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Decouple openmicroscopy/openmicroscopy for 5.5.0-m3
Squashed commit of the following: commit 1dea6f8397bd131f1cfbe7bbd8d315df8944c3ed Merge: dba6312 648c95d Author: Josh Moore <[email protected]> Date: Thu Feb 14 12:42:00 2019 +0100 Merge pull request ome#12 from rgozim/develop Develop commit 648c95def1ab980ae20b41b14239caa1500c0ae6 Author: Jean-Marie Burel <[email protected]> Date: Wed Feb 13 11:33:20 2019 +0000 specify ice version commit dc240eaf655c9dd151b11643d772a9f79fccd2f0 Author: Jean-Marie Burel <[email protected]> Date: Wed Feb 13 11:32:24 2019 +0000 use method since there is no shortname field commit 43f2158aac722b4305c2ff606165ec4c5410689d Author: Jean-Marie Burel <[email protected]> Date: Thu Jan 31 21:20:21 2019 +0000 roll back change now that spring 2.0 is not included commit 90428fb495ae4a92213c6af1406f04dd047a2ccd Author: Jean-Marie Burel <[email protected]> Date: Thu Jan 31 14:58:40 2019 +0000 upgrade gradle commit 4163f840b0605fab3f71b0258d19d1dfee043c44 Author: Jean-Marie Burel <[email protected]> Date: Wed Jan 30 13:45:06 2019 +0000 add custom manifest commit bcae1b48df8dd3984bd521d9505a871abe971b4b Author: Jean-Marie Burel <[email protected]> Date: Wed Jan 30 13:02:52 2019 +0000 set outputdir commit 988910a55e17ae9c52b331a7d6261c4969c68deb Author: Jean-Marie Burel <[email protected]> Date: Tue Jan 29 22:32:45 2019 +0000 fix path commit 69b63e042b8b9177261e042378fd6bb2abee1fdb Author: Jean-Marie Burel <[email protected]> Date: Wed Jan 23 12:44:48 2019 +0000 Use MailException commit 580ea28da5393f3260c260fefd9dce23fe69fb59 Author: Jean-Marie Burel <[email protected]> Date: Wed Jan 23 12:21:08 2019 +0000 replace by SQLException commit dcb5d4c80dc0c92f80996747762fc79b69d7420b Author: Riad Gozim <[email protected]> Date: Tue Jan 29 09:53:15 2019 +0000 Removed some lines for convention commit 0f4c35fa6b9c386cf338d12996f4863bc975d288 Author: Riad Gozim <[email protected]> Date: Mon Jan 28 23:29:29 2019 +0000 build.gradle with predefined databaseTypes and omeXmlFiles in dsl block commit 5c6b0b85fdce5300d141aab83b6a456cdcbf32af Merge: 128e5f0 e3af300 Author: Riad Gozim <[email protected]> Date: Mon Jan 28 18:14:49 2019 +0000 Added combined.vm file and updated build.gradle commit e3af300e8e5dcf7c3af9b7ceacdbc9bcc4b02280 Author: Jean-Marie Burel <[email protected]> Date: Mon Jan 28 11:37:45 2019 +0000 bump version commit 128e5f0d2a5d346d93be6ced07bf2b3a6669f396 Author: Riad Gozim <[email protected]> Date: Fri Jan 25 23:16:25 2019 +0000 Changes to build.gradle files to prevent gradle lifecycle clash commit 68f2d722df7599e625c9222fcf6e2627dcb55cf6 Author: Riad Gozim <[email protected]> Date: Fri Jan 25 20:21:17 2019 +0000 Updated to use latest blitzplugin commit 3deb9dafd465437419dc20c29369afb727b06aa6 Author: Riad Gozim <[email protected]> Date: Thu Jan 24 22:59:57 2019 +0000 Updated to use latest plugin syntax commit 9553b36f6b09b27fde31742cf4a6095a0ce0f5c2 Author: Riad Gozim <[email protected]> Date: Wed Jan 23 17:38:39 2019 +0000 WIP added ome maven to build.gradle commit 20e7507be056a8ef6499c1f8dd4c66a5b8f45329 Author: Jean-Marie Burel <[email protected]> Date: Tue Jan 22 13:17:08 2019 +0000 Replace :: by _ This is needed b/c of usage of perf4j commit 98acf15508481433b3018761eeba66a324f91262 Author: Riad Gozim <[email protected]> Date: Tue Jan 22 18:00:46 2019 +0000 Removed unused repository using latest blitz and dsl plugins commit 0d15e725c52733b4c24584437018f934e5659dab Author: Riad Gozim <[email protected]> Date: Tue Jan 22 16:09:12 2019 +0000 Changes to work with latest blitz plugin commit dba63124b44cef30621f9eeee29ff5099f32d795 Merge: 5738482 b4bd167 Author: jean-marie burel <[email protected]> Date: Tue Jan 15 11:29:47 2019 +0000 Merge pull request ome#8 from rgozim/fix/schema Updated xml files to use latest schema commit b4bd167c7c55d28042d42e9c20e16ea7df71fa5a Author: jean-marie burel <[email protected]> Date: Sun Jan 13 09:11:44 2019 +0000 move to existing section commit 901020c6ecbc0d94bc23f392b799b017912d1660 Author: Riad Gozim <[email protected]> Date: Fri Jan 11 15:58:19 2019 +0000 Fixed incorrect EventContext usage commit 0aa2b4402e176d035543e9b7bf1fc4c733a976ca Author: Riad Gozim <[email protected]> Date: Fri Jan 11 15:22:36 2019 +0000 Removed IRoles commit 1a8285853f678723ab148d323392fbd6b7d419e8 Author: Riad Gozim <[email protected]> Date: Fri Jan 11 14:52:11 2019 +0000 Renamed IEventContext to EventContext Moved EventContext from omero.api to omero.sys commit 7fb8a8bbd91cfcd502886d58066db5bfbf790702 Author: Riad Gozim <[email protected]> Date: Fri Jan 11 13:34:09 2019 +0000 Updated xml files to use