[Biopython-dev] [Bug 2395] New: Need a commit in db.load (BioSQL with MySQL)

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2395

           Summary: Need a commit in db.load (BioSQL with MySQL)
           Product: Biopython
           Version: 1.44
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


As noted in bug 1921 and more recently on the mailing and bug 2390, it seem
Biopython should be doing a database commit with MySQL.

e.g.  Leighton Pritchard wrote on bug 1921 comment 3

>>> from BioSQL import BioSeqDatabase
>>> server = BioSeqDatabase.open_database(driver="MySQLdb", user="root", passwd=
"<db root password>", host="localhost", db="bioseqdb")
>>> db = server.new_database("cold")
>>> from Bio import GenBank
>>> parser = GenBank.FeatureParser()
>>> iterator = GenBank.Iterator(file("cor6_6.gb"), parser)
>>> db.load(iterator)
6
>>> 

However, there is now an additional new problem when using MySQL5, as the
necessary commit is not automatically executed, and a direct call of 

>>> server.adaptor.commit()

seems to be necessary after the above in order to commit the changes to the
database.


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