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Task #12278 (closed)

Opened 10 years ago

Closed 10 years ago

Bug: In-place imports and omero.data.dir error (Windows)

Reported by: bpindelski Owned by:
Priority: blocker Milestone: 5.0.3
Component: Services Version: 5.0.1
Keywords: n.a. Cc: jamoore, spli
Resources: n.a. Referenced By: https://trello.com/c/EOL8YL14/54-bug-import
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by bpindelski)

While testing https://github.com/openmicroscopy/openmicroscopy/pull/2242, it has been discovered that using omero.data.dir with an in-place import causes the import to fail. The scenario is following:

  1. Start the server without setting omero.data.dir - images are assumed to be saved to C:\OMERO
  2. Conduct an in-place import
  3. Stop the server, set omero.data.dir to e.g. C:\OMERO.data, rename the binary repo to the new name
  4. Start the server, try an in-place import. It fails with
    2014-05-14 13:45:36,403 10750      [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: C:\Users\ome\Desktop\test\dv_single\test11_R3D.dv
    2014-05-14 13:45:36,528 10875      [      main] WARN   s.importer.transfers.SymlinkFileTransfer - Failed to deleted C:\OMERO\ManagedRepository\root_0\2014-05\14\13-45-33.575\test11_R3D.dv
    2014-05-14 13:45:36,543 10890      [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: C:\Users\ome\Desktop\test\dv_single\test11_R3D.dv
    java.io.FileNotFoundException: File 'C:\OMERO\ManagedRepository\root_0\2014-05\14\13-45-33.575\test11_R3D.dv' does not exist
            at org.apache.commons.io.FileUtils.openInputStream(FileUtils.java:137) ~[commons-io.jar:1.4]
            at org.apache.commons.io.FileUtils.readFileToString(FileUtils.java:1102) ~[commons-io.jar:1.4]
            at org.apache.commons.io.FileUtils.readFileToString(FileUtils.java:1120) ~[commons-io.jar:1.4]
            at ome.formats.importer.transfers.AbstractExecFileTransfer.checkLocation(AbstractExecFileTransfer.java:119) ~[blitz.jar:na]
            at ome.formats.importer.transfers.AbstractExecFileTransfer.transfer(AbstractExecFileTransfer.java:61) ~[blitz.jar:na]
            at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:414) [blitz.jar:na]
            at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:477) [blitz.jar:na]
            at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271) [blitz.jar:na]
            at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216) [blitz.jar:na]
            at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:721) [blitz.jar:na]
    2014-05-14 13:45:36,559 10906      [      main] ERROR        ome.formats.importer.ImportLibrary - Error on import
    java.io.FileNotFoundException: File 'C:\OMERO\ManagedRepository\root_0\2014-05\14\13-45-33.575\test11_R3D.dv' does not exist
            at org.apache.commons.io.FileUtils.openInputStream(FileUtils.java:137) ~[commons-io.jar:1.4]
            at org.apache.commons.io.FileUtils.readFileToString(FileUtils.java:1102) ~[commons-io.jar:1.4]
            at org.apache.commons.io.FileUtils.readFileToString(FileUtils.java:1120) ~[commons-io.jar:1.4]
            at ome.formats.importer.transfers.AbstractExecFileTransfer.checkLocation(AbstractExecFileTransfer.java:119) ~[blitz.jar:na]
            at ome.formats.importer.transfers.AbstractExecFileTransfer.transfer(AbstractExecFileTransfer.java:61) ~[blitz.jar:na]
            at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:414) ~[blitz.jar:na]
            at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:477) ~[blitz.jar:na]
            at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271) ~[blitz.jar:na]
            at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216) [blitz.jar:na]
            at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:721) [blitz.jar:na]
    2014-05-14 13:45:36,559 10906      [      main] INFO         ome.formats.importer.ImportLibrary - Exiting on error
    

This only happens on Windows. Impossible to reproduce on Linux or OS X.

Change History (6)

comment:1 Changed 10 years ago by bpindelski

  • Cc jamoore added

comment:2 Changed 10 years ago by bpindelski

  • Description modified (diff)
  • Summary changed from Bug: In-place imports and omero.data.dir error to Bug: In-place imports and omero.data.dir error (Windows)

comment:3 Changed 10 years ago by jburel

comment:4 Changed 10 years ago by jamoore

  • Cc spli added

Simon, would it make sense to take a blank Windows VM from modern.ie and try using your scripts to set up a server to reproduce this? i.e. that should work?

comment:5 Changed 10 years ago by spli

Yes, it should work.

comment:6 Changed 10 years ago by bpindelski

  • Resolution set to worksforme
  • Status changed from new to closed
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