Changeset 417

Timestamp:

Sep 11, 2007, 5:45:06 PM (16 years ago)

Author:

dominic

Message:

latest tab2mage importer code

Location:

trunk/uk/ac/ebi/Tab2MageImporter

Files:

• ChangeLog.txt (modified) (1 diff)
• README.txt (modified) (1 diff)
• src (added)
• src/java (added)
• src/java/log4j.xml (added)
• src/java/org (added)
• src/java/org/embl (added)
• src/java/org/embl/cg (added)
• src/java/org/embl/cg/affyexport (added)
• src/java/org/embl/cg/affyexport/AffyConvert.java (added)
• src/java/org/embl/cg/affyexport/ExportCDF.java (added)
• src/java/org/embl/cg/affyexport/ExportCHP.java (added)
• src/java/org/embl/cg/affyexport/ExportExp.java (added)
• src/java/org/embl/cg/bloader (added)
• src/java/org/embl/cg/bloader/conf (added)
• src/java/org/embl/cg/bloader/conf/ConfigurationInit.java (added)
• src/java/org/embl/cg/bloader/core (added)
• src/java/org/embl/cg/bloader/core/BASELoader.java (added)
• src/java/org/embl/cg/bloader/dbAccess (added)
• src/java/org/embl/cg/bloader/dbAccess/DatabaseAccess.java (added)
• src/java/org/embl/cg/bloader/dbAccess/DatabaseAccessFactory.java (added)
• src/java/org/embl/cg/bloader/dbAccess/DatabaseRollback.java (added)
• src/java/org/embl/cg/bloader/dbAccess/base1 (added)
• src/java/org/embl/cg/bloader/dbAccess/base1/DatabaseUtils.java (added)
• src/java/org/embl/cg/bloader/dbAccess/base1/Rollback.java (added)
• src/java/org/embl/cg/bloader/exceptions (added)
• src/java/org/embl/cg/bloader/exceptions/AccessException.java (added)
• src/java/org/embl/cg/bloader/exceptions/BaseException.java (added)
• src/java/org/embl/cg/bloader/exceptions/ConfigurationException.java (added)
• src/java/org/embl/cg/bloader/exceptions/InvalidHeaderException.java (added)
• src/java/org/embl/cg/bloader/exceptions/InvalidLoginException.java (added)
• src/java/org/embl/cg/bloader/exceptions/ParsingException.java (added)
• src/java/org/embl/cg/bloader/exceptions/PropertyNotFoundException.java (added)
• src/java/org/embl/cg/bloader/exceptions/RawDataParserException.java (added)
• src/java/org/embl/cg/bloader/exceptions/RawDataWriterException.java (added)
• src/java/org/embl/cg/bloader/exceptions/TAB2MAGEException.java (added)
• src/java/org/embl/cg/bloader/exceptions/UtilityException.java (added)
• src/java/org/embl/cg/bloader/exceptions/ValidationException.java (added)
• src/java/org/embl/cg/bloader/io (added)
• src/java/org/embl/cg/bloader/io/ExperimentalDataAccess.java (added)
• src/java/org/embl/cg/bloader/io/RawDataAccess.java (added)
• src/java/org/embl/cg/bloader/io/SampleTissueResolver.java (added)
• src/java/org/embl/cg/bloader/io/rawdataparser (added)
• src/java/org/embl/cg/bloader/io/rawdataparser/AffymetrixRDParser.java (added)
• src/java/org/embl/cg/bloader/io/rawdataparser/CodeLinkRDParser.java (added)
• src/java/org/embl/cg/bloader/io/rawdataparser/GenePixRDParser.java (added)
• src/java/org/embl/cg/bloader/io/rawdataparser/RawDataParser.java (added)
• src/java/org/embl/cg/bloader/io/rawdatawriter (added)
• src/java/org/embl/cg/bloader/io/rawdatawriter/RawDataWriter.java (added)
• src/java/org/embl/cg/bloader/io/rawdatawriter/RawDataWriterFactory.java (added)
• src/java/org/embl/cg/bloader/io/rawdatawriter/base1 (added)
• src/java/org/embl/cg/bloader/io/rawdatawriter/base1/AffymetrixRDWriter.java (added)
• src/java/org/embl/cg/bloader/io/rawdatawriter/base1/DefaultRawDataWriter.java (added)
• src/java/org/embl/cg/bloader/io/tab2mageparser (added)
• src/java/org/embl/cg/bloader/io/tab2mageparser/ExperimentalDataReader.java (added)
• src/java/org/embl/cg/bloader/io/tab2mageparser/GeneCoreDbReader.java (added)
