diff --git a/gemma-core/pom.xml b/gemma-core/pom.xml index 7de3fc5d33..0db3d3e02c 100644 --- a/gemma-core/pom.xml +++ b/gemma-core/pom.xml @@ -112,8 +112,8 @@ 1.5 - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} runtime diff --git a/gemma-core/src/main/java/ubic/gemma/core/security/audit/AuditAdvice.java b/gemma-core/src/main/java/ubic/gemma/core/security/audit/AuditAdvice.java index f42cf946cf..3b8427c9d3 100644 --- a/gemma-core/src/main/java/ubic/gemma/core/security/audit/AuditAdvice.java +++ b/gemma-core/src/main/java/ubic/gemma/core/security/audit/AuditAdvice.java @@ -26,6 +26,7 @@ import org.hibernate.*; import org.hibernate.engine.spi.CascadeStyle; import org.hibernate.engine.spi.CascadingAction; +import org.hibernate.engine.spi.CascadingActions; import org.hibernate.persister.entity.EntityPersister; import org.hibernate.type.Type; import org.slf4j.Logger; @@ -180,7 +181,7 @@ private void processAuditable( Signature method, OperationType operationType, Au */ private void addCreateAuditEvent( Signature method, Auditable auditable, User user, Date date ) { addAuditEvent( method, auditable, AuditAction.CREATE, "", user, date ); - cascadeAuditEvent( method, AuditAction.CREATE, auditable, user, date, CascadingAction.PERSIST ); + cascadeAuditEvent( method, AuditAction.CREATE, auditable, user, date, CascadingActions.PERSIST ); } private void addSaveAuditEvent( Signature method, Auditable auditable, User user, Date date ) { @@ -188,10 +189,10 @@ private void addSaveAuditEvent( Signature method, Auditable auditable, User user CascadingAction cascadingAction; if ( auditable.getId() != null ) { auditAction = AuditAction.UPDATE; - cascadingAction = CascadingAction.MERGE; + cascadingAction = CascadingActions.MERGE; } else { auditAction = AuditAction.CREATE; - cascadingAction = CascadingAction.PERSIST; + cascadingAction = CascadingActions.PERSIST; } addAuditEvent( method, auditable, auditAction, "", user, date ); // we only propagate a CREATE event through cascade for entities that were created in the save @@ -214,7 +215,7 @@ private void addUpdateAuditEvent( Signature method, Auditable auditable, User us addAuditEvent( method, auditable, AuditAction.UPDATE, "", user, date ); // we only propagate a CREATE event through cascade for entities that were created in the update // Note: CREATE events are skipped if the audit trail already contains one - cascadeAuditEvent( method, AuditAction.CREATE, auditable, user, date, CascadingAction.SAVE_UPDATE ); + cascadeAuditEvent( method, AuditAction.CREATE, auditable, user, date, CascadingActions.SAVE_UPDATE ); } private void addDeleteAuditEvent( Signature method, Auditable auditable, User user, Date date ) { @@ -222,7 +223,7 @@ private void addDeleteAuditEvent( Signature method, Auditable auditable, User us throw new IllegalArgumentException( String.format( "Transient instance passed to delete auditing [%s on %s by %s]", method, auditable, user.getUserName() ) ); } addAuditEvent( method, auditable, AuditAction.DELETE, "", user, date ); - cascadeAuditEvent( method, AuditAction.DELETE, auditable, user, date, CascadingAction.DELETE ); + cascadeAuditEvent( method, AuditAction.DELETE, auditable, user, date, CascadingActions.DELETE ); } /** diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/util/ObjectFilter.java b/gemma-core/src/main/java/ubic/gemma/persistence/util/ObjectFilter.java index e89002d12b..37af94be6b 100644 --- a/gemma-core/src/main/java/ubic/gemma/persistence/util/ObjectFilter.java +++ b/gemma-core/src/main/java/ubic/gemma/persistence/util/ObjectFilter.java @@ -62,7 +62,7 @@ public class ObjectFilter { */ private static final ConfigurableConversionService conversionService = new GenericConversionService(); - private static void addConverter( Class targetClass, Converter converter ) { + private static void addConverter( Class targetClass, Converter converter ) { conversionService.addConverter( String.class, targetClass, converter ); } diff --git a/gemma-core/src/main/resources/ubic/gemma/applicationContext-search.xml b/gemma-core/src/main/resources/ubic/gemma/applicationContext-search.xml index 21521fd2cf..05adea749f 100644 --- a/gemma-core/src/main/resources/ubic/gemma/applicationContext-search.xml +++ b/gemma-core/src/main/resources/ubic/gemma/applicationContext-search.xml @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -48,7 +48,7 @@ - + @@ -57,7 +57,7 @@ - + @@ -66,7 +66,7 @@ - + @@ -75,7 +75,7 @@ - + @@ -84,7 +84,7 @@ - + @@ -93,7 +93,7 @@ - + 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 e9bbb33f35..6b76983d9b 100644 --- a/gemma-core/src/main/resources/ubic/gemma/applicationContext-serviceBeans.xml +++ b/gemma-core/src/main/resources/ubic/gemma/applicationContext-serviceBeans.xml @@ -20,9 +20,7 @@ are listed in a resource. If the resource is in your classpath, list in in 'locations'. Other config files can be added by defining PropertiesConfiguration instances --> - - - + @@ -31,9 +29,7 @@ - - - + classpath:default.properties diff --git a/gemma-core/src/test/resources/test.spring.config.xml b/gemma-core/src/test/resources/test.spring.config.xml index 55b9d5bc1c..9b6afb8071 100644 --- a/gemma-core/src/test/resources/test.spring.config.xml +++ b/gemma-core/src/test/resources/test.spring.config.xml @@ -5,9 +5,7 @@ - - - + classpath:default.properties @@ -18,9 +16,7 @@ - - - + diff --git a/gemma-web/pom.xml b/gemma-web/pom.xml index 81d407485b..67f8b6aa22 100644 --- a/gemma-web/pom.xml +++ b/gemma-web/pom.xml @@ -102,6 +102,30 @@ maven-war-plugin 3.3.2 + + org.apache.maven.plugins + maven-dependency-plugin + 3.3.0 + + + generate-sources + + unpack + + + + + org.springframework + spring-webmvc + 3.2.18.RELEASE + + + org/springframework/web/servlet/mvc/AbstractFormController.class,org/springframework/web/servlet/mvc/BaseCommandController.class,org/springframework/web/servlet/mvc/SimpleFormController.class + ${project.build.directory}/classes + + + + @@ -187,18 +211,18 @@ - + org.springframework.social spring-social-core - 1.0.3.RELEASE + 1.1.6.RELEASE runtime - + org.springframework.ws spring-ws-core - 2.1.4.RELEASE + 2.4.7.RELEASE @@ -224,19 +248,19 @@ org.quartz-scheduler quartz - 1.8.6 + 2.3.2 - rome + com.rometools rome - 1.0 + 1.18.0 - rome + com.rometools rome-fetcher - 1.0 + 1.18.0 @@ -250,7 +274,7 @@ org.directwebremoting dwr - 2.0.11-RELEASE + 3.0.2-RELEASE @@ -274,7 +298,7 @@ runtime - + org.glassfish.jersey.core jersey-server @@ -288,7 +312,7 @@ org.glassfish.jersey.ext - jersey-spring3 + jersey-spring4 ${jersey.version} @@ -312,7 +336,7 @@ javax.ws.rs javax.ws.rs-api - 2.0.1 + 2.1.1 diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/common/rss/CustomRssViewer.java b/gemma-web/src/main/java/ubic/gemma/web/controller/common/rss/CustomRssViewer.java index d132d5d928..490c54aa51 100644 --- a/gemma-web/src/main/java/ubic/gemma/web/controller/common/rss/CustomRssViewer.java +++ b/gemma-web/src/main/java/ubic/gemma/web/controller/common/rss/CustomRssViewer.java @@ -18,9 +18,9 @@ */ package ubic.gemma.web.controller.common.rss; -import com.sun.syndication.feed.rss.Channel; -import com.sun.syndication.feed.rss.Content; -import com.sun.syndication.feed.rss.Item; +import