[ome-devel] Python import API (was: Release of OMERO 5.2.2)

Mon Feb 29 17:56:40 GMT 2016

Hi Niko,

congratulations to the release and many many thanks for all the effort!

On behalf of the team, thanks!

I do have one small question though: as discussed with J-M and Sebastien during last year's meeting in Paris, it would be extremely helpful if the Python API call for importing an image into OMERO would report the ID of the new image after a successful import.

We are currently in the process of shifting one processing workflow to use OMERO as the *only* backend, meaning the files being processed are managed by OMERO, fully automated processing is happening on some network nodes and the results will be re-uploaded into OMERO. For being able to create meaningful links between numerical / human readable results and images, it is crucial to be able to attach them to an image imported into OMERO - which does require the ID...

The same holds for the OMERO-connector integrated into the latest HRM release [1]. For being able to upload parameter settings, coloc results, statistics etc. along a deconvolved dataset from the HRM, we'd need to know the ID of a newly created image.

Does 5.2.2 expose the ID via its Python API already?

Have you looked at some of our Python integrations tests, for example:

<https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tools/OmeroPy/test/integration/clitest/test_import.py#L674>

Here we capture the stdout and stderr. The Pixels IDs are in stdout (just the IDs each on a new line), for example:

“
9
10
11
12
"

And the Image IDs can be parsed from stderr, which is, for example:

“
Imported pixels:
Other imported objects:
Fileset:6
Image:9
Image:10
Image:11
Image:12
“

Is this the sort of thing you are after or are you looking at getting these IDs at some other point in your workflow?

Cheers,

Colin

On 29 Feb 2016, at 16:23, Niko Ehrenfeuchter <nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch>> wrote:

Dear all,

congratulations to the release and many many thanks for all the effort!

I do have one small question though: as discussed with J-M and Sebastien during last year's meeting in Paris, it would be extremely helpful if the Python API call for importing an image into OMERO would report the ID of the new image after a successful import.

We are currently in the process of shifting one processing workflow to use OMERO as the *only* backend, meaning the files being processed are managed by OMERO, fully automated processing is happening on some network nodes and the results will be re-uploaded into OMERO. For being able to create meaningful links between numerical / human readable results and images, it is crucial to be able to attach them to an image imported into OMERO - which does require the ID...

The same holds for the OMERO-connector integrated into the latest HRM release [1]. For being able to upload parameter settings, coloc results, statistics etc. along a deconvolved dataset from the HRM, we'd need to know the ID of a newly created image.

Does 5.2.2 expose the ID via its Python API already?

Many thanks,
~Niko

[1] http://www.huygens-rm.org/wp/?p=193

On 29.02.2016 16:17, Jean-Marie Burel (Staff) wrote:

Dear All,

Today we are releasing OMERO 5.2.2, a bug-fix release which also
introduces some new client features. Improvements include:

* display of ROI masks in OMERO.web image viewer
* display of OMERO.tables data for Wells in the OMERO.web right hand panel
* 'Populate Metadata' script to enable generation of OMERO.tables for
Wells is now usable from both OMERO.web and OMERO.insight (note this is
still in development and has some limitations)
* measurement tool fixes
* fixed pixel size metadata and scalebar in OMERO.web image viewer for
images with pixel size units other than micrometer
* fixed OMERO.web handling of turning off interpolation of pixels
* previous and next buttons fixed in OMERO.web image viewer
* delete and change group performance improvements
* better handling of dates in search
* client support for map annotations in OME-TIFF
* disabled orphaned container feature
* OMERO.web clean-up to remove obsolete volume viewer

 Developer updates include:
* Python API examples for creating Polygon and Mask shapes
* Python API example for "Populate Metadata" to create OMERO.tables for
Wells
* OMERO.tables documentation extended
* updated 'What's New for developers' to clarify that 'pojos' has been
renamed as 'omero.gateway.model'
* dynamic scripts functionality documented
* dynamic loading of omero.client server settings into HTTP sessions

System administrator updates include:
* clarification of OMERO.web documentation for nginx deployment,
including an experimental solution to resolve download issues
* documentation of hard-linking issues for in-place import on linux systems

This release also upgrades the version of Bio-Formats which OMERO uses to
5.1.8. For more information see
https://www.openmicroscopy.org/site/support/bio-formats5.1/about/whats-new.html.

Note that the OMERO Virtual Appliance has been discontinued and will not
be updated for version 5.2.2 or any later releases.

The software is available at:
http://downloads.openmicroscopy.org/omero/5.2.2

Upgrade information is at
http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade.html.

Regards,

The OME Team

The University of Dundee is a registered Scottish Charity, No: SC015096

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Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch>
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