diff --git a/.idea/runConfigurations/Gemma_Web.xml b/.idea/runConfigurations/Gemma_Web.xml
index b03a91f317..7231e4b6d5 100644
--- a/.idea/runConfigurations/Gemma_Web.xml
+++ b/.idea/runConfigurations/Gemma_Web.xml
@@ -1,6 +1,6 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="Gemma Web" type="#com.intellij.j2ee.web.tomcat.TomcatRunConfigurationFactory" factoryName="Local" APPLICATION_SERVER_NAME="Tomcat 8.5.83" ALTERNATIVE_JRE_ENABLED="false">
-    <option name="COMMON_VM_ARGUMENTS" value="-Dspring.profiles.active=dev -Dlog4j.configuration=$PROJECT_DIR$/gemma-web/src/main/config/log4j-dev.properties" />
+    <option name="COMMON_VM_ARGUMENTS" value="-Dspring.profiles.active=dev -Dlog4j.configuration=$PROJECT_DIR$/gemma-web/src/main/config/log4j-dev.properties -Dcom.mysql.cj.disableAbandonedConnectionCleanup=true" />
     <option name="UPDATE_ON_FRAME_DEACTIVATION" value="true" />
     <option name="UPDATING_POLICY" value="redeploy-artifacts" />
     <deployment>
diff --git a/gemma-cli/pom.xml b/gemma-cli/pom.xml
index 0716dc7590..816ba5e589 100644
--- a/gemma-cli/pom.xml
+++ b/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>
diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/GemmaCLI.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/GemmaCLI.java
index 81157abeeb..de7f546db0 100644
--- a/gemma-cli/src/main/java/ubic/gemma/core/apps/GemmaCLI.java
+++ b/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 ============" );
 
diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/GenericGenelistDesignGenerator.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/GenericGenelistDesignGenerator.java
index 9cf90200a5..50fc65f0be 100644
--- a/gemma-cli/src/main/java/ubic/gemma/core/apps/GenericGenelistDesignGenerator.java
+++ b/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 ) {
diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLI.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLI.java
index f6c46e645e..553c09305f 100755
--- a/gemma-cli/src/main/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLI.java
+++ b/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 );
diff --git a/gemma-cli/src/test/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLITest.java b/gemma-cli/src/test/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLITest.java
index 9a7d26e649..abee3f0023 100644
--- a/gemma-cli/src/test/java/ubic/gemma/core/apps/NCBIGene2GOAssociationLoaderCLITest.java
+++ b/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() );
     }
diff --git a/gemma-core/pom.xml b/gemma-core/pom.xml
index 31459be9f6..cc7fde0ea7 100644
--- a/gemma-core/pom.xml
+++ b/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>
diff --git a/gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/PreprocessingException.java b/gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/PreprocessingException.java
index c9504dca44..ee599ed137 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/PreprocessingException.java
+++ b/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 );
     }
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/SplitExperimentServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/SplitExperimentServiceImpl.java
index 1129bae145..c6b5da277b 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/SplitExperimentServiceImpl.java
+++ b/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 ) {
diff --git a/gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNew.java b/gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNew.java
index 61eeec321b..741b2379d3 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNew.java
+++ b/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;
     }
 
diff --git a/gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNewService.java b/gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNewService.java
index a3789f9c9b..ddfcdf952c 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNewService.java
+++ b/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();
 }
\ No newline at end of file
diff --git a/gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNewServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNewServiceImpl.java
index b3c339c81a..75f49d531c 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNewServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNewServiceImpl.java
@@ -18,12 +18,19 @@
  */
 package ubic.gemma.core.analysis.report;
 
+import gemma.gsec.AuthorityConstants;
 import gemma.gsec.SecurityService;
 import org.apache.commons.lang3.time.DateUtils;
 import org.apache.commons.lang3.time.StopWatch;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.security.authentication.AnonymousAuthenticationToken;
+import org.springframework.security.concurrent.DelegatingSecurityContextCallable;
+import org.springframework.security.core.authority.SimpleGrantedAuthority;
+import org.springframework.security.core.context.SecurityContext;
+import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.stereotype.Component;
 import org.springframework.transaction.annotation.Transactional;
 import ubic.basecode.util.FileTools;
@@ -34,9 +41,9 @@
 import ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService;
 import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
-import ubic.gemma.persistence.util.Settings;
 
 import java.io.*;
+import java.nio.file.Paths;
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -49,188 +56,133 @@
 @SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use
 public class WhatsNewServiceImpl implements WhatsNewService {
 
+    private static final Log log = LogFactory.getLog( WhatsNewServiceImpl.class.getName() );
+
     private static final String WHATS_NEW_DIR = "WhatsNew";
     private static final String WHATS_NEW_FILE = "WhatsNew";
-    private static final Log log = LogFactory.getLog( WhatsNewServiceImpl.class.getName() );
-    private final String HOME_DIR = Settings.getString( "gemma.appdata.home" );
+
     @Autowired
-    private ArrayDesignService arrayDesignService = null;
+    private ArrayDesignService arrayDesignService;
     @Autowired
     private AuditEventService auditEventService;
     @Autowired
-    private ExpressionExperimentService expressionExperimentService = null;
+    private ExpressionExperimentService expressionExperimentService;
     @Autowired
-    private SecurityService securityService = null;
+    private SecurityService securityService;
 
-    @Override
-    @Transactional
-    public void generateWeeklyReport() {
-        Calendar c = Calendar.getInstance();
-        Date date = c.getTime();
-        date = DateUtils.addDays( date, -7 );
-        this.saveReport( date );
-    }
+    @Value("${gemma.appdata.home}")
+    private String homeDir;
 
-    /**
-     * save the report from the date specified. This will be the report that will be used by the WhatsNew box.
-     */
     @Override
     @Transactional(readOnly = true)
-    public void saveReport( Date date ) {
-        WhatsNew wn = this.getReport( date );
-        this.initDirectories();
-        this.saveFile( wn );
+    public WhatsNew getDailyReport() {
+        Calendar c = Calendar.getInstance();
+        Date date = c.getTime();
+        date = DateUtils.addDays( date, -1 );
+        return this.getReportAsAnonymousUser( date );
     }
 
     @Override
     @Transactional(readOnly = true)
-    public WhatsNew getReport( Date date ) {
-        WhatsNew wn = new WhatsNew( date );
-
-        Collection<Auditable> updatedObjects = auditEventService.getUpdatedSinceDate( date );
-        wn.setUpdatedObjects( updatedObjects );
-        WhatsNewServiceImpl.log.info( wn.getUpdatedObjects().size() + " updated objects since " + date );
-
-        Collection<Auditable> newObjects = auditEventService.getNewSinceDate( date );
-        wn.setNewObjects( newObjects );
-        WhatsNewServiceImpl.log.info( wn.getNewObjects().size() + " new objects since " + date );
-
-        Collection<ExpressionExperiment> updatedExpressionExperiments = this.getExpressionExperiments( updatedObjects );
-        Collection<ExpressionExperiment> newExpressionExperiments = this.getExpressionExperiments( newObjects );
-        Collection<ArrayDesign> updatedArrayDesigns = this.getArrayDesigns( updatedObjects );
-        Collection<ArrayDesign> newArrayDesigns = this.getArrayDesigns( newObjects );
-
-        // don't show things that are "new" as "updated" too (if they were updated after being loaded)
-        updatedExpressionExperiments.removeAll( newExpressionExperiments );
-        updatedArrayDesigns.removeAll( newArrayDesigns );
-
-        // build total, new and updated counts by taxon to display in data summary widget on front page
-        wn.setNewEEIdsPerTaxon( this.getExpressionExperimentIdsByTaxon( newExpressionExperiments ) );
-        wn.setUpdatedEEIdsPerTaxon( this.getExpressionExperimentIdsByTaxon( updatedExpressionExperiments ) );
-
-        wn.setNewBioMaterialCount( this.getBioMaterialCount( newExpressionExperiments ) );
-
-        return wn;
+    public WhatsNew getWeeklyReport() {
+        Calendar c = Calendar.getInstance();
+        Date date = c.getTime();
+        date = DateUtils.addWeeks( date, -1 );
+        return this.getReportAsAnonymousUser( date );
     }
 
     @Override
     @Transactional(readOnly = true)
-    public WhatsNew getWeeklyReport() {
+    public WhatsNew generateWeeklyReport() {
         Calendar c = Calendar.getInstance();
         Date date = c.getTime();
-        date = DateUtils.addWeeks( date, -1 );
-        return this.getReport( date );
+        WhatsNew wn = this.getReportAsAnonymousUser( DateUtils.addWeeks( date, -1 ) );
+        this.initDirectories();
+        this.saveLatestWeeklyReport( wn, date );
+        return wn;
     }
 
     @Override
     @Transactional(readOnly = true)
     public WhatsNew getLatestWeeklyReport() {
         WhatsNew wn = new WhatsNew();
-        try {
-            File newObjects = new File(
-                    HOME_DIR + File.separatorChar + WhatsNewServiceImpl.WHATS_NEW_DIR + File.separatorChar
-                            + WhatsNewServiceImpl.WHATS_NEW_FILE + ".new" );
-            File updatedObjects = new File(
-                    HOME_DIR + File.separatorChar + WhatsNewServiceImpl.WHATS_NEW_DIR + File.separatorChar
-                            + WhatsNewServiceImpl.WHATS_NEW_FILE + ".updated" );
-            if ( !newObjects.exists() && !updatedObjects.exists() ) {
-                return null;
-            }
+        File newObjects = new File(
+                homeDir + File.separatorChar + WhatsNewServiceImpl.WHATS_NEW_DIR + File.separatorChar
+                        + WhatsNewServiceImpl.WHATS_NEW_FILE + ".new" );
+        File updatedObjects = new File(
+                homeDir + File.separatorChar + WhatsNewServiceImpl.WHATS_NEW_DIR + File.separatorChar
+                        + WhatsNewServiceImpl.WHATS_NEW_FILE + ".updated" );
+        if ( !newObjects.exists() && !updatedObjects.exists() ) {
+            return null;
+        }
 
-            StopWatch timer = StopWatch.createStarted();
-            StopWatch loadNewObjectsTimer = StopWatch.create();
-            StopWatch loadUpdatedObjectsTimer = StopWatch.create();
-
-            // load up all new objects
-            loadNewObjectsTimer.start();
-            if ( newObjects.exists() ) {
-                Collection<AuditableObject> aos = this.loadAuditableObjects( newObjects );
-                Map<String, List<AuditableObject>> aosByType = aos.stream()
-                        .collect( Collectors.groupingBy( AuditableObject::getType, Collectors.toList() ) );
-                for ( Map.Entry<String, List<AuditableObject>> entry : aosByType.entrySet() ) {
-                    Collection<? extends Auditable> objects = this.fetchAllByType( entry.getValue(), entry.getKey() );
-                    for ( AuditableObject ao : entry.getValue() ) {
-                        this.updateDate( wn, ao );
-                    }
-                    wn.addNewObjects( objects );
+        StopWatch timer = StopWatch.createStarted();
+        StopWatch loadNewObjectsTimer = StopWatch.create();
+        StopWatch loadUpdatedObjectsTimer = StopWatch.create();
+
+        // restore the date from the last modified -1 week
+        wn.setDate( DateUtils.addWeeks( new Date( newObjects.lastModified() ), -1 ) );
+
+        // load up all new objects
+        loadNewObjectsTimer.start();
+        if ( newObjects.exists() ) {
+            Collection<AuditableObject> aos = this.loadAuditableObjects( newObjects );
+            Map<String, List<AuditableObject>> aosByType = aos.stream()
+                    .collect( Collectors.groupingBy( AuditableObject::getType, Collectors.toList() ) );
+            for ( Map.Entry<String, List<AuditableObject>> entry : aosByType.entrySet() ) {
+                Collection<? extends Auditable> objects = this.fetchAllByType( entry.getValue(), entry.getKey() );
+                for ( AuditableObject ao : entry.getValue() ) {
+                    this.updateDate( wn, ao );
                 }
+                wn.addNewObjects( objects );
             }
-            loadNewObjectsTimer.stop();
-
-            // load up all updated objects
-            loadUpdatedObjectsTimer.start();
-            if ( updatedObjects.exists() ) {
-                Collection<AuditableObject> aos = this.loadAuditableObjects( updatedObjects );
-                Map<String, List<AuditableObject>> aosByType = aos.stream()
-                        .collect( Collectors.groupingBy( AuditableObject::getType, Collectors.toList() ) );
-                for ( Map.Entry<String, List<AuditableObject>> entry : aosByType.entrySet() ) {
-                    /*
-                     * This call takes ~ 15-20 ms but it can be called many times if there are a lot of updated
-                     * experiments, meaning this loop can take >8500 ms (over tunnel for ~450 experiments).
-                     *
-                     * Loading objects could be avoided since we only need ids on the front end, but we would need to
-                     * refactor the cache, because object-type is used to calculate counts for updated array design
-                     * objects vs updated experiments
-                     *
-                     * This is probably not necessary because usually the number of updated or new experiments will be
-                     * much lower than 450.
-                     */
-                    Collection<? extends Auditable> objects = this.fetchAllByType( entry.getValue(), entry.getKey() );
-                    for ( AuditableObject ao : entry.getValue() ) {
-                        this.updateDate( wn, ao );
-                    }
-                    wn.addUpdatedObjects( objects );
+        }
+        loadNewObjectsTimer.stop();
+
+        // load up all updated objects
+        loadUpdatedObjectsTimer.start();
+        if ( updatedObjects.exists() ) {
+            Collection<AuditableObject> aos = this.loadAuditableObjects( updatedObjects );
+            Map<String, List<AuditableObject>> aosByType = aos.stream()
+                    .collect( Collectors.groupingBy( AuditableObject::getType, Collectors.toList() ) );
+            for ( Map.Entry<String, List<AuditableObject>> entry : aosByType.entrySet() ) {
+                /*
+                 * This call takes ~ 15-20 ms, but it can be called many times if there are a lot of updated
+                 * experiments, meaning this loop can take >8500 ms (over tunnel for ~450 experiments).
+                 *
+                 * Loading objects could be avoided since we only need ids on the front end, but we would need to
+                 * refactor the cache, because object-type is used to calculate counts for updated array design
+                 * objects vs updated experiments
+                 *
+                 * This is probably not necessary because usually the number of updated or new experiments will be
+                 * much lower than 450.
+                 */
+                Collection<? extends Auditable> objects = this.fetchAllByType( entry.getValue(), entry.getKey() );
+                for ( AuditableObject ao : entry.getValue() ) {
+                    this.updateDate( wn, ao );
                 }
+                wn.addUpdatedObjects( objects );
             }
-            loadUpdatedObjectsTimer.stop();
-
-            // build total, new and updated counts by taxon to display in data summary widget on front page
-            StopWatch funkyMapGenerationTimer = StopWatch.createStarted();
-            wn.setNewEEIdsPerTaxon( this.getExpressionExperimentIdsByTaxon( wn.getNewExpressionExperiments() ) );
-            wn.setUpdatedEEIdsPerTaxon(
-                    this.getExpressionExperimentIdsByTaxon( wn.getUpdatedExpressionExperiments() ) );
-            funkyMapGenerationTimer.stop();
-            timer.stop();
-
-            if ( timer.getTime() > 500 ) {
-                log.info( "Retrieving report took " + timer.getTime() + "ms ("
-                        + "loading new: " + loadNewObjectsTimer.getTime() + " ms, "
-                        + "loading updated: " + loadUpdatedObjectsTimer.getTime() + " ms, "
-                        + "ee by taxon map creation: " + funkyMapGenerationTimer.getTime() + "ms)." );
-            }
+        }
+        loadUpdatedObjectsTimer.stop();
 
-        } catch ( Throwable e ) {
-            WhatsNewServiceImpl.log.error( e, e );
-            return null;
+        // build total, new and updated counts by taxon to display in data summary widget on front page
+        StopWatch funkyMapGenerationTimer = StopWatch.createStarted();
+        wn.setNewEEIdsPerTaxon( this.getExpressionExperimentIdsByTaxon( wn.getNewExpressionExperiments() ) );
+        wn.setUpdatedEEIdsPerTaxon(
+                this.getExpressionExperimentIdsByTaxon( wn.getUpdatedExpressionExperiments() ) );
+        funkyMapGenerationTimer.stop();
+        timer.stop();
+
+        if ( timer.getTime() > 500 ) {
+            log.info( "Retrieving report took " + timer.getTime() + "ms ("
+                    + "loading new: " + loadNewObjectsTimer.getTime() + " ms, "
+                    + "loading updated: " + loadUpdatedObjectsTimer.getTime() + " ms, "
+                    + "ee by taxon map creation: " + funkyMapGenerationTimer.getTime() + "ms)." );
         }
         return wn;
     }
 
-    /**
-     * @param arrayDesignService the arrayDesignService to set
-     */
-    public void setArrayDesignService( ArrayDesignService arrayDesignService ) {
-        this.arrayDesignService = arrayDesignService;
-    }
-
-    public void setAuditEventService( AuditEventService auditEventService ) {
-        this.auditEventService = auditEventService;
-    }
-
-    /**
-     * @param expressionExperimentService the expressionExperimentService to set
-     */
-    public void setExpressionExperimentService( ExpressionExperimentService expressionExperimentService ) {
-        this.expressionExperimentService = expressionExperimentService;
-    }
-
-    /**
-     * @param securityService the securityService to set
-     */
-    public void setSecurityService( SecurityService securityService ) {
-        this.securityService = securityService;
-    }
-
     private Collection<? extends Auditable> fetchAllByType( List<AuditableObject> object, String type ) {
         if ( object == null )
             return null;
@@ -245,6 +197,50 @@ private Collection<? extends Auditable> fetchAllByType( List<AuditableObject> ob
         }
     }
 
+    /**
+     * Obtain the report from the perspective of an anonymous user.
+     */
+    private WhatsNew getReportAsAnonymousUser( Date date ) {
+        // generate the report from an anonymous user perspective
+        SecurityContext context = SecurityContextHolder.createEmptyContext();
+        context.setAuthentication( new AnonymousAuthenticationToken( "1234", AuthorityConstants.ANONYMOUS_USER_NAME,
+                Collections.singleton( new SimpleGrantedAuthority( AuthorityConstants.ANONYMOUS_GROUP_AUTHORITY ) ) ) );
+        try {
+            return new DelegatingSecurityContextCallable<>( () -> getReport( date ), context ).call();
+        } catch ( Exception e ) {
+            throw new RuntimeException( e );
+        }
+    }
+
+    private WhatsNew getReport( Date date ) {
+        WhatsNew wn = new WhatsNew( date );
+
+        Collection<Auditable> updatedObjects = auditEventService.getUpdatedSinceDate( date );
+        wn.setUpdatedObjects( updatedObjects );
+        WhatsNewServiceImpl.log.info( wn.getUpdatedObjects().size() + " updated objects since " + date );
+
+        Collection<Auditable> newObjects = auditEventService.getNewSinceDate( date );
+        wn.setNewObjects( newObjects );
+        WhatsNewServiceImpl.log.info( wn.getNewObjects().size() + " new objects since " + date );
+
+        Collection<ExpressionExperiment> updatedExpressionExperiments = this.getExpressionExperiments( updatedObjects );
+        Collection<ExpressionExperiment> newExpressionExperiments = this.getExpressionExperiments( newObjects );
+        Collection<ArrayDesign> updatedArrayDesigns = this.getArrayDesigns( updatedObjects );
+        Collection<ArrayDesign> newArrayDesigns = this.getArrayDesigns( newObjects );
+
+        // don't show things that are "new" as "updated" too (if they were updated after being loaded)
+        updatedExpressionExperiments.removeAll( newExpressionExperiments );
+        updatedArrayDesigns.removeAll( newArrayDesigns );
+
+        // build total, new and updated counts by taxon to display in data summary widget on front page
+        wn.setNewEEIdsPerTaxon( this.getExpressionExperimentIdsByTaxon( newExpressionExperiments ) );
+        wn.setUpdatedEEIdsPerTaxon( this.getExpressionExperimentIdsByTaxon( updatedExpressionExperiments ) );
+
+        wn.setNewBioMaterialCount( this.getBioMaterialCount( newExpressionExperiments ) );
+
+        return wn;
+    }
+
     /**
      * @param items a collection of objects that may include array designs
      * @return the array design subset of the collection passed in
@@ -264,9 +260,8 @@ private Collection<ArrayDesign> getArrayDesigns( Collection<Auditable> items ) {
      * @param ees a collection of expression experiments
      * @return the number of biomaterials in all the expression experiments passed in
      */
-    private int getBioMaterialCount( Collection<ExpressionExperiment> ees ) {
-
-        int count = 0;
+    private long getBioMaterialCount( Collection<ExpressionExperiment> ees ) {
+        long count = 0;
         for ( ExpressionExperiment ee : ees ) {
             count += this.expressionExperimentService.getBioMaterialCount( ee );
         }
@@ -280,18 +275,7 @@ private Map<Taxon, Collection<Long>> getExpressionExperimentIdsByTaxon( Collecti
         /*
          * Sort taxa by name.
          */
-        TreeMap<Taxon, Collection<Long>> eesPerTaxon = new TreeMap<>( new Comparator<Taxon>() {
-            @Override
-            public int compare( Taxon o1, Taxon o2 ) {
-                if ( o1 == null ) {
-                    return 1;
-                } else if ( o2 == null ) {
-                    return -1;
-                } else {
-                    return o1.getScientificName().compareTo( o2.getScientificName() );
-                }
-            }
-        } );
+        SortedMap<Taxon, Collection<Long>> eesPerTaxon = new TreeMap<>( Comparator.comparing( Taxon::getScientificName, Comparator.nullsLast( Comparator.naturalOrder() ) ) );
 
         if ( ees.isEmpty() )
             return eesPerTaxon;
@@ -333,9 +317,9 @@ private Collection<ExpressionExperiment> getExpressionExperiments( Collection<Au
     private void initDirectories() {
         // check to see if the home directory exists. If it doesn't, create it.
         // check to see if the reports directory exists. If it doesn't, create it.
-        FileTools.createDir( HOME_DIR );
-        FileTools.createDir( HOME_DIR + File.separatorChar + WhatsNewServiceImpl.WHATS_NEW_DIR );
-        File f = new File( HOME_DIR + File.separatorChar + WhatsNewServiceImpl.WHATS_NEW_DIR );
+        FileTools.createDir( homeDir );
+        FileTools.createDir( homeDir + File.separatorChar + WhatsNewServiceImpl.WHATS_NEW_DIR );
+        File f = new File( homeDir + File.separatorChar + WhatsNewServiceImpl.WHATS_NEW_DIR );
         Collection<File> files = new ArrayList<>();
         File[] fileArray = f.listFiles();
         if ( fileArray != null ) {
@@ -345,65 +329,61 @@ private void initDirectories() {
         FileTools.deleteFiles( files );
     }
 
-    private Collection<AuditableObject> loadAuditableObjects( File newObjects )
-            throws IOException, ClassNotFoundException {
+    private Collection<AuditableObject> loadAuditableObjects( File newObjects ) {
         try ( FileInputStream fis = new FileInputStream( newObjects );
                 ObjectInputStream ois = new ObjectInputStream( fis ) ) {
             @SuppressWarnings("unchecked")
             Collection<AuditableObject> aos = ( Collection<AuditableObject> ) ois
                     .readObject();
             return aos;
+        } catch ( IOException | ClassNotFoundException e ) {
+            throw new RuntimeException( e );
         }
     }
 
-    private void saveFile( WhatsNew wn ) {
-        try {
-            // remove file first
-            File newOutput = new File(
-                    HOME_DIR + File.separatorChar + WhatsNewServiceImpl.WHATS_NEW_DIR + File.separatorChar
-                            + WhatsNewServiceImpl.WHATS_NEW_FILE + ".new" );
-            File updatedOutput = new File(
-                    HOME_DIR + File.separatorChar + WhatsNewServiceImpl.WHATS_NEW_DIR + File.separatorChar
-                            + WhatsNewServiceImpl.WHATS_NEW_FILE + ".updated" );
-            if ( newOutput.exists() ) {
-                if ( !newOutput.delete() ) {
-                    WhatsNewServiceImpl.log.error( "Could not delete " + newOutput.getName() );
-                }
-            }
-            if ( updatedOutput.exists() ) {
-                if ( !updatedOutput.delete() ) {
-                    WhatsNewServiceImpl.log.error( "Could not delete " + updatedOutput.getName() );
-                }
-            }
-            Calendar c = Calendar.getInstance();
-            Date date = c.getTime();
-
-            Collection<ArrayDesign> ads = wn.getNewArrayDesigns();
-            Collection<ExpressionExperiment> ees = wn.getNewExpressionExperiments();
-            // save the IDs for new Auditables
-            Collection<AuditableObject> newObjects = new ArrayList<>();
-            this.addAllADs( date, ads, newObjects );
-            this.addAllEEs( date, ees, newObjects );
-
-            // save the ids for updated Auditables
-            ads = wn.getUpdatedArrayDesigns();
-            ees = wn.getUpdatedExpressionExperiments();
-            // save the IDs for new Auditables
-            Collection<AuditableObject> updatedObjects = new ArrayList<>();
-            this.addAllADs( date, ads, updatedObjects );
-            this.addAllEEs( date, ees, updatedObjects );
-            try ( FileOutputStream fos = new FileOutputStream( newOutput );
-                    ObjectOutputStream oos = new ObjectOutputStream( fos ) ) {
-                oos.writeObject( newObjects );
-            }
+    private void saveLatestWeeklyReport( WhatsNew wn, Date dateRetrieved ) {
+        // remove file first
+        File newOutput = Paths.get( homeDir, WhatsNewServiceImpl.WHATS_NEW_DIR, WhatsNewServiceImpl.WHATS_NEW_FILE + ".new" ).toFile();
+        File updatedOutput = Paths.get( homeDir, WhatsNewServiceImpl.WHATS_NEW_DIR, WhatsNewServiceImpl.WHATS_NEW_FILE + ".updated" ).toFile();
+        if ( newOutput.exists() && !newOutput.delete() ) {
+            throw new RuntimeException( "Could not delete " + newOutput.getName() );
+        }
+        if ( updatedOutput.exists() && !updatedOutput.delete() ) {
+            throw new RuntimeException( "Could not delete " + updatedOutput.getName() );
+        }
 
-            try ( FileOutputStream fos = new FileOutputStream( updatedOutput );
-                    ObjectOutputStream oos = new ObjectOutputStream( fos ) ) {
-                oos.writeObject( updatedObjects );
-            }
+        Collection<ArrayDesign> ads = wn.getNewArrayDesigns();
+        Collection<ExpressionExperiment> ees = wn.getNewExpressionExperiments();
+        // save the IDs for new Auditables
+        Collection<AuditableObject> newObjects = new ArrayList<>();
+        this.addAllADs( dateRetrieved, ads, newObjects );
+        this.addAllEEs( dateRetrieved, ees, newObjects );
+
+        // save the ids for updated Auditables
+        ads = wn.getUpdatedArrayDesigns();
+        ees = wn.getUpdatedExpressionExperiments();
+        // save the IDs for new Auditables
+        Collection<AuditableObject> updatedObjects = new ArrayList<>();
+        this.addAllADs( dateRetrieved, ads, updatedObjects );
+        this.addAllEEs( dateRetrieved, ees, updatedObjects );
+        try ( FileOutputStream fos = new FileOutputStream( newOutput );
+                ObjectOutputStream oos = new ObjectOutputStream( fos ) ) {
+            oos.writeObject( newObjects );
+        } catch ( IOException e ) {
+            throw new RuntimeException( e );
+        }
+
+        try ( FileOutputStream fos = new FileOutputStream( updatedOutput );
+                ObjectOutputStream oos = new ObjectOutputStream( fos ) ) {
+            oos.writeObject( updatedObjects );
+        } catch ( IOException e ) {
+            throw new RuntimeException( e );
+        }
 
-        } catch ( Throwable e ) {
-            log.error( "Error while saving the what's new file.", e );
+        // set the last modified on the generated files, so that we can restore the report date when it's loaded at a
+        // later point
+        if ( !newOutput.setLastModified( dateRetrieved.getTime() ) || !updatedOutput.setLastModified( dateRetrieved.getTime() ) ) {
+            log.warn( "Failed to set the last modified date on the WhatsNew files, the date might be inaccurate when loading the report." );
         }
     }
 
diff --git a/gemma-core/src/main/java/ubic/gemma/core/association/phenotype/PhenotypeAssociationManagerServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/core/association/phenotype/PhenotypeAssociationManagerServiceImpl.java
index 28c3f1a172..2aeb9676f2 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/association/phenotype/PhenotypeAssociationManagerServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/association/phenotype/PhenotypeAssociationManagerServiceImpl.java
@@ -28,6 +28,7 @@
 import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 import ubic.basecode.ontology.model.OntologyTerm;
@@ -145,13 +146,19 @@ public class PhenotypeAssociationManagerServiceImpl implements PhenotypeAssociat
     @Autowired
     private Future<HomologeneService> homologeneService;
 
+    /**
+     * Indicate if ontologies are loaded on startup.
+     */
+    @Value("${load.ontologies}")
+    private boolean autoLoadOntologies;
+
     @Override
     public void afterPropertiesSet() {
         this.pubMedXmlFetcher = new PubMedXMLFetcher();
         Set<ubic.basecode.ontology.providers.OntologyService> disabledOntologies = ontologyHelper.getOntologyServices().stream()
                 .filter( os -> !os.isEnabled() )
                 .collect( Collectors.toSet() );
-        if ( !disabledOntologies.isEmpty() ) {
+        if ( autoLoadOntologies && !disabledOntologies.isEmpty() ) {
             log.warn( String.format( "The following ontologies are required by Phenocarta are not enabled:\n\t%s.",
                     disabledOntologies.stream().map( Object::toString ).collect( Collectors.joining( "\n\t" ) ) ) );
         }
diff --git a/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneService.java b/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneService.java
index b6727cb66c..be06f9f84e 100755
--- a/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneService.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneService.java
@@ -198,4 +198,7 @@ public interface GeneService extends BaseService<Gene>, FilteringVoEnabledServic
     Gene thawLiter( Gene gene );
 
     Collection<GeneValueObject> searchGenes( String query, Long taxonId ) throws SearchException;
+
+    @Secured({ "GROUP_ADMIN" })
+    int removeAll();
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneServiceImpl.java
index af33356cc2..0b21f1338d 100755
--- a/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneServiceImpl.java
@@ -517,4 +517,10 @@ public Collection<GeneValueObject> searchGenes( String query, Long taxonId ) thr
         return geneValueObjects;
     }
 
+    @Override
+    @Transactional
+    public int removeAll() {
+        return geneDao.removeAll();
+    }
+
 }
\ No newline at end of file
diff --git a/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneSetService.java b/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneSetService.java
index b5785bcf72..762dee961b 100755
--- a/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneSetService.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneSetService.java
@@ -328,9 +328,5 @@ Collection<DatabaseBackedGeneSetValueObject> updateDatabaseEntity(
     void remove( Long id );
 
     @Secured({ "GROUP_ADMIN" })
-    void removeAll();
-
-    @Override
-    @Secured({ "GROUP_ADMIN" })
-    void removeAllInBatch();
+    int removeAll();
 }
\ No newline at end of file
diff --git a/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneSetServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneSetServiceImpl.java
index 4be1dcd5ba..c2566e8a79 100755
--- a/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneSetServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/genome/gene/service/GeneSetServiceImpl.java
@@ -27,7 +27,6 @@
 import org.springframework.transaction.annotation.Transactional;
 import ubic.gemma.core.genome.gene.GeneSetValueObjectHelper;
 import ubic.gemma.core.genome.gene.SessionBoundGeneSetValueObject;
-import ubic.gemma.core.search.BaseCodeOntologySearchException;
 import ubic.gemma.core.search.GeneSetSearch;
 import ubic.gemma.core.search.SearchException;
 import ubic.gemma.model.genome.Gene;
@@ -516,7 +515,7 @@ private void checkGeneList( GeneSet gset, Collection<GeneSetMember> updatedGenel
 
     @Override
     @Transactional
-    public void removeAll() {
-        this.geneSetDao.removeAllInBatch();
+    public int removeAll() {
+        return geneSetDao.removeAll();
     }
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/core/loader/association/NCBIGene2GOAssociationParser.java b/gemma-core/src/main/java/ubic/gemma/core/loader/association/NCBIGene2GOAssociationParser.java
index 8909689248..d1b66abebc 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/loader/association/NCBIGene2GOAssociationParser.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/loader/association/NCBIGene2GOAssociationParser.java
@@ -176,8 +176,12 @@ public Gene2GOAssociation mapFromGene2GO( String line ) {
                 return null;
             }
 
-            evcode = GOEvidenceCode.valueOf( evidenceCode );
-
+            try {
+                evcode = GOEvidenceCode.valueOf( evidenceCode );
+            } catch ( IllegalArgumentException e ) {
+                log.warn( String.format( "Unknown GO evidence code %s, will be mapping it as %s.", evidenceCode, GOEvidenceCode.OTHER ) );
+                evcode = GOEvidenceCode.OTHER;
+            }
         }
         Gene2GOAssociation g2GOAss = Gene2GOAssociation.Factory.newInstance( gene, oe, evcode );
 
diff --git a/gemma-core/src/main/java/ubic/gemma/core/loader/expression/geo/service/GeoBrowserServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/core/loader/expression/geo/service/GeoBrowserServiceImpl.java
index ea622ec441..8a4b541473 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/loader/expression/geo/service/GeoBrowserServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/loader/expression/geo/service/GeoBrowserServiceImpl.java
@@ -24,6 +24,7 @@
 import org.springframework.beans.factory.DisposableBean;
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
 import org.springframework.stereotype.Component;
 import org.w3c.dom.Document;
 import org.w3c.dom.NodeList;
@@ -51,8 +52,10 @@
 import java.util.concurrent.Executors;
 
 /**
+ * This is marked as {@link Lazy} since we don't use it outside Gemma Web, so it won't be loaded unless it's needed.
  * @author pavlidis
  */
+@Lazy
 @Component
 public class GeoBrowserServiceImpl implements GeoBrowserService, InitializingBean, DisposableBean {
     private static final int MIN_SAMPLES = 5;
diff --git a/gemma-core/src/main/java/ubic/gemma/core/loader/genome/gene/ncbi/homology/HomologeneServiceFactory.java b/gemma-core/src/main/java/ubic/gemma/core/loader/genome/gene/ncbi/homology/HomologeneServiceFactory.java
index 6519187cb5..5ecf429511 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/loader/genome/gene/ncbi/homology/HomologeneServiceFactory.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/loader/genome/gene/ncbi/homology/HomologeneServiceFactory.java
@@ -50,9 +50,6 @@ protected HomologeneService createObject() throws Exception {
         HomologeneService homologeneService = new HomologeneServiceImpl( geneService, taxonService, homologeneFile );
         if ( loadHomologene ) {
             homologeneService.refresh();
-        } else {
-            log.warn( String.format( "Homologene is not enabled, set %s=true in Gemma.properties to load it on startup.",
-                    LOAD_HOMOLOGENE_CONFIG ) );
         }
         return homologeneService;
     }
diff --git a/gemma-core/src/main/java/ubic/gemma/core/metrics/binder/database/package-info.java b/gemma-core/src/main/java/ubic/gemma/core/metrics/binder/database/package-info.java
new file mode 100644
index 0000000000..313a1f7b46
--- /dev/null
+++ b/gemma-core/src/main/java/ubic/gemma/core/metrics/binder/database/package-info.java
@@ -0,0 +1,7 @@
+/**
+ *
+ */
+@ParametersAreNonnullByDefault
+package ubic.gemma.core.metrics.binder.database;
+
+import javax.annotation.ParametersAreNonnullByDefault;
\ No newline at end of file
diff --git a/gemma-core/src/main/java/ubic/gemma/core/metrics/binder/jpa/Hibernate4Metrics.java b/gemma-core/src/main/java/ubic/gemma/core/metrics/binder/jpa/Hibernate4Metrics.java
index 6f5fec2b67..33fe61b30b 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/metrics/binder/jpa/Hibernate4Metrics.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/metrics/binder/jpa/Hibernate4Metrics.java
@@ -15,7 +15,6 @@
  *
  * @author poirigui
  * @see io.micrometer.core.instrument.binder.jpa.HibernateMetrics
- * @see io.micrometer.core.instrument.binder.jpa.HibernateQueryMetrics
  */
 public class Hibernate4Metrics implements MeterBinder {
 
@@ -26,30 +25,6 @@ public class Hibernate4Metrics implements MeterBinder {
     @Nullable
     private final Statistics statistics;
 
