RBUELS / Bio-Chado-Schema-0.20000 / Changes

0.20000   2012-07-06 15:04:34 America/New_York

 * added Bio::Chado::NaturalDiversity::Reports, which has some canned
   reporting functions for working with natural diversity data (nmenda)
 * added greate_genotypeprops to Genetic::Genotype (nmenda)
 * added stock_phenotypes_rs, recursive_phenotypes_rs,
   stock_genotypes_rs, and stock_project_phenotypes to Stock::Stock
   (nmenda)

0.10010   2011-11-08 16:39:15 America/New_York

 * fix (in cleanup) errors related to schema object DESTROY function
   on some versions of DBIC
 * added create_phenotypeprop function (naama)
 * fix filenames of Chado-module-level POD files.  For instance,
   Bio::Chado::Schema::Result::Sequence POD is now rightly in
   lib/Bio/Chado/Schema/Result/Sequence.pod

0.10000   2011-11-07 13:22:41 America/Los_Angeles

 * add support for phenotypeprop table from Chado svn r25232

0.09040   2011-11-04 09:31:11 America/Los_Angeles

 * fix a memory-leak bug present in 0.9010 through 0.9030

0.09030   2011-11-03 14:58:58 America/Los_Angeles

 * fix some issues with repeated sections in the POD

0.09020   2011-11-02 17:30:03 America/Los_Angeles

 * implemented alphabet() function for Feature rows using as a silly
   heuristic that works in many cases.  alphabet() is needed by things
   like revcom() in newer versions of BioPerl.

0.09010   2011-10-24 11:25:25 America/Los_Angeles

 * added get_cvterm and get_cvterm_or_die convenience methods directly
   to the schema object, since cvterms are so pervasive in chado
 * added to_range to Featureloc class that makes a Bio::Range object
   for that location.

0.09000   2011-09-22 09:27:36 America/Los_Angeles

 * update for Chado 1.2, including:
    + add classes for new Chado 1.2 tables chadoprop (Cv::Chadoprop)
      genotypeprop (Genetic::Genotypeprop)
    + adds type to nd_protocol (NaturalDiversity::NdProtocol)
    + adds name column to phenotype table (Phenotype::Phenotype)
    + corrects misspelled name of stock_relationship_id column
      accessor for stock_relationship_cvterm
      (Stock::StockRelationshipCvterm), adds stock_relationship DBIC
      relation

0.08200   2011-09-19 09:35:03 America/Los_Angeles

 * fix inconsistencies in behavior for features with null residues
   and/or seqlens

0.08100   2011-03-21 16:01:00 America/Los_Angeles

 * add support for literal sql in property values set using
   create_*props helper functions
 * add 'features' many-to-many relation to the Synonym result class.
 * add 'synonyms' many-to-many relation to the Feature result class.
 * add new class for stock_cvtermprop table, and new is_not and rank
   columns for stock_cvterm

0.08002   2011-02-22 11:17:13 America/Los_Angeles

 * Added support for new cvprop table.
 * Added plugin_add_relationship class method to Bio::Chado::Schema
   main class, which makes it possible to do BCS plugins: sets of
   classes in the Bio::Chado::Schema namespace that are loaded as part
   of BCS.  plugin_add_relationship lets plugins inject relationships
   into the core BCS classes.

0.07300   2010-11-28 17:19:08 PST8PDT

 * Add convenient featureloc length() method.
 * Add better support for large sequences: a subseq() method to
   Feature class with support for checking a 'large_residues'
   featureprop for sequence, and doing substring calls on that.

0.07100   2010-11-16 12:28:17 PST8PDT

 * Fix bug with Cvterm add_secondary_dbxref, only caught under
   DBIx::Class >= 0.08124
 * add convenience methods for creating stock_dbxrefprops,
   nd_experimentprops, projectprops, and geolocationprops
 * add methods for working with parent and child terms of cvterms
 * Convert t/lib/BCSTest.pm to Bio::Chado::Schema::Test so other
   CPAN modules can have test suites that use an
   automagically-created SQLite db

0.06400   2010-10-20 20:54:37 PST8PDT

 * added naama's stock_dbxrefprop from upstream chado

0.06302   2010-10-20 09:58:19 PST8PDT

 * corrected homepage url in CPAN upload

0.06301   2010-10-19 17:49:41 PST8PDT

 * corrected missing DBIx::Class::Tree::NestedSet dep

0.06300   2010-10-18 17:38:29 PST8PDT

 * converted build system to Dist::Zilla
 * applied nmenda's type_id corrections from chado trunk
 * fix permission denied test failure caused by shipping a
   t/var/BCS.db file by accident

0.06200

 * removed erroneous duplicate General/Project.pm module
 * Updated natdiv module from Chado upstream (fixed upstream by nmenda).
 * Added create_stockprops method to stock module (nmenda).

