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Changeset [5b3100d26be47cfba359cea256db1059d3d5a55d] by Nathan Dunn

Revision 5b3100d26be47cfba359cea256db1059d3d5a55d, committed by Nathan Dunn · September 8th, 2014 @ 03:21 PM

218 changed files

  • A src/main/java/net/crackstation/PasswordHash.java
  • A src/main/java/org/bbop/apollo/web/AnnotationChangeNotificationService.java
  • A src/main/java/org/bbop/apollo/web/AnnotationEditorService.java
  • A src/main/java/org/bbop/apollo/web/ErrorReportValve.java
  • A src/main/java/org/bbop/apollo/web/Login.java
  • A src/main/java/org/bbop/apollo/web/ProxyService.java
  • A src/main/java/org/bbop/apollo/web/UserManagerService.java
  • A src/main/java/org/bbop/apollo/web/config/CannedComments.java
  • A src/main/java/org/bbop/apollo/web/config/ServerConfiguration.java
  • A src/main/java/org/bbop/apollo/web/data/FeatureLazyResidues.java
  • A src/main/java/org/bbop/apollo/web/data/FeatureSequenceChunkManager.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/DataAdapter.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/IOService.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/chado/ChadoDataAdapter.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/chado/ChadoIO.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/chado/ChadoJEDatabaseIO.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/fasta/FastaDataAdapter.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/fasta/FastaIO.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/fasta/FastaJEDatabaseIO.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/gff3/Gff3DataAdapter.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/gff3/Gff3IO.java
  • A src/main/java/org/bbop/apollo/web/dataadapter/gff3/Gff3JEDatabaseIO.java
  • A src/main/java/org/bbop/apollo/web/datastore/AbstractDataStore.java
  • A src/main/java/org/bbop/apollo/web/datastore/AbstractDataStoreManager.java
  • A src/main/java/org/bbop/apollo/web/datastore/DataStoreChangeEvent.java
  • A src/main/java/org/bbop/apollo/web/datastore/DataStoreChangeListener.java
  • A src/main/java/org/bbop/apollo/web/datastore/JEDatabase.java
  • A src/main/java/org/bbop/apollo/web/datastore/JEDatabaseIterator.java
  • A src/main/java/org/bbop/apollo/web/datastore/JEDatabaseSessionDataStore.java-2013-10-23
  • A src/main/java/org/bbop/apollo/web/datastore/JESerializedDatabase.java
  • A src/main/java/org/bbop/apollo/web/datastore/history/AbstractHistoryStore.java
  • A src/main/java/org/bbop/apollo/web/datastore/history/AbstractHistoryStoreManager.java
  • A src/main/java/org/bbop/apollo/web/datastore/history/CompoundTransaction.java
  • A src/main/java/org/bbop/apollo/web/datastore/history/JEHistoryDatabase.java
  • A src/main/java/org/bbop/apollo/web/datastore/history/Transaction.java
  • A src/main/java/org/bbop/apollo/web/datastore/history/TransactionList.java
  • A src/main/java/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridArrayDataStore.java
  • A src/main/java/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridBetterDataStore.java
  • A src/main/java/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridDataStore.java
  • A src/main/java/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridWithTreeDataStore.java
  • A src/main/java/org/bbop/apollo/web/datastore/session/JEDatabaseSessionMemoryDataStore.java
  • A src/main/java/org/bbop/apollo/web/name/AbstractNameAdapter.java
  • A src/main/java/org/bbop/apollo/web/name/FeatureNameAdapter.java
  • A src/main/java/org/bbop/apollo/web/name/HttpSessionNameAdapter.java
  • A src/main/java/org/bbop/apollo/web/name/HttpSessionTimeStampNameAdapter.java
  • A src/main/java/org/bbop/apollo/web/name/PreDefinedNameAdapter.java
  • A src/main/java/org/bbop/apollo/web/name/TemplateNameAdapter.java
