Task #12211 (new)
Opened 10 years ago
Last modified 9 years ago
BUG: Bulk annotations script - Insight — at Version 5
Reported by: | pwalczysko | Owned by: | jburel |
---|---|---|---|
Priority: | critical | Milestone: | 5.0.3 |
Component: | Insight | Version: | 5.0.1 |
Keywords: | n.a. | Cc: | ux@…, cxallan, cblackburn, spli |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description (last modified by pwalczysko)
The result of the Bulk annotations script (populate_metadata.py) is not visible in Insight when Plate is inside a Screen.
Gretzky
user-4
read-write-1
Screen ID: 651 (this Screen has a plate inside which should have been annotated by the script)
Plate ID: 1752 (=the orphaned plate with no Screen)
When executing the https://www.openmicroscopy.org/private/ome-internal/testing_scenarios/BulkAnnotations.html, the execution of the script went well (user-4 in read-write-1, which is the default group, but see also https://trac.openmicroscopy.org.uk/ome/ticket/12210 for permissions problems here).
The annotations are visible in Insight in case of orphaned Plate (see screenslhot). If the script is executed on a Screen (with the plate inside), the annotations are not displayed in Insight.
see screenshot
This was repeated on localhost (5.0.1 release server) as well as on gretzky (merge build)
Web
The annotations which are missing in Insight are displayed in Web only partially, with the row titles there, but the values say "undefined" (see screenshot).
The output of the command line (first paragraph is the fully successful run of the script on orphaned plate, second paragraph the semi-successful run on a screen):
Clasifying as a blocker because this is a regression in comparison with the situation when the script was tested last time (4.4.x times)
Note that the annotation Bulk Annotation was attached to the Screen as expected (attached also to this ticket), but no annotations were visible on single wells in Insight.
[petr@LS25165 ~/Work/omero5-server/OMERO.server-5.0.1-190-e58c9fb-ice33-b208/lib/python]$ PYTHONPATH=$PYTHONPATH:. python omero/util/populate_metadata.py -s gretzky.openmicroscopy.org.uk -u user-4 -w ome Plate:1752 ~/Desktop/test_plate.csv INFO:omero.util.Resources:Starting INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Missing plate name column, skipping. INFO:omero.util.populate_metadata:Created new table OriginalFile:66092 INFO:omero.util.populate_metadata:Table initialized with 9 columns. INFO:omero.util.populate_metadata:Added data column data. INFO:omero.util.Resources:Halted [petr@LS25165 ~/Work/omero5-server/OMERO.server-5.0.1-190-e58c9fb-ice33-b208/lib/python]$ PYTHONPATH=$PYTHONPATH:. python omero/util/populate_metadata.py -s gretzky.openmicroscopy.org.uk -u user-4 -w ome Screen:651 ~/Desktop/test_screen.csv INFO:omero.util.Resources:Starting WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641 INFO:omero.util.populate_metadata:Created new table OriginalFile:66093 INFO:omero.util.populate_metadata:Table initialized with 11 columns. INFO:omero.util.populate_metadata:Added data column data. INFO:omero.util.Resources:Halted [petr@LS25165 ~/Work/omero5-server/OMERO.server-5.0.1-190-e58c9fb-ice33-b208/lib/python]$
Change History (12)
Changed 10 years ago by pwalczysko
Changed 10 years ago by pwalczysko
Changed 10 years ago by pwalczysko
Changed 10 years ago by pwalczysko
Changed 10 years ago by pwalczysko
Changed 10 years ago by pwalczysko
comment:1 Changed 10 years ago by pwalczysko
- Description modified (diff)
Changed 10 years ago by pwalczysko
comment:2 Changed 10 years ago by pwalczysko
comment:3 Changed 10 years ago by jburel
- Milestone changed from 5.0.2 to 5.0.3
- Priority changed from blocker to critical
comment:4 Changed 10 years ago by pwalczysko
See also https://trac.openmicroscopy.org.uk/ome/ticket/12235 - populate_roi.py has also problems.
comment:5 Changed 10 years ago by pwalczysko
- Description modified (diff)
Moving to 5.0.3. Good to have it fixed but no real blocker since our HCS support is limited in clients