Changeset 3533
- Timestamp:
- Jun 27, 2007, 11:22:48 PM (16 years ago)
- Location:
- branches/webservices
- Files:
-
- 2 deleted
- 268 edited
- 18 copied
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base2.license.txt (modified) (view diffs)
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bin/set_classpath.bat (modified) (view diffs)
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bin/set_classpath.sh (modified) (view diffs)
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build.xml (modified) (view diffs)
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config/dist/log4j.properties (modified) (view diffs)
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config/dist/raw-data-types.xml (modified) (view diffs)
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credits.txt (modified) (view diffs)
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doc/3rd-party-components.txt (modified) (view diffs)
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doc/licenses/tar.license.txt (copied) (copied from trunk/doc/licenses/tar.license.txt) (view diffs)
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doc/src/docbook/admindoc/installation_upgrade.xml (modified) (view diffs)
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doc/src/docbook/admindoc/plugin_installation.xml (modified) (view diffs)
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doc/src/docbook/appendix/base.config.xml (modified) (view diffs)
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doc/src/docbook/appendix/incompatible.xml (modified) (view diffs)
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doc/src/docbook/appendix/jobagent.properties.xml (modified) (view diffs)
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doc/src/docbook/appendix/jobagent.sh.xml (modified) (view diffs)
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doc/src/docbook/appendix/other_config.xml (modified) (view diffs)
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doc/src/docbook/developerdoc/api_overview.xml (modified) (view diffs)
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doc/src/docbook/developerdoc/core_ref.xml (modified) (view diffs)
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doc/src/docbook/developerdoc/plugin_developer.xml (modified) (view diffs)
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doc/src/docbook/developerdoc/write_docbook_doc.xml (modified) (view diffs)
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doc/src/docbook/faq/faqs.xml (modified) (view diffs)
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doc/src/docbook/overviewdoc/resources.xml (modified) (view diffs)
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doc/src/docbook/userdoc/annotations.xml (modified) (view diffs)
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doc/src/docbook/userdoc/array_lims.xml (modified) (view diffs)
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doc/src/docbook/userdoc/biomaterials.xml (modified) (view diffs)
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doc/src/docbook/userdoc/file_system.xml (modified) (view diffs)
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doc/src/docbook/userdoc/import_export_data.xml (modified) (view diffs)
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doc/src/docbook/userdoc/jobs.xml (modified) (view diffs)
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doc/src/docbook/userdoc/project_permission.xml (modified) (view diffs)
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doc/src/docbook/userdoc/reporters.xml (modified) (view diffs)
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doc/src/docbook/userdoc/trashcan.xml (modified) (view diffs)
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doc/src/docbook/userdoc/webclient.xml (modified) (view diffs)
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lib/dist/AffxFusion.jar (copied) (copied from trunk/lib/dist/AffxFusion.jar) (view diffs)
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lib/dist/bzip2.jar (copied) (copied from trunk/lib/dist/bzip2.jar) (view diffs)
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lib/dist/hibernate3.jar (modified) (view diffs)
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lib/dist/mysql-connector-java-5.0.4-bin.jar (deleted)
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lib/dist/mysql-connector-java-5.0.6-bin.jar (copied) (copied from trunk/lib/dist/mysql-connector-java-5.0.6-bin.jar) (view diffs)
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lib/dist/tar.jar (copied) (copied from trunk/lib/dist/tar.jar) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/AnnotationTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/AnnotationTypeTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ArrayBatchTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ArrayBlockTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ArraySlideTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ArrayTypePlateTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ArrayTypeTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/CommonItemTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ExperimentTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ExtractTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/FileTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/GroupTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/HardwareTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/HybridizationTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ImageFileTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/LabelTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/LabeledExtractTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/Manager.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/MappedPlateTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/MeasuredBioMaterialTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/Migrater.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/NewsTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/PlateEventTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/PlateEventTypeTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/PlateTypeTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/PluginTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ProgressThread.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ProtocolTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ProtocolTypeTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/QuotaTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayDataTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ReporterTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/RoleTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/SampleTissueTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/SampleTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/ScanTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/SharedItemTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/SoftwareTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/Transfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/UnmappedPlateTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/UploadFileTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/UserTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/WellTransfer.java (modified) (view diffs)
