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Introduce the Specification<T> interface for find() and findOrCreate()
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@arteymix
arteymix committed Aug 25, 2023
1 parent 9ccaee3 commit 15a4d6a
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15 changes: 8 additions & 7 deletions gemma-cli/src/main/java/ubic/gemma/core/apps/GenericGenelistDesignGenerator.java
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Expand Up @@ -14,15 +14,10 @@
*/
package ubic.gemma.core.apps;

import java.util.Collection;
import java.util.HashMap;
import java.util.Map;

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.core.analysis.report.ArrayDesignReportService;
import ubic.gemma.core.analysis.service.ArrayDesignAnnotationService;
import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
Expand All @@ -49,6 +44,12 @@
import ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService;
import ubic.gemma.persistence.service.genome.taxon.TaxonService;

import java.util.Collection;
import java.util.HashMap;
import java.util.Map;

import static ubic.gemma.persistence.util.Specifications.byIdentifiable;

/**
* Create (or update) an array design based on the current set of transcripts for a taxon.
* This is used to create a 'platform' for linking non-array based data to the system, or data for which we have only
Expand Down Expand Up @@ -116,9 +117,9 @@ protected void doWork() throws Exception {
arrayDesign.setDescription( "Created by Gemma" );
arrayDesign.setTechnologyType( TechnologyType.GENELIST ); // this is key

if ( arrayDesignService.find( arrayDesign ) != null ) {
if ( arrayDesignService.find( byIdentifiable( arrayDesign ) ) != null ) {
AbstractCLI.log.info( "Platform for " + taxon + " already exists, will update" );
arrayDesign = arrayDesignService.findOrFail( arrayDesign );
arrayDesign = arrayDesignService.findOrFail( byIdentifiable( arrayDesign ) );
arrayDesignService.deleteGeneProductAnnotationAssociations( arrayDesign );
arrayDesign = arrayDesignService.loadOrFail( arrayDesign.getId() );

Expand Down
18 changes: 5 additions & 13 deletions ...ore/src/main/java/ubic/gemma/core/annotation/reference/BibliographicReferenceService.java
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Expand Up @@ -27,6 +27,7 @@
import ubic.gemma.model.expression.experiment.ExpressionExperiment;
import ubic.gemma.persistence.service.BaseImmutableService;
import ubic.gemma.persistence.service.BaseVoEnabledService;
import ubic.gemma.persistence.util.Specification;

import javax.annotation.ParametersAreNonnullByDefault;
import java.util.Collection;
Expand All @@ -45,18 +46,9 @@ public interface BibliographicReferenceService

List<BibliographicReference> browse( int start, int limit, String orderField, boolean descending );

/**
* check to see if the object already exists
*
* @param bibliographicReference reference
* @return reference
*/
@Override
BibliographicReference find( BibliographicReference bibliographicReference );

@Override
@Secured({ "GROUP_USER" })
BibliographicReference findOrCreate( BibliographicReference BibliographicReference );
BibliographicReference findOrCreate( Specification<BibliographicReference> spec );

@Override
@Secured({ "GROUP_USER" })
Expand All @@ -74,7 +66,7 @@ public interface BibliographicReferenceService
* @param id id
* @return reference
*/
BibliographicReference findByExternalId( java.lang.String id );
BibliographicReference findByExternalId( String id );

/**
* Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').
Expand All @@ -83,7 +75,7 @@ public interface BibliographicReferenceService
* @param databaseName db name
* @return reference
*/
BibliographicReference findByExternalId( java.lang.String id, java.lang.String databaseName );
BibliographicReference findByExternalId( String id, String databaseName );

/**
* <p>
Expand All @@ -93,7 +85,7 @@ public interface BibliographicReferenceService
* @param id id
* @return reference VO
*/
BibliographicReferenceValueObject findVOByExternalId( java.lang.String id );
BibliographicReferenceValueObject findVOByExternalId( String id );

/**
* Return all the BibRefs that are linked to ExpressionExperiments.
Expand Down
4 changes: 3 additions & 1 deletion gemma-core/src/main/java/ubic/gemma/core/loader/expression/DataUpdaterImpl.java
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Expand Up @@ -64,6 +64,8 @@
import java.io.IOException;
import java.util.*;

import static ubic.gemma.persistence.util.Specifications.byIdentifiable;

