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Task #12235 (closed)

Opened 10 years ago

Closed 8 years ago

Last modified 8 years ago

BUG: populate_roi.py on omero 5

Reported by: pwalczysko Owned by: spli
Priority: blocker Milestone: OMERO-5.2.2
Component: Scripting Version: 5.0.1
Keywords: n.a. Cc: ux@…, cxallan, spli, exwilliams, ejrozbicki, cblackburn
Resources: n.a. Referenced By: https://trello.com/c/hZNSNO3h/53-bug-roi-5-0-3
References: n.a. Remaining Time: 0.0d
Sprint: n.a.

Description

The populate_roi.py script does not work on 5.0.1 server ran locally. The same script works fine with 4.4.10 server.

To repeat, import from_skyking/mias/frans/siRNA…. plate and note plate ID. Then cd into the /lib/python folder of your server and execute command as below: (the plate ID in the OMERO 4 example was "61" - see below for syntax)

Output in OMERO 4:

[petr@ls25165 ~/Work/omero4-server/OMERO.server-4.4.10-39-0a20827-ice33-b461/lib/python]$ PYTHONPATH=$PYTHONPATH:. python omero/util/populate_roi.py -s localhost -u will 61
Password: 
INFO:omero.util.Resources:Starting
INFO:omero.util.populate_roi:Parsing: Well0001_mode1_z000_t000_detail_2008-09-18-10h48m54s.txt
INFO:omero.util.populate_roi:Downloading original file: 747
INFO:omero.util.populate_roi:Batch 1 ROI update took 583ms
INFO:omero.util.populate_roi:Created new table: 1215
INFO:omero.util.populate_roi:Table update took 43ms
INFO:omero.util.Resources:Halted
[petr@ls25165 ~/Work/omero4-server/OMERO.server-4.4.10-39-0a20827-ice33-b461/lib/python]$ 

OMERO 5

[petr@ls25165 ~/Work/omero5-server/OMERO-CURRENT/lib/python]$ PYTHONPATH=$PYTHONPATH:. python omero/util/populate_roi.py -s localhost -u petr 2 
Password: 
INFO:omero.util.Resources:Starting
Traceback (most recent call last):
  File "omero/util/populate_roi.py", line 1259, in <module>
    analysis_ctx = factory.get_analysis_ctx(plate_id)
  File "omero/util/populate_roi.py", line 516, in get_analysis_ctx
    plate_id)
__main__.MeasurementError: Unable to find suitable analysis context for plate: 2
INFO:omero.util.Resources:Halted
[petr@ls25165 ~/Work/omero5-server/OMERO-CURRENT/lib/python]$ 

Note similar ticket for populate_metadata.py http://trac.openmicroscopy.org.uk/ome/ticket/12211#comment:3

Change History (21)

comment:1 Changed 10 years ago by jburel

comment:2 Changed 9 years ago by sbesson

  • Cc changed from ux@openmicroscopy.org.uk, cxallan, spli, to ux@openmicroscopy.org.uk, cxallan, spli
  • Owner set to sbesson

comment:3 Changed 9 years ago by sbesson

  • Milestone changed from 5.1.0-m4 to 5.1.1

Discussed with jburel, mtbcarroll and jamoore. Work on companion files is upcoming for 5.1.0 (see https://github.com/openmicroscopy/openmicroscopy/pull/3384). Pushing the milestone to 5.1.1 to fix the script.

comment:4 Changed 9 years ago by sbesson

  • Milestone changed from 5.1.1 to 5.1.2

comment:5 Changed 9 years ago by jamoore

Note: PR to be opened from Glencoe on this. Testing likely to happen via IDR imports.

comment:6 Changed 9 years ago by jburel

  • Milestone changed from 5.1.2 to 5.1.4

Pushing to 5.1.4. We can bring it forward if required

comment:7 Changed 9 years ago by jamoore

  • Cc exwilliams added
  • Milestone changed from 5.1.4 to 5.1.3

Can I propose a first look in 5.1.3 in case we need it for data-in in IDR?

comment:8 Changed 9 years ago by sbesson

  • Owner changed from sbesson to ejrozbicki

comment:9 Changed 9 years ago by jamoore

  • Cc ejrozbicki added
  • Owner changed from ejrozbicki to jamoore

comment:11 Changed 9 years ago by pwalczysko

  • Priority changed from major to blocker

The fix seems to be still in progress. Also after discussion with spli and considering the rising importance of this workflow, upping the priority.

comment:12 Changed 9 years ago by pwalczysko

  • Cc cblackburn added

comment:13 Changed 9 years ago by spli

  • Owner changed from jamoore to spli
  • Status changed from new to accepted

Is there any additional data we can use to test this apart from the one test scenario?

comment:14 Changed 9 years ago by pwalczysko

@ spli Sorry, not that I know of, but I might simply not know of them (did not look for them strenuously)

comment:15 Changed 9 years ago by pwalczysko

@ spli maybe Josh or Chris know ?

comment:16 Changed 9 years ago by jburel

  • Milestone changed from 5.1.4 to 5.2.0

Part of the metadata work, not for 5.1.4 moving to 5.2

comment:17 Changed 9 years ago by jamoore

  • Milestone changed from 5.2.0 to OMERO-5.2.0

Splitting due to milestone decoupling.

comment:18 Changed 8 years ago by jburel

  • Milestone changed from OMERO-5.2.1 to OMERO-5.2.2

Milestone OMERO-5.2.1 deleted

comment:19 Changed 8 years ago by jburel

  • Milestone changed from OMERO-5.2.2 to OMERO-5.2.1

Milestone OMERO-5.2.2 deleted

comment:20 Changed 8 years ago by jamoore

  • Resolution set to fixed
  • Status changed from accepted to closed

Petr: I'm assuming that this is handled by https://github.com/openmicroscopy/openmicroscopy/pull/4426 -- Closing.

comment:21 Changed 8 years ago by jmoore <josh@…>

  • Remaining Time set to 0

(In [0b34a0000be0464ac2495957e11bfbf4b5c7beed/ome.git] on branch develop) populate_roi.py: add support for OMERO 5 (Fix #12235)

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