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src/clients/migrate/net/sf/basedb/clients/migrate/WizzzardTransfer.java (modified) (view diffs)
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src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (view diffs)
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src/clients/web/net/sf/basedb/clients/web/DuplicateWizardException.java (copied) (copied from trunk/src/clients/web/net/sf/basedb/clients/web/DuplicateWizardException.java) (view diffs)
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src/clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java (modified) (view diffs)
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src/clients/web/net/sf/basedb/clients/web/taglib/Body.java (modified) (view diffs)
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src/clients/web/net/sf/basedb/clients/web/taglib/table/PresetSelector.java (modified) (view diffs)
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src/core/common-queries.xml (modified) (view diffs)
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src/core/net/sf/basedb/core/AbstractBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/AbstractQuery.java (modified) (view diffs)
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src/core/net/sf/basedb/core/AbstractSqlQuery.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Affymetrix.java (modified) (view diffs)
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src/core/net/sf/basedb/core/AnnotationType.java (modified) (view diffs)
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src/core/net/sf/basedb/core/AnyToAny.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Application.java (modified) (view diffs)
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src/core/net/sf/basedb/core/ArrayDesign.java (modified) (view diffs)
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src/core/net/sf/basedb/core/BasicBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Client.java (modified) (view diffs)
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src/core/net/sf/basedb/core/DataCube.java (modified) (view diffs)
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src/core/net/sf/basedb/core/DbControl.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Directory.java (modified) (view diffs)
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src/core/net/sf/basedb/core/DiskUsageStatistics.java (modified) (view diffs)
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src/core/net/sf/basedb/core/ExtendedProperty.java (modified) (view diffs)
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src/core/net/sf/basedb/core/ExtraValueType.java (modified) (view diffs)
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src/core/net/sf/basedb/core/FeatureBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/File.java (modified) (view diffs)
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src/core/net/sf/basedb/core/FilterBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Formula.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Group.java (modified) (view diffs)
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src/core/net/sf/basedb/core/HibernateUtil.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Install.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Item.java (modified) (view diffs)
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src/core/net/sf/basedb/core/ItemContext.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Job.java (modified) (view diffs)
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src/core/net/sf/basedb/core/JobAgent.java (modified) (view diffs)
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src/core/net/sf/basedb/core/MappingBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/PluginDefinition.java (modified) (view diffs)
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src/core/net/sf/basedb/core/PluginResponse.java (modified) (view diffs)
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src/core/net/sf/basedb/core/PluginType.java (modified) (view diffs)
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src/core/net/sf/basedb/core/PositionBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/PositionExtraValueBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Project.java (modified) (view diffs)
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src/core/net/sf/basedb/core/PropertyFilter.java (modified) (view diffs)
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src/core/net/sf/basedb/core/QuotaException.java (modified) (view diffs)
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src/core/net/sf/basedb/core/RawBioAssay.java (modified) (view diffs)
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src/core/net/sf/basedb/core/RawDataBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Reporter.java (modified) (view diffs)
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src/core/net/sf/basedb/core/ReporterBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Role.java (modified) (view diffs)
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src/core/net/sf/basedb/core/SessionControl.java (modified) (view diffs)
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src/core/net/sf/basedb/core/SpotBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/SpotExtraValueBatcher.java (modified) (view diffs)
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src/core/net/sf/basedb/core/StringUtil.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Trashcan.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Type.java (modified) (view diffs)
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src/core/net/sf/basedb/core/Update.java (modified) (view diffs)
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src/core/net/sf/basedb/core/User.java (modified) (view diffs)
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src/core/net/sf/basedb/core/VirtualDb.java (modified) (view diffs)
