# # ChangeLog for trunk/src/misc # # Generated by Trac 1.2.3 # Jun 28, 2022, 6:32:57 PM Thu, 11 Sep 2008 20:05:50 GMT Jari Häkkinen [4512] * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/Agent.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/AgentController.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/AgentSignalReceiver.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/CmdLine.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/JobExecutor.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/JobQueueChecker.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/JobRunner.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/executors/DummyJobExecutor.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/executors/ProcessJobExecutor.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/executors/ThreadJobExecutor.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/handlers/DefaultRequestHandler.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/handlers/InfoRequestHandler.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/handlers/PauseRequestHandler.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/handlers/PingRequestHandler.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/handlers/SignalRequestHandler.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/handlers/StartRequestHandler.java (modified) * trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/handlers/StopRequestHandler.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/AnnotationTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/AnnotationTypeTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArrayBatchTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArrayBlockTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArraySlideTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArrayTypePlateTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArrayTypeTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/CommonItemTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ExperimentTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ExtractTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/FileTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/GroupTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/HardwareTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/HybridizationTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ImageFileTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/LabelTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/LabeledExtractTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/Manager.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/MappedPlateTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/MeasuredBioMaterialTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/Migrater.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/NewsTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/PlateEventTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/PlateEventTypeTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/PlateTypeTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/PluginTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ProgressThread.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ProtocolTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ProtocolTypeTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/QuotaTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayDataTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ReporterProxy.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ReporterTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/RoleTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/SampleTissueTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/SampleTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ScanTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/SharedItemTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/SoftwareTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/Transfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/UnmappedPlateTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/UploadFileTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/UserTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/WellTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/WizzzardTransfer.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/WrappedDataItem.java (modified) * trunk/src/clients/migrate/net/sf/basedb/clients/migrate/WrappedItem.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/Base.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/DuplicateWizardException.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/ModeInfo.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/PermissionUtil.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/WebException.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/dtd/export.dtd (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/dtd/tableinfo.dtd (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/AbstractJspActionFactory.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/AbstractJspFactory.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/AbstractJspRendererFactory.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/ExtensionsControl.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/ExtensionsDirectory.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/ExtensionsFile.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/JspContext.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/ScanResults.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/ServletLoader.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/ServletWrapper.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/Settings.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/menu/FixedMenuItemFactory.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/menu/MenuItemAction.