0.06001

 * Corrected missing stuff in the manifest.

0.06000

 * Added DBIx::Class::Tree::NestedSet support to for Phylonodes.
 * Added Natural Diversity and Project module support.

0.05801

 * Fix bugs and add tests for child_features and parent_features on
   Sequence::Feature
 * Added parent_relationships and child_relationships rels to
   Sequence::Feature as more intuitive aliases for
   feature_relationship_*

0.05800
 
 * New aliases on Sequence::Feature
    child_features  -> featureloc_features
    parent_features -> featureloc_srcfeatures
 * Added a function for creating cvtermsynonyms ($cvterm->add_synonym)
 * Added a function for creating new cvtermprops ($cvterm->create_cvtermprops) 
 * Test suite can now deploy a Chado schema to a SQLite database
   if BCS_TEST_DSN is not defined. This means that smokers can
   now run these tests without setting up any databases.
        -- leto

0.05703

 * relaxed dependency on Carp 1.08

0.05702

 * that upload was a bit TOO clean, was missing the Build.PL!

0.05701

  * corrected a dirty cpan upload

0.05700

  * re-dumped with latest schema loader devel version
  * stripped _id suffixes for a number of relationships that still had
    them.  Hopefully the schema loader patch used for this will make
    it into schema loader releases.  List of changed relationship names:

     lib/Bio/Chado/Schema/CellLine/CellLine.pm
      cell_line_relationship_subject_ids -> cell_line_relationship_subjects
      cell_line_relationship_object_ids  -> cell_line_relationship_objects

     lib/Bio/Chado/Schema/Contact/Contact.pm
      contact_relationship_object_ids -> contact_relationship_objects
      contact_relationship_subject_ids -> contact_relationship_subjects

     lib/Bio/Chado/Schema/Cv/Cvterm.pm
      arraydesign_platformtype_ids -> arraydesign_platformtypes
      arraydesign_substratetype_ids -> arraydesign_substratetypes
      cvtermpath_type_ids -> cvtermpath_types
      cvtermpath_object_ids -> cvtermpath_objects
      cvtermpath_subject_ids -> cvtermpath_subjects
      cvtermprop_type_ids -> cvtermprop_types
      cvtermprop_cvterm_ids -> cvtermprop_cvterms
      cvterm_relationship_type_ids -> cvterm_relationship_types
      cvterm_relationship_object_ids -> cvterm_relationship_objects
      cvterm_relationship_subject_ids -> cvterm_relationship_subjects
      cvtermsynonym_type_ids -> cvtermsynonym_types
      cvtermsynonym_cvterm_ids -> cvtermsynonym_cvterms
      expression_cvterm_cvterm_ids -> expression_cvterm_cvterms
      expression_cvterm_cvterm_type_ids -> expression_cvterm_cvterm_types
      phenotype_assay_ids -> phenotype_assays
      phenotype_attr_ids -> phenotype_attrs
      phenotype_observable_ids -> phenotype_observables
      phenotype_cvalue_ids -> phenotype_cvalues
      protocolparam_unittype_ids -> protocolparam_unittypes
      protocolparam_datatype_ids -> protocolparam_datatypes

     lib/Bio/Chado/Schema/Genetic/Environment.pm
      phenotype_comparison_environment2_ids -> phenotype_comparison_environment2s
      phenotype_comparison_environment1_ids -> phenotype_comparison_environment1s

     lib/Bio/Chado/Schema/Genetic/Genotype.pm
      phenotype_comparison_genotype1_ids -> phenotype_comparison_genotype1s
      phenotype_comparison_genotype2_ids -> phenotype_comparison_genotype2s