-    /**
-     * Create {@code HibernateMetrics} and bind to the specified meter registry.
-     * @param registry meter registry to use
-     * @param sessionFactory session factory to use
-     * @param sessionFactoryName session factory name as a tag value
-     * @param tags additional tags
-     */
-    public static void monitor( MeterRegistry registry, SessionFactory sessionFactory, String sessionFactoryName,
-            String... tags ) {
-        monitor( registry, sessionFactory, sessionFactoryName, Tags.of( tags ) );
-    }
-
-    /**
-     * Create {@code HibernateMetrics} and bind to the specified meter registry.
-     * @param registry meter registry to use
-     * @param sessionFactory session factory to use
-     * @param sessionFactoryName session factory name as a tag value
-     * @param tags additional tags
-     */
-    public static void monitor( MeterRegistry registry, SessionFactory sessionFactory, String sessionFactoryName,
-            Iterable<Tag> tags ) {
-        new Hibernate4Metrics( sessionFactory, sessionFactoryName, tags ).bindTo( registry );
-    }
-
     /**
      * Create a {@code HibernateMetrics}.
      * @param sessionFactory session factory to use
@@ -175,43 +150,6 @@ public void bindTo( MeterRegistry registry ) {
                 Statistics::getQueryCacheMissCount, "result", "miss" );
         counter( registry, "hibernate.cache.query.puts", "The number of cacheable queries put in cache",
                 Statistics::getQueryCachePutCount );
-
-        for ( String query : statistics.getQueries() ) {
-            QueryStatistics queryStatistics = statistics.getQueryStatistics( query );
-
-            FunctionCounter
-                    .builder( "hibernate.query.cache.requests", queryStatistics, QueryStatistics::getCacheHitCount )
-                    .tags( tags ).tags( "result", "hit", "query", query ).description( "Number of query cache hits" )
-                    .register( registry );
-
-            FunctionCounter
-                    .builder( "hibernate.query.cache.requests", queryStatistics, QueryStatistics::getCacheMissCount )
-                    .tags( tags ).tags( "result", "miss", "query", query ).description( "Number of query cache misses" )
-                    .register( registry );
-
-            FunctionCounter
-                    .builder( "hibernate.query.cache.puts", queryStatistics, QueryStatistics::getCachePutCount )
-                    .tags( tags ).tags( "query", query ).description( "Number of cache puts for a query" )
-                    .register( registry );
-
-            TimeGauge
-                    .builder( "hibernate.query.execution.max", queryStatistics, TimeUnit.MILLISECONDS,
-                            QueryStatistics::getExecutionMaxTime )
-                    .tags( tags ).tags( "query", query ).description( "Query maximum execution time" )
-                    .register( registry );
-
-            TimeGauge
-                    .builder( "hibernate.query.execution.min", queryStatistics, TimeUnit.MILLISECONDS,
-                            QueryStatistics::getExecutionMinTime )
-                    .tags( tags ).tags( "query", query ).description( "Query minimum execution time" )
-                    .register( registry );
-
-            FunctionCounter
-                    .builder( "hibernate.query.execution.rows", queryStatistics,
-                            QueryStatistics::getExecutionRowCount )
-                    .tags( tags ).tags( "query", query ).description( "Number of rows processed for a query" )
-                    .register( registry );
-        }
     }
 
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/core/metrics/binder/jpa/Hibernate4QueryMetrics.java b/gemma-core/src/main/java/ubic/gemma/core/metrics/binder/jpa/Hibernate4QueryMetrics.java
new file mode 100644
index 0000000000..93765870ac
--- /dev/null
+++ b/gemma-core/src/main/java/ubic/gemma/core/metrics/binder/jpa/Hibernate4QueryMetrics.java
@@ -0,0 +1,106 @@
+package ubic.gemma.core.metrics.binder.jpa;
+
+import io.micrometer.core.instrument.*;
+import io.micrometer.core.instrument.binder.MeterBinder;
+import org.hibernate.SessionFactory;
+import org.hibernate.stat.QueryStatistics;
+import org.hibernate.stat.Statistics;
+
+import javax.annotation.Nullable;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ScheduledExecutorService;
+import java.util.concurrent.TimeUnit;
+
+/**
+ * Query metrics for Hibernate 4.
+ * @see io.micrometer.core.instrument.binder.jpa.HibernateQueryMetrics
+ * @author poirigui
+ */
+public class Hibernate4QueryMetrics implements MeterBinder, AutoCloseable {
+
+    private static final String SESSION_FACTORY_TAG_NAME = "entityManagerFactory";
+
+    private final Iterable<Tag> tags;
+
+    @Nullable
+    private final Statistics statistics;
+
+    private final ScheduledExecutorService executor = Executors.newSingleThreadScheduledExecutor();
+
+    /**
+     * Create a {@code HibernateQueryMetrics}.
+     * @param sessionFactory session factory to use
+     * @param sessionFactoryName session factory name as a tag value
+     * @param tags additional tags
+     */
+    public Hibernate4QueryMetrics( SessionFactory sessionFactory, String sessionFactoryName, Iterable<Tag> tags ) {
+        this.tags = Tags.concat( tags, SESSION_FACTORY_TAG_NAME, sessionFactoryName );
+        Statistics statistics = sessionFactory.getStatistics();
+        this.statistics = statistics.isStatisticsEnabled() ? statistics : null;
+    }
+
+    @Override
+    public void bindTo( MeterRegistry meterRegistry ) {
+        if ( statistics == null ) {
+            return;
+        }
+        executor.scheduleAtFixedRate( () -> {
+            registerQueryMetric( statistics, meterRegistry );
+        }, 0, 1000, TimeUnit.MILLISECONDS );
+    }
+
+    private void registerQueryMetric( Statistics statistics, MeterRegistry meterRegistry ) {
+        for ( String query : statistics.getQueries() ) {
+            QueryStatistics queryStatistics = statistics.getQueryStatistics( query );
+
+            FunctionCounter
+                    .builder( "hibernate.query.cache.requests", queryStatistics, QueryStatistics::getCacheHitCount )
+                    .tags( tags )
+                    .tags( "result", "hit", "query", query )
+                    .description( "Number of query cache hits" )
+                    .register( meterRegistry );
+
+            FunctionCounter
+                    .builder( "hibernate.query.cache.requests", queryStatistics, QueryStatistics::getCacheMissCount )
+                    .tags( tags )
+                    .tags( "result", "miss", "query", query )
+                    .description( "Number of query cache misses" )
+                    .register( meterRegistry );
+
+            FunctionCounter
+                    .builder( "hibernate.query.cache.puts", queryStatistics, QueryStatistics::getCachePutCount )
+                    .tags( tags )
+                    .tags( "query", query )
+                    .description( "Number of cache puts for a query" )
+                    .register( meterRegistry );
+
+            TimeGauge
+                    .builder( "hibernate.query.execution.max", queryStatistics, TimeUnit.MILLISECONDS,
+                            QueryStatistics::getExecutionMaxTime )
+                    .tags( tags )
+                    .tags( "query", query )
+                    .description( "Query maximum execution time" )
+                    .register( meterRegistry );
+
+            TimeGauge
+                    .builder( "hibernate.query.execution.min", queryStatistics, TimeUnit.MILLISECONDS,
+                            QueryStatistics::getExecutionMinTime )
+                    .tags( tags )
+                    .tags( "query", query )
+                    .description( "Query minimum execution time" )
+                    .register( meterRegistry );
+
+            FunctionCounter
+                    .builder( "hibernate.query.execution.rows", queryStatistics, QueryStatistics::getExecutionRowCount )
+                    .tags( tags )
+                    .tags( "query", query )
+                    .description( "Number of rows processed for a query" )
+                    .register( meterRegistry );
+        }
+    }
+
+    @Override
+    public void close() {
+        executor.shutdown();
+    }
+}
diff --git a/gemma-core/src/main/java/ubic/gemma/core/ontology/OntologyServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/core/ontology/OntologyServiceImpl.java
index 51311d8bf2..4732db8e41 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/ontology/OntologyServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/ontology/OntologyServiceImpl.java
@@ -25,6 +25,7 @@
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.cache.CacheManager;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.core.io.Resource;
@@ -123,6 +124,9 @@ public class OntologyServiceImpl implements OntologyService, InitializingBean {
     @Autowired
     private CacheManager cacheManager;
 
+    @Value("${load.ontologies}")
+    private boolean autoLoadOntologies;
+
     private OntologyCache ontologyCache;
     private Set<OntologyTermSimple> categoryTerms = null;
 
@@ -141,12 +145,12 @@ public void afterPropertiesSet() throws Exception {
                     } )
                     .filter( ubic.basecode.ontology.providers.OntologyService::isEnabled )
                     .collect( Collectors.toList() );
-            if ( enabledOntologyServices.isEmpty() ) {
-                log.warn( "No ontologies are enabled, consider enabling them by setting 'load.{name}Ontology' options in Gemma.properties." );
-            } else {
+            if ( !enabledOntologyServices.isEmpty() ) {
                 log.info( "The following ontologies are enabled:\n\t" + enabledOntologyServices.stream()
                         .map( ubic.basecode.ontology.providers.OntologyService::toString )
                         .collect( Collectors.joining( "\n\t" ) ) );
+            } else if ( autoLoadOntologies ) {
+                log.warn( "No ontologies are enabled, consider enabling them by setting 'load.{name}Ontology' options in Gemma.properties." );
             }
         }
         // remove GeneOntologyService, it was originally not included in the list before bean injection was used
@@ -780,7 +784,7 @@ private void initializeCategoryTerms() throws IOException {
             }
             this.categoryTerms = Collections.unmodifiableSet( categoryTerms );
         }
-        if ( !experimentalFactorOntologyService.isEnabled() ) {
+        if ( autoLoadOntologies && !experimentalFactorOntologyService.isEnabled() ) {
             OntologyServiceImpl.log.warn( String.format( "%s is not enabled; using light-weight placeholder for categories.",
                     experimentalFactorOntologyService ) );
         }
diff --git a/gemma-core/src/main/java/ubic/gemma/core/ontology/providers/GeneOntologyServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/core/ontology/providers/GeneOntologyServiceImpl.java
index 6a9af0e3ad..7452044fc3 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/ontology/providers/GeneOntologyServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/ontology/providers/GeneOntologyServiceImpl.java
@@ -25,6 +25,7 @@
 import org.springframework.beans.factory.DisposableBean;
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.cache.Cache;
 import org.springframework.cache.CacheManager;
 import org.springframework.stereotype.Service;
@@ -32,7 +33,6 @@
 import ubic.basecode.ontology.model.AnnotationProperty;
 import ubic.basecode.ontology.model.OntologyTerm;
 import ubic.basecode.ontology.search.OntologySearchException;
-import ubic.basecode.util.Configuration;
 import ubic.gemma.core.genome.gene.service.GeneService;
 import ubic.gemma.model.common.description.Characteristic;
 import ubic.gemma.model.genome.Gene;
@@ -40,7 +40,6 @@
 import ubic.gemma.model.genome.Taxon;
 import ubic.gemma.persistence.service.association.Gene2GOAssociationService;
 import ubic.gemma.persistence.util.CacheUtils;
-import ubic.gemma.persistence.util.Settings;
 
 import java.util.*;
 import java.util.stream.Collectors;
@@ -57,7 +56,6 @@ public enum GOAspect {
         BIOLOGICAL_PROCESS, CELLULAR_COMPONENT, MOLECULAR_FUNCTION
     }
 
-    private final static String GO_URL = Settings.getString( "url.geneOntology" );
     private static final Log log = LogFactory.getLog( GeneOntologyServiceImpl.class.getName() );
 
     /**
@@ -91,7 +89,7 @@ protected String getOntologyName() {
 
     @Override
     protected String getOntologyUrl() {
-        return Settings.getString( "url.geneOntology" );
+        return ontologyUrl;
     }
 
     /**
@@ -110,7 +108,11 @@ private static String toUri( String goId ) {
     @Autowired
     private CacheManager cacheManager;
 
-    private final boolean autoLoad;
+    @Value("${load.ontologies}")
+    private boolean autoLoadOntologies;
+
+    @Value("${url.geneOntology}")
+    private String ontologyUrl;
 
     /**
      * Cache of gene -> go terms.
@@ -122,37 +124,19 @@ private static String toUri( String goId ) {
      */
     private Cache term2Aspect;
 
-    /**
-     * If this load.ontologies is NOT configured, we go ahead (per-ontology config will be checked).
-     */
-    private static boolean isAutoLoad() {
-        String doLoad = Configuration.getString( "load.ontologies" );
-        return StringUtils.isBlank( doLoad ) || Configuration.getBoolean( "load.ontologies" );
-    }
-
-    public GeneOntologyServiceImpl() {
-        this( isAutoLoad() );
-    }
-
-    public GeneOntologyServiceImpl( boolean autoLoad ) {
-        this.autoLoad = autoLoad;
-    }
-
 
     @Override
     public void afterPropertiesSet() throws InterruptedException {
         goTerms = CacheUtils.getCache( cacheManager, "GeneOntologyService.goTerms" );
         term2Aspect = CacheUtils.getCache( cacheManager, "GeneOntologyService.term2Aspect" );
-        if ( autoLoad ) {
+        if ( autoLoadOntologies ) {
             startInitializationThread( false, false );
-        } else {
-            log.info( "Auto-loading of ontologies is disabled, GO terms will not be available." );
         }
     }
 
     @Override
     public void destroy() throws Exception {
-        if ( isAutoLoad() ) {
+        if ( isInitializationThreadAlive() ) {
             cancelInitializationThread();
         }
     }
@@ -163,7 +147,7 @@ public Map<Long, Collection<OntologyTerm>> calculateGoTermOverlap( Gene queryGen
         Map<Long, Collection<OntologyTerm>> overlap = new HashMap<>();
         if ( queryGene == null )
             return null;
-        if ( geneIds.size() == 0 )
+        if ( geneIds.isEmpty() )
             return overlap;
 
         Collection<OntologyTerm> queryGeneTerms = this.getGOTerms( queryGene );
@@ -195,7 +179,7 @@ public Map<Long, Collection<OntologyTerm>> calculateGoTermOverlap( Long queryGen
         Map<Long, Collection<OntologyTerm>> overlap = new HashMap<>();
         if ( queryGene == null )
             return null;
-        if ( geneIds.size() == 0 )
+        if ( geneIds.isEmpty() )
             return overlap;
 
         Collection<OntologyTerm> queryGeneTerms = this.getGOTerms( queryGene, true, null );
@@ -282,10 +266,15 @@ public Collection<OntologyTerm> getGOTerms( Gene gene, boolean includePartOf, GO
 
             Collection<Characteristic> annotations = gene2GOAssociationService.findByGene( gene );
             for ( Characteristic c : annotations ) {
-                OntologyTerm term = getTerm( c.getValueUri() );
+                OntologyTerm term;
+                if ( c.getValueUri() == null ) {
+                    GeneOntologyServiceImpl.log.warn( String.format( "Term %s is free-text, cannot search GO ontology with it.", c ) );
+                    continue;
+                } else {
+                    term = getTerm( c.getValueUri() );
+                }
                 if ( term == null ) {
-                    GeneOntologyServiceImpl.log
-                            .warn( "Term " + c.getValueUri() + " not found in term list can't add to results (ontology not loaded?)" );
+                    GeneOntologyServiceImpl.log.warn( String.format( "Term %s not found in term list can't add to results (ontology not loaded?)", c ) );
                     continue;
                 }
                 allGOTermSet.add( term );
diff --git a/gemma-core/src/main/java/ubic/gemma/core/ontology/providers/OntologyServiceFactory.java b/gemma-core/src/main/java/ubic/gemma/core/ontology/providers/OntologyServiceFactory.java
index 234a7df0be..aa5218b5bc 100644
--- a/gemma-core/src/main/java/ubic/gemma/core/ontology/providers/OntologyServiceFactory.java
+++ b/gemma-core/src/main/java/ubic/gemma/core/ontology/providers/OntologyServiceFactory.java
@@ -23,12 +23,6 @@ public class OntologyServiceFactory<T extends OntologyService> extends AbstractF
      */
     private static final boolean isAutoLoad = ( StringUtils.isBlank( Configuration.getString( "load.ontologies" ) ) || Configuration.getBoolean( "load.ontologies" ) );
 
-    static {
-        if ( !isAutoLoad ) {
-            log.warn( "Auto-loading of ontologies is disabled, enable it by setting load.ontologies=true in Gemma.properties." );
-        }
-    }
-
     private final Class<T> ontologyServiceClass;
     private boolean forceLoad = false;
     private boolean forceIndexing = false;
diff --git a/gemma-core/src/main/java/ubic/gemma/model/association/GOEvidenceCode.java b/gemma-core/src/main/java/ubic/gemma/model/association/GOEvidenceCode.java
index 4dd8808ab9..70a7b53789 100644
--- a/gemma-core/src/main/java/ubic/gemma/model/association/GOEvidenceCode.java
+++ b/gemma-core/src/main/java/ubic/gemma/model/association/GOEvidenceCode.java
@@ -15,6 +15,8 @@
  * </ul>
  * And our own custom code IIA which means Inferred from Imported Annotation to distinguish IEAs that we ourselves have
  * computed
+ *
+ * See https://geneontology.org/docs/guide-go-evidence-codes/ for documentation of GO evidence codes.
  */
 public enum GOEvidenceCode {
     IC,
@@ -91,5 +93,31 @@ public enum GOEvidenceCode {
     /**
      * Quantitative Trait Measurement (RGD code)
      */
-    QTM;
-}
\ No newline at end of file
+    QTM,
+    /**
+     Inferred from High Throughput Direct Assay (HDA)
+     */
+    HDA,
+    /**
+     *  Inferred from High Throughput Expression Pattern (HEP)
+     */
+    HEP,
+    /**
+     *  Inferred from High Throughput Genetic Interaction (HGI)
+     */
+    HGI,
+
+    /**
+     * Inferred from High Throughput Mutant Phenotype (HMP)
+     */
+    HMP,
+
+    /**
+     *  Inferred from High Throughput Experiment (HTP)
+     */
+    HTP,
+    /**
+     * Unsupported/unknown GO evidence code are mapped to this value.
+     */
+    OTHER;
+}
diff --git a/gemma-core/src/main/java/ubic/gemma/model/expression/experiment/FactorValue.java b/gemma-core/src/main/java/ubic/gemma/model/expression/experiment/FactorValue.java
index c735ca67d8..26183c6364 100644
--- a/gemma-core/src/main/java/ubic/gemma/model/expression/experiment/FactorValue.java
+++ b/gemma-core/src/main/java/ubic/gemma/model/expression/experiment/FactorValue.java
@@ -201,22 +201,28 @@ public void setValue( String value ) {
         this.value = value;
     }
 
-    @SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use
+    /**
+     * Produce a descriptive string for this factor value.
+     */
     @Transient
     public String getDescriptiveString() {
-        if ( this.characteristics != null && this.characteristics.size() > 0 ) {
+        if ( this.characteristics != null && !this.characteristics.isEmpty() ) {
             StringBuilder fvString = new StringBuilder();
+            boolean first = true;
             for ( Characteristic c : this.characteristics ) {
-                fvString.append( c.getValue() ).append( " " );
+                if ( !first ) {
+                    fvString.append( " " );
+                }
+                fvString.append( StringUtils.strip( c.getValue() ) );
+                first = false;
             }
             return fvString.toString();
         } else if ( this.measurement != null ) {
-            return this.measurement.getValue();
-        } else if ( this.value != null && !this.value.isEmpty() ) {
-            return this.value;
+            return StringUtils.strip( this.measurement.getValue() );
+        } else if ( StringUtils.isNotBlank( this.value ) ) {
+            return StringUtils.strip( this.value );
         }
-
-        return "absent ";
+        return "absent";
     }
 
     private boolean checkGuts( FactorValue that ) {
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/AbstractDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/AbstractDao.java
index 711e0f69e1..e14091d257 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/AbstractDao.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/AbstractDao.java
@@ -21,7 +21,9 @@
 import org.apache.commons.lang3.time.StopWatch;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.hibernate.*;
+import org.hibernate.FlushMode;
+import org.hibernate.Hibernate;
+import org.hibernate.SessionFactory;
 import org.hibernate.criterion.Projections;
 import org.hibernate.criterion.Restrictions;
 import org.hibernate.metadata.ClassMetadata;
@@ -46,46 +48,25 @@ public abstract class AbstractDao<T extends Identifiable> implements BaseDao<T>
 
     protected static final Log log = LogFactory.getLog( AbstractDao.class );
 
-    /**
-     * Default batch size to reach before flushing and clearing the Hibernate session when a batch-supporting method
-     * used in a batch-advisable flush mode.
-     */
-    protected static final int DEFAULT_BATCH_SIZE = 100;
-
     protected final Class<? extends T> elementClass;
-
     private final SessionFactory sessionFactory;
-    private final int batchSize;
     private final ClassMetadata classMetadata;
 
     protected AbstractDao( Class<? extends T> elementClass, SessionFactory sessionFactory ) {
         this( elementClass, sessionFactory, requireNonNull( sessionFactory.getClassMetadata( elementClass ),
-                String.format( "%s is missing from Hibernate mapping.", elementClass.getName() ) ), DEFAULT_BATCH_SIZE );
-    }
-
-    protected AbstractDao( Class<? extends T> elementClass, SessionFactory sessionFactory, ClassMetadata classMetadata ) {
-        this( elementClass, sessionFactory, classMetadata, DEFAULT_BATCH_SIZE );
+                String.format( "%s is missing from Hibernate mapping.", elementClass.getName() ) ) );
     }
 
     /**
      * @param classMetadata the class metadata to use to retrieve information about {@link T}
-     * @param batchSize     a strictly positive batch size for creating, updating or deleting collection of entities.
-     *                      Use {@link Integer#MAX_VALUE} to effectively disable batching and '1' to flush changes right
-     *                      away. Batching only applies if the current flush mode is {@link FlushMode#MANUAL} or
-     *                      {@link FlushMode#AUTO} in a batch-supporting method such as {@link #createInBatch(Collection)}.
-     *                      This value should be adjusted to an optimal one for the DAO. Large model should have a
-     *                      relatively small batch size to reduce memory usage. See <a href="https://docs.jboss.org/hibernate/core/4.2/manual/en-US/html/ch15.html">Chapter 15. Batch processing</a>
-     *                      for more details.
      */
-    protected AbstractDao( Class<? extends T> elementClass, SessionFactory sessionFactory, ClassMetadata classMetadata, int batchSize ) {
+    protected AbstractDao( Class<? extends T> elementClass, SessionFactory sessionFactory, ClassMetadata classMetadata ) {
         Assert.isTrue( elementClass.isAssignableFrom( ( Class<?> ) classMetadata.getMappedClass() ),
                 String.format( "The mapped class must be assignable from %s.", elementClass.getName() ) );
         Assert.notNull( classMetadata.getIdentifierPropertyName(), String.format( "%s does not have a ID.", elementClass.getName() ) );
-        Assert.isTrue( batchSize >= 1, "Batch size must be greater or equal to 1." );
         this.elementClass = elementClass;
         this.sessionFactory = sessionFactory;
         this.classMetadata = classMetadata;
-        this.batchSize = batchSize;
     }
 
     @Override
@@ -109,22 +90,6 @@ public Collection<T> create( Collection<T> entities ) {
         return results;
     }
 
-    @Override
-    public void createInBatch( Collection<T> entities ) {
-        StopWatch stopWatch = StopWatch.createStarted();
-        warnIfBatchingIsNotAdvisable( "create", entities );
-        int i = 0;
-        for ( T t : entities ) {
-            //noinspection ResultOfMethodCallIgnored
-            this.create( t );
-            if ( ++i % batchSize == 0 && isBatchingAdvisable() ) {
-                flushAndClear();
-                AbstractDao.log.debug( String.format( "Flushed and cleared after creating %d/%d %s entities.", i, entities.size(), elementClass ) );
-            }
-        }
-        AbstractDao.log.debug( String.format( "Created %d %s entities in %s ms.", entities.size(), elementClass.getSimpleName(), stopWatch.getTime( TimeUnit.MILLISECONDS ) ) );
-    }
-
     @Override
     @OverridingMethodsMustInvokeSuper
     public T create( T entity ) {
@@ -144,21 +109,6 @@ public Collection<T> save( Collection<T> entities ) {
         return results;
     }
 
-    @Override
-    public void saveInBatch( Collection<T> entities ) {
-        StopWatch timer = StopWatch.createStarted();
-        int i = 0;
-        for ( T entity : entities ) {
-            //noinspection ResultOfMethodCallIgnored
-            this.save( entity );
-            if ( ++i % batchSize == 0 && isBatchingAdvisable() ) {
-                flushAndClear();
-                AbstractDao.log.trace( String.format( "Flushed and cleared after saving %d/%d %s entities.", i, entities.size(), elementClass ) );
-            }
-        }
-        AbstractDao.log.debug( String.format( "Saved %d entities in %d ms.", entities.size(), timer.getTime( TimeUnit.MILLISECONDS ) ) );
-    }
-
     @Override
     @OverridingMethodsMustInvokeSuper
     public T save( T entity ) {
@@ -271,21 +221,6 @@ public void remove( Collection<T> entities ) {
         AbstractDao.log.debug( String.format( "Removed %d entities in %d ms.", entities.size(), timer.getTime( TimeUnit.MILLISECONDS ) ) );
     }
 
-    @Override
-    public void removeInBatch( Collection<T> entities ) {
-        StopWatch timer = StopWatch.createStarted();
-        warnIfBatchingIsNotAdvisable( "remove", entities );
-        int i = 0;
-        for ( T e : entities ) {
-            this.remove( e );
-            if ( ++i % batchSize == 0 && isBatchingAdvisable() ) {
-                flushAndClear();
-                AbstractDao.log.trace( String.format( "Flushed and cleared after removing %d/%d %s entities.", i, entities.size(), elementClass ) );
-            }
-        }
-        AbstractDao.log.debug( String.format( "Removed %d entities in %d ms.", entities.size(), timer.getTime( TimeUnit.MILLISECONDS ) ) );
-    }
-
     @Override
     public void remove( Long id ) {
         T entity = this.load( id );
@@ -303,22 +238,6 @@ public void remove( T entity ) {
         AbstractDao.log.trace( String.format( "Removed %s.", formatEntity( entity ) ) );
     }
 
-    @Override
-    public void removeAllInBatch() {
-        StopWatch timer = StopWatch.createStarted();
-        while ( true ) {
-            //noinspection unchecked
-            List<T> results = sessionFactory.getCurrentSession().createCriteria( elementClass )
-                    .setMaxResults( batchSize )
-                    .list();
-            if ( results.isEmpty() ) {
-                break;
-            }
-            this.removeInBatch( results );
-        }
-        AbstractDao.log.debug( String.format( "Removed all %s entities in %d ms.", elementClass.getSimpleName(), timer.getTime( TimeUnit.MILLISECONDS ) ) );
-    }
-
     @Override
     public void update( Collection<T> entities ) {
         StopWatch timer = StopWatch.createStarted();
@@ -328,21 +247,6 @@ public void update( Collection<T> entities ) {
         AbstractDao.log.debug( String.format( "Updated %d %s entities in %d ms.", entities.size(), elementClass.getSimpleName(), timer.getTime( TimeUnit.MILLISECONDS ) ) );
     }
 
-    @Override
-    public void updateInBatch( Collection<T> entities ) {
-        StopWatch timer = StopWatch.createStarted();
-        warnIfBatchingIsNotAdvisable( "update", entities );
-        int i = 0;
-        for ( T entity : entities ) {
-            this.update( entity );
-            if ( ++i % batchSize == 0 && isBatchingAdvisable() ) {
-                flushAndClear();
-                AbstractDao.log.trace( String.format( "Flushed and cleared after updating %d/%d %s entities.", i, entities.size(), elementClass ) );
-            }
-        }
-        AbstractDao.log.debug( String.format( "Updated %d %s entities in %d ms.", entities.size(), elementClass.getSimpleName(), timer.getTime( TimeUnit.MILLISECONDS ) ) );
-    }
-
     @Override
     @OverridingMethodsMustInvokeSuper
     public void update( T entity ) {
@@ -421,46 +325,6 @@ protected List<T> findByPropertyIn( String propertyName, Collection<?> propertyV
                 .list();
     }
 
-    /**
-     * Flush pending changes to the persistent storage.
-     */
-    protected void flush() {
-        sessionFactory.getCurrentSession().flush();
-    }
-
-    /**
-     * Flush pending changes and clear the session.
-     * <p>
-     * Use this carefully, cleared entities referenced later will be retrieved from the persistent storage.
-     */
-    private void flushAndClear() {
-        this.getSessionFactory().getCurrentSession().flush();
-        this.getSessionFactory().getCurrentSession().clear();
-    }
-
-    /**
-     * Emit a warning if the current flush mode does not allow batching the given collection.
-     */
-    private void warnIfBatchingIsNotAdvisable( String operation, Collection<?> entities ) {
-        if ( entities.size() >= DEFAULT_BATCH_SIZE && !isBatchingAdvisable() ) {
-            AbstractDao.log.warn( String.format( "Batching is not advisable with current flush mode %s, will proceed with %s on %d entities without invoking Session.flush() and Session.clear().",
-                    sessionFactory.getCurrentSession().getFlushMode(),
-                    operation,
-                    entities.size() ) );
-        }
-    }
-
-    /**
-     * Check if batching is currently advisable.
-     * <p>
-     * In certain cases, such as when the flush mode is set to {@link FlushMode#MANUAL}, we would want to prevent any
-     * unintended flushes.
-     */
-    private boolean isBatchingAdvisable() {
-        FlushMode flushMode = sessionFactory.getCurrentSession().getFlushMode();
-        return flushMode == FlushMode.AUTO || flushMode == FlushMode.ALWAYS;
-    }
-
     private String formatEntity( @Nullable T entity ) {
         if ( entity == null ) {
             return String.format( "null %s", elementClass.getSimpleName() );
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/AbstractService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/AbstractService.java
index 69f1d388cf..2cd5547515 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/AbstractService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/AbstractService.java
@@ -10,6 +10,8 @@
 import javax.annotation.Nonnull;
 import javax.annotation.OverridingMethodsMustInvokeSuper;
 import java.util.*;
+import java.util.function.Function;
+import java.util.function.Supplier;
 
 import static java.util.Objects.requireNonNull;
 
@@ -96,10 +98,32 @@ public O load( Long id ) {
     @Override
     @Transactional(readOnly = true)
     public O loadOrFail( Long id ) {
-        return requireNonNull( mainDao.load( id ),
+        return loadOrFail( id, NullPointerException::new,
                 String.format( "No %s with ID %d.", mainDao.getElementClass().getName(), id ) );
     }
 
+    @Nonnull
+    @Override
+    @Transactional(readOnly = true)
+    public <T extends Exception> O loadOrFail( Long id, Supplier<T> exceptionSupplier ) throws T {
+        O entity = mainDao.load( id );
+        if ( entity == null ) {
+            throw exceptionSupplier.get();
+        }
+        return entity;
+    }
+
+    @Nonnull
+    @Override
+    @Transactional(readOnly = true)
+    public <T extends Exception> O loadOrFail( Long id, Function<String, T> exceptionSupplier, String message ) throws T {
+        O entity = mainDao.load( id );
+        if ( entity == null ) {
+            throw exceptionSupplier.apply( message );
+        }
+        return entity;
+    }
+
     @Override
     @Transactional(readOnly = true)
     public Collection<O> loadAll() {
@@ -131,12 +155,6 @@ public void remove( O entity ) {
         mainDao.remove( entity );
     }
 
-    @Override
-    @Transactional
-    public void removeAllInBatch() {
-        mainDao.removeAllInBatch();
-    }
-
     @Override
     @Transactional
     public void update( Collection<O> entities ) {
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseDao.java
index e1c52e6673..7d664feb63 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseDao.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseDao.java
@@ -20,7 +20,9 @@
 
 import ubic.gemma.model.common.Identifiable;
 
-import javax.annotation.*;
+import javax.annotation.CheckReturnValue;
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import java.io.Serializable;
 import java.util.Collection;
 
@@ -51,11 +53,6 @@ public interface BaseDao<T> {
     @CheckReturnValue
     Collection<T> create( Collection<T> entities );
 
-    /**
-     * Create all the given entities in batch.
-     */
-    void createInBatch( Collection<T> entities );
-
     /**
      * Create an object. If the entity type is immutable, this may also remove any existing entities identified by an
      * appropriate 'find' method.
@@ -78,8 +75,6 @@ public interface BaseDao<T> {
     @CheckReturnValue
     Collection<T> save( Collection<T> entities );
 
-    void saveInBatch( Collection<T> entities );
-
     /**
      * Create or update an entity whether it is transient.
      * <p>
@@ -147,11 +142,6 @@ public interface BaseDao<T> {
 
     void remove( Collection<T> entities );
 
-    /**
-     * Remove all given instances in batch.
-     */
-    void removeInBatch( Collection<T> entities );
-
     /**
      * Remove a persistent instance based on its ID.
      *
@@ -171,18 +161,11 @@ public interface BaseDao<T> {
      */
     void remove( T entity );
 
-    /**
-     * Remove all entities from persistent storage.
-     */
-    void removeAllInBatch();
-
     /**
      * @param entities Update the entities. Not supported if the entities are immutable.
      */
     void update( Collection<T> entities );
 
-    void updateInBatch( Collection<T> entities );
-
     /**
      * @param entity Update the entity. Not supported if the entity is immutable.
      */
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseImmutableService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseImmutableService.java
index c61dccb5ca..4b426fbbce 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseImmutableService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseImmutableService.java
@@ -60,9 +60,4 @@ public interface BaseImmutableService<O extends Identifiable> extends BaseReadOn
      * @param entity the entity to be removed.
      */
     void remove( O entity );
-
-    /**
-     * Remove all entities from the persistent storage.
-     */
-    void removeAllInBatch();
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseReadOnlyService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseReadOnlyService.java
index 3dce4cca34..e5fa7f1fcd 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseReadOnlyService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/BaseReadOnlyService.java
@@ -6,6 +6,8 @@
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import java.util.Collection;
+import java.util.function.Function;
+import java.util.function.Supplier;
 
 /**
  * Interface for read-only services.
@@ -25,9 +27,15 @@ public interface BaseReadOnlyService<O extends Identifiable> {
     @CheckReturnValue
     O find( O entity );
 
+    /**
+     * Does a search for the entity in the persistent storage, raising a {@link NullPointerException} if not found.
+     * @param entity the entity to be searched for
+     * @return the version of entity retrieved from persistent storage
+     * @throws NullPointerException if the entity is not found
+     */
     @Nonnull
     @CheckReturnValue
-    O findOrFail( O entity );
+    O findOrFail( O entity ) throws NullPointerException;
 
     /**
      * Loads objects with given ids.
@@ -55,6 +63,12 @@ public interface BaseReadOnlyService<O extends Identifiable> {
     @Nonnull
     O loadOrFail( Long id ) throws NullPointerException;
 
+    @Nonnull
+    <T extends Exception> O loadOrFail( Long id, Supplier<T> exceptionSupplier ) throws T;
+
+    @Nonnull
+    <T extends Exception> O loadOrFail( Long id, Function<String, T> exceptionSupplier, String message ) throws T;
+
     /**
      * Loads all the entities of specific type.
      *
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/coexpression/CoexpressionAnalysisService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/coexpression/CoexpressionAnalysisService.java
index 77759b675f..efb18f633d 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/coexpression/CoexpressionAnalysisService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/coexpression/CoexpressionAnalysisService.java
@@ -45,7 +45,7 @@ public interface CoexpressionAnalysisService extends BaseService<CoexpressionAna
     void update( CoexpressionAnalysis o );
 
     @Override
-    @Secured({ "GROUP_USER", "ACL_SECURABLE_EDIT" })
+    @Secured({ "GROUP_USER", "ACL_SECURABLE_COLLECTION_EDIT" })
     void update( Collection<CoexpressionAnalysis> o );
 
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "ACL_SECURABLE_READ" })
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/coexpression/CoexpressionAnalysisServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/coexpression/CoexpressionAnalysisServiceImpl.java
index cbe9f5715b..fae31db592 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/coexpression/CoexpressionAnalysisServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/coexpression/CoexpressionAnalysisServiceImpl.java
@@ -122,11 +122,6 @@ public void remove( Long id ) {
         throw new UnsupportedOperationException( "Removing a coexpression analysis by ID is not supported." );
     }
 
-    @Override
-    public void removeAllInBatch() {
-        throw new UnsupportedOperationException( "Removing all coexpression analyses in batch is not supported." );
-    }
-
     @Override
     @Transactional(readOnly = true)
     public Collection<CoexpressionAnalysis> findByExperiment( BioAssaySet investigation ) {
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisDaoImpl.java
index 8a09739925..82bb4e86a4 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisDaoImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisDaoImpl.java
@@ -21,15 +21,14 @@
 import org.apache.commons.collections4.ListUtils;
 import org.apache.commons.lang3.time.StopWatch;
 import org.apache.commons.lang3.tuple.Pair;
-import org.hibernate.Hibernate;
-import org.hibernate.HibernateException;
-import org.hibernate.SQLQuery;
-import org.hibernate.SessionFactory;
+import org.hibernate.*;
 import org.hibernate.engine.jdbc.spi.SqlStatementLogger;
+import org.hibernate.engine.spi.SessionImplementor;
+import org.hibernate.id.IdentifierGeneratorHelper;
 import org.hibernate.internal.SessionFactoryImpl;
-import org.hibernate.internal.SessionImpl;
 import org.hibernate.jdbc.Expectations;
 import org.hibernate.persister.entity.EntityPersister;
+import org.hibernate.type.Type;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 import ubic.gemma.model.analysis.expression.diff.*;
@@ -42,8 +41,10 @@
 import ubic.gemma.persistence.util.CommonQueries;
 import ubic.gemma.persistence.util.EntityUtils;
 
+import java.io.Serializable;
 import java.math.BigInteger;
 import java.sql.PreparedStatement;
+import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.Types;
 import java.util.*;
@@ -146,15 +147,16 @@ public DifferentialExpressionAnalysis create( DifferentialExpressionAnalysis ent
         // create the analysis, result sets, pvalue distributions, etc.
         DifferentialExpressionAnalysis finalEntity = super.create( entity );
 
