Open Microscopy Environment

Hi,

is any way to add or create bulk user id's creation in omero ? more than 40 user in single file in csv or excel formats to omero id creation

thanks

There's no built in way to bulk add, but it's fairly easy to script. Assuming your user CSV looks like this:

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bulk-user1,Albert,A.,bulk-groups,abc123
bulk-user2,Barbara,B.,bulk-groups,def456


then you can use the following code to add the users:

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#!/usr/bin/env python
import omero
import omero.cli
import fileinput

with omero.cli.cli_login() as cli:
    for line in fileinput.input():
        line = line.strip()
        parts = line.split(",")
        assert len(parts) == 5
        omeName, firstName, lastName, groupName, password  = parts
        cli.invoke(["-q", "user", "add", "--ignore-existing",
                    omeName, firstName, lastName, groupName,
                    "--userpassword", password],
                   strict=True)


For example,

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$ bin/omero login root@localhost
Created session for root@localhost:4064. Idle timeout: 10 min. Current group: system
$ bin/omero group add bulk-groups
Added group bulk-groups (id=4) with permissions rw----
$ PYTHONPATH=lib/python ./bulk.py bulk.csv
Added user bulk-user1 (id=3) with password
Added user bulk-user2 (id=4) with password


The "--ignore-existing" flag means that if you update the CSV and re-run the code, you'll see that some users have already been added:

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$ PYTHONPATH=lib/python ./bulk.py bulk.csv
User exists: bulk-user1 (id=3)
User exists: bulk-user2 (id=4)


Hi

Thanks for reply

The group is added successfully, but user creation show some error

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omero@ubuntu-14:~/OMERO.server$ PYTHONPATH=lib/python ./bulk.py bulk.csv
Traceback (most recent call last):
  File "./bulk.py", line 6, in <module>
    with omero.cli.cli_login() as cli:
AttributeError: 'module' object has no attribute 'cli_login'

Hmm...what version of OMERO are you using? (cli_login was added in 5.3.0) but the code is simple enough to be copied into your script completely. Another alternative would be to do the same with bash.

~Josh

Hi

My Omero Version is 5.2

Thanks

Gotcha. For being able to maintain this script, would you rather see more Python or Bash? ~J

Bash

Bash script:

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#!/usr/bin/env bash

set -e
set -u
CSVFILE="$1"

omero login

IFS=","
while read omeName firstName lastName groupName password
do
   omero -q user add --ignore-existing \
     "$omeName" "$firstName" "$lastName" "$groupName" \
     --userpassword "$password"
done < "$CSVFILE"


Example:

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$ export PATH=$PATH:/opt/omero/server/OMERO.server/bin/
$ ./bulk.sh bulk.csv
Previous session expired for root on localhost:4064
Server: [localhost:4064]
Username: [root]
Password:
Created session for root@localhost:4064. Idle timeout: 10 min. Current group: system
User exists: bulk-user1 (id=3)
User exists: bulk-user2 (id=4)


~Josh

Hi

it working good, but first line user only created. It skips all other lines without any errors.
And how to delete the unused or unwanted user and group ?

Thanks

Hmmm.... that's surprising. Is there any other output that you can share with us that might give a clue as to what's going on?