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src/core/net/sf/basedb/core/data/ContextData.java (modified) (view diffs)
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src/core/net/sf/basedb/core/data/ExtraValueTypeData.java (modified) (view diffs)
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src/core/net/sf/basedb/core/data/FileData.java (modified) (view diffs)
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src/core/net/sf/basedb/core/data/FormulaData.java (modified) (view diffs)
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src/core/net/sf/basedb/core/data/GroupData.java (modified) (view diffs)
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src/core/net/sf/basedb/core/data/JobData.java (modified) (view diffs)
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src/core/net/sf/basedb/core/data/RoleData.java (modified) (view diffs)
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src/core/net/sf/basedb/core/dbengine/DbEngine.java (modified) (view diffs)
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src/core/net/sf/basedb/core/dbengine/DefaultDbEngine.java (modified) (view diffs)
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src/core/net/sf/basedb/core/dbengine/MySQLEngine.java (modified) (view diffs)
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src/core/net/sf/basedb/core/dbengine/PostgresDbEngine.java (modified) (view diffs)
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src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java (modified) (view diffs)
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src/core/net/sf/basedb/core/plugin/AbstractPlugin.java (modified) (view diffs)
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src/core/net/sf/basedb/core/plugin/InteractivePlugin.java (modified) (view diffs)
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src/core/net/sf/basedb/core/query/Aggregations.java (modified) (view diffs)
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src/core/net/sf/basedb/core/query/EqRestriction.java (modified) (view diffs)
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src/core/net/sf/basedb/core/query/GeometricMeanExpression.java (copied) (copied from trunk/src/core/net/sf/basedb/core/query/GeometricMeanExpression.java) (view diffs)
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src/core/net/sf/basedb/core/query/MeanExpression.java (modified) (view diffs)
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src/core/net/sf/basedb/core/query/NeqRestriction.java (modified) (view diffs)
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src/core/net/sf/basedb/core/query/Restrictions.java (modified) (view diffs)
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src/core/net/sf/basedb/core/templates/hibernate-properties-RawData.xml (modified) (view diffs)
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src/core/net/sf/basedb/util/ClassUtil.java (modified) (view diffs)
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src/core/net/sf/basedb/util/ContextUtil.java (copied) (copied from trunk/src/core/net/sf/basedb/util/ContextUtil.java) (view diffs)
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src/core/net/sf/basedb/util/Enumeration.java (modified) (view diffs)
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src/core/net/sf/basedb/util/FileUtil.java (modified) (view diffs)
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src/core/net/sf/basedb/util/InputStreamTracker.java (copied) (copied from trunk/src/core/net/sf/basedb/util/InputStreamTracker.java) (view diffs)
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src/core/net/sf/basedb/util/JarClassLoader.java (modified) (view diffs)
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src/core/net/sf/basedb/util/jep/Jep.java (modified) (view diffs)
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src/core/net/sf/basedb/util/overview/ExperimentOverview.java (modified) (view diffs)
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src/core/net/sf/basedb/util/parser/ColumnMapper.java (modified) (view diffs)
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src/core/net/sf/basedb/util/parser/CompoundMapper.java (modified) (view diffs)
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src/core/net/sf/basedb/util/parser/ConstantMapper.java (modified) (view diffs)
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src/core/net/sf/basedb/util/parser/FlatFileParser.java (modified) (view diffs)
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src/core/net/sf/basedb/util/parser/NullIfExceptionMapper.java (copied) (copied from trunk/src/core/net/sf/basedb/util/parser/NullIfExceptionMapper.java) (view diffs)
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src/core/net/sf/basedb/util/zip/AbstractFileUnpacker.java (modified) (view diffs)
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src/install/net/sf/basedb/install/Webclient.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/AbstractFlatFileImporter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/CdfFileReporterImporter.java (copied) (copied from trunk/src/plugins/core/net/sf/basedb/plugins/CdfFileReporterImporter.java) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/FormulaFilter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/IntensityCalculatorPlugin.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/JepIntensityTransformer.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/PlateFlatFileImporter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/PluginConfigurationExporter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/PluginConfigurationImporter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/PrintMapFlatFileImporter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/RawDataFlatFileImporter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/ReporterFlatFileImporter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/ReporterMapFlatFileImporter.java (modified) (view diffs)
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src/plugins/core/net/sf/basedb/plugins/TarFileUnpacker.java (copied) (copied from trunk/src/plugins/core/net/sf/basedb/plugins/TarFileUnpacker.java) (view diffs)
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src/test/TestAll.java (modified) (view diffs)
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src/test/TestAnalyzePluginUtil.java (modified) (view diffs)
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src/test/TestAnnotationType.java (modified) (view diffs)
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src/test/TestAnyToAny.java (modified) (view diffs)
