I'm using Python and its MySQLdb module to import some measurement data into a Mysql database. The amount of data that we have is quite high (currently about ~250 MB of csv files and plenty of more to come).

Currently I use cursor.execute(...) to import some metadata. This isn't problematic as there are only a few entries for these.

The problem is that when I try to use cursor.executemany() to import larger quantities of the actual measurement data, MySQLdb raises a

TypeError: not all arguments converted during string formatting

My current code is

def __insert_values(self, values):cursor = self.connection.cursor()cursor.executemany("""insert into values (ensg, value, sampleid)values (%s, %s, %s)""", values)cursor.close()

where values is a list of tuples containing three strings each. Any ideas what could be wrong with this?

Edit:

The values are generated by

yield (prefix + row['id'], row['value'], sample_id)

and then read into a list one thousand at a time where row is and iterator coming from csv.DictReader.

In retrospective this was a really stupid but hard to spot mistake. Values is a keyword in sql so the table name values needs quotes around it.

def __insert_values(self, values):cursor = self.connection.cursor()cursor.executemany("""insert into `values` (ensg, value, sampleid)values (%s, %s, %s)""", values)cursor.close()