  • A src/main/java/org/bbop/apollo/web/overlap/NoOverlapper.java
  • A src/main/java/org/bbop/apollo/web/overlap/OrfOverlapper.java
  • A src/main/java/org/bbop/apollo/web/overlap/Overlapper.java
  • A src/main/java/org/bbop/apollo/web/overlap/SimpleOverlapper.java
  • A src/main/java/org/bbop/apollo/web/proxy/AbstractProxy.java
  • A src/main/java/org/bbop/apollo/web/proxy/EUtilsProxy.java
  • A src/main/java/org/bbop/apollo/web/tools/FixGeneBoundaries.java
  • A src/main/java/org/bbop/apollo/web/tools/JEDatabaseMerger.java
  • A src/main/java/org/bbop/apollo/web/tools/RemoveIsoforms.java
  • A src/main/java/org/bbop/apollo/web/tools/RemoveOrphanFeatures.java
  • A src/main/java/org/bbop/apollo/web/tools/RemoveTopLevelFeaturesById.java
  • A src/main/java/org/bbop/apollo/web/tools/UpdateSequenceAlterations.java
  • A src/main/java/org/bbop/apollo/web/tools/UpdateTranscriptToMrna.java
  • A src/main/java/org/bbop/apollo/web/track/AmelTrackNameComparator.java
  • A src/main/java/org/bbop/apollo/web/track/BtauTrackNameComparator.java
  • A src/main/java/org/bbop/apollo/web/track/DecreasingLengthTrackNameComparator.java
  • A src/main/java/org/bbop/apollo/web/track/DefaultTrackNameComparator.java
  • A src/main/java/org/bbop/apollo/web/track/IncreasingLengthTrackNameComparator.java
  • A src/main/java/org/bbop/apollo/web/track/TrackNameComparator.java
  • A src/main/java/org/bbop/apollo/web/user/Permission.java
  • A src/main/java/org/bbop/apollo/web/user/UserAuthentication.java
  • A src/main/java/org/bbop/apollo/web/user/UserAuthenticationException.java
  • A src/main/java/org/bbop/apollo/web/user/UserManager.java
  • A src/main/java/org/bbop/apollo/web/user/browserid/BrowserIdUserAuthentication.java
  • A src/main/java/org/bbop/apollo/web/user/encryptedlocaldb/EncryptedLocalDbUserAuthentication.java
  • A src/main/java/org/bbop/apollo/web/user/localdb/LocalDbUserAuthentication.java
  • A src/main/java/org/bbop/apollo/web/util/FeatureIterator.java
  • A src/main/java/org/bbop/apollo/web/util/FormatUtil.java
  • A src/main/java/org/bbop/apollo/web/util/JSONUtil.java
  • A src/main/java/org/bbop/apollo/web/util/Pair.java
  • A src/test/java/org/bbop/apollo/web/test/AnnotationEditorServiceTest.java
  • A src/test/java/org/bbop/apollo/web/test/AnnotationEditorServiceWithPersistentStorageTest.java
  • A src/test/java/org/bbop/apollo/web/test/FeatureLazyResiduesTest.java
  • A src/test/java/org/bbop/apollo/web/test/FormatUtilTest.java
  • A src/test/java/org/bbop/apollo/web/test/JEDatabasePrintValues.java
  • A src/test/java/org/bbop/apollo/web/test/JEDatabaseTest.java
  • A src/test/java/org/bbop/apollo/web/test/JEHistoryDatabasePrintValues.java
  • A src/test/java/org/bbop/apollo/web/test/JSONUtilTest.java
  • R Archive/GBOL/lib/HibernateConfigurationExporter.jar
  • R Archive/GBOL/lib/SimpleObjectFactoryExporter.jar
  • R Archive/GBOL/lib/Tidy.jar
  • R Archive/GBOL/lib/ant-1.6.5.jar
  • R Archive/GBOL/lib/ant-antlr-1.6.5.jar
  • R Archive/GBOL/lib/ant-junit-1.6.5.jar
  • R Archive/GBOL/lib/ant-launcher-1.6.5.jar
  • R Archive/GBOL/lib/ant-swing-1.6.5.jar
  • R Archive/GBOL/lib/antlr-2.7.6.jar
  • R Archive/GBOL/lib/asm-attrs.jar
  • R Archive/GBOL/lib/asm.jar
  • R Archive/GBOL/lib/c3p0-0.9.1.jar
  • R Archive/GBOL/lib/cglib-2.1.3.jar
  • R Archive/GBOL/lib/checkstyle-all.jar
  • R Archive/GBOL/lib/cleanimports.jar
  • R Archive/GBOL/lib/commons-collections-2.1.1.jar
  • R Archive/GBOL/lib/commons-logging-1.0.4.jar
  • R Archive/GBOL/lib/commons-logging-api-1.1.1.jar
  • R Archive/GBOL/lib/concurrent-1.3.2.jar
  • R Archive/GBOL/lib/dom4j-1.6.1.jar
  • R Archive/GBOL/lib/ehcache-1.2.3.jar
  • R Archive/GBOL/lib/freemarker.jar
  • R Archive/GBOL/lib/hibernate-tools.jar
