Changeset 3827

Timestamp:

Oct 12, 2007, 9:04:29 PM (16 years ago)

Author:

Jari Häkkinen

Message:

Merged log:trunk#3795:3824 into webservices branch.

Location:

branches/webservices

Files:

• build.xml (modified) (view diffs)
• config/dist/base.config (modified) (view diffs)
• config/dist/mysql-migration-queries.sql (modified) (view diffs)
• config/dist/raw-data-types.xml (modified) (view diffs)
• doc (modified) (view diffs)
• doc/3rd-party-components.txt (modified) (view diffs)
• doc/development/overview/core/data_in_files.html (modified) (view diffs)
• doc/development/overview/data/authentication.png (deleted)
• doc/development/overview/data/basic-class-hierarchy.png (modified) (view diffs)
• doc/development/overview/data/data_in_files.html (modified) (view diffs)
• doc/development/overview/data/files.png (modified) (view diffs)
• doc/src/docbook/admindoc/installation_upgrade.xml (modified) (view diffs)
• doc/src/docbook/admindoc/plugin_installation.xml (modified) (view diffs)
• doc/src/docbook/appendix/base.config.xml (modified) (view diffs)
• doc/src/docbook/appendix/menuguide.xml (modified) (view diffs)
• doc/src/docbook/appendix/raw_data_types.xml (modified) (view diffs)
• doc/src/docbook/developerdoc/api_overview.xml (modified) (view diffs)
• doc/src/docbook/developerdoc/core_ref.xml (modified) (view diffs)
• doc/src/docbook/developerdoc/index.xml (modified) (view diffs)
• doc/src/docbook/developerdoc/plugin_developer.xml (modified) (view diffs)
• doc/src/docbook/developerdoc/write_docbook_doc.xml (deleted)
• doc/src/docbook/figures/magicdraw (copied) (copied from trunk/doc/src/docbook/figures/magicdraw) (view diffs)
• doc/src/docbook/figures/plugin_autoinstall.png (copied) (copied from trunk/doc/src/docbook/figures/plugin_autoinstall.png) (view diffs)
• doc/src/docbook/figures/select_install.png (copied) (copied from trunk/doc/src/docbook/figures/select_install.png) (view diffs)
• doc/src/docbook/figures/uml (copied) (copied from trunk/doc/src/docbook/figures/uml) (view diffs)
• doc/src/docbook/figures/uml/corelayer.datainfiles.png (copied) (copied from trunk/doc/src/docbook/figures/uml/corelayer.datainfiles.png) (view diffs)
• doc/src/docbook/figures/uml/datalayer.files.png (copied) (copied from trunk/doc/src/docbook/figures/uml/datalayer.files.png) (view diffs)
• doc/src/docbook/figures/uml/datalayer.platforms.png (copied) (copied from trunk/doc/src/docbook/figures/uml/datalayer.platforms.png) (view diffs)
• doc/src/docbook/figures/upload_file.png (modified) (view diffs)
• doc/src/docbook/overviewdoc/resources.xml (modified) (view diffs)
• doc/src/docbook/userdoc/about.xml (deleted)
• doc/src/docbook/userdoc/file_system.xml (modified) (view diffs)
• doc/src/docbook/userdoc/index.xml (modified) (view diffs)
• doc/src/docbook/userdoc/overview.xml (copied) (copied from trunk/doc/src/docbook/userdoc/overview.xml) (view diffs)
• doc/src/docbook/userdoc/project_permission.xml (modified) (view diffs)
• doc/src/docbook/userdoc/webclient.xml (modified) (view diffs)
• doc/src/uml (copied) (copied from trunk/doc/src/uml) (view diffs)
• lib/dist/AffxFusion.jar (modified) (view diffs)
• lib/docbook/custom-styles/docbook/plain/xsl/customized.chunked.xsl (modified) (view diffs)
• lib/docbook/docbook/xsl/html/table.xsl (modified) (view diffs)
• lib/docbook/preprocess/dweiss-docbook-extensions.dtd (modified) (view diffs)
• src/clients/migrate/net/sf/basedb/clients/migrate/ArrayTypeTransfer.java (modified) (view diffs)
• src/clients/migrate/net/sf/basedb/clients/migrate/FileTransfer.java (modified) (view diffs)
• src/clients/migrate/net/sf/basedb/clients/migrate/Migrater.java (modified) (view diffs)
• src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayDataTransfer.java (modified) (view diffs)
• src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayTransfer.java (modified) (view diffs)
