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Use AsyncFactoryBean for loading ontologies #621

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Use AsyncFactoryBean for loading ontologies #621

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42 changes: 25 additions & 17 deletions ...core/src/main/java/ubic/gemma/core/analysis/service/ArrayDesignAnnotationServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,13 @@
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.stereotype.Component;
import ubic.basecode.ontology.model.OntologyTerm;
import ubic.basecode.util.DateUtil;
import ubic.basecode.util.FileTools;
import ubic.gemma.core.ontology.providers.GeneOntologyService;
import ubic.gemma.core.ontology.providers.GeneOntologyServiceFactory;
import ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl;
import ubic.gemma.model.association.BioSequence2GeneProduct;
import ubic.gemma.model.common.description.Characteristic;
Expand All @@ -40,14 +42,18 @@
import ubic.gemma.persistence.service.association.Gene2GOAssociationService;
import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
import ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService;
import ubic.gemma.persistence.util.AsyncFactoryBeanUtils;
import ubic.gemma.persistence.util.EntityUtils;
import ubic.gemma.persistence.util.Settings;

import java.io.*;
import java.util.*;
import java.util.concurrent.Future;
import java.util.regex.Pattern;
import java.util.zip.GZIPOutputStream;

import static ubic.gemma.persistence.util.AsyncFactoryBeanUtils.getSilently;

/**
* @author Paul
* @see ArrayDesignAnnotationService
Expand All @@ -68,7 +74,7 @@ public static File getFileName( String fileBaseName ) {
* Remove file separators (e.g., "/") from the file names.
*
* @param fileBaseName file base name
* @return munged name
* @return munged name
*/
public static String mungeFileName( String fileBaseName ) {
if ( fileBaseName == null ) {
Expand All @@ -79,7 +85,7 @@ public static String mungeFileName( String fileBaseName ) {

/**
* @param arrayDesign array design
* @return Map of composite sequence ids and transient (incomplete) genes. The genes only have the
* @return Map of composite sequence ids and transient (incomplete) genes. The genes only have the
* symbol filled in.
*/
public static Map<Long, Collection<Gene>> readAnnotationFile( ArrayDesign arrayDesign ) {
Expand All @@ -95,7 +101,7 @@ public static Map<Long, Collection<Gene>> readAnnotationFile( ArrayDesign arrayD
Map<String, Long> probeNameToId = new HashMap<>();
ArrayDesignAnnotationServiceImpl.populateProbeNameToIdMap( arrayDesign, results, probeNameToId );
ArrayDesignAnnotationServiceImpl.log.info( "Reading annotations from: " + f );
try (InputStream is = FileTools.getInputStreamFromPlainOrCompressedFile( f.getAbsolutePath() )) {
try ( InputStream is = FileTools.getInputStreamFromPlainOrCompressedFile( f.getAbsolutePath() ) ) {
return ArrayDesignAnnotationServiceImpl.parseAnnotationFile( results, is, probeNameToId );
} catch ( IOException e ) {
throw new RuntimeException( e );
Expand All @@ -107,7 +113,7 @@ public static Map<Long, Collection<Gene>> readAnnotationFile( ArrayDesign arrayD
* GO annotations are not part of the result.
*
* @param arrayDesign array design
* @return Map of composite sequence ids to an array of delimited strings: [probe name,genes symbol,
* @return Map of composite sequence ids to an array of delimited strings: [probe name,genes symbol,
* gene Name,
* gemma gene id, ncbi id] for a given probe id. format of string is geneSymbol then geneNames
* same as found
Expand Down Expand Up @@ -155,8 +161,8 @@ public static Map<Long, String[]> readAnnotationFileAsString( ArrayDesign arrayD
probeNameToId.put( cs.getName(), cs.getId() );
}

try (InputStream is = FileTools.getInputStreamFromPlainOrCompressedFile( f.getAbsolutePath() );
BufferedReader br = new BufferedReader( new InputStreamReader( is ) )) {
try ( InputStream is = FileTools.getInputStreamFromPlainOrCompressedFile( f.getAbsolutePath() );
BufferedReader br = new BufferedReader( new InputStreamReader( is ) ) ) {
ArrayDesignAnnotationServiceImpl.log.info( "Reading annotations from: " + f );