-        getSessionFactory().getCurrentSession().doWork( work -> {
-            PreparedStatement insertResultStmt = work.prepareStatement( INSERT_RESULT_SQL );
-            PreparedStatement insertContrastStmt = work.prepareStatement( INSERT_CONTRAST_SQL );
-            int numResults = 0;
-            int numContrasts = 0;
+        Session session = getSessionFactory().getCurrentSession();
+
+        session.doWork( work -> {
+            PreparedStatement insertResultStmt = work.prepareStatement( INSERT_RESULT_SQL, PreparedStatement.RETURN_GENERATED_KEYS );
+            PreparedStatement insertContrastStmt = work.prepareStatement( INSERT_CONTRAST_SQL, PreparedStatement.RETURN_GENERATED_KEYS );
+            List<DifferentialExpressionAnalysisResult> results = new ArrayList<>();
+            List<ContrastResult> contrasts = new ArrayList<>();
             for ( ExpressionAnalysisResultSet rs : finalEntity.getResultSets() ) {
                 for ( DifferentialExpressionAnalysisResult result : rs.getResults() ) {
-                    result.setId( ( Long ) resultPersister.getIdentifierGenerator().generate( ( SessionImpl ) getSessionFactory().getCurrentSession(), result ) );
-                    insertResultStmt.setLong( 1, result.getId() );
+                    insertResultStmt.setNull( 1, Types.BIGINT );
                     insertResultStmt.setObject( 2, result.getPvalue(), Types.DOUBLE );
                     insertResultStmt.setObject( 3, result.getCorrectedPvalue(), Types.DOUBLE );
                     insertResultStmt.setObject( 4, result.getRank(), Types.DOUBLE );
@@ -162,10 +164,16 @@ public DifferentialExpressionAnalysis create( DifferentialExpressionAnalysis ent
                     insertResultStmt.setLong( 6, result.getProbe().getId() );
                     insertResultStmt.setLong( 7, rs.getId() );
                     insertResultStmt.addBatch();
-                    numResults++;
+                    results.add( result );
+                }
+            }
+
+            insertRowsAndAssignGeneratedKeys( INSERT_RESULT_SQL, insertResultStmt, results, resultPersister, ( SessionImplementor ) session );
+
+            for ( ExpressionAnalysisResultSet rs : finalEntity.getResultSets() ) {
+                for ( DifferentialExpressionAnalysisResult result : rs.getResults() ) {
                     for ( ContrastResult cr : result.getContrasts() ) {
-                        cr.setId( ( Long ) contrastPersister.getIdentifierGenerator().generate( ( SessionImpl ) getSessionFactory().getCurrentSession(), cr ) );
-                        insertContrastStmt.setLong( 1, cr.getId() );
+                        insertContrastStmt.setNull( 1, Types.BIGINT );
                         insertContrastStmt.setObject( 2, cr.getPvalue(), Types.DOUBLE );
                         insertContrastStmt.setObject( 3, cr.getTstat(), Types.DOUBLE );
                         if ( cr.getFactorValue() != null ) {
@@ -182,20 +190,29 @@ public DifferentialExpressionAnalysis create( DifferentialExpressionAnalysis ent
                             insertContrastStmt.setNull( 8, Types.BIGINT );
                         }
                         insertContrastStmt.addBatch();
-                        numContrasts++;
+                        contrasts.add( cr );
                     }
                 }
             }
 
-            statementLogger.logStatement( INSERT_RESULT_SQL + String.format( " [repeated %d times]", numResults ) );
-            ensureExpectedRowsAreInserted( insertResultStmt, insertResultStmt.executeBatch() );
-            statementLogger.logStatement( INSERT_CONTRAST_SQL + String.format( " [repeated %d times]", numContrasts ) );
-            ensureExpectedRowsAreInserted( insertContrastStmt, insertContrastStmt.executeBatch() );
+            insertRowsAndAssignGeneratedKeys( INSERT_CONTRAST_SQL, insertContrastStmt, contrasts, contrastPersister, ( SessionImplementor ) session );
         } );
 
         return finalEntity;
     }
 
+    private void insertRowsAndAssignGeneratedKeys( String insertSql, PreparedStatement insertStmt, List<?> objects, EntityPersister persister, SessionImplementor session ) throws SQLException {
+        statementLogger.logStatement( insertSql + String.format( " [repeated %d times]", objects.size() ) );
+        ensureExpectedRowsAreInserted( insertStmt, insertStmt.executeBatch() );
+        ResultSet rs = insertStmt.getGeneratedKeys();
+        String idProp = persister.getIdentifierPropertyName();
+        Type idType = persister.getIdentifierType();
+        for ( Object object : objects ) {
+            Serializable id = IdentifierGeneratorHelper.getGeneratedIdentity( rs, idProp, idType );
+            persister.setIdentifier( object, id, session );
+        }
+    }
+
     private void ensureExpectedRowsAreInserted( PreparedStatement statement, int[] batchStatus ) throws
             HibernateException, SQLException {
         int i = 0;
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisServiceImpl.java
index 27e542c8c3..fd79cec015 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisServiceImpl.java
@@ -242,19 +242,12 @@ public void remove( Long id ) {
         throw new UnsupportedOperationException( "Removing an analysis by ID is not supported, use remove() with an entity instead." );
     }
 
-    @Override
-    public void removeAllInBatch() {
-        throw new UnsupportedOperationException( "Removing all analyses in batch is not supported." );
-    }
-
     @Override
     @Transactional
     public void removeForExperiment( BioAssaySet ee ) {
         Collection<DifferentialExpressionAnalysis> diffAnalyses = this.differentialExpressionAnalysisDao
                 .findByExperiment( ee );
-        for ( DifferentialExpressionAnalysis de : diffAnalyses ) {
-            this.remove( de );
-        }
+        this.remove( diffAnalyses );
     }
 
     @Override
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationDao.java
index 3c10c0882c..d45ca5d586 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationDao.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationDao.java
@@ -56,5 +56,5 @@ public interface Gene2GOAssociationDao extends BaseDao<Gene2GOAssociation> {
 
     Collection<Gene> getGenes( Collection<String> ids, @Nullable Taxon taxon );
 
-    void removeAllInBatch();
+    int removeAll();
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationDaoImpl.java
index b1769f171c..b7f1d97786 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationDaoImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationDaoImpl.java
@@ -21,7 +21,6 @@
 import org.apache.commons.lang3.time.StopWatch;
 import org.hibernate.Criteria;
 import org.hibernate.Query;
-import org.hibernate.Session;
 import org.hibernate.SessionFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
@@ -147,6 +146,29 @@ public Collection<Gene> getGenes( Collection<String> ids, @Nullable Taxon taxon
                 .setParameterList( "goIDs", ids ).setParameter( "tax", taxon ).list();
     }
 
+    @Override
+    public int removeAll() {
+        //noinspection unchecked
+        List<Long> cIds = getSessionFactory().getCurrentSession()
+                .createQuery( "select c.id from Gene2GOAssociation g2g join g2g.ontologyEntry c" )
+                .list();
+        int removedAssociations = this.getSessionFactory().getCurrentSession()
+                .createQuery( "delete from Gene2GOAssociation" )
+                .executeUpdate();
+        int removedCharacteristics;
+        if ( !cIds.isEmpty() ) {
+            removedCharacteristics = getSessionFactory().getCurrentSession()
+                    .createQuery( "delete from Characteristic where id in :cIds" )
+                    .setParameterList( "cIds", cIds )
+                    .executeUpdate();
+        } else {
+            removedCharacteristics = 0;
+        }
+        log.debug( String.format( "Removed all %d Gene2GOAssociation. %d Characteristic were removed in cascade.",
+                removedAssociations, removedCharacteristics ) );
+        return removedAssociations;
+    }
+
     private Map<? extends Gene, ? extends Collection<Characteristic>> fetchBatch( Set<Gene> batch ) {
         Map<Long, Gene> giMap = EntityUtils.getIdMap( batch );
         //language=HQL
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationService.java
index 09c4ea0e28..c9219c212e 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationService.java
@@ -24,7 +24,6 @@
 import ubic.gemma.model.genome.Gene;
 import ubic.gemma.model.genome.Taxon;
 import ubic.gemma.persistence.service.BaseImmutableService;
-import ubic.gemma.persistence.service.BaseService;
 
 import javax.annotation.Nullable;
 import java.util.Collection;
@@ -53,8 +52,11 @@ public interface Gene2GOAssociationService extends BaseImmutableService<Gene2GOA
 
     Collection<Gene> findByGOTerm( String goID, Taxon taxon );
 
+    /**
+     * Remove all Gene2GO associations in batch.
+     */
     @Secured({ "GROUP_ADMIN" })
-    void removeAllInBatch();
+    int removeAll();
 
     /**
      * @param  termsToFetch terms
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationServiceImpl.java
index cdaa26b051..874397e7e4 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/Gene2GOAssociationServiceImpl.java
@@ -120,6 +120,12 @@ public Collection<Gene> findByGOTerm( String goID, Taxon taxon ) {
         return this.gene2GOAssociationDao.findByGoTerm( goID, taxon );
     }
 
+    @Override
+    @Transactional
+    public int removeAll() {
+        return this.gene2GOAssociationDao.removeAll();
+    }
+
     @Override
     @Transactional(readOnly = true)
     public Collection<Gene> findByGOTerms( Collection<String> termsToFetch, @Nullable Taxon taxon ) {
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/PhenotypeAssociationDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/PhenotypeAssociationDao.java
index 6844e0283a..eca5d9b2b6 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/PhenotypeAssociationDao.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/PhenotypeAssociationDao.java
@@ -203,4 +203,5 @@ Collection<DifferentialExpressionEvidence> loadEvidenceWithGeneDifferentialExpre
      */
     void removePhenotypePublication( PhenotypeAssociationPublication phenotypeAssociationPublicationId );
 
+    int removeAll();
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/PhenotypeAssociationDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/PhenotypeAssociationDaoImpl.java
index cc804fcfdb..afbdf0e4d9 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/PhenotypeAssociationDaoImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/PhenotypeAssociationDaoImpl.java
@@ -37,6 +37,7 @@
 import ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject;
 import ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject;
 import ubic.gemma.persistence.service.AbstractDao;
+import ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDao;
 import ubic.gemma.persistence.util.EntityUtils;
 
 import javax.annotation.Nullable;
@@ -59,6 +60,9 @@ public class PhenotypeAssociationDaoImpl extends AbstractDao<PhenotypeAssociatio
             + "'ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence') ";
     private static final Log log = LogFactory.getLog( PhenotypeAssociationDaoImpl.class );
 
+    @Autowired
+    private AuditTrailDao auditTrailDao;
+
     @Autowired
     public PhenotypeAssociationDaoImpl( SessionFactory sessionFactory ) {
         super( PhenotypeAssociation.class, sessionFactory );
@@ -761,6 +765,25 @@ public void removePhenotypePublication( PhenotypeAssociationPublication phenotyp
                 .executeUpdate();
     }
 
+    @Override
+    public int removeAll() {
+        //noinspection unchecked
+        List<Long> atIds = getSessionFactory().getCurrentSession()
+                .createQuery( "select at.id from PhenotypeAssociation pa join pa.auditTrail at" )
+                .list();
+        getSessionFactory().getCurrentSession()
+                .createSQLQuery( "delete from CHARACTERISTIC where PHENOTYPE_ASSOCIATION_FK is not null" )
+                .executeUpdate();
+        getSessionFactory().getCurrentSession()
+                .createSQLQuery( "delete from PHENOTYPE_ASSOCIATION_PUBLICATIONS where PHENOTYPE_ASSOCIATION_FK is not null" )
+                .executeUpdate();
+        int associationsRemoved = this.getSessionFactory().getCurrentSession()
+                .createQuery( "delete from PhenotypeAssociation" )
+                .executeUpdate();
+        auditTrailDao.removeByIds( atIds );
+        return associationsRemoved;
+    }
+
     @SuppressWarnings("ConstantConditions") // Better readability
     private String addExternalDatabaseQuery( @Nullable Collection<Long> externalDatabaseIds ) {
 
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/service/PhenotypeAssociationService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/service/PhenotypeAssociationService.java
index e0b919acc6..339196928f 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/service/PhenotypeAssociationService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/service/PhenotypeAssociationService.java
@@ -146,4 +146,7 @@ Collection<DifferentialExpressionEvidence> loadEvidenceWithGeneDifferentialExpre
     ExternalDatabaseStatisticsValueObject loadStatisticsOnAllEvidence( String downloadFile );
 
     void removePhenotypePublication( PhenotypeAssociationPublication phenotypeAssociationPublicationId );
+
+    @Secured({ "GROUP_ADMIN" })
+    int removeAll();
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/service/PhenotypeAssociationServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/service/PhenotypeAssociationServiceImpl.java
index 24a2f3055f..ac5da1a78e 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/service/PhenotypeAssociationServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/association/phenotype/service/PhenotypeAssociationServiceImpl.java
@@ -341,4 +341,9 @@ public void removePhenotypePublication( PhenotypeAssociationPublication phenotyp
         this.phenotypeAssociationDao.removePhenotypePublication( phenotypeAssociationPublication );
     }
 
+    @Override
+    @Transactional
+    public int removeAll() {
+        return this.phenotypeAssociationDao.removeAll();
+    }
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/common/auditAndSecurity/AuditTrailDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/common/auditAndSecurity/AuditTrailDao.java
index 140334a715..4814b52e40 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/common/auditAndSecurity/AuditTrailDao.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/common/auditAndSecurity/AuditTrailDao.java
@@ -21,9 +21,19 @@
 import ubic.gemma.model.common.auditAndSecurity.AuditTrail;
 import ubic.gemma.persistence.service.BaseDao;
 
+import java.util.Collection;
+
 /**
  * @see ubic.gemma.model.common.auditAndSecurity.AuditTrail
  */
 public interface AuditTrailDao extends BaseDao<AuditTrail> {
 
+    /**
+     * Remove the given audit trails by IDs.
+     * <p>
+     * This is more efficient than using {@link #remove(Collection)} because batch operations are performed without
+     * retrieving entities.
+     * @return number of entities removed
+     */
+    int removeByIds( Collection<Long> ids );
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/common/auditAndSecurity/AuditTrailDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/common/auditAndSecurity/AuditTrailDaoImpl.java
index efb771c07f..266cf83fa1 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/common/auditAndSecurity/AuditTrailDaoImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/common/auditAndSecurity/AuditTrailDaoImpl.java
@@ -24,6 +24,9 @@
 import ubic.gemma.model.common.auditAndSecurity.AuditTrail;
 import ubic.gemma.persistence.service.AbstractDao;
 
+import java.util.Collection;
+import java.util.List;
+
 /**
  * @author pavlidis
  * @see AuditTrailDao
@@ -35,4 +38,34 @@ public class AuditTrailDaoImpl extends AbstractDao<AuditTrail> implements AuditT
     public AuditTrailDaoImpl( SessionFactory sessionFactory ) {
         super( AuditTrail.class, sessionFactory );
     }
+
+    @Override
+    public int removeByIds( Collection<Long> ids ) {
+        if ( ids.isEmpty() )
+            return 0;
+        //noinspection unchecked
+        List<Long> aeIds = getSessionFactory().getCurrentSession()
+                .createQuery( "select ae.id from AuditTrail at join at.events ae" )
+                .list();
+        //noinspection unchecked
+        List<Long> aetIds = getSessionFactory().getCurrentSession()
+                .createQuery( "select aet.id from AuditTrail at join at.events ae join ae.eventType aet" )
+                .list();
+        if ( !aeIds.isEmpty() ) {
+            getSessionFactory().getCurrentSession()
+                    .createQuery( "delete from AuditEvent ae where ae.id in :aeIds" )
+                    .setParameterList( "aeIds", aeIds )
+                    .executeUpdate();
+        }
+        if ( !aetIds.isEmpty() ) {
+            getSessionFactory().getCurrentSession()
+                    .createQuery( "delete from AuditEventType aet where aet.id in :aetIds" )
+                    .setParameterList( "aetIds", aetIds )
+                    .executeUpdate();
+        }
+        return getSessionFactory().getCurrentSession()
+                .createQuery( "delete from AuditTrail at where at.id in :atIds" )
+                .setParameterList( "atIds", ids )
+                .executeUpdate();
+    }
 }
\ No newline at end of file
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/common/description/ExternalDatabaseService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/common/description/ExternalDatabaseService.java
index b970142289..9f0a508ec0 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/common/description/ExternalDatabaseService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/common/description/ExternalDatabaseService.java
@@ -76,9 +76,5 @@ public interface ExternalDatabaseService extends BaseService<ExternalDatabase> {
     @Secured({ "GROUP_ADMIN" })
     void remove( Collection<ExternalDatabase> entities );
 
-    @Override
-    @Secured({ "GROUP_ADMIN" })
-    void removeAllInBatch();
-
     List<ExternalDatabase> findAllByNameIn( List<String> names );
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignDaoImpl.java
index d7475576d3..8f3bbb180d 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignDaoImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignDaoImpl.java
@@ -205,7 +205,7 @@ public void deleteGeneProductAssociations( ArrayDesign arrayDesign ) {
                     "Done deleting " + blatAssociations.size() + " blat associations for " + arrayDesign );
         }
 
-        flush();
+        getSessionFactory().getCurrentSession().flush();
 
         final String annotationAssociationQueryString = "select ba from CompositeSequence cs "
                 + " inner join cs.biologicalCharacteristic bs, AnnotationAssociation ba "
@@ -873,10 +873,10 @@ public Boolean updateSubsumingStatus( ArrayDesign candidateSubsumer, ArrayDesign
         candidateSubsumee.setSubsumingArrayDesign( candidateSubsumer );
 
         this.update( candidateSubsumer );
-        flush();
+        getSessionFactory().getCurrentSession().flush();
 
         this.update( candidateSubsumee );
-        flush();
+        getSessionFactory().getCurrentSession().flush();
 
         return true;
     }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignService.java
index f6f0c2050e..bd4c575a5b 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignService.java
@@ -37,10 +37,17 @@
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
+import java.util.function.Function;
 
 @SuppressWarnings("unused") // Possible external use
 public interface ArrayDesignService extends CuratableService<ArrayDesign, ArrayDesignValueObject> {
 
+    /**
+     * Load a platform by ID and thaw it with {@link #thawLite(ArrayDesign)}
+     */
+    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ" })
+    <T extends Exception> ArrayDesign loadAndThawLiteOrFail( Long id, Function<String, T> exceptionSupplier, String message ) throws T;
+
     @Secured({ "GROUP_ADMIN" })
     void addProbes( ArrayDesign arrayDesign, Collection<CompositeSequence> newProbes );
 
@@ -370,4 +377,6 @@ public interface ArrayDesignService extends CuratableService<ArrayDesign, ArrayD
 
     @Secured("IS_AUTHENTICATED_ANONYMOUSLY")
     Collection<ArrayDesignValueObject> loadValueObjectsWithCache( @Nullable Filters filters, @Nullable Sort sort );
+
+    long countWithCache( @Nullable Filters filters );
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignServiceImpl.java
index 8eeda8ffcb..3f89231947 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignServiceImpl.java
@@ -36,6 +36,7 @@
 
 import javax.annotation.Nullable;
 import java.util.*;
+import java.util.function.Function;
 
 /**
  * @author klc
@@ -57,6 +58,14 @@ public ArrayDesignServiceImpl( ArrayDesignDao arrayDesignDao, AuditEventDao audi
         this.auditEventDao = auditEventDao;
     }
 
+    @Override
+    @Transactional(readOnly = true)
+    public <T extends Exception> ArrayDesign loadAndThawLiteOrFail( Long id, Function<String, T> exceptionSupplier, String message ) throws T {
+        ArrayDesign ad = loadOrFail( id, exceptionSupplier, message );
+        arrayDesignDao.thawLite( ad );
+        return ad;
+    }
+
     @Override
     @Transactional
     public void addProbes( ArrayDesign arrayDesign, Collection<CompositeSequence> newProbes ) {
@@ -270,6 +279,12 @@ public Collection<ArrayDesignValueObject> loadValueObjectsWithCache( @Nullable F
         return arrayDesignDao.loadValueObjectsWithCache( filters, sort );
     }
 
+    @Override
+    @Transactional(readOnly = true)
+    public long countWithCache( @Nullable Filters filters ) {
+        return arrayDesignDao.countWithCache( filters );
+    }
+
     @Override
     @Transactional(readOnly = true)
     public Map<Long, Boolean> isMerged( Collection<Long> ids ) {
@@ -416,7 +431,7 @@ public Collection<ArrayDesign> thaw( Collection<ArrayDesign> aas ) {
     @Transactional(readOnly = true)
     public ArrayDesign thawLite( ArrayDesign arrayDesign ) {
         arrayDesign = ensureInSession( arrayDesign );
-        arrayDesignDao.thaw( arrayDesign );
+        arrayDesignDao.thawLite( arrayDesign );
         return arrayDesign;
     }
 
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/CuratableService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/CuratableService.java
index d54f4f1e2b..3654e2de0a 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/CuratableService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/arrayDesign/CuratableService.java
@@ -13,6 +13,8 @@
 import javax.annotation.Nullable;
 import java.util.Collection;
 import java.util.List;
+import java.util.function.Function;
+import java.util.function.Supplier;
 
 /**
  * Interface for curatable services.
@@ -43,6 +45,7 @@ public interface CuratableService<C extends Curatable, VO extends AbstractCurata
     Collection<C> load( Collection<Long> ids );
 
     @Override
+    @Nullable
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ_QUIET" })
     C load( Long id );
 
@@ -51,6 +54,16 @@ public interface CuratableService<C extends Curatable, VO extends AbstractCurata
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ" })
     C loadOrFail( Long id ) throws NullPointerException;
 
+    @Nonnull
+    @Override
+    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ" })
+    <T extends Exception> C loadOrFail( Long id, Supplier<T> exceptionSupplier ) throws T;
+
+    @Nonnull
+    @Override
+    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ" })
+    <T extends Exception> C loadOrFail( Long id, Function<String, T> exceptionSupplier, String message ) throws T;
+
     @Override
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_COLLECTION_READ" })
     Collection<C> loadAll();
@@ -100,26 +113,12 @@ public interface CuratableService<C extends Curatable, VO extends AbstractCurata
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_VALUE_OBJECT_COLLECTION_READ" })
     List<VO> loadAllValueObjects();
 
-    /**
-     * {@inheritDoc}
-     * <p>
-     * TODO: add ACL_SECURABLE_EDIT, but this method accepts transient entities which do not have ACLs yet.
-     * @deprecated do not use this until the issue with ACLs is resolved.
-     */
-    @Deprecated
     @Override
-    @Secured({ "GROUP_USER" })
+    @Secured({ "GROUP_USER", "ACL_SECURABLE_COLLECTION_EDIT_IGNORE_TRANSIENT" })
     Collection<C> save( Collection<C> entities );
 
-    /**
-     * {@inheritDoc}
-     * <p>
-     * TODO: add ACL_SECURABLE_EDIT, but this method accepts transient entities which do not have ACLs yet.
-     * @deprecated do not use this until the issue with ACLs is resolved.
-     */
-    @Deprecated
     @Override
-    @Secured({ "GROUP_USER" })
+    @Secured({ "GROUP_USER", "ACL_SECURABLE_EDIT_IGNORE_TRANSIENT" })
     C save( C entity );
 
     @Override
@@ -142,13 +141,4 @@ public interface CuratableService<C extends Curatable, VO extends AbstractCurata
     @Override
     @Secured({ "GROUP_USER", "ACL_SECURABLE_EDIT" })
     void remove( C expressionExperiment );
-
-    /**
-     * {@inheritDoc}
-     * <p>
-     * Only administrators are allowed to remove all entities in batch.
-     */
-    @Override
-    @Secured({ "GROUP_ADMIN" })
-    void removeAllInBatch();
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDao.java
index fd37b49e9d..9fbfe47bb6 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDao.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDao.java
@@ -45,4 +45,6 @@ public interface BlacklistedEntityDao extends BaseVoEnabledDao<BlacklistedEntity
     boolean isBlacklisted( ExpressionExperiment dataset );
 
     Collection<ExpressionExperiment> getNonBlacklistedExpressionExperiments( ArrayDesign arrayDesign );
+
+    int removeAll();
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDaoImpl.java
index b5b3b1cfb1..c50b11c44d 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDaoImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDaoImpl.java
@@ -19,19 +19,12 @@
 
 package ubic.gemma.persistence.service.expression.experiment;
 
-import java.util.Collection;
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-import java.util.stream.Collectors;
-
 import org.hibernate.Criteria;
 import org.hibernate.SessionFactory;
 import org.hibernate.criterion.Projections;
 import org.hibernate.criterion.Restrictions;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
-
 import ubic.gemma.model.common.description.DatabaseEntry;
 import ubic.gemma.model.expression.BlacklistedEntity;
 import ubic.gemma.model.expression.BlacklistedValueObject;
@@ -40,6 +33,12 @@
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.AbstractVoEnabledDao;
 
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.stream.Collectors;
+
 /**
  *
  * @author paul
@@ -130,4 +129,25 @@ public Collection<ExpressionExperiment> getNonBlacklistedExpressionExperiments(
                 .setParameter( "ad", arrayDesign )
                 .list();
     }
+
+    @Override
+    public int removeAll() {
+        //noinspection unchecked
+        List<Long> deIds = getSessionFactory().getCurrentSession()
+                .createQuery( "select ea.id from BlacklistedEntity be join be.externalAccession ea" ).list();
+        int removedBe = getSessionFactory().getCurrentSession()
+                .createQuery( "delete from BlacklistedEntity" )
+                .executeUpdate();
+        int removedDe;
+        if ( !deIds.isEmpty() ) {
+            removedDe = getSessionFactory().getCurrentSession()
+                    .createQuery( "delete from DatabaseEntry where id in :deIds" )
+                    .setParameterList( "deIds", deIds )
+                    .executeUpdate();
+        } else {
+            removedDe = 0;
+        }
+        log.debug( String.format( "Removed all %d BlacklistedEntity. %d DatabaseEntry were removed in cascade.", removedBe, removedDe ) );
+        return removedBe;
+    }
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityService.java
index b90c76a590..ea86f8f66c 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityService.java
@@ -50,4 +50,10 @@ public interface BlacklistedEntityService extends BaseImmutableService<Blacklist
      */
     @Secured({ "GROUP_ADMIN", "ACL_SECURABLE_EDIT" })
     BlacklistedPlatform blacklistPlatform( ArrayDesign platform, String reason );
+
+    /**
+     * Remove all blacklisted platforms and experiments.
+     */
+    @Secured({ "GROUP_ADMIN" })
+    int removeAll();
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityServiceImpl.java
index a269421121..5782382adb 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityServiceImpl.java
@@ -12,7 +12,6 @@
 import ubic.gemma.model.expression.experiment.BlacklistedExperiment;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.AbstractVoEnabledService;
-import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
 
 import java.util.HashSet;
 import java.util.Set;
@@ -112,6 +111,12 @@ public BlacklistedPlatform blacklistPlatform( ArrayDesign platform, String reaso
         return bp;
     }
 
+    @Override
+    @Transactional
+    public int removeAll() {
+        return blacklistedEntityDao.removeAll();
+    }
+
     private BlacklistedExperiment doBlacklistExpressionExperiment( ExpressionExperiment dataset, String reason ) {
         BlacklistedExperiment be = new BlacklistedExperiment();
         be.setShortName( dataset.getShortName() );
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExperimentalFactorService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExperimentalFactorService.java
index ce90fadbf2..31342df499 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExperimentalFactorService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExperimentalFactorService.java
@@ -59,10 +59,6 @@ public interface ExperimentalFactorService
     @Secured({ "GROUP_ADMIN" })
     void remove( Long id );
 
-    @Override
-    @Secured({ "GROUP_ADMIN" })
-    void removeAllInBatch();
-
     @Override
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ" })
     ExperimentalFactor find( ExperimentalFactor experimentalFactor );
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExperimentalFactorServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExperimentalFactorServiceImpl.java
index ef0f60cbe8..4f430ae5ed 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExperimentalFactorServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExperimentalFactorServiceImpl.java
@@ -71,11 +71,6 @@ public void remove( Long id ) {
         throw new UnsupportedOperationException( "Removing an experimental factor by ID is not supported" );
     }
 
-    @Override
-    public void removeAllInBatch() {
-        throw new UnsupportedOperationException( "Removing all experimental factors in batch is not supported." );
-    }
-
     @Override
     @Transactional(readOnly = true)
     public ExperimentalFactor thaw( ExperimentalFactor ef ) {
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentDao.java
index 9750e030c3..e000510fa8 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentDao.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentDao.java
@@ -41,6 +41,9 @@ public interface ExpressionExperimentDao
 
     String OBJECT_ALIAS = "ee";
 
+    @Nullable
+    BioAssaySet loadBioAssaySet( Long id );
+
     Collection<Long> filterByTaxon( Collection<Long> ids, Taxon taxon );
 
     ExpressionExperiment findByShortName( String shortName );
@@ -292,4 +295,11 @@ Map<ExpressionExperiment, Collection<AuditEvent>> getSampleRemovalEvents(
     Collection<ExpressionExperiment> getExperimentsLackingPublications();
 
     MeanVarianceRelation updateMeanVarianceRelation( ExpressionExperiment ee, MeanVarianceRelation mvr );
+
+    /**
+     * Count the number of biomaterials of datasets satisfying the given filters.
+     * <p>
+     * The result is stored in the standard query cache.
+     */
+    long countBioMaterials( @Nullable Filters filters );
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentDaoImpl.java
index 4f57f86885..b7df0b34a5 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentDaoImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentDaoImpl.java
@@ -114,6 +114,11 @@ public List<ExpressionExperiment> browse( int start, int limit, String orderFiel
         throw new NotImplementedException( "Browsing ExpressionExperiment in a specific order is not supported." );
     }
 
+    @Override
+    public BioAssaySet loadBioAssaySet( Long id ) {
+        return ( BioAssaySet ) getSessionFactory().getCurrentSession().get( BioAssaySet.class, id );
+    }
+
     @Override
     public Collection<Long> filterByTaxon( @Nullable Collection<Long> ids, Taxon taxon ) {
 
@@ -780,6 +785,16 @@ public MeanVarianceRelation updateMeanVarianceRelation( ExpressionExperiment ee,
         return mvr;
     }
 
+    @Override
+    public long countBioMaterials( @Nullable Filters filters ) {
+        //language=HQL
+        Query query = finishFilteringQuery( "select count(distinct bm) from ExpressionExperiment ee "
+                        + "join ee.bioAssays ba "
+                        + "join ba.sampleUsed bm",
+                filters, null, null );
+        return ( Long ) query.setCacheable( true ).uniqueResult();
+    }
+
     @Override
     public Collection<ArrayDesign> getArrayDesignsUsed( BioAssaySet bas ) {
 
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentService.java
index 696aa98ce1..c44e58fa86 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentService.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentService.java
@@ -49,6 +49,7 @@
 import javax.annotation.CheckReturnValue;
 import javax.annotation.Nullable;
 import java.util.*;
+import java.util.function.Function;
 
 /**
  * @author kelsey
@@ -103,9 +104,30 @@ ExpressionExperiment addRawVectors( ExpressionExperiment eeToUpdate,
      */
     Collection<Long> filterByTaxon( Collection<Long> ids, Taxon taxon );
 
+    @Nullable
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ_QUIET" })
     ExpressionExperiment loadWithCharacteristics( Long id );
 
+    /**
+     * Load a {@link BioAssaySet} by ID which can be either a {@link ExpressionExperiment} or a {@link ExpressionExperimentSubSet}.
+     */
+    @Nullable
+    BioAssaySet loadBioAssaySet( Long id );
+
+    /**
+     * Load an experiment and thaw it as per {@link #thawLite(ExpressionExperiment)} or fail with the supplied exception
+     * and message.
+     */
+    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ" })
+    <T extends Exception> ExpressionExperiment loadAndThawLiteOrFail( Long id, Function<String, T> exceptionSupplier, String message ) throws T;
+
+    /**
+     * Load an experiment and thaw it as per {@link #thawLite(ExpressionExperiment)} or fail with the supplied exception
+     * and message.
+     */
+    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ" })
+    <T extends Exception> ExpressionExperiment loadAndThawOrFail( Long id, Function<String, T> exceptionSupplier, String message ) throws T;
+
     List<Long> loadIdsWithCache( @Nullable Filters filters, @Nullable Sort sort );
 
     long countWithCache( @Nullable Filters filters );
@@ -113,9 +135,11 @@ ExpressionExperiment addRawVectors( ExpressionExperiment eeToUpdate,
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_VALUE_OBJECT_COLLECTION_READ" })
     Slice<ExpressionExperimentValueObject> loadValueObjectsWithCache( @Nullable Filters filters, @Nullable Sort sort, int offset, int limit );
 
+    @Nullable
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ_QUIET" })
     ExpressionExperiment loadWithPrimaryPublication( Long id );
 
+    @Nullable
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ_QUIET" })
     ExpressionExperiment loadWithMeanVarianceRelation( Long id );
 
@@ -193,6 +217,7 @@ ExpressionExperiment addRawVectors( ExpressionExperiment eeToUpdate,
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ" })
     ExpressionExperiment findByQuantitationType( QuantitationType type );
 
+    @Nullable
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ_QUIET" })
     ExpressionExperiment findByShortName( String shortName );
 
@@ -593,4 +618,9 @@ Map<ExpressionExperiment, Collection<AuditEvent>> getSampleRemovalEvents(
 
     @Secured({ "GROUP_USER" })
     MeanVarianceRelation updateMeanVarianceRelation( ExpressionExperiment ee, MeanVarianceRelation mvr );
+
+    /**
+     * @see ExpressionExperimentDao#countBioMaterials(Filters)
+     */
+    long countBioMaterials( @Nullable Filters filters );
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentServiceImpl.java
index cec3458c4f..2a28b13281 100755
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentServiceImpl.java
@@ -75,6 +75,7 @@
 
 import javax.annotation.Nullable;
 import java.util.*;
+import java.util.function.Function;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -621,6 +622,28 @@ public ExpressionExperiment loadWithCharacteristics( Long id ) {
         return ee;
     }
 
+    @Override
+    @Transactional(readOnly = true)
+    public BioAssaySet loadBioAssaySet( Long id ) {
+        return expressionExperimentDao.loadBioAssaySet( id );
+    }
+
+    @Override
+    @Transactional(readOnly = true)
+    public <T extends Exception> ExpressionExperiment loadAndThawLiteOrFail( Long id, Function<String, T> exceptionSupplier, String message ) throws T {
+        ExpressionExperiment ee = loadOrFail( id, exceptionSupplier, message );
+        this.expressionExperimentDao.thawWithoutVectors( ee );
+        return ee;
+    }
+
+    @Override
+    @Transactional(readOnly = true)
+    public <T extends Exception> ExpressionExperiment loadAndThawOrFail( Long id, Function<String, T> exceptionSupplier, String message ) throws T {
+        ExpressionExperiment ee = loadOrFail( id, exceptionSupplier, message );
+        this.expressionExperimentDao.thaw( ee );
+        return ee;
+    }
+
     @Override
     @Transactional(readOnly = true)
     public List<Long> loadIdsWithCache( @Nullable Filters filters, @Nullable Sort sort ) {
@@ -1384,12 +1407,6 @@ public void remove( Collection<ExpressionExperiment> entities ) {
         entities.forEach( this::remove );
     }
 
-    @Override
-    @Transactional
-    public void removeAllInBatch() {
-        throw new UnsupportedOperationException( "That would be nut." );
-    }
-
     private Collection<? extends AnnotationValueObject> getAnnotationsByFactorValues( Long eeId ) {
         return this.expressionExperimentDao.getAnnotationsByFactorvalues( eeId );
     }
@@ -1457,6 +1474,12 @@ public MeanVarianceRelation updateMeanVarianceRelation( ExpressionExperiment ee,
         return expressionExperimentDao.updateMeanVarianceRelation( ee, mvr );
     }
 
+    @Override
+    @Transactional(readOnly = true)
+    public long countBioMaterials( @Nullable Filters filters ) {
+        return expressionExperimentDao.countBioMaterials( filters );
+    }
+
     /**
      * Checks for special properties that are allowed to be referenced on certain objects. E.g. characteristics on EEs.
      * {@inheritDoc}
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentSubSetServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentSubSetServiceImpl.java
index 077fea1261..8c5b7f2cff 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentSubSetServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentSubSetServiceImpl.java
@@ -91,9 +91,4 @@ public void remove( Collection<ExpressionExperimentSubSet> entities ) {
     public void remove( Long id ) {
         throw new UnsupportedOperationException( "Removing an experiment subset by ID is not supported." );
     }
-
-    @Override
-    public void removeAllInBatch() {
-        throw new UnsupportedOperationException( "This would be nuts." );
-    }
 }
\ No newline at end of file
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/GeneDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/GeneDao.java
index 75fd98bb4c..f68c7c6ae0 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/GeneDao.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/GeneDao.java
@@ -140,4 +140,6 @@ public interface GeneDao extends FilteringVoEnabledDao<Gene, GeneValueObject> {
     Gene thawLite( Gene gene );
 
     Gene thawLiter( Gene gene );
+
+    int removeAll();
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/GeneDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/GeneDaoImpl.java
index c025825c01..dab99bac9b 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/GeneDaoImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/GeneDaoImpl.java
@@ -426,6 +426,71 @@ public Gene thawLiter( final Gene gene ) {
                 .uniqueResult();
     }
 
