Getting error while using "ExportToDatabase" function to create properties file for CPA



I’m try to create a properties file to use for CPA. So I tried using the ExportToDatabase function for the first time at the end of my pipeline. I wanted to store the CSV files locally on the computer rather than using the mySQL database.

So, it creates a properties file and the workspace file, but when I try to open the file on cellprofiler analyst by clicking on my newly created properties file, it doesn’t open. I think it has to do with the error that I get when I use the ExportToDatabase module.

Below is the error:

“Traceback (most recent call last):
File “cellprofiler\gui\pipelinecontroller.pyc”, line 2444, in module_display_request
File “cellprofiler\modules\exporttodatabase.pyc”, line 3227, in display
AttributeError: ‘DisplayData’ object has no attribute ‘columns’”



Can you post your pipeline and some sample images? That’s the only way we’ll be able to diagnose and/or reproduce the issue. Thanks!


I’ve attached the pipeline and a few of the images. Thanks!

testpipe.cppipe (9.4 KB)



1)The error appears to be a small bug in the ExportToDatabase module that as far as I can tell is specific to the MySQL/CSV setting- if the “eye” is open for that module and it’s trying to create a display window, it doesn’t have a display to generate and the error is generated. Closing the eye so that a display window is never generated fixes the issue, though I’ll file a bug report.

  1. Even after you fix the first thing, you will need to create some sort of database to use CPA- the MySQL/CSV merely gives you a script to create a database from those CSVs but CPA needs a database to work. If you’re not super comfortable with databases, I STRONGLY recommend that rather than choosing MySQL/CSV in ExportToDatabase you choose SQLite instead, which is just a little container “wrapper” file around the data tables that can be run locally just on your machine without needing networked infrastructure. You can always add an ExportToSpreadsheet module to your pipeline before/or after the ExportToDatabase to generate CSVs at the same time, or the information can usually be easily exported into CSVs from any database program.