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Commits on Jun 22, 2009

• Deprecating psycopg support in BioSQL code (use psycopg2 instead)

  

  peterc

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Commits on Jun 8, 2009

• PostgreSQL RULES hack now works with psycopg, psycop2 and pgdb (aka PyGreSQL). Patch from Cymon Cox (Bug 2851)

  

  peterc

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Commits on Jun 5, 2009

• Fix BioSQL with PyGresql (pgdb) PostgreSQL driver (Bug 2849), patch from Cymon Cox.

  

  peterc

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Commits on Jun 4, 2009

• Cymon's patch to try and cope with the PostgreSQL RULES in BioSQL default schema (Bug 2833 and 2839)

  

  peterc

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Commits on Jun 3, 2009

• Get mixed-strand features to work when parsing GenBank files and to/from BioSQL

  

  peterc

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  16148dc

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• Strict strand checking and an inverted location warning when reading records from BioSQL

  

  peterc

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• Adding a warning about unsupported location operators (like order).

  

  peterc

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Commits on Jun 2, 2009

• Adding a warning regarding the PostgreSQL BioSQL schema's rules (see Bug 2833 and 2839). Based on a patch from Cymon Cox.

  

  peterc

  committed
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Commits on Jun 1, 2009

• Unit tests and a fix for an issue with loading a DBSeqRecord into BioSQL where references lack a location (Bug 2840). Based on a patch from Cymon Cox.

  

  peterc

  committed
  1697081

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Commits on May 23, 2009

• Define empty per-letter-annotations dictionary in DBSeqRecord so the __str__ methods work (Bug 2838 part two)

  

  peterc

  committed
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Commits on May 22, 2009

• Cope with importing a DBSeqRecord where the date annotation is a list (Bug 2838)

  

  peterc

  committed
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Commits on Apr 1, 2009

• Support UnknownSeq (Bug 2799) in BioSQL. Cope when comments is a list (Bug 2802)

  

  peterc

  committed
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Commits on Mar 20, 2009

• Adding transaction methods to DBServer object (Bug 2795)

  

  peterc

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Commits on Feb 18, 2009

• Retrieve the comment (my fault, bug wasn't in Cymon's original patch). Fixes Bug 2761

  

  peterc

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Commits on Nov 21, 2008

• Stricter testing of record's annotations dictionary, requiring a small fix for references and actually fetching comments from the database. Based very much on a patch by Cymon Cox (Bug 2681)

  

  peterc

  committed
  110056a

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• Included NC_005816.1 GenBank file in the BioSQL unit test which required fixing a couple of minor things on references (handling missing authors, not testing consortium)

  

  peterc

  committed
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• Based on a patch from Cymon Cox (Bug 2766), this addresses feature location's strand, db ref and the sub-feature order. It does not yet record the feature operator (which still defaults to 'join')

  

  peterc

  committed
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Commits on Nov 13, 2008

• Feature and sub-features should be sorted in the database by their rank, don't try and resort them. This also resolves the related TODO item in the unit test (Fix from Cymon Cox, see Bug 2655).

  

  peterc

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Commits on Nov 12, 2008

• Patch from Cymon Cox to Include explicit ordering by rank for qualifiers and dbxrefs, fixing the cor6_6.gb unit test example. I'm also recording the SeqFeature primary key as a private property.

  

  peterc

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Commits on Nov 11, 2008

• Support adding BioSQL DBSeq objects, an oversight reported on the mailing list by Cymon Cox (no bug filed).

  

  peterc

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Commits on Nov 5, 2008

• Fixes for bugs 2544 and 2622.

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  chapmanb

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Commits on Oct 23, 2008

• Updating raise exception style (see PEP8)

  

  peterc

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Commits on Oct 17, 2008

• Support for Psycopg2 PostgreSQL driver, patch from Cymon J. Cox

  

  peterc

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Commits on Oct 10, 2008

• Switching from <> to != for future python 3.0 compatibility

  

  peterc

  committed
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• Switch from 'dict.has_key(key)' to 'key in dict' for compatibility with python 3.x

  

  peterc

  committed
  27719a4

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Commits on Sep 30, 2008

• Option to fetch the NCBI taxonomy via Bio.Entrez while importing SeqRecords into BioSQL, based in part on code from Eric Gibert (see Bug 2475)

  

  peterc

  committed
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Commits on Sep 29, 2008

• Restructuring _get_taxon_id (see Bug 2475)

  

  peterc

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Commits on Sep 26, 2008

• Fixes to cope with loading a FASTA file into a BioSQL database (Bug 2425)

  

  peterc

  committed
  e319c61

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• Shouldn't assume sequences in the database use unambiguous IUPAC alphabets (problem found testing FASTA files giving sequences with generic alphabets)

  

  peterc

  committed
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Commits on Aug 27, 2008

• Added a few docstrings.

  

  peterc

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Commits on Jun 20, 2008

• Don't assume SeqFeature qualifier values are always lists of strings (in particular, we should cope with a plain string).

  

  peterc

  committed
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Commits on Jun 5, 2008

• Ignore left/right values when retrieving taxonomy (Bug 2494). Other tweaks to be more robust to changes in the underlying Seq class.

  

  peterc

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Commits on May 30, 2008

• Use single quotes rather than double quotes for greater cross-database compatibility (e.g. PostgreSQL). See bug 2506

  

  peterc

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Commits on May 19, 2008

• Small improvements to the doc strings, still needs work.

  

  peterc

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Commits on Mar 21, 2008

• Added missing copyright and licence header, explicitly stating that while these files are part of Biopython, BioSQL itself (database schema and scipts) is available and licensed separately.

  

  peterc

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