latest schema commit 98af77f739d1158aec35f61b75771bfd0daa7e9c Author: Riad Gozim <[email protected]> Date: Fri Jan 11 10:44:50 2019 +0000 Added generated folder to gitignore commit d1192d30afacff2f52d4afb3c0d718d3d5732af5 Author: Riad Gozim <[email protected]> Date: Thu Jan 10 22:52:26 2019 +0000 Removed afterEval block from blitzPython publish and updated python task syntax to latest commit of zeroc plugin commit 57384821149e327290da475d034d8c7333d290c5 Merge: 3ae3812 ddf202a Author: Josh Moore <[email protected]> Date: Thu Jan 10 18:59:28 2019 +0100 Merge pull request ome#7 from rgozim/feature/local-zeroc Updated build.gradle to use zeroc local plugin commit ddf202a3572bbf126304e64b43a7485252be1cd8 Author: Riad Gozim <[email protected]> Date: Thu Jan 10 15:37:14 2019 +0000 Placed pythonTask includeDir in project.file commit a7707299ebe6c01cdcda21254bd1ce947bbcdc14 Author: Riad Gozim <[email protected]> Date: Thu Jan 10 15:10:19 2019 +0000 Updated pythonTask(s) to filter for files in top level dirs commit 81a759af4efebb4fd4c2b3e898d60029c0f3dd3b Author: Riad Gozim <[email protected]> Date: Thu Jan 10 10:10:35 2019 +0000 Added task for generation of ObjectFactoryRegistrar.py commit ead7781f776d6b53b61a172197a9a29e2c9ae155 Author: jmoore <[email protected]> Date: Thu Jan 10 08:59:15 2019 +0000 Try adding prefix to model files commit bc0bacbd29319c75be955b7023d967b97a27d14e Author: Riad Gozim <[email protected]> Date: Wed Jan 9 20:38:39 2019 +0000 Changed output dir of splitPython task commit 6c77a4e8253fdc20b1b0ed1d7902a7d2523a32ba Author: Riad Gozim <[email protected]> Date: Tue Jan 8 18:45:26 2019 +0000 Experimenting with gradle local plugin Added custom python tasks for compiling ice files into python Set pythonZip to depend on pythonTaskGroup commit 2cb75b7b4f75089a4f20939fdf11ebc8e30b5fed Author: Josh Moore <[email protected]> Date: Tue Jan 8 09:52:42 2019 +0100 Drop gradle.plugin prefix commit a2689c88805959b6361be4249a34e9a83e65aa02 Author: Riad Gozim <[email protected]> Date: Mon Jan 7 16:37:56 2019 +0000 Updated build.gradle to use zeroc local plugin commit 3ae38123f67bdda04ca30c9f6b5d00b199d10671 Author: Riad Gozim <[email protected]> Date: Thu Dec 20 15:29:05 2018 +0000 Cleaned syntax up a little bit commit 2290bd9da5c10c1da3f3b17d32056bdd9459923f Author: Riad Gozim <[email protected]> Date: Thu Dec 20 15:11:05 2018 +0000 Added publication for python sources commit 7b8d2d45603aa337764c124b40026f4c8807a83f Author: Riad Gozim <[email protected]> Date: Wed Dec 19 13:16:32 2018 +0000 Removed old mappings.gradle (not used) commit 40ce0081e7fd0febbad01e660b5d35a5593fb0ad Author: Riad Gozim <[email protected]> Date: Wed Dec 19 13:03:47 2018 +0000 Split publish code from build.gradle to publish.gradle Added javadoc jar commit 9f8c79b48a19657703f939b70808da7ff3b54746 Author: jmoore <[email protected]> Date: Tue Dec 18 19:26:12 2018 +0000 Fix version in mappings.gradle commit 4a15984e7b12cfe6d6a642c071e4126a9e8a5383 Author: jmoore <[email protected]> Date: Tue Dec 18 15:47:16 2018 +0000 Add gradle 5.0 wrapper commit 051ea27c87401dbd5d840ce7a332189287380750 Author: jmoore <[email protected]> Date: Tue Dec 18 12:43:39 2018 +0000 Resurrect file() fix commit f3ef837deb1333e2f33450086c983afe7ba98dca Author: Riad Gozim <[email protected]> Date: Mon Jun 18 18:01:28 2018 +0100 Removed combined file and made tweaks to build.gradle commit 1d7243801e109de5800a1a68f08c5aa3f9c57af1 Author: Riad Gozim <[email protected]> Date: Thu Jan 3 15:03:55 2019 +0000 initial commit incl. renames Conflicts: src/main/ice36/ome/services/blitz/fire/Registry.java src/main/ice36/ome/services/blitz/fire/TopicManager.java src/main/java/loci/ome/io/OMECredentials.java src/main/java/loci/ome/io/OmeroReader.java src/main/java/loci/ome/io/ome-logo.png src/main/java/loci/ome/io/package.html src/main/java/loci/ome/io/services/OMEReaderWriterService.java src/main/java/loci/ome/io/services/OMEReaderWriterServiceImpl.java src/main/java/ome/formats/ImageNameMetadataStore.java src/main/java/ome/formats/Index.java src/main/java/ome/formats/OMEROImportFixture.java src/main/java/ome/formats/OMEROMetadataStoreClient.java src/main/java/ome/formats/OMEROMetadataStoreClientRoot.java src/main/java/ome/formats/OMEXMLModelComparator.java src/main/java/ome/formats/OverlayMetadataStore.java src/main/java/ome/formats/SortDatasetsByName.java src/main/java/ome/formats/SortProjectsByName.java src/main/java/ome/formats/StringEnumeration.java src/main/java/ome/formats/enums/EnumerationException.java src/main/java/ome/formats/enums/EnumerationProvider.java src/main/java/ome/formats/enums/IQueryEnumProvider.java src/main/java/ome/formats/enums/handler/CorrectionEnumHandler.java