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213 changes: 73 additions & 140 deletions
213
gemma-cli/src/main/java/ubic/gemma/core/apps/IndexGemmaCLI.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,168 +1,101 @@ | ||
| /* | ||
| /* | ||
| * The Gemma project | ||
| * | ||
| * Copyright (c) 2006 University of British Columbia | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| * | ||
| */ | ||
| package ubic.gemma.core.apps; | ||
|
|
||
| import org.apache.commons.cli.CommandLine; | ||
| import org.apache.commons.cli.Option; | ||
| import org.apache.commons.cli.Options; | ||
| import org.compass.gps.spi.CompassGpsInterfaceDevice; | ||
| import ubic.gemma.core.apps.GemmaCLI.CommandGroup; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.beans.factory.annotation.Value; | ||
| import org.springframework.stereotype.Component; | ||
| import ubic.gemma.core.search.IndexerService; | ||
| import ubic.gemma.core.util.AbstractCLI; | ||
| import ubic.gemma.core.util.AbstractCLIContextCLI; | ||
| import ubic.gemma.persistence.util.CompassUtils; | ||
| import ubic.gemma.model.analysis.expression.ExpressionExperimentSet; | ||
| import ubic.gemma.model.common.Identifiable; | ||
| import ubic.gemma.model.common.description.BibliographicReference; | ||
| import ubic.gemma.model.expression.arrayDesign.ArrayDesign; | ||
| import ubic.gemma.model.expression.designElement.CompositeSequence; | ||
| import ubic.gemma.model.expression.experiment.ExpressionExperiment; | ||
| import ubic.gemma.model.genome.Gene; | ||
| import ubic.gemma.model.genome.biosequence.BioSequence; | ||
| import ubic.gemma.model.genome.gene.GeneSet; | ||
|
|
||
| import java.io.File; | ||
| import java.util.HashSet; | ||
| import java.util.Set; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| @Component | ||
| public class IndexGemmaCLI extends AbstractCLI { | ||
|
|
||
| /** | ||
| * A list of all searchable entities this CLI supports. | ||
| */ | ||
| private static final IndexableEntity[] indexableEntities = { | ||
| new IndexableEntity( "g", "genes", Gene.class ), | ||
| new IndexableEntity( "e", "datasets", ExpressionExperiment.class ), | ||
| new IndexableEntity( "a", "platforms", ArrayDesign.class ), | ||
| new IndexableEntity( "b", "bibliographic references", BibliographicReference.class ), | ||
| new IndexableEntity( "s", "probes", CompositeSequence.class ), | ||
| new IndexableEntity( "q", "sequences", BioSequence.class ), | ||
| new IndexableEntity( "x", "datasets groups", ExpressionExperimentSet.class ), | ||
| new IndexableEntity( "y", "gene sets", GeneSet.class ) | ||
| }; | ||
|
|
||
| @lombok.Value | ||
| private static class IndexableEntity { | ||
| String option; | ||
| String description; | ||
| Class<? extends Identifiable> clazz; | ||
| } | ||
|
|
||
| /** | ||
| * Simple command line to index the gemma db. Can index gene's, Expression experiments or array Designs | ||
| * | ||
| * @author klc | ||
| */ | ||
| public class IndexGemmaCLI extends AbstractCLIContextCLI { | ||
| @Autowired | ||
| private IndexerService indexerService; | ||
|
|
||
| private boolean indexAD = false; | ||
| private boolean indexB = false; | ||
| private boolean indexEE = false; | ||
| private boolean indexG = false; | ||
| private boolean indexP = false; | ||
| private boolean indexQ = false; | ||
| private boolean indexX = false; | ||
| private boolean indexY = false; | ||
| @Value("${gemma.search.dir}") | ||
| private File searchDir; | ||
|
|
||
| @Override | ||
| public CommandGroup getCommandGroup() { | ||
| return CommandGroup.SYSTEM; | ||
| } | ||
| private final Set<Class<? extends Identifiable>> classesToIndex = new HashSet<>(); | ||
|
|
||
| @Override | ||
| public String getCommandName() { | ||
| return "searchIndex"; | ||
| } | ||
|
|
||
| @SuppressWarnings("static-access") | ||
| @Override | ||
| protected void buildOptions( Options options ) { | ||
| Option geneOption = Option.builder( "g" ).desc( "Index genes" ).longOpt( "genes" ).build(); | ||
| options.addOption( geneOption ); | ||
|
|
||
| Option eeOption = Option.builder( "g" ).desc( "Index Expression Experiments" ) | ||
| .longOpt( "ExpressionExperiments" ).build(); | ||
| options.addOption( eeOption ); | ||
|
|
||
| Option adOption = Option.builder( "a" ).desc( "Index Array Designs" ).longOpt( "ArrayDesigns" ) | ||
| .build(); | ||
| options.addOption( adOption ); | ||
|
|
||
| Option bibliographicOption = Option.builder( "b" ).desc( "Index Bibliographic References" ) | ||
| .longOpt( "Bibliographic" ).build(); | ||
| options.addOption( bibliographicOption ); | ||
|
|
||
