[ome-devel] in place import failed

[Josh Moore]

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
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