[ome-devel] command line importer

[Will Moore]

Hi Chris,

I didn't write this, and I'm not too familiar with the code, but this  
is something we use in our Python testing framework to import images.
components/tools/OmeroPy/test/integration/libraray.py


     def import_image(self, filename = None):
         if filename is None:
             filename = self.OmeroPy / ".." / ".." / ".." /  
"components" / "common" / "test" / "tinyTest.d3d.dv"

         server = self.client.getProperty("omero.host")
         port = self.client.getProperty("omero.port")
         key = self.client.getSessionId()

         # Search up until we find "OmeroPy"
         dist_dir = self.OmeroPy / ".." / ".." / ".." / "dist"
         args = ["python"]
         args.append(str(path(".") / "bin" / "omero"))
         args.extend(["-s", server, "-k", key, "-p", port, "import",  
filename])
         popen = subprocess.Popen(args, cwd=str(dist_dir),  
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         out, err = popen.communicate()
         rc = popen.wait()
         if rc != 0:
             raise exceptions.Exception("import failed: [%r] %s\n%s" %  
(args, rc, err))
         pix_ids = []
         for x in out.split("\n"):
             if x and x.find("Created") < 0 and x.find("#") < 0:
                 try:    # if the line has an image ID...
                     imageId = str(long(x.strip()))
                     pix_ids.append(imageId)
                 except: pass
         return pix_ids


Hopefully you can work out what you need from this.

   Will.

On 18 May 2011, at 17:16, Wood, Christopher wrote:

> Also, when I use the command line importer (using the python  
> subprocess module), is there a good way to get the image id?
>
> Thanks again.
> Chris
>
> From: ome-devel-bounces at lists.openmicroscopy.org.uk [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk 
> ] On Behalf Of Wood, Christopher
> Sent: Wednesday, May 18, 2011 11:10 AM
> To: ome-devel at lists.openmicroscopy.org.uk
> Subject: [ome-devel] command line importer
>
> Hi,
>
> Is there an option for the command line importer to archive the  
> imported file(s) (so the originals can be downloaded later)?
>
> Thanks
> Chris
>
> --
> Chris Wood, Ph.D | Group Head - Stowers Microscopy Center
> Stowers Institute for Medical Research
> 1000 E 50th |Kansas City, MO 64110
> http://www.stowers.org | cjw at stowers.org
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Phone 01382 386364
http://openmicroscopy.org





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