  • R Archive/GBOL/lib/hibernate3.jar
  • R Archive/GBOL/lib/jaas.jar
  • R Archive/GBOL/lib/jacc-1_0-fr.jar
  • R Archive/GBOL/lib/javassist.jar
  • R Archive/GBOL/lib/jaxen-1.1-beta-7.jar
  • R Archive/GBOL/lib/jboss-cache.jar
  • R Archive/GBOL/lib/jboss-common.jar
  • R Archive/GBOL/lib/jboss-jmx.jar
  • R Archive/GBOL/lib/jboss-system.jar
  • R Archive/GBOL/lib/jgroups-2.2.8.jar
  • R Archive/GBOL/lib/jta.jar
  • R Archive/GBOL/lib/junit-3.8.1.jar
  • R Archive/GBOL/lib/log4j-1.2.11.jar
  • R Archive/GBOL/lib/oscache-2.1.jar
  • R Archive/GBOL/lib/postgresql-8.2-504.jdbc3.jar
  • R Archive/GBOL/lib/postgresql-8.3-603.jdbc3.jar
  • R Archive/GBOL/lib/proxool-0.8.3.jar
  • R Archive/GBOL/lib/resources.jar
  • R Archive/GBOL/lib/swarmcache-1.0rc2.jar
  • R Archive/GBOL/lib/syndiag2.jar
  • R Archive/GBOL/lib/version.properties
  • R Archive/GBOL/lib/versioncheck.jar
  • R Archive/GBOL/lib/xerces-2.6.2.jar
  • R Archive/GBOL/lib/xml-apis.jar
  • R server/WebApollo/src/net/crackstation/PasswordHash.java
  • R server/WebApollo/src/org/bbop/apollo/web/AnnotationChangeNotificationService.java
  • R server/WebApollo/src/org/bbop/apollo/web/AnnotationEditorService.java
  • R server/WebApollo/src/org/bbop/apollo/web/ErrorReportValve.java
  • R server/WebApollo/src/org/bbop/apollo/web/Login.java
  • R server/WebApollo/src/org/bbop/apollo/web/ProxyService.java
  • R server/WebApollo/src/org/bbop/apollo/web/UserManagerService.java
  • R server/WebApollo/src/org/bbop/apollo/web/config/CannedComments.java
  • R server/WebApollo/src/org/bbop/apollo/web/config/ServerConfiguration.java
  • R server/WebApollo/src/org/bbop/apollo/web/data/FeatureLazyResidues.java
  • R server/WebApollo/src/org/bbop/apollo/web/data/FeatureSequenceChunkManager.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/DataAdapter.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/IOService.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/chado/ChadoDataAdapter.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/chado/ChadoIO.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/chado/ChadoJEDatabaseIO.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/fasta/FastaDataAdapter.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/fasta/FastaIO.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/fasta/FastaJEDatabaseIO.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/gff3/Gff3DataAdapter.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/gff3/Gff3IO.java
  • R server/WebApollo/src/org/bbop/apollo/web/dataadapter/gff3/Gff3JEDatabaseIO.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/AbstractDataStore.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/AbstractDataStoreManager.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/DataStoreChangeEvent.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/DataStoreChangeListener.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/JEDatabase.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/JEDatabaseIterator.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/JEDatabaseSessionDataStore.java-2013-10-23
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/JESerializedDatabase.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/history/AbstractHistoryStore.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/history/AbstractHistoryStoreManager.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/history/CompoundTransaction.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/history/JEHistoryDatabase.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/history/Transaction.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/history/TransactionList.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridArrayDataStore.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridBetterDataStore.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridDataStore.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridWithTreeDataStore.java