/**
* Update or fill in the data associated with an experiment. Cases include reprocessing data from CEL files (Affymetrix,
* GEO only), inserting data for RNA-seq data sets but also generic cases where data didn't come from GEO and we need to
Expand Down Expand Up @@ -993,7 +995,7 @@ private Collection<RawExpressionDataVector> makeNewVectors( ExpressionExperiment
assert bioAssayDimension != null;
assert !bioAssayDimension.getBioAssays().isEmpty();

bioAssayDimension = assayDimensionService.findOrCreate( bioAssayDimension );
bioAssayDimension = assayDimensionService.findOrCreate( byIdentifiable( bioAssayDimension ) );

assert !bioAssayDimension.getBioAssays().isEmpty();

Expand Down
9 changes: 5 additions & 4 deletions ...ic/gemma/core/loader/expression/arrayDesign/ArrayDesignSequenceProcessingServiceImpl.java
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Expand Up @@ -23,7 +23,6 @@
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.access.method.P;
import org.springframework.stereotype.Component;
import ubic.gemma.core.analysis.report.ArrayDesignReportService;
import ubic.gemma.core.analysis.sequence.SequenceManipulation;
Expand All @@ -47,6 +46,8 @@
import java.io.*;
import java.util.*;

import static ubic.gemma.persistence.util.Specifications.byIdentifiable;

/**
* Handles collapsing the sequences, attaching sequences to DesignElements, either from provided input or via a fetch.
*
Expand Down Expand Up @@ -650,14 +651,14 @@ private BioSequence createOrUpdateGenbankSequence( BioSequence found, boolean fo

BioSequence existing;

existing = bioSequenceService.findByAccession( sequenceDatabaseEntry );
existing = bioSequenceService.findByAccession( byIdentifiable( sequenceDatabaseEntry ) );

BioSequence result;
if ( existing == null ) {
if ( ArrayDesignSequenceProcessingServiceImpl.log.isDebugEnabled() )
ArrayDesignSequenceProcessingServiceImpl.log.debug( "Find (or creating) new sequence " + found );

result = bioSequenceService.find( found ); // there still might be a match.
result = bioSequenceService.find( byIdentifiable( found ) ); // there still might be a match.

if ( result == null ) {
result = bioSequenceService.create( found );
Expand Down Expand Up @@ -722,7 +723,7 @@ private Map<String, BioSequence> findLocalSequences( Collection<String> identifi
BioSequence template = BioSequence.Factory.newInstance();
template.setTaxon( taxon );
template.setName( id );
BioSequence seq = bioSequenceService.find( template );
BioSequence seq = bioSequenceService.find( byIdentifiable( template ) );
if ( seq != null ) {
seq = bioSequenceService.thaw( seq );
found.put( id, seq );
Expand Down
5 changes: 3 additions & 2 deletions .../java/ubic/gemma/core/loader/expression/simple/SimpleExpressionDataLoaderServiceImpl.java
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Expand Up @@ -27,7 +27,6 @@
import ubic.basecode.dataStructure.matrix.DoubleMatrixFactory;
import ubic.basecode.io.ByteArrayConverter;
import ubic.basecode.io.reader.DoubleMatrixReader;
import ubic.gemma.core.analysis.preprocess.PreprocessingException;
import ubic.gemma.core.analysis.preprocess.PreprocessorService;
import ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcher;
import ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData;
Expand All @@ -51,6 +50,8 @@
import java.io.InputStream;
import java.util.*;

import static ubic.gemma.persistence.util.Specifications.byIdentifiable;

/**
* Convert a simple matrix and some meta-data into an ExpressionExperiment. Used to handle flat file conversion.
*
Expand Down Expand Up @@ -357,7 +358,7 @@ private Taxon convertTaxon( Taxon taxon ) {
if ( taxonService == null ) {
return taxon; // for tests
}
return taxonService.findOrCreate( taxon );
return taxonService.findOrCreate( byIdentifiable( taxon ) );

}

Expand Down
13 changes: 8 additions & 5 deletions gemma-core/src/main/java/ubic/gemma/persistence/persister/CommonPersister.java
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Expand Up @@ -40,6 +40,8 @@
import java.util.Collection;
import java.util.Map;

import static ubic.gemma.persistence.util.Specifications.byIdentifiable;

/**
* Persister for ubic.gemma.model.common package classes.
*
Expand Down Expand Up @@ -128,7 +130,7 @@ protected AuditTrail persistAuditTrail( AuditTrail entity ) {
}

protected Contact persistContact( Contact contact ) {
return this.contactDao.findOrCreate( contact );
return this.contactDao.findOrCreate( byIdentifiable( contact ) );
}

protected ExternalDatabase persistExternalDatabase( ExternalDatabase database, Caches caches ) {
Expand All @@ -140,7 +142,7 @@ protected ExternalDatabase persistExternalDatabase( ExternalDatabase database, C
return seenDatabases.get( name );
}

