[ome-devel] OME python binding

Fri Sep 26 14:28:44 BST 2014

It is not in OMERO 5 series. The latest develop allows you to set omero.web.ui.tree.orphaned but it only updates OMERO.web, Insight will not pick it. It will definitely be available for both clients in 5.1 release.

Kind regards
Ola

From: Yanling Liu <vrnova at gmail.com<mailto:vrnova at gmail.com>>
Date: Fri, 26 Sep 2014 09:20:44 -0400
To: Aleksandra Tarkowska <a.tarkowska at dundee.ac.uk<mailto:a.tarkowska at dundee.ac.uk>>
Cc: "ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>" <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-devel] OME python binding

Where do I changed the name of "Orphaned Images"? I would prefer to use "Unmapped Images" instead.

Thanks,

On Fri, Sep 26, 2014 at 9:13 AM, Aleksandra Tarkowska <A.Tarkowska at dundee.ac.uk<mailto:A.Tarkowska at dundee.ac.uk>> wrote:
Hi Yanling

> Dropbox documentation says NAS is not supported, is a NFS mount considered a network attached share (NAS) to OMERO?

Dropbox can monitor only local hard drive. But you can set up samba dir locally to drop files and set configuration parameters like: "--transfer=ln_rm" or "--transfer=upload_rm" to delete when they are imported. If you prefer to use NFS you can use In-place import https://www.openmicroscopy.org/site/support/omero5/sysadmins/in-place-import.html. That should simplify your workflow.

> Dropbox import new images under "Orphaned Images", then user has to login to organise new images into projects and datasets, is that correct?

That is correct. Extended path /OMERO/DropBox/user/group/project/dataset/ is on our list to do http://trac.openmicroscopy.org.uk/ome/ticket/4032 as well as templates http://trac.openmicroscopy.org.uk/ome/ticket/12039

You can customise name of  "Orphaned Images" if is not suitable.

Kind regards
Ola

On Fri, Sep 26, 2014 at 8:38 AM, Aleksandra Tarkowska <A.Tarkowska at dundee.ac.uk<mailto:A.Tarkowska at dundee.ac.uk>> wrote:
Hi Yanling

As Carne mentioned you can invoke import process via python script.
Similar test is available on
https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/to
ols/OmeroPy/test/integration/library.py#L187<https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tools/OmeroPy/test/integration/library.py#L187>

args.extend(["-s", server, "-k", key, "-p", port, "import", "--"])

Allows you to pass all parameters you normally pass via bin/omero import Š
For more details refer to --help.

Can I ask why you just simply cannot use dropbox to do that work
automatically for you?
Did you see
http://www.openmicroscopy.org/site/support/omero5/sysadmins/dropbox.html

Kind regards
Ola

On 26/09/2014 12:48, "Carnë Draug" <carandraug+dev at gmail.com<mailto:carandraug%2Bdev at gmail.com>> wrote:

>On Thu, 25 Sep 2014 13:31:53 -0400, Yanling Liu <vrnova at gmail.com<mailto:vrnova at gmail.com>> wrote:
>> Hi,
>>
>> I was able to use the CLI import (bin/omero import) to import
>> images into OMERO. My question is that if OMERO python binding has
>> similar capability? Can I write a little python script and call OMERO
>> import function to upload some images to OMERO?
>>
>> What I mean is if there's python binding to the import function,
>> rather than doing system call in python script to call bin/omero.
>
>You can do something like the following:
>
>    import omero
>    import omero.cli
>
>    client = omero.client (host = server_ip_or_hostname)
>    client.createSession (username = "username", password = "password")
>
>    cli = omero.cli.CLI()
>    cli.loadplugins()
>    cli._client = client.createClient(secure = True)
>    cli.invoke(["import", path_to_image_file])
>
>Note that you need to create a copy of the client when setting `_client`
>because that session will be closed after the image import.
>
>To find out the ID of the image you imported, you will need to get
>this call STDOUT.  I have routinely [1] been doing the following (note
>that this imports a single file but should be easy to adjust for
>multiple files):
>
>
>    cli = omero.cli.CLI()
>    cli.loadplugins()
>    cli._client = self.client.createClient(secure = True)
>      cmd = [
>      "import",
>      "--debug", "ERROR",
>    ]
>    if self.datasetID:
>      cmd.extend(["-d", str(self.datasetID)])
>    if self.child_name:
>      cmd.extend(["-n", self.child_name])
>
>    cid = None
>    with tempfile.NamedTemporaryFile(suffix=".stdout") as stdout:
>      cmd.extend([
>        "---errs", os.devnull,
>        "---file", stdout.name<http://stdout.name>,
>      ])
>      cmd.append(self.fout.name<http://self.fout.name>)
>
>      STDERR = sys.stderr
>      try:
>        with open(os.devnull, 'w') as DEVNULL:
>          sys.stderr = DEVNULL
>          cli.invoke(cmd)
>      finally:
>        sys.stderr = STDERR
>        ret_code = cli.rv
>        if ret_code == 0:
>          ## we only need to read one line or something is very wrong
>          cid = int(stdout.readline())
>          if not cid:
>            raise Exception("unable to get exported image ID")
>        else:
>          raise Exception("failed to import processed image")
>
>    self.child = self.conn.getObject("Image", cid)
>
>
>[1]
>https://github.com/MicronOxford/omero_scripts_processing/blob/40e29af8/ome
>ro_scripts_processing.py#L293
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