Bio-Chado-Schema

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.