ExternalDatabase existingDatabase = externalDatabaseDao.find( database );
ExternalDatabase existingDatabase = externalDatabaseDao.find( byIdentifiable( database ) );

// don't use findOrCreate to avoid flush.
if ( existingDatabase == null ) {
Expand Down Expand Up @@ -196,16 +198,17 @@ protected QuantitationType persistQuantitationType( QuantitationType qType, Cach
}

protected Unit persistUnit( Unit unit ) {
return this.unitDao.findOrCreate( unit );
return this.unitDao.findOrCreate( byIdentifiable( unit ) );
}

private Object persistBibliographicReference( BibliographicReference reference, Caches caches ) {
this.fillInDatabaseEntry( reference.getPubAccession(), caches );
return this.bibliographicReferenceDao.findOrCreate( reference );
return this.bibliographicReferenceDao.findOrCreate( byIdentifiable( reference ) );
}

@Deprecated
private Person persistPerson( Person person ) {
return this.personDao.findOrCreate( person );
return this.personDao.findOrCreate( byIdentifiable( person ) );
}

}
12 changes: 7 additions & 5 deletions gemma-core/src/main/java/ubic/gemma/persistence/persister/ExpressionPersister.java
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Expand Up @@ -45,6 +45,8 @@
import javax.annotation.Nullable;
import java.util.*;

import static ubic.gemma.persistence.util.Specifications.byIdentifiable;

/**
* @author pavlidis
*/
Expand Down Expand Up @@ -390,7 +392,7 @@ private BioAssayDimension persistBioAssayDimension( BioAssayDimension bioAssayDi
assert persistedBioAssays.size() > 0;
bioAssayDimension.setBioAssays( persistedBioAssays );
// bioAssayDimension.setId( null ); // in case of retry.
return bioAssayDimensionDao.findOrCreate( bioAssayDimension );
return bioAssayDimensionDao.findOrCreate( byIdentifiable( bioAssayDimension ) );
}

private BioMaterial persistBioMaterial( BioMaterial entity, Caches caches ) {
Expand All @@ -408,14 +410,14 @@ private BioMaterial persistBioMaterial( BioMaterial entity, Caches caches ) {
AbstractPersister.log.debug( "taxon done" );

AbstractPersister.log.debug( "start save" );
BioMaterial bm = bioMaterialDao.findOrCreate( entity );
BioMaterial bm = bioMaterialDao.findOrCreate( byIdentifiable( entity ) );
AbstractPersister.log.debug( "save biomaterial done" );

return bm;
}

private Compound persistCompound( Compound compound ) {
return compoundDao.findOrCreate( compound );
return compoundDao.findOrCreate( byIdentifiable( compound ) );
}

/**
Expand All @@ -434,7 +436,7 @@ private ExpressionExperimentSubSet persistExpressionExperimentSubSet( Expression
throw new IllegalArgumentException(
"Subsets are only supported for expression experiments that are already persistent" );
} else {
return expressionExperimentSubSetDao.findOrCreate( entity );
return expressionExperimentSubSetDao.findOrCreate( byIdentifiable( entity ) );
}
}

Expand All @@ -447,7 +449,7 @@ private FactorValue persistFactorValue( FactorValue factorValue, Caches caches )
"You must fill in the experimental factor before persisting a factorvalue" );
}
this.fillInFactorValueAssociations( factorValue, caches );
return factorValueDao.findOrCreate( factorValue );
return factorValueDao.findOrCreate( byIdentifiable( factorValue ) );
}

/**
Expand Down
22 changes: 12 additions & 10 deletions gemma-core/src/main/java/ubic/gemma/persistence/persister/GenomePersister.java
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Expand Up @@ -43,6 +43,8 @@
import javax.annotation.Nullable;
import java.util.*;

import static ubic.gemma.persistence.util.Specifications.byIdentifiable;

/**
* @author pavlidis
*/
Expand Down Expand Up @@ -207,7 +209,7 @@ private Gene updateGene( Gene existingGene, Gene newGeneInfo, Caches caches ) {
GeneProduct existingGeneProduct = updatedGpMap.get( newGeneProductInfo.getNcbiGi() );
this.updateGeneProduct( existingGeneProduct, newGeneProductInfo, caches );
} else {
GeneProduct existingGeneProduct = geneProductDao.find( newGeneProductInfo );
GeneProduct existingGeneProduct = geneProductDao.find( byIdentifiable( newGeneProductInfo ) );
if ( existingGeneProduct == null ) {
// it is, in fact, new, so far as we can tell.
newGeneProductInfo.setGene( existingGene );
Expand Down Expand Up @@ -297,7 +299,7 @@ private Gene updateGene( Gene existingGene, Gene newGeneInfo, Caches caches ) {
}

protected BioSequence persistBioSequence( BioSequence bioSequence, Caches caches ) {
BioSequence existingBioSequence = bioSequenceDao.find( bioSequence );
BioSequence existingBioSequence = bioSequenceDao.find( byIdentifiable( bioSequence ) );

