[Biopython-dev] [Bug 2795] New: Add commit, rollback, close to DBServer object
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Fri Mar 20 17:32:50 UTC 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2795
Summary: Add commit, rollback, close to DBServer object
Product: Biopython
Version: Not Applicable
Platform: All
OS/Version: All
Status: NEW
Severity: enhancement
Priority: P2
Component: BioSQL
AssignedTo: biopython-dev at biopython.org
ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk
The DBServer object is defined in file BioSQL/BioSeqDatabase.py and it might
make sense to add the following methods to it:
def commit(self):
"""Commits the current transaction to the database."""
return self.adaptor.commit()
def rollback(self):
"""Rolls backs the current transaction."""
return self.adaptor.rollback()
def close(self):
"""Close the connection. No further activity possible."""
return self.adaptor.close()
I think the adaptor is intended to hide internal implementation details, so we
shouldn't be forcing people to use it directly for transaction support.
Consider this example from http://www.biopython.org/wiki/BioSQL currently:
from Bio import Entrez
from Bio import SeqIO
from BioSQL import BioSeqDatabase
server = BioSeqDatabase.open_database(driver="MySQLdb", user="root",
passwd = "", host = "localhost", db="bioseqdb")
db = server["orchids"]
handle = Entrez.efetch(db="nuccore", id="6273291,6273290,6273289",
rettype="genbank")
db.load(SeqIO.parse(handle, "genbank"))
server.adaptor.commit()
The last line would become just:
server.commit()
This seems cleaner. Patch to follow...
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