<div dir="ltr">Has anyone seen this import error? It's pretty vague. I imported a test jpg to make sure import was working in general and it was fine. I updated to the latest OMERO and still seeing the problem.<div><br></div><div>Any ideas?</div><div><br></div><div>Thanks<br><div><div><br></div><div><b>Import attempt:</b></div><div><br></div><div><div>bash-4.2$ /opt/omero/server/OMERO.server/bin/omero import -g "public-group" -- --transfer=ln_s /OMERO/data/ss240_802/2017-04/10/07-20-11.268/130722.nd</div><div>Using session 69309e1b-15bb-4eef-80ef-62018c661a28 (root@localhost:4064). Idle timeout: 10 min. Current group: public-group</div><div>2017-12-19 23:46:10,097 202        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.4.1-ice36-b75</div><div>2017-12-19 23:46:10,109 214        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.7.2 revision: 6909f51c1786b58fe5a0765cea2ad6a278ebc1c2 date: 21 November 2017</div><div>2017-12-19 23:46:10,146 251        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting transfer to ln_s</div><div>2017-12-19 23:46:10,149 254        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO</div><div>2017-12-19 23:46:10,449 554        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM</div><div>2017-12-19 23:46:25,767 15872      [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 978ms. (15317ms total) [0 unknowns]</div><div>2017-12-19 23:46:26,655 16760      [      main] INFO       ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064</div><div>2017-12-19 23:46:27,008 17113      [      main] INFO       ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back</div><div>2017-12-19 23:46:27,303 17408      [      main] INFO       ome.formats.OMEROMetadataStoreClient - Server: 5.4.1</div><div>2017-12-19 23:46:27,303 17408      [      main] INFO       ome.formats.OMEROMetadataStoreClient - Client: 5.4.1-ice36-b75</div><div>2017-12-19 23:46:27,303 17408      [      main] INFO       ome.formats.OMEROMetadataStoreClient - Java Version: 1.8.0_151</div><div>2017-12-19 23:46:27,303 17408      [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Name: Linux</div><div>2017-12-19 23:46:27,303 17408      [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Arch: amd64</div><div>2017-12-19 23:46:27,303 17408      [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Version: 4.4.51-40.58.amzn1.x86_64</div><div>2017-12-19 23:46:27,387 17492      [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION</div><div>2017-12-19 23:46:34,669 24774      [      main] ERROR        ome.formats.importer.ImportLibrary - Error on import</div><div>Ice.UnknownLocalException: null</div><div><span style="white-space:pre">    </span>at IceInternal.AsyncResultI.__wait(AsyncResultI.java:276) ~[ice.jar:na]</div><div><span style="white-space:pre">       </span>at omero.grid.ManagedRepositoryPrxHelper.end_importFileset(ManagedRepositoryPrxHelper.java:171) ~[blitz.jar:na]</div><div><span style="white-space:pre">       </span>at omero.grid.ManagedRepositoryPrxHelper.importFileset(ManagedRepositoryPrxHelper.java:46) ~[blitz.jar:na]</div><div><span style="white-space:pre">    </span>at omero.grid.ManagedRepositoryPrxHelper.importFileset(ManagedRepositoryPrxHelper.java:33) ~[blitz.jar:na]</div><div><span style="white-space:pre">    </span>at ome.formats.importer.ImportLibrary.createImport(ImportLibrary.java:374) ~[blitz.jar:na]</div><div><span style="white-space:pre">    </span>at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:499) ~[blitz.jar:na]</div><div><span style="white-space:pre">     </span>at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289) ~[blitz.jar:na]</div><div><span style="white-space:pre">        </span>at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:289) [blitz.jar:na]</div><div><span style="white-space:pre">    </span>at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:958) [blitz.jar:na]</div><div>2017-12-19 23:46:34,679 24784      [      main] INFO         ome.formats.importer.ImportLibrary - Exiting on error</div><div><br></div><div>==> Summary</div><div>0 files uploaded, 0 filesets created, 0 images imported, 0 errors in 0:00:07.297</div><div>2017-12-19 23:46:34,702 24807      [      main] WARN       ome.formats.OMEROMetadataStoreClient - Exception closing 69309e1b-15bb-4eef-80ef-62018c661a28/83ca5b32-2fa1-4771-a6bb-d52e794fa9c8omero.api.RawFileStore -t -e 1.0:tcp -h 172.17.0.9 -p 44181 -t 60000</div><div>Ice.UnknownLocalException: null</div><div><span style="white-space:pre">    </span>at IceInternal.AsyncResultI.