src/main/java/ome/formats/enums/handler/DetectorTypeEnumHandler.java src/main/java/ome/formats/enums/handler/EnumHandlerFactory.java src/main/java/ome/formats/enums/handler/EnumerationHandler.java src/main/java/ome/formats/enums/handler/ImmersionEnumHandler.java src/main/java/ome/formats/enums/handler/NoopEnumHandler.java src/main/java/ome/formats/enums/handler/OriginalFileFormatEnumHandler.java src/main/java/ome/formats/enums/handler/PatternSet.java src/main/java/ome/formats/importer/IObservable.java src/main/java/ome/formats/importer/IObserver.java src/main/java/ome/formats/importer/ImportCandidates.java src/main/java/ome/formats/importer/ImportConfig.java src/main/java/ome/formats/importer/ImportContainer.java src/main/java/ome/formats/importer/ImportEvent.java src/main/java/ome/formats/importer/ImportFixture.java src/main/java/ome/formats/importer/ImportLibrary.java src/main/java/ome/formats/importer/ImportSize.java src/main/java/ome/formats/importer/OMEROWrapper.java src/main/java/ome/formats/importer/Version.java src/main/java/ome/formats/importer/cli/CommandLineImporter.java src/main/java/ome/formats/importer/cli/ErrorHandler.java src/main/java/ome/formats/importer/cli/ImportCloser.java src/main/java/ome/formats/importer/cli/ImportOutput.java src/main/java/ome/formats/importer/cli/LoggingImportMonitor.java src/main/java/ome/formats/importer/exclusions/AbstractFileExclusion.java src/main/java/ome/formats/importer/exclusions/ClientPathExclusion.java src/main/java/ome/formats/importer/exclusions/FileExclusion.java src/main/java/ome/formats/importer/exclusions/FilenameExclusion.java src/main/java/ome/formats/importer/exclusions/package-info.java src/main/java/ome/formats/importer/targets/ImportTarget.java src/main/java/ome/formats/importer/targets/ModelImportTarget.java src/main/java/ome/formats/importer/targets/ServerTemplateImportTarget.java src/main/java/ome/formats/importer/targets/TargetBuilder.java src/main/java/ome/formats/importer/targets/TemplateImportTarget.java src/main/java/ome/formats/importer/transfers/AbstractExecFileTransfer.java src/main/java/ome/formats/importer/transfers/AbstractFileTransfer.java src/main/java/ome/formats/importer/transfers/CleanupFailure.java src/main/java/ome/formats/importer/transfers/CopyFileTransfer.java src/main/java/ome/formats/importer/transfers/CopyMoveFileTransfer.java src/main/java/ome/formats/importer/transfers/FileTransfer.java src/main/java/ome/formats/importer/transfers/HardlinkFileTransfer.java src/main/java/ome/formats/importer/transfers/MoveFileTransfer.java src/main/java/ome/formats/importer/transfers/SymlinkFileTransfer.java src/main/java/ome/formats/importer/transfers/TransferState.java src/main/java/ome/formats/importer/transfers/UploadFileTransfer.java src/main/java/ome/formats/importer/transfers/UploadRmFileTransfer.java src/main/java/ome/formats/importer/transfers/package-info.java src/main/java/ome/formats/importer/util/ClientKeepAlive.java src/main/java/ome/formats/importer/util/ErrorContainer.java src/main/java/ome/formats/importer/util/ErrorHandler.java src/main/java/ome/formats/importer/util/FileUploader.java src/main/java/ome/formats/importer/util/HtmlMessenger.java src/main/java/ome/formats/importer/util/HtmlMessengerException.java src/main/java/ome/formats/importer/util/IniFileLoader.java src/main/java/ome/formats/importer/util/ProportionalTimeEstimatorImpl.java src/main/java/ome/formats/importer/util/TimeEstimator.java src/main/java/ome/formats/model/BlitzInstanceProvider.java src/main/java/ome/formats/model/ChannelData.java src/main/java/ome/formats/model/ChannelProcessor.java src/main/java/ome/formats/model/ColorsFactory.java src/main/java/ome/formats/model/IObjectContainerStore.java src/main/java/ome/formats/model/InstanceProvider.java src/main/java/ome/formats/model/InstrumentProcessor.java src/main/java/ome/formats/model/ModelException.java src/main/java/ome/formats/model/ModelProcessor.java src/main/java/ome/formats/model/PixelsProcessor.java src/main/java/ome/formats/model/PlaneInfoProcessor.java src/main/java/ome/formats/model/ReferenceProcessor.java src/main/java/ome/formats/model/ShapeProcessor.java src/main/java/ome/formats/model/TargetProcessor.java src/main/java/ome/formats/model/UnitsFactory.java src/main/java/ome/formats/model/WellProcessor.java src/main/java/ome/formats/model/handler/ArcHandler.java src/main/java/ome/formats/model/handler/DetectorHandler.java src/main/java/ome/formats/model/handler/ExperimentHandler.java src/main/java/ome/formats/model/handler/FilamentHandler.java src/main/java/ome/formats/model/handler/LaserHandler.java src/main/java/ome/formats/model/handler/LogicalChannelHandler.java