• src/clients/migrate/net/sf/basedb/clients/migrate/UploadFileTransfer.java (modified) (view diffs)
• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (view diffs)
• src/clients/web/net/sf/basedb/clients/web/PermissionUtil.java (modified) (view diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/Navigator.java (modified) (view diffs)
• src/core/common-queries.xml (modified) (view diffs)
• src/core/net/sf/basedb/core/Affymetrix.java (modified) (view diffs)
• src/core/net/sf/basedb/core/Application.java (modified) (view diffs)
• src/core/net/sf/basedb/core/ArrayDesign.java (modified) (view diffs)
• src/core/net/sf/basedb/core/BasicChildItem.java (copied) (copied from trunk/src/core/net/sf/basedb/core/BasicChildItem.java) (view diffs)
• src/core/net/sf/basedb/core/Config.java (modified) (view diffs)
• src/core/net/sf/basedb/core/DataFileType.java (copied) (copied from trunk/src/core/net/sf/basedb/core/DataFileType.java) (view diffs)
• src/core/net/sf/basedb/core/Directory.java (modified) (view diffs)
• src/core/net/sf/basedb/core/Experiment.java (modified) (view diffs)
• src/core/net/sf/basedb/core/FeatureBatcher.java (modified) (view diffs)
• src/core/net/sf/basedb/core/File.java (modified) (view diffs)
• src/core/net/sf/basedb/core/FileSet.java (copied) (copied from trunk/src/core/net/sf/basedb/core/FileSet.java) (view diffs)
• src/core/net/sf/basedb/core/FileSetMember.java (copied) (copied from trunk/src/core/net/sf/basedb/core/FileSetMember.java) (view diffs)
• src/core/net/sf/basedb/core/FileStoreEnabled.java (copied) (copied from trunk/src/core/net/sf/basedb/core/FileStoreEnabled.java) (view diffs)
• src/core/net/sf/basedb/core/FileStoreUtil.java (copied) (copied from trunk/src/core/net/sf/basedb/core/FileStoreUtil.java) (view diffs)
• src/core/net/sf/basedb/core/Install.java (modified) (view diffs)
• src/core/net/sf/basedb/core/InvalidPathException.java (modified) (view diffs)
• src/core/net/sf/basedb/core/InvalidRelationException.java (copied) (copied from trunk/src/core/net/sf/basedb/core/InvalidRelationException.java) (view diffs)
• src/core/net/sf/basedb/core/Item.java (modified) (view diffs)
• src/core/net/sf/basedb/core/ItemContext.java (modified) (view diffs)
• src/core/net/sf/basedb/core/Job.java (modified) (view diffs)
• src/core/net/sf/basedb/core/Metadata.java (modified) (view diffs)
• src/core/net/sf/basedb/core/MimeType.java (modified) (view diffs)
• src/core/net/sf/basedb/core/ParameterType.java (modified) (view diffs)
• src/core/net/sf/basedb/core/ParameterValuesImpl.java (modified) (view diffs)
• src/core/net/sf/basedb/core/Path.java (modified) (view diffs)
• src/core/net/sf/basedb/core/PathParameterType.java (modified) (view diffs)
• src/core/net/sf/basedb/core/Platform.java (copied) (copied from trunk/src/core/net/sf/basedb/core/Platform.java) (view diffs)
• src/core/net/sf/basedb/core/PlatformFileType.java (copied) (copied from trunk/src/core/net/sf/basedb/core/PlatformFileType.java) (view diffs)
• src/core/net/sf/basedb/core/PlatformVariant.java (copied) (copied from trunk/src/core/net/sf/basedb/core/PlatformVariant.java) (view diffs)
• src/core/net/sf/basedb/core/PluginConfiguration.java (modified) (view diffs)
• src/core/net/sf/basedb/core/PluginDefinition.java (modified) (view diffs)
• src/core/net/sf/basedb/core/RawBioAssay.java (modified) (view diffs)
• src/core/net/sf/basedb/core/RawDataBatcher.java (modified) (view diffs)
• src/core/net/sf/basedb/core/RawDataType.java (modified) (view diffs)
• src/core/net/sf/basedb/core/RawDataTypes.java (modified) (view diffs)
• src/core/net/sf/basedb/core/Scan.java (modified) (view diffs)
• src/core/net/sf/basedb/core/SimpleProgressReporter.java (modified) (view diffs)
• src/core/net/sf/basedb/core/SpotImages.java (modified) (view diffs)
• src/core/net/sf/basedb/core/SystemItem.java (modified) (view diffs)
• src/core/net/sf/basedb/core/Update.java (modified) (view diffs)