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src/test/TestBase1PluginExecuter.java (modified) (view diffs)
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src/test/TestDirty.java (copied) (copied from trunk/src/test/TestDirty.java) (view diffs)
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src/test/TestNumberFormat.java (modified) (view diffs)
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src/test/TestProject.java (modified) (view diffs)
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src/test/TestRawBioAssay.java (modified) (view diffs)
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src/test/TestRawDataFlatFileImporter.java (modified) (view diffs)
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src/test/TestReporter.java (modified) (view diffs)
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src/test/TestUser.java (modified) (view diffs)
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src/test/data/test.import.dirty.txt (copied) (copied from trunk/src/test/data/test.import.dirty.txt) (view diffs)
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src/test/nullbase1plugin.jar (deleted)
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src/test/runplugin.sh (modified) (view diffs)
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src/test/set_classpath.bat (modified) (view diffs)
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src/test/set_classpath.sh (modified) (view diffs)
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www/WEB-INF/table.tld (modified) (view diffs)
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www/admin/annotationtypes/list_annotationtypes.jsp (modified) (view diffs)
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www/admin/diskusage/details/index.jsp (modified) (view diffs)
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www/admin/diskusage/details/view_details.jsp (modified) (view diffs)
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www/admin/diskusage/list_groups.jsp (modified) (view diffs)
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www/admin/diskusage/list_users.jsp (modified) (view diffs)
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www/admin/diskusage/overview.jsp (modified) (view diffs)
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www/admin/groups/edit_group.jsp (modified) (view diffs)
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www/admin/groups/index.jsp (modified) (view diffs)
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www/admin/groups/list_groups.jsp (modified) (view diffs)
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www/admin/groups/view_group.jsp (modified) (view diffs)
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www/admin/pluginconfigurations/index.jsp (modified) (view diffs)
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www/admin/pluginconfigurations/list_configurations.jsp (modified) (view diffs)
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www/admin/plugindefinitions/edit_plugin.jsp (modified) (view diffs)
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www/admin/plugindefinitions/index.jsp (modified) (view diffs)
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www/admin/plugindefinitions/list_plugins.jsp (modified) (view diffs)
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www/admin/plugindefinitions/view_plugin.jsp (modified) (view diffs)
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www/admin/roles/edit_role.jsp (modified) (view diffs)
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www/admin/roles/index.jsp (modified) (view diffs)
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www/admin/roles/list_roles.jsp (modified) (view diffs)
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www/admin/roles/view_role.jsp (modified) (view diffs)
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www/admin/users/edit_default_membership.jsp (copied) (copied from trunk/www/admin/users/edit_default_membership.jsp) (view diffs)
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www/admin/users/edit_user.jsp (modified) (view diffs)
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www/admin/users/index.jsp (modified) (view diffs)
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www/admin/users/list_users.jsp (modified) (view diffs)
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www/common/annotations/annotate.jsp (modified) (view diffs)
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www/common/expression_builder.jsp (modified) (view diffs)
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www/common/import/index.jsp (modified) (view diffs)
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www/common/import/select_plugin.jsp (modified) (view diffs)
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www/common/plugin/configure.jsp (modified) (view diffs)
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www/common/plugin/download_immediately.jsp (modified) (view diffs)
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www/common/plugin/finish_job.jsp (modified) (view diffs)
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www/common/plugin/index.jsp (modified) (view diffs)
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www/common/plugin/select_plugin.jsp (modified) (view diffs)
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www/exception/duplicate_wizard.jsp (copied) (copied from trunk/www/exception/duplicate_wizard.jsp) (view diffs)
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www/exception/exception.jsp (modified) (view diffs)
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www/exception/invalid_data.jsp (modified) (view diffs)
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www/exception/permission_denied.jsp (modified) (view diffs)
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www/exception/web.jsp (modified) (view diffs)
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www/favicon.ico (copied) (copied from trunk/www/favicon.ico) (view diffs)
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www/filemanager/files/edit_file.jsp (modified) (view diffs)
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www/filemanager/files/index.jsp (modified) (view diffs)
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www/filemanager/files/list_files.jsp (modified) (view diffs)
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www/filemanager/files/view_file.jsp (modified) (view diffs)
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www/filemanager/upload/select.jsp (modified) (view diffs)
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