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Commits on Aug 14, 2015
  1. @hlapp

    Merge pull request #1 from dvs/master

    hlapp committed
    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
    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


    bosborne committed
  2. @bosborne


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

    Chris Fields committed
  2. update skipped files

    Chris Fields committed

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

    buzgilla -> redmine

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

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

    Chris Fields committed
  2. ignore conf file

    Chris Fields committed
  3. add minimal .gitignore file

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

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

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

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

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

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

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

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

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

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

    cjfields committed
    * 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
    svn path=/bioperl-db/trunk/; revision=15910
  2. @sendu

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

    sendu committed
    …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
    svn path=/bioperl-db/trunk/; revision=15904
  4. remove Data::Dumper

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

    cjfields committed
    * 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
    * these need to be mapped to their bp_*.PLS counterparts
    svn path=/bioperl-db/trunk/; revision=15900
Commits on Aug 7, 2009
  1. * convert over to Module::Build

    cjfields committed
    * add concrete MANIFEST.SKIP (no point on generating this for only one file)
    svn path=/bioperl-db/trunk/; revision=15899
Commits on Mar 19, 2009
  1. [bug 2757]

    cjfields committed
    * patch for error handling, per Mark Johnson
    svn path=/bioperl-db/trunk/; revision=15601
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