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Commits on Jun 17, 2016
Commits on Jun 16, 2016
  1. Bug fix: Only do gsub on bio_ref.reference.authors if it exists.

    binnisb authored and ngoto committed Dec 9, 2013
     * Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
       Fix bioruby/bioruby#89
  2. Bug fix: Missing require when generating genbank output for BioSQL se…

    binnisb authored and ngoto committed Dec 9, 2013
    …quence
    
     * Bug fix: Missing require when generating genbank output for BioSQL
       sequence. Partly fix bioruby/bioruby#89
  3. The "libpath magic" in tests are replaced by the load of helper routine.

    ngoto committed Nov 12, 2009
     * In all unit tests, the "libpath magic" are replaced by the load
       of helper routine.
     * Changed to use a constant BioRubyTestDataPath for generating test
       data file path.
     * Some "require" lines are modified.
     * "File.open(...).read" in some tests are replaced by "File.read(...)".
     * Header comment lines of some tests with wrong filename and/or
       class/module name information are fixed.
  4. Fixed: taxonomy, do not report node_rank of type "class".

    helios authored and ngoto committed Mar 10, 2009
    GenBanks Tests I/O passed.
  5. Fix: reference deletion from bioentry deletion, when reference is a l…

    helios authored and ngoto committed Mar 6, 2009
    …eaf ( no more bioentries connected to it)
  6. Added: relation between bioentry and refernces, also through referenc…

    helios authored and ngoto committed Mar 6, 2009
    …es by bioentry_reference. This is useful to accomplish complete bioentry's delete.
  7. Fixed: title test

    helios authored and ngoto committed Mar 6, 2009
  8. Add: bioentry_qualifier_value recognize if it's handling data (reader…

    helios authored and ngoto committed Mar 6, 2009
    …) and format it accordingly with GenBank/EMBL format ex: 26-SEP-2006
  9. Fixed: date_modified, the code is moved to Bio::SQL::Sequence#bioentr…

    helios authored and ngoto committed Mar 6, 2009
    …y_qualifier_anchor#method_reader. It's most an exercise of style than good programming. date_modifier reader should be a method apart.
  10. Add: BioSQL's TestSuite, alpha stage

    helios authored and ngoto committed Mar 6, 2009
  11. Fix: date_modifier biosequence adapter

    helios authored and ngoto committed Mar 5, 2009
  12. Added preliminar tests using connection with jdbcmysql. Test are focu…

    helios authored and ngoto committed Mar 5, 2009
    …sed on input/output coherence.
  13. Fixed: GI:xxxx reference on VERSION's line using biosql/to_biosequenc…

    helios authored and ngoto committed Mar 5, 2009
    …e.output(:genbank)
  14. added other_seqids as alias of identifier, for the adapter. Export pr…

    helios authored and ngoto committed Mar 4, 2009
    …oblem of GI in output(:genbank) from biosql/biosequence.
  15. TODO: .to_biosequence.output(:genbank) some major and minor problems.

    helios authored and ngoto committed Mar 4, 2009
    1) Major. GI: is not exported IN(VERSION     X64011.1  GI:44010),OUT(VERSION     X64011.1)
    1.1) Db storage is ok, GI is saved into identifier of bioentry
    2) Moderate. date wrong format IN(26-SEP-2006), OUT(2006-09-26)
    3) Minor. Organism in output as more terms.
    4) Minor. Title has a dot at the end, input was without
    
    ref for GI in genbank are functions ncbi_gi_number/other_seqids
  16. establish_connection rewrite and update Class.first call with ActiveR…

    helios authored and ngoto committed Mar 3, 2009
    …ecord sintax. Coming from DataMapper.
  17. Version developed with DataMapper, need to be tested with ActiveRecor…

    helios authored and ngoto committed Mar 3, 2009
    …d -current ORM-.
  18. Newly added lib/bio/io/biosql/ar-biosql.rb: In one file definition of…

    helios authored and ngoto committed Mar 3, 2009
    … all BioSQL's ActiveRecords classes.
  19. Separated connection (see lib/bio/io/biosql.rb) from definition of pu…

    helios authored and ngoto committed Mar 3, 2009
    …blic methods.
  20. Temporal removal of BioSQL ActiveRecords classes (being restored soon).

    helios authored and ngoto committed Mar 3, 2009
    To integrate BioSQL ActiveRecords classes to one file, as the first
    step, files listed below are deleted. In the later commit, they will
    be integrated into one file, lib/bio/io/biosql/ar-biosql.rb.
    
    This is a combination of 28 commits made by Raoul Jean Pierre Bonnal.
    
    Deleted files:
     * lib/bio/io/biosql/biodatabase.rb
     * lib/bio/io/biosql/bioentry.rb
     * lib/bio/io/biosql/bioentry_dbxref.rb
     * lib/bio/io/biosql/bioentry_path.rb
     * lib/bio/io/biosql/bioentry_qualifier_value.rb
     * lib/bio/io/biosql/bioentry_reference.rb
     * lib/bio/io/biosql/bioentry_relationship.rb
     * lib/bio/io/biosql/biosequence.rb
     * lib/bio/io/biosql/comment.rb
     * lib/bio/io/biosql/dbxref.rb
     * lib/bio/io/biosql/dbxref_qualifier_value.rb
     * lib/bio/io/biosql/location.rb
     * lib/bio/io/biosql/location_qualifier_value.rb
     * lib/bio/io/biosql/ontology.rb
     * lib/bio/io/biosql/reference.rb
     * lib/bio/io/biosql/seqfeature.rb
     * lib/bio/io/biosql/seqfeature_dbxref.rb
     * lib/bio/io/biosql/seqfeature_path.rb
     * lib/bio/io/biosql/seqfeature_qualifier_value.rb
     * lib/bio/io/biosql/seqfeature_relationship.rb
     * lib/bio/io/biosql/taxon.rb
     * lib/bio/io/biosql/taxon_name.rb
     * lib/bio/io/biosql/term.rb
     * lib/bio/io/biosql/term_dbxref.rb
     * lib/bio/io/biosql/term_path.rb
     * lib/bio/io/biosql/term_relationship.rb
     * lib/bio/io/biosql/term_relationship_term.rb
     * lib/bio/io/biosql/term_synonym.rb
  21. Test

    Ra authored and ngoto committed Oct 14, 2008
  22. Fix: typing error

    Ra authored and ngoto committed Oct 14, 2008
  23. Merging patches by Raoul in commit 496561a70784d3a1a82bf3117b2d267c76…

    ngoto committed Oct 14, 2008
    …25afac which are ignored when rebasing, probably because of manually editing during merge
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