I’m testing cellprofiler with Azure Database for MySQL server. I have no problems connecting to the database via the command line, or MySQLWorkbench.
In cellprofiler I get a successful connection when I test it, however it throws up the following error if you try to run the pipeline:
ProgrammingError: (1064, “You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ‘’ at line 1”)
It is related to the fact that my username from the Azure database is “nel56@othcellprof” apparently the “@” symbol is an invalid character. The portion after the “@” is the name of the database. In fact the only way I could get the test connection to work is by leaving the database name blank in cellprofiler, however as I say that is when I get the above error. I cannot change this username. Is there a way around this? Because I cannot export the batch file to run on our cluster.