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/menu/MenuItemBean.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/menu/PermissionMenuItemFactory.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/service/DummyService.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/service/ServiceControllerAction.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/service/Services.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/service/ServicesEventHandler.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/service/StartServiceRenderer.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/service/StopServiceRenderer.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/ButtonAction.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/ButtonBean.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/CompactButtonRenderer.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/CompactButtonRendererFactory.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/FixedButtonFactory.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/PermissionButtonFactory.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/fileupload/FileUpload.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/fileupload/FileUploadProgress.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/fileupload/UploadAbortedException.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/fileupload/UploadedFile.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/fileupload/package.html (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/formatter/ColorFormatter.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/formatter/ExtendedPropertyFormatter.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/formatter/FormatterFactory.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/formatter/FormatterSettings.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/formatter/SpotImageFormatter.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/formatter/StringFormatter.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/plugins/DataQueryWrapper.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/plugins/DynamicQueryWrapper.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/plugins/ExportTemplate.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/plugins/ExportedProperty.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/plugins/ItemQueryWrapper.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/plugins/PlainTextTemplate.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/plugins/QueryWrapper.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/plugins/ReporterScoreQueryWrapper.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/plugins/XMLTemplate.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/servlet/CharacterEncodingFilter.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/servlet/CompileAll.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/servlet/Download.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/servlet/ExtensionsServlet.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/servlet/PlotServlet.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/servlet/StartStopServlet.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/servlet/ViewSpotImage.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Body.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Button.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/ButtonGroup.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Head.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Help.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/HideableSection.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Icon.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Note.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Page.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/PropertyValue.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Select.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/extensions/Render.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/extensions/Scripts.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/extensions/Stylesheets.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/menu/Menu.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/menu/Menuitem.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/menu/Menuseparator.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/menu/Submenu.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/menu/package.html (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/path/Path.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/path/PathElement.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/tab/Tab.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/tab/TabControl.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/tab/package.html (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/tab/tab.css (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/tab/tab.js (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/tab/tab.tld (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Button.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Cell.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/CellValue.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/ColumnDef.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Columns.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Data.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Header.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Hidden.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Label.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Navigator.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Panel.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/PresetSelector.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/PropertyFilter.