• src/core/net/sf/basedb/core/data/ArrayDesignData.java (modified) (view diffs)
• src/core/net/sf/basedb/core/data/DataFileTypeData.java (copied) (copied from trunk/src/core/net/sf/basedb/core/data/DataFileTypeData.java) (view diffs)
• src/core/net/sf/basedb/core/data/DirectoryData.java (modified) (view diffs)
• src/core/net/sf/basedb/core/data/FileData.java (modified) (view diffs)
• src/core/net/sf/basedb/core/data/FileSetData.java (copied) (copied from trunk/src/core/net/sf/basedb/core/data/FileSetData.java) (view diffs)
• src/core/net/sf/basedb/core/data/FileSetMemberData.java (copied) (copied from trunk/src/core/net/sf/basedb/core/data/FileSetMemberData.java) (view diffs)
• src/core/net/sf/basedb/core/data/FileStoreEnabledData.java (copied) (copied from trunk/src/core/net/sf/basedb/core/data/FileStoreEnabledData.java) (view diffs)
• src/core/net/sf/basedb/core/data/FileTypeIndex.java (copied) (copied from trunk/src/core/net/sf/basedb/core/data/FileTypeIndex.java) (view diffs)
• src/core/net/sf/basedb/core/data/MimeTypeData.java (modified) (view diffs)
• src/core/net/sf/basedb/core/data/PlatformData.java (copied) (copied from trunk/src/core/net/sf/basedb/core/data/PlatformData.java) (view diffs)
• src/core/net/sf/basedb/core/data/PlatformFileTypeData.java (copied) (copied from trunk/src/core/net/sf/basedb/core/data/PlatformFileTypeData.java) (view diffs)
• src/core/net/sf/basedb/core/data/PlatformVariantData.java (copied) (copied from trunk/src/core/net/sf/basedb/core/data/PlatformVariantData.java) (view diffs)
• src/core/net/sf/basedb/core/data/RawBioAssayData.java (modified) (view diffs)
• src/core/net/sf/basedb/core/data/SystemData.java (modified) (view diffs)
• src/core/net/sf/basedb/core/filehandler (copied) (copied from trunk/src/core/net/sf/basedb/core/filehandler) (view diffs)
• src/core/net/sf/basedb/core/filehandler/AbstractDataFileHandler.java (copied) (copied from trunk/src/core/net/sf/basedb/core/filehandler/AbstractDataFileHandler.java) (view diffs)
• src/core/net/sf/basedb/core/filehandler/AffymetrixFileHandler.java (copied) (copied from trunk/src/core/net/sf/basedb/core/filehandler/AffymetrixFileHandler.java) (view diffs)
• src/core/net/sf/basedb/core/filehandler/CdfFileHandler.java (copied) (copied from trunk/src/core/net/sf/basedb/core/filehandler/CdfFileHandler.java) (view diffs)
• src/core/net/sf/basedb/core/filehandler/CelFileHandler.java (copied) (copied from trunk/src/core/net/sf/basedb/core/filehandler/CelFileHandler.java) (view diffs)
• src/core/net/sf/basedb/core/filehandler/DataFileHandler.java (copied) (copied from trunk/src/core/net/sf/basedb/core/filehandler/DataFileHandler.java) (view diffs)
• src/core/net/sf/basedb/core/filehandler/DataFileMetadataReader.java (copied) (copied from trunk/src/core/net/sf/basedb/core/filehandler/DataFileMetadataReader.java) (view diffs)
• src/core/net/sf/basedb/core/filehandler/DataFileValidator.java (copied) (copied from trunk/src/core/net/sf/basedb/core/filehandler/DataFileValidator.java) (view diffs)
• src/core/net/sf/basedb/core/query/Hql.java (modified) (view diffs)
• src/core/net/sf/basedb/util/ClassUtil.java (modified) (view diffs)
• src/core/net/sf/basedb/util/ConsoleProgressReporter.java (modified) (view diffs)
• src/core/net/sf/basedb/util/FileUtil.java (modified) (view diffs)
• src/core/net/sf/basedb/util/IntensityCalculatorUtil.java (modified) (view diffs)
• src/core/net/sf/basedb/util/JarClassLoader.java (modified) (view diffs)
• src/core/net/sf/basedb/util/overview/ExperimentOverview.java (modified) (view diffs)
• src/examples/plugins/base-configurations.xml (copied) (copied from trunk/src/examples/plugins/base-configurations.xml) (view diffs)
• src/examples/plugins/base-plugins.xml (copied) (copied from trunk/src/examples/plugins/base-plugins.xml) (view diffs)
• src/examples/plugins/build.xml (modified) (view diffs)