+    @Override
+    public int removeAll() {
+        // remove associations
+        this.getSessionFactory().getCurrentSession()
+                .createQuery( "delete from BioSequence2GeneProduct ba where ba.geneProduct in (select gp from GeneProduct gp where gp.gene is not null)" )
+                .executeUpdate();
+        this.getSessionFactory().getCurrentSession()
+                .createQuery( "delete from GeneSetMember gm where gm.gene is not null" )
+                .executeUpdate();
+        this.getSessionFactory().getCurrentSession()
+                .createQuery( "delete from Gene2GOAssociation g2g where g2g.gene is not null" )
+                .executeUpdate();
+        int removedAccessions = getSessionFactory().getCurrentSession()
+                .createSQLQuery( "delete from DATABASE_ENTRY where GENE_FK is not null" )
+                .executeUpdate();
+        // we have to do some manual deletion because no cascading is performed when deleting in batch
+        //noinspection unchecked
+        List<Long> gpIds = getSessionFactory().getCurrentSession()
+                .createQuery( "select gp.id from Gene g join g.products gp" )
+                .list();
+        int removedGeneProductsAccessions;
+        if ( !gpIds.isEmpty() ) {
+            removedGeneProductsAccessions = getSessionFactory().getCurrentSession()
+                    .createSQLQuery( "delete from DATABASE_ENTRY where GENE_PRODUCT_FK in :gpIds" )
+                    .setParameterList( "gpIds", gpIds )
+                    .executeUpdate();
+        } else {
+            removedGeneProductsAccessions = 0;
+        }
+        int removedProducts = getSessionFactory().getCurrentSession()
+                .createQuery( "delete from GeneProduct gp where gp.gene is not null" )
+                .executeUpdate();
+        //noinspection unchecked
+        List<Long> gaIds = getSessionFactory().getCurrentSession()
+                .createQuery( "select ga.id from Gene g join g.aliases ga" )
+                .list();
+        int removedAliases;
+        if ( !gaIds.isEmpty() ) {
+            removedAliases = getSessionFactory().getCurrentSession()
+                    .createQuery( "delete from GeneAlias ga where ga.id in :gaIds" )
+                    .setParameterList( "gaIds", gaIds )
+                    .executeUpdate();
+        } else {
+            removedAliases = 0;
+        }
+        //noinspection unchecked
+        List<Long> plIds = getSessionFactory().getCurrentSession()
+                .createQuery( "select pl.id from Gene g join g.physicalLocation pl" )
+                .list();
+        int removedGenes = getSessionFactory().getCurrentSession()
+                .createQuery( "delete from Gene" )
+                .executeUpdate();
+        int removedPhysicalLocations;
+        if ( !plIds.isEmpty() ) {
+            removedPhysicalLocations = getSessionFactory().getCurrentSession()
+                    .createQuery( "delete from PhysicalLocation pl where pl.id in :plIds" )
+                    .executeUpdate();
+        } else {
+            removedPhysicalLocations = 0;
+        }
+        log.debug( String.format( "Removed all %d Gene. %d GeneProduct, %d DatabaseEntry, %d GeneAlias and %d PhysicalLocation were also removed in cascade.",
+                removedGenes, removedProducts, removedAccessions + removedGeneProductsAccessions, removedAliases, removedPhysicalLocations ) );
+        return removedGenes;
+    }
+
     @Override
     public void remove( Gene gene ) {
         // remove associations
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneProductServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneProductServiceImpl.java
index 2d63298542..c170fd0d07 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneProductServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneProductServiceImpl.java
@@ -132,9 +132,4 @@ public void remove( Collection<GeneProduct> toRemove ) {
     public void remove( Long id ) {
         throw new UnsupportedOperationException( "Removing a gene product by ID is not supported." );
     }
-
-    @Override
-    public void removeAllInBatch() {
-        throw new UnsupportedOperationException( "Removing all gene products in batch is not supported." );
-    }
 }
\ No newline at end of file
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDao.java
index 127dc471b7..df97afc243 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDao.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDao.java
@@ -74,4 +74,6 @@ public interface GeneSetDao extends BaseVoEnabledDao<GeneSet, DatabaseBackedGene
      * @param geneSet gene set
      */
     void thaw( GeneSet geneSet );
+
+    int removeAll();
 }
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDaoImpl.java
index 6bfbba575e..d48cb7513a 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDaoImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDaoImpl.java
@@ -32,6 +32,7 @@
 import ubic.gemma.model.genome.gene.GeneSetMember;
 import ubic.gemma.model.genome.gene.GeneSetValueObject;
 import ubic.gemma.persistence.service.AbstractDao;
+import ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDao;
 
 import javax.annotation.Nullable;
 import javax.annotation.ParametersAreNonnullByDefault;
@@ -209,6 +210,34 @@ public void thaw( final GeneSet geneSet ) {
         }
     }
 
+    @Autowired
+    private AuditTrailDao auditTrailDao;
+
+    @Override
+    public int removeAll() {
+        //noinspection unchecked
+        List<Long> atIds = getSessionFactory().getCurrentSession()
+                .createQuery( "select at.id from GeneSet gs join gs.auditTrail at" )
+                .list();
+        int removedMembers = getSessionFactory().getCurrentSession()
+                .createQuery( "delete from GeneSetMember gsm" )
+                .executeUpdate();
+        // FIXME: use HQL delete from Characteristic
+        int removedCharacteristics = getSessionFactory().getCurrentSession()
+                .createSQLQuery( "delete from CHARACTERISTIC where GENE_SET_FK is not null" )
+                .executeUpdate();
+        //noinspection SqlWithoutWhere
+        int removedLiteratureSourcesAssociations = getSessionFactory().getCurrentSession()
+                .createSQLQuery( "delete from GENE_SETS2LITERATURE_SOURCES" )
+                .executeUpdate();
+        int removedGeneSet = getSessionFactory().getCurrentSession().createQuery( "delete from GeneSet" )
+                .executeUpdate();
+        auditTrailDao.removeByIds( atIds );
+        log.debug( String.format( "Removed all %d GeneSet. %d GeneSetMember, %d Characteristic and %d BibliographicReference associations were removed in cascade.",
+                removedGeneSet, removedMembers, removedCharacteristics, removedLiteratureSourcesAssociations ) );
+        return removedGeneSet;
+    }
+
     @Override
     public final void update( Collection<GeneSet> entities ) {
         super.update( entities );
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/util/EntityUtils.java b/gemma-core/src/main/java/ubic/gemma/persistence/util/EntityUtils.java
index 3f3c1b2867..b37888600e 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/util/EntityUtils.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/util/EntityUtils.java
@@ -23,11 +23,8 @@
 import gemma.gsec.acl.domain.AclGrantedAuthoritySid;
 import gemma.gsec.acl.domain.AclObjectIdentity;
 import gemma.gsec.acl.domain.AclPrincipalSid;
-import gemma.gsec.model.Securable;
 import gemma.gsec.util.SecurityUtil;
-import org.hibernate.Query;
 import org.hibernate.SQLQuery;
-import org.hibernate.Session;
 import org.hibernate.SessionFactory;
 import org.hibernate.proxy.HibernateProxy;
 import org.springframework.security.acls.domain.BasePermission;
@@ -36,7 +33,6 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.math.BigInteger;
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -93,7 +89,7 @@ public static <T extends Identifiable> Map<Long, T> getIdMap( Collection<T> enti
         }
         return result;
     }
-    
+
     public static Class<?> getImplClass( Class<?> type ) {
         String canonicalName = type.getName();
         try {
@@ -229,8 +225,7 @@ public static boolean[] getPermissions( AclObjectIdentity aoi ) {
             } else if ( SecurityUtil.isUserAnonymous() ) {
                 canWrite = false;
             } else {
-                if ( ace.getPermission().getMask() == BasePermission.WRITE.getMask() || ace.getPermission().getMask() == BasePermission.ADMINISTRATION
-                        .getMask() ) {
+                if ( ( ace.getMask() & BasePermission.WRITE.getMask() ) != 0 || ( ace.getMask() & BasePermission.ADMINISTRATION.getMask() ) != 0 ) {
                     Sid sid = ace.getSid();
                     if ( sid instanceof AclGrantedAuthoritySid ) {
                         //noinspection unused //FIXME if user is in granted group then he can write probably
@@ -244,7 +239,7 @@ public static boolean[] getPermissions( AclObjectIdentity aoi ) {
             }
 
             // Check public and shared - code adapted from SecurityUtils, only we do not hold an ACL object.
-            if ( ace.getPermission().equals( BasePermission.READ ) ) {
+            if ( ( ace.getMask() & BasePermission.READ.getMask() ) != 0 ) {
                 Sid sid = ace.getSid();
                 if ( sid instanceof AclGrantedAuthoritySid ) {
                     String grantedAuthority = ( ( AclGrantedAuthoritySid ) sid ).getGrantedAuthority();
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/util/PropertySourcesConfigurer.java b/gemma-core/src/main/java/ubic/gemma/persistence/util/PropertySourcesConfigurer.java
deleted file mode 100644
index 48033a4dab..0000000000
--- a/gemma-core/src/main/java/ubic/gemma/persistence/util/PropertySourcesConfigurer.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package ubic.gemma.persistence.util;
-
-import org.springframework.beans.factory.InitializingBean;
-import org.springframework.context.EnvironmentAware;
-import org.springframework.core.env.ConfigurableEnvironment;
-import org.springframework.core.env.Environment;
-import org.springframework.core.env.PropertySource;
-import org.springframework.util.Assert;
-
-import java.util.List;
-
-/**
- * Add a given list of {@link PropertySource} to the {@link Environment}.
- * @author poirigui
- */
-public class PropertySourcesConfigurer implements EnvironmentAware, InitializingBean {
-
-    private final List<PropertySource<?>> propertySources;
-    private ConfigurableEnvironment env;
-
-    public PropertySourcesConfigurer( List<PropertySource<?>> propertySources ) {
-        this.propertySources = propertySources;
-    }
-
-    @Override
-    public void afterPropertiesSet() throws Exception {
-        Assert.notNull( env, "A ConfigurableEnvironment was not set, property sources cannot be added." );
-        for ( int i = propertySources.size() - 1; i >= 0; i-- ) {
-            env.getPropertySources().addFirst( propertySources.get( i ) );
-        }
-    }
-
-    @Override
-    public void setEnvironment( Environment environment ) {
-        if ( environment instanceof ConfigurableEnvironment ) {
-            this.env = ( ConfigurableEnvironment ) environment;
-        }
-    }
-}
\ No newline at end of file
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/util/Settings.java b/gemma-core/src/main/java/ubic/gemma/persistence/util/Settings.java
index 73704682c7..d66dc7a1d1 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/util/Settings.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/util/Settings.java
@@ -33,6 +33,7 @@
 import java.math.BigDecimal;
 import java.math.BigInteger;
 import java.net.MalformedURLException;
+import java.nio.file.Paths;
 import java.util.*;
 
 /**
@@ -41,8 +42,8 @@
  *
  * @author pavlidis
  * @see org.apache.commons.configuration2.CompositeConfiguration
- * @deprecated Use {@link org.springframework.beans.factory.annotation.Value} to inject configurations. You can either
- *             use {@code @Value("#{environment['property']}")} or the shorthand {@code @Value("${property}")}.
+ * @deprecated This has been replaced with Spring-based configuration {@link SettingsConfig} and usage of {@link org.springframework.beans.factory.annotation.Value}
+ *             to inject configurations. You can use {@code @Value("${property}")} as replacement.
  */
 @SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use
 @Deprecated
@@ -85,12 +86,26 @@ public class Settings {
          * will be checked"
          */
 
-        try {
-            PropertiesConfiguration pc = ConfigUtils.loadConfig( Settings.USER_CONFIGURATION );
+        boolean userConfigLoaded = false;
 
-            Settings.config.addConfiguration( pc );
+        String catalinaBase;
+        if ( ( catalinaBase = System.getenv( "CATALINA_BASE" ) ) != null ) {
+            File f = Paths.get( catalinaBase, Settings.USER_CONFIGURATION ).toFile();
+            log.debug( "Loading configuration from " + f.getAbsolutePath() + " since $CATALINA_BASE is defined." );
+            try {
+                Settings.config.addConfiguration( ConfigUtils.loadConfig( f ) );
+                userConfigLoaded = true;
+            } catch ( ConfigurationException e ) {
+                throw new RuntimeException( f.getAbsolutePath() + " could not be loaded.", e );
+            }
+        }
+
+        try {
+            Settings.config.addConfiguration( ConfigUtils.loadConfig( Settings.USER_CONFIGURATION ) );
         } catch ( ConfigurationException e ) {
-            Settings.log.warn( Settings.USER_CONFIGURATION + " not found" );
+            if ( !userConfigLoaded ) {
+                throw new RuntimeException( Settings.USER_CONFIGURATION + " could not be loaded and no other user configuration were supplied.", e );
+            }
         }
 
         try {
diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/util/SettingsConfig.java b/gemma-core/src/main/java/ubic/gemma/persistence/util/SettingsConfig.java
new file mode 100644
index 0000000000..78fe3defc0
--- /dev/null
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/util/SettingsConfig.java
@@ -0,0 +1,94 @@
+package ubic.gemma.persistence.util;
+
+import lombok.extern.apachecommons.CommonsLog;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
+import org.springframework.core.env.MutablePropertySources;
+import org.springframework.core.env.PropertySources;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.core.io.FileSystemResource;
+import org.springframework.core.io.support.ResourcePropertySource;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.attribute.PosixFilePermission;
+import java.util.Set;
+
+/**
+ * Beans declaration for making the settings available via the Spring Environment and placeholder substitution.
+ * @author poirigui
+ */
+@CommonsLog
+@Configuration
+public class SettingsConfig {
+
+    /**
+     * Allow for substitution placeholders with values from the settings.
+     */
+    @Bean
+    public static PropertySourcesPlaceholderConfigurer propertySourcesPlaceholderConfigurer() throws IOException {
+        PropertySourcesPlaceholderConfigurer configurer = new PropertySourcesPlaceholderConfigurer();
+        configurer.setPropertySources( propertySources() );
+        return configurer;
+    }
+
+    private static PropertySources propertySources() throws IOException {
+        MutablePropertySources result = new MutablePropertySources();
+        boolean userConfigLoaded = false;
+
+        // load configuration from $CATALINA_BASE
+        // TODO: move this in Gemma Web
+        String catalinaBase = System.getenv( "CATALINA_BASE" );
+        if ( catalinaBase != null ) {
+            Path p = Paths.get( catalinaBase, "Gemma.properties" );
+            File f = p.toFile();
+            log.debug( "Loading configuration from " + f.getAbsolutePath() + " since $CATALINA_BASE is defined." );
+            FileSystemResource r = new FileSystemResource( f );
+            if ( !r.exists() ) {
+                throw new RuntimeException( f.getAbsolutePath() + " could not be loaded." );
+            }
+            warnIfReadableByGroupOrOthers( p );
+            result.addLast( new ResourcePropertySource( r ) );
+            userConfigLoaded = true;
+        }
+
+        // load configuration from the home directory
+        // TODO: move this in Gemma CLI
+        Path p = Paths.get( System.getProperty( "user.home" ), "Gemma.properties" );
+        FileSystemResource r = new FileSystemResource( p.toFile() );
+        if ( r.exists() ) {
+            warnIfReadableByGroupOrOthers( p );
+            result.addLast( new ResourcePropertySource( r ) );
+            userConfigLoaded = true;
+        }
+
+        // at least one user configuration should be loaded
+        if ( !userConfigLoaded ) {
+            throw new RuntimeException( "Gemma.properties could not be loaded and no other user configuration were supplied." );
+        }
+
+        result.addLast( new ResourcePropertySource( new ClassPathResource( "default.properties" ) ) );
+        result.addLast( new ResourcePropertySource( new ClassPathResource( "project.properties" ) ) );
+        // FIXME: local local.properties from ${gemma.appdata.home}
+        result.addLast( new ResourcePropertySource( new ClassPathResource( "ubic/gemma/version.properties" ) ) );
+
+        return result;
+    }
+
+    private static void warnIfReadableByGroupOrOthers( Path path ) throws IOException {
+        Set<PosixFilePermission> permissions;
+        try {
+            permissions = Files.getPosixFilePermissions( path );
+        } catch ( UnsupportedOperationException e ) {
+            return;
+        }
+        if ( permissions.contains( PosixFilePermission.GROUP_READ ) || permissions.contains( PosixFilePermission.OTHERS_READ ) ) {
+            log.warn( String.format( "%s may contain credentials and is not exclusively readable by its owner. Adjust the permissions by running 'chmod go-r %s' to remove this warning.",
+                    path.getFileName(), path.toAbsolutePath() ) );
+        }
+    }
+}
diff --git a/gemma-core/src/main/resources/default.properties b/gemma-core/src/main/resources/default.properties
index ffad8458f1..8f57484d88 100755
--- a/gemma-core/src/main/resources/default.properties
+++ b/gemma-core/src/main/resources/default.properties
@@ -126,6 +126,8 @@ quartzOn=false
 # Other ontologies are configured with defaults through basecode.properties
 # by default, same place as other search indices
 ontology.index.dir=${gemma.search.dir}
+# Auto-load ontologies on startup
+load.ontologies=false
 # GO
 load.geneOntology=false
 url.geneOntology=http://purl.obolibrary.org/obo/go.owl
diff --git a/gemma-core/src/main/resources/ubic/gemma/applicationContext-serviceBeans.xml b/gemma-core/src/main/resources/ubic/gemma/applicationContext-serviceBeans.xml
index e250ac0acc..489761263f 100644
--- a/gemma-core/src/main/resources/ubic/gemma/applicationContext-serviceBeans.xml
+++ b/gemma-core/src/main/resources/ubic/gemma/applicationContext-serviceBeans.xml
@@ -3,10 +3,9 @@
 <beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
        xmlns="http://www.springframework.org/schema/beans"
        xmlns:aop="http://www.springframework.org/schema/aop"
-       xmlns:context="http://www.springframework.org/schema/context"
        xsi:schemaLocation="http://www.springframework.org/schema/beans
             http://www.springframework.org/schema/beans/spring-beans.xsd
-       http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop.xsd http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context.xsd">
+       http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop.xsd">
 
     <!-- Local tasks executor -->
     <bean id="taskExecutor" class="org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor">
@@ -24,30 +23,6 @@
         <property name="fallbackToSystemLocale" value="false"/>
     </bean>
 
-    <bean id="propertySourcesConfigurer" class="ubic.gemma.persistence.util.PropertySourcesConfigurer">
-        <constructor-arg>
-            <list>
-                <bean class="org.springframework.core.io.support.ResourcePropertySource">
-                    <constructor-arg value="file:${user.home}/Gemma.properties"/>
-                </bean>
-                <bean class="org.springframework.core.io.support.ResourcePropertySource">
-                    <constructor-arg value="classpath:default.properties"/>
-                </bean>
-                <bean class="org.springframework.core.io.support.ResourcePropertySource">
-                    <constructor-arg value="classpath:project.properties"/>
-                </bean>
-                <bean class="org.springframework.core.io.support.ResourcePropertySource">
-                    <constructor-arg value="classpath:ubic/gemma/version.properties"/>
-                </bean>
-            </list>
-        </constructor-arg>
-    </bean>
-
-    <context:property-placeholder location="file:${user.home}/Gemma.properties" ignore-unresolvable="true"/>
-    <context:property-placeholder location="classpath:default.properties" ignore-unresolvable="true"/>
-    <context:property-placeholder location="classpath:project.properties" ignore-unresolvable="true"/>
-    <context:property-placeholder location="classpath:ubic/gemma/version.properties"/>
-
     <!-- Configure Velocity for sending e-mail -->
     <bean id="velocityEngine" class="org.apache.velocity.app.VelocityEngine">
         <constructor-arg>
@@ -85,6 +60,13 @@
                             <list/>
                         </constructor-arg>
                     </bean>
+                    <bean class="ubic.gemma.core.metrics.binder.jpa.Hibernate4QueryMetrics">
+                        <constructor-arg ref="sessionFactory"/>
+                        <constructor-arg value="sessionFactory"/>
+                        <constructor-arg>
+                            <list/>
+                        </constructor-arg>
+                    </bean>
                     <bean class="ubic.gemma.core.metrics.binder.database.HikariCPMetrics">
                         <constructor-arg ref="dataSource"/>
                     </bean>
diff --git a/gemma-core/src/main/resources/ubic/gemma/core/loader/affy.cdfs.properties b/gemma-core/src/main/resources/ubic/gemma/core/loader/affy.cdfs.properties
index 39e6adfcda..196f6ce033 100644
--- a/gemma-core/src/main/resources/ubic/gemma/core/loader/affy.cdfs.properties
+++ b/gemma-core/src/main/resources/ubic/gemma/core/loader/affy.cdfs.properties
@@ -2,6 +2,8 @@
 # defines map of platform short names to CDF file names. The path to the CDFs must be defined by affy.power.tools.cdf.path
 # Do not add exon arrays to this file. They are handled as a special case. See affy.mps.properties.
 GPL32=MG_U74A.CDF
+GPL33=MG_U74B.CDF
+GPL34=MG_U74C.CDF
 GPL72=DrosGenome1.CDF
 GPL201=HG-Focus.CDF
 GPL80=Hu6800.CDF
diff --git a/gemma-core/src/main/resources/ubic/gemma/core/loader/affy.celmappings.properties b/gemma-core/src/main/resources/ubic/gemma/core/loader/affy.celmappings.properties
index 56e5f5a87c..0e44a7b9f4 100644
--- a/gemma-core/src/main/resources/ubic/gemma/core/loader/affy.celmappings.properties
+++ b/gemma-core/src/main/resources/ubic/gemma/core/loader/affy.celmappings.properties
@@ -42,7 +42,11 @@ U133_X3P=GPL1352
 U133_X3Pa520049=GPL1352	
 HG-U219=GPL13667
 # Mouse
+Mu11KsubA=GPL75
+Mu11KsubB=GPL76
 MG_U74A=GPL32
+MG-U74B=GPL33
+MG-U74C=GPL34
 MG_U74Av2=GPL81
 MG_U74Bv2=GPL82
 MG_U74Cv2=GPL83
diff --git a/gemma-core/src/main/resources/ubic/gemma/core/ontology/valueStringToOntologyTermMappings.txt b/gemma-core/src/main/resources/ubic/gemma/core/ontology/valueStringToOntologyTermMappings.txt
index ea66ff7d77..e631e4a7f2 100644
--- a/gemma-core/src/main/resources/ubic/gemma/core/ontology/valueStringToOntologyTermMappings.txt
+++ b/gemma-core/src/main/resources/ubic/gemma/core/ontology/valueStringToOntologyTermMappings.txt
@@ -320,7 +320,7 @@ K-ras Status: Wt	wild type genotype	http://www.ebi.ac.uk/efo/EFO_0005168	genotyp
 KCl	potassium chloride	http://purl.obolibrary.org/obo/CHEBI_32588	treatment	http://www.ebi.ac.uk/efo/EFO_0000727
 kidney	kidney	http://purl.obolibrary.org/obo/UBERON_0002113	organism part	http://www.ebi.ac.uk/efo/EFO_0000635
 kidney tissue	kidney	http://purl.obolibrary.org/obo/UBERON_0002113	organism part	http://www.ebi.ac.uk/efo/EFO_0000635
-knockdown	Knockdown	http://gemma.msl.ubc.ca/ont/TGEMO_00007	genotype	http://www.ebi.ac.uk/efo/EFO_0000513
+knockdown	gene knockdown	http://purl.obolibrary.org/obo/OBI_0002625	genotype	http://www.ebi.ac.uk/efo/EFO_0000513
 left liver lobe	left lobe of liver	http://purl.obolibrary.org/obo/UBERON_0001115	organism part	http://www.ebi.ac.uk/efo/EFO_0000635
 Left ventricle	heart left ventricle	http://purl.obolibrary.org/obo/UBERON_0002084	organism part	http://www.ebi.ac.uk/efo/EFO_0000635
 Left ventricle of heart	heart left ventricle	http://purl.obolibrary.org/obo/UBERON_0002084	organism part	http://www.ebi.ac.uk/efo/EFO_0000635
diff --git a/gemma-core/src/main/resources/ubic/gemma/model/analysis/expression/diff/ContrastResult.hbm.xml b/gemma-core/src/main/resources/ubic/gemma/model/analysis/expression/diff/ContrastResult.hbm.xml
index 7704889e79..d7bfc0439b 100644
--- a/gemma-core/src/main/resources/ubic/gemma/model/analysis/expression/diff/ContrastResult.hbm.xml
+++ b/gemma-core/src/main/resources/ubic/gemma/model/analysis/expression/diff/ContrastResult.hbm.xml
@@ -8,7 +8,7 @@
     >
         <id name="id" type="java.lang.Long" unsaved-value="null">
             <column name="ID" sql-type="BIGINT"/>
-            <generator class="org.hibernate.id.MultipleHiLoPerTableGenerator"/>
+            <generator class="native"/>
         </id>
         <property name="pvalue" type="java.lang.Double">
             <column name="PVALUE" not-null="false" unique="false" sql-type="DOUBLE"/>
diff --git a/gemma-core/src/main/resources/ubic/gemma/model/analysis/expression/diff/DifferentialExpressionAnalysisResult.hbm.xml b/gemma-core/src/main/resources/ubic/gemma/model/analysis/expression/diff/DifferentialExpressionAnalysisResult.hbm.xml
index b15e2a2e69..880adf9082 100644
--- a/gemma-core/src/main/resources/ubic/gemma/model/analysis/expression/diff/DifferentialExpressionAnalysisResult.hbm.xml
+++ b/gemma-core/src/main/resources/ubic/gemma/model/analysis/expression/diff/DifferentialExpressionAnalysisResult.hbm.xml
@@ -8,7 +8,7 @@
            table="DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT" mutable="false">
         <id name="id" type="java.lang.Long" unsaved-value="null">
             <column name="ID" sql-type="BIGINT"/>
-            <generator class="org.hibernate.id.MultipleHiLoPerTableGenerator"/>
+            <generator class="native"/>
         </id>
         <property name="pvalue" type="java.lang.Double">
             <column name="PVALUE" not-null="false" unique="false" sql-type="DOUBLE"/>
diff --git a/gemma-core/src/test/java/ubic/gemma/core/analysis/expression/diff/DiffExMetaAnalyzerServiceTest.java b/gemma-core/src/test/java/ubic/gemma/core/analysis/expression/diff/DiffExMetaAnalyzerServiceTest.java
index 7a0d2047aa..e2e7b86947 100644
--- a/gemma-core/src/test/java/ubic/gemma/core/analysis/expression/diff/DiffExMetaAnalyzerServiceTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/core/analysis/expression/diff/DiffExMetaAnalyzerServiceTest.java
@@ -531,7 +531,7 @@ private void cleanup() {
             arrayDesignService.remove( gpl97 );
         }
 
-        geneService.removeAllInBatch();
+        geneService.removeAll();
     }
 
     private void deleteSet( String shortName ) {
diff --git a/gemma-core/src/test/java/ubic/gemma/core/analysis/preprocess/SplitExperimentTest.java b/gemma-core/src/test/java/ubic/gemma/core/analysis/preprocess/SplitExperimentTest.java
index 252dcc05da..a9e83fed14 100644
--- a/gemma-core/src/test/java/ubic/gemma/core/analysis/preprocess/SplitExperimentTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/core/analysis/preprocess/SplitExperimentTest.java
@@ -32,16 +32,19 @@
 import ubic.gemma.core.util.test.BaseSpringContextTest;
 import ubic.gemma.core.util.test.category.SlowTest;
 import ubic.gemma.model.analysis.expression.ExpressionExperimentSet;
+import ubic.gemma.model.common.description.Characteristic;
 import ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector;
 import ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector;
 import ubic.gemma.model.expression.experiment.BioAssaySet;
 import ubic.gemma.model.expression.experiment.ExperimentalFactor;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
+import ubic.gemma.model.expression.experiment.FactorValue;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
 
 import java.io.InputStream;
 import java.util.Collection;
 
+import static org.assertj.core.api.Assertions.assertThatThrownBy;
 import static org.junit.Assert.*;
 import static org.junit.Assume.assumeNoException;
 
@@ -179,6 +182,36 @@ public void testSplitGSE123753ByCollectionOfMaterial() throws Exception {
         assertEquals( splitOn.getFactorValues().size(), results.getExperiments().size() );
     }
 
+    @Test
+    public void testGenerateName() {
+        ExpressionExperiment ee = new ExpressionExperiment();
+        ee.setName( "test" );
+        Characteristic c = new Characteristic();
+        c.setValue( "bar" );
+        FactorValue fv = new FactorValue();
+        fv.getCharacteristics().add( c );
+        ExperimentalFactor ef = new ExperimentalFactor();
+        ef.setName( "foo" );
+        fv.setExperimentalFactor( ef );
+        assertEquals( "Split part 1 of: test [foo = bar]", SplitExperimentServiceImpl.generateNameForSplit( ee, 1, fv ) );
+        ee.setName( String.join( "", java.util.Collections.nCopies( 255, "a" ) ) );
+        String name = SplitExperimentServiceImpl.generateNameForSplit( ee, 1, fv );
+        assertEquals( 255, name.length() );
+        assertEquals( "Split part 1 of: aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa… [foo = bar]", name );
+        ee.setName( "test" );
+        c.setValue( String.join( "", java.util.Collections.nCopies( 255, "a" ) ) );
+        assertThatThrownBy( () -> SplitExperimentServiceImpl.generateNameForSplit( ee, 1, fv ) )
+                .isInstanceOf( IllegalArgumentException.class )
+                .hasMessageContaining( "It's not possible to truncate the name of the split such that it won't exceed 255 characters." );
+
+        // make sure that whitespaces before the ellipsis are trimmed
+        int lengthOfEverythingElse = "Split part 1 of:  [foo = bar]".length();
+        ee.setName( String.join( "", java.util.Collections.nCopies( 255 - lengthOfEverythingElse - 1, "a" ) ) + " " );
+        c.setValue( "bar" );
+        assertEquals( 254, SplitExperimentServiceImpl.generateNameForSplit( ee, 1, fv ).length() );
+        assertEquals( "Split part 1 of: aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa… [foo = bar]", name );
+    }
+
     @After
     public void teardown() throws Exception {
         if ( ees != null ) {
diff --git a/gemma-core/src/test/java/ubic/gemma/core/analysis/report/WhatsNewServiceTest.java b/gemma-core/src/test/java/ubic/gemma/core/analysis/report/WhatsNewServiceTest.java
new file mode 100644
index 0000000000..658c31b6d4
--- /dev/null
+++ b/gemma-core/src/test/java/ubic/gemma/core/analysis/report/WhatsNewServiceTest.java
@@ -0,0 +1,41 @@
+package ubic.gemma.core.analysis.report;
+
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import ubic.gemma.core.util.test.BaseSpringContextTest;
+
+import java.nio.file.Paths;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class WhatsNewServiceTest extends BaseSpringContextTest {
+
+    @Autowired
+    private WhatsNewService whatsNewService;
+
+    @Value("${gemma.appdata.home}")
+    private String appDataHome;
+
+    @Test
+    public void testGeneratePublicWeeklyReport() {
+        // FIXME: generate some test data because we currently rely on other tests left-overs
+        WhatsNew initialReport = whatsNewService.generateWeeklyReport();
+        assertThat( Paths.get( appDataHome, "WhatsNew", "WhatsNew.new" ) ).exists();
+        assertThat( Paths.get( appDataHome, "WhatsNew", "WhatsNew.updated" ) ).exists();
+        WhatsNew report = whatsNewService.getLatestWeeklyReport();
+        assertThat( report ).isNotNull();
+        assertThat( report.getDate() ).isEqualTo( initialReport.getDate() );
+        assertThat( report.getNewArrayDesigns() )
+                .containsExactlyElementsOf( initialReport.getNewArrayDesigns() );
+        assertThat( report.getUpdatedArrayDesigns() )
+                .containsExactlyElementsOf( initialReport.getUpdatedArrayDesigns() );
+        assertThat( report.getNewExpressionExperiments() )
+                .containsExactlyElementsOf( initialReport.getNewExpressionExperiments() );
+        assertThat( report.getUpdatedExpressionExperiments() )
+                .containsExactlyElementsOf( initialReport.getUpdatedExpressionExperiments() );
+        assertThat( report.getNewEEIdsPerTaxon() ).isEqualTo( initialReport.getNewEEIdsPerTaxon() );
+        assertThat( report.getUpdatedEEIdsPerTaxon() ).isEqualTo( initialReport.getUpdatedEEIdsPerTaxon() );
+        assertThat( report.getEeCountPerTaxon() ).isEqualTo( initialReport.getEeCountPerTaxon() );
+    }
+}
\ No newline at end of file
diff --git a/gemma-core/src/test/java/ubic/gemma/core/loader/association/NCBIGene2GOAssociationParserTest.java b/gemma-core/src/test/java/ubic/gemma/core/loader/association/NCBIGene2GOAssociationParserTest.java
index 753c55e3c5..87855b863d 100644
--- a/gemma-core/src/test/java/ubic/gemma/core/loader/association/NCBIGene2GOAssociationParserTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/core/loader/association/NCBIGene2GOAssociationParserTest.java
@@ -48,7 +48,7 @@ public class NCBIGene2GOAssociationParserTest extends BaseSpringContextTest {
      */
     @Before
     public void setup() {
-        gene2GOAssociationService.removeAllInBatch();
+        gene2GOAssociationService.removeAll();
         gene2GOAssLoader = new NCBIGene2GOAssociationLoader();
         gene2GOAssLoader.setParser( new NCBIGene2GOAssociationParser( taxonService.loadAll() ) );
         gene2GOAssLoader.setPersisterHelper( this.persisterHelper );
diff --git a/gemma-core/src/test/java/ubic/gemma/core/loader/entrez/pubmed/PubMedSearchTest.java b/gemma-core/src/test/java/ubic/gemma/core/loader/entrez/pubmed/PubMedSearchTest.java
index 025700c8b6..ad448dce2a 100644
--- a/gemma-core/src/test/java/ubic/gemma/core/loader/entrez/pubmed/PubMedSearchTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/core/loader/entrez/pubmed/PubMedSearchTest.java
@@ -18,25 +18,18 @@
  */
 package ubic.gemma.core.loader.entrez.pubmed;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.junit.Before;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
-import org.xml.sax.SAXException;
 import ubic.gemma.core.util.test.category.PubMedTest;
 import ubic.gemma.core.util.test.category.SlowTest;
 import ubic.gemma.model.common.description.BibliographicReference;
 
-import javax.xml.parsers.ParserConfigurationException;
-import java.io.IOException;
-import java.net.UnknownHostException;
 import java.util.Collection;
 import java.util.HashSet;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assume.assumeNoException;
+import static org.junit.Assert.*;
+import static ubic.gemma.core.util.test.Assumptions.assumeThatResourceIsAvailable;
 
 /**
  * @author pavlidis
@@ -44,32 +37,31 @@
 @Category(PubMedTest.class)
 public class PubMedSearchTest {
 
+    @Before
+    public void setUp() throws Exception {
+        assumeThatResourceIsAvailable( "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" );
+    }
+
     /*
      * Test method for 'ubic.gemma.core.loader.entrez.pubmed.PubMedSearch.searchAndRetriveByHTTP(Collection<String>)'
      */
     @Test
     @Category(SlowTest.class)
     public void testSearchAndRetrieveByHTTP() throws Exception {
-        try {
-            PubMedSearch pms = new PubMedSearch();
-            Collection<String> searchTerms = new HashSet<>();
-            searchTerms.add( "brain" );
-            searchTerms.add( "hippocampus" );
-            searchTerms.add( "habenula" );
-            searchTerms.add( "glucose" );
-            Collection<BibliographicReference> actualResult = pms.searchAndRetrieveByHTTP( searchTerms );
-            assertTrue( "Expected at least 5 results, got " + actualResult.size(), actualResult.size() >= 5 );
-            /*
-             * at least, this was the result on 4/2008.
-             */
-            BibliographicReference r = actualResult.iterator().next();
-            assertNotNull( r.getAuthorList() );
-            assertNotNull( r.getPublicationDate() );
-        } catch ( java.io.IOException e ) {
-            checkCause( e );
-        } catch ( ESearchException e ) {
-            assumeNoException( e );
-        }
+        PubMedSearch pms = new PubMedSearch();
+        Collection<String> searchTerms = new HashSet<>();
+        searchTerms.add( "brain" );
+        searchTerms.add( "hippocampus" );
+        searchTerms.add( "habenula" );
+        searchTerms.add( "glucose" );
+        Collection<BibliographicReference> actualResult = pms.searchAndRetrieveByHTTP( searchTerms );
+        assertTrue( "Expected at least 5 results, got " + actualResult.size(), actualResult.size() >= 5 );
+        /*
+         * at least, this was the result on 4/2008.
+         */
+        BibliographicReference r = actualResult.iterator().next();
+        assertNotNull( r.getAuthorList() );
+        assertNotNull( r.getPublicationDate() );
     }
 
     /*
@@ -78,66 +70,37 @@ public void testSearchAndRetrieveByHTTP() throws Exception {
     @Test
     @Category(SlowTest.class)
     public void testSearchAndRetrieveByHTTPInChunks() throws Exception {
-        try {
-            PubMedSearch pms = new PubMedSearch();
-            Collection<String> searchTerms = new HashSet<>();
-            searchTerms.add( "brain" );
-            searchTerms.add( "hippocampus" );
-            searchTerms.add( "habenula" );
-            Collection<BibliographicReference> actualResult = pms.searchAndRetrieveByHTTP( searchTerms );
-            /*
-             * at least, this was the result on 4/2008.
-             */
-            assertTrue( "Expected at least 10, got " + actualResult.size(), actualResult.size() >= 10 );
-        } catch ( java.io.IOException e ) {
-            this.checkCause( e );
-        } catch ( ESearchException e ) {
-            assumeNoException( e );
-        }
+        PubMedSearch pms = new PubMedSearch();
+        Collection<String> searchTerms = new HashSet<>();
+        searchTerms.add( "brain" );
+        searchTerms.add( "hippocampus" );
+        searchTerms.add( "habenula" );
+        Collection<BibliographicReference> actualResult = pms.searchAndRetrieveByHTTP( searchTerms );
+        /*
+         * at least, this was the result on 4/2008.
+         */
+        assertTrue( "Expected at least 10, got " + actualResult.size(), actualResult.size() >= 10 );
     }
 
     @Test
     @Category(SlowTest.class)
     public void testSearchAndRetrieveIdByHTTPBookshelf() throws Exception {
-        try {
-            PubMedSearch pms = new PubMedSearch();
-            Collection<String> searchTerms = new HashSet<>();
-            searchTerms.add( "23865096" );
-            Collection<BibliographicReference> actualResult = pms.searchAndRetrieveIdByHTTP( searchTerms );
-            assertEquals( 1, actualResult.size() );
-        } catch ( java.io.IOException e ) {
-            this.checkCause( e );
-        }
+        PubMedSearch pms = new PubMedSearch();
+        Collection<String> searchTerms = new HashSet<>();
+        searchTerms.add( "23865096" );
+        Collection<BibliographicReference> actualResult = pms.searchAndRetrieveIdByHTTP( searchTerms );
+        assertEquals( 1, actualResult.size() );
     }
 
