Task #11781 (closed)
Opened 10 years ago
Closed 10 years ago
Bug: flex mount points may not be available to the server
Reported by: | jamoore | Owned by: | mlinkert |
---|---|---|---|
Priority: | critical | Milestone: | 5.0.0-rc1 |
Component: | Bio-Formats | Version: | 5.0.0-beta1 |
Keywords: | n.a. | Cc: | christophe.trefois@…, bf@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
See: http://lists.openmicroscopy.org.uk/pipermail/ome-users/2013-November/004083.html
Flex files can be configured to read files from a net share. This happens on the client-side. In OMERO5, with the client being re-used to read the files server-side, the files are not being found:
2013-11-28 13:40:30,060 INFO [ loci.formats.FormatHandler] (3-thread-5) Building list of valid .flex files 2013-11-28 13:40:30,060 INFO [ loci.formats.FormatHandler] (3-thread-5) Looking for files that are in the same dataset as /home/omero/OMERO.data/ManagedRepository/root_0/2013-11/28/13-37-47.221/Y;/OperaDB_Backups/20 13/2013_11/OperaDB_2013_Nov/Christophe Trefois/CT 2013.11.08_Rotenone_Paraquat/CT 20131108_Rot_Para_P1/Meas_01/Meas_01(2013-11-08_12-29-06).mea 2013-11-28 13:40:30,060 DEBUG [ loci.formats.Memoizer] (3-thread-5) start[1385646029916] time[144] tag[loci.formats.Memoizer.setId] 2013-11-28 13:40:30,061 INFO [ o.s.b.r.ManagedImportRequestI.@18e2742] (3-thread-5) Cancelled 2013-11-28 13:40:30,061 INFO [ org.perf4j.TimingLogger] (3-thread-5) start[1385646029839] time[221] tag[omero.request] 2013-11-28 13:40:30,062 INFO [ org.perf4j.TimingLogger] (3-thread-5) start[1385646029827] time[234] tag[omero.call.exception] 2013-11-28 13:40:30,062 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Excp: omero.cmd.HandleI$Cancel: error-on-init 2013-11-28 13:40:30,062 DEBUG [ o.s.b.r.ManagedImportRequestI.@18e2742] (3-thread-5) Request cancelled by loci.formats.FormatException: .flex files were not found. Did you forget to specify the server names?
from the log file in QA 7752.
Change History (1)
comment:1 Changed 10 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
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Should be fixed with https://github.com/openmicroscopy/bioformats/pull/819 and https://github.com/openmicroscopy/openmicroscopy/pull/1867. Server-side server mappings are not required; this just uses Bio-Formats' ID mapping to allow ImportLibrary to send all files to the same directory on import into the server.