package Bio::Chado::Schema::Result::Pub::Pub; BEGIN { $Bio::Chado::Schema::Result::Pub::Pub::AUTHORITY = 'cpan:RBUELS'; } BEGIN { $Bio::Chado::Schema::Result::Pub::Pub::VERSION = '0.10010'; } # Created by DBIx::Class::Schema::Loader # DO NOT MODIFY THE FIRST PART OF THIS FILE use strict; use warnings; use base 'DBIx::Class::Core'; =head1 NAME Bio::Chado::Schema::Result::Pub::Pub =head1 DESCRIPTION A documented provenance artefact - publications, documents, personal communication. =cut __PACKAGE__->table("pub"); =head1 ACCESSORS =head2 pub_id data_type: 'integer' is_auto_increment: 1 is_nullable: 0 sequence: 'pub_pub_id_seq' =head2 title data_type: 'text' is_nullable: 1 Descriptive general heading. =head2 volumetitle data_type: 'text' is_nullable: 1 Title of part if one of a series. =head2 volume data_type: 'varchar' is_nullable: 1 size: 255 =head2 series_name data_type: 'varchar' is_nullable: 1 size: 255 Full name of (journal) series. =head2 issue data_type: 'varchar' is_nullable: 1 size: 255 =head2 pyear data_type: 'varchar' is_nullable: 1 size: 255 =head2 pages data_type: 'varchar' is_nullable: 1 size: 255 Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii. =head2 miniref data_type: 'varchar' is_nullable: 1 size: 255 =head2 uniquename data_type: 'text' is_nullable: 0 =head2 type_id data_type: 'integer' is_foreign_key: 1 is_nullable: 0 The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv. =head2 is_obsolete data_type: 'boolean' default_value: false is_nullable: 1 =head2 publisher data_type: 'varchar' is_nullable: 1 size: 255 =head2 pubplace data_type: 'varchar' is_nullable: 1 size: 255 =cut __PACKAGE__->add_columns( "pub_id", { data_type => "integer", is_auto_increment => 1, is_nullable => 0, sequence => "pub_pub_id_seq", }, "title", { data_type => "text", is_nullable => 1 }, "volumetitle", { data_type => "text", is_nullable => 1 }, "volume", { data_type => "varchar", is_nullable => 1, size => 255 }, "series_name", { data_type => "varchar", is_nullable => 1, size => 255 }, "issue", { data_type => "varchar", is_nullable => 1, size => 255 }, "pyear", { data_type => "varchar", is_nullable => 1, size => 255 }, "pages", { data_type => "varchar", is_nullable => 1, size => 255 }, "miniref", { data_type => "varchar", is_nullable => 1, size => 255 }, "uniquename", { data_type => "text", is_nullable => 0 }, "type_id", { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, "is_obsolete", { data_type => "boolean", default_value => \"false", is_nullable => 1 }, "publisher", { data_type => "varchar", is_nullable => 1, size => 255 }, "pubplace", { data_type => "varchar", is_nullable => 1, size => 255 }, ); __PACKAGE__->set_primary_key("pub_id"); __PACKAGE__->add_unique_constraint("pub_c1", ["uniquename"]); =head1 RELATIONS =head2 cell_line_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "cell_line_cvterms", "Bio::Chado::Schema::Result::CellLine::CellLineCvterm", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cell_line_features Type: has_many Related object: L =cut __PACKAGE__->has_many( "cell_line_features", "Bio::Chado::Schema::Result::CellLine::CellLineFeature", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cell_line_libraries Type: has_many Related object: L =cut __PACKAGE__->has_many( "cell_line_libraries", "Bio::Chado::Schema::Result::CellLine::CellLineLibrary", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cell_lineprop_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "cell_lineprop_pubs", "Bio::Chado::Schema::Result::CellLine::CellLinepropPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cell_line_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "cell_line_pubs", "Bio::Chado::Schema::Result::CellLine::CellLinePub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cell_line_synonyms Type: has_many Related object: L =cut __PACKAGE__->has_many( "cell_line_synonyms", "Bio::Chado::Schema::Result::CellLine::CellLineSynonym", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 expression_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "expression_pubs", "Bio::Chado::Schema::Result::Expression::ExpressionPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_cvterms", "Bio::Chado::Schema::Result::Sequence::FeatureCvterm", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_cvterm_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_cvterm_pubs", "Bio::Chado::Schema::Result::Sequence::FeatureCvtermPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_expressions Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_expressions", "Bio::Chado::Schema::Result::Expression::FeatureExpression", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 featureloc_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "featureloc_pubs", "Bio::Chado::Schema::Result::Sequence::FeaturelocPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 featuremap_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "featuremap_pubs", "Bio::Chado::Schema::Result::Map::FeaturemapPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 featureprop_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "featureprop_pubs", "Bio::Chado::Schema::Result::Sequence::FeaturepropPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_pubs", "Bio::Chado::Schema::Result::Sequence::FeaturePub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_relationshipprop_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_relationshipprop_pubs", "Bio::Chado::Schema::Result::Sequence::FeatureRelationshippropPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_relationship_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_relationship_pubs", "Bio::Chado::Schema::Result::Sequence::FeatureRelationshipPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_synonyms Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_synonyms", "Bio::Chado::Schema::Result::Sequence::FeatureSynonym", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 library_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "library_cvterms", "Bio::Chado::Schema::Result::Library::LibraryCvterm", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 libraryprop_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "libraryprop_pubs", "Bio::Chado::Schema::Result::Library::LibrarypropPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 