• src/java/org/embl/cg/bloader/io/tab2mageparser/Tab2MAGEFileReader.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/Tab2MAGEExperimentWriter.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/Tab2MAGEHybridizationWriter.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/Tab2MAGEProtocolWriter.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/Tab2MAGEWriterFactory.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/base1 (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/base1/Tab2MAGEExperimentWriterBASE1MySQL.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/base1/Tab2MAGEExperimentWriterBASE1PostgreSQL.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/base1/Tab2MAGEHybridizationWriterBASE1.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/base1/Tab2MAGEHybridizationWriterBASE1MySQL.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/base1/Tab2MAGEHybridizationWriterBASE1PostgreSQL.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/base1/Tab2MAGEProtocolWriterBASE1MySQL.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/base1/Tab2MAGEProtocolWriterBASE1PostgreSQL.java (added)
• src/java/org/embl/cg/bloader/io/tab2magewriter/base2 (added)
• src/java/org/embl/cg/bloader/models (added)
• src/java/org/embl/cg/bloader/models/AffymetrixRawData.java (added)
• src/java/org/embl/cg/bloader/models/CodeLinkRawData.java (added)
• src/java/org/embl/cg/bloader/models/Feature.java (added)
• src/java/org/embl/cg/bloader/models/GenePixRawData.java (added)
• src/java/org/embl/cg/bloader/models/Position.java (added)
• src/java/org/embl/cg/bloader/models/RawBioAssayMap.java (added)
• src/java/org/embl/cg/bloader/models/RawData.java (added)
• src/java/org/embl/cg/bloader/models/Tab2MAGEExperiment.java (added)
• src/java/org/embl/cg/bloader/models/Tab2MAGEHybridization.java (added)
• src/java/org/embl/cg/bloader/models/Tab2MAGEHybridizationLine.java (added)
• src/java/org/embl/cg/bloader/models/Tab2MAGEHybridizationMap.java (added)
• src/java/org/embl/cg/bloader/models/Tab2MAGEProtocol.java (added)
• src/java/org/embl/cg/bloader/scheduler (added)
• src/java/org/embl/cg/bloader/scheduler/Scheduler.java (added)
• src/java/org/embl/cg/bloader/test (added)
• src/java/org/embl/cg/bloader/test/DyeSwapTesting.java (added)
• src/java/org/embl/cg/bloader/test/EMailerTesting.java (added)
• src/java/org/embl/cg/bloader/test/ParserTesting.java (added)
• src/java/org/embl/cg/bloader/test/TransactionTesting.java (added)
• src/java/org/embl/cg/bloader/test/WebUtilTesting.java (added)
• src/java/org/embl/cg/bloader/ums (added)
• src/java/org/embl/cg/bloader/ums/IAuthentication.java (added)
• src/java/org/embl/cg/bloader/ums/SecurityService.java (added)
• src/java/org/embl/cg/bloader/ums/User.java (added)
• src/java/org/embl/cg/bloader/utils (added)
• src/java/org/embl/cg/bloader/utils/AffymetrixProbeSetPositionHandler.java (added)
• src/java/org/embl/cg/bloader/utils/ApplicationConfiguration.java (added)
• src/java/org/embl/cg/bloader/utils/Constants.java (added)
• src/java/org/embl/cg/bloader/utils/DatabaseUtils_Web.java (added)
• src/java/org/embl/cg/bloader/utils/EMailer.java (added)
• src/java/org/embl/cg/bloader/utils/FileUtil.java (added)
• src/java/org/embl/cg/bloader/utils/HeaderDescriptor.java (added)
• src/java/org/embl/cg/bloader/utils/LoadShellScript.java (added)
• src/java/org/embl/cg/bloader/utils/PropertyReader.java (added)
• src/java/org/embl/cg/bloader/utils/RollbackHandling.java (added)
• src/java/org/embl/cg/bloader/utils/SampleTissue.java (added)
• src/java/org/embl/cg/bloader/utils/Upload.java (added)
• src/java/org/embl/cg/bloader/utils/Utils.java (added)
• src/java/org/embl/cg/bloader/utils/WebConstants.java (added)
• src/java/org/embl/cg/bloader/validation (added)
• src/java/org/embl/cg/bloader/validation/AffymetrixValidation.java (added)
• src/java/org/embl/cg/bloader/validation/ExperimentValidation.java (added)
• src/java/org/embl/cg/bloader/validation/GenePixValidation.java (added)
• src/java/org/embl/cg/bloader/validation/HybridizationValidation.java (added)
