Merge branch 'hotfix-1.30.3'

gemma-cli/pom.xml

@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.30.2</version>
+ <version>1.30.3</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-cli</artifactId>

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

@@ -24,10 +24,10 @@
 import org.apache.commons.lang3.exception.ExceptionUtils;
 import org.springframework.context.ApplicationContext;
 import org.springframework.security.core.context.SecurityContextHolder;
+import ubic.gemma.core.logging.LoggingConfigurer;
+import ubic.gemma.core.logging.log4j.Log4jConfigurer;
 import ubic.gemma.core.util.AbstractCLI;
 import ubic.gemma.core.util.CLI;
-import ubic.gemma.core.logging.log4j.Log4jConfigurer;
-import ubic.gemma.core.logging.LoggingConfigurer;
 import ubic.gemma.persistence.util.Settings;
 import ubic.gemma.persistence.util.SpringContextUtil;
 import ubic.gemma.persistence.util.SpringProfiles;
@@ -151,6 +151,8 @@ public static void main( String[] args ) {
  profiles.add( SpringProfiles.TEST );
  }
 
+ lintConfiguration();
+
  ApplicationContext ctx = SpringContextUtil.getApplicationContext( profiles.toArray( new String[0] ) );
 
  /*
@@ -216,6 +218,21 @@ static String getOptStringForLogging( Object[] argsToPass ) {
  return matcher.replaceAll( "$1 XXXXXX" );
  }
 
+ private static void lintConfiguration() {
+ // check some common settings that might affect initialization time
+ if ( Settings.getBoolean( "load.ontologies" ) ) {
+ log.warn( "Auto-loading of ontologies is enabled, this is not recommended for the CLI. Disable it by setting load.ontologies=false in Gemma.properties." );
+ }
+
+ if ( Settings.getBoolean( "load.homologene" ) ) {
+ log.warn( "Homologene is enabled, this is not recommended for the CLI. Disable it by setting load.homologene=false in Gemma.properties." );
+ }
+
+ if ( Settings.getString( "gemma.hibernate.hbm2ddl.auto" ).equals( "validate" ) ) {
+ log.warn( "Hibernate is configured to validate the database schema, this is not recommended for the CLI. Disable it by setting gemma.hibernate.hbm2ddl.auto= in Gemma.properties." );
+ }
+ }
+
  private static void printHelp( Options options, @Nullable SortedMap<CommandGroup, SortedMap<String, CLI>> commands ) {
  System.err.println( "============ Gemma CLI tools ============" );
 

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

@@ -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;
@@ -49,6 +44,10 @@
 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;
+
 /**
  * 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
@@ -242,12 +241,19 @@ protected void doWork() throws Exception {
  }
  bioSequence.setSequenceDatabaseEntry( de );
  } else {
- bioSequence.setSequenceDatabaseEntry( accessions.iterator().next() );
- existing = bioSequenceService.findByAccession( accessions.iterator().next() );
-
  // FIXME It is possible that this sequence will have been aligned to the genome, which is a bit
  // confusing. So it will map to a gene. Worse case: it maps to more than one gene ...
-
+ existing = bioSequenceService.findByAccession( accessions.iterator().next() );
+ if ( existing == null ) {
+ // create a copy, each biosequence must own their database entry
+ DatabaseEntry databaseEntry = accessions.iterator().next();
+ DatabaseEntry clone = DatabaseEntry.Factory.newInstance();
+ clone.setAccession( databaseEntry.getAccession() );
+ clone.setAccessionVersion( databaseEntry.getAccessionVersion() );
+ clone.setUri( databaseEntry.getUri() );
+ clone.setExternalDatabase( databaseEntry.getExternalDatabase() );
+ bioSequence.setSequenceDatabaseEntry( clone );
+ }
  }
 
  if ( existing == null ) {

gemma-cli/src/main/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLI.java

@@ -106,7 +106,7 @@ protected void doWork() throws Exception {
  assert files.size() == 1;
  LocalFile gene2Gofile = files.iterator().next();
  AbstractCLI.log.info( "Removing all old GO associations" );
- gene2GOAssociationService.removeAllInBatch();
+ gene2GOAssociationService.removeAll();
 
