Open Microscopy Environment

Hi Josh,

I test the invoke login with cli import and get the following error:

Code: Select all

File "./script", line 82, in upload_to_omero_cli
    cli.invoke(cmd)
  File "/home/omero/OMERO.server-5.3.5-ice36-b73/lib/python/omero/cli.py", line 992, in invoke
    stop = self.onecmd(line, previous_args)
  File "/home/omero/OMERO.server-5.3.5-ice36-b73/lib/python/omero/cli.py", line 1069, in onecmd
    self.execute(line, previous_args)
  File "/home/omero/OMERO.server-5.3.5-ice36-b73/lib/python/omero/cli.py", line 1151, in execute
    args.func(args)
  File "/home/omero/OMERO.server-5.3.5-ice36-b73/lib/python/omero/plugins/import.py", line 480, in importer
    command_args = CommandArguments(self.ctx, args)
  File "/home/omero/OMERO.server-5.3.5-ice36-b73/lib/python/omero/plugins/import.py", line 114, in __init__
    self.set_login_arguments(ctx, args)
  File "/home/omero/OMERO.server-5.3.5-ice36-b73/lib/python/omero/plugins/import.py", line 229, in set_login_arguments
    client = ctx.conn(args)
  File "/home/omero/OMERO.server-5.3.5-ice36-b73/lib/python/omero/cli.py", line 1327, in conn
    self.controls["sessions"].login(args)
  File "/home/omero/OMERO.server-5.3.5-ice36-b73/lib/python/omero/plugins/sessions.py", line 406, in login
    server, name, port = self._get_server(store, name, port)
  File "/home/omero/OMERO.server-5.3.5-ice36-b73/lib/python/omero/plugins/sessions.py", line 886, in _get_server
    rv = self.ctx.input("Server: [%s:%s]" % (defserver, port))
  File "/home/omero/OMERO.server-5.3.5-ice36-b73/lib/python/omero/cli.py", line 555, in input
    rv = raw_input(prompt)
EOFError: EOF when reading a line
!! 06/21/18 13:07:03.763 error: communicator not destroyed during global destruction.


Script:

Code: Select all

def upload_to_omero_cli(conn,imagePath,imgSrc):
    dataset = imgSrc.getParent()

    # import via cli
    client = conn.c
    cmd = "import %s -d %s" % (imagePath, dataset.id)
    print cmd

    cli = omero.cli.CLI()
    cli.loadplugins()
    cli.set_client(client)
    #invoke login
    cli.invoke("hql -q 'select g.name from ExperimenterGroup g'")
    cli.invoke(cmd)


Regards,
Susanne

Hi Susanne,

sorry for the confusion. Please replace:

Code: Select all

    cli.set_client(client)
    #invoke login


with

Code: Select all

    cli.invoke("login")


Gruß,
~Josh.

Hi Josh, Hi Will,

now it works. I was wonder that the import failed with all the hints you gave me, but after killing all the orphaned script sessions it works.
So thank you very much for the help!

Regards
Susanne