CellProfiler/CellProfiler — Issue #254: ExportToDatabase error
Author: dlogan
Created: 2011-12-21 21:14:44+00:00
State: open
Labels: current

Batch 3479 (http://imagingweb.broadinstitute.org/batchprofiler/cgi-bin/CellProfiler2.0/CellProfiler/BatchProfiler/ViewBatch.py?batch_id=3479)

has a few failed jobs, like this one:
http://imagingweb.broadinstitute.org/batchprofiler/cgi-bin/CellProfiler2.0/CellProfiler/BatchProfiler/ViewTextFile.py?run_id=1509709
(stack trace at bottom)

The reason seems to be "OperationalError: (1048, "Column 'SynAll_Number_Object_Number' cannot be null")". My first thought was that the FlagImage module which does skip the rest of the pipeline might be causing a problem, but in the xample below, it does not seem to be aborting the rest of the pipeline.

I resubmitted one of these Failed jobs, but I don't think it will help.

******
...
Wed Dec 21 13:59:55 2011: Image # 4858, module SaveImages # 71: 0.04 sec (bg)
ERROR:cellprofiler.modules.exporttodatabase:Failed to write measurements to database
Traceback (most recent call last):
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/11675/cellprofiler/modules/exporttodatabase.py", line 2124, in write_data_to_db
self.cursor.executemany(stmt, my_rows)
File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 206, in executemany
r = r + self.execute(query, a)
File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 174, in execute
self.errorhandler(self, exc, value)
File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler
raise errorclass, errorvalue
OperationalError: (1048, "Column 'SynAll_Number_Object_Number' cannot be null")
Failed to write measurements to database
Traceback (most recent call last):
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/11675/cellprofiler/modules/exporttodatabase.py", line 2124, in write_data_to_db
self.cursor.executemany(stmt, my_rows)
File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 206, in executemany
r = r + self.execute(query, a)
File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 174, in execute
self.errorhandler(self, exc, value)
File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler
raise errorclass, errorvalue
OperationalError: (1048, "Column 'SynAll_Number_Object_Number' cannot be null")
ERROR:cellprofiler.pipeline:Error detected during run of module ExportToDatabase
Traceback (most recent call last):
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/11675/cellprofiler/pipeline.py", line 1283, in run_with_yield
module.run(workspace)
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/11675/cellprofiler/modules/exporttodatabase.py", line 1357, in run
self.write_data_to_db(workspace)
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/11675/cellprofiler/modules/exporttodatabase.py", line 2124, in write_data_to_db
self.cursor.executemany(stmt, my_rows)
File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 206, in executemany
r = r + self.execute(query, a)
File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 174, in execute
self.errorhandler(self, exc, value)
File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler
raise errorclass, errorvalue
OperationalError: (1048, "Column 'SynAll_Number_Object_Number' cannot be null")
Error detected during run of module ExportToDatabase
Traceback (most recent call last):
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/11675/cellprofiler/pipeline.py", line 1283, in run_with_yield
module.run(workspace)
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/11675/cellprofiler/modules/exporttodatabase.py", line 1357, in run
self.write_data_to_db(workspace)
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/11675/cellprofiler/modules/exporttodatabase.py", line 2124, in write_data_to_db
self.cursor.executemany(stmt, my_rows)
File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 206, in executemany
r = r + self.execute(query, a)
File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 174, in execute
self.errorhandler(self, exc, value)
File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler
raise errorclass, errorvalue
OperationalError: (1048, "Column 'SynAll_Number_Object_Number' cannot be null")
INFO:PipelineStatistics:Wed Dec 21 13:59:56 2011: Image # 4858, module ExportToDatabase # 72: 5.15 sec
Wed Dec 21 13:59:56 2011: Image # 4858, module ExportToDatabase # 72: 5.15 sec
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.