com.rometools.rome.feed.rss.Channel; +import com.rometools.rome.feed.rss.Content; +import com.rometools.rome.feed.rss.Item; import org.apache.commons.lang3.time.DateUtils; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/gemma-web/src/main/java/ubic/gemma/web/feed/FeedReader.java b/gemma-web/src/main/java/ubic/gemma/web/feed/FeedReader.java index 2698aba1c8..b5b71c3aa4 100644 --- a/gemma-web/src/main/java/ubic/gemma/web/feed/FeedReader.java +++ b/gemma-web/src/main/java/ubic/gemma/web/feed/FeedReader.java @@ -18,12 +18,12 @@ */ package ubic.gemma.web.feed; -import com.sun.syndication.feed.synd.SyndEntry; -import com.sun.syndication.feed.synd.SyndFeed; -import com.sun.syndication.fetcher.FeedFetcher; -import com.sun.syndication.fetcher.impl.FeedFetcherCache; -import com.sun.syndication.fetcher.impl.HashMapFeedInfoCache; -import com.sun.syndication.fetcher.impl.HttpURLFeedFetcher; +import com.rometools.fetcher.FeedFetcher; +import com.rometools.fetcher.impl.FeedFetcherCache; +import com.rometools.fetcher.impl.HashMapFeedInfoCache; +import com.rometools.fetcher.impl.HttpURLFeedFetcher; +import com.rometools.rome.feed.synd.SyndEntry; +import com.rometools.rome.feed.synd.SyndFeed; import org.apache.commons.lang3.StringUtils; import org.springframework.beans.factory.InitializingBean; import org.springframework.stereotype.Controller; diff --git a/gemma-web/src/main/java/ubic/gemma/web/remote/CharacteristicConverter.java b/gemma-web/src/main/java/ubic/gemma/web/remote/CharacteristicConverter.java index fe83589a5e..d7c57a7e2e 100644 --- a/gemma-web/src/main/java/ubic/gemma/web/remote/CharacteristicConverter.java +++ b/gemma-web/src/main/java/ubic/gemma/web/remote/CharacteristicConverter.java @@ -19,30 +19,26 @@ package ubic.gemma.web.remote; +import org.directwebremoting.ConversionException; import org.directwebremoting.convert.BeanConverter; -import org.directwebremoting.dwrp.ParseUtil; -import org.directwebremoting.dwrp.ProtocolConstants; import org.directwebremoting.extend.*; -import org.directwebremoting.util.LocalUtil; -import org.directwebremoting.util.Messages; - import ubic.gemma.model.common.description.Characteristic; import java.util.ArrayList; import java.util.HashSet; -import java.util.Iterator; import java.util.Map; import java.util.Map.Entry; +import static org.directwebremoting.extend.ConvertUtil.splitInbound; + /** * @author kelsey - * */ public class CharacteristicConverter extends BeanConverter { @SuppressWarnings("unchecked") @Override - public Object convertInbound( Class paramType, InboundVariable iv, InboundContext inctx ) throws MarshallException { + public Object convertInbound( Class paramType, InboundVariable iv ) throws ConversionException { String value = iv.getValue(); // If the text is null then the whole bean is null @@ -51,13 +47,12 @@ public Object convertInbound( Class paramType, InboundVariable iv, InboundContex } if ( !value.startsWith( ProtocolConstants.INBOUND_MAP_START ) ) { - throw new MarshallException( paramType, Messages.getString( "BeanConverter.FormatError", - ProtocolConstants.INBOUND_MAP_START ) ); + throw new ConversionException( paramType, String.format( "Inbound variable does not start with '%s'.", ProtocolConstants.INBOUND_MAP_START ) ); } if ( !value.endsWith( ProtocolConstants.INBOUND_MAP_END ) ) { - throw new MarshallException( paramType, Messages.getString( "BeanConverter.FormatError", - ProtocolConstants.INBOUND_MAP_START ) ); + throw new ConversionException( paramType, String.format( "Inbound variable does not end with '%s'.", ProtocolConstants.INBOUND_MAP_END ) ); + // ProtocolConstants.INBOUND_MAP_START ) ); } value = value.substring( 1, value.length() - 1 ); @@ -68,17 +63,16 @@ public Object convertInbound( Class paramType, InboundVariable iv, InboundContex Object bean = Characteristic.Factory.newInstance(); if ( instanceType != null ) { - inctx.addConverted( iv, instanceType, bean ); + iv.getContext().addConverted( iv, instanceType, bean ); } else { - inctx.addConverted( iv, paramType, bean ); + iv.getContext().addConverted( iv, paramType, bean ); } Map properties = getPropertyMapFromObject( bean, false, true ); // Loop through the properties passed in - for ( Iterator> it = tokens.entrySet().iterator(); it.hasNext(); ) { - Map.Entry entry = it.next(); + for ( Entry entry : tokens.entrySet() ) { String key = entry.getKey(); String val = entry.getValue(); @@ -89,14 +83,14 @@ public Object convertInbound( Class paramType, InboundVariable iv, InboundContex Class propType = property.getPropertyType(); - String[] split = ParseUtil.splitInbound( val ); - String splitValue = split[LocalUtil.INBOUND_INDEX_VALUE]; - String splitType = split[LocalUtil.INBOUND_INDEX_TYPE]; + String[] split = splitInbound( val ); + String splitValue = split[ConvertUtil.INBOUND_INDEX_VALUE]; + String splitType = split[ConvertUtil.INBOUND_INDEX_TYPE]; - InboundVariable nested = new InboundVariable( iv.getLookup(), null, splitType, splitValue ); - TypeHintContext incc = createTypeHintContext( inctx, property ); + InboundVariable nested = new InboundVariable( iv.getContext(), null, splitType, splitValue ); + Property incc = createTypeHintContext( iv.getContext(), property ); - Object output = converterManager.convertInbound( propType, nested, inctx, incc ); + Object output = converterManager.convertInbound( propType, nested, incc ); // Unfortunate hack. Change the properties association to be a Set instead of a Collection in the // model; Model think this is a generic Collection, Hibernate thinks its a Set. DWR converts collections @@ -111,10 +105,10 @@ public Object convertInbound( Class paramType, InboundVariable iv, InboundContex } return bean; - } catch ( MarshallException ex ) { + } catch ( ConversionException ex ) { throw ex; } catch ( Exception ex ) { - throw new MarshallException( paramType, ex ); + throw new ConversionException( paramType, ex ); } } } diff --git a/gemma-web/src/main/java/ubic/gemma/web/remote/DirectionConverter.java b/gemma-web/src/main/java/ubic/gemma/web/remote/DirectionConverter.java index c8af77ec56..e08d8bce20 100644 --- a/gemma-web/src/main/java/ubic/gemma/web/remote/DirectionConverter.java +++ b/gemma-web/src/main/java/ubic/gemma/web/remote/DirectionConverter.java @@ -2,7 +2,7 @@ * The gemma-web project * * Copyright (c) 2013 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 * @@ -14,24 +14,22 @@ */ package ubic.gemma.web.remote; +import org.directwebremoting.ConversionException; import org.directwebremoting.convert.StringConverter; -import org.directwebremoting.extend.InboundContext; import org.directwebremoting.extend.InboundVariable; -import org.directwebremoting.extend.MarshallException; import ubic.gemma.model.analysis.expression.diff.Direction; /** * DWR converter for Direction type. * * @author Paul - * * @see ubic.gemma.model.analysis.expression.diff.Direction */ public class DirectionConverter extends StringConverter { @Override - public Object convertInbound( Class paramType, InboundVariable iv, InboundContext inctx ) throws MarshallException { - String value = ( String ) super.convertInbound( paramType, iv, inctx ); + public Object convertInbound( Class paramType, InboundVariable