     @Test
     public void testSearchAndRetrieveIdsByHTTP() throws Exception {
-        try {
-            PubMedSearch pms = new PubMedSearch();
-            Collection<String> searchTerms = new HashSet<>();
-            searchTerms.add( "brain" );
-            searchTerms.add( "hippocampus" );
-            searchTerms.add( "habenula" );
-            searchTerms.add( "glucose" );
-            Collection<String> actualResult = pms.searchAndRetrieveIdsByHTTP( searchTerms );
-            assertTrue( "Expect at least 5 results, got " + actualResult.size(), actualResult.size() >= 5 );
-            /*
-             * at least, this was the result on 4/2008.
-             */
-        } catch ( java.io.IOException e ) {
-            this.checkCause( e );
-        } catch ( ESearchException e ) {
-            assumeNoException( e );
-        }
-    }
-
-    private void checkCause( java.io.IOException e ) throws IOException {
-        if ( e instanceof UnknownHostException ) {
-            assumeNoException( "Test skipped due to unknown host exception", e );
-        } else if ( e.getMessage().contains( "503" ) || e.getMessage().contains( "502" ) ) {
-            assumeNoException( "Test skipped due to a 50x from NCBI", e );
-        } else {
-            throw e;
-        }
+        PubMedSearch pms = new PubMedSearch();
+        Collection<String> searchTerms = new HashSet<>();
+        searchTerms.add( "brain" );
+        searchTerms.add( "hippocampus" );
+        searchTerms.add( "habenula" );
+        searchTerms.add( "glucose" );
+        Collection<String> actualResult = pms.searchAndRetrieveIdsByHTTP( searchTerms );
+        assertTrue( "Expect at least 5 results, got " + actualResult.size(), actualResult.size() >= 5 );
     }
 }
diff --git a/gemma-core/src/test/java/ubic/gemma/core/ontology/OntologyServiceTest.java b/gemma-core/src/test/java/ubic/gemma/core/ontology/OntologyServiceTest.java
index f2623723be..3b318d840a 100644
--- a/gemma-core/src/test/java/ubic/gemma/core/ontology/OntologyServiceTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/core/ontology/OntologyServiceTest.java
@@ -18,6 +18,7 @@
 import ubic.gemma.core.ontology.providers.GeneOntologyService;
 import ubic.gemma.core.search.SearchException;
 import ubic.gemma.core.search.SearchService;
+import ubic.gemma.core.util.test.TestPropertyPlaceholderConfigurer;
 import ubic.gemma.model.common.search.SearchSettings;
 import ubic.gemma.model.genome.Gene;
 import ubic.gemma.persistence.service.common.description.CharacteristicService;
@@ -37,6 +38,11 @@ public class OntologyServiceTest extends AbstractJUnit4SpringContextTests {
     @TestComponent
     static class OntologyServiceTestContextConfiguration {
 
+        @Bean
+        public static TestPropertyPlaceholderConfigurer testPropertyPlaceholderConfigurer() {
+            return new TestPropertyPlaceholderConfigurer( "load.ontologies=false" );
+        }
+
         @Bean
         public OntologyService ontologyService() {
             return new OntologyServiceImpl();
diff --git a/gemma-core/src/test/java/ubic/gemma/core/ontology/providers/GeneOntologyService2Test.java b/gemma-core/src/test/java/ubic/gemma/core/ontology/providers/GeneOntologyService2Test.java
index 9380c2ead9..5548064438 100644
--- a/gemma-core/src/test/java/ubic/gemma/core/ontology/providers/GeneOntologyService2Test.java
+++ b/gemma-core/src/test/java/ubic/gemma/core/ontology/providers/GeneOntologyService2Test.java
@@ -14,6 +14,7 @@
  */
 package ubic.gemma.core.ontology.providers;
 
+import org.junit.Before;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -28,6 +29,7 @@
 import ubic.gemma.core.genome.gene.service.GeneService;
 import ubic.gemma.core.ontology.OntologyTestUtils;
 import ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect;
+import ubic.gemma.core.util.test.TestPropertyPlaceholderConfigurer;
 import ubic.gemma.core.util.test.category.SlowTest;
 import ubic.gemma.persistence.service.association.Gene2GOAssociationService;
 import ubic.gemma.persistence.util.TestComponent;
@@ -53,13 +55,15 @@ public class GeneOntologyService2Test extends AbstractJUnit4SpringContextTests {
     @Configuration
     @TestComponent
     public static class GeneOntologyService2TestContextConfiguration {
+
+        @Bean
+        public static TestPropertyPlaceholderConfigurer testPropertyPlaceholderConfigurer() {
+            return new TestPropertyPlaceholderConfigurer( "load.ontologies=false", "url.geneOntology=dummy" );
+        }
+
         @Bean
         public GeneOntologyService geneOntologyService() throws IOException, InterruptedException {
-            GeneOntologyServiceImpl gos = new GeneOntologyServiceImpl( false );
-            InputStream is = new GZIPInputStream(
-                    new ClassPathResource( "/data/loader/ontology/go.bptest.owl.gz" ).getInputStream() );
-            OntologyTestUtils.initialize( gos, is );
-            return gos;
+            return new GeneOntologyServiceImpl();
         }
 
         @Bean
@@ -81,6 +85,13 @@ public CacheManager cacheManager() {
     @Autowired
     private GeneOntologyService gos;
 
+    @Before
+    public void setUp() throws InterruptedException, IOException {
+        InputStream is = new GZIPInputStream(
+                new ClassPathResource( "/data/loader/ontology/go.bptest.owl.gz" ).getInputStream() );
+        OntologyTestUtils.initialize( gos, is );
+    }
+
     @Test
     @Category(SlowTest.class)
     public final void testParents() {
diff --git a/gemma-core/src/test/java/ubic/gemma/core/ontology/providers/GeneOntologyServiceTest.java b/gemma-core/src/test/java/ubic/gemma/core/ontology/providers/GeneOntologyServiceTest.java
index f201961991..49fdd0f1a3 100644
--- a/gemma-core/src/test/java/ubic/gemma/core/ontology/providers/GeneOntologyServiceTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/core/ontology/providers/GeneOntologyServiceTest.java
@@ -20,6 +20,7 @@
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.cache.CacheManager;
@@ -33,6 +34,7 @@
 import ubic.basecode.ontology.search.OntologySearchException;
 import ubic.gemma.core.genome.gene.service.GeneService;
 import ubic.gemma.core.ontology.OntologyTestUtils;
+import ubic.gemma.core.util.test.TestPropertyPlaceholderConfigurer;
 import ubic.gemma.persistence.service.association.Gene2GOAssociationService;
 import ubic.gemma.persistence.util.TestComponent;
 
@@ -54,17 +56,15 @@ public class GeneOntologyServiceTest extends AbstractJUnit4SpringContextTests {
     @Configuration
     @TestComponent
     static class GeneOntologyServiceTestContextConfiguration {
+
+        @Bean
+        public static TestPropertyPlaceholderConfigurer testPropertyPlaceholderConfigurer() {
+            return new TestPropertyPlaceholderConfigurer( "load.ontologies=false", "url.geneOntology=dummy" );
+        }
+
         @Bean
         public GeneOntologyService geneOntologyService() throws IOException, InterruptedException {
-            GeneOntologyService goService = new GeneOntologyServiceImpl( false );
-            /*
-             * Note that this test file is out of date in some ways. See GeneOntologyServiceTest2
-             */
-            InputStream is = new GZIPInputStream(
-                    new ClassPathResource( "/data/loader/ontology/molecular-function.test.owl.gz" ).getInputStream() );
-            // we must force indexing to get consistent test results
-            OntologyTestUtils.initialize( goService, is );
-            return goService;
+            return new GeneOntologyServiceImpl();
         }
 
         @Bean
@@ -86,6 +86,17 @@ public CacheManager cacheManager() {
     @Autowired
     private GeneOntologyService gos;
 
+    @Before
+    public void setUp() throws InterruptedException, IOException {
+        /*
+         * Note that this test file is out of date in some ways. See GeneOntologyServiceTest2
+         */
+        InputStream is = new GZIPInputStream(
+                new ClassPathResource( "/data/loader/ontology/molecular-function.test.owl.gz" ).getInputStream() );
+        // we must force indexing to get consistent test results
+        OntologyTestUtils.initialize( gos, is );
+    }
+
     @Test
     public void testFindTerm() throws OntologySearchException {
         Collection<OntologyTerm> matches = gos.findTerm( "toxin" );
diff --git a/gemma-core/src/test/java/ubic/gemma/core/util/test/TestPropertyPlaceholderConfigurer.java b/gemma-core/src/test/java/ubic/gemma/core/util/test/TestPropertyPlaceholderConfigurer.java
new file mode 100644
index 0000000000..81823f0c1b
--- /dev/null
+++ b/gemma-core/src/test/java/ubic/gemma/core/util/test/TestPropertyPlaceholderConfigurer.java
@@ -0,0 +1,32 @@
+package ubic.gemma.core.util.test;
+
+import org.springframework.beans.factory.config.PropertyPlaceholderConfigurer;
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.StringReader;
+import java.util.Properties;
+
+/**
+ * Minimalistic placeholder configurer for usage in tests.
+ * <p>
+ * TODO: switch to <a href="https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/test/context/TestPropertySource.html">@TestPropertySource</a>
+ * once we migrate to Spring 4.
+ * @author poirigui
+ */
+public class TestPropertyPlaceholderConfigurer extends PropertyPlaceholderConfigurer {
+
+    public TestPropertyPlaceholderConfigurer( String... properties ) {
+        setProperties( createTestProperties( properties ) );
+    }
+
+    private static Properties createTestProperties( String... properties ) {
+        Properties props = new Properties();
+        try ( Reader reader = new StringReader( String.join( "\n", properties ) ) ) {
+            props.load( reader );
+        } catch ( IOException e ) {
+            throw new RuntimeException( e );
+        }
+        return props;
+    }
+}
diff --git a/gemma-core/src/test/java/ubic/gemma/model/association/phenotype/PhenotypeAssociationTest.java b/gemma-core/src/test/java/ubic/gemma/model/association/phenotype/PhenotypeAssociationTest.java
index 2c5a94f99c..8d47a8f404 100644
--- a/gemma-core/src/test/java/ubic/gemma/model/association/phenotype/PhenotypeAssociationTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/model/association/phenotype/PhenotypeAssociationTest.java
@@ -97,7 +97,7 @@ public void setUp() throws Exception {
     @After
     public void tearDown() {
         this.runAsAdmin();
-        phenotypeAssociationService.removeAllInBatch();
+        phenotypeAssociationService.removeAll();
     }
 
     @Test
diff --git a/gemma-core/src/test/java/ubic/gemma/model/common/auditAndSecurity/AuditTrailDaoTest.java b/gemma-core/src/test/java/ubic/gemma/model/common/auditAndSecurity/AuditTrailDaoTest.java
index 499c4c9991..3bec882fe4 100644
--- a/gemma-core/src/test/java/ubic/gemma/model/common/auditAndSecurity/AuditTrailDaoTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/model/common/auditAndSecurity/AuditTrailDaoTest.java
@@ -22,7 +22,6 @@
 import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
-
 import ubic.gemma.core.util.test.BaseSpringContextTest;
 import ubic.gemma.model.common.Auditable;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
@@ -96,5 +95,4 @@ public void testHandleAddEventAuditableAuditEvent() {
         assertTrue( auditable.getAuditTrail().getEvents().size() > 1 );
 
     }
-
 }
diff --git a/gemma-core/src/test/java/ubic/gemma/model/expression/experiment/ExpressionExperimentServiceIntegrationTest.java b/gemma-core/src/test/java/ubic/gemma/model/expression/experiment/ExpressionExperimentServiceIntegrationTest.java
index e35e22f53c..d197f10649 100644
--- a/gemma-core/src/test/java/ubic/gemma/model/expression/experiment/ExpressionExperimentServiceIntegrationTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/model/expression/experiment/ExpressionExperimentServiceIntegrationTest.java
@@ -25,6 +25,8 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.access.AccessDeniedException;
 import ubic.gemma.core.util.test.BaseSpringContextTest;
+import ubic.gemma.model.common.auditAndSecurity.AuditAction;
+import ubic.gemma.model.common.auditAndSecurity.AuditEvent;
 import ubic.gemma.model.common.auditAndSecurity.Contact;
 import ubic.gemma.model.common.description.Characteristic;
 import ubic.gemma.model.common.description.DatabaseEntry;
@@ -51,6 +53,7 @@
 import java.util.function.Consumer;
 
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.assertThatThrownBy;
 import static org.junit.Assert.*;
 
 /**
@@ -454,4 +457,28 @@ public void testCacheInvalidationWhenACharacteristicIsDeleted() {
         assertThat( expressionExperimentService.getAnnotationsUsageFrequency( null, 0, 0, null, null, null, null ) )
                 .noneSatisfy( consumer );
     }
+
+    @Test
+    public void testSaveWithTransientEntity() {
+        ExpressionExperiment ee = new ExpressionExperiment();
+        ExpressionExperiment createdEE = expressionExperimentService.save( ee );
+        assertNotNull( createdEE.getId() );
+        // ees.add( createdEE );
+        assertThat( createdEE.getAuditTrail().getEvents() )
+                .extracting( AuditEvent::getAction )
+                .containsExactly( AuditAction.CREATE );
+        ExpressionExperiment updatedEE = expressionExperimentService.save( ee );
+        assertThat( updatedEE.getId() ).isEqualTo( createdEE.getId() );
+        assertThat( createdEE.getAuditTrail().getEvents() )
+                .extracting( AuditEvent::getAction )
+                .containsExactly( AuditAction.CREATE, AuditAction.UPDATE );
+    }
+
+    @Test
+    public void testUpdateWithTransientEntity() {
+        ExpressionExperiment ee = new ExpressionExperiment();
+        assertThatThrownBy( () -> expressionExperimentService.update( ee ) )
+                .isInstanceOf( IllegalArgumentException.class )
+                .hasMessageContaining( "ID is required to be non-null" );
+    }
 }
diff --git a/gemma-core/src/test/java/ubic/gemma/model/genome/gene/GeneSetServiceTest.java b/gemma-core/src/test/java/ubic/gemma/model/genome/gene/GeneSetServiceTest.java
index 4a8b513a21..84ef6582a6 100644
--- a/gemma-core/src/test/java/ubic/gemma/model/genome/gene/GeneSetServiceTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/model/genome/gene/GeneSetServiceTest.java
@@ -84,7 +84,7 @@ public void setUp() throws Exception {
     @After
     public void tearDown() {
         geneSetService.removeAll();
-        gene2GoService.removeAllInBatch();
+        gene2GoService.removeAll();
     }
 
     /**
diff --git a/gemma-core/src/test/java/ubic/gemma/persistence/service/AbstractDaoTest.java b/gemma-core/src/test/java/ubic/gemma/persistence/service/AbstractDaoTest.java
index 1a05787084..4483de2c45 100644
--- a/gemma-core/src/test/java/ubic/gemma/persistence/service/AbstractDaoTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/persistence/service/AbstractDaoTest.java
@@ -17,12 +17,8 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
-import java.util.stream.Collectors;
-import java.util.stream.LongStream;
 
-import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.*;
-import static org.mockito.internal.verification.VerificationModeFactory.noInteractions;
 
 public class AbstractDaoTest {
 
@@ -45,10 +41,6 @@ public static class MyDao extends AbstractDao<MyEntity> {
         public MyDao( SessionFactory sessionFactory ) {
             super( MyEntity.class, sessionFactory );
         }
-
-        public MyDao( SessionFactory sessionFactory, int batchSize ) {
-            super( MyEntity.class, sessionFactory, sessionFactory.getClassMetadata( MyEntity.class ), batchSize );
-        }
     }
 
     private SessionFactory sessionFactory;
@@ -67,43 +59,6 @@ public void setUp() {
         when( session.getFlushMode() ).thenReturn( FlushMode.AUTO );
     }
 
-    @Test
-    public void testBatchSizeFlushRightAway() {
-        myDao = new MyDao( sessionFactory, 1 );
-        myDao.createInBatch( generateEntities( 10 ) );
-        verify( session, times( 10 ) ).persist( any( MyEntity.class ) );
-        verify( session, times( 10 ) ).flush();
-        verify( session, times( 10 ) ).clear();
-    }
-
-    @Test
-    public void testBatchSizeUnlimited() {
-        myDao = new MyDao( sessionFactory, Integer.MAX_VALUE );
-        myDao.createInBatch( generateEntities( 10 ) );
-        verify( session, times( 10 ) ).persist( any( MyEntity.class ) );
-        verify( session, VerificationModeFactory.times( 0 ) ).flush();
-        verify( session, times( 0 ) ).clear();
-    }
-
-    @Test
-    public void testBatchSizeSmall() {
-        myDao = new MyDao( sessionFactory, 10 );
-        myDao.createInBatch( generateEntities( 10 ) );
-        verify( session, times( 10 ) ).persist( any( MyEntity.class ) );
-        verify( session, VerificationModeFactory.times( 1 ) ).flush();
-        verify( session, times( 1 ) ).clear();
-    }
-
-    @Test
-    public void testBatchingNotAdvisableWhenFlushModeIsManual() {
-        myDao = new MyDao( sessionFactory, 10 );
-        when( session.getFlushMode() ).thenReturn( FlushMode.MANUAL );
-        myDao.createInBatch( generateEntities( 20 ) );
-        verify( session, times( 20 ) ).persist( any( MyEntity.class ) );
-        verify( session, times( 0 ) ).flush();
-        verify( session, times( 0 ) ).clear();
-    }
-
     private static abstract class MyEntityProxy extends MyEntity implements HibernateProxy {
 
     }
@@ -134,12 +89,4 @@ public void testLoadByCollection() {
         verify( mockCriteria ).add( argThat( criterion -> criterion.toString().equals( Restrictions.in( "id", ids ).toString() ) ) );
         verify( mockCriteria ).list();
     }
-
-    private Collection<MyEntity> generateEntities( int count ) {
-        Collection<MyEntity> result = new ArrayList<>();
-        for ( int i = 0; i < count; i++ ) {
-            result.add( new MyEntity() );
-        }
-        return result;
-    }
 }
diff --git a/gemma-core/src/test/java/ubic/gemma/persistence/service/AbstractServiceTest.java b/gemma-core/src/test/java/ubic/gemma/persistence/service/AbstractServiceTest.java
index 0fa3e64b7a..f3a7ddb911 100644
--- a/gemma-core/src/test/java/ubic/gemma/persistence/service/AbstractServiceTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/persistence/service/AbstractServiceTest.java
@@ -19,6 +19,7 @@
 import java.util.List;
 
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.failBecauseExceptionWasNotThrown;
 
 @ContextConfiguration
 public class AbstractServiceTest extends BaseDatabaseTest {
@@ -43,6 +44,37 @@ public MyService myService( ExternalDatabaseDao dao ) {
 
     private int i = 0;
 
+    public static class ExceptionWithoutMessage extends Exception {
+
+        public ExceptionWithoutMessage() {
+        }
+    }
+
+    public static class ExceptionWithMessage extends Exception {
+
+        public ExceptionWithMessage( String message ) {
+            super( message );
+        }
+    }
+
+    @Test
+    public void testLoadOrFail() {
+        try {
+            myService.loadOrFail( 12L, ExceptionWithoutMessage::new );
+            failBecauseExceptionWasNotThrown( ExceptionWithoutMessage.class );
+        } catch ( ExceptionWithoutMessage e ) {
+            assertThat( e ).hasMessage( null );
+        }
+        try {
+            myService.loadOrFail( 12L, ExceptionWithMessage::new, "No ExternalDatabase with ID 12." );
+            failBecauseExceptionWasNotThrown( ExceptionWithMessage.class );
+        } catch ( ExceptionWithMessage e ) {
+            assertThat( e )
+                    .hasMessageContaining( "ExternalDatabase" )
+                    .hasMessageContaining( "12" );
+        }
+    }
+
     @Test
     public void testEnsureInSession() {
         ExternalDatabase ed = ExternalDatabase.Factory.newInstance( "test", DatabaseType.OTHER );
diff --git a/gemma-core/src/test/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDaoImplTest.java b/gemma-core/src/test/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDaoImplTest.java
new file mode 100644
index 0000000000..94692d8cad
--- /dev/null
+++ b/gemma-core/src/test/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityDaoImplTest.java
@@ -0,0 +1,48 @@
+package ubic.gemma.persistence.service.expression.experiment;
+
+import org.hibernate.SessionFactory;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.test.context.ContextConfiguration;
+import ubic.gemma.core.util.test.BaseDatabaseTest;
+import ubic.gemma.model.common.description.DatabaseEntry;
+import ubic.gemma.model.common.description.DatabaseType;
+import ubic.gemma.model.common.description.ExternalDatabase;
+import ubic.gemma.model.expression.arrayDesign.BlacklistedPlatform;
+import ubic.gemma.persistence.util.TestComponent;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+@ContextConfiguration
+public class BlacklistedEntityDaoImplTest extends BaseDatabaseTest {
+
+    @Configuration
+    @TestComponent
+    static class BlacklistedEntityDaoContextConfiguration extends BaseDatabaseTestContextConfiguration {
+
+        @Bean
+        public BlacklistedEntityDao blacklistedEntityDao( SessionFactory sessionFactory ) {
+            return new BlacklistedEntityDaoImpl( sessionFactory );
+        }
+    }
+
+    @Autowired
+    private BlacklistedEntityDao blacklistedEntityDao;
+
+    @Test
+    public void testDeleteAll() {
+        BlacklistedPlatform bp = new BlacklistedPlatform();
+        ExternalDatabase ed = ExternalDatabase.Factory.newInstance( "test", DatabaseType.OTHER );
+        sessionFactory.getCurrentSession().persist( ed );
+        bp.setExternalAccession( DatabaseEntry.Factory.newInstance( ed ) );
+        bp = ( BlacklistedPlatform ) blacklistedEntityDao.create( bp );
+        assertEquals( 1, blacklistedEntityDao.removeAll() );
+        sessionFactory.getCurrentSession().flush();
+        sessionFactory.getCurrentSession().clear();
+        assertNull( sessionFactory.getCurrentSession().get( BlacklistedPlatform.class, bp.getId() ) );
+        assertNull( sessionFactory.getCurrentSession().get( DatabaseEntry.class, bp.getExternalAccession().getId() ) );
+    }
+}
\ No newline at end of file
diff --git a/gemma-core/src/test/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityServiceTest.java b/gemma-core/src/test/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityServiceTest.java
index 5ee423306d..2a0d68c3b0 100644
--- a/gemma-core/src/test/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityServiceTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/persistence/service/expression/experiment/BlacklistedEntityServiceTest.java
@@ -5,7 +5,6 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.access.AccessDeniedException;
 import ubic.gemma.core.util.test.BaseSpringContextTest;
-import ubic.gemma.model.expression.BlacklistedEntity;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
 import ubic.gemma.model.expression.experiment.BlacklistedExperiment;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
@@ -34,7 +33,7 @@ public void tearDown() {
             expressionExperimentService.remove( ee );
         if ( ad != null )
             arrayDesignService.remove( ad );
-        blacklistedEntityService.removeAllInBatch();
+        blacklistedEntityService.removeAll();
     }
 
     @Test
diff --git a/gemma-core/src/test/java/ubic/gemma/core/util/ConfigurationTest.java b/gemma-core/src/test/java/ubic/gemma/persistence/util/SettingsConfigTest.java
similarity index 56%
rename from gemma-core/src/test/java/ubic/gemma/core/util/ConfigurationTest.java
rename to gemma-core/src/test/java/ubic/gemma/persistence/util/SettingsConfigTest.java
index 2855ac095a..6bdd02d9b0 100644
--- a/gemma-core/src/test/java/ubic/gemma/core/util/ConfigurationTest.java
+++ b/gemma-core/src/test/java/ubic/gemma/persistence/util/SettingsConfigTest.java
@@ -1,56 +1,45 @@
-package ubic.gemma.core.util;
+package ubic.gemma.persistence.util;
 
 import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
-import org.springframework.core.env.Environment;
 import org.springframework.core.env.MutablePropertySources;
-import org.springframework.core.env.PropertySource;
+import org.springframework.core.env.PropertySources;
+import org.springframework.core.io.ClassPathResource;
 import org.springframework.core.io.support.ResourcePropertySource;
 import org.springframework.test.context.ActiveProfiles;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests;
-import ubic.gemma.persistence.util.PropertySourcesConfigurer;
-import ubic.gemma.persistence.util.SpringProfiles;
-import ubic.gemma.persistence.util.TestComponent;
 
 import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.Assert.*;
 
 @ActiveProfiles(SpringProfiles.TEST)
 @ContextConfiguration
-public class ConfigurationTest extends AbstractJUnit4SpringContextTests {
+public class SettingsConfigTest extends AbstractJUnit4SpringContextTests {
 
     @Configuration
     @TestComponent
     static class ConfigurationTestContextConfiguration {
 
         @Bean
-        public PropertySourcesPlaceholderConfigurer propertySourcesPlaceholderConfigurer() throws IOException {
+        public static PropertySourcesPlaceholderConfigurer propertySourcesPlaceholderConfigurer() throws IOException {
             PropertySourcesPlaceholderConfigurer configurer = new PropertySourcesPlaceholderConfigurer();
-            MutablePropertySources mps = new MutablePropertySources();
-            for ( PropertySource<?> ps : propertySources() ) {
-                mps.addLast( ps );
-            }
+            configurer.setPropertySources( propertySources() );
             return configurer;
         }
 
-        @Bean
-        public PropertySourcesConfigurer propertySourcesConfigurer() throws IOException {
-            return new PropertySourcesConfigurer( propertySources() );
-        }
-
-        private List<PropertySource<?>> propertySources() throws IOException {
-            return Arrays.asList( new ResourcePropertySource( "classpath:default.properties" ),
-                    new ResourcePropertySource( "classpath:project.properties" ),
-                    new ResourcePropertySource( "classpath:ubic/gemma/version.properties" ) );
+        private static PropertySources propertySources() throws IOException {
+            MutablePropertySources result = new MutablePropertySources();
+            result.addLast( new ResourcePropertySource( new ClassPathResource( "default.properties" ) ) );
+            result.addLast( new ResourcePropertySource( new ClassPathResource( "project.properties" ) ) );
+            // FIXME: local local.properties from ${gemma.appdata.home}
+            result.addLast( new ResourcePropertySource( new ClassPathResource( "ubic/gemma/version.properties" ) ) );
+            return result;
         }
     }
 
@@ -66,9 +55,6 @@ private List<PropertySource<?>> propertySources() throws IOException {
     @Value("${gemma.compass.dir}")
     public String compassDir;
 
-    @Value("#{environment['gemma.search.dir']}")
-    public String searchDirFromEnv;
-
     @Value("${cors.allowedOrigins}")
     private String allowedOrigins;
 
@@ -81,22 +67,16 @@ private List<PropertySource<?>> propertySources() throws IOException {
     @Value("${gemma.hosturl}")
     private String hostUrl;
 
-    @Autowired
-    private Environment env;
-
     @Test
     public void test() {
         assertNotNull( version );
         assertTrue( allowedOrigins.contains( hostUrl ) );
-        assertEquals( version, env.getProperty( "gemma.version" ) );
         assertThat( featuredExternalDatabases )
                 .isNotNull()
                 .contains( "hg38", "mm10" );
         assertEquals( "/var/tmp/gemmaData", appDataHome );
         assertEquals( appDataHome + "/download", downloadPath );
         assertEquals( appDataHome + "/searchIndices", searchDir );
-        assertEquals( searchDir, searchDirFromEnv );
         assertEquals( searchDir, compassDir );
-        assertEquals( searchDir, env.getProperty( "gemma.compass.dir" ) );
     }
 }
diff --git a/gemma-groovy-support/pom.xml b/gemma-groovy-support/pom.xml
index 2722de5d9d..4ec7c34125 100644
--- a/gemma-groovy-support/pom.xml
+++ b/gemma-groovy-support/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>gemma</groupId>
         <artifactId>gemma</artifactId>
-        <version>1.30.2</version>
+        <version>1.30.3</version>
     </parent>
 
     <artifactId>gemma-groovy-support</artifactId>
diff --git a/gemma-rest/pom.xml b/gemma-rest/pom.xml
index 1eb9d135d8..907726be81 100644
--- a/gemma-rest/pom.xml
+++ b/gemma-rest/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gemma</artifactId>
         <groupId>gemma</groupId>
-        <version>1.30.2</version>
+        <version>1.30.3</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
diff --git a/gemma-rest/src/main/java/ubic/gemma/rest/DatasetsWebService.java b/gemma-rest/src/main/java/ubic/gemma/rest/DatasetsWebService.java
index bd2f4864ce..fc177a5c4b 100644
--- a/gemma-rest/src/main/java/ubic/gemma/rest/DatasetsWebService.java
+++ b/gemma-rest/src/main/java/ubic/gemma/rest/DatasetsWebService.java
@@ -61,7 +61,6 @@
 import ubic.gemma.model.genome.TaxonValueObject;
 import ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService;
 import ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService;
-import ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService;
 import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
 import ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
@@ -117,8 +116,6 @@ public class DatasetsWebService {
     @Autowired
     private AuditEventService auditEventService;
     @Autowired
-    private QuantitationTypeService quantitationTypeService;
-    @Autowired
     private DatasetArgService datasetArgService;
     @Autowired
     private GeneArgService geneArgService;
@@ -653,6 +650,7 @@ public Response getDatasetDifferentialExpressionAnalysesResultSets(
      *                   is more efficient. Only datasets that user has access to will be available.
      */
     @GET
+    @CacheControl(maxAge = 1200)
     @Path("/{dataset}/annotations")
     @Produces(MediaType.APPLICATION_JSON)
     @Operation(summary = "Retrieve the annotations of a dataset", responses = {
@@ -1009,7 +1007,7 @@ private Response outputFile( File file, String error, String shortName ) {
     private List<DifferentialExpressionAnalysisValueObject> getDiffExVos( Long eeId, int offset, int limit ) {
         Map<ExpressionExperimentDetailsValueObject, List<DifferentialExpressionAnalysisValueObject>> map = differentialExpressionAnalysisService
                 .getAnalysesByExperiment( Collections.singleton( eeId ), offset, limit );
-        if ( map == null || map.size() < 1 ) {
+        if ( map == null || map.isEmpty() ) {
             return Collections.emptyList();
         }
         return map.get( map.keySet().iterator().next() );
diff --git a/gemma-rest/src/main/java/ubic/gemma/rest/TaxaWebService.java b/gemma-rest/src/main/java/ubic/gemma/rest/TaxaWebService.java
index fc09107eb5..b23859e20d 100644
--- a/gemma-rest/src/main/java/ubic/gemma/rest/TaxaWebService.java
+++ b/gemma-rest/src/main/java/ubic/gemma/rest/TaxaWebService.java
@@ -218,7 +218,7 @@ public ResponseDataObject<List<PhysicalLocationValueObject>> getGeneLocationsInT
     }
 
     /**
-     * Retrieves datasets for the given taxon. Filtering allowed exactly like in {@link DatasetsWebService#getDatasets(String, Double, FilterArg, OffsetArg, LimitArg, SortArg)}.
+     * Retrieves datasets for the given taxon. Filtering allowed exactly like in {@link DatasetsWebService#getDatasets(String, FilterArg, OffsetArg, LimitArg, SortArg)}.
      *
      * @param taxonArg can either be Taxon ID, Taxon NCBI ID, or one of its string identifiers:
      *                 scientific name, common name. It is recommended to use the ID for efficiency.
diff --git a/gemma-rest/src/test/java/ubic/gemma/rest/DatasetsWebServiceTest.java b/gemma-rest/src/test/java/ubic/gemma/rest/DatasetsWebServiceTest.java
index 2d42ababc2..eb6734077a 100644
--- a/gemma-rest/src/test/java/ubic/gemma/rest/DatasetsWebServiceTest.java
+++ b/gemma-rest/src/test/java/ubic/gemma/rest/DatasetsWebServiceTest.java
@@ -441,4 +441,15 @@ public void testGetBlacklistedDatasets() {
                 .hasMediaTypeCompatibleWith( MediaType.APPLICATION_JSON_TYPE );
         verify( expressionExperimentService ).loadBlacklistedValueObjects( Filters.empty(), Sort.by( "ee", "id", Sort.Direction.ASC, "id" ), 0, 20 );
     }
+
+    @Test
+    public void testGetDatasetAnnotations() {
+        ee.setId( 1L );
+        when( expressionExperimentService.load( 1L ) ).thenReturn( ee );
+        assertThat( target( "/datasets/1/annotations" ).request().get() )
+                .hasStatus( Response.Status.OK )
+                .hasHeader( "Cache-Control", "max-age=1200" );
+        verify( expressionExperimentService ).load( 1L );
+        verify( expressionExperimentService ).getAnnotationsById( 1L );
+    }
 }
\ No newline at end of file
diff --git a/gemma-rest/src/test/java/ubic/gemma/rest/PlatformsWebServiceTest.java b/gemma-rest/src/test/java/ubic/gemma/rest/PlatformsWebServiceTest.java
index e46696a3b3..dbf79acb60 100644
--- a/gemma-rest/src/test/java/ubic/gemma/rest/PlatformsWebServiceTest.java
+++ b/gemma-rest/src/test/java/ubic/gemma/rest/PlatformsWebServiceTest.java
@@ -54,7 +54,7 @@ public void setUp() throws Exception {
     public void tearDown() {
         eeService.remove( expressionExperiment );
         arrayDesignService.remove( arrayDesign );
-        blacklistedEntityService.removeAllInBatch();
+        blacklistedEntityService.removeAll();
     }
 
     @Test
diff --git a/gemma-web/pom.xml b/gemma-web/pom.xml
index b64ac9b12b..b9d682efc5 100644
--- a/gemma-web/pom.xml
+++ b/gemma-web/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-web</artifactId>
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/ExpressionExperimentReportGenerationController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/ExpressionExperimentReportGenerationController.java
index 95016535a7..bb280fec97 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/ExpressionExperimentReportGenerationController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/ExpressionExperimentReportGenerationController.java
@@ -24,6 +24,7 @@
 import ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 /**
  * @author klc
@@ -39,7 +40,7 @@ public class ExpressionExperimentReportGenerationController {
     public String run( Long id ) {
         ExpressionExperiment ee = expressionExperimentService.load( id );
         if ( ee == null ) {
-            throw new IllegalArgumentException( "Could not access experiment with id=" + id );
+            throw new EntityNotFoundException( "Could not access experiment with id=" + id );
         }
 
         ExpressionExperimentReportTaskCommand cmd = new ExpressionExperimentReportTaskCommand( ee );
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/expression/coexpression/links/LinkAnalysisController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/expression/coexpression/links/LinkAnalysisController.java
index 70b0f109ae..7f77bd8976 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/expression/coexpression/links/LinkAnalysisController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/expression/coexpression/links/LinkAnalysisController.java
@@ -27,6 +27,7 @@
 import ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 /**
  * A controller to pre-process expression data vectors.
@@ -49,7 +50,7 @@ public String run( Long id ) {
         ExpressionExperiment ee = expressionExperimentService.load( id );
 
         if ( ee == null ) {
-            throw new IllegalArgumentException( "Cannot access experiment with id=" + id );
+            throw new EntityNotFoundException( "Cannot access experiment with id=" + id );
         }
 
         experimentReportService.evictFromCache( id );
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/BatchInfoFetchController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/BatchInfoFetchController.java
index 26b4b9f312..0aafe58504 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/BatchInfoFetchController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/BatchInfoFetchController.java
@@ -26,6 +26,7 @@
 import ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskCommand;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 /**
  * For populating "batch" information about experiments.
@@ -46,10 +47,8 @@ public String run( Long id ) {
         if ( id == null )
             throw new IllegalArgumentException( "ID cannot be null" );
 
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null )
-            throw new IllegalArgumentException( "Could not load experiment with id=" + id );
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, "Could not load experiment with id=" + id );
 
         /*
          * Check preconditions.
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/PreprocessController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/PreprocessController.java
index 3e276c6727..a5fe17dee2 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/PreprocessController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/PreprocessController.java
@@ -25,6 +25,7 @@
 import ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 /**
  * A controller to pre-process expression data (including updating diagnostics)
@@ -47,17 +48,14 @@ public class PreprocessController {
      * Update the processed data vectors as well as diagnostics
      *
      * @param  id of the experiment
-     * @return    status
+     * @return status
      */
     public String run( Long id ) {
         if ( id == null )
             throw new IllegalArgumentException( "ID cannot be null" );
 
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null )
-            throw new IllegalArgumentException( "Could not load experiment with id=" + id );
-
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, "Could not load experiment with id=" + id );
 
         PreprocessTaskCommand cmd = new PreprocessTaskCommand( ee );
         experimentReportService.evictFromCache( id );
@@ -68,17 +66,14 @@ public String run( Long id ) {
      * Only update the daignostics
      *
      * @param  id of experiment
-     * @return    status
+     * @return status
      */
     public String diagnostics( Long id ) {
         if ( id == null )
             throw new IllegalArgumentException( "ID cannot be null" );
 
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null )
-            throw new IllegalArgumentException( "Could not load experiment with id=" + id );
-
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, "Could not load experiment with id=" + id );
 
         PreprocessTaskCommand cmd = new PreprocessTaskCommand( ee );
         cmd.setDiagnosticsOnly( true );
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/SvdController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/SvdController.java
index 079944b636..66068905b5 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/SvdController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/SvdController.java
@@ -26,6 +26,7 @@
 import ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 /**
  * Run SVD on a data set.
@@ -48,11 +49,10 @@ public class SvdController {
     public String run( Long id ) {
         if ( id == null )
             throw new IllegalArgumentException( "ID cannot be null" );
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null )
-            throw new IllegalArgumentException( "Could not load experiment with id=" + id );
 
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, "Could not load experiment with id=" + id );
+
         experimentReportService.evictFromCache( id );
         SvdTaskCommand cmd = new SvdTaskCommand( ee );
 
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/TwoChannelMissingValueController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/TwoChannelMissingValueController.java
index 69cbbed1f6..a2f25cb34f 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/TwoChannelMissingValueController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/analysis/preprocess/TwoChannelMissingValueController.java
@@ -25,6 +25,7 @@
 import ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 /**
  * Run misssing value computation via web request.
@@ -45,12 +46,8 @@ public class TwoChannelMissingValueController {
      * AJAX entry point. -- uses default settings
      */
     public String run( Long id ) {
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Cannot access experiment with id=" + id );
-        }
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, "Cannot access experiment with id=" + id );
 