  AbstractCLI.log.info( "Done, loading new ones" );
  gene2GOAssLoader.load( gene2Gofile );

gemma-cli/src/test/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLITest.java

@@ -7,7 +7,6 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.security.test.context.support.WithMockUser;
 import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.TestExecutionListeners;
 import ubic.gemma.core.util.test.BaseCliTest;
 import ubic.gemma.core.util.test.category.SlowTest;
 import ubic.gemma.model.common.description.DatabaseType;
@@ -65,7 +64,7 @@ public void test() throws Exception {
  ExternalDatabase gene2go = ExternalDatabase.Factory.newInstance( "go", DatabaseType.OTHER );
  when( externalDatabaseService.findByNameWithAuditTrail( "go" ) ).thenReturn( gene2go );
  ncbiGene2GOAssociationLoaderCLI.executeCommand( new String[] {} );
- verify( gene2GOAssociationService ).removeAllInBatch();
+ verify( gene2GOAssociationService ).removeAll();
  verify( externalDatabaseService ).findByNameWithAuditTrail( "go" );
  verify( externalDatabaseService ).updateReleaseLastUpdated( same( gene2go ), isNull(), any() );
  }

gemma-core/pom.xml

@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.30.2</version>
+ <version>1.30.3</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-core</artifactId>

gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/PreprocessingException.java

@@ -14,6 +14,7 @@
  */
 package ubic.gemma.core.analysis.preprocess;
 
+import org.apache.commons.lang3.exception.ExceptionUtils;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 
 /**
@@ -33,6 +34,6 @@ public PreprocessingException( ExpressionExperiment ee, String message ) {
  }
 
  public PreprocessingException( ExpressionExperiment ee, Throwable cause ) {
- super( String.format( "Failed to pre-process %s", ee.getShortName() ), cause );
+ super( String.format( "Failed to pre-process %s: %s", ee.getShortName(), ExceptionUtils.getRootCauseMessage( cause ) ), cause );
  }
 }

gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/SplitExperimentServiceImpl.java

@@ -30,7 +30,6 @@
 import ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix;
 import ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix;
 import ubic.gemma.model.analysis.expression.ExpressionExperimentSet;
-import ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails;
 import ubic.gemma.model.common.description.Characteristic;
 import ubic.gemma.model.common.description.DatabaseEntry;
 import ubic.gemma.model.common.measurement.Measurement;
@@ -65,6 +64,8 @@ public class SplitExperimentServiceImpl implements SplitExperimentService {
 
  private static final Log log = LogFactory.getLog( SplitExperimentServiceImpl.class );
 
+ private static final int MAX_SPLIT_NAME_LENGTH = 255;
+
  @Autowired
  private PreprocessorService preprocessor;
 
@@ -156,17 +157,7 @@ public ExpressionExperimentSet split( ExpressionExperiment toSplit, Experimental
  split.setShortName( sourceShortName + "." + splitNumber );
 
  // copy everything but samples over
- String factorValueString = splitValue.getValue();
- if ( StringUtils.isBlank( factorValueString ) ) {
- factorValueString = splitValue.getDescriptiveString();
- }
- split.setName( String.format( "Split part %d of: %s [%s = %s]",
- splitNumber,
- toSplit.getName(),
- splitValue.getExperimentalFactor().getCategory() != null ?
- splitValue.getExperimentalFactor().getCategory().getValue() :
- splitValue.getExperimentalFactor().getName(),
- factorValueString ) );
+ split.setName( generateNameForSplit( toSplit, splitNumber, splitValue ) );
  split.setDescription( "This experiment was created by Gemma splitting another: \n" + toSplit + toSplit.getDescription() );
 
  split.setCharacteristics( this.cloneCharacteristics( toSplit.getCharacteristics() ) );
@@ -350,6 +341,31 @@ public ExpressionExperimentSet split( ExpressionExperiment toSplit, Experimental
  return g;
  }
 
