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Task #6732 (closed)

Opened 13 years ago

Closed 12 years ago

Last modified 12 years ago

BUG: FileAnnotation without OriginalFile attached to it

Reported by: atarkowska Owned by: jamoore
Priority: major Milestone: OMERO-4.4.4
Component: Import Version: n.a.
Keywords: n.a. Cc: wmoore, jamoore, jburel
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2012-08-28 (3)

Description

I end up with the woried state in my database where I had FileAnnotation? without OriginalFile?

"/type/OriginalFile/";111;"NEOlog2008-09-18-14h37m07s";-7;"openmicroscopy.org/omero/measurement";;"";"";;"";;;3282;;5;2;3282;

Would be good to figure out how this annotation was created and why file does not exist.

Change History (17)

comment:1 Changed 13 years ago by mlinkert

  • Cc jmoore added
  • Owner mlinkert-x deleted

I can duplicate this by importing mias/frans/siRNA_PRIM1_03102008 via Insight, then running:

select * from annotation where id>5156;

(the id specified is just the largest one from prior to importing the plate)

and getting the following output:

    discriminator    |  id  |        description         | permissions |                      ns                       | version | timevalue | textvalue | boolvalue | termvalue | longvalue | doublevalue | creation_id | external_id | group_id | owner_id | update_id | file 
---------------------+------+----------------------------+-------------+-----------------------------------------------+---------+-----------+-----------+-----------+-----------+-----------+-------------+-------------+-------------+----------+----------+-----------+------
 /type/OriginalFile/ | 5201 |                            |        -103 | openmicroscopy.org/omero/import/companionFile |         |           |           |           |           |           |             |       27170 |             |        0 |        0 |     27170 | 5651
 /type/OriginalFile/ | 5202 |                            |        -103 | openmicroscopy.org/omero/import/companionFile |         |           |           |           |           |           |             |       27170 |             |        0 |        0 |     27170 | 5652
 /type/OriginalFile/ | 5203 |                            |        -103 | openmicroscopy.org/omero/import/companionFile |         |           |           |           |           |           |             |       27170 |             |        0 |        0 |     27170 | 5653
 /type/OriginalFile/ | 5204 |                            |        -103 | openmicroscopy.org/omero/import/companionFile |         |           |           |           |           |           |             |       27170 |             |        0 |        0 |     27170 | 5654
 /type/OriginalFile/ | 5205 |                            |        -103 | openmicroscopy.org/omero/import/companionFile |         |           |           |           |           |           |             |       27170 |             |        0 |        0 |     27170 | 5655
 /type/OriginalFile/ | 5206 | NEOlog2008-09-18-14h37m07s |        -103 | openmicroscopy.org/omero/measurement          |         |           |           |           |           |           |             |       27193 |             |        0 |        0 |     27193 |     
(6 rows)

Server is running locally, built from the tip of develop and with OMERO.tables installed. On a hunch, I had a peek at /OMERO/Files/5656, which has the following
contents:

Traceback (most recent call last):
  File "./script", line 34, in <module>
    measurement_ctx.parse_and_populate()
  File "/home/melissa/code/openmicroscopy/dist/lib/python/omero/util/populate_roi.py", line 668, in parse_and_populate
    self.parse_and_populate_roi(columns)
  File "/home/melissa/code/openmicroscopy/dist/lib/python/omero/util/populate_roi.py", line 873, in parse_and_populate_roi
    self._parse_neo_roi(columns)
  File "/home/melissa/code/openmicroscopy/dist/lib/python/omero/util/populate_roi.py", line 821, in _parse_neo_roi
    thread_pool.add_task(self.update_rois, rois, batches, batch_no)
AttributeError: 'NoneType' object has no attribute 'add_task'

That looks to me like a Python bug and not an import bug; unassigning and CC'ing Josh. Happy to test further as needed.

comment:2 Changed 13 years ago by jburel

  • Milestone changed from Unscheduled to OMERO-Beta4.4

comment:3 Changed 13 years ago by jburel

  • Cc jburel added; cxallan removed
  • Owner set to cxallan
  • Sprint set to 2012-03-13 (10)

comment:4 Changed 13 years ago by jburel

  • Sprint changed from 2012-03-13 (10) to 2012-03-27 (11)

Moved from sprint 2012-03-13 (10)

comment:5 Changed 12 years ago by jburel

  • Sprint changed from 2012-03-27 (11) to 2012-04-10 (12)

Chris is off. Moving to next sprint.

comment:6 Changed 12 years ago by cxallan

  • Sprint changed from 2012-04-10 (12) to 2012-04-24 (13)

comment:7 Changed 12 years ago by jburel

  • Sprint changed from 2012-04-24 (13) to 2012-05-08 (14)

Moved from sprint 2012-04-24 (13)

comment:8 Changed 12 years ago by jburel

  • Sprint changed from 2012-05-08 (14) to 2012-05-22 (15)

Moved from sprint 2012-05-08 (14)

comment:9 Changed 12 years ago by jburel

  • Sprint changed from 2012-05-22 (15) to 2012-06-05 (16)

Moved from sprint 2012-05-22 (15)

comment:10 Changed 12 years ago by jburel

  • Sprint changed from 2012-06-05 (16) to 2012-06-19 (17)

Moved from sprint 2012-06-05 (16)

comment:11 Changed 12 years ago by cxallan

  • Remaining Time set to 0.25
  • Status changed from new to accepted

comment:12 Changed 12 years ago by cxallan

  • Owner cxallan deleted
  • Status changed from accepted to new

comment:13 Changed 12 years ago by cxallan

  • Owner set to cxallan
  • Sprint 2012-06-19 (17) deleted

comment:14 Changed 12 years ago by cxallan

  • Milestone changed from OMERO-Beta4.4 to OMERO-Beta4.4.1

comment:15 Changed 12 years ago by jmoore

  • Component changed from General to Import
  • Owner changed from cxallan to jmoore
  • Remaining Time changed from 0.25 to 0.1
  • Sprint set to 2012-08-28 (3)
  • Status changed from new to accepted

comment:16 Changed 12 years ago by jmoore

  • Remaining Time changed from 0.1 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

Pushed to ​https://github.com/openmicroscopy/openmicroscopy/pull/292

comment:17 Changed 12 years ago by jmoore <josh@…>

(In [b460a250e6ef346e7ae8ff1178bb867d8ff38162/ome.git] on branch develop) Add get_thread_pool function to ctor in populate_rois.py (Fix #6732)

Ctors of the measurement contexts now call get_thread_pool,
which will instantiate the global "thread_pool" if it is None.

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