// try to avoid making the instance 'dirty' if we don't have to, to avoid updates.
if ( existingBioSequence != null ) {
Expand Down Expand Up @@ -328,7 +330,7 @@ protected Taxon persistTaxon( Taxon taxon, Caches caches ) {
} else if ( commonName != null && seenTaxa.containsKey( commonName.toLowerCase() ) ) {
return seenTaxa.get( commonName.toLowerCase() );
} else {
Taxon fTaxon = taxonDao.findOrCreate( taxon );
Taxon fTaxon = taxonDao.findOrCreate( byIdentifiable( taxon ) );
assert fTaxon != null;
assert fTaxon.getId() != null;

Expand Down Expand Up @@ -377,7 +379,7 @@ private void removeGeneProducts( Collection<GeneProduct> toRemove ) {
Collection<DatabaseEntry> accessions = gpt.getAccessions();
Collection<DatabaseEntry> toRelease = new HashSet<>();
for ( DatabaseEntry de : accessions ) {
if ( this.bioSequenceDao.findByAccession( de ) != null ) {
if ( this.bioSequenceDao.findByAccession( byIdentifiable( de ) ) != null ) {
toRelease.add( de );
}
}
Expand Down Expand Up @@ -420,7 +422,7 @@ private BioSequence2GeneProduct persistBlatAssociation( BlatAssociation associat

private Gene persistGene( Gene gene, boolean checkFirst, Caches caches ) {
if ( checkFirst ) {
Gene existingGene = geneDao.find( gene );
Gene existingGene = geneDao.find( byIdentifiable( gene ) );

if ( existingGene != null ) {
if ( AbstractPersister.log.isDebugEnabled() )
Expand Down Expand Up @@ -450,7 +452,7 @@ private Gene persistGene( Gene gene, boolean checkFirst, Caches caches ) {

Set<GeneProduct> geneProductsForNewGene = new HashSet<>();
for ( GeneProduct product : tempGeneProduct ) {
GeneProduct existingProduct = geneProductDao.find( product );
GeneProduct existingProduct = geneProductDao.find( byIdentifiable( product ) );
if ( existingProduct != null ) {
/*
* A geneProduct is being moved to a gene that didn't exist in the system already
Expand Down Expand Up @@ -494,7 +496,7 @@ private Gene persistGene( Gene gene, boolean checkFirst, Caches caches ) {
}

private GeneProduct persistGeneProduct( GeneProduct geneProduct, Caches caches ) {
GeneProduct existing = geneProductDao.find( geneProduct );
GeneProduct existing = geneProductDao.find( byIdentifiable( geneProduct ) );

if ( existing != null ) {
if ( AbstractPersister.log.isDebugEnabled() )
Expand Down Expand Up @@ -525,7 +527,7 @@ private GeneProduct persistGeneProduct( GeneProduct geneProduct, Caches caches )
private BioSequence persistOrUpdateBioSequence( BioSequence bioSequence, Caches caches ) {
// Note that this method is only really used by the ArrayDesignSequencePersister: it's for filling in
//information about probes on arrays.
BioSequence existingBioSequence = bioSequenceDao.find( bioSequence );
BioSequence existingBioSequence = bioSequenceDao.find( byIdentifiable( bioSequence ) );

if ( existingBioSequence == null ) {
if ( AbstractPersister.log.isDebugEnabled() )
Expand Down Expand Up @@ -597,7 +599,7 @@ private Gene persistOrUpdateGene( Gene gene, Caches caches ) {
if ( gene.getId() != null ) {
existingGene = geneDao.load( gene.getId() );
} else {
existingGene = geneDao.find( gene );
existingGene = geneDao.find( byIdentifiable( gene ) );
}

if ( existingGene == null ) {
Expand All @@ -615,7 +617,7 @@ private GeneProduct persistOrUpdateGeneProduct( GeneProduct geneProduct, Caches
if ( geneProduct.getId() != null ) {
existing = geneProductDao.load( geneProduct.getId() );
} else {
existing = geneProductDao.find( geneProduct );
existing = geneProductDao.find( byIdentifiable( geneProduct ) );
}

if ( existing == null ) {
Expand Down
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