| Option probeOption = Option.builder( "s" ).desc( "Index probes" ).longOpt( "probes" ).build(); | ||
| options.addOption( probeOption ); | ||
|
|
||
| Option sequenceOption = Option.builder( "q" ).desc( "Index sequences" ).longOpt( "sequences" ) | ||
| .build(); | ||
| options.addOption( sequenceOption ); | ||
|
|
||
| options.addOption( Option.builder( "x" ).desc( "Index EE sets" ).longOpt( "eesets" ).build() ); | ||
|
|
||
| options.addOption( Option.builder( "y" ).desc( "Index gene sets" ).longOpt( "genesets" ).build() ); | ||
| public String getShortDesc() { | ||
| return "Create or update the searchable indexes for a Gemma production system"; | ||
| } | ||
|
|
||
| @Override | ||
| protected void doWork() throws Exception { | ||
| /* | ||
| * These beans are defined in Spring XML. | ||
| */ | ||
| if ( this.indexG ) { | ||
| this.rebuildIndex( this.getBean( "geneGps", CompassGpsInterfaceDevice.class ), "Gene index" ); | ||
| } | ||
| if ( this.indexEE ) { | ||
| this.rebuildIndex( this.getBean( "expressionGps", CompassGpsInterfaceDevice.class ), | ||
| "Expression Experiment index" ); | ||
| } | ||
| if ( this.indexAD ) { | ||
| this.rebuildIndex( this.getBean( "arrayGps", CompassGpsInterfaceDevice.class ), "Array Design index" ); | ||
| } | ||
| if ( this.indexB ) { | ||
| this.rebuildIndex( this.getBean( "bibliographicGps", CompassGpsInterfaceDevice.class ), | ||
| "Bibliographic Reference Index" ); | ||
| } | ||
| if ( this.indexP ) { | ||
| this.rebuildIndex( this.getBean( "probeGps", CompassGpsInterfaceDevice.class ), | ||
| "Probe Reference Index" ); | ||
| } | ||
| if ( this.indexQ ) { | ||
| this.rebuildIndex( this.getBean( "biosequenceGps", CompassGpsInterfaceDevice.class ), | ||
| "BioSequence Index" ); | ||
| } | ||
|
|
||
| if ( this.indexY ) { | ||
| this.rebuildIndex( this.getBean( "experimentSetGps", CompassGpsInterfaceDevice.class ), | ||
| "Experiment set Index" ); | ||
| } | ||
|
|
||
| if ( this.indexX ) { | ||
| this.rebuildIndex( this.getBean( "geneSetGps", CompassGpsInterfaceDevice.class ), "Gene set Index" ); | ||
| } | ||
| public GemmaCLI.CommandGroup getCommandGroup() { | ||
| return GemmaCLI.CommandGroup.SYSTEM; | ||
| } | ||
|
|
||
| @Override | ||
| public String getShortDesc() { | ||
| return "Create or update the searchable indexes for a Gemma production system"; | ||
| protected void buildOptions( Options options ) { | ||
| for ( IndexableEntity ie : indexableEntities ) { | ||
| options.addOption( ie.option, null, false, "Index " + ie.description ); | ||
| } | ||
| addThreadsOption( options ); | ||
| } | ||
|
|
||
| @Override | ||
| protected void processOptions( CommandLine commandLine ) { | ||
| if ( commandLine.hasOption( 'e' ) ) | ||
| indexEE = true; | ||
|
|
||
| if ( commandLine.hasOption( 'a' ) ) | ||
| indexAD = true; | ||
|
|
||
| if ( commandLine.hasOption( 'g' ) ) | ||
| indexG = true; | ||
|
|
||
| if ( commandLine.hasOption( 'b' ) ) | ||
| indexB = true; | ||
|
|
||
| if ( commandLine.hasOption( 's' ) ) | ||
| indexP = true; | ||
|
|
||
| if ( commandLine.hasOption( 'q' ) ) | ||
| indexQ = true; | ||
| if ( commandLine.hasOption( 'x' ) ) | ||
| indexX = true; | ||
| if ( commandLine.hasOption( 'y' ) ) | ||
| indexY = true; | ||
|
|
||
| protected void processOptions( CommandLine commandLine ) throws Exception { | ||
| for ( IndexableEntity ie : indexableEntities ) { | ||
| if ( commandLine.hasOption( ie.option ) ) { | ||
| classesToIndex.add( ie.clazz ); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| private void rebuildIndex( CompassGpsInterfaceDevice device, String whatIndexingMsg ) { | ||
|
|
||
| long time = System.currentTimeMillis(); | ||
|
|
||
| AbstractCLI.log.info( "Rebuilding " + whatIndexingMsg ); | ||
| CompassUtils.rebuildCompassIndex( device ); | ||
| time = System.currentTimeMillis() - time; | ||
|
|
||
| AbstractCLI.log.info( "Finished rebuilding " + whatIndexingMsg + ". Took (ms): " + time ); | ||
| AbstractCLI.log.info( " \n " ); | ||
|
|
||
| @Override | ||
| protected void doWork() throws Exception { | ||
| if ( classesToIndex.isEmpty() ) { | ||
| log.info( String.format( "All entities will be indexed under %s.", searchDir.getAbsolutePath() ) ); | ||
| indexerService.index( numThreads ); | ||
| } else { | ||
| log.info( String.format( "The following entities will be indexed under %s:\n\t%s", | ||
| searchDir.getAbsolutePath(), | ||
| classesToIndex.stream().map( Class::getName ).collect( Collectors.joining( "\n\t" ) ) ) ); | ||
| indexerService.index( classesToIndex, numThreads ); | ||
| } | ||
| } | ||
| } |
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