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Row.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Rows.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Table.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/TableColumn.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Toolbar.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/package.html (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/util/HTML.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/util/NameablePluginAdaptor.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/util/ServletExportOutputStream.java (modified) * trunk/src/clients/web/net/sf/basedb/clients/web/util/SimpleSignalProgressReporter.java (modified) * trunk/src/info/net/sf/basedb/info/AnnotatedItemInfo.java (modified) * trunk/src/info/net/sf/basedb/info/AnnotationInfo.java (modified) * trunk/src/info/net/sf/basedb/info/AnnotationTypeInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ArrayDesignInfo.java (modified) * trunk/src/info/net/sf/basedb/info/BasicItemInfo.java (modified) * trunk/src/info/net/sf/basedb/info/BioAssaySetInfo.java (modified) * trunk/src/info/net/sf/basedb/info/CommonItemInfo.java (modified) * trunk/src/info/net/sf/basedb/info/DataFileTypeInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ExperimentInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ExtendedPropertyInfo.java (modified) * trunk/src/info/net/sf/basedb/info/NameableInfo.java (modified) * trunk/src/info/net/sf/basedb/info/OwnedItemInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ProjectInfo.java (modified) * trunk/src/info/net/sf/basedb/info/QueryOptions.java (modified) * trunk/src/info/net/sf/basedb/info/QueryParameter.java (modified) * trunk/src/info/net/sf/basedb/info/RawBioAssayInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ReporterListInfo.java (modified) * trunk/src/info/net/sf/basedb/info/SharedItemInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ToTransferable.java (modified) * trunk/src/info/net/sf/basedb/info/Transferable.java (modified) * trunk/src/info/net/sf/basedb/info/VersionInfo.java (modified) * trunk/src/info/net/sf/basedb/info/package.html (modified) * trunk/src/install/net/sf/basedb/install/InitDB.java (modified) * trunk/src/install/net/sf/basedb/install/OneTimeFix.java (modified) * trunk/src/install/net/sf/basedb/install/Webclient.java (modified) * trunk/src/misc/compiler/net/sf/basedb/clients/web/extensions/XJspCompiler.java (modified) Addresses #1106. Missed to change reference wherefrom retrive GPLv3 ... Fri, 05 Sep 2008 15:16:58 GMT Jari Häkkinen [4480] * trunk/.svndigest/config (modified) * trunk/src/info/net/sf/basedb/info/AnnotatedItemInfo.java (modified) * trunk/src/info/net/sf/basedb/info/AnnotationInfo.java (modified) * trunk/src/info/net/sf/basedb/info/AnnotationTypeInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ArrayDesignInfo.java (modified) * trunk/src/info/net/sf/basedb/info/BasicItemInfo.java (modified) * trunk/src/info/net/sf/basedb/info/BioAssaySetInfo.java (modified) * trunk/src/info/net/sf/basedb/info/CommonItemInfo.java (modified) * trunk/src/info/net/sf/basedb/info/DataFileTypeInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ExperimentInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ExtendedPropertyInfo.java (modified) * trunk/src/info/net/sf/basedb/info/NameableInfo.java (modified) * trunk/src/info/net/sf/basedb/info/OwnedItemInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ProjectInfo.java (modified) * trunk/src/info/net/sf/basedb/info/QueryOptions.java (modified) * trunk/src/info/net/sf/basedb/info/QueryParameter.java (modified) * trunk/src/info/net/sf/basedb/info/RawBioAssayInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ReporterListInfo.java (modified) * trunk/src/info/net/sf/basedb/info/SharedItemInfo.java (modified) * trunk/src/info/net/sf/basedb/info/ToTransferable.java (modified) * trunk/src/info/net/sf/basedb/info/Transferable.java (modified) * trunk/src/info/net/sf/basedb/info/VersionInfo.java (modified) * trunk/src/info/net/sf/basedb/info/package.html (modified) * trunk/src/install/net/sf/basedb/install/InitDB.java (modified) * trunk/src/install/net/sf/basedb/install/OneTimeFix.java (modified) * trunk/src/install/net/sf/basedb/install/Webclient.java (modified) * trunk/src/misc/compiler/net/sf/basedb/clients/web/extensions/XJspCompiler.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/AbstractFlatFileImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/CdfFileReporterImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/FormulaFilter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/GalExporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/HelpExporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/HelpImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/IntensityCalculatorPlugin.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/JepExtraValueCalculator.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/JepIntensityTransformer.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/LowessNormalization.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/PackedFileExporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/PlateFlatFileImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/PlateMappingExporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/PlateMappingImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/PluginConfigurationExporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/PluginConfigurationImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/PrintMapFlatFileImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/RawDataFlatFileImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/ReporterFlatFileImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/ReporterMapFlatFileImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/SpotImageCreator.