Hi,
I’m facing some issues with the ExportToDatabase
module in CellProfiler. I’ve created a local empty MySQL database and a very simple pipeline that just extracts features from images. It works well when I export them in a CSV file with the ExportToSpreadsheet
module, but now, I would like to export them to a MySQL database.
- System 1: macOS 10.14.6, CellProfiler 3.1.8, mysql 8.0.17
Here, when I click the “Test connection” it works, but when the analysis starts running, it gives me this error (even before processing the images):
Encountered unrecoverable error in ExportToDatabase during startup:
'ascii' codec can't decode byte 0xff in position 254: ordinal not in range(128)
The workaround suggested here didn’t work for me.
- System 2: Ubuntu 18.04, CellProfiler 3.1.9, mysql 14.14
“Test connection” fails in this case with the following error:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cellprofiler/gui/moduleview.py", line 1267, in callback
self.__on_do_something(event, setting)
File "/usr/local/lib/python2.7/dist-packages/cellprofiler/gui/moduleview.py", line 2231, in __on_do_something
setting.on_event_fired()
File "/usr/local/lib/python2.7/dist-packages/cellprofiler/setting.py", line 2148, in on_event_fired
self.__callback(*self.__args)
File "/usr/local/lib/python2.7/dist-packages/cellprofiler/modules/exporttodatabase.py", line 1890, in test_connection
self.db_name.value)
File "/usr/local/lib/python2.7/dist-packages/cellprofiler/modules/exporttodatabase.py", line 308, in connect_mysql
connection = MySQLdb.connect(host=host, user=user, passwd=pw, db=db)
File "/usr/local/lib/python2.7/dist-packages/MySQLdb/__init__.py", line 81, in Connect
return Connection(*args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/MySQLdb/connections.py", line 152, in __init__
from MySQLdb.converters import conversions
File "/usr/local/lib/python2.7/dist-packages/MySQLdb/converters.py", line 35, in <module>
from _mysql import string_literal, escape_sequence, escape_dict, escape, NULL
ImportError: cannot import name escape_sequence
My impression is that the error is related to the same issue on both systems. Could be something related to Python 2.7 and the MySQL version? Any hints on how to fix it?
Thanks a lot!
Beatriz