Bug: cli importer seems to not be submitted QA

[jamoore]

Tried with the latest server and got no QAs on a large number of NPEs from bioformats. Need to investigate.

[bwzloranger]

Seems to be submitting qa's OK in the lastest build. Was something specific causing the issue? --B

[jmoore]

Logs files and files as well? What was the command line you used?

[jmoore]

See previous comment for questions.

[bwzloranger]

All includes are also working (see ​http://qa.openmicroscopy.org.uk/qa/feedback/3188/ as an example)

commandline options used were:

-s <server> -u <user> -w <password> -d <id> --report --upload --logs <path to file>

Perhaps the NPE in bio-formats was preventing the importer from executing. Do you have access to the files that were generating the problem?

[jmoore]

Have you tried with the email parameter?

This may be the related issue:

http://dev.loci.wisc.edu/trac/java/ticket/562

On Tue, Sep 14, 2010 at 6:05 AM, Josh Moore <josh.moore@gmx.de> wrote:
Subj: MIAS import fails with NPE
Text:

Data: /ome/data_repo/from_skyking/mias/frans/NEO-Exp13072008-long-protokol/001-365700055641/
{{{
java.lang.NullPointerException
       at loci.formats.in.MIASReader.getChannelColorFromFile(MIASReader.java:793)
       at loci.formats.in.MIASReader.initFile(MIASReader.java:758)
       at loci.formats.FormatReader.setId(FormatReader.java:1074)
       at loci.formats.ImageReader.setId(ImageReader.java:650)
       at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
       at loci.formats.ChannelFiller.setId(ChannelFiller.java:244)
       at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
       at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
       at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
       at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:255)
       at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:447)
       at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:224)
       at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:133)
       at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:358)
}}}

See also:
 * http://qa.openmicroscopy.org.uk/qa/feedback/2714/
 to
 * http://qa.openmicroscopy.org.uk/qa/feedback/2720/

[jmoore]

I don't think this is fixed.

touch a.pic
bin/omero import --report --upload --logs --email=josh@glencoesoftware.com a.pic 

I don't see uploads here: ​http://qa.openmicroscopy.org.uk/qa/feedback/3197

[jmoore]

Is the missing "/" the issue?

[jburel]

Moved from sprint 2011-02-10 (5)

[bwzloranger <brian.loranger@…>]

(In [a86851588d247b8421d4c97e1aa023afdd063d42/ome.git] on branch develop) Fixes #3861 (CLI Importer upload error)

[jmoore <josh@…>]

(In [3c9b37787a0ec52a9cf22205d86a51f52ddaa2eb/ome.git] on branch dev_4_2) Fixes #3861 (CLI Importer upload error)