String line;
Expand Down Expand Up @@ -315,7 +321,8 @@ private static void populateProbeNameToIdMap( ArrayDesign arrayDesign, Map<Long,
private Gene2GOAssociationService gene2GOAssociationService;

@Autowired
private GeneOntologyService goService;
@Qualifier("geneOntologyServiceFactory")
private Future<GeneOntologyService> goService;

private final Transformer goTermExtractor = new Transformer() {
@Override
Expand All @@ -326,15 +333,15 @@ public Object transform( Object input ) {

/*
* (non-Javadoc)
*
*
* @see
* ubic.gemma.core.analysis.service.ArrayDesignAnnotationService#create(ubic.gemma.model.expression.arrayDesign.
* ArrayDesign, java.lang.Boolean)
*/
@Override
public void create( ArrayDesign inputAd, Boolean overWrite ) throws IOException {

if ( !goService.isOntologyLoaded() ) {
if ( !goService.isDone() ) {
throw new IllegalStateException( "GO was not loaded" );
}

Expand Down Expand Up @@ -387,8 +394,9 @@ public void create( ArrayDesign inputAd, Boolean overWrite ) throws IOException
* them (or no annotations)
*/
Collection<ExpressionExperiment> ees = arrayDesignService.getExpressionExperiments( ad );
if ( !ees.isEmpty() ) log.info( "Deleting data files for " + ees.size() + " experiments which use " + ad.getShortName()
+ ", that may have outdated annotations" );
if ( !ees.isEmpty() )
log.info( "Deleting data files for " + ees.size() + " experiments which use " + ad.getShortName()
+ ", that may have outdated annotations" );
for ( ExpressionExperiment ee : ees ) {
this.expressionDataFileService.deleteAllFiles( ee );
}
Expand Down Expand Up @@ -440,7 +448,7 @@ public void deleteExistingFiles( ArrayDesign ad ) {

/*
* (non-Javadoc)
*
*
* @see ubic.gemma.core.analysis.service.ArrayDesignAnnotationService#generateAnnotationFile(java.io.Writer,
* java.util.Collection)
*/
Expand Down Expand Up @@ -573,7 +581,7 @@ private Map<Gene, Collection<Characteristic>> getGOMappings(
/**
* @param ty Configures which GO terms to return: With all parents, biological process only, or direct annotations
* only.
* @return the goTerms for a given gene, as configured
* @return the goTerms for a given gene, as configured
*/
private Collection<OntologyTerm> getGoTerms( Collection<Characteristic> ontologyTerms, OutputType ty ) {

Expand All @@ -582,14 +590,14 @@ private Collection<OntologyTerm> getGoTerms( Collection<Characteristic> ontology
return results;

for ( Characteristic vc : ontologyTerms ) {
results.add( goService.getTermForId( vc.getValue() ) );
results.add( getSilently( goService, GeneOntologyServiceFactory.class ).getTermForId( vc.getValue() ) );
}

if ( ty.equals( OutputType.SHORT ) )
return results;

if ( ty.equals( OutputType.LONG ) ) {
Collection<OntologyTerm> oes = goService.getAllParents( results );
Collection<OntologyTerm> oes = getSilently( goService, GeneOntologyServiceFactory.class ).getAllParents( results );
results.addAll( oes );
} else if ( ty.equals( OutputType.BIOPROCESS ) ) {
Collection<OntologyTerm> toRemove = new HashSet<>();
Expand All @@ -598,7 +606,7 @@ private Collection<OntologyTerm> getGoTerms( Collection<Characteristic> ontology
if ( ( ont == null ) ) {
continue; // / shouldn't happen!
}
if ( !goService.isBiologicalProcess( ont ) ) {
if ( !getSilently( goService, GeneOntologyServiceFactory.class ).isBiologicalProcess( ont ) ) {
toRemove.add( ont );
}
}
Expand Down Expand Up @@ -663,7 +671,7 @@ private void processCompositeSequences( ArrayDesign arrayDesign, String fileBase
return;
}

try (Writer writer = initOutputFile( arrayDesign, fileBaseName, overWrite )) {
try ( Writer writer = initOutputFile( arrayDesign, fileBaseName, overWrite ) ) {

