched to anther platform) still exist for platform" );
                     continue;

gemma-core/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>gemma</artifactId>
         <groupId>gemma</groupId>
-        <version>1.29.14</version>
+        <version>1.29.15</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>gemma-core</artifactId>

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

@@ -46,7 +46,6 @@
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.model.expression.experiment.FactorValue;
 import ubic.gemma.persistence.persister.Persister;
-import ubic.gemma.persistence.service.common.auditAndSecurity.CurationDetailsService;
 import ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService;
@@ -75,9 +74,6 @@ public class SplitExperimentServiceImpl implements SplitExperimentService {
     @Autowired
     private RawExpressionDataVectorService rawExpressionDataVectorService;
 
-    @Autowired
-    private CurationDetailsService curationDetailsService;
-
     @Autowired
     private Persister persister;
 

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

@@ -15,10 +15,12 @@
 package ubic.gemma.core.association.phenotype;
 
 import ubic.basecode.ontology.model.OntologyTerm;
+import ubic.basecode.ontology.providers.OntologyService;
 import ubic.basecode.ontology.search.OntologySearchException;
 import ubic.gemma.model.common.description.Characteristic;
 import ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject;
 
+import javax.annotation.Nullable;
 import java.util.Collection;
 import java.util.Set;
 
@@ -29,48 +31,50 @@
 public interface PhenotypeAssoOntologyHelper {
 
     /**
-     * @return Gemma might be ready but the ontology thread not finish loading
+     * Returns the ontology services this helper is using.
      */
-    boolean areOntologiesAllLoaded();
+    Collection<OntologyService> getOntologyServices();
 
     /**
      * CharacteristicValueObject to Characteristic with no valueUri given
      *
      * @param  characteristicValueObject characteristic VO
-     * @return                           vocab characteristic
+     * @return vocab characteristic
      */
     Characteristic characteristicValueObject2Characteristic( CharacteristicValueObject characteristicValueObject );
 
     /**
      * For a valueUri return the OntologyTerm found
      *
      * @param  valueUri value uri
-     * @return          ontology term
+     * @return ontology term
      */
-    OntologyTerm findOntologyTermByUri( String valueUri ) throws EntityNotFoundException;
+    @Nullable
+    OntologyTerm findOntologyTermByUri( String valueUri );
 
     /**
      * search the disease,hp and mp ontology for a searchQuery and return an ordered set of CharacteristicVO
      *
      * @param  searchQuery query
-     * @return             characteristic VOs
+     * @return characteristic VOs
      */
     Set<CharacteristicValueObject> findPhenotypesInOntology( String searchQuery ) throws OntologySearchException;
 
     /**
      * search the disease, hp and mp ontology for OntologyTerm
      *
      * @param  searchQuery free text query?
-     * @return             terms
+     * @return terms
      */
     Collection<OntologyTerm> findValueUriInOntology( String searchQuery ) throws OntologySearchException;
 
     /**
      * Helper method. For a valueUri return the Characteristic (represents a phenotype)
      *
      * @param  valueUri value uri
-     * @return          Characteristic
+     * @return Characteristic
      */
+    @Nullable
     Characteristic valueUri2Characteristic( String valueUri );
 