         TwoChannelMissingValueTaskCommand cmd = new TwoChannelMissingValueTaskCommand( ee );
         experimentReportService.evictFromCache( id );
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/SecurityControllerImpl.java b/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/SecurityControllerImpl.java
index 933ae2f18e..612331996b 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/SecurityControllerImpl.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/SecurityControllerImpl.java
@@ -50,6 +50,7 @@
 import ubic.gemma.persistence.util.MailEngine;
 import ubic.gemma.persistence.util.Settings;
 import ubic.gemma.web.remote.EntityDelegator;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 import javax.servlet.ServletContext;
 import java.util.*;
@@ -88,7 +89,7 @@ public boolean addUserToGroup( String userName, String groupName ) {
         User userTakingAction = userManager.getCurrentUser();
 
         if ( userTakingAction == null ) {
-            throw new IllegalStateException( "Cannot add user to group when user is not logged in" );
+            throw new AccessDeniedException( "Cannot add user to group when user is not logged in" );
         }
 
         User u;
@@ -108,7 +109,7 @@ public boolean addUserToGroup( String userName, String groupName ) {
             String uname = u.getUserName();
             securityService.addUserToGroup( uname, groupName );
         } else {
-            throw new IllegalArgumentException( "Sorry, there is no matching user." );
+            throw new EntityNotFoundException( "Sorry, there is no matching user." );
         }
 
         /*
@@ -541,8 +542,9 @@ private Securable getSecurable( EntityDelegator ed ) {
         }
 
         if ( s == null ) {
-            throw new IllegalArgumentException( "Entity does not exist or user does not have access." );
+            throw new EntityNotFoundException( clazz.getSimpleName() + " with ID " + ed.getId() + " does not exist or user does not have access." );
         }
+
         return s;
     }
 
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/UserFormMultiActionController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/UserFormMultiActionController.java
index e74829497c..b9b5b461bf 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/UserFormMultiActionController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/UserFormMultiActionController.java
@@ -23,6 +23,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.json.JSONObject;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.access.AccessDeniedException;
 import org.springframework.security.authentication.encoding.PasswordEncoder;
 import org.springframework.security.core.Authentication;
 import org.springframework.security.core.AuthenticationException;
@@ -85,7 +86,7 @@ public void editUser( @RequestParam("email") String email, @RequestParam("passwo
             String username = SecurityContextHolder.getContext().getAuthentication().getName();
 
             if ( !username.equals( originalUserName ) ) {
-                throw new RuntimeException( "You must be logged in to edit your profile." );
+                throw new AccessDeniedException( "You must be logged in to edit your profile." );
             }
 
             UserDetailsImpl user = ( UserDetailsImpl ) userManager.loadUserByUsername( username );
@@ -106,7 +107,7 @@ public void editUser( @RequestParam("email") String email, @RequestParam("passwo
 
             if ( password.length() > 0 ) {
                 if ( !StringUtils.equals( password, passwordConfirm ) ) {
-                    throw new RuntimeException( "Passwords do not match." );
+                    throw new IllegalArgumentException( "Passwords do not match." );
                 }
                 String encryptedPassword = passwordEncoder.encodePassword( password, user.getUsername() );
                 userManager.changePassword( oldPassword, encryptedPassword );
@@ -177,7 +178,7 @@ public void resetPassword( @RequestParam("email") String email, @RequestParam("u
         if ( StringUtils.isEmpty( email ) || StringUtils.isEmpty( username ) ) {
             String txt = "Email or username not specified.  These are required fields.";
             log.warn( txt );
-            throw new RuntimeException( txt );
+            throw new IllegalArgumentException( txt );
         }
 
         /* look up the user's information and reset password. */
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/UserListControllerImpl.java b/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/UserListControllerImpl.java
index 52661c5816..4a66f453ff 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/UserListControllerImpl.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/UserListControllerImpl.java
@@ -25,7 +25,6 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.jdbc.UncategorizedSQLException;
 import org.springframework.security.authentication.encoding.PasswordEncoder;
-import org.springframework.security.core.GrantedAuthority;
 import org.springframework.security.core.userdetails.UserDetailsService;
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.RequestMapping;
@@ -33,14 +32,12 @@
 import org.springframework.web.servlet.ModelAndView;
 import ubic.gemma.core.security.authentication.UserManager;
 import ubic.gemma.model.common.auditAndSecurity.User;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Date;
-import java.util.List;
-import java.util.stream.Collectors;
 
 /**
  * For display and editing of users. Note: do not use parametrized collections as parameters for ajax methods in this
@@ -107,7 +104,7 @@ public void saveUser( UserValueObject user ) {
         User u = userManager.findByUserName( userName );
 
         if ( u == null ) {
-            throw new IllegalArgumentException( String.format( "No user with username %s.", userName ) );
+            throw new EntityNotFoundException( String.format( "No user with username %s.", userName ) );
         }
 
         UserDetailsImpl userDetails;
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/WhatsNewController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/WhatsNewController.java
index 8a36f13bf3..19cd236f43 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/WhatsNewController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/common/auditAndSecurity/WhatsNewController.java
@@ -1,8 +1,8 @@
 /*
  * The Gemma project
- * 
+ *
  * Copyright (c) 2007 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
@@ -18,7 +18,6 @@
  */
 package ubic.gemma.web.controller.common.auditAndSecurity;
 
-import org.apache.commons.lang3.time.DateUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.RequestMapping;
@@ -30,8 +29,6 @@
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
-import java.util.Calendar;
-import java.util.Date;
 
 /**
  * Controller to provide information on "what's new" in the system
@@ -48,10 +45,7 @@ public class WhatsNewController {
     @RequestMapping("/daily.html")
     public ModelAndView daily( HttpServletRequest request, HttpServletResponse response ) {
         ModelAndView mav = new ModelAndView( "wnDay" );
-        Calendar c = Calendar.getInstance();
-        Date date = c.getTime();
-        date = DateUtils.addDays( date, -1 );
-        WhatsNew wn = whatsNewService.getReport( date );
+        WhatsNew wn = whatsNewService.getDailyReport();
         mav.addObject( "whatsnew", wn );
         mav.addObject( "timeSpan", "In the past day" );
         return mav;
@@ -61,11 +55,8 @@ public ModelAndView daily( HttpServletRequest request, HttpServletResponse respo
     public ModelAndView generateCache( HttpServletRequest request, HttpServletResponse response ) {
         ModelAndView mav = new ModelAndView( new RedirectView( WebConstants.HOME_PAGE, true ) );
 
-        Calendar c = Calendar.getInstance();
-        Date date = c.getTime();
-        date = DateUtils.addDays( date, -7 );
         // save a report for a week's duration
-        whatsNewService.saveReport( date );
+        whatsNewService.generateWeeklyReport();
 
         return mav;
     }
@@ -77,13 +68,9 @@ public void setWhatsNewService( WhatsNewService whatsNewService ) {
     @RequestMapping("/weekly.html")
     public ModelAndView weekly( HttpServletRequest request, HttpServletResponse response ) {
         ModelAndView mav = new ModelAndView( "wnWeek" );
-        Calendar c = Calendar.getInstance();
-        Date date = c.getTime();
-        date = DateUtils.addWeeks( date, -1 );
-        WhatsNew wn = whatsNewService.getReport( date );
+        WhatsNew wn = whatsNewService.getWeeklyReport();
         mav.addObject( "whatsnew", wn );
         mav.addObject( "timeSpan", "In the past week" );
         return mav;
     }
-
 }
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/common/description/bibref/BibliographicReferenceControllerImpl.java b/gemma-web/src/main/java/ubic/gemma/web/controller/common/description/bibref/BibliographicReferenceControllerImpl.java
index 939f5c2ce6..28d4b10095 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/common/description/bibref/BibliographicReferenceControllerImpl.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/common/description/bibref/BibliographicReferenceControllerImpl.java
@@ -43,7 +43,6 @@
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
-import java.security.InvalidParameterException;
 import java.util.*;
 import java.util.Map.Entry;
 
@@ -72,7 +71,7 @@ public ModelAndView add( HttpServletRequest request, HttpServletResponse respons
         String pubMedId = request.getParameter( "accession" ); // FIXME: allow use of the primary key as well.
 
         if ( StringUtils.isBlank( pubMedId ) ) {
-            throw new EntityNotFoundException( "Must provide a PubMed Id" );
+            throw new IllegalArgumentException( "Must provide a PubMed Id" );
         }
 
         BibliographicReference bibRef = bibliographicReferenceService.findByExternalId( pubMedId );
@@ -135,7 +134,7 @@ public ModelAndView delete( HttpServletRequest request, HttpServletResponse resp
 
         if ( pubMedId == null ) {
             // should be a validation error.
-            throw new EntityNotFoundException( "Must provide a PubMed Id" );
+            throw new IllegalArgumentException( "Must provide a PubMed Id" );
         }
 
         BibliographicReference bibRef = bibliographicReferenceService.findByExternalId( pubMedId );
@@ -159,7 +158,7 @@ public BibliographicReferenceValueObject load( Long id ) {
         if ( returnVal.getRecords() != null && !returnVal.getRecords().isEmpty() ) {
             return returnVal.getRecords().iterator().next();
         }
-        throw new InvalidParameterException( "Error retrieving bibliographic reference for id = " + id );
+        throw new EntityNotFoundException( "Error retrieving bibliographic reference for id = " + id );
 
     }
 
@@ -210,7 +209,7 @@ public ModelAndView show( HttpServletRequest request, HttpServletResponse respon
         // FIXME: allow use of the primary key as well.
 
         if ( StringUtils.isBlank( pubMedId ) && StringUtils.isBlank( gemmaId ) ) {
-            throw new EntityNotFoundException( "Must provide a gamma database id or a PubMed id" );
+            throw new IllegalArgumentException( "Must provide a gamma database id or a PubMed id" );
         }
 
         if ( !StringUtils.isBlank( gemmaId ) ) {
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/diff/DifferentialExpressionAnalysisController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/diff/DifferentialExpressionAnalysisController.java
index 515a87d16a..d66daf7373 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/diff/DifferentialExpressionAnalysisController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/diff/DifferentialExpressionAnalysisController.java
@@ -36,6 +36,7 @@
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 import java.util.Collection;
 import java.util.HashSet;
@@ -64,15 +65,11 @@ public class DifferentialExpressionAnalysisController {
      * Ajax method. Pick the analysis type when we want it to be completely automated. Does not support subset factors
      *
      * @param  id id
-     * @return    analysis info
+     * @return analysis info
      */
     public DifferentialExpressionAnalyzerInfo determineAnalysisType( Long id ) {
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Cannot access experiment with id=" + id );
-        }
-
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, "Cannot access experiment with id=" + id );
 
         Collection<ExperimentalFactor> factorsWithoutBatch = ExperimentalDesignUtils
                 .factorsWithoutBatch( ee.getExperimentalDesign().getExperimentalFactors() );
@@ -106,33 +103,23 @@ public DifferentialExpressionAnalyzerInfo determineAnalysisType( Long id ) {
      *
      * @param  eeId ee id
      * @param  id   id
-     * @return      string
+     * @return string
      */
     public String redo( Long eeId, Long id ) {
-        ExpressionExperiment ee = expressionExperimentService.load( eeId );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Cannot access experiment with id=" + eeId );
-        }
-
-        DifferentialExpressionAnalysis toRedo = differentialExpressionAnalysisService.load( id );
-        if ( toRedo == null ) {
-            throw new IllegalArgumentException( "Cannot access analysis with id=" + id );
-        }
+        ExpressionExperiment ee = expressionExperimentService.loadOrFail( eeId,
+                EntityNotFoundException::new, "Cannot access experiment with id=" + eeId );
+        DifferentialExpressionAnalysis toRedo = differentialExpressionAnalysisService.loadOrFail( id,
+                EntityNotFoundException::new, "Cannot access analysis with id=" + id );
         this.experimentReportService.evictFromCache( ee.getId() );
         DifferentialExpressionAnalysisTaskCommand cmd = new DifferentialExpressionAnalysisTaskCommand( ee, toRedo );
         return taskRunningService.submitTaskCommand( cmd );
     }
 
     public String refreshStats( Long eeId, Long id ) {
-        ExpressionExperiment ee = expressionExperimentService.load( eeId );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Cannot access experiment with id=" + eeId );
-        }
-
-        DifferentialExpressionAnalysis toRefresh = differentialExpressionAnalysisService.load( id );
-        if ( toRefresh == null ) {
-            throw new IllegalArgumentException( "Cannot access analysis with id=" + id );
-        }
+        ExpressionExperiment ee = expressionExperimentService.loadOrFail( eeId,
+                EntityNotFoundException::new, "Cannot access experiment with id=" + eeId );
+        DifferentialExpressionAnalysis toRefresh = differentialExpressionAnalysisService.loadOrFail( id,
+                EntityNotFoundException::new, "Cannot access analysis with id=" + id );
         this.experimentReportService.evictFromCache( ee.getId() );
         DifferentialExpressionAnalysisTaskCommand cmd = new DifferentialExpressionAnalysisTaskCommand( ee, toRefresh );
         return taskRunningService.submitTaskCommand( cmd );
@@ -142,18 +129,13 @@ public String refreshStats( Long eeId, Long id ) {
      * AJAX entry point to remove an analysis given by the ID
      *
      * @param  id id
-     * @return    string
+     * @return string
      */
     public String remove( Long eeId, Long id ) {
-        ExpressionExperiment ee = expressionExperimentService.load( eeId );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Cannot access experiment with id=" + eeId );
-        }
-
-        DifferentialExpressionAnalysis toRemove = differentialExpressionAnalysisService.load( id );
-        if ( toRemove == null ) {
-            throw new IllegalArgumentException( "Cannot access analysis with id=" + id );
-        }
+        ExpressionExperiment ee = expressionExperimentService.loadOrFail( eeId,
+                EntityNotFoundException::new, "Cannot access experiment with id=" + eeId );
+        DifferentialExpressionAnalysis toRemove = differentialExpressionAnalysisService.loadOrFail( id,
+                EntityNotFoundException::new, "Cannot access analysis with id=" + id );
         DifferentialExpressionAnalysisRemoveTaskCommand cmd = new DifferentialExpressionAnalysisRemoveTaskCommand( ee,
                 toRemove );
         this.experimentReportService.evictFromCache( ee.getId() );
@@ -164,16 +146,12 @@ public String remove( Long eeId, Long id ) {
      * AJAX entry point when running completely automatically.
      *
      * @param  id id
-     * @return    string
+     * @return string
      */
     public String run( Long id ) {
-
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Cannot access experiment with id=" + id );
-        }
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, "Cannot access experiment with id=" + id );
         this.experimentReportService.evictFromCache( ee.getId() );
-        ee = expressionExperimentService.thawLite( ee );
 
         DifferentialExpressionAnalysisTaskCommand cmd = new DifferentialExpressionAnalysisTaskCommand( ee );
         boolean rnaSeq = expressionExperimentService.isRNASeq( ee );
@@ -187,12 +165,12 @@ public String run( Long id ) {
 
     /**
      * Perform a customized DEA based on user input on web interface.
-     * 
+     *
      * @param  id                  of the experiment
      * @param  factorids           to include
      * @param  includeInteractions if possible
      * @param  subsetFactorId      if required
-     * @return                     task identifier
+     * @return task identifier
      */
     public String runCustom( Long id, Collection<Long> factorids, boolean includeInteractions, Long subsetFactorId ) {
 
@@ -200,12 +178,8 @@ public String runCustom( Long id, Collection<Long> factorids, boolean includeInt
             throw new IllegalArgumentException( "You must provide at least one factor to analyze" );
         }
 
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Cannot access experiment with id=" + id );
-        }
-
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, "Cannot access experiment with id=" + id );
 
         /*
          * Get the factors matching the factorids
@@ -234,8 +208,7 @@ public String runCustom( Long id, Collection<Long> factorids, boolean includeInt
             }
 
             if ( factors.contains( subsetFactor ) ) {
-                throw new IllegalArgumentException(
-                        "Subset factor must not be one of the factors used in the analysis" );
+                throw new IllegalArgumentException( "Subset factor must not be one of the factors used in the analysis" );
             }
         }
 
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/diff/DifferentialExpressionSearchController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/diff/DifferentialExpressionSearchController.java
index fae6d831cf..083cd12ca7 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/diff/DifferentialExpressionSearchController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/diff/DifferentialExpressionSearchController.java
@@ -208,8 +208,10 @@ public String scheduleDiffExpSearchTask( Long taxonId, ExpressionExperimentSetVa
             } else if ( eevo.getName() != null ) {
                 Collection<ExpressionExperimentSet> eesets = expressionExperimentSetService
                         .findByName( eevo.getName() );
-                if ( eesets.isEmpty() || eesets.size() > 1 ) {
-                    throw new IllegalArgumentException( "Experiment set not found by name=" + eevo.getName() );
+                if ( eesets.isEmpty() ) {
+                    throw new EntityNotFoundException( "No experiment set found by name=" + eevo.getName() );
+                } else if ( eesets.size() > 1 ) {
+                    throw new IllegalArgumentException( "A unique experiment set not found by name=" + eevo.getName() );
                 }
                 experiments = expressionExperimentSetService
                         .getExperimentValueObjectsInSet( eesets.iterator().next().getId() );
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignController.java
index 459b7a1dc0..87cccd15ac 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignController.java
@@ -14,9 +14,6 @@
  */
 package ubic.gemma.web.controller.expression.arrayDesign;
 
-import org.springframework.core.io.FileSystemResource;
-import org.springframework.core.io.Resource;
-import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.servlet.ModelAndView;
@@ -27,9 +24,7 @@
 import ubic.gemma.web.remote.JsonReaderResponse;
 import ubic.gemma.web.remote.ListBatchCommand;
 
-import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
-import java.io.File;
 import java.io.IOException;
 import java.util.Collection;
 import java.util.Map;
@@ -57,7 +52,7 @@ JsonReaderResponse<ArrayDesignValueObject> browse( ListBatchCommand batch, Long[
      * Delete an arrayDesign.
      */
     @RequestMapping("/deleteArrayDesign.html")
-    ModelAndView delete( HttpServletRequest request, HttpServletResponse response );
+    ModelAndView delete( @RequestParam("id") Long id );
 
     @RequestMapping("/downloadAnnotationFile.html")
     void downloadAnnotationFile( @RequestParam("id") Long arrayDesignId, @RequestParam(value = "fileType", required = false) String fileType, HttpServletResponse httpServletResponse ) throws IOException;
@@ -66,13 +61,13 @@ JsonReaderResponse<ArrayDesignValueObject> browse( ListBatchCommand batch, Long[
      * Show array designs that match search criteria.
      */
     @RequestMapping("/filterArrayDesigns.html")
-    ModelAndView filter( HttpServletRequest request, HttpServletResponse response );
+    ModelAndView filter( @RequestParam("filter") String filter );
 
     /**
      * Build summary report for an array design
      */
     @RequestMapping("/generateArrayDesignSummary.html")
-    ModelAndView generateSummary( HttpServletRequest request, HttpServletResponse response );
+    ModelAndView generateSummary( @RequestParam(value = "id", required = false) Long id );
 
     Collection<ArrayDesignValueObject> getArrayDesigns( Long[] arrayDesignIds, boolean showMergees,
             boolean showOrphans );
@@ -101,16 +96,19 @@ Collection<ArrayDesignValueObject> getArrayDesigns( Long[] arrayDesignIds, boole
      * Show all array designs, or according to a list of IDs passed in.
      */
     @RequestMapping("/showAllArrayDesigns.html")
-    ModelAndView showAllArrayDesigns( HttpServletRequest request, HttpServletResponse response );
+    ModelAndView showAllArrayDesigns();
 
-    @RequestMapping({ "/showArrayDesign.html", "/" })
-    ModelAndView showArrayDesign( HttpServletRequest request, HttpServletResponse response );
+    @RequestMapping(value = { "/showArrayDesign.html", "/" }, params = { "id" })
+    ModelAndView showArrayDesign( @RequestParam("id") Long id );
+
+    @RequestMapping(value = { "/showArrayDesign.html", "/" }, params = { "name" })
+    ModelAndView showArrayDesignByName( @RequestParam("name") String name );
 
     /**
      * Show (some of) the probes from an array.
      */
     @RequestMapping("/showCompositeSequenceSummary.html")
-    ModelAndView showCompositeSequences( HttpServletRequest request );
+    ModelAndView showCompositeSequences( @RequestParam("id") Long id );
 
     /**
      * shows a list of BioAssays for an expression experiment subset
@@ -118,7 +116,7 @@ Collection<ArrayDesignValueObject> getArrayDesigns( Long[] arrayDesignIds, boole
      * @return ModelAndView
      */
     @RequestMapping("/showExpressionExperiments.html")
-    ModelAndView showExpressionExperiments( HttpServletRequest request );
+    ModelAndView showExpressionExperiments( @RequestParam("id") Long id );
 
     String updateReport( EntityDelegator ed );
 
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignControllerImpl.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignControllerImpl.java
index 31499cbc31..560e9ed1d1 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignControllerImpl.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignControllerImpl.java
@@ -63,7 +63,6 @@
 import ubic.gemma.web.taglib.arrayDesign.ArrayDesignHtmlUtil;
 import ubic.gemma.web.util.EntityNotFoundException;
 
-import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import java.io.*;
 import java.util.*;
@@ -107,10 +106,7 @@ public class ArrayDesignControllerImpl implements ArrayDesignController {
 
     @Override
     public String addAlternateName( Long arrayDesignId, String alternateName ) {
-        ArrayDesign ad = arrayDesignService.load( arrayDesignId );
-        if ( ad == null ) {
-            throw new IllegalArgumentException( "No such platform with id=" + arrayDesignId );
-        }
+        ArrayDesign ad = arrayDesignService.loadOrFail( arrayDesignId, EntityNotFoundException::new, "No such platform with id=" + arrayDesignId );
 
         if ( StringUtils.isBlank( alternateName ) ) {
             return formatAlternateNames( ad );
@@ -143,30 +139,14 @@ public JsonReaderResponse<ArrayDesignValueObject> browse( ListBatchCommand batch
 
     @Override
     @RequestMapping("/deleteArrayDesign.html")
-    public ModelAndView delete( HttpServletRequest request, HttpServletResponse response ) {
-        String stringId = request.getParameter( "id" );
-
-        if ( stringId == null ) {
-            // should be a validation error.
-            throw new EntityNotFoundException( "Must provide an id" );
-        }
-
-        Long id;
-        try {
-            id = Long.parseLong( stringId );
-        } catch ( NumberFormatException e ) {
-            throw new EntityNotFoundException( "Identifier was invalid" );
-        }
-
-        ArrayDesign arrayDesign = arrayDesignService.load( id );
-        if ( arrayDesign == null ) {
-            throw new EntityNotFoundException( "Platform with id=" + id + " not found" );
-        }
+    public ModelAndView delete( @RequestParam("id") Long id ) {
+        ArrayDesign arrayDesign = arrayDesignService.loadOrFail( id,
+                EntityNotFoundException::new, "Platform with id=" + id + " not found" );
 
         // check that no EE depend on the arraydesign we want to remove
         // Do this by checking if there are any bioassays that depend this AD
         Collection<BioAssay> assays = arrayDesignService.getAllAssociatedBioAssays( arrayDesign );
-        if ( assays.size() != 0 ) {
+        if ( !assays.isEmpty() ) {
             return new ModelAndView( new RedirectView( "/arrays/showAllArrayDesigns.html", true ) )
                     .addObject( "message", "Array  " + arrayDesign.getName()
                             + " can't be deleted. Dataset has a dependency on this Array." );
@@ -221,20 +201,17 @@ public void downloadAnnotationFile( @RequestParam("id") Long arrayDesignId, @Req
 
     @Override
     @RequestMapping("/filterArrayDesigns.html")
-    public ModelAndView filter( HttpServletRequest request, HttpServletResponse response ) {
-
+    public ModelAndView filter( @RequestParam("filter") String filter ) {
         StopWatch overallWatch = new StopWatch();
         overallWatch.start();
 
-        String filter = request.getParameter( "filter" );
-
         // Validate the filtering search criteria.
         if ( StringUtils.isBlank( filter ) ) {
             return new ModelAndView( new RedirectView( "/arrays/showAllArrayDesigns.html", true ) )
                     .addObject( "message", "No search criteria provided" );
         }
 
-        Collection<SearchResult<ArrayDesign>> searchResults = null;
+        Collection<SearchResult<ArrayDesign>> searchResults;
         try {
             searchResults = searchService.search( SearchSettings.arrayDesignSearch( filter ) )
                     .getByResultObjectType( ArrayDesign.class );
@@ -243,7 +220,7 @@ public ModelAndView filter( HttpServletRequest request, HttpServletResponse resp
                     .addObject( "message", "Invalid search settings: " + e.getMessage() );
         }
 
-        if ( ( searchResults == null ) || ( searchResults.size() == 0 ) ) {
+        if ( ( searchResults == null ) || ( searchResults.isEmpty() ) ) {
             return new ModelAndView( new RedirectView( "/arrays/showAllArrayDesigns.html", true ) )
                     .addObject( "message", "No search criteria provided" );
 
@@ -264,7 +241,7 @@ public ModelAndView filter( HttpServletRequest request, HttpServletResponse resp
         }
 
         overallWatch.stop();
-        Long overallElapsed = overallWatch.getTime();
+        long overallElapsed = overallWatch.getTime();
         log.info( "Generating the AD list:  (" + list + ") took: " + overallElapsed / 1000 + "s " );
 
         return new ModelAndView( new RedirectView( "/arrays/showAllArrayDesigns.html?id=" + list, true ) )
@@ -274,29 +251,20 @@ public ModelAndView filter( HttpServletRequest request, HttpServletResponse resp
 
     @Override
     @RequestMapping("/generateArrayDesignSummary.html")
-    public ModelAndView generateSummary( HttpServletRequest request, HttpServletResponse response ) {
-
-        String sId = request.getParameter( "id" );
-
+    public ModelAndView generateSummary( @RequestParam(value = "id", required = false) Long id ) {
         // if no IDs are specified, then load all expressionExperiments and show the summary (if available)
         GenerateArraySummaryLocalTask job;
-        if ( StringUtils.isBlank( sId ) ) {
+        if ( id == null ) {
             job = new GenerateArraySummaryLocalTask( new TaskCommand() );
             String taskId = taskRunningService.submitTask( job );
             return new ModelAndView( new RedirectView( "/arrays/showAllArrayDesigns.html", true ) )
                     .addObject( "taskId", taskId );
         }
 
-        try {
-            Long id = Long.parseLong( sId );
-            job = new GenerateArraySummaryLocalTask( new TaskCommand( id ) );
-            String taskId = taskRunningService.submitTask( job );
-            return new ModelAndView( new RedirectView( "/arrays/showAllArrayDesigns.html?id=" + id, true ) )
-                    .addObject( "taskId", taskId );
-        } catch ( NumberFormatException e ) {
-            throw new RuntimeException( "Invalid ID: " + sId );
-        }
-
+        job = new GenerateArraySummaryLocalTask( new TaskCommand( id ) );
+        String taskId = taskRunningService.submitTask( job );
+        return new ModelAndView( new RedirectView( "/arrays/showAllArrayDesigns.html?id=" + id, true ) )
+                .addObject( "taskId", taskId );
     }
 
     @Override
@@ -355,7 +323,7 @@ public ArrayDesignValueObjectExt getDetails( Long id ) {
 
         ArrayDesignValueObject vo = arrayDesignService.loadValueObject( arrayDesign );
         if ( vo == null ) {
-            throw new IllegalArgumentException(
+            throw new EntityNotFoundException(
                     "You do not have appropriate rights to see this platform. This is likely due "
                             + "to the platform being marked as unusable." );
         }
@@ -385,15 +353,8 @@ private ArrayDesign getADSafely( Long id ) {
         if ( id == null ) {
             throw new IllegalArgumentException( "ID cannot be null" );
         }
-
-        ArrayDesign arrayDesign = arrayDesignService.load( id );
-
-        if ( arrayDesign == null ) {
-            throw new IllegalArgumentException( "No platform with id=" + id + " could be loaded" );
-        }
-
-        arrayDesign = arrayDesignService.thawLite( arrayDesign );
-        return arrayDesign;
+        return arrayDesignService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, "No platform with id=" + id + " could be loaded" );
     }
 
     /**
@@ -498,9 +459,8 @@ public String remove( EntityDelegator ed ) {
             throw new EntityNotFoundException( ed.getId() + " not found" );
         }
         Collection<BioAssay> assays = arrayDesignService.getAllAssociatedBioAssays( arrayDesign );
-        if ( assays.size() != 0 ) {
-            throw new IllegalArgumentException(
-                    "Cannot remove " + arrayDesign + ", it is used by an expression experiment" );
+        if ( !assays.isEmpty() ) {
+            throw new IllegalArgumentException( "Cannot remove " + arrayDesign + ", it is used by an expression experiment" );
         }
 
         RemoveArrayLocalTask job = new RemoveArrayLocalTask( new TaskCommand( arrayDesign.getId() ) );
@@ -511,71 +471,47 @@ public String remove( EntityDelegator ed ) {
 
     @Override
     @RequestMapping("/showAllArrayDesigns.html")
-    public ModelAndView showAllArrayDesigns( HttpServletRequest request, HttpServletResponse response ) {
+    public ModelAndView showAllArrayDesigns() {
         return new ModelAndView( "arrayDesigns" );
     }
 
     @Override
-    @RequestMapping({ "/showArrayDesign.html", "/" })
-    public ModelAndView showArrayDesign( HttpServletRequest request, HttpServletResponse response ) {
-        String name = request.getParameter( "name" );
-        String idStr = request.getParameter( "id" );
-
-        if ( ( name == null ) && ( idStr == null ) ) {
-            throw new IllegalArgumentException( "Must provide a platform identifier or name" );
-        }
-
-        ArrayDesign arrayDesign;
-        if ( idStr != null ) {
-            arrayDesign = arrayDesignService.load( Long.parseLong( idStr ) );
-            request.setAttribute( "id", idStr );
-        } else {
-            arrayDesign = arrayDesignService.findByShortName( name );
-            request.setAttribute( "name", name );
-
-            if ( arrayDesign == null ) {
-                Collection<ArrayDesign> byName = arrayDesignService.findByName( name );
-                if ( byName.isEmpty() ) {
-                    throw new IllegalArgumentException( "Must provide a valid platform identifier or name" );
+    @RequestMapping(value = { "/showArrayDesign.html", "/" }, params = { "id" })
+    public ModelAndView showArrayDesign( @RequestParam("id") Long id ) {
+        return showArrayDesignInternal( arrayDesignService.loadOrFail( id, EntityNotFoundException::new, "No platform was found for ID " + id + "." ) );
+    }
 
-                }
-                arrayDesign = byName.iterator().next();
-            }
+    @Override
+    @RequestMapping(value = { "/showArrayDesign.html", "/" }, params = { "name" })
+    public ModelAndView showArrayDesignByName( @RequestParam("name") String name ) {
+        ArrayDesign arrayDesign = arrayDesignService.findByShortName( name );
+        if ( arrayDesign == null ) {
+            arrayDesign = arrayDesignService.findByName( name ).iterator().next();
         }
-
         if ( arrayDesign == null ) {
-            throw new IllegalArgumentException( "Must provide a valid platform identifier or name" );
+            throw new EntityNotFoundException( "No platform was found for the provided name." );
         }
+        return showArrayDesignInternal( arrayDesign );
+    }
 
-        long id = arrayDesign.getId();
-
-        ModelAndView mav = new ModelAndView( "arrayDesign.detail" );
-
-        mav.addObject( "arrayDesignId", id );
-        mav.addObject( "arrayDesignShortName", arrayDesign.getShortName() );
-        mav.addObject( "arrayDesignName", arrayDesign.getName() );
-
-        return mav;
+    private ModelAndView showArrayDesignInternal( ArrayDesign arrayDesign ) {
+        return new ModelAndView( "arrayDesign.detail" )
+                .addObject( "arrayDesignId", arrayDesign.getId() )
+                .addObject( "arrayDesignShortName", arrayDesign.getShortName() )
+                .addObject( "arrayDesignName", arrayDesign.getName() );
     }
 
     @Override
     @RequestMapping("/showCompositeSequenceSummary.html")
-    public ModelAndView showCompositeSequences( HttpServletRequest request ) {
-
-        String arrayDesignIdStr = request.getParameter( "id" );
-
-        if ( arrayDesignIdStr == null ) {
-            // should be a validation error, on 'submit'.
-            throw new EntityNotFoundException( "Must provide a platform name or Id" );
-        }
-
-        ArrayDesign arrayDesign = arrayDesignService.load( Long.parseLong( arrayDesignIdStr ) );
+    public ModelAndView showCompositeSequences( @RequestParam("id") Long id ) {
+        ArrayDesign arrayDesign = arrayDesignService.loadOrFail( id,
+                EntityNotFoundException::new, "No platform was found for ID " + id + "." );
         ModelAndView mav = new ModelAndView( "compositeSequences.geneMap" );
 
         if ( !AJAX ) {
             Collection<CompositeSequenceMapValueObject> compositeSequenceSummary = getDesignSummaries( arrayDesign );
-            if ( compositeSequenceSummary == null || compositeSequenceSummary.size() == 0 ) {
-                throw new RuntimeException( "No probes found for " + arrayDesign );
+            if ( compositeSequenceSummary == null || compositeSequenceSummary.isEmpty() ) {
+                throw new EntityNotFoundException( "No probes found for " + arrayDesign );
             }
             mav.addObject( "sequenceData", compositeSequenceSummary );
             mav.addObject( "numCompositeSequences", compositeSequenceSummary.size() );
@@ -588,11 +524,10 @@ public ModelAndView showCompositeSequences( HttpServletRequest request ) {
 
     @Override
     @RequestMapping("/showExpressionExperiments.html")
-    public ModelAndView showExpressionExperiments( HttpServletRequest request ) {
-        Long id = Long.parseLong( request.getParameter( "id" ) );
-
+    public ModelAndView showExpressionExperiments( @RequestParam("id") Long id ) {
         ArrayDesign arrayDesign = arrayDesignService.load( id );
         if ( arrayDesign == null ) {
+            // FIXME: treat this as a 404 instead
             return new ModelAndView( new RedirectView( "/arrays/showAllArrayDesigns.html", true ) )
                     .addObject( "message", "Platform with id=" + id + " not found" );
         }
@@ -699,10 +634,8 @@ public RemoveArrayLocalTask( TaskCommand command ) {
 
         @Override
         public TaskResult call() {
-            ArrayDesign ad = arrayDesignService.load( taskCommand.getEntityId() );
-            if ( ad == null ) {
-                throw new IllegalArgumentException( "Could not load platform with id=" + taskCommand.getEntityId() );
-            }
+            ArrayDesign ad = arrayDesignService.loadOrFail( taskCommand.getEntityId(),
+                    EntityNotFoundException::new, "Could not load platform with id=" + taskCommand.getEntityId() );
             arrayDesignService.remove( ad );
             return new TaskResult( taskCommand,
                     new ModelAndView( new RedirectView( "/arrays/showAllArrayDesigns.html", true ) )
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignFormController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignFormController.java
index 467f970907..4b27e9fa17 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignFormController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignFormController.java
@@ -1,8 +1,8 @@
 /*
  * 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
@@ -110,7 +110,7 @@ protected Object formBackingObject( HttpServletRequest request ) {
             try {
                 id = Long.parseLong( idString );
             } catch ( NumberFormatException e ) {
-                throw new IllegalArgumentException();
+                throw new IllegalArgumentException( "Invalid ID for platform.", e );
             }
             Collection<Long> ids = new HashSet<Long>();
             ids.add( id );
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/bioAssay/BioAssayController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/bioAssay/BioAssayController.java
index d058805422..ca296406fd 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/bioAssay/BioAssayController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/bioAssay/BioAssayController.java
@@ -27,8 +27,6 @@
 import org.springframework.web.servlet.ModelAndView;
 import ubic.gemma.core.analysis.preprocess.OutlierDetails;
 import ubic.gemma.core.analysis.preprocess.OutlierDetectionService;
-import ubic.gemma.core.analysis.preprocess.filter.FilteringException;
-import ubic.gemma.core.analysis.preprocess.filter.NoRowsLeftAfterFilteringException;
 import ubic.gemma.core.job.executor.webapp.TaskRunningService;
 import ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand;
 import ubic.gemma.model.expression.bioAssay.BioAssay;
@@ -70,12 +68,9 @@ public class BioAssayController {
     private OutlierDetectionService outlierDetectionService;
 
     public Collection<BioAssayValueObject> getBioAssays( Long eeId ) {
-        ExpressionExperiment ee = eeService.load( eeId );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Could not load experiment with ID=" + eeId );
-        }
+        ExpressionExperiment ee = eeService.loadAndThawLiteOrFail( eeId,
+                EntityNotFoundException::new, "Could not load experiment with ID=" + eeId );
 
-        ee = this.eeService.thawLite( ee );
         Collection<BioAssayValueObject> result = new HashSet<>();
         Collection<OutlierDetails> outliers = outlierDetectionService.getOutlierDetails( ee );
 