iv ) throws ConversionException { + String value = ( String ) super.convertInbound( paramType, iv ); return Direction.fromString( value ); } diff --git a/gemma-web/src/main/java/ubic/gemma/web/remote/DoublePointConverter.java b/gemma-web/src/main/java/ubic/gemma/web/remote/DoublePointConverter.java index 0f9dd8a9cf..e89d3a9b23 100644 --- a/gemma-web/src/main/java/ubic/gemma/web/remote/DoublePointConverter.java +++ b/gemma-web/src/main/java/ubic/gemma/web/remote/DoublePointConverter.java @@ -18,15 +18,14 @@ */ package ubic.gemma.web.remote; +import org.directwebremoting.ConversionException; import org.directwebremoting.convert.BeanConverter; -import org.directwebremoting.dwrp.ObjectOutboundVariable; -import org.directwebremoting.extend.MarshallException; +import org.directwebremoting.extend.ObjectOutboundVariable; import org.directwebremoting.extend.OutboundContext; import org.directwebremoting.extend.OutboundVariable; import org.directwebremoting.extend.Property; import ubic.basecode.dataStructure.DoublePoint; -import java.util.Iterator; import java.util.Map; import java.util.Map.Entry; import java.util.TreeMap; @@ -41,7 +40,7 @@ public class DoublePointConverter extends BeanConverter { @Override - public OutboundVariable convertOutbound( Object data, OutboundContext outctx ) throws MarshallException { + public OutboundVariable convertOutbound( Object data, OutboundContext outctx ) throws ConversionException { if ( !( data instanceof DoublePoint ) ) return super.convertOutbound( data, outctx ); @@ -54,8 +53,7 @@ public OutboundVariable convertOutbound( Object data, OutboundContext outctx ) t try { Map properties = getPropertyMapFromObject( data, true, false ); - for ( Iterator> it = properties.entrySet().iterator(); it.hasNext(); ) { - Entry entry = it.next(); + for ( Entry entry : properties.entrySet() ) { String name = entry.getKey(); Property property = entry.getValue(); @@ -73,13 +71,13 @@ public OutboundVariable convertOutbound( Object data, OutboundContext outctx ) t } ovs.put( name, nested ); } - } catch ( MarshallException ex ) { + } catch ( ConversionException ex ) { throw ex; } catch ( Exception ex ) { - throw new MarshallException( data.getClass(), ex ); + throw new ConversionException( data.getClass(), ex ); } - ov.init( ovs, getJavascript() ); + ov.setChildren( ovs ); return ov; } diff --git a/gemma-web/src/main/java/ubic/gemma/web/remote/GOEvidenceCodeConverter.java b/gemma-web/src/main/java/ubic/gemma/web/remote/GOEvidenceCodeConverter.java index 964399e961..86ee564d0f 100755 --- a/gemma-web/src/main/java/ubic/gemma/web/remote/GOEvidenceCodeConverter.java +++ b/gemma-web/src/main/java/ubic/gemma/web/remote/GOEvidenceCodeConverter.java @@ -19,20 +19,18 @@ package ubic.gemma.web.remote; import org.apache.commons.lang3.StringUtils; +import org.directwebremoting.ConversionException; import org.directwebremoting.convert.StringConverter; -import org.directwebremoting.extend.InboundContext; import org.directwebremoting.extend.InboundVariable; -import org.directwebremoting.extend.MarshallException; import ubic.gemma.model.association.GOEvidenceCode; /** * @author luke - * */ public class GOEvidenceCodeConverter extends StringConverter { @Override - public Object convertInbound( Class paramType, InboundVariable iv, InboundContext inctx ) throws MarshallException { - String value = ( String ) super.convertInbound( paramType, iv, inctx ); + public Object convertInbound( Class paramType, InboundVariable iv ) throws ConversionException { + String value = ( String ) super.convertInbound( paramType, iv ); if ( StringUtils.isBlank( value ) ) { return null; } diff --git a/gemma-web/src/main/java/ubic/gemma/web/remote/ScaleTypeConverter.java b/gemma-web/src/main/java/ubic/gemma/web/remote/ScaleTypeConverter.java index be887888ee..90dfad5d5c 100755 --- a/gemma-web/src/main/java/ubic/gemma/web/remote/ScaleTypeConverter.java +++ b/gemma-web/src/main/java/ubic/gemma/web/remote/ScaleTypeConverter.java @@ -18,10 +18,9 @@ */ package ubic.gemma.web.remote; +import org.directwebremoting.ConversionException; import org.directwebremoting.convert.StringConverter; -import org.directwebremoting.extend.InboundContext; import org.directwebremoting.extend.InboundVariable; -import org.directwebremoting.extend.MarshallException; import ubic.gemma.model.common.quantitationtype.ScaleType; /** @@ -29,8 +28,8 @@ */ public class ScaleTypeConverter extends StringConverter { @Override - public Object convertInbound( Class paramType, InboundVariable iv, InboundContext inctx ) throws MarshallException { - String value = ( String ) super.convertInbound( paramType, iv, inctx ); + public Object convertInbound( Class paramType, InboundVariable iv ) throws ConversionException { + String value = ( String ) super.convertInbound( paramType, iv ); return ScaleType.fromString( value ); } } diff --git a/gemma-web/src/main/java/ubic/gemma/web/remote/StandardQuantitationTypeConverter.java b/gemma-web/src/main/java/ubic/gemma/web/remote/StandardQuantitationTypeConverter.java index ef38b8f3dd..5bbe8a94a6 100755 --- a/gemma-web/src/main/java/ubic/gemma/web/remote/StandardQuantitationTypeConverter.java +++ b/gemma-web/src/main/java/ubic/gemma/web/remote/StandardQuantitationTypeConverter.java @@ -18,10 +18,9 @@ */ package ubic.gemma.web.remote; +import org.directwebremoting.ConversionException; import org.directwebremoting.convert.StringConverter; -import org.directwebremoting.extend.InboundContext; import org.directwebremoting.extend.InboundVariable; -import org.directwebremoting.extend.MarshallException; import ubic.gemma.model.common.quantitationtype.StandardQuantitationType; /** @@ -30,8 +29,8 @@ */ public class StandardQuantitationTypeConverter extends StringConverter { @Override - public Object convertInbound( Class paramType, InboundVariable iv, InboundContext inctx ) throws MarshallException { - String value = ( String ) super.convertInbound( paramType, iv, inctx ); + public Object convertInbound( Class paramType, InboundVariable iv ) throws ConversionException { + String value = ( String ) super.convertInbound( paramType, iv ); return StandardQuantitationType.fromString( value ); } } diff --git a/gemma-web/src/main/java/ubic/gemma/web/util/EhcacheCacheMonitorImpl.java b/gemma-web/src/main/java/ubic/gemma/web/util/EhcacheCacheMonitorImpl.java index efe74f83ef..7f3079fe16 100644 --- a/gemma-web/src/main/java/ubic/gemma/web/util/EhcacheCacheMonitorImpl.java +++ b/gemma-web/src/main/java/ubic/gemma/web/util/EhcacheCacheMonitorImpl.java @@ -19,8 +19,8 @@ package ubic.gemma.web.util; import net.sf.ehcache.Ehcache; -import net.sf.ehcache.Statistics; import net.sf.ehcache.config.CacheConfiguration; +import net.sf.ehcache.statistics.StatisticsGateway; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.springframework.beans.factory.annotation.Autowired; @@ -113,9 +113,9 @@ public String getStats() { int count = 0; for ( String rawCacheName : cacheNames ) { Cache cache = cacheManager.getCache( rawCacheName ); - Statistics statistics = ( ( Ehcache ) cache.getNativeCache() ).getStatistics(); + StatisticsGateway statistics = ( ( Ehcache ) cache.getNativeCache() ).getStatistics(); - long