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.