[ome-devel] in place import failed

[Yanling Liu]

Success!

Thank you Josh.

On Wed, Oct 1, 2014 at 1:13 PM, Josh Moore <josh at glencoesoftware.com> wrote:

>
> On Oct 1, 2014, at 6:08 PM, Yanling Liu wrote:
>
> > Hi, it's me, again, :-)
>
> Hi Yanling!
>
> > Trying to do in place import to inject existing images into OMERO but
> failed.
> >
> > Previously I created python script to invoke bin/omero to do import:
> >
> > omeroBin = "/home/omero/omero/OMERO.server/bin/omero"
> > createImport = omeroBin + " import -d " + datasetId + " -u " + username
> + " --sudo root -w " + rootPWD + " -s localhost '" + path + "'"
> > subprocess.call(createImport, shell=True)
> >
> > Essentially what I am doing is to import existing images for other users
> using the root account.
> >
> > It works well till I try to use in place import. Based on omero
> documentation (
> https://www.openmicroscopy.org/site/support/omero5/sysadmins/in-place-import.html),
> I modified my script to be like this:
> >
> > createImport = omeroBin + " import -- --transfer=ln_s -d " + datasetId +
> " -u " + username + " --sudo root -w " + rootPWD + " -s localhost '" + path
> + "'"
> >
> > The only difference is to add "-- --transfer=ln_s" in the command line
> string.
>
> The "--" means "stop parsing the other arguments in Python".
> Unfortunately, "--sudo" is needed on the Python side of things. The
> following should work:
>
> createImport = omeroBin + " import -d " + datasetId + " -u " + username +
> " --sudo root -w " + rootPWD + " -s localhost -- --transfer=ln_s '" + path
> + "'"
>
> Cheers,
> ~Josh.
>
> > However, I got something like this:
> >
> > 2014-10-01 12:59:46,180 177        [      main] INFO
> ome.formats.importer.ImportConfig - OMERO Version: 5.0.3-ice34-b41
> > 2014-10-01 12:59:46,193 190        [      main] INFO
> ome.formats.importer.ImportConfig - Bioformats version: 5.0.3-ice34-b41
> revision: 5f987c0 date: 5 August 2014
> > 2014-10-01 12:59:46,198 195        [      main] INFO
>  formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
> > importer-cli: unrecognized option '--sudo'
> >
> >
> > Any help?
> >
> > Thanks,
> > Yanling
> > _______________________________________________
> > ome-devel mailing list
> > ome-devel at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20141001/76f69fc1/attachment.html>