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/AnnotationController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/AnnotationController.java
index b7ef204d2c..12890d3eb6 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/AnnotationController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/AnnotationController.java
@@ -37,6 +37,7 @@
 import ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
 import ubic.gemma.persistence.service.genome.taxon.TaxonService;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 import java.util.Collection;
 import java.util.HashSet;
@@ -78,10 +79,8 @@ public Collection<OntologyTerm> getCategoryTerms() {
     }
 
     public void createBiomaterialTag( Characteristic vc, Long id ) {
-        BioMaterial bm = bioMaterialService.load( id );
-        if ( bm == null ) {
-            throw new IllegalArgumentException( "No such BioMaterial with id=" + id );
-        }
+        BioMaterial bm = bioMaterialService.loadOrFail( id,
+                EntityNotFoundException::new, "No such BioMaterial with id=" + id );
         bm = bioMaterialService.thaw( bm );
         ontologyService.saveBioMaterialStatement( vc, bm );
     }
@@ -93,11 +92,8 @@ public void createBiomaterialTag( Characteristic vc, Long id ) {
      * @param id of the expression experiment
      */
     public void createExperimentTag( Characteristic vc, Long id ) {
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "No such experiment with id=" + id );
-        }
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, "No such experiment with id=" + id );
         ontologyService.addExpressionExperimentStatement( vc, ee );
         expressionExperimentService.update( ee );
     }
@@ -149,10 +145,7 @@ public void reinitializeOntologyIndices() {
     }
 
     public void removeBiomaterialTag( Characteristic vc, Long id ) {
-        BioMaterial bm = bioMaterialService.load( id );
-        if ( bm == null ) {
-            throw new IllegalArgumentException( "No such BioMaterial with id=" + id );
-        }
+        BioMaterial bm = bioMaterialService.loadOrFail( id, EntityNotFoundException::new, "No such BioMaterial with id=" + id );
         bm = bioMaterialService.thaw( bm );
         ontologyService.removeBioMaterialStatement( vc.getId(), bm );
     }
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/DEDVController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/DEDVController.java
index 5c145d31ba..f52afba6ec 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/DEDVController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/DEDVController.java
@@ -409,7 +409,7 @@ public VisualizationValueObject[] getDEDVForDiffExVisualizationByThreshold( Long
             Double givenThreshold ) {
 
         if ( resultSetId == null ) {
-            throw new IllegalArgumentException( "Results    etId cannot be null" );
+            throw new IllegalArgumentException( "The resultSetId parameter cannot be null" );
         }
 
         double threshold = DEFAULT_THRESHOLD;
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExperimentalDesignControllerImpl.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExperimentalDesignControllerImpl.java
index 1213b18fbf..2b8a08788a 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExperimentalDesignControllerImpl.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExperimentalDesignControllerImpl.java
@@ -29,7 +29,6 @@
 import ubic.gemma.core.analysis.report.ExpressionExperimentReportService;
 import ubic.gemma.core.expression.experiment.FactorValueDeletion;
 import ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporter;
-import ubic.gemma.web.util.AnchorTagUtil;
 import ubic.gemma.model.association.GOEvidenceCode;
 import ubic.gemma.model.common.auditAndSecurity.eventType.ExperimentalDesignUpdatedEvent;
 import ubic.gemma.model.common.description.Characteristic;
@@ -48,6 +47,7 @@
 import ubic.gemma.persistence.util.EntityUtils;
 import ubic.gemma.web.controller.BaseController;
 import ubic.gemma.web.remote.EntityDelegator;
+import ubic.gemma.web.util.AnchorTagUtil;
 import ubic.gemma.web.util.EntityNotFoundException;
 
 import javax.servlet.http.HttpServletRequest;
@@ -94,16 +94,11 @@ public class ExperimentalDesignControllerImpl extends BaseController implements
 
     @Override
     public void createDesignFromFile( Long eeid, String filePath ) {
-        ExpressionExperiment ee = expressionExperimentService.loadOrFail( eeid );
-        ee = expressionExperimentService.thaw( ee );
-
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Could not access experiment with id=" + eeid );
-        }
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawOrFail( eeid,
+                EntityNotFoundException::new, "Could not access experiment with id=" + eeid );
 
-        if ( ee.getExperimentalDesign().getExperimentalFactors().size() > 0 ) {
-            throw new IllegalArgumentException(
-                    "Cannot import an experimental design for an experiment that already has design data populated." );
+        if ( !ee.getExperimentalDesign().getExperimentalFactors().isEmpty() ) {
+            throw new IllegalArgumentException( "Cannot import an experimental design for an experiment that already has design data populated." );
         }
 
         File f = new File( filePath );
@@ -177,8 +172,7 @@ public void createFactorValue( EntityDelegator e ) {
         }
         if ( chars.isEmpty() ) {
             if ( ef.getCategory() == null ) {
-                throw new IllegalArgumentException(
-                        "You cannot create new factor values on a experimental factor that is not defined by a formal Category" );
+                throw new IllegalArgumentException( "You cannot create new factor values on a experimental factor that is not defined by a formal Category" );
             }
             chars.add( this.createTemplateCharacteristic( ef.getCategory() ) );
         }
@@ -622,8 +616,7 @@ public void updateExperimentalFactors( ExperimentalFactorValueObject[] efvos ) {
                 if ( ef.getFactorValues().isEmpty() ) {
                     ef.setType( newType );
                 } else {
-                    throw new IllegalArgumentException(
-                            "You cannot change the 'type' of a factor once it has factor values. Delete the factor values first." );
+                    throw new IllegalArgumentException( "You cannot change the 'type' of a factor once it has factor values. Delete the factor values first." );
                 }
             }
 
@@ -649,7 +642,7 @@ public void updateExperimentalFactors( ExperimentalFactorValueObject[] efvos ) {
         ExperimentalFactor ef = experimentalFactorService.loadOrFail( efvos[0].getId() );
         ExpressionExperiment ee = expressionExperimentService.findByFactor( ef );
         if ( ee == null )
-            throw new IllegalArgumentException( "No experiment for factor: " + ef );
+            throw new EntityNotFoundException( "No experiment for factor: " + ef );
         this.experimentReportService.evictFromCache( ee.getId() );
     }
 
@@ -667,10 +660,7 @@ public void updateFactorValueCharacteristics( FactorValueValueObject[] fvvos ) {
                 throw new IllegalArgumentException( "Factor value id must be supplied" );
             }
 
-            FactorValue fv = this.factorValueService.load( fvID );
-            if ( fv == null ) {
-                throw new IllegalArgumentException( "Could not load factorvalue with id=" + fvID );
-            }
+            FactorValue fv = this.factorValueService.loadOrFail( fvID, EntityNotFoundException::new, "Could not load factorvalue with id=" + fvID );
 
             if ( !securityService.isEditable( fv ) ) {
                 /*
@@ -696,8 +686,7 @@ public void updateFactorValueCharacteristics( FactorValueValueObject[] fvvos ) {
                 }
 
                 if ( !fv.getCharacteristics().contains( c ) ) {
-                    throw new IllegalArgumentException(
-                            "Characteristic with id=" + charId + " does not belong to factorvalue with id=" + fvID );
+                    throw new IllegalArgumentException( "Characteristic with id=" + charId + " does not belong to factorvalue with id=" + fvID );
                 }
 
             } else {
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentController.java
index 02ad9ba168..c6ce82e0d4 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentController.java
@@ -25,9 +25,11 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.i18n.LocaleContextHolder;
 import org.springframework.security.access.AccessDeniedException;
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.view.RedirectView;
 import ubic.gemma.core.analysis.preprocess.MeanVarianceService;
@@ -88,6 +90,7 @@
 import javax.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.text.DateFormat;
+import java.text.NumberFormat;
 import java.util.*;
 import java.util.concurrent.TimeUnit;
 
@@ -209,9 +212,10 @@ public JsonReaderResponse<ExpressionExperimentDetailsValueObject> browseSpecific
      * AJAX returns a JSON string encoding whether the current user owns the experiment and whether they can edit it
      */
     public boolean canCurrentUserEditExperiment( Long eeId ) {
+        ExpressionExperiment ee = getExperimentById( eeId, false );
         boolean userCanEditGroup;
         try {
-            userCanEditGroup = securityService.isEditable( expressionExperimentService.load( eeId ) );
+            userCanEditGroup = securityService.isEditable( ee );
         } catch ( org.springframework.security.access.AccessDeniedException ade ) {
             return false;
         }
@@ -239,9 +243,10 @@ public String deleteById( Long id ) {
      * AJAX returns a JSON string encoding whether the current user owns the experiment and whether they can edit it
      */
     public boolean doesCurrentUserOwnExperiment( Long eeId ) {
+        ExpressionExperiment ee = getExperimentById( eeId, false );
         boolean userOwnsGroup;
         try {
-            userOwnsGroup = securityService.isOwnedByCurrentUser( expressionExperimentService.load( eeId ) );
+            userOwnsGroup = securityService.isOwnedByCurrentUser( ee );
         } catch ( org.springframework.security.access.AccessDeniedException ade ) {
             return false;
         }
@@ -325,31 +330,25 @@ public Collection<AnnotationValueObject> getAnnotation( EntityDelegator e ) {
      *         expander)
      */
     public String getDescription( Long id ) {
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null ) return null;
-
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = getExperimentById( id, true );
 
         Collection<ExperimentalFactor> efs = ee.getExperimentalDesign().getExperimentalFactors();
 
         StringBuilder descriptive = new StringBuilder();
 
-        String eeDescription = ee.getDescription() == null ? "" : ee.getDescription().trim();
-
-        // Need to trim?
-        if ( eeDescription.length() < ExpressionExperimentController.TRIM_SIZE + 1 )
-            descriptive.append( eeDescription );
-        else
-            descriptive.append( eeDescription.substring( 0, ExpressionExperimentController.TRIM_SIZE ) ).append( "...&nbsp;&nbsp;" );
+        if ( ee.getDescription() != null ) {
+            descriptive.append( StringUtils.abbreviate( StringUtils.strip( ee.getDescription() ), "…",
+                    ExpressionExperimentController.TRIM_SIZE ) );
+        }
 
         // Is there any factor info to add?
-        if ( efs.size() < 1 ) return descriptive.append( "</br><b>(No Factors)</b>" ).toString();
+        if ( efs.isEmpty() ) return descriptive.append( "</br><b>(No Factors)</b>" ).toString();
 
         String efUri = "&nbsp;<a target='_blank' href='" + servletContext.getContextPath()
                 + "/experimentalDesign/showExperimentalDesign.html?eeid=" + ee.getId() + "'>(details)</a >";
         int MAX_TAGS_TO_SHOW = 15;
         Collection<Characteristic> tags = ee.getCharacteristics();
-        if ( tags.size() > 0 ) {
+        if ( !tags.isEmpty() ) {
             descriptive.append( "</br>&nbsp;<b>Tags:</b>&nbsp;" );
             int i = 0;
             for ( Characteristic tag : tags ) {
@@ -378,12 +377,10 @@ public String getDescription( Long id ) {
      * AJAX
      */
     public Collection<DesignMatrixRowValueObject> getDesignMatrixRows( EntityDelegator e ) {
-
-        if ( e == null || e.getId() == null ) return null;
-        ExpressionExperiment ee = this.expressionExperimentService.load( e.getId() );
-        if ( ee == null ) return null;
-
-        ee = expressionExperimentService.thawLite( ee );
+        if ( e == null || e.getId() == null ) {
+            throw new IllegalArgumentException( "A non-null experiment ID must be supplied." );
+        }
+        ExpressionExperiment ee = getExperimentById( e.getId(), true );
         return DesignMatrixRowValueObject.Factory.getDesignMatrix( ee, true ); // ignore "batch"
     }
 
@@ -393,10 +390,11 @@ public Collection<DesignMatrixRowValueObject> getDesignMatrixRows( EntityDelegat
      * @return a collection of factor value objects that represent the factors of a given experiment
      */
     public Collection<ExperimentalFactorValueObject> getExperimentalFactors( EntityDelegator e ) {
+        if ( e == null || e.getId() == null ) {
+            throw new IllegalArgumentException( "A non-null experiment ID must be supplied." );
+        }
 
-        if ( e == null || e.getId() == null ) return null;
-
-        ExpressionExperiment ee = this.expressionExperimentService.loadOrFail( e.getId() );
+        ExpressionExperiment ee = getExperimentById( e.getId(), false );
 
         Collection<ExperimentalFactorValueObject> result = new HashSet<>();
 
@@ -416,11 +414,11 @@ public Collection<ExperimentalFactorValueObject> getExperimentalFactors( EntityD
      * @return A collection of factor value objects for the specified experimental factor
      */
     public Collection<FactorValueValueObject> getFactorValues( EntityDelegator e ) {
+        if ( e == null || e.getId() == null ) {
+            throw new IllegalArgumentException( "A non-null ExperimentalFactor ID must be supplied." );
+        }
 
-        if ( e == null || e.getId() == null ) return null;
-
-        ExperimentalFactor ef = this.experimentalFactorService.load( e.getId() );
-        if ( ef == null ) return null;
+        ExperimentalFactor ef = this.experimentalFactorService.loadOrFail( e.getId(), EntityNotFoundException::new, "ExperimentalFactor with ID " + e.getId() + " does not exist." );
 
         Collection<FactorValueValueObject> result = new HashSet<>();
 
@@ -451,10 +449,8 @@ public String getQCTagHTML( ExpressionExperiment ee ) {
         qc.setNumOutliersRemoved( this.numOutliersRemoved( ee ) );
         try {
             qc.setNumPossibleOutliers( this.numPossibleOutliers( ee ) );
-        } catch ( java.lang.ArrayIndexOutOfBoundsException e ) {
-            ExpressionExperimentController.log.error( e );
-        } catch ( IllegalStateException e ) {
-            ExpressionExperimentController.log.error( e );
+        } catch ( ArrayIndexOutOfBoundsException | IllegalStateException e ) {
+            ExpressionExperimentController.log.error( "Error while setting the number of possible outliers for " + ee + ".", e );
         }
         return qc.getQChtml();
     }
@@ -471,12 +467,12 @@ public Map<String, Object> loadCountsForDataSummaryTable() {
         StopWatch reportTimer = StopWatch.create();
 
         Map<String, Object> summary = new HashMap<>();
-        List<Map<String, Object>> taxonEntries = new ArrayList();
+        List<Map<String, Object>> taxonEntries = new ArrayList<>();
 
         countTimer.start();
-        long bioMaterialCount = bioMaterialService.countAll();
-        long arrayDesignCount = arrayDesignService.countAll();
-        long expressionExperimentCount = expressionExperimentService.countAll();
+        long bioMaterialCount = expressionExperimentService.countBioMaterials( null );
+        long arrayDesignCount = arrayDesignService.countWithCache( null );
+        long expressionExperimentCount = expressionExperimentService.countWithCache( null );
         Map<Taxon, Long> eesPerTaxon = expressionExperimentService.getPerTaxonCount();
         countTimer.stop();
 
@@ -490,7 +486,7 @@ public Map<String, Object> loadCountsForDataSummaryTable() {
         reportTimer.stop();
 
         // Get count for new assays
-        int newBioMaterialCount = wn.getNewBioMaterialCount();
+        long newBioMaterialCount = wn.getNewBioMaterialCount();
 
         Collection<ExpressionExperiment> newExpressionExperiments = wn.getNewExpressionExperiments();
         Collection<Long> newExpressionExperimentIds = ( newExpressionExperiments != null ) ? EntityUtils.getIds( newExpressionExperiments ) : new ArrayList<>();
@@ -504,17 +500,20 @@ public Map<String, Object> loadCountsForDataSummaryTable() {
         Map<Taxon, Collection<Long>> newEEsPerTaxon = wn.getNewEEIdsPerTaxon();
         Map<Taxon, Collection<Long>> updatedEEsPerTaxon = wn.getUpdatedEEIdsPerTaxon();
 
+        Locale locale = LocaleContextHolder.getLocale();
+        NumberFormat integerFormat = NumberFormat.getIntegerInstance( locale );
+
         for ( Taxon t : eesPerTaxon.keySet() ) {
             Map<String, Object> taxLine = new HashMap<>();
             taxLine.put( "taxonId", t.getId() );
             taxLine.put( "taxonName", t.getScientificName() );
-            taxLine.put( "totalCount", eesPerTaxon.get( t ) );
+            taxLine.put( "totalCount", integerFormat.format( eesPerTaxon.get( t ) ) );
             if ( newEEsPerTaxon.containsKey( t ) ) {
-                taxLine.put( "newCount", newEEsPerTaxon.get( t ).size() );
+                taxLine.put( "newCount", integerFormat.format( newEEsPerTaxon.get( t ).size() ) );
                 taxLine.put( "newIds", newEEsPerTaxon.get( t ) );
             }
             if ( updatedEEsPerTaxon.containsKey( t ) ) {
-                taxLine.put( "updatedCount", updatedEEsPerTaxon.get( t ).size() );
+                taxLine.put( "updatedCount", integerFormat.format( updatedEEsPerTaxon.get( t ).size() ) );
                 taxLine.put( "updatedIds", updatedEEsPerTaxon.get( t ) );
             }
             taxonEntries.add( taxLine );
@@ -536,22 +535,24 @@ public Map<String, Object> loadCountsForDataSummaryTable() {
         summary.put( "updateDate", date );
         summary.put( "drawNewColumn", drawNewColumn );
         summary.put( "drawUpdatedColumn", drawUpdatedColumn );
-        if ( newBioMaterialCount != 0 ) summary.put( "newBioMaterialCount", ( long ) newBioMaterialCount );
-        if ( newArrayCount != 0 ) summary.put( "newArrayDesignCount", ( long ) newArrayCount );
-        if ( updatedArrayCount != 0 ) summary.put( "updatedArrayDesignCount", ( long ) updatedArrayCount );
+        if ( newBioMaterialCount != 0 )
+            summary.put( "newBioMaterialCount", integerFormat.format( newBioMaterialCount ) );
+        if ( newArrayCount != 0 ) summary.put( "newArrayDesignCount", integerFormat.format( newArrayCount ) );
+        if ( updatedArrayCount != 0 )
+            summary.put( "updatedArrayDesignCount", integerFormat.format( updatedArrayCount ) );
         if ( newExpressionExperimentCount != 0 )
-            summary.put( "newExpressionExperimentCount", newExpressionExperimentCount );
+            summary.put( "newExpressionExperimentCount", integerFormat.format( newExpressionExperimentCount ) );
         if ( updatedExpressionExperimentCount != 0 )
-            summary.put( "updatedExpressionExperimentCount", updatedExpressionExperimentCount );
+            summary.put( "updatedExpressionExperimentCount", integerFormat.format( updatedExpressionExperimentCount ) );
         if ( newExpressionExperimentCount != 0 )
             summary.put( "newExpressionExperimentIds", newExpressionExperimentIds );
         if ( updatedExpressionExperimentCount != 0 )
             summary.put( "updatedExpressionExperimentIds", updatedExpressionExperimentIds );
 
-        summary.put( "bioMaterialCount", bioMaterialCount );
-        summary.put( "arrayDesignCount", arrayDesignCount );
+        summary.put( "bioMaterialCount", integerFormat.format( bioMaterialCount ) );
+        summary.put( "arrayDesignCount", integerFormat.format( arrayDesignCount ) );
 
-        summary.put( "expressionExperimentCount", expressionExperimentCount );
+        summary.put( "expressionExperimentCount", integerFormat.format( expressionExperimentCount ) );
 
         if ( sw.getTime( TimeUnit.MILLISECONDS ) > 1000 ) {
             log.info( "Retrieving EE summary took " + sw.getTime( TimeUnit.MILLISECONDS ) + " ms (" + "counting: " + countTimer.getTime() + " ms, " + "report: " + reportTimer.getTime() + " ms)." );
@@ -567,12 +568,15 @@ public Map<String, Object> loadCountsForDataSummaryTable() {
      * @return ee details vo
      */
     public ExpressionExperimentDetailsValueObject loadExpressionExperimentDetails( Long id ) {
-
-        ExpressionExperiment ee = this.getEESafely( id );
+        ExpressionExperiment ee = getExperimentById( id, false );
+        ee = expressionExperimentService.thawLiter( ee );
+        if ( ee == null ) {
+            throw new EntityNotFoundException( "No experiment with ID " + id + "." );
+        }
         Collection<ExpressionExperimentDetailsValueObject> initialResults = expressionExperimentService.loadDetailsValueObjectsByIdsWithCache( Collections.singleton( id ) );
 
-        if ( initialResults.size() == 0 ) {
-            return null;
+        if ( initialResults.isEmpty() ) {
+            throw new EntityNotFoundException( "No experiment with ID " + id + "." );
         }
 
         expressionExperimentReportService.populateReportInformation( initialResults );
@@ -603,19 +607,19 @@ public ExpressionExperimentDetailsValueObject loadExpressionExperimentDetails( L
     }
 
     public void recalculateBatchConfound( Long id ) {
-        ExpressionExperiment ee = expressionExperimentService.loadOrFail( id );
+        ExpressionExperiment ee = getExperimentById( id, false );
         ee.setBatchConfound( expressionExperimentService.getBatchConfound( ee ) );
         expressionExperimentService.update( ee );
     }
 
     public void recalculateBatchEffect( Long id ) {
-        ExpressionExperiment ee = expressionExperimentService.loadOrFail( id );
+        ExpressionExperiment ee = getExperimentById( id, false );
         ee.setBatchEffect( expressionExperimentService.getBatchEffect( ee ) );
         expressionExperimentService.update( ee );
     }
 
     public void runGeeq( Long id, String mode ) {
-        ExpressionExperiment ee = expressionExperimentService.loadOrFail( id );
+        ExpressionExperiment ee = getExperimentById( id, false );
         geeqService.calculateScore( ee, GeeqService.ScoreMode.valueOf( mode ) );
     }
 
@@ -639,7 +643,7 @@ public Collection<ExpressionExperimentDetailsValueObject> loadExpressionExperime
      * @return collection of experiments that use this platform -- including those that were switched
      */
     public Collection<ExpressionExperimentDetailsValueObject> loadExperimentsForPlatform( Long id ) {
-        ArrayDesign ad = arrayDesignService.loadOrFail( id );
+        ArrayDesign ad = arrayDesignService.loadOrFail( id, EntityNotFoundException::new, "No platform with ID " + id + "." );
 
         Collection<ExpressionExperimentDetailsValueObject> switchedExperiments = getFilteredExpressionExperimentValueObjects( null,
                 EntityUtils.getIds( arrayDesignService.getSwitchedExperiments( ad ) ), 0, true );
@@ -680,15 +684,14 @@ public JsonReaderResponse<Map<String, Object>> loadExpressionExperimentsWithQcIs
 
         Collection<ExpressionExperiment> outlierEEs = expressionExperimentService.getExperimentsWithOutliers();
 
-        Collection<ExpressionExperiment> ees = new HashSet<>();
-        ees.addAll( outlierEEs );
-        // ees.addAll( batchEffectEEs );
+        Collection<ExpressionExperiment> ees = new HashSet<>( outlierEEs );
+        // TODO: ees.addAll( batchEffectEEs );
 
         List<Map<String, Object>> jsonRecords = new ArrayList<>();
 
         for ( ExpressionExperiment ee : ees ) {
             //noinspection MismatchedQueryAndUpdateOfCollection
-            Map<String, Object> record = new HashMap();
+            Map<String, Object> record = new HashMap<>();
             record.put( "id", ee.getId() );
             record.put( "shortName", ee.getShortName() );
             record.put( "name", ee.getName() );
@@ -712,11 +715,8 @@ public JsonReaderResponse<Map<String, Object>> loadExpressionExperimentsWithQcIs
      * @return security-filtered set of value objects.
      */
     public Collection<QuantitationTypeValueObject> loadQuantitationTypes( Long eeId ) {
-
-        ExpressionExperiment ee = expressionExperimentService.loadOrFail( eeId );
         // need to thawRawAndProcessed?
-        ee = expressionExperimentService.thawLite( ee );
-
+        ExpressionExperiment ee = getExperimentById( eeId, true );
         return expressionExperimentService.getQuantitationTypeValueObjects( ee );
     }
 
@@ -800,7 +800,6 @@ public String removePrimaryPublication( Long eeId ) {
      */
     public List<SearchResultDisplayObject> searchExperimentsAndExperimentGroups( String query, Long taxonId ) {
         boolean taxonLimited = ( taxonId != null );
-        List<SearchResultDisplayObject> displayResults = new ArrayList<>();
 
         // add session bound sets
         // get any session-bound groups
@@ -809,7 +808,7 @@ public List<SearchResultDisplayObject> searchExperimentsAndExperimentGroups( Str
         List<SearchResultDisplayObject> sessionSets = new ArrayList<>();
 
         // create SearchResultDisplayObjects
-        if ( sessionResult != null && sessionResult.size() > 0 ) {
+        if ( sessionResult != null && !sessionResult.isEmpty() ) {
             for ( SessionBoundExpressionExperimentSetValueObject eevo : sessionResult ) {
                 SearchResultDisplayObject srdo = new SearchResultDisplayObject( eevo );
                 srdo.setUserOwned( true );
@@ -819,7 +818,7 @@ public List<SearchResultDisplayObject> searchExperimentsAndExperimentGroups( Str
 
         // keep sets in proper order (session-bound groups first)
         Collections.sort( sessionSets );
-        displayResults.addAll( sessionSets );
+        List<SearchResultDisplayObject> displayResults = new ArrayList<>( sessionSets );
         try {
             displayResults.addAll( expressionExperimentSearchService.searchExperimentsAndExperimentGroups( query, taxonId ) );
         } catch ( SearchException e ) {
@@ -867,46 +866,17 @@ public ModelAndView showAllLinkSummaries( HttpServletRequest request, HttpServle
     }
 
     @RequestMapping(value = { "/showBioAssaysFromExpressionExperiment.html", "/bioAssays" })
-    public ModelAndView showBioAssays( HttpServletRequest request, HttpServletResponse response ) {
-        String idStr = request.getParameter( "id" );
-
-        if ( idStr == null ) {
-            // should be a validation error, on 'submit'.
-            throw new EntityNotFoundException( identifierNotFound );
-        }
-        Long id = Long.parseLong( idStr );
-
-        ExpressionExperiment expressionExperiment = expressionExperimentService.loadOrFail( id );
-
-        expressionExperiment = expressionExperimentService.thawLite( expressionExperiment );
-
-        if ( expressionExperiment == null ) {
-            throw new EntityNotFoundException( id + " not found" );
-        }
-        request.setAttribute( "id", id );
+    public ModelAndView showBioAssays( @RequestParam("id") Long id ) {
+        ExpressionExperiment expressionExperiment = getExperimentById( id, true );
         ModelAndView mv = new ModelAndView( "bioAssays" ).addObject( "bioAssays", bioAssayService.thaw( expressionExperiment.getBioAssays() ) );
-
         this.addQCInfo( expressionExperiment, mv );
         mv.addObject( "expressionExperiment", expressionExperiment );
         return mv;
     }
 
     @RequestMapping(value = { "/showBioMaterialsFromExpressionExperiment.html", "/bioMaterials" })
-    public ModelAndView showBioMaterials( HttpServletRequest request, HttpServletResponse response ) {
-        String idStr = request.getParameter( "id" );
-
-        if ( idStr == null ) {
-            // should be a validation error, on 'submit'.
-            throw new EntityNotFoundException( identifierNotFound );
-        }
-        Long id = Long.parseLong( idStr );
-
-        ExpressionExperiment expressionExperiment = expressionExperimentService.loadOrFail( id );
-        expressionExperiment = expressionExperimentService.thawLite( expressionExperiment );
-
-        if ( expressionExperiment == null ) {
-            throw new EntityNotFoundException( id + " not found" );
-        }
+    public ModelAndView showBioMaterials( @RequestParam("id") Long id ) {
+        ExpressionExperiment expressionExperiment = getExperimentById( id, true );
 
         Collection<BioAssay> bioAssays = expressionExperiment.getBioAssays();
         Collection<BioMaterial> bioMaterials = new ArrayList<>();
@@ -931,25 +901,30 @@ public ModelAndView showBioMaterials( HttpServletRequest request, HttpServletRes
         return mav;
     }
 
-    @RequestMapping({ "/showExpressionExperiment.html", "/", "/show" })
-    public ModelAndView showExpressionExperiment( HttpServletRequest request, HttpServletResponse response ) {
-
-        StopWatch timer = new StopWatch();
-        timer.start();
-
-        ModelAndView mav = new ModelAndView( "expressionExperiment.detail" );
-        BioAssaySet expExp = this.getExpressionExperimentFromRequest( request );
-
-        mav.addObject( "expressionExperiment", expExp );
-
-        mav.addObject( "eeId", expExp.getId() );
-        mav.addObject( "eeClass", ExpressionExperiment.class.getName() );
+    @RequestMapping(value = { "/showExpressionExperiment.html", "/", "/show" }, params = { "id" })
+    public ModelAndView showExpressionExperiment( @RequestParam(value = "id") Long id ) {
+        BioAssaySet bioAssaySet;
+        bioAssaySet = expressionExperimentService.loadBioAssaySet( id );
+        if ( bioAssaySet == null ) {
+            throw new EntityNotFoundException( "No experiment with ID " + id + "." );
+        }
+        return showBioAssaySet( bioAssaySet );
+    }
 
-        if ( timer.getTime() > 200 ) {
-            ExpressionExperimentController.log.info( "Show Experiment was slow: id=" + expExp.getId() + " " + timer.getTime() + "ms" );
+    @RequestMapping(value = { "/showExpressionExperiment.html", "/", "/show" }, params = { "shortName" })
+    public ModelAndView showExpressionExperimentByShortName( @RequestParam(value = "shortName") String shortName ) {
+        ExpressionExperiment experimentExperiment = expressionExperimentService.findByShortName( shortName );
+        if ( experimentExperiment == null ) {
+            throw new EntityNotFoundException( "No experiment with short name " + shortName + "." );
         }
+        return showBioAssaySet( experimentExperiment );
+    }
 
-        return mav;
+    private ModelAndView showBioAssaySet( BioAssaySet ee ) {
+        return new ModelAndView( "expressionExperiment.detail" )
+                .addObject( "expressionExperiment", ee )
+                .addObject( "eeId", ee.getId() )
+                .addObject( "eeClass", ee.getClass() );
     }
 
     /**
@@ -973,18 +948,14 @@ public ModelAndView showSubSet( HttpServletRequest request, HttpServletResponse
     }
 
     /**
-     * Completely reset the pairing of bioassays to biomaterials so they are no longer paired. New biomaterials are
+     * Completely reset the pairing of bioassays to biomaterials, so they are no longer paired. New biomaterials are
      * constructed where necessary; they retain the characteristics of the original. Experimental design might need to
      * be redone after this operation. (AJAX)
      *
      * @param eeId ee id
      */
     public void unmatchAllBioAssays( Long eeId ) {
-        ExpressionExperiment ee = this.expressionExperimentService.load( eeId );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Could not load experiment with id=" + eeId );
-        }
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = getExperimentById( eeId, true );
 
         Collection<BioMaterial> needToProcess = new HashSet<>();
 
@@ -1020,20 +991,19 @@ public void unmatchAllBioAssays( Long eeId ) {
 
     }
 
-    public ExpressionExperimentDetailsValueObject updateBasics( UpdateEEDetailsCommand command ) throws Exception {
+    public ExpressionExperimentDetailsValueObject updateBasics( UpdateEEDetailsCommand command ) {
         if ( command.getEntityId() == null ) {
             throw new IllegalArgumentException( "Id cannot be null" );
         }
 
         /*
-         * This should be fast so I'm not using a background task.
+         * This should be fast, so I'm not using a background task.
          */
         String details = "Changed: ";
         boolean changed = false;
         Long entityId = command.getEntityId();
-        ExpressionExperiment ee = expressionExperimentService.load( entityId );
-        if ( ee == null )
-            throw new IllegalArgumentException( "Cannot locate or access experiment with id=" + entityId );
+        ExpressionExperiment ee = expressionExperimentService.loadOrFail( entityId,
+                EntityNotFoundException::new, "Cannot locate or access experiment with id=" + entityId );
 
         if ( StringUtils.isNotBlank( command.getShortName() ) && !command.getShortName().equals( ee.getShortName() ) ) {
             if ( expressionExperimentService.findByShortName( command.getShortName() ) != null ) {
@@ -1102,7 +1072,7 @@ public ModelAndView handleRequestInternal( HttpServletRequest request ) {
         String eeSetName = request.getParameter( "esn" ); // might not be there
 
         ModelAndView mav = new ModelAndView( new TextView() );
-        if ( ( eeIds == null || eeIds.isEmpty() ) && ( eeSetIds == null || eeSetIds.isEmpty() ) ) {
+        if ( eeIds.isEmpty() && eeSetIds.isEmpty() ) {
             mav.addObject( TextView.TEXT_PARAM, "Could not find genes to match expression experiment ids: {" + eeIds + "} or expression experiment set ids {" + eeSetIds + "}" );
             return mav;
         }
@@ -1115,7 +1085,7 @@ public ModelAndView handleRequestInternal( HttpServletRequest request ) {
 
         mav.addObject( TextView.TEXT_PARAM, this.format4File( ees, eeSetName ) );
         watch.stop();
-        Long time = watch.getTime();
+        long time = watch.getTime();
 
         if ( time > 100 ) {
             ExpressionExperimentController.log.info( "Retrieved and Formated" + ees.size() + " genes in : " + time + " ms." );
@@ -1189,7 +1159,6 @@ private int numOutliersRemoved( ExpressionExperiment ee ) {
      *
      * @param  ee          ee
      * @param  finalResult result
-     * @return ee details vo
      */
     private void setBatchInfo( ExpressionExperimentDetailsValueObject finalResult, ExpressionExperiment ee ) {
         boolean hasBatchInformation = expressionExperimentService.checkHasBatchInfo( ee );
@@ -1206,7 +1175,6 @@ private void setBatchInfo( ExpressionExperimentDetailsValueObject finalResult, E
      *
      * @param  ee          ee
      * @param  finalResult result
-     * @return ee details vo
      */
     private void setPublicationAndAuthor( ExpressionExperimentDetailsValueObject finalResult, ExpressionExperiment ee ) {
 
@@ -1232,36 +1200,19 @@ private void setPublicationAndAuthor( ExpressionExperimentDetailsValueObject fin
      */
     private Collection<ArrayDesign> getADsSafely( ExpressionExperiment ee ) {
         Collection<ArrayDesign> ads = expressionExperimentService.getArrayDesignsUsed( ee );
-        if ( ads == null ) {
-            throw new IllegalArgumentException( "No array designs for experiment " + ee.getId() + " could be loaded." );
+        if ( ads.isEmpty() ) {
+            throw new EntityNotFoundException( "No array designs for experiment " + ee.getId() + " could be loaded." );
         }
         ads = arrayDesignService.thawLite( ads );
 
         return ads;
     }
 
-    /**
-     * Loads, checks not null, and thaws the ee with given ID;
-     *
-     * @param  id id
-     * @return ee
-     */
-    private ExpressionExperiment getEESafely( Long id ) {
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "No experiment with id=" + id + " could be loaded" );
-        }
-        ee = expressionExperimentService.thawLiter( ee );
-
-        return ee;
-    }
-
     /**
      * Checks and sets multiple technology types and RNA-seq status
      *
      * @param  ee          ee
      * @param  finalResult result
-     * @return ee details vo
      */
     private void setTechTypeInfo( ExpressionExperimentDetailsValueObject finalResult, ExpressionExperiment ee ) {
         Collection<TechnologyType> techTypes = new HashSet<>();
@@ -1279,7 +1230,6 @@ private void setTechTypeInfo( ExpressionExperimentDetailsValueObject finalResult
      *
      * @param  ee          ee
      * @param  finalResult result
-     * @return ee details vo
      */
     private void setPreferredAndReprocessed( ExpressionExperimentDetailsValueObject finalResult, ExpressionExperiment ee ) {
 
@@ -1415,7 +1365,7 @@ private String format4File( Collection<ExpressionExperimentValueObject> ees, Str
         strBuff.append( "# Generated by Gemma\n# " ).append( new Date() ).append( "\n" );
         strBuff.append( ExpressionDataFileService.DISCLAIMER + "#\n" );
 
-        if ( eeSetName != null && eeSetName.length() != 0 )
+        if ( eeSetName != null && !eeSetName.isEmpty() )
             strBuff.append( "# Experiment Set: " ).append( eeSetName ).append( "\n" );
         strBuff.append( "# " ).append( ees.size() ).append( ( ees.size() > 1 ) ? " experiments" : " experiment" ).append( "\n#\n" );
 
@@ -1445,7 +1395,7 @@ private Collection<ExpressionExperimentDetailsValueObject> getEEVOsForManager( L
 
         Taxon taxon;
         if ( taxonId != null ) {
-            taxon = taxonService.loadOrFail( taxonId );
+            taxon = taxonService.loadOrFail( taxonId, EntityNotFoundException::new, "No taxon with ID " + taxonId + "." );
         } else {
             taxon = null;
         }
@@ -1460,49 +1410,8 @@ private Collection<ExpressionExperimentDetailsValueObject> getEEVOsForManager( L
         if ( filter != null && filter > 0 ) {
             eeVos = this.applyFilter( eeVos, filter );
         }
-        if ( eeVos.isEmpty() ) {
-            return eeVos;
-        }
 
         return eeVos;
-
-    }
-
-    /**
-     * @param  request                  request
-     * @return bio assay set
-     * @throws IllegalArgumentException if a matching EE can't be loaded
-     */
-    private BioAssaySet getExpressionExperimentFromRequest( HttpServletRequest request ) {
-
-        BioAssaySet expressionExperiment = null;
-        Long id;
-
-        if ( request.getParameter( "id" ) == null ) {
-
-            String shortName = request.getParameter( "shortName" );
-
-            if ( StringUtils.isNotBlank( shortName ) ) {
-                expressionExperiment = expressionExperimentService.findByShortName( shortName );
-            }
-
-            if ( expressionExperiment == null ) {
-                throw new IllegalArgumentException( "Unable to access experiment with shortName=" + shortName );
-            }
-
-        } else {
-            try {
-                id = Long.parseLong( request.getParameter( "id" ) );
-            } catch ( NumberFormatException e ) {
-                throw new IllegalArgumentException( "You must provide a valid numerical identifier" );
-            }
-            expressionExperiment = expressionExperimentService.load( id );
-
-            if ( expressionExperiment == null ) {
-                throw new IllegalArgumentException( "Unable to access experiment with id=" + id );
-            }
-        }
-        return expressionExperiment;
     }
 
     private Collection<ExpressionExperimentSetValueObject> getExpressionExperimentSets( BioAssaySet ee ) {
@@ -1621,12 +1530,7 @@ private List<ExpressionExperimentDetailsValueObject> returnNeedsAttention( Colle
      * @param id id
      */
     private void updateCorrelationMatrixFile( Long id ) {
-        ExpressionExperiment ee;
-        ee = expressionExperimentService.loadOrFail( id );
-        ee = expressionExperimentService.thawLiter( ee );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Unable to access experiment with id=" + id );
-        }
+        ExpressionExperiment ee = getExperimentById( id, true );
         try {
             sampleCoexpressionAnalysisService.compute( ee );
         } catch ( Exception e ) {
@@ -1636,11 +1540,7 @@ private void updateCorrelationMatrixFile( Long id ) {
     }
 
     private void updateMV( Long id ) {
-        ExpressionExperiment expressionExperiment;
-        expressionExperiment = expressionExperimentService.load( id );
-        if ( expressionExperiment == null ) {
-            throw new IllegalArgumentException( "Unable to access experiment with id=" + id );
-        }
+        ExpressionExperiment expressionExperiment = getExperimentById( id, false );
         try {
             meanVarianceService.create( expressionExperiment, true );
         } catch ( Exception e ) {
@@ -1677,9 +1577,7 @@ public RemovePubMed( TaskCommand command ) {
 