// if no writer then we should abort (this could happen in case where we don't want to overwrite files)
if ( writer == null ) {
Expand Down
30 changes: 9 additions & 21 deletions ...in/java/ubic/gemma/core/analysis/service/GeneMultifunctionalityPopulationServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,12 +22,13 @@
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.stereotype.Component;
import ubic.basecode.math.Rank;
import ubic.basecode.ontology.model.OntologyTerm;
import ubic.gemma.core.genome.gene.service.GeneService;
import ubic.gemma.core.ontology.OntologyService;
import ubic.gemma.core.ontology.providers.GeneOntologyService;
import ubic.gemma.core.ontology.providers.GeneOntologyServiceFactory;
import ubic.gemma.model.common.description.Characteristic;
import ubic.gemma.model.common.description.ExternalDatabase;
import ubic.gemma.model.common.description.ExternalDatabases;
Expand All @@ -39,6 +40,9 @@
import ubic.gemma.persistence.service.genome.taxon.TaxonService;

import java.util.*;
import java.util.concurrent.Future;

import static ubic.gemma.persistence.util.AsyncFactoryBeanUtils.getSilently;

/**
* Compute gene multifunctionality and store it in the database.
Expand All @@ -57,10 +61,8 @@ public class GeneMultifunctionalityPopulationServiceImpl implements GeneMultifun
private GeneService geneService;

@Autowired
private GeneOntologyService goService;

@Autowired
private OntologyService ontologyService;
@Qualifier("geneOntologyServiceFactory")
private Future<GeneOntologyService> goService;

@Autowired
private ExternalDatabaseService externalDatabaseService;
Expand Down Expand Up @@ -209,20 +211,6 @@ private Map<Gene, Multifunctionality> computeMultifunctionality( Map<Gene, Colle
}

private Map<Gene, Collection<String>> fetchGoAnnotations( Collection<Gene> genes ) {

if ( !goService.isOntologyLoaded() ) {
goService.startInitializationThread( true, false );
}

while ( !goService.isOntologyLoaded() ) {
try {
Thread.sleep( 2000 );
} catch ( InterruptedException e ) {
//
}
GeneMultifunctionalityPopulationServiceImpl.log.info( "Waiting for GO to load" );
}

/*
* Build the GO 'matrix'.
*/
Expand All @@ -243,7 +231,7 @@ private Map<Gene, Collection<String>> fetchGoAnnotations( Collection<Gene> genes
*/
Set<OntologyTerm> terms = new HashSet<>( annots.size() );
for ( Characteristic t : annots ) {
OntologyTerm term = goService.getTerm( t.getValueUri() );
OntologyTerm term = getSilently( goService, GeneOntologyServiceFactory.class ).getTerm( t.getValueUri() );
if ( term == null || term.isObsolete() ) {
GeneMultifunctionalityPopulationServiceImpl.log
.warn( "Obsolete term annotated to " + gene + " : " + t );
Expand All @@ -254,7 +242,7 @@ private Map<Gene, Collection<String>> fetchGoAnnotations( Collection<Gene> genes
}

// add all the parents
Collection<OntologyTerm> parents = goService.getAllParents( terms );
Collection<OntologyTerm> parents = getSilently( goService, GeneOntologyServiceFactory.class ).getAllParents( terms );
for ( OntologyTerm p : parents ) {
if ( p.isObsolete() ) {
continue;
Expand Down
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