[ome-devel] OME python binding

Yanling Liu vrnova at gmail.com
Wed Oct 1 19:07:59 BST 2014


Excellent!

So if I want to use this with DropBox I simply put --transfer=upload_rm to
omero.fs.importArgs in  etc/grid/templates.xml, right?

Thanks,
Yanling


On Wed, Oct 1, 2014 at 1:30 PM, Colin Blackburn <C.Blackburn at dundee.ac.uk>
wrote:

> Hi Yanling,
>
> Although we plan to release this in 5.1 it is already available in 5.0.5
> as an experimental feature. However, it is not exposed in the help or
> documentation as it is only intended as an experimental feature for testing
> purposes. To import a file by first uploading and then deleting the
> original source files you would need to use this transfer option:
>
> -—transfer=upload_rm
>
> Please note that you should use this for test purposes only! Please do not
> use it in a production system and please ensure that any data you use for
> testing is backed-up elsewhere.
>
> Any feedback would be most welcome.
>
> Cheers,
>
> Colin
>
> On 1 Oct 2014, at 17:35, Yanling Liu <vrnova at gmail.com> wrote:
>
> > Colin,
> >
> > I'd be more than glad to test this feature.
> >
> > Best,
> > Yanling
> >
> > On Wed, Oct 1, 2014 at 12:30 PM, Colin Blackburn <
> C.Blackburn at dundee.ac.uk> wrote:
> > Hi Yanling,
> >
> > Again, we are planning to release a transfer mode that uploads, imports
> and then deletes the original files. It would do this only on a successful
> upload (all files checked against their sha1s) and a successful import
> (completes without error). This transfer mode could then be used for
> DropBox to effectively clean the DropBox directories of files once imported.
> >
> > This feature is intended to be available in the 5.1 release. If you
> would like to test the this feature prior to that release please do let us
> know.
> >
> > Cheers,
> >
> > Colin
> >
> > On 1 Oct 2014, at 16:54, Yanling Liu <vrnova at gmail.com> wrote:
> >
> > > This is fabulous!
> > >
> > > Then the only thing I need to work on is to setup a cron job to delete
> old files from the DropBox folder.
> > >
> > > Can I dream about DropBox facility to be able to auto-delete imported
> files? I know there's in-place auto-delete but our data is 20TB+ on NFS
> storage and OME doesn't support NFS.
> > >
> > > Cheers,
> > >
> > > Yanling
> > >
> > > On Wed, Oct 1, 2014 at 11:40 AM, Colin Blackburn <
> C.Blackburn at dundee.ac.uk> wrote:
> > > Hi Yanling,
> > >
> > > We are planning to implement a DropBox facility for selecting the
> destination container for imports in our next major release, 5.1.
> > >
> > > Cheers,
> > >
> > > Colin
> > >
> > >
> > > On 30 Sep 2014, at 19:33, Yanling Liu <vrnova at gmail.com> wrote:
> > >
> > > > Tested Dropbox and it works very well.
> > > >
> > > > Just wondering when will the extended path
> /OMERO/DropBox/user/group/project/dataset being implemented? This is very
> very useful to make OME "useful" for imaging facilities where imaging
> facilities upload images for users instead of users themselves, which is
> exactly the case we have.
> > > >
> > > > Thanks,
> > > >
> > > > Yanling
> > > >
> > > > 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
> > > >
> > > > 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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