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!