+ static String generateNameForSplit( ExpressionExperiment toSplit, int splitNumber, FactorValue splitValue ) {
+ String template = "Split part %d of: %s [%s = %s]";
+ String originalName = StringUtils.strip( toSplit.getName() );
+ String factorValueString = splitValue.getDescriptiveString();
+ String newFullName = String.format( template, splitNumber, originalName,
+ StringUtils.strip( splitValue.getExperimentalFactor().getCategory() != null ?
+ splitValue.getExperimentalFactor().getCategory().getValue() :
+ splitValue.getExperimentalFactor().getName() ),
+ factorValueString );
+ if ( newFullName.length() <= MAX_SPLIT_NAME_LENGTH )
+ return newFullName;
+ // truncate the original name
+ int lengthOfEverythingElse = newFullName.length() - String.format( "%s", originalName ).length();
+ // we want at least 100 characters of the original name
+ if ( lengthOfEverythingElse > MAX_SPLIT_NAME_LENGTH - 100 ) {
+ throw new IllegalArgumentException( "It's not possible to truncate the name of the split such that it won't exceed 255 characters." );
+ }
+ return String.format( template, splitNumber, StringUtils.abbreviate( originalName, "…", 255 - lengthOfEverythingElse )
+ .replace( "\\s+…$", "…" ),
+ StringUtils.strip( splitValue.getExperimentalFactor().getCategory() != null ?
+ splitValue.getExperimentalFactor().getCategory().getValue() :
+ splitValue.getExperimentalFactor().getName() ),
+ factorValueString );
+ }
+
  private void enforceOtherParts( Collection<ExpressionExperiment> result ) {
  // Enforce relation to other parts of the split.
  for ( ExpressionExperiment split : result ) {

gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNew.java

@@ -38,7 +38,7 @@ public class WhatsNew {
  private Map<Taxon, Long> eeCountPerTaxon;
  private Map<Taxon, Collection<Long>> newEEIdsPerTaxon;
  private Map<Taxon, Collection<Long>> updatedEEIdsPerTaxon;
- private int newBioMaterialCount = 0;
+ private long newBioMaterialCount = 0L;
  private Date date;
 
  public WhatsNew( Date date ) {
@@ -195,11 +195,11 @@ public void setUpdatedEEIdsPerTaxon( Map<Taxon, Collection<Long>> map ) {
  /**
  * @return get a count of the number of biomaterials in the new expression experiments
  */
- public int getNewBioMaterialCount() {
+ public long getNewBioMaterialCount() {
  return this.newBioMaterialCount;
  }
 
- public void setNewBioMaterialCount( int count ) {
+ public void setNewBioMaterialCount( long count ) {
  this.newBioMaterialCount = count;
  }
 

gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNewService.java

@@ -20,43 +20,39 @@
 
 import org.springframework.security.access.annotation.Secured;
 
-import java.util.Date;
+import javax.annotation.Nullable;
 
 /**
  * Creates reports that can be shown on the web pages or in social media feeds.
+ * <p>
+ * Reports are always generated from an anonymous user's perspective.
  *
  * @author paul
  */
 public interface WhatsNewService {
 
  /**
- * save the report from last week.
+ * Generate the report from yesterday.
+ * @return new or updated objects from within a day ago.
  */
- @Secured({ "GROUP_AGENT" })
- void generateWeeklyReport();
+ WhatsNew getDailyReport();
 
  /**
- * save the report from the date specified.
- *
- * @param date the date of the report
- */
- void saveReport( Date date );
-
- /**
- * @param date the date of the report
- * @return representing the updated or new objects.
+ * Generate the report from last week.
+ * @return new or updated objects from within one week ago.
  */
- WhatsNew getReport( Date date );
+ WhatsNew getWeeklyReport();
 
  /**
- * @return new or updated objects from within one week ago.
+ * Generate and save the report from last week. It can later be retrieved with {@link #getLatestWeeklyReport()}.
  */
- WhatsNew getWeeklyReport();
+ @Secured({ "GROUP_AGENT" })
+ WhatsNew generateWeeklyReport();
 
  /**
- * Retrieve the latest WhatsNew report.
- *
- * @return WhatsNew the latest WhatsNew report cache, or null if it hasn't been computed
+ * Retrieve the latest weekly report if available.
+ * @return the latest weekly report, or null if unavailable
  */
+ @Nullable
  WhatsNew getLatestWeeklyReport();
 }