objectCount = statistics.getObjectCount(); + long objectCount = statistics.getSize(); if ( objectCount == 0 ) { continue; @@ -126,13 +126,13 @@ public String getStats() { buf.append( "" ).append( this.getClearCacheHtml( rawCacheName ) ).append( cacheName ) .append( "" ); - long hits = statistics.getCacheHits(); - long misses = statistics.getCacheMisses(); - long inMemoryHits = statistics.getInMemoryHits(); - long inMemoryMisses = statistics.getInMemoryMisses(); + long hits = statistics.cacheHitCount(); + long misses = statistics.cacheMissCount(); + long inMemoryHits = statistics.localHeapHitCount(); + long inMemoryMisses = statistics.localHeapMissCount(); - long onDiskHits = statistics.getOnDiskHits(); - long evictions = statistics.getEvictionCount(); + long onDiskHits = statistics.localDiskHitCount(); + long evictions = statistics.localDiskRemoveCount(); if ( hits + misses > 0 ) { @@ -191,7 +191,7 @@ private String makeTableCellForStat( String s ) { private synchronized void setStatisticsEnabled( boolean b ) { for ( String rawCacheName : cacheManager.getCacheNames() ) { Cache cache = cacheManager.getCache( rawCacheName ); - ( ( Ehcache ) cache.getNativeCache() ).setSampledStatisticsEnabled( b ); + // ( ( Ehcache ) cache.getNativeCache() ).setSampledStatisticsEnabled( b ); } } diff --git a/gemma-web/src/main/resources/ubic/gemma/applicationContext-schedule.xml b/gemma-web/src/main/resources/ubic/gemma/applicationContext-schedule.xml index a702b526ae..aec20b0d3c 100644 --- a/gemma-web/src/main/resources/ubic/gemma/applicationContext-schedule.xml +++ b/gemma-web/src/main/resources/ubic/gemma/applicationContext-schedule.xml @@ -18,15 +18,15 @@ - - - - - - - - - + + + + + + + + + @@ -36,31 +36,31 @@ W Month 1-12 or JAN-DEC , - * / Day-of-Week 1-7 or SUN-SAT , - * ? / L # Year (Optional) empty, 1970-2099 , - * / See http://www.opensymphony.com/quartz/api/org/quartz/CronExpression.html for details, http://www.opensymphony.com/quartz/api/org/quartz/CronTrigger.html for examples. If you want a schedule that fire frequently for testing, try 0 0/2 * ? * *. --> - + - + - + - + - + - + - + diff --git a/gemma-web/src/main/webapp/WEB-INF/gemma-ws-servlet.xml b/gemma-web/src/main/webapp/WEB-INF/gemma-ws-servlet.xml index 5f3355b515..d9c6735c97 100644 --- a/gemma-web/src/main/webapp/WEB-INF/gemma-ws-servlet.xml +++ b/gemma-web/src/main/webapp/WEB-INF/gemma-ws-servlet.xml @@ -68,7 +68,7 @@ - + diff --git a/gemma-web/src/test/java/ubic/gemma/web/services/rest/AnnotationsWebServiceTest.java b/gemma-web/src/test/java/ubic/gemma/web/services/rest/AnnotationsWebServiceTest.java index d3192d4af6..997d7bb9cd 100644 --- a/gemma-web/src/test/java/ubic/gemma/web/services/rest/AnnotationsWebServiceTest.java +++ b/gemma-web/src/test/java/ubic/gemma/web/services/rest/AnnotationsWebServiceTest.java @@ -39,7 +39,7 @@ public class AnnotationsWebServiceTest extends AbstractJUnit4SpringContextTests { @Configuration - public static class AnnotationsWebServiceContextConfiguration { + static class AnnotationsWebServiceContextConfiguration { @Bean public OntologyService ontologyService() { diff --git a/pom.xml b/pom.xml index 78c9a952e5..9e024cd9d0 100644 --- a/pom.xml +++ b/pom.xml @@ -16,7 +16,7 @@ ubc.pavlab pavlab-starter-parent - 1.2.4 + 1.3.0-SNAPSHOT gemma-core @@ -234,11 +234,10 @@ org.hibernate hibernate-ehcache - compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j @@ -250,7 +249,7 @@ net.sf.ehcache - ehcache-core + ehcache @@ -617,10 +616,10 @@ - 0.0.10 - 3.2.18.RELEASE + 0.0.11-SNAPSHOT + 4.3.30.RELEASE 3.2.10.RELEASE - 2.25.1 + 2.27 2.14.1 2.2.7 3.9