Properties file


I just started using Cell Profiler and CPA. So far, I can work nicely with the CPA example files.
However, when I analyze my own images with Cell Profiler and then start CPA I get the following error message:

“AssertionError: PROPERTIES ERROR (db_host): Field is required with db_type=mysql.”

The properties file is generated by Cell Profiler and actually contains the requested field:

#Fri Apr 15 18:26:02 2011


CellProfiler Analyst 2.0 properties file


==== Database Info ====

db_type = mysql
db_port =
db_host =
db_name = HoechstTestDB
db_user =
db_passwd =

==== Database Tables ====

image_table = Per_Image
object_table = Per_Object

Does anybody know how to solve this?

HoechstAssay pipeline_3.cp (9.37 KB)

Hi Carlos,

In your ExportToDatabase, you chose MySQL/CSV as the database type. The “?” help section for this option reads:

Did you run this *.SQL script? It is needed to upload your data to the MySQL database. Do you have a MySQL database set up? You didn’t fill in these fields in ExportToDatabase

[quote] Database host:

which are necessary for CPA to access your MySQL server. If you don’t have MySQL, then I would suggest using the SQLite “Database Type”, since you won’t need to install or configure other software.

Does this help?

Hi David,

Since I don’t have a MySQL database set up I actually wanted to use the CSV option.
I mistakenly thought MySQL/CSV would be the database type of choice in this case.
Changing to SQLite solved the problem.

Many thanks,