Warning: Can't synchronize with repository "(default)" (/home/git/ome.git does not appear to be a Git repository.). Look in the Trac log for more information.
Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Bug #1584 (closed)

Opened 15 years ago

Closed 14 years ago

CSV exception from populate_rois.py

Reported by: jamoore Owned by: cxallan
Priority: major Cc:
Sprint: n.a.
Total Remaining Time: n.a.

Description

While populating siRNA:

josh@mac:~/code/omero.git/dist$ PYTHONPATH=lib/python python lib/python/omero/util/populate_roi.py -h localhost -u root 551
Password: 
Parsing: Well0001_mode1_z000_t000_detail_2008-09-18-10h48m54s.txt
Downloading original file: 854
Traceback (most recent call last):
  File "lib/python/omero/util/populate_roi.py", line 1051, in <module>
    measurement_ctx.parse_and_populate()
  File "lib/python/omero/util/populate_roi.py", line 519, in parse_and_populate
    result = self.parse()
  File "lib/python/omero/util/populate_roi.py", line 604, in parse
    rows = list(csv.reader(data, delimiter='\t'))
_csv.Error: line contains NULL byte

plate upload was successful, but original file on disk (`/OMERO/Files/854') is empty.

cli log:

2009-10-18 17:03:17,100 798        [      main] INFO          ome.formats.importer.ImportConfig  - Bioformats version: 4.0.1 revision: 5610 date: 16 October 2009
2009-10-18 17:03:22,224 5922       [      main] INFO      ome.formats.importer.ImportCandidates  - 164 file(s) parsed into 1 groups with 25 call(s) to setId in 4733ms. (4756ms total) [24 unknowns]
2009-10-18 17:08:48,119 331817     [      main] INFO   ormats.importer.cli.LoggingImportMonitor  - IMPORT_DONE
Imported pixels:
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
2009-10-18 17:08:48,121 331819     [      main] INFO      ome.formats.importer.cli.ErrorHandler  - Number of errors: 0

Change History (1)

comment:1 Changed 14 years ago by cxallan

  • Resolution set to worksforme
  • Status changed from new to closed

Haven't seen this ever again. Re-open as necessary.

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.64198 sec.)

We're Hiring!