src/main/java/ome/formats/model/handler/MicroscopeHandler.java src/main/java/ome/formats/model/handler/ModelObjectHandler.java src/main/java/ome/formats/model/handler/ModelObjectHandlerFactory.java src/main/java/ome/formats/model/handler/NoopModelObjectHandler.java src/main/java/ome/formats/model/handler/ObjectiveHandler.java src/main/java/ome/services/blitz/Entry.java src/main/java/ome/services/blitz/Router.java src/main/java/ome/services/blitz/Status.java src/main/java/ome/services/blitz/fire/AopContextInitializer.java src/main/java/ome/services/blitz/fire/PermissionsVerifierI.java src/main/java/ome/services/blitz/fire/Ring.java src/main/java/ome/services/blitz/fire/SessionManagerI.java src/main/java/ome/services/blitz/impl/AbstractAmdServant.java src/main/java/ome/services/blitz/impl/AbstractCloseableAmdServant.java src/main/java/ome/services/blitz/impl/AbstractPyramidServant.java src/main/java/ome/services/blitz/impl/AdminI.java src/main/java/ome/services/blitz/impl/ConfigI.java src/main/java/ome/services/blitz/impl/ContainerI.java src/main/java/ome/services/blitz/impl/ExporterI.java src/main/java/ome/services/blitz/impl/JobHandleI.java src/main/java/ome/services/blitz/impl/LdapI.java src/main/java/ome/services/blitz/impl/MetadataI.java src/main/java/ome/services/blitz/impl/MetadataStoreI.java src/main/java/ome/services/blitz/impl/OmeroMetadata.java src/main/java/ome/services/blitz/impl/PixelsI.java src/main/java/ome/services/blitz/impl/ProcessorCallbackI.java src/main/java/ome/services/blitz/impl/ProjectionI.java src/main/java/ome/services/blitz/impl/QueryI.java src/main/java/ome/services/blitz/impl/RawFileStoreI.java src/main/java/ome/services/blitz/impl/RawPixelsStoreI.java src/main/java/ome/services/blitz/impl/RenderingEngineI.java src/main/java/ome/services/blitz/impl/RenderingSettingsI.java src/main/java/ome/services/blitz/impl/RepositoryInfoI.java src/main/java/ome/services/blitz/impl/RoiI.java src/main/java/ome/services/blitz/impl/ScriptI.java src/main/java/ome/services/blitz/impl/ScriptProcessI.java src/main/java/ome/services/blitz/impl/SearchI.java src/main/java/ome/services/blitz/impl/ServiceFactoryI.java src/main/java/ome/services/blitz/impl/SessionI.java src/main/java/ome/services/blitz/impl/ShareI.java src/main/java/ome/services/blitz/impl/SharedResourcesI.java src/main/java/ome/services/blitz/impl/ThumbnailStoreI.java src/main/java/ome/services/blitz/impl/TimelineI.java src/main/java/ome/services/blitz/impl/TypesI.java src/main/java/ome/services/blitz/impl/UpdateI.java src/main/java/ome/services/blitz/impl/commands/RequestObjectFactoryRegistry.java src/main/java/ome/services/blitz/impl/commands/SaveI.java src/main/java/ome/services/blitz/measurements/Helper.java src/main/java/ome/services/blitz/measurements/MeasurementStore.java src/main/java/ome/services/blitz/measurements/OmeroMeasurementStore.java src/main/java/ome/services/blitz/measurements/SmartColumns.java src/main/java/ome/services/blitz/redirect/AbstractRedirector.java src/main/java/ome/services/blitz/redirect/ConfigRedirector.java src/main/java/ome/services/blitz/redirect/NullRedirector.java src/main/java/ome/services/blitz/redirect/Redirector.java src/main/java/ome/services/blitz/redirect/ScaleRedirector.java src/main/java/ome/services/blitz/repo/AbstractRepositoryI.java src/main/java/ome/services/blitz/repo/BfPixelsStoreI.java src/main/java/ome/services/blitz/repo/CheckedPath.java src/main/java/ome/services/blitz/repo/FileMaker.java src/main/java/ome/services/blitz/repo/InternalRepositoryConfig.java src/main/java/ome/services/blitz/repo/InternalRepositoryI.java src/main/java/ome/services/blitz/repo/LegacyRepositoryI.java src/main/java/ome/services/blitz/repo/ManagedImportLocationI.java src/main/java/ome/services/blitz/repo/ManagedImportProcessI.java src/main/java/ome/services/blitz/repo/ManagedImportRequestI.java src/main/java/ome/services/blitz/repo/ManagedRepositoryI.java src/main/java/ome/services/blitz/repo/ProcessContainer.java src/main/java/ome/services/blitz/repo/PublicRepositoryI.java src/main/java/ome/services/blitz/repo/RawAccessRequestI.java src/main/java/ome/services/blitz/repo/RepoRawFileStoreI.java src/main/java/ome/services/blitz/repo/RepositoryDao.java src/main/java/ome/services/blitz/repo/RepositoryDaoImpl.java src/main/java/ome/services/blitz/repo/RequestObjectFactoryRegistry.java src/main/java/ome/services/blitz/repo/ScriptRepositoryI.java src/main/java/ome/services/blitz/repo/TemporaryRepositoryI.java src/main/java/ome/services/blitz/repo/path/ClientFilePathTransformer.java src/main/java/ome/services/blitz/repo/path/FilePathNamingValidator.java