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Task #12211 (closed)

Opened 10 years ago

Closed 9 years ago

BUG: Bulk annotations script - Insight AND Web

Reported by: pwalczysko Owned by: spli
Priority: blocker Milestone: OMERO-5.2.0
Component: Client 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=$PYTHONPATH:. python omero/util/populate_metadata.py -s gretzky.openmicroscopy.org.uk -u user-4 -w ome Screen:651 ~/Desktop/test_screen.csv
INFO:omero.util.Resources:Starting
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
WARNING:omero.util.populate_metadata:Screen is missing plate: 365700055641
INFO:omero.util.populate_metadata:Created new table OriginalFile:66093
INFO:omero.util.populate_metadata:Table initialized with 11 columns.
INFO:omero.util.populate_metadata:Added data column data.
INFO:omero.util.Resources:Halted
[petr@LS25165 ~/Work/omero5-server/OMERO.server-5.0.1-190-e58c9fb-ice33-b208/lib/python]$

Attachments (7)

Insight - complete failure in Screen.png​ (119.7 KB) - added by pwalczysko 10 years ago.
Insight full success in orphaned plate.png​ (150.3 KB) - added by pwalczysko 10 years ago.
Insight - the attachment was produced in Screen.png​ (90.7 KB) - added by pwalczysko 10 years ago.
in Web - full success in orphaned plate.png​ (71.0 KB) - added by pwalczysko 10 years ago.
in Web - partial success & display in Screen.png​ (48.5 KB) - added by pwalczysko 10 years ago.
in Web - the script was not run at all for comparison.png​ (20.7 KB) - added by pwalczysko 10 years ago.
bulk_annotations​ (7.6 KB) - added by pwalczysko 10 years ago.

Download all attachments as: .zip

Change History (22)

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

Moving to 5.0.3. Good to have it fixed but no real blocker since our HCS support is limited in clients

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)

comment:6 Changed 10 years ago by pwalczysko

Note that this problem occurs analogicaly also in 5.1, see ​https://github.com/openmicroscopy/openmicroscopy/pull/2445

comment:7 Changed 10 years ago by pwalczysko

@wmoore @jburel : As discussed on the UX meeting yesterday, this ticket here describes in my opinion the status Quo concerning the populate_metadata.py script -> it works only to some 60% , the "in the Screen" case is not good -> this situation PRECEDES the PR of @wmoore regarding the changes in the Full Viewer as described here ​https://github.com/openmicroscopy/openmicroscopy/pull/2907 => any bugs described here are NOT the fault of the mentioned PR.

comment:8 Changed 10 years ago by pwalczysko

  • Component changed from Insight to Client
  • Summary changed from BUG: Bulk annotations script - Insight to BUG: Bulk annotations script - Insight AND Web

comment:9 Changed 9 years ago by jburel

  • Milestone changed from 5.1.0 to 5.1.1

Pushing to 5.1.1.

comment:10 Changed 9 years ago by jburel

  • Milestone changed from 5.1.1 to 5.1.2

I won't have a chance to look at it for 5.1.1

comment:11 Changed 9 years ago by jburel

  • Milestone changed from 5.1.2 to 5.1.4

comment:12 Changed 9 years ago by pwalczysko

  • Cc spli added
  • Priority changed from critical to blocker

Upping the priority, also because the discussions about populate_metadata.py and populate_roi.py are more intesive and the workflow grows in importance.

comment:13 Changed 9 years ago by jamoore

  • Milestone changed from 5.1.4 to OMERO-5.1.4

Splitting 5.1.4 due to milestone decoupling

comment:14 Changed 9 years ago by sbesson

  • Milestone changed from OMERO-5.1.4 to 5.x
  • Owner changed from jburel to spli

Assigning to Simon to see if the problem can be fixed via the IDR effort.

comment:15 Changed 9 years ago by jamoore

  • Milestone changed from 5.x to OMERO-5.2.0
  • Resolution set to duplicate
  • Status changed from new to closed

Moving to ​https://trello.com/c/8nwXuLsS/69-bulk-annotations-script-populate-metadata-py-is-not-visible-in-insight-when-plate-is-inside-a-screen

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