[ome-devel] OME python binding
Yanling Liu
vrnova at gmail.com
Wed Oct 1 16:54:05 BST 2014
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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> > >ome-devel at lists.openmicroscopy.org.uk
> > >http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> >
> >
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> >
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> >
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>
>
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