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114 changes: 114 additions & 0 deletions
114
gemma-cli/src/main/java/ubic/gemma/core/apps/FixOntologyTermLabelsCli.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,114 @@ | ||
| package ubic.gemma.core.apps; | ||
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| import org.apache.commons.cli.CommandLine; | ||
| import org.apache.commons.cli.Options; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.beans.factory.annotation.Qualifier; | ||
| import org.springframework.beans.factory.annotation.Value; | ||
| import org.springframework.core.task.AsyncTaskExecutor; | ||
| import ubic.basecode.ontology.model.OntologyTerm; | ||
| import ubic.gemma.core.ontology.OntologyService; | ||
| import ubic.gemma.core.util.AbstractAuthenticatedCLI; | ||
| import ubic.gemma.core.util.CLI; | ||
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| import java.util.ArrayList; | ||
| import java.util.LinkedHashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.concurrent.CompletionService; | ||
| import java.util.concurrent.ExecutorCompletionService; | ||
| import java.util.concurrent.Future; | ||
| import java.util.concurrent.TimeUnit; | ||
| import java.util.stream.Collectors; | ||
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| public class FixOntologyTermLabelsCli extends AbstractAuthenticatedCLI { | ||
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| boolean dryRun = false; | ||
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| @Autowired | ||
| private OntologyService ontologyService; | ||
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| @Autowired | ||
| @Qualifier("ontologyTaskExecutor") | ||
| private AsyncTaskExecutor ontologyTaskExecutor; | ||
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| @Value("${load.ontologies}") | ||
| private boolean autoLoadOntologies; | ||
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| @Autowired | ||
| private List<ubic.basecode.ontology.providers.OntologyService> ontologies; | ||
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| @Override | ||
| public GemmaCLI.CommandGroup getCommandGroup() { | ||
| return GemmaCLI.CommandGroup.METADATA; | ||
| } | ||
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| @Override | ||
| public String getShortDesc() { | ||
| return "Check and correct characteristics & statements using the wrong label for an ontology term"; | ||
| } | ||
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| @Override | ||
| protected void processOptions( CommandLine commandLine ) { | ||
| if ( commandLine.hasOption( 'd' ) ) { | ||
| dryRun = true; | ||
| } | ||
| } | ||
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| @Override | ||
| public String getCommandName() { | ||
| return "fixOntologyTermLabels"; | ||
| } | ||
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| @Override | ||
| protected void buildOptions( Options options ) { | ||
| options.addOption( "d", "dryRun", false, "Dry run, do not update the database [default: " + dryRun + "]" ); | ||
| } | ||
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| @Override | ||
| protected void doWork() throws Exception { | ||
| if ( autoLoadOntologies ) { | ||
| throw new IllegalArgumentException( "Auto-loading of ontologies is enabled, disable it by setting load.ontologies=false in Gemma.properties." ); | ||
| } | ||
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| List<ubic.basecode.ontology.providers.OntologyService> ontologiesLoading = new ArrayList<>( ); | ||
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| log.info( String.format( "Warming up %d ontologies ...", ontologies.size() ) ); | ||
| CompletionService<ubic.basecode.ontology.providers.OntologyService> completionService = new ExecutorCompletionService<>( ontologyTaskExecutor ); | ||
| Map<ubic.basecode.ontology.providers.OntologyService, Future<ubic.basecode.ontology.providers.OntologyService>> futures = new LinkedHashMap<>(); | ||
| for ( ubic.basecode.ontology.providers.OntologyService ontology : ontologies ) { | ||
| ontologiesLoading.add( ontology ); | ||
| futures.put( ontology, completionService.submit( () -> { | ||
| // we don't need all those features | ||
| ontology.setSearchEnabled( false ); | ||
| ontology.setInferenceMode( ubic.basecode.ontology.providers.OntologyService.InferenceMode.NONE ); | ||
| ontology.initialize( true, false ); | ||
| return ontology; | ||
| } ) ); | ||
| } | ||
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| for ( int i = 0; i < ontologiesLoading.size(); i++ ) { | ||
| ubic.basecode.ontology.providers.OntologyService os = completionService.take().get(); | ||
| log.info( String.format( " === Ontology (%d/%d) warmed up: %s", i + 1, ontologies.size(), os ) ); | ||
| int remainingToLoad = ontologies.size() - ( i + 1 ); | ||
| if ( remainingToLoad > 0 && remainingToLoad <= 5 ) { | ||
| log.info( "Still loading:\n\t" + futures.entrySet().stream().filter( e -> !e.getValue().isDone() ) | ||
| .map( Map.Entry::getKey ) | ||
| .map( ubic.basecode.ontology.providers.OntologyService::toString ) | ||
| .collect( Collectors.joining( "\n\t" ) ) ); | ||
| } | ||
| } | ||
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| log.info( "Ontologies warmed up, starting check..." ); | ||
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| Map<String, OntologyTerm> mismatches = ontologyService.fixOntologyTermLabels( dryRun, 4, TimeUnit.HOURS ); | ||
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| System.out.println("Wrong_label\tCorrect_Label\tURI"); | ||
| for ( Map.Entry<String, OntologyTerm> entry : mismatches.entrySet() ) { | ||
| System.out.println( entry.getKey() + "\t" + entry.getValue().getLabel() + "\t" + entry.getValue().getUri()); | ||
| } | ||
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| } | ||
| } |
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