     lib/Bio/Chado/Schema/Mage/Acquisition.pm
      acquisition_relationship_subject_ids -> acquisition_relationship_subjects
      acquisition_relationship_object_ids -> acquisition_relationship_objects

     lib/Bio/Chado/Schema/Mage/Biomaterial.pm
      biomaterial_relationship_subject_ids -> biomaterial_relationship_subjects
      biomaterial_relationship_object_ids -> biomaterial_relationship_objects

     lib/Bio/Chado/Schema/Mage/Element.pm
      element_relationship_object_ids -> element_relationship_objects
      element_relationship_subject_ids -> element_relationship_subjects

     lib/Bio/Chado/Schema/Mage/Elementresult.pm
      elementresult_relationship_subject_ids -> elementresult_relationship_subjects
      elementresult_relationship_object_ids -> elementresult_relationship_objects

     lib/Bio/Chado/Schema/Mage/Quantification.pm
      quantification_relationship_subject_ids -> quantification_relationship_subjects
      quantification_relationship_object_ids -> quantification_relationship_objects

     lib/Bio/Chado/Schema/Phenotype/Phenotype.pm
      phenotype_comparison_phenotype1_ids -> phenotype_comparison_phenotype1s
      phenotype_comparison_phenotype2_ids -> phenotype_comparison_phenotype2s

     lib/Bio/Chado/Schema/Phylogeny/Phylonode.pm
      phylonode_relationship_object_ids -> phylonode_relationship_objects
      phylonode_relationship_subject_ids -> phylonode_relationship_subjects

     lib/Bio/Chado/Schema/Pub/Pub.pm
      pub_relationship_object_ids -> pub_relationship_objects
      pub_relationship_subject_ids -> pub_relationship_subjects

     lib/Bio/Chado/Schema/Sequence/Feature.pm
      feature_genotype_feature_ids -> feature_genotype_features
      feature_genotype_chromosome_ids -> feature_genotype_chromosomes
      featureloc_feature_ids -> featureloc_features
      featureloc_srcfeature_ids -> featureloc_srcfeatures
      featurepos_feature_ids -> featurepos_features
      featurepos_map_feature_ids -> featurepos_map_features
      featurerange_leftendf_ids -> featurerange_leftendfs
      featurerange_rightstartf_ids -> featurerange_rightstartfs
      featurerange_rightendf_ids -> featurerange_rightendfs
      featurerange_leftstartf_ids -> featurerange_leftstartfs
      featurerange_feature_ids -> featurerange_features
      feature_relationship_subject_ids -> feature_relationship_subjects
      feature_relationship_object_ids -> feature_relationship_objects

     lib/Bio/Chado/Schema/Stock/Stock.pm
      stock_relationship_subject_ids -> stock_relationship_subjects
      stock_relationship_object_ids -> stock_relationship_objects

  * new create_with() function for creating new cvterms
  * more POD tweaking to improve CPAN indexing

0.05501

  * tweaked per-chado-module POD for better CPAN indexing

0.05500

  * much better POD, added autogenerated links from Schema.pm to
    per-chado-module POD files, and links to chado module pod files
    in Schema.pm
  * improved slide presentation to the version given at January 2010
    GMOD meeting

0.05001

  * test count bugfix

0.05000

  * Added DBICSL-generated POD
  * Turned off DBIC's cascade_delete and cascade_copy on all relations
    (thanks to Siddhartha Basu for troubleshooting).  Things break if
    these are on and you don't have every part of the schema installed.

0.04300

  * Corrected a rather dirty CPAN upload, Util.pod file was in the
    wrong place.

0.04200

  * removed Util.pm, replaced with Util.pod for documentation, moved
    the actual Util methods into a separate package inside Schema.pm.
    Thanks to Aure Bombarely.

0.04100

  * added missing dependency on BioPerl

0.04000

  * added new modules and relationships for the newly released
    cell_line module in Chado

0.03100

  * added $VERSION to Bio::Chado::Schema to support CPAN indexer,
    bumped version by several numbers to force CPAN reindexing

0.022

  * update to schema dumping script now finds many more inter-module
    relationships
  * added the new inter-module relationships found by the dumping
    script

0.01_03

  * changed namespace to Bio::Chado instead of Chado

0.01_01

  * Initial release.



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