• src/java/org/embl/cg/bloader/validation/ProtocolValidation.java (added)
• src/java/org/embl/cg/bloader/validation/Validation.java (added)
• src/java/org/embl/cg/bloader/validation/ValidationFactory.java (added)
• src/java/org/embl/cg/bloader/validation/base1 (added)
• src/java/org/embl/cg/bloader/validation/base1/Tab2MAGEExperimentValidation.java (added)
• src/java/org/embl/cg/bloader/validation/base1/Tab2MAGEHybridizationValidation.java (added)
• src/java/org/embl/cg/bloader/validation/base1/Tab2MAGEProtocolValidation.java (added)
• src/java/org/embl/cg/bloader/validation/base2 (added)
• src/java/org/embl/cg/bloader/validation/defaultImplementation (added)
• src/java/org/embl/cg/bloader/validation/defaultImplementation/Tab2MAGEExperimentValidation.java (added)
• src/java/org/embl/cg/bloader/validation/defaultImplementation/Tab2MAGEHybridizationValidation.java (added)
• src/java/org/embl/cg/bloader/validation/defaultImplementation/Tab2MAGEProtocolValidation.java (added)
• src/java/org/embl/cg/bloader/web (added)
• src/java/org/embl/cg/bloader/web/actions (added)
• src/java/org/embl/cg/bloader/web/actions/BLoaderInputAction.java (added)
• src/java/org/embl/cg/bloader/web/actions/BLoaderRenderAction.java (added)
• src/java/org/embl/cg/bloader/web/actions/ConvertCHPAction.java (added)
• src/java/org/embl/cg/bloader/web/actions/LoginAction.java (added)
• src/java/org/embl/cg/bloader/web/actions/LogoutAction.java (added)
• src/java/org/embl/cg/bloader/web/business (added)
• src/java/org/embl/cg/bloader/web/business/Hybridizations.java (added)
• src/java/org/embl/cg/bloader/web/business/Samples.java (added)
• src/java/org/embl/cg/bloader/web/business/Summary.java (added)
• src/java/org/embl/cg/bloader/web/filter (added)
• src/java/org/embl/cg/bloader/web/filter/LoggedInFilter.java (added)
• src/java/org/embl/cg/bloader/web/forms (added)
• src/java/org/embl/cg/bloader/web/forms/CompleteForm.java (added)
• src/java/org/embl/cg/bloader/web/forms/ConvertCHPForm.java (added)
• src/java/org/embl/cg/bloader/web/forms/LoginForm.java (added)
• src/java/org/embl/cg/bloader/web/listeners (added)
• src/java/org/embl/cg/bloader/web/listeners/SessionCounter.java (added)
• src/java/org/embl/cg/bloader/web/listeners/UserCounter.java (added)
• src/java/org/embl/cg/bloader/web/rules (added)
• src/java/org/embl/cg/bloader/web/rules/BLoaderWizard.java (added)
• src/java/org/embl/cg/bloader/web/rules/BasicBLoaderStep.java (added)
• src/java/org/embl/cg/bloader/web/rules/StepChangeSummary.java (added)
• src/java/org/embl/cg/bloader/web/rules/StepExperiment.java (added)
• src/java/org/embl/cg/bloader/web/rules/StepFinish.java (added)
• src/java/org/embl/cg/bloader/web/rules/StepHybridization.java (added)
• src/java/org/embl/cg/bloader/web/rules/StepLaunchBASELoader.java (added)
• src/java/org/embl/cg/bloader/web/rules/StepOrigin.java (added)
• src/java/org/embl/cg/bloader/web/rules/StepProtocol.java (added)
• src/java/org/embl/cg/bloader/web/rules/StepSamples.java (added)
• src/java/org/embl/cg/bloader/web/rules/StepSummary.java (added)
• src/java/org/embl/cg/utilitytools (added)
• src/java/org/embl/cg/utilitytools/parser (added)
• src/java/org/embl/cg/utilitytools/parser/KeyValue.java (added)
• src/java/org/embl/cg/utilitytools/parser/ParserUtil.java (added)
• src/java/org/embl/cg/utilitytools/parser/csv (added)
• src/java/org/embl/cg/utilitytools/parser/csv/CSVLine.java (added)
• src/java/org/embl/cg/utilitytools/parser/csv/CSVParser.java (added)
• src/java/org/embl/cg/utilitytools/parser/csv/InvalidCSVSetUpException.java (added)
• src/uk (added)
• src/uk/ac (added)
• src/uk/ac/ebi (added)
• src/uk/ac/ebi/nugo (added)
• src/uk/ac/ebi/nugo/common (added)
• src/uk/ac/ebi/nugo/common/Helper.java (added)
• src/uk/ac/ebi/nugo/common/NutribasePluginException.java (added)