         @Override
         public TaskResult call() {
-            ExpressionExperiment ee = expressionExperimentService.loadOrFail( taskCommand.getEntityId() );
-
-            ee = expressionExperimentService.thawLite( ee );
+            ExpressionExperiment ee = getExperimentById( taskCommand.getEntityId(), true );
 
             if ( ee.getPrimaryPublication() == null ) {
                 return new TaskResult( taskCommand, false );
@@ -1706,7 +1604,7 @@ public TaskResult call() {
             Long eeId = taskCommand.getEntityId();
             ExpressionExperiment expressionExperiment = expressionExperimentService.loadWithPrimaryPublication( eeId );
             if ( expressionExperiment == null )
-                throw new IllegalArgumentException( "Cannot access experiment with id=" + eeId );
+                throw new EntityNotFoundException( "Cannot access experiment with id=" + eeId );
 
             String pubmedId = taskCommand.getPubmedId();
             BibliographicReference publication = bibliographicReferenceService.findByExternalId( pubmedId );
@@ -1738,9 +1636,9 @@ public TaskResult call() {
                 }
                 // check to see if there are publications found
                 // if there are none, or more than one, add an error message and do nothing
-                if ( publications.size() == 0 ) {
+                if ( publications.isEmpty() ) {
                     ExpressionExperimentController.log.info( "No matching publication found" );
-                    throw new IllegalArgumentException( "No matching publication found" );
+                    throw new EntityNotFoundException( "No matching publication found" );
                 } else if ( publications.size() > 1 ) {
                     ExpressionExperimentController.log.info( "Multiple matching publications found!" );
                     throw new IllegalArgumentException( "Multiple matching publications found!" );
@@ -1775,4 +1673,16 @@ public TaskResult call() {
 
     }
 
+    /**
+     * Load an {@link ExpressionExperiment} by ID, optionally thawing it with {@link ExpressionExperimentService#thawLite}.
+     */
+    private ExpressionExperiment getExperimentById( Long id, boolean thawLite ) throws EntityNotFoundException {
+        if ( thawLite ) {
+            return this.expressionExperimentService.loadAndThawLiteOrFail( id,
+                    EntityNotFoundException::new, "No experiment with ID " + id + "." );
+        } else {
+            return this.expressionExperimentService.loadOrFail( id,
+                    EntityNotFoundException::new, "No experiment with ID " + id + "." );
+        }
+    }
 }
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentDataFetchController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentDataFetchController.java
index 9dc5b5383d..e1d63dca5d 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentDataFetchController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentDataFetchController.java
@@ -42,13 +42,15 @@
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.util.*;
+import java.util.Collection;
+import java.util.HashSet;
 
 /**
  * For the download of data files from the browser. We can send the 'raw' data for any one quantitation type, with gene
@@ -122,11 +124,8 @@ public void downloadMetaFile( HttpServletRequest request, HttpServletResponse re
      * @return an array of files available in the metadata directory for the given experiment.
      */
     public MetaFile[] getMetadataFiles( Long eeId ) {
-
-        ExpressionExperiment ee = expressionExperimentService.load( eeId );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Experiment with given ID does not exist." );
-        }
+        ExpressionExperiment ee = expressionExperimentService.loadOrFail( eeId,
+                EntityNotFoundException::new, "Experiment with given ID does not exist." );
 
         MetaFile[] metaFiles = new MetaFile[ExpressionExperimentMetaFileType.values().length];
 
@@ -436,8 +435,7 @@ public TaskResult call() {
                     + " milliseconds" );
 
             if ( files.isEmpty() ) {
-                throw new IllegalArgumentException(
-                        "No data available (either due to no analyses being present, lack of authorization, or use of an invalid entity identifier)" );
+                throw new EntityNotFoundException( "No data available (either due to no analyses being present, lack of authorization, or use of an invalid entity identifier)" );
                 // } else if ( files.size() > 1 ) {
                 // throw new UnsupportedOperationException(
                 // "Sorry, you can't get multiple analyses at once using this method." );
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentFormController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentFormController.java
index bff06d4623..46a9f9bc6d 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentFormController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentFormController.java
@@ -45,6 +45,7 @@
 import ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService;
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
 import ubic.gemma.web.controller.BaseFormController;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
@@ -174,12 +175,8 @@ protected Object formBackingObject( HttpServletRequest request ) {
         BaseFormController.log.debug( id );
         ExpressionExperimentEditValueObject obj;
 
-        ExpressionExperiment ee = expressionExperimentService.load( id );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Could not load experiment with id=" + id );
-        }
-
-        ee = expressionExperimentService.thawLite( ee );
+        ExpressionExperiment ee = expressionExperimentService.loadAndThawLiteOrFail( id,
+                EntityNotFoundException::new, String.format( "No experiment with ID %d", id ) );
 
         List<QuantitationTypeValueObject> qts = new ArrayList<>(
                 quantitationTypeService.loadValueObjects( expressionExperimentService.getQuantitationTypes( ee ) ) );
@@ -187,7 +184,7 @@ protected Object formBackingObject( HttpServletRequest request ) {
         ExpressionExperimentValueObject vo = expressionExperimentService.loadValueObject( ee );
 
         if ( vo == null ) {
-            throw new IllegalArgumentException( String.format( "Could load experiment VO with ID %d", id ) );
+            throw new EntityNotFoundException( String.format( "Could load experiment VO with ID %d", id ) );
         }
 
         obj = new ExpressionExperimentEditValueObject( vo );
@@ -234,13 +231,8 @@ public ModelAndView onSubmit( HttpServletRequest request, HttpServletResponse re
             BindException errors ) {
 
         ExpressionExperimentEditValueObject eeCommand = ( ExpressionExperimentEditValueObject ) command;
-        ExpressionExperiment expressionExperiment = expressionExperimentService.load( eeCommand.getId() );
-
-        if ( expressionExperiment == null ) {
-            throw new IllegalArgumentException( "Could not load experiment" );
-        }
-
-        expressionExperiment = expressionExperimentService.thawLite( expressionExperiment );
+        ExpressionExperiment expressionExperiment = expressionExperimentService.loadAndThawLiteOrFail( eeCommand.getId(),
+                EntityNotFoundException::new, String.format( "No experiment with ID %d", eeCommand.getId() ) );
 
         /*
          * Much more complicated
@@ -305,12 +297,10 @@ private boolean updateBioMaterialMap( HttpServletRequest request, ExpressionExpe
                 newMaterialId = bioAssay2BioMaterialMap.getLong( bioAssayKey );
             }
 
-            BioAssay bioAssay = bioAssayService.load( bioAssayId ); // maybe we need to do
-            // this load to avoid stale data?
+            BioAssay bioAssay = bioAssayService.loadOrFail( bioAssayId, EntityNotFoundException::new, "No Bioassay with ID " + bioAssayId ); // maybe we need to do
 
-            if ( bioAssay == null ) {
-                throw new IllegalArgumentException(
-                        "Bioassay with id=" + bioAssayId + " was not associated with the experiment" );
+            if ( !expressionExperiment.getBioAssays().contains( bioAssay ) ) {
+                throw new IllegalArgumentException( "Bioassay with id=" + bioAssayId + " was not associated with the experiment" );
             }
 
             BioMaterial currentBioMaterial = bioAssay.getSampleUsed();
@@ -329,11 +319,8 @@ private boolean updateBioMaterialMap( HttpServletRequest request, ExpressionExpe
                 newBioMaterialCount++;
             } else {
                 // FIXME can we just use this from the experiment, probably no need to fetch it again.
-                newMaterial = bioMaterialService.load( newMaterialId );
-                if ( newMaterial == null ) {
-                    throw new IllegalArgumentException(
-                            "BioMaterial with id=" + newMaterialId + " could not be loaded" );
-                }
+                newMaterial = bioMaterialService.loadOrFail( newMaterialId, EntityNotFoundException::new,
+                        "BioMaterial with id=" + newMaterialId + " could not be loaded" );
             }
             anyChanges = true;
             BaseFormController.log.info( "Associating " + bioAssay + " with " + newMaterial );
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentQCController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentQCController.java
index 47a1cedc18..3eee6a65e9 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentQCController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentQCController.java
@@ -86,6 +86,7 @@
 import ubic.gemma.persistence.util.EntityUtils;
 import ubic.gemma.persistence.util.Settings;
 import ubic.gemma.web.controller.BaseController;
+import ubic.gemma.web.util.EntityNotFoundException;
 import ubic.gemma.web.view.TextView;
 
 import javax.imageio.ImageIO;
@@ -434,10 +435,8 @@ public ModelAndView visualizeProbeCorrDist( Long id, OutputStream os ) throws Ex
     @RequestMapping(value = "/expressionExperiment/visualizePvalueDist.html", produces = "image/png")
     public void visualizePvalueDist( Long id, Long analysisId, Long rsid, String factorName, Integer size,
             OutputStream os ) throws Exception {
-        ExpressionExperiment ee = this.expressionExperimentService.load( id );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Could not load experiment with id " + id );
-        }
+        ExpressionExperiment ee = this.expressionExperimentService.loadOrFail( id, EntityNotFoundException::new,
+                "Could not load experiment with id " + id );
 
         if ( size == null ) {
             if ( !this.writePValueHistImage( os, ee, analysisId, rsid, factorName ) ) {
@@ -452,10 +451,8 @@ public void visualizePvalueDist( Long id, Long analysisId, Long rsid, String fac
 
     @RequestMapping("/expressionExperiment/eigenGenes.html")
     public ModelAndView writeEigenGenes( Long eeid ) throws IOException {
-        ExpressionExperiment ee = expressionExperimentService.load( eeid );
-        if ( ee == null ) {
-            throw new IllegalArgumentException( "Could not load experiment with id " + eeid ); // or access deined.
-        }
+        ExpressionExperiment ee = expressionExperimentService.loadOrFail( eeid,
+                EntityNotFoundException::new, "Could not load experiment with id " + eeid );// or access deined.
         SVDValueObject svdo = svdService.getSvd( ee.getId() );
 
         DoubleMatrix<Long, Integer> vMatrix = svdo.getvMatrix();
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentSetController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentSetController.java
index c4afe3fedd..1c8384f0d6 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentSetController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentSetController.java
@@ -37,6 +37,7 @@
 import ubic.gemma.persistence.util.EntityUtils;
 import ubic.gemma.web.controller.BaseController;
 import ubic.gemma.web.persistence.SessionListManager;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 import javax.annotation.Nullable;
 import javax.servlet.http.HttpServletRequest;
@@ -168,7 +169,7 @@ public Collection<Long> getExperimentIdsInSet( Long id ) {
 
         ExpressionExperimentSetValueObject vo = expressionExperimentSetService.loadValueObjectById( id );
         if ( vo == null ) {
-            throw new IllegalArgumentException( "No such set with id=" + id );
+            throw new EntityNotFoundException( "No such set with id=" + id );
         }
         // FIXME this is a bit inefficient, for security filtering ... could have an ID-filtering interceptor.
         return EntityUtils.getIds( expressionExperimentSetService.getExperimentValueObjectsInSet( id ) );
@@ -472,7 +473,7 @@ private ExpressionExperimentSetValueObject getExpressionExperimentSetFromRequest
             set = expressionExperimentSetService.loadValueObjectById( id );
 
             if ( set == null ) {
-                throw new IllegalArgumentException( "Unable to access experiment set with id=" + id );
+                throw new EntityNotFoundException( "Unable to access experiment set with id=" + id );
             }
         } else {
             throw new IllegalArgumentException( "You must provide an id" );
diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneSetController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneSetController.java
index be33027c11..5f144c029d 100755
--- a/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneSetController.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneSetController.java
@@ -35,6 +35,7 @@
 import ubic.gemma.model.genome.gene.GeneSetValueObject;
 import ubic.gemma.model.genome.gene.GeneValueObject;
 import ubic.gemma.web.persistence.SessionListManager;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 import javax.servlet.http.HttpServletRequest;
 import java.util.ArrayList;
@@ -140,7 +141,7 @@ public String canCurrentUserEditGroup( GeneSetValueObject gsvo ) {
         if ( gsvo instanceof DatabaseBackedGeneSetValueObject ) {
             groupIsDBBacked = true;
             try {
-                userCanEditGroup = securityService.isEditable( geneSetService.load( gsvo.getId() ) );
+                userCanEditGroup = securityService.isEditable( geneSetService.loadOrFail( gsvo.getId(), EntityNotFoundException::new, "No gene set with ID " + gsvo.getId() ) );
             } catch ( org.springframework.security.access.AccessDeniedException ade ) {
                 return "{groupIsDBBacked:" + groupIsDBBacked + ",userCanEditGroup:" + false + "}";
             }
@@ -284,12 +285,14 @@ public Collection<DatabaseBackedGeneSetValueObject> getUsersGeneGroups( boolean
      * @return gene set vos
      */
     public DatabaseBackedGeneSetValueObject load( Long id ) {
-
         if ( id == null ) {
             throw new IllegalArgumentException( "Cannot load a gene set with a null id." );
         }
-        return geneSetService.loadValueObjectById( id );
-
+        DatabaseBackedGeneSetValueObject gsvo = geneSetService.loadValueObjectById( id );
+        if ( gsvo == null ) {
+            throw new EntityNotFoundException( "No GeneSet with ID " + id + "." );
+        }
+        return gsvo;
     }
 
     /**
@@ -496,7 +499,7 @@ private GeneSetValueObject getGeneSetFromRequest( HttpServletRequest request ) {
             geneSet = geneSetService.loadValueObjectById( id );
 
             if ( geneSet == null ) {
-                throw new IllegalArgumentException( "Unable to access gene set with id=" + id );
+                throw new EntityNotFoundException( "Unable to access gene set with id=" + id );
             }
         } else {
             throw new IllegalArgumentException( "You must provide an id" );
diff --git a/gemma-web/src/main/java/ubic/gemma/web/listener/StartupListener.java b/gemma-web/src/main/java/ubic/gemma/web/listener/StartupListener.java
index 1d2fc0d4a7..6f5edff754 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/listener/StartupListener.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/listener/StartupListener.java
@@ -105,6 +105,8 @@ public void contextInitialized( ServletContextEvent event ) {
 
         this.loadTrackerInformation( config );
 
+        this.lintConfiguration();
+
         ApplicationContext ctx = WebApplicationContextUtils.getRequiredWebApplicationContext( servletContext );
 
         servletContext.setAttribute( Constants.CONFIG, config );
@@ -118,6 +120,18 @@ public void contextInitialized( ServletContextEvent event ) {
                 String.join( ", ", ctx.getEnvironment().getActiveProfiles() ) ) );
     }
 
+    /**
+     * Perform some basic sanity checks for the configuration.
+     */
+    private void lintConfiguration() {
+        if ( !Settings.getBoolean( "load.ontologies" ) ) {
+            log.warn( "Auto-loading of ontologies is disabled, enable it by setting load.ontologies=true in Gemma.properties." );
+        }
+        if ( !Settings.getBoolean( "load.homologene" ) ) {
+            log.warn( "Homologene is not enabled, set load.homologene=true in Gemma.properties to load it on startup." );
+        }
+    }
+
     private static final String JAWR_DEBUG_ON_SYSTEM_PROPERTY = "net.jawr.debug.on";
 
     /**
diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/Probe2GeneEndpoint.java b/gemma-web/src/main/java/ubic/gemma/web/services/Probe2GeneEndpoint.java
index 1ee71db69c..711b433be1 100644
--- a/gemma-web/src/main/java/ubic/gemma/web/services/Probe2GeneEndpoint.java
+++ b/gemma-web/src/main/java/ubic/gemma/web/services/Probe2GeneEndpoint.java
@@ -29,6 +29,7 @@
 import ubic.gemma.model.genome.Gene;
 import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
 import ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService;
+import ubic.gemma.web.util.EntityNotFoundException;
 
 import java.util.Collection;
 import java.util.HashSet;
@@ -90,7 +91,7 @@ protected Element invokeInternal( Element requestElement, Document document ) {
         for ( String id : adResults ) {
             adid = id;
         }
-        ArrayDesign ad = arrayDesignService.loadOrFail( Long.parseLong( adid ) );
+        ArrayDesign ad = arrayDesignService.loadOrFail( Long.parseLong( adid ), EntityNotFoundException::new, "No platform with ID " + adid + "." );
 
         // get genes, given probe (which is unique to an Array Design
         // therefore, the Array Design Identifier input is not really necessary
diff --git a/gemma-web/src/main/webapp/WEB-INF/gemma-servlet.xml b/gemma-web/src/main/webapp/WEB-INF/gemma-servlet.xml
index 0c8460cecd..4c82364d5e 100644
--- a/gemma-web/src/main/webapp/WEB-INF/gemma-servlet.xml
+++ b/gemma-web/src/main/webapp/WEB-INF/gemma-servlet.xml
@@ -18,13 +18,6 @@
         <context:exclude-filter type="annotation" expression="ubic.gemma.persistence.util.TestComponent"/>
     </context:component-scan>
 
-    <!-- perform placeholder substitution in the servlet environment (i.e. web.xml init params) -->
-    <bean class="org.springframework.context.support.PropertySourcesPlaceholderConfigurer">
-        <property name="environment">
-            <bean class="org.springframework.web.context.support.StandardServletEnvironment"/>
-        </property>
-    </bean>
-
     <!-- Mapping URLS to controllers -->
 
 
diff --git a/gemma-web/src/main/webapp/pages/error/404.jsp b/gemma-web/src/main/webapp/pages/error/404.jsp
index 882803b7bf..d6d52274db 100644
--- a/gemma-web/src/main/webapp/pages/error/404.jsp
+++ b/gemma-web/src/main/webapp/pages/error/404.jsp
@@ -15,4 +15,8 @@
             </fmt:param>
         </fmt:message>
     </p>
+
+    <hr class="normal">
+
+    <p><c:out value="${exception.message}"/></p>
 </div>
\ No newline at end of file
diff --git a/gemma-web/src/main/webapp/scripts/api/entities/experiment/ExpressionExperimentsSummaryPanel.js b/gemma-web/src/main/webapp/scripts/api/entities/experiment/ExpressionExperimentsSummaryPanel.js
index 456e00ff8c..75d9daa317 100755
--- a/gemma-web/src/main/webapp/scripts/api/entities/experiment/ExpressionExperimentsSummaryPanel.js
+++ b/gemma-web/src/main/webapp/scripts/api/entities/experiment/ExpressionExperimentsSummaryPanel.js
@@ -1,4 +1,4 @@
-Ext.namespace('Gemma');
+Ext.namespace( 'Gemma' );
 
 /**
  * A panel for displaying by-taxon counts of all existing, new and updated experiments in Gemma, with a column for each
@@ -6,163 +6,155 @@ Ext.namespace('Gemma');
  *
  * a similar table appeared on the classic Gemma's front page
  */
-Gemma.ExpressionExperimentsSummaryPanel = Ext.extend(Ext.Panel,
-    {
-        title: 'Summary & updates in the past week',
-        collapsible: true,
-        titleCollapse: true,
-        animCollapse: false,
+Gemma.ExpressionExperimentsSummaryPanel = Ext.extend( Ext.Panel,
+   {
+      title : 'Summary & updates in the past week',
+      collapsible : true,
+      titleCollapse : true,
+      animCollapse : false,
 
-        listeners: {
-            render: function () {
-                if (!this.collapsed) {
-                    this.loadCounts();
-                }
-            },
-            expand: function () {
-                if (!this.countsLoaded) {
-                    this.loadCounts();
-                }
+      listeners : {
+         render : function() {
+            if ( !this.collapsed ) {
+               this.loadCounts();
             }
-        },
+         },
+         expand : function() {
+            if ( !this.countsLoaded ) {
+               this.loadCounts();
+            }
+         }
+      },
 
-        stateful: true,
-        stateId: 'showAllExpressionExperimentsSummaryGridState',
+      stateful : true,
+      stateId : 'showAllExpressionExperimentsSummaryGridState',
 
-        // what describes the state of this panel - in this case it is the "collapsed" field
-        getState: function () {
-            return {
-                collapsed: this.collapsed
-            };
-        },
+      // what describes the state of this panel - in this case it is the "collapsed" field
+      getState : function() {
+         return {
+            collapsed : this.collapsed
+         };
+      },
 
-        // specify when the state should be saved - in this case after panel was collapsed or expanded
-        stateEvents: ['collapse', 'expand'],
+      // specify when the state should be saved - in this case after panel was collapsed or expanded
+      stateEvents : [ 'collapse', 'expand' ],
 
-        constructor: function (config) {
-            Gemma.ExpressionExperimentsSummaryPanel.superclass.constructor.call(this, config);
-        },
+      constructor : function( config ) {
+         Gemma.ExpressionExperimentsSummaryPanel.superclass.constructor.call( this, config );
+      },
 
-        initComponent: function () {
-            Gemma.ExpressionExperimentsSummaryPanel.superclass.initComponent.call(this);
-        }, // end of initComponent
+      initComponent : function() {
+         Gemma.ExpressionExperimentsSummaryPanel.superclass.initComponent.call( this );
+      }, // end of initComponent
 
-        /**
-         * @memberOf Gemma.ExpressionExperimentsSummaryPanel
-         */
-        loadCounts: function () {
-            if (this.getEl() && !this.loadMask) {
-                this.loadMask = new Ext.LoadMask(this.getEl(), {
-                    msg: "Loading summary ...",
-                    msgCls: 'absolute-position-loading-mask ext-el-mask-msg x-mask-loading'
-                });
-            }
-            if (this.loadMask) {
-                this.loadMask.show();
-            }
+      /**
+       * @memberOf Gemma.ExpressionExperimentsSummaryPanel
+       */
+      loadCounts : function() {
+         if ( this.getEl() && !this.loadMask ) {
+            this.loadMask = new Ext.LoadMask( this.getEl(), {
+               msg : "Loading summary ...",
+               msgCls : 'absolute-position-loading-mask ext-el-mask-msg x-mask-loading'
+            } );
+         }
+         if ( this.loadMask ) {
+            this.loadMask.show();
+         }
 
-            var parent = this;
-            ExpressionExperimentController.loadCountsForDataSummaryTable(function (json) {
-                // update the panel with counts
-                json.cmpId = Ext.id(this);
-                this.update(json);
-                this.countsLoaded = true;
+         var parent = this;
+         ExpressionExperimentController.loadCountsForDataSummaryTable( function( json ) {
+            // update the panel with counts
+            json.cmpId = Ext.id( this );
+            this.update( json );
+            this.countsLoaded = true;
 
-                if (parent.loadMask) {
-                    parent.loadMask.hide();
-                }
+            if ( parent.loadMask ) {
+               parent.loadMask.hide();
+            }
 
-            }.createDelegate(this));
-        },
+         }.createDelegate( this ) );
+      },
 
-        // this is so long because it is lifted from the original version of the summary table
-        tpl: new Ext.XTemplate(
-            '<div id="dataSummaryTable">'
-            + '<div class="roundedcornr_box_777249" style="margin-bottom: 15px; padding: 10px; -moz-border-radius: 15px; border-radius: 15px;">'
-            + '<div class="roundedcornr_content_777249">'
-          //  + '<td align="right" style="padding-right: 10px">'
-            // + '<div style="font-size: small; padding-bottom: 5px;">'
-            // + '<b>Data Summary</b>'
-            // + '<tpl if="drawNewColumn == true && drawUpdatedColumn == true ">'
-            // + '<b> and Changes in the Last Week:</b>'
-            // + '</tpl>'
-            // + '<tpl if="drawNewColumn == true && drawUpdatedColumn == false ">'
-            // + '<b> and Additions in the Last Week:</b>'
-            // + '</tpl>'
-            // + '<tpl if="drawNewColumn == false && drawUpdatedColumn == true ">'
-            // + '<b> and Updates in the Last Week:</b>'
-            // + '</tpl>'
-            // + '</div>'
-          //  + '</td>'
-            + '<div id="dataSummary" style="margin-left: 15px; margin-right: 15px">'
-            + '<table style="white-space: nowrap">'
-            + '<tr>'
-            + '<td style="padding-right: 10px">'
-            + '<span style="white-space: nowrap">'
-            + '&nbsp; </span>'
-            + '</td>'
-            + '<td style="padding-right: 10px" align="right">'
-            + 'Total'
-            + '</td>'
-            + '<tpl if="drawUpdatedColumn == true">'
-            + '<td align="right" style="padding-right: 10px">'
-            + 'Updated'
-            + '</td>'
-            + '</tpl>'
-            + '<tpl if="drawNewColumn == true">'
-            + '<td align="right" style="padding-right: 10px">'
-            + 'New'
-            + '</td>'
-            + '</tpl>'
-            + '</tr><tr>'
-            + '<td style="padding-right: 10px">'
-            + '<span style="white-space: nowrap"> <!-- for IE --> '
-            + '<b>Expression Experiments:</b></span>'
-            + '</td>'
-            + '<td align="right" style="padding-right: 10px">'
-            + '<b><a href="' + ctxBasePath + '/expressionExperiment/showAllExpressionExperiments.html">{expressionExperimentCount}</b>'
-            + '</td>'
-            + '<td align="right" style="padding-right: 10px">'
-            + '<b><a style="cursor:pointer" onClick="Gemma.ExpressionExperimentsSummaryPanel.handleIdsLink([{updatedExpressionExperimentIds}],\'{cmpId}\');">'
-            + '{updatedExpressionExperimentCount}</a></b>&nbsp;&nbsp;'
-            + '</td>'
-            + '<td align="right">'
-            + '<b><a style="cursor:pointer" onClick="Gemma.ExpressionExperimentsSummaryPanel.handleIdsLink([{newExpressionExperimentIds}],\'{cmpId}\');">'
-            + '{newExpressionExperimentCount}</a></b>&nbsp;'
-            + '</td>'
-            + '</tr>'
-            + '<tpl for="sortedCountsPerTaxon">'
-            + '<tr>'
-            + '<td style="padding-right: 10px">'
-            + '<span style="white-space: nowrap"> <!-- for IE --> &emsp;'
-            + '{taxonName}'
-            + '</td><td align="right" style="padding-right: 10px">'
-            + '<a style="cursor:pointer" onClick="Gemma.ExpressionExperimentsSummaryPanel.handleTaxonLink({taxonId},\'{parent.cmpId}\');">'
-            + '{totalCount}</a>'
-            + '</td><td align="right" style="padding-right: 10px">'
-            + '<b><a style="cursor:pointer" onClick="Gemma.ExpressionExperimentsSummaryPanel.handleIdsLink([{updatedIds}],\'{parent.cmpId}\');">'
-            + '{updatedCount}</a></b>&nbsp;&nbsp;'
-            + '</a>'
-            + '</td><td align="right">'
-            + '<b><a style="cursor:pointer" onClick="Gemma.ExpressionExperimentsSummaryPanel.handleIdsLink([{newIds}],\'{parent.cmpId}\');">'
-            + '{newCount}</a></b>&nbsp;' + '</a>' + '</td>' + '</tr>' + '</tpl>' + '<tr>'
-            + '<td style="padding-right: 10px">' + '<span style="white-space: nowrap"> <!-- for IE -->'
-            + '<b>Platforms:</b>  </span>' + '</td>' + '<td align="right" style="padding-right: 10px">'
-            + '<a href="' + ctxBasePath + '/arrays/showAllArrayDesigns.html">' + '<b>{arrayDesignCount}</b></a>' + '</td>'
-            + '<td align="right" style="padding-right: 10px">' + '<b>{updatedArrayDesignCount}</b>&nbsp;&nbsp;'
-            + '</td>' + '<td align="right">' + '<b>{newArrayDesignCount}</b>&nbsp;' + '</td>' + '</tr>' + '<tr>'
-            + '<td style="padding-right: 10px">'
-            + '<span style="white-space: nowrap"> <!-- for IE --> <b>Samples:</b>' + '</span>' + '</td>'
-            + '<td align="right" style="padding-right: 10px">' + '{bioMaterialCount}' + '</td>'
-            + '<td align="right" style="padding-right: 10px">' + '&nbsp;&nbsp;' + '</td>' + '<td align="right">'
-            + '<b>{newBioMaterialCount}</b>&nbsp;' + '</td>' + '</tr>' + '</table>' + '</div>' + '</div>' + '</div>'
-            + '</div>')
-    });
+      // this is so long because it is lifted from the original version of the summary table
+      tpl : new Ext.XTemplate(
+         '<div id="dataSummaryTable">'
+         + '<div class="roundedcornr_box_777249" style="margin-bottom: 15px; padding: 10px; -moz-border-radius: 15px; border-radius: 15px;">'
+         + '<div class="roundedcornr_content_777249">'
+         //  + '<td align="right" style="padding-right: 10px">'
+         // + '<div style="font-size: small; padding-bottom: 5px;">'
+         // + '<b>Data Summary</b>'
+         // + '<tpl if="drawNewColumn == true && drawUpdatedColumn == true ">'
+         // + '<b> and Changes in the Last Week:</b>'
+         // + '</tpl>'
+         // + '<tpl if="drawNewColumn == true && drawUpdatedColumn == false ">'
+         // + '<b> and Additions in the Last Week:</b>'
+         // + '</tpl>'
+         // + '<tpl if="drawNewColumn == false && drawUpdatedColumn == true ">'
+         // + '<b> and Updates in the Last Week:</b>'
+         // + '</tpl>'
+         // + '</div>'
+         //  + '</td>'
+         + '<div id="dataSummary" style="margin-left: 15px; margin-right: 15px">'
+         + '<table style="border-spacing: 10px 2px;">'
+         + '<tr>'
+         + '<td></td>'
+         + '<td style="text-align: right;">Total</td>'
+         + '<tpl if="drawUpdatedColumn == true">'
+         + '<td style="text-align: right;">Updated</td>'
+         + '</tpl>'
+         + '<tpl if="drawNewColumn == true">'
+         + '<td style="text-align: right;">New</td>'
+         + '</tpl>'
+         + '</tr><tr>'
+         + '<td><b>Expression Experiments:</b></td>'
+         + '<td style="text-align: right;">'
+         + '<a href="' + ctxBasePath + '/expressionExperiment/showAllExpressionExperiments.html">{expressionExperimentCount}'
+         + '</td>'
+         + '<td style="text-align: right;">'
+         + '<b><a style="cursor:pointer" onClick="Gemma.ExpressionExperimentsSummaryPanel.handleIdsLink([{updatedExpressionExperimentIds}],\'{cmpId}\');">{updatedExpressionExperimentCount}</a></b>'
+         + '</td>'
+         + '<td style="text-align: right;">'
+         + '<b><a style="cursor:pointer" onClick="Gemma.ExpressionExperimentsSummaryPanel.handleIdsLink([{newExpressionExperimentIds}],\'{cmpId}\');">{newExpressionExperimentCount}</a></b>'
+         + '</td>'
+         + '</tr>'
+         + '<tpl for="sortedCountsPerTaxon">'
+         + '<tr>'
+         + '<td>&emsp;{taxonName}</td>'
+         + '<td style="text-align: right;">'
+         + '<a style="cursor:pointer" onClick="Gemma.ExpressionExperimentsSummaryPanel.handleTaxonLink({taxonId},\'{parent.cmpId}\');">{totalCount}</a>'
+         + '</td>'
+         + '<td style="text-align: right;">'
+         + '<b><a style="cursor:pointer" onClick="Gemma.ExpressionExperimentsSummaryPanel.handleIdsLink([{updatedIds}],\'{parent.cmpId}\');">{updatedCount}</a></b></a>'
+         + '</td>'
+         + '<td style="text-align: right;">'
+         + '<b><a style="cursor:pointer" onClick="Gemma.ExpressionExperimentsSummaryPanel.handleIdsLink([{newIds}],\'{parent.cmpId}\');">{newCount}</a></b></a>'
+         + '</td>'
+         + '</tr>'
+         + '</tpl>'
+         + '<tr>'
+         + '<td><b>Platforms:</b></td>'
+         + '<td style="text-align: right;">'
+         + '<a href="' + ctxBasePath + '/arrays/showAllArrayDesigns.html">{arrayDesignCount}</a></td>'
+         + '<td style="text-align: right;"><b>{updatedArrayDesignCount}</b></td>'
+         + '<td style="text-align: right;"><b>{newArrayDesignCount}</b></td>'
+         + '</tr>'
+         + '<tr>'
+         + '<td><b>Samples:</b></td>'
+         + '<td style="text-align: right;">{bioMaterialCount}</td>'
+         + '<td style="text-align: right;"><b>{updatedBioMaterialCount}</b></td>'
+         + '<td style="text-align: right;"><b>{newBioMaterialCount}</b></td>'
+         + '</tr>'
+         + '</table>'
+         + '</div>'
+         + '</div>'
+         + '</div>'
+         + '</div>' )
+   } );
 
-Gemma.ExpressionExperimentsSummaryPanel.handleIdsLink = function (ids, cmpId) {
-    Ext.getCmp(cmpId).fireEvent('showExperimentsByIds', ids);
+Gemma.ExpressionExperimentsSummaryPanel.handleIdsLink = function( ids, cmpId ) {
+   Ext.getCmp( cmpId ).fireEvent( 'showExperimentsByIds', ids );
 };
 
-Gemma.ExpressionExperimentsSummaryPanel.handleTaxonLink = function (id, cmpId) {
-    Ext.getCmp(cmpId).fireEvent('showExperimentsByTaxon', id);
+Gemma.ExpressionExperimentsSummaryPanel.handleTaxonLink = function( id, cmpId ) {
+   Ext.getCmp( cmpId ).fireEvent( 'showExperimentsByTaxon', id );
 };
\ No newline at end of file
diff --git a/gemma-web/src/test/java/ubic/gemma/web/controller/common/rss/RssFeedControllerTest.java b/gemma-web/src/test/java/ubic/gemma/web/controller/common/rss/RssFeedControllerTest.java
index 6a66f369a6..b685ba5aef 100644
--- a/gemma-web/src/test/java/ubic/gemma/web/controller/common/rss/RssFeedControllerTest.java
+++ b/gemma-web/src/test/java/ubic/gemma/web/controller/common/rss/RssFeedControllerTest.java
@@ -55,8 +55,7 @@ public void setUp() throws Exception {
         super.getTestPersistentExpressionExperiment();
         super.getTestPersistentExpressionExperiment();
 
-        whatsNewService.generateWeeklyReport();
-        WhatsNew wn = whatsNewService.getLatestWeeklyReport();
+        WhatsNew wn = whatsNewService.generateWeeklyReport();
 
         Collection<ExpressionExperiment> updatedExperiments = wn.getUpdatedExpressionExperiments();
         Collection<ExpressionExperiment> newExperiments = wn.getNewExpressionExperiments();
diff --git a/gemma-web/src/test/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignControllerTest.java b/gemma-web/src/test/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignControllerTest.java
index 085b903288..28839a8896 100644
--- a/gemma-web/src/test/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignControllerTest.java
+++ b/gemma-web/src/test/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignControllerTest.java
@@ -20,12 +20,9 @@
 
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.mock.web.MockHttpServletRequest;
 import org.springframework.web.servlet.ModelAndView;
-import ubic.gemma.persistence.util.Settings;
 import ubic.gemma.web.util.BaseSpringWebTest;
 
-import javax.servlet.http.HttpServletResponse;
 import java.util.Collection;
 
 import static org.junit.Assert.assertEquals;
@@ -36,16 +33,12 @@
  */
 public class ArrayDesignControllerTest extends BaseSpringWebTest {
 
-    private MockHttpServletRequest request;
-
     @Autowired
     private ArrayDesignController arrayDesignController;
 
     @Test
-    public void testShowAllArrayDesigns() throws Exception {
-        request = this.newPost( "/arrayDesign/showAllArrayDesigns.html" );
-
-        ModelAndView mav = arrayDesignController.showAllArrayDesigns( request, ( HttpServletResponse ) null );
+    public void testShowAllArrayDesigns() {
+        ModelAndView mav = arrayDesignController.showAllArrayDesigns();
         Collection<Object> c = mav.getModel().values();
         assertNotNull( c );
         assertEquals( "arrayDesigns", mav.getViewName() );
diff --git a/pom.xml b/pom.xml
index 3a31ba6292..29dc92c92e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
 	<name>Gemma</name>
 	<groupId>gemma</groupId>
 	<artifactId>gemma</artifactId>
-	<version>1.30.2</version>
+	<version>1.30.3</version>
 	<inceptionYear>2005</inceptionYear>
 	<description>The Gemma Project for meta-analysis of genomics data</description>
 	<url>https://gemma.msl.ubc.ca</url>
@@ -635,7 +635,7 @@
 		</plugins>
 	</reporting>
 	<properties>
-		<gsec.version>0.0.14</gsec.version>
+		<gsec.version>0.0.15</gsec.version>
 		<spring.version>3.2.18.RELEASE</spring.version>
 		<spring.security.version>3.2.10.RELEASE</spring.security.version>
 		<jersey.version>2.25.1</jersey.version>