src/main/java/ome/services/blitz/repo/path/FilePathRestrictionInstance.java src/main/java/ome/services/blitz/repo/path/FilePathRestrictions.java src/main/java/ome/services/blitz/repo/path/FsFile.java src/main/java/ome/services/blitz/repo/path/MakeNextDirectory.java src/main/java/ome/services/blitz/repo/path/MakePathComponentSafe.java src/main/java/ome/services/blitz/repo/path/ServerFilePathTransformer.java src/main/java/ome/services/blitz/util/ApiConsistencyCheck.java src/main/java/ome/services/blitz/util/BlitzConfiguration.java src/main/java/ome/services/blitz/util/BlitzExecutor.java src/main/java/ome/services/blitz/util/BlitzOnly.java src/main/java/ome/services/blitz/util/CheckAllJobs.java src/main/java/ome/services/blitz/util/ChecksumAlgorithmMapper.java src/main/java/ome/services/blitz/util/ConvertToBlitzExceptionMessage.java src/main/java/ome/services/blitz/util/CurrentPlatform.java src/main/java/ome/services/blitz/util/ExpiredServantMessage.java src/main/java/ome/services/blitz/util/FindServiceFactoryMessage.java src/main/java/ome/services/blitz/util/IceMethodInvoker.java src/main/java/ome/services/blitz/util/ParamsCache.java src/main/java/ome/services/blitz/util/RegisterServantMessage.java src/main/java/ome/services/blitz/util/ResultHolder.java src/main/java/ome/services/blitz/util/ServiceFactoryAware.java src/main/java/ome/services/blitz/util/UnregisterServantMessage.java src/main/java/ome/services/formats/OmeroReader.java src/main/java/ome/services/roi/GeomTool.java src/main/java/ome/services/roi/PixelData.java src/main/java/ome/services/roi/PopulateRoiJob.java src/main/java/ome/services/roi/RoiTypes.java src/main/java/ome/services/scripts/ScriptFinder.java src/main/java/ome/services/throttling/AbstractThrottlingStrategy.java src/main/java/ome/services/throttling/Adapter.java src/main/java/ome/services/throttling/Callback.java src/main/java/ome/services/throttling/Callback2.java src/main/java/ome/services/throttling/InThreadThrottlingStrategy.java src/main/java/ome/services/throttling/Queue.java src/main/java/ome/services/throttling/SerialThrottlingStrategy.java src/main/java/ome/services/throttling/Slot.java src/main/java/ome/services/throttling/Task.java src/main/java/ome/services/throttling/ThrottlingStrategy.java src/main/java/omero/ClientError.java src/main/java/omero/IllegalArgumentException.java src/main/java/omero/UnloadedCollectionException.java src/main/java/omero/UnloadedEntityException.java src/main/java/omero/client.java src/main/java/omero/cmd/CallContext.java src/main/java/omero/cmd/CmdCallbackI.java src/main/java/omero/cmd/HandleFactory.java src/main/java/omero/cmd/HandleI.java src/main/java/omero/cmd/Helper.java src/main/java/omero/cmd/IHandle.java src/main/java/omero/cmd/IRequest.java src/main/java/omero/cmd/RequestObjectFactoryRegistry.java src/main/java/omero/cmd/SessionAware.java src/main/java/omero/cmd/SessionI.java src/main/java/omero/cmd/admin/CurrentSessionsRequestI.java src/main/java/omero/cmd/admin/ResetPasswordRequestI.java src/main/java/omero/cmd/admin/UpdateSessionTimeoutRequestI.java src/main/java/omero/cmd/basic/DoAllI.java src/main/java/omero/cmd/basic/ListRequestsI.java src/main/java/omero/cmd/basic/TimingI.java src/main/java/omero/cmd/fs/FindPyramidsI.java src/main/java/omero/cmd/fs/ManageImageBinariesI.java src/main/java/omero/cmd/fs/OriginalMetadataRequestI.java src/main/java/omero/cmd/fs/UsedFilesRequestI.java src/main/java/omero/cmd/graphs/BaseGraphPolicyAdjuster.java src/main/java/omero/cmd/graphs/BaseGraphTraversalProcessor.java src/main/java/omero/cmd/graphs/Chgrp2I.java src/main/java/omero/cmd/graphs/ChildOptionI.java src/main/java/omero/cmd/graphs/ChildOptionsPolicy.java src/main/java/omero/cmd/graphs/Chmod2I.java src/main/java/omero/cmd/graphs/Chown2I.java src/main/java/omero/cmd/graphs/Delete2I.java src/main/java/omero/cmd/graphs/DiskUsage2I.java src/main/java/omero/cmd/graphs/DiskUsageI.java src/main/java/omero/cmd/graphs/DuplicateI.java src/main/java/omero/cmd/graphs/FindChildrenI.java src/main/java/omero/cmd/graphs/FindParentsI.java src/main/java/omero/cmd/graphs/GraphHelper.java src/main/java/omero/cmd/graphs/GraphRequestFactory.java src/main/java/omero/cmd/graphs/GraphUtil.java src/main/java/omero/cmd/graphs/IgnoreTypePolicy.java src/main/java/omero/cmd/graphs/LegalGraphTargetsI.java src/main/java/omero/cmd/graphs/NullGraphTraversalProcessor.java src/main/java/omero/cmd/graphs/SkipHeadI.java src/main/java/omero/cmd/graphs/SkipHeadPolicy.java src/main/java/omero/cmd/graphs/SkipTailPolicy.java src/main/java/omero/cmd/graphs/SpecificityClassifier.java src/main/java/omero/cmd/graphs/StopBeforeHelper.java src/main/java/omero/cmd/graphs/WrappableRequest.java