• src/uk/ac/ebi/nugo/common/Tab2MageConstants.java (added)
• src/uk/ac/ebi/nugo/common/ValueFormatter.java (added)
• src/uk/ac/ebi/nugo/common/ZipUnpacker.java (added)
• src/uk/ac/ebi/nugo/plugins (added)
• src/uk/ac/ebi/nugo/plugins/AnnotationTypeCvImporter.java (added)
• src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/AgilentDataColumns.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/AnnotationTypeFileMapping.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/DetectablePluginTypes.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/ExperimentPlatformsLibrary.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/GenePixDataColumns.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/ImageLibrary.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/Tab2MageExperiment.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/Tab2MageProtocol.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/AnnotationTypeFileWriter.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/AnnotationTypeOutputStreamWriter.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/AnnotationTypesWriter.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/Base2Tab2MageFileReader.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/RawDataImport.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/Tab2MageDataImportFactory.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/Tab2MageExperimentWriter.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/Tab2MageHybWriter.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/Tab2MageProtocolWriter.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/Tab2MageWriterFactory.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/parser (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/parser/AgilentRDParser.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/parser/Base2GenePixRDParser.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/parser/CSVParser.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/mail (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/mail/MessagingConstants.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/mail/Tab2MageEMessaging.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/AgilentValidation.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/GenePixFileValidation.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/RawDataValidation.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageExperimentValidation.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageHybridizationValidation.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageImportValidatorUtils.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageImportValidatorUtils.txt (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageProtocolValidation.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageValidationFactory.java (added)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageValidationFactory.txt (added)
• src/uk/ac/ebi/nugo/plugins/util (added)
• src/uk/ac/ebi/nugo/plugins/util/tab2mage (added)
• src/uk/ac/ebi/nugo/plugins/util/tab2mage/ClassPreamble2.java (added)
• src/uk/ac/ebi/nugo/plugins/util/tab2mage/PluginConfigDetector.java (added)
• src/uk/ac/ebi/nugo/plugins/util/tab2mage/Tab2MageHelper.java (added)

trunk/uk/ac/ebi/Tab2MageImporter/ChangeLog.txt

@@ -1 @@
-,____First release
+,____Second release
+
+
+-- pooling support added
+-- isisues relating to agilent files
+-- logging
+-- 
+
 
 This file will contain information about changes iin subsequent releases.

trunk/uk/ac/ebi/Tab2MageImporter/README.txt

@@ -117 +117 @@
   If this happens, you can simply ask your administrator to allow your machine to connect to the email server using port 25.
 
-  The email alert should work on a linux / unix and may be mac machines.
+  The email alert works on a linux / unix and may be mac machines.