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Commits on Dec 3, 2015
  1. @hlapp

    Merge pull request #9 from dvs/master

    hlapp committed Dec 3, 2015
    add_association - bugfix, sort the SQL arguments
  2. @dvs

    add_association - bugfix, sort the SQL arguments

    dvs committed Dec 3, 2015
    This is similar to the latest bugfix for _find_by_unique_key().
Commits on Aug 14, 2015
  1. @hlapp

    Merge pull request #1 from dvs/master

    hlapp committed Aug 14, 2015
    Merging bug fix for relying on same order when doing simple hash key iteration.
Commits on Aug 5, 2015
  1. @dvs

    _find_by_unique_key - bugfix

    dvs committed Aug 5, 2015
    There was a wrong order of the argument binding.
    Both the orders of the fields of the unique key: (1)
    in the SQL statement and (2) in $dbd->bind_param() were
    determined by the simple hash key iteration.
    
    This accidentally worked with some old Perl versions but
    with Perl v.5.18 (Ubuntu 14.04 LTS) it is not working anymore.
    
    As a result, during the saving of RichSeq into the BioSQL database
    `term` entries were sometimes not found by its unique key.
    It led to the automatical creation of duplicated entries in the
    `term` table. This, in its turn, lead to a crash later, when
    the search by name or ontology_id brought several rows whereas just
    one is expected. The unique key of the table:
    
    UNIQUE KEY `name` (`name`,`ontology_id`, `is_obsolete`)
    
    did not prevent the duplications because `is_obsolete` is always
    NULL (it seems that this field is itself obsolete) and, since
    SQL standard assumes NULL is not equal NULL, the duplications
    are "unique" do not violate the constraint.
    
    In order to resolve this issuet the sorting was added so that
    the two argument orders were always the same.
Commits on Jun 19, 2015
  1. @bosborne

    Format

    bosborne committed Jun 19, 2015
  2. @bosborne

    Update

    bosborne committed Jun 19, 2015
  3. @bosborne
  4. @bosborne
Commits on Apr 28, 2014
  1. @bosborne
Commits on Apr 27, 2014
  1. @bosborne

    Add some useful example code

    bosborne committed Apr 27, 2014
Commits on Apr 15, 2011
  1. updates since last release

    Chris Fields committed Apr 15, 2011
  2. update skipped files

    Chris Fields committed Apr 15, 2011
  3. add MANIFEST.SKIP

    Chris Fields committed Apr 14, 2011
Commits on Mar 27, 2011
  1. @hyphaltip

    buzgilla -> redmine

    hyphaltip committed with hyphaltip Mar 28, 2011
Commits on Jul 23, 2010
  1. [RT 44466] remove corba-related scripts, now obsolete

    Chris Fields committed Jul 23, 2010
Commits on Jun 30, 2010
  1. squash perl 5.12 warning

    Chris Fields committed Jun 30, 2010
  2. ignore conf file

    Chris Fields committed Jun 30, 2010
  3. add minimal .gitignore file

    Chris Fields committed Jun 30, 2010
Commits on Dec 7, 2009
  1. weird duplication removed

    maj committed Dec 7, 2009
    svn path=/bioperl-db/trunk/; revision=16448
  2. committing patch for bug #2958

    maj committed Dec 7, 2009
    svn path=/bioperl-db/trunk/; revision=16447
Commits on Nov 2, 2009
  1. test commit to check SVN::Notify

    cjfields committed Nov 2, 2009
    svn path=/bioperl-db/trunk/; revision=16310
  2. Build.PL now checks for DBD drivers and attempts to DTRT

    cjfields committed Nov 2, 2009
    svn path=/bioperl-db/trunk/; revision=16309
Commits on Sep 30, 2009
  1. remove MANIFEST.SKIP

    cjfields committed Sep 30, 2009
    svn path=/bioperl-db/trunk/; revision=16224
  2. update Changes

    cjfields committed Sep 30, 2009
    svn path=/bioperl-db/trunk/; revision=16214
Commits on Sep 29, 2009
  1. fix empty POD section

    cjfields committed Sep 29, 2009
    svn path=/bioperl-db/trunk/; revision=16206
  2. some pod cleaning

    cjfields committed Sep 29, 2009
    svn path=/bioperl-db/trunk/; revision=16205
Commits on Sep 22, 2009
  1. main trunk version is wrong

    cjfields committed Sep 22, 2009
    svn path=/bioperl-db/trunk/; revision=16157
Commits on Aug 25, 2009
  1. * 02species.t now compared to similarly behaving instance, also creat…

    cjfields committed Aug 25, 2009
    …es comparable array
    
    * remove debugging lines
    
    svn path=/bioperl-db/trunk/; revision=15998
  2. [bug 2092]

    cjfields committed Aug 25, 2009
    * commit Sendu's patch
    * comment out lines in SpeciesAdaptor that munge genus/species names (old behavior)
    * 02species.t tests now failing, checking to see what the problem is
    
    svn path=/bioperl-db/trunk/; revision=15997
Commits on Aug 9, 2009
  1. @sendu

    moved Bio into lib to make Module::Build installation more normal

    sendu committed Aug 9, 2009
    svn path=/bioperl-db/trunk/; revision=15910
  2. @sendu

    fixed up capitalisation; allowed --accept; improved script install; w…

    sendu committed Aug 9, 2009
    …ill install modules from lib
    
    svn path=/bioperl-db/trunk/; revision=15906
  3. @sendu

    fix up shebang lines so they can be converted during install

    sendu committed Aug 9, 2009
    svn path=/bioperl-db/trunk/; revision=15904
  4. remove Data::Dumper

    cjfields committed Aug 9, 2009
    svn path=/bioperl-db/trunk/; revision=15903
  5. * scripts now convert over properly.

    cjfields committed Aug 9, 2009
    * should probably consider actually going through the scripts and adding the 'bp_foo.PLS' directly instead of working around this 
    * not sure why we are going through the trouble of running the conversion just prior to installation, anyone know?
    
    
    svn path=/bioperl-db/trunk/; revision=15902
Commits on Aug 8, 2009
  1. * get scripts working, module installation from Bio as well

    cjfields committed Aug 8, 2009
    * these need to be mapped to their bp_*.PLS counterparts
    
    svn path=/bioperl-db/trunk/; revision=15900
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