src/main/java/omero/cmd/mail/SendEmailRequestI.java src/main/java/omero/grid/InteractiveProcessorI.java src/main/java/omero/grid/ParamsHelper.java src/main/java/omero/grid/ProcessCallbackI.java src/main/java/omero/log/LogMessage.java src/main/java/omero/log/Logger.java src/main/java/omero/log/NullLogger.java src/main/java/omero/log/SimpleLogger.java src/main/java/omero/model/DetailsI.java src/main/java/omero/model/ElectricPotentialI.java src/main/java/omero/model/FrequencyI.java src/main/java/omero/model/LengthI.java src/main/java/omero/model/PermissionsI.java src/main/java/omero/model/PowerI.java src/main/java/omero/model/PressureI.java src/main/java/omero/model/SmartEllipseI.java src/main/java/omero/model/SmartLineI.java src/main/java/omero/model/SmartMaskI.java src/main/java/omero/model/SmartPathI.java src/main/java/omero/model/SmartPointI.java src/main/java/omero/model/SmartPolygonI.java src/main/java/omero/model/SmartPolylineI.java src/main/java/omero/model/SmartRectI.java src/main/java/omero/model/SmartShape.java src/main/java/omero/model/SmartTextI.java src/main/java/omero/model/TemperatureI.java src/main/java/omero/model/TimeI.java src/main/java/omero/rtypes.java src/main/java/omero/sys/ParametersI.java src/main/java/omero/util/CloseableServant.java src/main/java/omero/util/IceMapper.java src/main/java/omero/util/ObjectFactoryRegistry.java src/main/java/omero/util/RPSTileData.java src/main/java/omero/util/RPSTileLoop.java src/main/java/omero/util/RTypeMapper.java src/main/java/omero/util/ReadOnlyByteArray.java src/main/java/omero/util/Resources.java src/main/java/omero/util/ServantHolder.java src/main/java/omero/util/TempFileManager.java src/main/java/omero/util/TieAware.java src/main/java/omero/util/TileData.java src/main/java/omero/util/TileLoop.java src/main/java/omero/util/TileLoopIteration.java src/main/java/org/hibernate/stat/ConcurrentStatisticsImpl.java src/main/resources/README.ice src/main/resources/beanRefContext.xml src/main/resources/footer.txt src/main/resources/header.txt src/main/resources/mock_filters.hbm.xml src/main/resources/ome/services/blitz-config.xml src/main/resources/ome/services/blitz-graph-rules.xml src/main/resources/ome/services/blitz-repositories.xml src/main/resources/ome/services/blitz-servantDefinitions.xml src/main/resources/ome/services/graph-rules/blitz-chgrp-rules.xml src/main/resources/ome/services/graph-rules/blitz-chmod-rules.xml src/main/resources/ome/services/graph-rules/blitz-chown-rules.xml src/main/resources/ome/services/graph-rules/blitz-contained-rules.xml src/main/resources/ome/services/graph-rules/blitz-container-rules.xml src/main/resources/ome/services/graph-rules/blitz-delete-rules.xml src/main/resources/ome/services/graph-rules/blitz-disk-usage-rules.xml src/main/resources/ome/services/graph-rules/blitz-duplicate-rules.xml src/main/resources/ome/services/objectfactories.xml src/main/resources/ome/services/repository/repository.xml src/main/resources/ome/services/throttling/throttling.xml src/main/resources/templates/combined.vm src/main/resources/templates/cpp_obj_reg.vm src/main/resources/templates/java_ice_map.vm src/main/resources/templates/java_obj_reg.vm src/main/resources/templates/py_obj_reg.vm src/main/slice/omero/API.ice src/main/slice/omero/Collections.ice src/main/slice/omero/Constants.ice src/main/slice/omero/FS.ice src/main/slice/omero/Internal.ice src/main/slice/omero/ModelF.ice src/main/slice/omero/ROMIO.ice src/main/slice/omero/RTypes.ice src/main/slice/omero/Repositories.ice src/main/slice/omero/Scripts.ice src/main/slice/omero/ServerErrors.ice src/main/slice/omero/ServicesF.ice src/main/slice/omero/SharedResources.ice src/main/slice/omero/System.ice src/main/slice/omero/SystemF.ice src/main/slice/omero/Tables.ice src/main/slice/omero/api/Exporter.ice src/main/slice/omero/api/IAdmin.ice src/main/slice/omero/api/IConfig.ice src/main/slice/omero/api/IContainer.ice src/main/slice/omero/api/ILdap.ice src/main/slice/omero/api/IMetadata.ice src/main/slice/omero/api/IPixels.ice src/main/slice/omero/api/IProjection.ice src/main/slice/omero/api/IQuery.ice src/main/slice/omero/api/IRenderingSettings.ice src/main/slice/omero/api/IRepositoryInfo.ice src/main/slice/omero/api/IRoi.ice src/main/slice/omero/api/IScript.ice src/main/slice/omero/api/ISession.ice src/main/slice/omero/api/IShare.ice src/main/slice/omero/api/ITimeline.ice src/main/slice/omero/api/ITypes.ice src/main/slice/omero/api/IUpdate.ice src/main/slice/omero/api/JobHandle.ice src/main/slice/omero/api/MetadataStore.ice src/main/slice/omero/api/PyramidService.ice src/main/slice/omero/api/RawFileStore.ice src/main/slice/omero/api/RawPixelsStore.ice