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

[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.

[jamoore]

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?

[spli]

Yes, it should work.

[bpindelski]

Re-tried with the server build from ​http://ci.openmicroscopy.org/job/OMERO-5.0-merge-build/ICE=3.4,label=ome-c6100-1/59/. This issue disappeared. I wonder if ​https://github.com/openmicroscopy/openmicroscopy/pull/2673 fixed it. Closing.