[ome-devel] CLI import: create project and dataset

[Petr Walczysko]

Hi Yanling

further information to the answer of Sebastien Besson below:

Please note that you have to take care about which group you are importing to (depends on the user you are importing-as).

You might want to switch the group. Please note that there is a bug, see
 http://trac.openmicroscopy.org.uk/ome/ticket/12288

For workaround, to be able to switch groups please follow following steps:


  *   bin/omero login --sudo=<admin> <user>@localhost

  *   bin/omero sessions group <group_name> - the output of which should be similar to:

Using session 5d7d8cd2-13e7-4a1d-988b-e65b02cf7f2f (user-8 at localhost:4064). Current group: private-1
Group 'private-1' (id=7) switched to 'read-only-1' (id=8)

  *   bin/omero import <path/to/images>

This should make sure you are importing for the <user> into the <group_name>.

All the best
Petr

There is a workflow described in the ticket.

Cheers
Petr

On 30 May 2014, at 10:24, Sebastien Besson <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>>
 wrote:

Hi Yanling,

Yes the --sudo flag was also part of the 5.0.2 release and definitely applies to the import.
So you should be able to call the following to perform a import-as operation via CLI:

$ bin/omero import --sudo root -d 'Dataset:51' -s localhost -u user /path_to_file

Note that this functionality is currently restricted to admins although we plan to extend
it to group owners in the future.

Sebastien


On 29 May 2014, at 20:18, Yanling Liu <vrnova at gmail.com<mailto:vrnova at gmail.com>> wrote:

Hello Sebastien,

Thanks for your message. I have performed OMERO upgrade to 5.0.2. The bin/omero obj command worked as described. Great!

I can see the obj command has the option to create projects for other users with --sudo flag. Does the flag apply to bin/omero import too? In other words, can I import data as administrator for other users without typing each user's password using bin/omero import?

I have tried to do following command but failed, of course dataset #51 does not belong to the root user.

bin/omero import -d 'Dataset:51' -s localhost -u root /path_to_file

Thanks,


On Thu, May 29, 2014 at 11:06 AM, Sebastien Besson <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>> wrote:
Hi Yanling,

as part of the last 5.0.2 release of OMERO, the CLI now supports a new `obj` command [1].
This command allows the creation of containers amongst other things. As an example, the
creation of projects and datasets should now be achievable via

$ bin/omero obj new Project name=project
$ bin/omero obj new Dataset name=dataset

As an aside, we have started working on a script to setup our training material which combines
`bin/omero obj` and `bin/omero import` and may be informative:
https://github.com/openmicroscopy/openmicroscopy/pull/2561/files
Note our next step is the extension of the CLI documentation [2] to add some description on this
command and its usage.

Best,
Sebastien


[1] https://github.com/openmicroscopy/openmicroscopy/pull/2409<http://www.openmicroscopy.org/site/support/omero5/sysadmins/server-webstart-codesigning.html>

[2] http://www.openmicroscopy.org/site/support/omero5/users/command-line-interface.html


On 29 May 2014, at 15:50, Yanling Liu <vrnova at gmail.com<mailto:vrnova at gmail.com>> wrote:

Hello,

Is it possible to create new project and dataset in CLI import?

For example, it would be great if I can use following command to import a set of images to a user while creating new project and dataset on the fly.

bin/omero -s localhost -u user import path_to_file -project project_name_or_id -dataset dataset_name_or_id

The reason I am asking is because we have 10TB existing images to be imported into OMERO. Create new project and dataset and import images into them would save us a lot of time.

Thanks,
Yanling
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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364


The University of Dundee is a registered Scottish Charity, No: SC015096


Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364


The University of Dundee is a registered Scottish Charity, No: SC015096
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