src/main/slice/omero/api/RenderingEngine.ice src/main/slice/omero/api/Search.ice src/main/slice/omero/api/ThumbnailStore.ice src/main/slice/omero/cmd/API.ice src/main/slice/omero/cmd/Admin.ice src/main/slice/omero/cmd/Basic.ice src/main/slice/omero/cmd/FS.ice src/main/slice/omero/cmd/Graphs.ice src/main/slice/omero/cmd/Mail.ice src/main/slice/omero/model/Details.ice src/main/slice/omero/model/ElectricPotential.ice src/main/slice/omero/model/Frequency.ice src/main/slice/omero/model/IObject.ice src/main/slice/omero/model/Length.ice src/main/slice/omero/model/NamedValue.ice src/main/slice/omero/model/Permissions.ice src/main/slice/omero/model/Power.ice src/main/slice/omero/model/Pressure.ice src/main/slice/omero/model/RTypes.ice src/main/slice/omero/model/Temperature.ice src/main/slice/omero/model/Time.ice src/main/slice/omero/model/Units.ice src/test/java/loci/ome/OmeroReaderTest.java src/test/java/loci/ome/utests/MissingOMEReaderWriterServiceTest.java src/test/java/loci/ome/utests/testng-no-ome-io.xml src/test/java/loci/ome/utests/testng.xml src/test/java/ome/formats/MockedOMEROImportFixture.java src/test/java/ome/formats/fixture.xml src/test/java/ome/formats/importer/ImportCandidatesTest.java src/test/java/ome/formats/importer/OMEROWrapperTest.java src/test/java/ome/formats/test/util/IniWritingInterceptor.java src/test/java/ome/formats/test/util/TestEngine.java src/test/java/ome/formats/test/util/TestEngineConfig.java src/test/java/ome/formats/test/util/TestEngineIniFile.java src/test/java/ome/formats/utests/BasicImporterClientTest.java src/test/java/ome/formats/utests/ChannelDataTest.java src/test/java/ome/formats/utests/ChannelProcessorTest.java src/test/java/ome/formats/utests/ContainerCacheOrderTest.java src/test/java/ome/formats/utests/CorrectionEnumTest.java src/test/java/ome/formats/utests/DetectorSettingsTest.java src/test/java/ome/formats/utests/ErrorHandlerTest.java src/test/java/ome/formats/utests/IObjectContainerStoreTest.java src/test/java/ome/formats/utests/ImportCandidatesTest.java src/test/java/ome/formats/utests/ImportConfigTest.java src/test/java/ome/formats/utests/IniFileLoaderTest.java src/test/java/ome/formats/utests/InstrumentTest.java src/test/java/ome/formats/utests/LaserTest.java src/test/java/ome/formats/utests/LightSourceSettingsArcTest.java src/test/java/ome/formats/utests/LightSourceSettingsFilamentTest.java src/test/java/ome/formats/utests/LightSourceSettingsLaserTest.java src/test/java/ome/formats/utests/MetadataValidatorTest.java src/test/java/ome/formats/utests/ObjectiveSettingsTest.java src/test/java/ome/formats/utests/PlaneInfoProcessorTest.java src/test/java/ome/formats/utests/ShapeProcessorTest.java src/test/java/ome/formats/utests/TargetsTest.java src/test/java/ome/formats/utests/TestEnumerationProvider.java src/test/java/ome/formats/utests/TestReader.java src/test/java/ome/formats/utests/TestServiceFactory.java src/test/java/ome/formats/utests/UnitsTest.java src/test/java/ome/formats/utests/WellProcessorTest.java src/test/java/ome/services/blitz/test/AbstractGraphTest.java src/test/java/ome/services/blitz/test/AbstractServantTest.java src/test/java/ome/services/blitz/test/AdminITest.java src/test/java/ome/services/blitz/test/ClientConstructorsTest.java src/test/java/ome/services/blitz/test/ClusteredRingTest.java src/test/java/ome/services/blitz/test/DoAllITest.java src/test/java/ome/services/blitz/test/ExporterITest.java src/test/java/ome/services/blitz/test/FakeAdapter.java src/test/java/ome/services/blitz/test/LoginInterceptor.java src/test/java/ome/services/blitz/test/ManagedContextFixture.java src/test/java/ome/services/blitz/test/ManagedRepositoryITest.java src/test/java/ome/services/blitz/test/MetadataStoreITest.java src/test/java/ome/services/blitz/test/ShareITest.java src/test/java/ome/services/blitz/test/TimelineITest.java src/test/java/ome/services/blitz/test/UpdateITest.java src/test/java/ome/services/blitz/test/fixtures/BlitzServerFixture.java src/test/java/ome/services/blitz/test/fixtures/ExecutorMockFactory.java src/test/java/ome/services/blitz/test/fixtures/SessionFactoryMockFactory.java src/test/java/ome/services/blitz/test/geom/GeomToolTest.java src/test/java/ome/services/blitz/test/mock/BlitzConfigurationTest.java src/test/java/ome/services/blitz/test/mock/BlitzEntryTest.java src/test/java/ome/services/blitz/test/mock/ClientCallbackTest.java src/test/java/ome/services/blitz/test/mock/ClusteredBlitzTest.java src/test/java/ome/services/blitz/test/mock/MockDeclarer.java src/test/java/ome/services/blitz/test/mock/MockFixture.java src/test/java/ome/services/blitz/test/mock/RTypesObjectFactoryTest.java src/test/java/ome/services/blitz/test/mock/ReflectiveApiTest.java