• src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (view diffs)
• src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (view diffs)
• src/plugins/core/net/sf/basedb/plugins/CdfFileReporterImporter.java (modified) (view diffs)
• src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java (modified) (view diffs)
• src/plugins/core/net/sf/basedb/plugins/IntensityCalculatorPlugin.java (modified) (view diffs)
• src/plugins/core/net/sf/basedb/plugins/PackedFileExporter.java (modified) (view diffs)
• src/plugins/core/net/sf/basedb/plugins/PluginConfigurationImporter.java (modified) (view diffs)
• src/plugins/core/net/sf/basedb/plugins/PrintMapFlatFileImporter.java (modified) (view diffs)
• src/plugins/core/net/sf/basedb/plugins/RawDataFlatFileImporter.java (modified) (view diffs)
• src/plugins/core/net/sf/basedb/plugins/ReporterMapFlatFileImporter.java (modified) (view diffs)
• src/test/TestAll.java (modified) (view diffs)
• src/test/TestAnalyzePluginUtil.java (modified) (view diffs)
• src/test/TestAnnotation.java (modified) (view diffs)
• src/test/TestAnnotationFlatFileImporter.java (modified) (view diffs)
• src/test/TestAnyToAny.java (modified) (view diffs)
• src/test/TestArrayBatch.java (modified) (view diffs)
• src/test/TestArrayDesign.java (modified) (view diffs)
• src/test/TestArrayDesignBlock.java (modified) (view diffs)
• src/test/TestArraySlide.java (modified) (view diffs)
• src/test/TestBase1PluginExecuter.java (modified) (view diffs)
• src/test/TestBioAsssaySetExporter.java (modified) (view diffs)
• src/test/TestDataFileType.java (copied) (copied from trunk/src/test/TestDataFileType.java) (view diffs)
• src/test/TestDirectory.java (modified) (view diffs)
• src/test/TestDirty.java (modified) (view diffs)
• src/test/TestDiskUsage.java (modified) (view diffs)
• src/test/TestExperiment.java (modified) (view diffs)
• src/test/TestFile.java (modified) (view diffs)
• src/test/TestHybridization.java (modified) (view diffs)
• src/test/TestIlluminaImporter.java (modified) (view diffs)
• src/test/TestMimeType.java (modified) (view diffs)
• src/test/TestPath.java (modified) (view diffs)
• src/test/TestPlateFlatFileImporter.java (modified) (view diffs)
• src/test/TestPlatform.java (copied) (copied from trunk/src/test/TestPlatform.java) (view diffs)
• src/test/TestPrintMapFlatFileImporter.java (modified) (view diffs)
• src/test/TestProject.java (modified) (view diffs)
• src/test/TestProtocol.java (modified) (view diffs)
• src/test/TestRawBioAssay.java (modified) (view diffs)
• src/test/TestRawDataFlatFileImporter.java (modified) (view diffs)
• src/test/TestReporterFlatFileImporter.java (modified) (view diffs)
• src/test/TestReporterMapFlatFileImporter.java (modified) (view diffs)
• src/test/TestSpotImages.java (modified) (view diffs)
• src/test/data/test.affymetrix.cdf (copied) (copied from trunk/src/test/data/test.affymetrix.cdf) (view diffs)
• src/test/data/test.affymetrix.cel (copied) (copied from trunk/src/test/data/test.affymetrix.cel) (view diffs)
• src/test/net/sf/basedb/test/merge/MergeTest.java (modified) (view diffs)
• src/test/net/sf/basedb/test/performance/PrepareTest.java (modified) (view diffs)
• src/test/net/sf/basedb/test/performance/RawDataTest.java (modified) (view diffs)
• src/test/net/sf/basedb/test/performance/Util.java (modified) (view diffs)
• src/test/net/sf/basedb/test/roles/PowerUserTest.java (modified) (view diffs)
• src/test/net/sf/basedb/test/roles/UserTest.java (modified) (view diffs)
• www/admin/datafiletypes (copied) (copied from trunk/www/admin/datafiletypes) (view diffs)
• www/admin/datafiletypes/edit_filetype.jsp (copied) (copied from trunk/www/admin/datafiletypes/edit_filetype.jsp) (view diffs)
• www/admin/datafiletypes/index.jsp (copied) (copied from trunk/www/admin/datafiletypes/index.jsp) (view diffs)
• www/admin/datafiletypes/list_filetypes.jsp (copied) (copied from trunk/www/admin/datafiletypes/list_filetypes.jsp) (view diffs)
