[ome-devel] OME python binding

[Aleksandra Tarkowska]

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

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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