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.