Fix slow RNG by using commons-math RandomUtils instead of commons-lang3

This also removes a deprecated API usage from commons-lang3. The other
problematic class that has a slow RNG is RandomStringUtils.

Author: arteymix

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

@@ -22,7 +22,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
-import org.apache.commons.lang3.RandomUtils;
+import org.apache.commons.lang.math.RandomUtils;
 import ubic.gemma.core.util.AbstractAuthenticatedCLI;
 import ubic.gemma.model.common.description.BibliographicReference;
 import ubic.gemma.persistence.service.common.description.BibliographicReferenceService;
@@ -104,7 +104,7 @@ protected void doWork() throws Exception {
             } catch ( Exception e ) {
                 log.info( "Failed to update: " + bibref + " (" + e.getMessage() + ")" );
             }
-            Thread.sleep( RandomUtils.nextInt( 0, 1000 ) );
+            Thread.sleep( RandomUtils.nextInt( 1000 ) );
         }
     }
 

gemma-core/src/main/java/ubic/gemma/core/ontology/OntologyServiceImpl.java

@@ -19,7 +19,7 @@
 package ubic.gemma.core.ontology;
 
 import io.micrometer.core.annotation.Timed;
-import org.apache.commons.lang3.RandomUtils;
+import org.apache.commons.lang.math.RandomUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.exception.ExceptionUtils;
 import org.apache.commons.lang3.time.StopWatch;
@@ -43,7 +43,6 @@
 import ubic.basecode.ontology.providers.ObiService;
 import ubic.basecode.ontology.search.OntologySearchException;
 import ubic.basecode.ontology.search.OntologySearchResult;
-import ubic.gemma.persistence.service.genome.gene.GeneService;
 import ubic.gemma.core.ontology.providers.GeneOntologyService;
 import ubic.gemma.core.ontology.providers.OntologyServiceFactory;
 import ubic.gemma.core.search.*;
@@ -56,6 +55,7 @@
 import ubic.gemma.model.genome.Taxon;
 import ubic.gemma.model.genome.gene.GeneValueObject;
 import ubic.gemma.persistence.service.common.description.CharacteristicService;
+import ubic.gemma.persistence.service.genome.gene.GeneService;
 
 import javax.annotation.Nullable;
 import java.io.BufferedReader;
@@ -979,7 +979,7 @@ private <T> T pollCompletionService( ExecutorCompletionService<T> completionServ
         double recheckMs = Math.min( checkFrequencyMillis, timeoutMs );
         // a fuzz factor to prevent concurrent tasks from all timing out at the same time
         // up to 10% of the initial timeout
-        double fuzzyMs = RandomUtils.nextDouble( 0.0, checkFrequencyMillis / 10.0 );
+        double fuzzyMs = RandomUtils.nextDouble() * checkFrequencyMillis / 10.0;
         while ( ( future = completionService.poll( ( long ) recheckMs, TimeUnit.MILLISECONDS ) ) == null ) {
             long remainingTimeMs = Math.max( timeoutMs - timer.getTime(), 0 );
             long i = futures.stream().filter( Future::isDone ).count();

gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExperimentalDesignDaoImpl.java

@@ -18,7 +18,7 @@
  */
 package ubic.gemma.persistence.service.expression.experiment;
 
-import org.apache.commons.lang3.RandomUtils;
+import org.apache.commons.lang.math.RandomUtils;
 import org.hibernate.SessionFactory;
 import org.hibernate.criterion.Restrictions;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -28,7 +28,7 @@
 import ubic.gemma.persistence.service.AbstractDao;
 
 import javax.annotation.Nullable;
-import java.util.List;
+import java.util.Random;
 
 /**
  * @see ubic.gemma.model.expression.experiment.ExperimentalDesign
@@ -79,7 +79,7 @@ public ExperimentalDesign getRandomExperimentalDesignThatNeedsAttention( Experim
                 .createQuery( "select distinct ed from ExperimentalDesign ed join ed.experimentalFactors ef "
                         + "join ef.factorValues fv where ed.id != :edId and fv.needsAttention = true" )
                 .setParameter( "edId", excludedDesign.getId() )
-                .setFirstResult( RandomUtils.nextInt( 0, numThatNeedsAttention.intValue() ) )
+                .setFirstResult( RandomUtils.nextInt( numThatNeedsAttention.intValue() ) )
                 .setMaxResults( 1 )
                 .uniqueResult();
     }

gemma-core/src/test/java/ubic/gemma/core/analysis/service/GeneMultifunctionalityPopulationServiceTest.java

@@ -19,16 +19,15 @@
 
 package ubic.gemma.core.analysis.service;
 
+import org.apache.commons.lang.math.RandomUtils;
 import org.apache.commons.lang3.RandomStringUtils;
-import org.apache.commons.lang3.RandomUtils;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.test.annotation.DirtiesContext;
-import ubic.gemma.persistence.service.genome.gene.GeneService;
 import ubic.gemma.core.ontology.providers.GeneOntologyService;
 import ubic.gemma.core.util.test.BaseSpringContextTest;
 import ubic.gemma.core.util.test.category.SlowTest;
@@ -44,6 +43,7 @@
 import ubic.gemma.model.genome.Taxon;
 import ubic.gemma.persistence.service.association.Gene2GOAssociationService;
 import ubic.gemma.persistence.service.common.description.ExternalDatabaseService;
+import ubic.gemma.persistence.service.genome.gene.GeneService;
 
 import java.io.InputStream;
 import java.util.Collection;
@@ -95,7 +95,7 @@ public void setUp() throws Exception {
 
         testTaxon = taxonService.findOrCreate( Taxon.Factory
                 .newInstance( "foobly" + RandomStringUtils.randomAlphabetic( 2 ),
-                        "doobly" + RandomStringUtils.randomAlphabetic( 2 ), RandomUtils.nextInt( 0, 5000 ), true ) );
+                        "doobly" + RandomStringUtils.randomAlphabetic( 2 ), RandomUtils.nextInt( 5000 ), true ) );
 
         /*
          * Create genes