 }

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

@@ -46,23 +46,12 @@ public class PhenotypeAssoOntologyHelperImpl implements PhenotypeAssoOntologyHel
     @Autowired
     public PhenotypeAssoOntologyHelperImpl( OntologyService ontologyService, MondoOntologyService diseaseOntologyService, MammalianPhenotypeOntologyService mammalianPhenotypeOntologyService, HumanPhenotypeOntologyService humanPhenotypeOntologyService ) {
         this.ontologyService = ontologyService;
-        //  We add them even when they aren't available so we can use unit tests that mock or fake the ontologies.
-        this.ontologies = Arrays.asList( diseaseOntologyService, mammalianPhenotypeOntologyService, humanPhenotypeOntologyService );
-        if ( !diseaseOntologyService.isEnabled() ) {
-            log.debug( "DO is not enabled, phenotype tools will not work correctly" );
-        }
-        if ( !mammalianPhenotypeOntologyService.isEnabled() ) {
-            log.debug( "MPO is not enabled, phenotype tools will not work correctly" );
-        }
-        if ( !humanPhenotypeOntologyService.isEnabled() ) {
-            log.debug( "HPO is not enabled, phenotype tools will not work correctly" );
-        }
+        this.ontologies = Collections.unmodifiableList( Arrays.asList( diseaseOntologyService, mammalianPhenotypeOntologyService, humanPhenotypeOntologyService ) );
     }
 
     @Override
-    public boolean areOntologiesAllLoaded() {
-        // if these ontologies are not configured, we will never be ready. Check for valid configuration.
-        return ontologies.stream().allMatch( ubic.basecode.ontology.providers.OntologyService::isOntologyLoaded );
+    public Collection<ubic.basecode.ontology.providers.OntologyService> getOntologyServices() {
+        return ontologies;
     }
 
     @Override
@@ -81,7 +70,7 @@ public Characteristic characteristicValueObject2Characteristic(
             // format the query for lucene to look for ontology terms with an exact match for the value
             String value = "\"" + StringUtils.join( characteristicValueObject.getValue().trim().split( " " ), " AND " ) + "\"";
 
-            Collection<OntologyTerm> ontologyTerms = null;
+            Collection<OntologyTerm> ontologyTerms;
             try {
                 ontologyTerms = this.ontologyService.findTerms( value );
                 for ( OntologyTerm ontologyTerm : ontologyTerms ) {
@@ -99,7 +88,7 @@ public Characteristic characteristicValueObject2Characteristic(
     }
 
     @Override
-    public OntologyTerm findOntologyTermByUri( String valueUri ) throws EntityNotFoundException {
+    public OntologyTerm findOntologyTermByUri( String valueUri ) {
 
         if ( valueUri == null || valueUri.isEmpty() ) {
             throw new IllegalArgumentException( "URI to load was blank." );
@@ -112,7 +101,7 @@ public OntologyTerm findOntologyTermByUri( String valueUri ) throws EntityNotFou
                 return ontologyTerm;
         }
 
-        throw new EntityNotFoundException( valueUri + " - term not found" );
+        return null;
     }
 
     @Override
@@ -149,22 +138,15 @@ public Collection<OntologyTerm> findValueUriInOntology( String searchQuery ) thr
 
     @Override
     public Characteristic valueUri2Characteristic( String valueUri ) {
-
-        try {
-            OntologyTerm o = findOntologyTermByUri( valueUri );
-            if ( o == null )
-                return null;
-            Characteristic myPhenotype = Characteristic.Factory.newInstance();
-            myPhenotype.setValueUri( o.getUri() );
-            myPhenotype.setValue( o.getLabel() );
-            myPhenotype.setCategory( PhenotypeAssociationConstants.PHENOTYPE );
-            myPhenotype.setCategoryUri( PhenotypeAssociationConstants.PHENOTYPE_CATEGORY_URI );
-            return myPhenotype;
-        } catch ( EntityNotFoundException e ) {
-            e.printStackTrace();
+        OntologyTerm o = findOntologyTermByUri( valueUri );
+        if ( o == null )
             return null;
-        }
-
+        Characteristic myPhenotype = Characteristic.Factory.newInstance();
+        myPhenotype.setValueUri( o.getUri() );
+        myPhenotype.setValue( o.getLabel() );
+        myPhenotype.setCategory( PhenotypeAssociationConstants.PHENOTYPE );
+        myPhenotype.setCategoryUri( PhenotypeAssociationConstants.PHENOTYPE_CATEGORY_URI );
+        return myPhenotype;
     }
 
     /**