<div dir="ltr"><div><div><div>Server configuration: Ubuntu 12.04 VM with 3TB NFS storage attached. OME 5 is installed and the ManagedRepository is located on the 3TB NFS storage.<br><br></div>When using command line import tool to inject one user folder plus its subfolders to one dataset in OME, I have got following error on certain TIFF images (file path removed from log info) :<br>
<br>Using session 0267110d-87b6-446a-92b8-0a6aa5b707f9 (acharyaj@localhost:4064). Current group: EMLAB<br>2014-06-06 16:43:36,419 181 [ main] INFO ome.formats.importer.ImportConfig - OMERO Version: 5.0.2-ice34-b26<br>
2014-06-06 16:43:36,432 194 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 5.0.2-ice34-b26 revision: 0c4215a date: 27 May 2014<br>2014-06-06 16:43:36,440 202 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO<br>
2014-06-06 16:43:36,677 439 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM<br>2014-06-06 16:43:37,710 1472 [ main] INFO ome.formats.importer.ImportCandidates - 9 file(s) parsed into 8 group(s) with 9 call(s) to setId in 1003ms. (1033ms total) [1 unknowns]<br>
2014-06-06 16:43:39,695 3457 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064<br>2014-06-06 16:43:40,131 3893 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back<br>
2014-06-06 16:43:40,371 4133 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.0.2<br>2014-06-06 16:43:40,371 4133 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.0.2-ice34-b26<br>
2014-06-06 16:43:40,371 4133 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 1.6.0_30<br>2014-06-06 16:43:40,371 4133 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux<br>
2014-06-06 16:43:40,371 4133 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64<br>2014-06-06 16:43:40,371 4133 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 3.2.0-34-generic<br>
2014-06-06 16:43:40,509 4271 [ main] INFO ome.formats.OMEROMetadataStoreClient - Call context: {omero.group:3}<br>2014-06-06 16:43:40,527 4289 [ main] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION<br>
2014-06-06 16:43:40,760 4522 [ main] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START<br>2014-06-06 16:43:40,773 4535 [ main] INFO ts.importer.transfers.UploadFileTransfer - Transferring /../51-11.tif...<br>
2014-06-06 16:43:40,790 4552 [ main] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /../51-11.tif<br>2014-06-06 16:43:40,872 4634 [ main] ERROR ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /../51-11.tif<br>
omero.ResourceError: null<br> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.6.0_30]<br> at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.6.0_30]<br>
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.6.0_30]<br> at java.lang.reflect.Constructor.newInstance(Constructor.java:534) ~[na:1.6.0_30]<br> at java.lang.Class.newInstance(Class.java:374) ~[na:1.6.0_30]<br>
at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2142) ~[ice.jar:na]<br> at IceInternal.BasicStream.throwException(BasicStream.java:1564) ~[ice.jar:na]<br> at IceInternal.Outgoing.throwUserException(Outgoing.java:443) ~[ice.jar:na]<br>
at omero.api._RawFileStoreDelM.save(_RawFileStoreDelM.java:183) ~[blitz.jar:na]<br> at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:527) ~[blitz.jar:na]<br> at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:500) ~[blitz.jar:na]<br>
at ome.formats.importer.transfers.TransferState.save(TransferState.java:113) ~[blitz.jar:na]<br> at ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:107) ~[blitz.jar:na]<br> at ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:85) ~[blitz.jar:na]<br>
at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:414) [blitz.jar:na]<br> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:477) [blitz.jar:na]<br> at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271) [blitz.jar:na]<br>
at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216) ~[blitz.jar:na]<br> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:721) ~[blitz.jar:na]<br>2014-06-06 16:43:40,879 4641 [ main] ERROR ome.formats.importer.ImportLibrary - Error on import: Cannot find path. Deleted? /../ManagedRepository/acharyaj_52/2014-06/06/16-43-40.589/51-11.tif<br>
omero.ResourceError: null<br> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.6.0_30]<br> at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.6.0_30]<br>
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.6.0_30]<br> at java.lang.reflect.Constructor.newInstance(Constructor.java:534) ~[na:1.6.0_30]<br> at java.lang.Class.newInstance(Class.java:374) ~[na:1.6.0_30]<br>
at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2142) ~[ice.jar:na]<br> at IceInternal.BasicStream.throwException(BasicStream.java:1564) ~[ice.jar:na]<br> at IceInternal.Outgoing.throwUserException(Outgoing.java:443) ~[ice.jar:na]<br>
at omero.api._RawFileStoreDelM.save(_RawFileStoreDelM.java:183) ~[blitz.jar:na]<br> at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:527) ~[blitz.jar:na]<br> at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:500) ~[blitz.jar:na]<br>
at ome.formats.importer.transfers.TransferState.save(TransferState.java:113) ~[blitz.jar:na]<br> at ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:107) ~[blitz.jar:na]<br> at ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:85) ~[blitz.jar:na]<br>
at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:414) ~[blitz.jar:na]<br> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:477) ~[blitz.jar:na]<br> at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271) ~[blitz.jar:na]<br>
at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216) ~[blitz.jar:na]<br> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:721) ~[blitz.jar:na]<br>2014-06-06 16:43:40,879 4641 [ main] INFO ome.formats.importer.ImportLibrary - Exiting on error<br>
<br><br><br></div>I have verified the file 51-11.tif exists as ManagedRepository/acharyaj_52/2014-06/06/16-43-40.589/51-11.tif. Tried run tiffinfo tool again the image file and found no problem. Don't know why OME report an existing file as non-exist...<br>
<br></div><div>Any help?<br><br></div>Thanks,<br>Yanling<br></div>