library_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "library_pubs", "Bio::Chado::Schema::Result::Library::LibraryPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 library_synonyms Type: has_many Related object: L =cut __PACKAGE__->has_many( "library_synonyms", "Bio::Chado::Schema::Result::Library::LibrarySynonym", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_experiment_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_experiment_pubs", "Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phendescs Type: has_many Related object: L =cut __PACKAGE__->has_many( "phendescs", "Bio::Chado::Schema::Result::Genetic::Phendesc", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenotype_comparisons Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenotype_comparisons", "Bio::Chado::Schema::Result::Genetic::PhenotypeComparison", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenotype_comparison_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenotype_comparison_cvterms", "Bio::Chado::Schema::Result::Genetic::PhenotypeComparisonCvterm", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenstatements Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenstatements", "Bio::Chado::Schema::Result::Genetic::Phenstatement", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phylonode_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "phylonode_pubs", "Bio::Chado::Schema::Result::Phylogeny::PhylonodePub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phylotree_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "phylotree_pubs", "Bio::Chado::Schema::Result::Phylogeny::PhylotreePub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 project_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "project_pubs", "Bio::Chado::Schema::Result::Project::ProjectPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 protocols Type: has_many Related object: L =cut __PACKAGE__->has_many( "protocols", "Bio::Chado::Schema::Result::Mage::Protocol", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 type Type: belongs_to Related object: L =cut __PACKAGE__->belongs_to( "type", "Bio::Chado::Schema::Result::Cv::Cvterm", { cvterm_id => "type_id" }, { cascade_copy => 0, cascade_delete => 0, is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE", }, ); =head2 pubauthors Type: has_many Related object: L =cut __PACKAGE__->has_many( "pubauthors", "Bio::Chado::Schema::Result::Pub::Pubauthor", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 pub_dbxrefs Type: has_many Related object: L =cut __PACKAGE__->has_many( "pub_dbxrefs", "Bio::Chado::Schema::Result::Pub::PubDbxref", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 pubprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "pubprops", "Bio::Chado::Schema::Result::Pub::Pubprop", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 pub_relationship_objects Type: has_many Related object: L =cut __PACKAGE__->has_many( "pub_relationship_objects", "Bio::Chado::Schema::Result::Pub::PubRelationship", { "foreign.object_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 pub_relationship_subjects Type: has_many Related object: L =cut __PACKAGE__->has_many( "pub_relationship_subjects", "Bio::Chado::Schema::Result::Pub::PubRelationship", { "foreign.subject_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stock_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "stock_cvterms", "Bio::Chado::Schema::Result::Stock::StockCvterm", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stockprop_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "stockprop_pubs", "Bio::Chado::Schema::Result::Stock::StockpropPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stock_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "stock_pubs", "Bio::Chado::Schema::Result::Stock::StockPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stock_relationship_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "stock_relationship_cvterms", "Bio::Chado::Schema::Result::Stock::StockRelationshipCvterm", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stock_relationship_pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "stock_relationship_pubs", "Bio::Chado::Schema::Result::Stock::StockRelationshipPub", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 studies Type: has_many Related object: L =cut __PACKAGE__->has_many( "studies", "Bio::Chado::Schema::Result::Mage::Study", { "foreign.pub_id" => "self.pub_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); # Created by DBIx::Class::Schema::Loader v0.07010 @ 2011-03-16 23:09:59 # DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:IREmDNM5PFZA6eqAwr7Pqg =head2 create_pubprops Usage: $set->create_pubprops({ baz => 2, foo => 'bar' }); Desc : convenience method to create pubprop properties using cvterms from the ontology with the given name Args : hashref of { propname => value, ...}, options hashref as: { autocreate => 0, (optional) boolean, if passed, automatically create cv, cvterm, and dbxref rows if one cannot be found for the given pubprop name. Default false. cv_name => cv.name to use for the given pubprops. Defaults to 'pub_property', db_name => db.name to use for autocreated dbxrefs, default 'null', dbxref_accession_prefix => optional, default 'autocreated:', definitions => optional hashref of: { cvterm_name => definition, } to load into the cvterm table when autocreating cvterms rank => force numeric rank. Be careful not to pass ranks that already exist for the property type. The function will die in such case. allow_duplicate_values => default false. If true, allow duplicate instances of the same cvterm and value in the properties of the pubprop. Duplicate values will have different ranks. } Ret : hashref of { propname => new pubprop object } =cut sub create_pubprops { my ($self, $props, $opts) = @_; # process opts $opts->{cv_name} = 'pub_property' unless defined $opts->{cv_name}; return Bio::Chado::Schema::Util->create_properties ( properties => $props, options => $opts, row => $self, prop_relation_name => 'pubprops', ); } # You can replace this text with custom content, and it will be preserved on regeneration 1;