src/test/java/ome/services/blitz/test/mock/SessionDestructionTest.java src/test/java/ome/services/blitz/test/mock/StandaloneRepositoryTest.java src/test/java/ome/services/blitz/test/mock/TemporaryRepositoryTest.java src/test/java/ome/services/blitz/test/old/IceTest.java src/test/java/ome/services/blitz/test/old/SecurityTest.java src/test/java/ome/services/blitz/test/old/ServiceFactoryTest.java src/test/java/ome/services/blitz/test/utests/AccessorsTest.java src/test/java/ome/services/blitz/test/utests/AdapterTest.java src/test/java/ome/services/blitz/test/utests/ApiConsistencyCheckTest.java src/test/java/ome/services/blitz/test/utests/CallbackTest.java src/test/java/ome/services/blitz/test/utests/CheckedPathTest.java src/test/java/ome/services/blitz/test/utests/ChecksumBitwidthTest.java src/test/java/ome/services/blitz/test/utests/ClientFilePathTransformerTest.java src/test/java/ome/services/blitz/test/utests/EhCacheTest.java src/test/java/ome/services/blitz/test/utests/FilePathNamingValidatorTest.java src/test/java/ome/services/blitz/test/utests/FilePathRestrictionsTest.java src/test/java/ome/services/blitz/test/utests/FilePathTransformerTestBase.java src/test/java/ome/services/blitz/test/utests/FleetingDirectory.java src/test/java/ome/services/blitz/test/utests/FsFileTest.java src/test/java/ome/services/blitz/test/utests/IceMethodInvokerUnitTest.java src/test/java/ome/services/blitz/test/utests/MakePathComponentSafeTest.java src/test/java/ome/services/blitz/test/utests/ManagedRepositoryITest.java src/test/java/ome/services/blitz/test/utests/ModelTest.java src/test/java/ome/services/blitz/test/utests/ParametersIToPojoOptionsTest.java src/test/java/ome/services/blitz/test/utests/ParametersTest.java src/test/java/ome/services/blitz/test/utests/PermissionsITest.java src/test/java/ome/services/blitz/test/utests/RTypesTest.java src/test/java/ome/services/blitz/test/utests/ResourcesTest.java src/test/java/ome/services/blitz/test/utests/RingTest.java src/test/java/ome/services/blitz/test/utests/ServerFilePathTransformerTest.java src/test/java/ome/services/blitz/test/utests/ServiceFactoryKeepAliveUnitTest.java src/test/java/ome/services/blitz/test/utests/ServiceFactoryServiceCreationDestructionTest.java src/test/java/ome/services/blitz/test/utests/TestCache.java src/test/java/ome/services/repo/test/AbstractRepoUnitTest.java src/test/java/ome/services/repo/test/FileMakerUnitTest.java src/test/java/ome/services/repo/test/LegacyRepositoryUnitTest.java src/test/java/ome/services/repo/test/ProcessContainerUnitTest.java src/test/java/ome/services/roi/test/AbstractRoiITest.java src/test/java/ome/services/roi/test/ContainedPointsTest.java src/test/java/ome/services/roi/test/ImageMeasurementsTest.java src/test/java/ome/services/roi/test/MeasurementStoreUnitTest.java src/test/java/ome/services/roi/test/RoiPerformanceTest.java src/test/java/ome/services/roi/test/ShapeStatsTest.java src/test/java/ome/services/roi/test/ShapeUnitTest.java src/test/java/ome/services/sec/test/AbstractAccountTest.java src/test/java/ome/services/sec/test/AbstractChangeDetailClientTest.java src/test/java/ome/services/sec/test/AbstractPermissionsTest.java src/test/java/ome/services/sec/test/AbstractSecurityTest.java src/test/java/ome/services/sec/test/AccountCreationTest.java src/test/java/ome/services/sec/test/AdminTest.java src/test/java/ome/services/sec/test/ChgrpClientTest.java src/test/java/ome/services/sec/test/ChmodClientTest.java src/test/java/ome/services/sec/test/ChownClientTest.java src/test/java/ome/services/sec/test/PasswordTest.java src/test/java/ome/services/sec/test/ReadSecurityTest.java src/test/java/ome/services/sec/test/SessionTest.java src/test/java/ome/services/sec/test/UseSecurityTest.java src/test/java/ome/services/sec/test/WriteSecurityTest.java src/test/java/omero/cmd/admin/ResetPasswordRequestTest.java src/test/java/omero/cmd/fs/OriginalMetadataRequestTest.java src/test/java/omero/cmd/graphs/GraphUtilTest.java src/test/java/omero/cmd/graphs/SpecificityClassifierTest.java src/test/java/omero/cmd/mail/SendEmailRequestTest.java src/test/java/omero/model/MaskDataTest.java src/test/java/omero/model/MaskTest.java src/test/java/omero/model/ROICoordinateTest.java src/test/java/omero/model/ROIDataTest.java src/test/java/omero/model/UnitsTest.java src/test/java/omero/test.xml src/test/java/omero/test2.xml src/test/java/omero/util/test/TempFileManagerTest.java src/test/resources/fs.testng.xml src/test/resources/integration.testng.xml src/test/resources/manual.config src/test/resources/rois.testng.xml src/test/resources/unit.testng.xml
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