• www/admin/datafiletypes/view_filetype.jsp (copied) (copied from trunk/www/admin/datafiletypes/view_filetype.jsp) (view diffs)
• www/admin/mimetypes/edit_mimetype.jsp (modified) (view diffs)
• www/admin/mimetypes/index.jsp (modified) (view diffs)
• www/admin/mimetypes/list_mimetypes.jsp (modified) (view diffs)
• www/admin/mimetypes/view_mimetype.jsp (modified) (view diffs)
• www/admin/platforms (copied) (copied from trunk/www/admin/platforms) (view diffs)
• www/admin/platforms/edit_platform.jsp (copied) (copied from trunk/www/admin/platforms/edit_platform.jsp) (view diffs)
• www/admin/platforms/index.jsp (copied) (copied from trunk/www/admin/platforms/index.jsp) (view diffs)
• www/admin/platforms/list_platforms.jsp (copied) (copied from trunk/www/admin/platforms/list_platforms.jsp) (view diffs)
• www/admin/platforms/variants (copied) (copied from trunk/www/admin/platforms/variants) (view diffs)
• www/admin/platforms/variants/edit_variant.jsp (copied) (copied from trunk/www/admin/platforms/variants/edit_variant.jsp) (view diffs)
• www/admin/platforms/variants/index.jsp (copied) (copied from trunk/www/admin/platforms/variants/index.jsp) (view diffs)
• www/admin/platforms/variants/list_variants.jsp (copied) (copied from trunk/www/admin/platforms/variants/list_variants.jsp) (view diffs)
• www/admin/platforms/variants/view_variant.jsp (copied) (copied from trunk/www/admin/platforms/variants/view_variant.jsp) (view diffs)
• www/admin/platforms/view_platform.jsp (copied) (copied from trunk/www/admin/platforms/view_platform.jsp) (view diffs)
• www/admin/plugindefinitions/index.jsp (modified) (view diffs)
• www/common/annotations/list_annotations.jsp (modified) (view diffs)
• www/common/datafiles (copied) (copied from trunk/www/common/datafiles) (view diffs)
• www/common/datafiles/list_files.jsp (copied) (copied from trunk/www/common/datafiles/list_files.jsp) (view diffs)
• www/common/datafiles/select_files.jsp (copied) (copied from trunk/www/common/datafiles/select_files.jsp) (view diffs)
• www/common/datafiles/wait.jsp (copied) (copied from trunk/www/common/datafiles/wait.jsp) (view diffs)
• www/filemanager/directories/edit_directory.jsp (modified) (view diffs)
• www/filemanager/directories/index.jsp (modified) (view diffs)
• www/filemanager/directories/list_directories.jsp (modified) (view diffs)
• www/filemanager/files/index.jsp (modified) (view diffs)
• www/filemanager/files/list_files.jsp (modified) (view diffs)
• www/filemanager/files/view_file.jsp (modified) (view diffs)
• www/filemanager/upload/select.jsp (modified) (view diffs)
• www/filemanager/upload/upload.jsp (modified) (view diffs)
• www/images/unchangeable.gif (copied) (copied from trunk/www/images/unchangeable.gif) (view diffs)
• www/include/menu.jsp (modified) (view diffs)
• www/include/scripts/main.js (modified) (view diffs)
• www/include/scripts/newjoust.js (modified) (view diffs)
• www/include/scripts/platforms.js (copied) (copied from trunk/www/include/scripts/platforms.js) (view diffs)
• www/include/styles/main.css (modified) (view diffs)
• www/lims/arraydesigns/edit_design.jsp (modified) (view diffs)
• www/lims/arraydesigns/index.jsp (modified) (view diffs)
• www/lims/arraydesigns/list_designs.jsp (modified) (view diffs)
• www/lims/arraydesigns/view_design.jsp (modified) (view diffs)
• www/views/experiments/edit_experiment.jsp (modified) (view diffs)
• www/views/experiments/list_experiments.jsp (modified) (view diffs)
• www/views/rawbioassays/edit_rawbioassay.jsp (modified) (view diffs)
• www/views/rawbioassays/index.jsp (modified) (view diffs)
• www/views/rawbioassays/list_rawbioassays.jsp (modified) (view diffs)
• www/views/rawbioassays/view_rawbioassay.jsp (modified) (view diffs)
• www/views/reporters/index.jsp (modified) (view diffs)

branches/webservices/doc

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