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/TarFileUnpacker.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/ZipFileUnpacker.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/AbstractItemImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ArrayBatchImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ArrayDesignImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ArraySlideImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/BioSourceImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ExtractImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/FallbackIdMethod.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/HybridizationImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/IdMethod.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/InternalIdMethod.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/LabeledExtractImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/MultiPropertyIdMethod.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/PropertyIdMethod.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/RawBioAssayImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/SampleImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ScanImporter.java (modified) * trunk/src/plugins/core/net/sf/basedb/plugins/util/Parameters.java (modified) * trunk/src/test/Base1NullPlugin.java (modified) * trunk/src/test/Base1TestPlugin.java (modified) * trunk/src/test/JarPlugin.java (modified) * trunk/src/test/JarPluginAbout.java (modified) * trunk/src/test/JarPluginInterface.java (modified) * trunk/src/test/JarPluginType.java (modified) * trunk/src/test/NullPlugin.java (modified) * trunk/src/test/NullPluginInterface.java (modified) * trunk/src/test/PermissionPlugin.java (modified) * trunk/src/test/TestAll.java (modified) * trunk/src/test/TestAnalyzePluginUtil.java (modified) * trunk/src/test/TestAnnotation.java (modified) * trunk/src/test/TestAnnotationFlatFileImporter.java (modified) * trunk/src/test/TestAnnotationType.java (modified) * trunk/src/test/TestAnnotationTypeCategory.java (modified) * trunk/src/test/TestAnyToAny.java (modified) * trunk/src/test/TestArrayBatch.java (modified) * trunk/src/test/TestArrayDesign.java (modified) * trunk/src/test/TestArrayDesignBlock.java (modified) * trunk/src/test/TestArraySlide.java (modified) * trunk/src/test/TestBase1PluginExecuter.java (modified) * trunk/src/test/TestBioAsssaySetExporter.java (modified) * trunk/src/test/TestBioSource.java (modified) * trunk/src/test/TestClient.java (modified) * trunk/src/test/TestClientDefaultSetting.java (modified) * trunk/src/test/TestContext.java (modified) * trunk/src/test/TestDataFileType.java (modified) * trunk/src/test/TestDbControl.java (modified) * trunk/src/test/TestDbInfo.java (modified) * trunk/src/test/TestDirectory.java (modified) * trunk/src/test/TestDirty.java (modified) * trunk/src/test/TestDiskUsage.java (modified) * trunk/src/test/TestDropIndexes.java (modified) * trunk/src/test/TestExperiment.java (modified) * trunk/src/test/TestExtensions.java (modified) * trunk/src/test/TestExternalPluginInstaller.java (modified) * trunk/src/test/TestExtraValueType.java (modified) * trunk/src/test/TestExtract.java (modified) * trunk/src/test/TestFile.java (modified) * trunk/src/test/TestFileType.java (modified) * trunk/src/test/TestFlatFileParser.java (modified) * trunk/src/test/TestFormula.java (modified) * trunk/src/test/TestGalExporter.java (modified) * trunk/src/test/TestGlobalDefaultSetting.java (modified) * trunk/src/test/TestGroup.java (modified) * trunk/src/test/TestHardware.java (modified) * trunk/src/test/TestHardwareType.java (modified) * trunk/src/test/TestHelp.java (modified) * trunk/src/test/TestHybridization.java (modified) * trunk/src/test/TestIlluminaImporter.java (modified) * trunk/src/test/TestInstall.java (modified) * trunk/src/test/TestItemImporter.java (modified) * trunk/src/test/TestItemKey.java (modified) * trunk/src/test/TestJarClassLoader.java (modified) * trunk/src/test/TestJep.java (modified) * trunk/src/test/TestJob.java (modified) * trunk/src/test/TestJobAgent.java (modified) * trunk/src/test/TestLabel.java (modified) * trunk/src/test/TestLabeledExtract.java (modified) * trunk/src/test/TestLowessNormalization.java (modified) * trunk/src/test/TestMedianRatioNormalization.java (modified) * trunk/src/test/TestMessage.java (modified) * trunk/src/test/TestMimeType.java (modified) * trunk/src/test/TestNews.java (modified) * trunk/src/test/TestNumberFormat.java (modified) * trunk/src/test/TestPackedFileExporter.java (modified) * trunk/src/test/TestParameterType.java (modified) * trunk/src/test/TestPath.java (modified) * trunk/src/test/TestPlate.java (modified) * trunk/src/test/TestPlateFlatFileImporter.java (modified) * trunk/src/test/TestPlateGeometry.java (modified) * trunk/src/test/TestPlateMapping.java (modified) * trunk/src/test/TestPlateType.java (modified) * trunk/src/test/TestPlatform.java (modified) * trunk/src/test/TestPluginConfiguration.java (modified) * trunk/src/test/TestPluginDefinition.java (modified) * trunk/src/test/TestPluginType.java (modified) * trunk/src/test/TestPresets.java (modified) * trunk/src/test/TestPrintMapFlatFileImporter.java (modified) * trunk/src/test/TestProject.java (modified) * trunk/src/test/TestProjectKey.java (modified) * trunk/src/test/TestProtocol.java (modified) * trunk/src/test/TestProtocolType.java (modified) * trunk/src/test/TestQuota.java (modified) * trunk/src/test/TestQuotaType.java (modified) * trunk/src/test/TestRawBioAssay.java (modified) * trunk/src/test/TestRawDataFlatFileImporter.java (modified) * trunk/src/test/TestReporter.java (modified) * trunk/src/test/TestReporterFlatFileImporter.java (modified) * trunk/src/test/TestReporterList.java (modified) * trunk/src/test/TestReporterMapFlatFileImporter.java (modified) * trunk/src/test/TestReporterType.java (modified) * trunk/src/test/TestRole.java (modified) * trunk/src/test/TestRoleKey.java (modified) * trunk/src/test/TestSample.java (modified) * trunk/src/test/TestScan.java (modified) * trunk/src/test/TestSession.java (modified) * trunk/src/test/TestSessionControl.java (modified) * trunk/src/test/TestSoftware.java (modified) * trunk/src/test/TestSoftwareType.java (modified) * trunk/src/test/TestSpotImages.java (modified) * trunk/src/test/TestTrashcan.java (modified) * trunk/src/test/TestUpdate.java (modified) * trunk/src/test/TestUpdateIndexes.java (modified) * trunk/src/test/TestUser.java (modified) * trunk/src/test/TestUserClientSetting.java (modified) * trunk/src/test/TestUserDefaultSetting.java (modified) * trunk/src/test/TestUtil.java (modified) * trunk/src/test/TestWebservices.java (modified) * trunk/src/test/TestXMLUtil.java (modified) * trunk/src/test/data/extended-properties.dtd (modified) * trunk/src/test/data/extended-properties.xml (modified) * trunk/src/test/data/test.extensions.xml (modified) * trunk/src/test/data/test.schema.xml (modified) * trunk/src/test/data/test.schema.xsd (modified) * trunk/src/test/net/sf/basedb/test/AffymetrixData.java (modified) * trunk/src/test/net/sf/basedb/test/CmdLine.java (modified) * trunk/src/test/net/sf/basedb/test/FileUtil.java (modified) * trunk/src/test/net/sf/basedb/test/MouseData.java (modified) * trunk/src/test/net/sf/basedb/test/PluginUtil.java (modified) * trunk/src/test/net/sf/basedb/test/TestUtil.java (modified) * trunk/src/test/net/sf/basedb/test/merge/MergeTest.java (modified) * trunk/src/test/net/sf/basedb/test/merge/Run.java (modified) * trunk/src/test/net/sf/basedb/test/performance/Config.java (modified) * trunk/src/test/net/sf/basedb/test/performance/FilterTest.java (modified) * trunk/src/test/net/sf/basedb/test/performance/LowessTest.java (modified) * trunk/src/test/net/sf/basedb/test/performance/PrepareTest.java (modified) * trunk/src/test/net/sf/basedb/test/performance/RawDataTest.java (modified) * trunk/src/test/net/sf/basedb/test/performance/RootTest.java (modified) * trunk/src/test/net/sf/basedb/test/performance/Run.java (modified) * trunk/src/test/net/sf/basedb/test/performance/Util.java (modified) * trunk/src/test/net/sf/basedb/test/roles/AdminTest.java (modified) * trunk/src/test/net/sf/basedb/test/roles/AnalysisTest.java (modified) * trunk/src/test/net/sf/basedb/test/roles/GuestTest.java (modified) * trunk/src/test/net/sf/basedb/test/roles/PowerUserTest.java (modified) * trunk/src/test/net/sf/basedb/test/roles/RootTest.java (modified) * trunk/src/test/net/sf/basedb/test/roles/Run.java (modified) * trunk/src/test/net/sf/basedb/test/roles/UserTest.java (modified) * trunk/src/test/net/sf/basedb/test/roles/Util.java (modified) * trunk/src/test/run.bat (modified) * trunk/src/test/run.sh (modified) * trunk/src/test/set_classpath.bat (modified) * trunk/src/test/set_classpath.sh (modified) * trunk/src/test/test.bat (modified) * trunk/src/test/test.sh (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/AbstractRPCClient.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/AnnotationTypeClient.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/ArrayDesignClient.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/BioAssaySetClient.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/ConfigurableServiceFactory.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/ExperimentClient.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/Factories.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/ProjectClient.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/RawBioAssayClient.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/ReporterClient.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/ServiceFactory.java (modified) * trunk/src/webservices/client/java/net/sf/basedb/ws/client/SessionClient.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/AbstractRPCService.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/AnnotationTypeService.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/ArrayDesignService.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/BaseFileDataSource.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/BioAssaySetService.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/ExperimentService.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/ProjectService.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/RawBioAssayService.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/ReporterService.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/ServicesUtil.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/SessionService.java (modified) * trunk/src/webservices/server/net/sf/basedb/ws/server/TempFileDataSource.java (modified) Addresses #1106. Moving to GPLv3 in chunked commits. Fri, 05 Sep 2008 15:09:28 GMT Jari Häkkinen [4472] * trunk/src/misc/compiler/net/sf/basedb/clients/web/extensions/XJspCompiler.java (modified) Fixing svn properties. Fri, 05 Sep 2008 15:09:05 GMT Jari Häkkinen [4471] * trunk/src/misc/compiler/net/sf/basedb/clients/web/extensions/XJspCompiler.java (modified) Fixing svn properties. Tue, 15 Apr 2008 12:24:33 GMT Nicklas Nordborg [4222] * trunk/build.xml (modified) * trunk/config/dist/web.xml (modified) * trunk/lib/servlet/jasper.jar (added) * trunk/lib/servlet/tomcat-juli.jar (added) * trunk/src/misc (added) * trunk/src/misc/compiler (added) * trunk/src/misc/compiler/net (added) * trunk/src/misc/compiler/net/sf (added) * trunk/src/misc/compiler/net/sf/basedb (added) * trunk/src/misc/compiler/net/sf/basedb/clients (added) * trunk/src/misc/compiler/net/sf/basedb/clients/web (added) * trunk/src/misc/compiler/net/sf/basedb/clients/web/extensions (added) * trunk/src/misc/compiler/net/sf/basedb/clients/web/extensions/XJspCompiler.java (added) References #989: Add support for using extension classes in custom ...