[ome-devel] OME python binding

[Yanling Liu]

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> 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> 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> wrote:
>>
>> >On Thu, 25 Sep 2014 13:31:53 -0400, Yanling Liu <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,
>> >      ])
>> >      cmd.append(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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>>
>>
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>>
>
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