  • R server/WebApollo/src/org/bbop/apollo/web/datastore/session/JEDatabaseSessionMemoryDataStore.java
  • R server/WebApollo/src/org/bbop/apollo/web/name/AbstractNameAdapter.java
  • R server/WebApollo/src/org/bbop/apollo/web/name/FeatureNameAdapter.java
  • R server/WebApollo/src/org/bbop/apollo/web/name/HttpSessionNameAdapter.java
  • R server/WebApollo/src/org/bbop/apollo/web/name/HttpSessionTimeStampNameAdapter.java
  • R server/WebApollo/src/org/bbop/apollo/web/name/PreDefinedNameAdapter.java
  • R server/WebApollo/src/org/bbop/apollo/web/name/TemplateNameAdapter.java
  • R server/WebApollo/src/org/bbop/apollo/web/overlap/NoOverlapper.java
  • R server/WebApollo/src/org/bbop/apollo/web/overlap/OrfOverlapper.java
  • R server/WebApollo/src/org/bbop/apollo/web/overlap/Overlapper.java
  • R server/WebApollo/src/org/bbop/apollo/web/overlap/SimpleOverlapper.java
  • R server/WebApollo/src/org/bbop/apollo/web/proxy/AbstractProxy.java
  • R server/WebApollo/src/org/bbop/apollo/web/proxy/EUtilsProxy.java
  • R server/WebApollo/src/org/bbop/apollo/web/test/AnnotationEditorServiceTest.java
  • R server/WebApollo/src/org/bbop/apollo/web/test/AnnotationEditorServiceWithPersistentStorageTest.java
  • R server/WebApollo/src/org/bbop/apollo/web/test/FeatureLazyResiduesTest.java
  • R server/WebApollo/src/org/bbop/apollo/web/test/FormatUtilTest.java
  • R server/WebApollo/src/org/bbop/apollo/web/test/JEDatabasePrintValues.java
  • R server/WebApollo/src/org/bbop/apollo/web/test/JEDatabaseTest.java
  • R server/WebApollo/src/org/bbop/apollo/web/test/JEHistoryDatabasePrintValues.java
  • R server/WebApollo/src/org/bbop/apollo/web/test/JSONUtilTest.java
  • R server/WebApollo/src/org/bbop/apollo/web/tools/FixGeneBoundaries.java
  • R server/WebApollo/src/org/bbop/apollo/web/tools/JEDatabaseMerger.java
  • R server/WebApollo/src/org/bbop/apollo/web/tools/RemoveIsoforms.java
  • R server/WebApollo/src/org/bbop/apollo/web/tools/RemoveOrphanFeatures.java
  • R server/WebApollo/src/org/bbop/apollo/web/tools/RemoveTopLevelFeaturesById.java
  • R server/WebApollo/src/org/bbop/apollo/web/tools/UpdateSequenceAlterations.java
  • R server/WebApollo/src/org/bbop/apollo/web/tools/UpdateTranscriptToMrna.java
  • R server/WebApollo/src/org/bbop/apollo/web/track/AmelTrackNameComparator.java
  • R server/WebApollo/src/org/bbop/apollo/web/track/BtauTrackNameComparator.java
  • R server/WebApollo/src/org/bbop/apollo/web/track/DecreasingLengthTrackNameComparator.java
  • R server/WebApollo/src/org/bbop/apollo/web/track/DefaultTrackNameComparator.java
  • R server/WebApollo/src/org/bbop/apollo/web/track/IncreasingLengthTrackNameComparator.java
  • R server/WebApollo/src/org/bbop/apollo/web/track/TrackNameComparator.java
  • R server/WebApollo/src/org/bbop/apollo/web/user/Permission.java
  • R server/WebApollo/src/org/bbop/apollo/web/user/UserAuthentication.java
  • R server/WebApollo/src/org/bbop/apollo/web/user/UserAuthenticationException.java
  • R server/WebApollo/src/org/bbop/apollo/web/user/UserManager.java
  • R server/WebApollo/src/org/bbop/apollo/web/user/browserid/BrowserIdUserAuthentication.java
  • R server/WebApollo/src/org/bbop/apollo/web/user/encryptedlocaldb/EncryptedLocalDbUserAuthentication.java
  • R server/WebApollo/src/org/bbop/apollo/web/user/localdb/LocalDbUserAuthentication.java
  • R server/WebApollo/src/org/bbop/apollo/web/util/FeatureIterator.java
  • R server/WebApollo/src/org/bbop/apollo/web/util/FormatUtil.java
  • R server/WebApollo/src/org/bbop/apollo/web/util/JSONUtil.java
  • R server/WebApollo/src/org/bbop/apollo/web/util/Pair.java
  • M pom.xml