__wait(AsyncResultI.java:276) ~[ice.jar:na]</div><div><span style="white-space:pre">       </span>at omero.api.RawFileStorePrxHelper.end_close(RawFileStorePrxHelper.java:1842) ~[blitz.jar:na]</div><div><span style="white-space:pre"> </span>at omero.api.RawFileStorePrxHelper.close(RawFileStorePrxHelper.java:1733) ~[blitz.jar:na]</div><div><span style="white-space:pre">     </span>at omero.api.RawFileStorePrxHelper.close(RawFileStorePrxHelper.java:1720) ~[blitz.jar:na]</div><div><span style="white-space:pre">     </span>at ome.formats.OMEROMetadataStoreClient.closeQuietly(OMEROMetadataStoreClient.java:1035) [blitz.jar:na]</div><div><span style="white-space:pre">       </span>at ome.formats.OMEROMetadataStoreClient.closeServices(OMEROMetadataStoreClient.java:1056) [blitz.jar:na]</div><div><span style="white-space:pre">      </span>at ome.formats.OMEROMetadataStoreClient.logout(OMEROMetadataStoreClient.java:1082) [blitz.jar:na]</div><div><span style="white-space:pre">     </span>at ome.formats.importer.cli.CommandLineImporter.cleanup(CommandLineImporter.java:335) [blitz.jar:na]</div><div><span style="white-space:pre">  </span>at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:964) [blitz.jar:na]</div></div></div><div><b><br></b></div><div><b>Diagnostics:</b></div><div><br></div><div><div>================================================================================</div><div>OMERO Diagnostics (admin) 5.4.1-ice36-b75</div><div>================================================================================</div><div><br></div><div>Commands:   java -version                  1.8.0     (/usr/bin/java)</div><div>Commands:   python -V                      2.7.5     (/usr/bin/python)</div><div>Commands:   icegridnode --version          3.6.4     (/usr/bin/icegridnode)</div><div>Commands:   icegridadmin --version         3.6.4     (/usr/bin/icegridadmin)</div><div>Commands:   psql --version                 9.4.15    (/usr/bin/psql)</div><div><br></div><div>Server:     icegridnode                    running</div><div>Server:     Blitz-0                        active (pid = 2558, enabled)</div><div>Server:     DropBox                        active (pid = 956, enabled)</div><div>Server:     FileServer                     active (pid = 957, enabled)</div><div>Server:     Indexer-0                      active (pid = 960, enabled)</div><div>Server:     MonitorServer                  active (pid = 959, enabled)</div><div>Server:     OMERO.Glacier2                 active (pid = 961, enabled)</div><div>Server:     OMERO.IceStorm                 active (pid = 970, enabled)</div><div>Server:     PixelData-0                    active (pid = 979, enabled)</div><div>Server:     Processor-0                    active (pid = 981, enabled)</div><div>Server:     Tables-0                       active (pid = 982, enabled)</div><div>Server:     TestDropBox                    inactive (enabled)</div><div><br></div><div>Log dir:    /opt/omero/server/OMERO.server/var/log exists</div><div>Log files:  Blitz-0.log                    3.0 MB        errors=0    warnings=11</div><div>Log files:  DropBox.log                    1.0 KB</div><div>Log files:  FileServer.log                 0.0 KB</div><div>Log files:  Indexer-0.log                  2.0 KB</div><div>Log files:  MonitorServer.log              1.0 KB</div><div>Log files:  PixelData-0.log                2.0 KB</div><div>Log files:  Processor-0.log                246.0 KB      errors=0    warnings=2</div><div>Log files:  Tables-0.log                   2.0 KB        errors=0    warnings=2</div><div>Log files:  TestDropBox.log                n/a</div><div>Log files:  master.err                     3.0 KB        errors=0    warnings=10</div><div>Log files:  master.out                     0.0 KB</div><div>Log files:  Total size                     3.84 MB</div><div><br></div><div><br></div><div>Environment:OMERO_HOME=(unset)</div><div>Environment:OMERO_NODE=(unset)</div><div>Environment:OMERO_MASTER=(unset)</div><div>Environment:OMERO_USERDIR=(unset)</div><div>Environment:OMERO_TMPDIR=(unset)</div><div>Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin</div><div>Environment:PYTHONPATH=(unset)</div><div>Environment:ICE_HOME=(unset)</div><div>Environment:LD_LIBRARY_PATH=(unset)</div><div>Environment:DYLD_LIBRARY_PATH=(unset)</div><div><br></div><div>OMERO SSL port:4064</div><div>OMERO TCP port:4063</div><div>OMERO data dir:'/OMERO'                       Exists? True<span style="white-space:pre">  </span>Is writable? True</div><div>OMERO temp dir:'/opt/omero/server/omero/tmp'  Exists? True<span style="white-space:pre">  </span>Is writable? True   (Size: 0)</div><div><br></div><div>JVM settings: Blitz-${index}                -Xmx5061m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions</div><div>JVM settings: Indexer-${index}              -Xmx3374m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions</div><div>JVM settings: PixelData-${index}            -Xmx5061m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions</div><div>JVM settings: Repository-${index}           -Xmx3374m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions</div></div></div></div>