[Biopython-dev] [Bug 2866] New: SQLite support for BioSQL

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2866

           Summary: SQLite support for BioSQL
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: FreeBSD
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: chapmanb at 50mail.com


Attached is a git patch to add SQLite support to the latest BioSQL. I've tested
this with SQLite and MySQL on my FreeBSD machine and both pass the test suite.
Cymon, Peter, and anyone else who is interested -- it would be great if you
could check on PostgreSQL and the various setups y'all have been using. A few
notes:

- SQLite does not support FOREIGN KEY constraints so I have dropped those from
the creation SQL.
- get_subseq_as_string used SUBSTRING, which does not seem to be supported on
SQLite. I switched to SUBSTR which I believe should be general.
- SQLite gives back unicode, which I explicitly convert to strings to be more
compatible with what was done previously.

If it's easier to check this on GitHub, I can do that when I'm back home. I
branched from the main trunk and internet is too slow to learn the right way to
do it now. Thanks.


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