From 88036825a985f08cf8a86345fc3ceb806a4267ed Mon Sep 17 00:00:00 2001 From: Naama Menda Date: Sat, 3 Mar 2012 12:39:57 -0500 Subject: [PATCH] updated dbic schema objects for sgn schema --- lib/SGN/Schema.pm | 7 +- lib/SGN/Schema/Accession.pm | 175 +++++++-- lib/SGN/Schema/AccessionName.pm | 91 +++-- lib/SGN/Schema/AnnotationTargetType.pm | 136 ++++--- lib/SGN/Schema/Author.pm | 104 +++--- lib/SGN/Schema/BlastAnnotation.pm | 133 +++++-- lib/SGN/Schema/BlastDb.pm | 309 ++++++++++------ lib/SGN/Schema/BlastDbGroup.pm | 68 +++- lib/SGN/Schema/BlastDefline.pm | 142 +++++--- lib/SGN/Schema/BlastHit.pm | 204 +++++++---- lib/SGN/Schema/BlastTarget.pm | 130 ++++--- lib/SGN/Schema/Cd.pm | 295 +++++++++------ lib/SGN/Schema/Clone.pm | 98 +++-- lib/SGN/Schema/CloningVector.pm | 61 +++- lib/SGN/Schema/CommonName.pm | 79 +++- lib/SGN/Schema/CommonNameprop.pm | 96 +++++ lib/SGN/Schema/CosMarker.pm | 319 +++++++++------- lib/SGN/Schema/CosiiOrtholog.pm | 206 +++++++---- lib/SGN/Schema/DeprecatedLinkageGroup.pm | 98 +++-- lib/SGN/Schema/DeprecatedMap.pm | 376 +++++++++++-------- lib/SGN/Schema/DeprecatedMapCross.pm | 92 ++++- lib/SGN/Schema/DeprecatedMapdata.pm | 147 ++++++-- lib/SGN/Schema/DeprecatedMarker.pm | 108 +++++- lib/SGN/Schema/DeprecatedMarkerConfidence.pm | 78 +++- lib/SGN/Schema/DeprecatedMarkerLocation.pm | 149 ++++++-- lib/SGN/Schema/DeprecatedMarkerType.pm | 86 +++-- lib/SGN/Schema/DerivedFromSource.pm | 100 +++-- lib/SGN/Schema/Domain.pm | 210 +++++++---- lib/SGN/Schema/DomainMatch.pm | 270 +++++++++----- lib/SGN/Schema/Enzyme.pm | 61 +++- lib/SGN/Schema/EnzymeRestrictionSite.pm | 55 ++- lib/SGN/Schema/Est.pm | 189 +++++++--- lib/SGN/Schema/EstDbxref.pm | 75 +++- lib/SGN/Schema/EstMappedByClone.pm | 85 +++++ lib/SGN/Schema/ExperimentType.pm | 73 +++- lib/SGN/Schema/Facility.pm | 278 ++++++++------ lib/SGN/Schema/Family.pm | 150 ++++++-- lib/SGN/Schema/FamilyBuild.pm | 165 ++++++--- lib/SGN/Schema/FamilyMember.pm | 182 ++++++---- lib/SGN/Schema/FamilyTree.pm | 157 +++++--- lib/SGN/Schema/FishChromatinDensityConstant.pm | 43 ++- lib/SGN/Schema/FishExperimenter.pm | 61 +++- lib/SGN/Schema/FishFile.pm | 106 +++--- lib/SGN/Schema/FishImage.pm | 51 ++- lib/SGN/Schema/FishKaryotypeConstant.pm | 136 ++++--- lib/SGN/Schema/FishKaryotypeConstantsOld.pm | 145 +++++--- lib/SGN/Schema/FishResult.pm | 255 ++++++++----- lib/SGN/Schema/FishResultComposite.pm | 257 ++++++++----- lib/SGN/Schema/FishResultImage.pm | 85 +++++ lib/SGN/Schema/Go.pm | 87 +++-- lib/SGN/Schema/Group.pm | 69 +++- lib/SGN/Schema/GroupLinkage.pm | 117 +++--- lib/SGN/Schema/IdLinkage.pm | 118 +++--- lib/SGN/Schema/IlInfo.pm | 184 ++++++---- lib/SGN/Schema/Interpro.pm | 87 +++-- lib/SGN/Schema/InterproGo.pm | 100 +++-- lib/SGN/Schema/Library.pm | 482 +++++++++++++++---------- lib/SGN/Schema/LinkageGroup.pm | 157 ++++++-- lib/SGN/Schema/LocType.pm | 108 +++--- lib/SGN/Schema/ManualAnnotation.pm | 149 +++++--- lib/SGN/Schema/ManualCensorReason.pm | 48 ++- lib/SGN/Schema/Map.pm | 237 ++++++++---- lib/SGN/Schema/MapVersion.pm | 163 +++++++-- lib/SGN/Schema/Marker.pm | 198 +++++++++- lib/SGN/Schema/MarkerAlias.pm | 89 +++++ lib/SGN/Schema/MarkerCollectible.pm | 144 +++++--- lib/SGN/Schema/MarkerCollection.pm | 72 +++- lib/SGN/Schema/MarkerConfidence.pm | 60 ++- lib/SGN/Schema/MarkerDerivedFrom.pm | 105 ++++-- lib/SGN/Schema/MarkerExperiment.pm | 170 ++++++--- lib/SGN/Schema/MarkerLocation.pm | 192 +++++++--- lib/SGN/Schema/MarkerToMap.pm | 191 ++++++---- lib/SGN/Schema/Metadata.pm | 127 +++++-- lib/SGN/Schema/Microarray.pm | 148 +++++--- lib/SGN/Schema/Misc.pm | 113 +++--- lib/SGN/Schema/Organism.pm | 304 +++++++++++----- lib/SGN/Schema/Organismgroup.pm | 81 +++++ lib/SGN/Schema/OrganismgroupMember.pm | 85 +++++ lib/SGN/Schema/PMarker.pm | 146 +++++--- lib/SGN/Schema/PcrExpAccession.pm | 115 ++++-- lib/SGN/Schema/PcrExperiment.pm | 316 +++++++++++----- lib/SGN/Schema/PcrExperimentSequence.pm | 103 ++++++ lib/SGN/Schema/PcrProduct.pm | 125 +++++-- lib/SGN/Schema/PrimerUnigeneMatch.pm | 219 +++++++---- lib/SGN/Schema/QcReport.pm | 246 +++++++++---- lib/SGN/Schema/RflpMarker.pm | 355 +++++++++++------- lib/SGN/Schema/RflpSequence.pm | 84 ++++- lib/SGN/Schema/RflpUnigeneAssociation.pm | 131 +++++-- lib/SGN/Schema/Seqread.pm | 296 +++++++++------ lib/SGN/Schema/Sequence.pm | 116 +++++- lib/SGN/Schema/Snp.pm | 209 +++++++++++ lib/SGN/Schema/SnpFile.pm | 80 ++++ lib/SGN/Schema/Snpprop.pm | 100 +++++ lib/SGN/Schema/Ssr.pm | 279 +++++++++----- lib/SGN/Schema/SsrPrimerUnigeneMatches.pm | 169 +++++++++ lib/SGN/Schema/SsrRepeat.pm | 173 ++++++--- lib/SGN/Schema/SubmitUser.pm | 228 +++++++----- lib/SGN/Schema/Taxonomy.pm | 104 +++++- lib/SGN/Schema/TempCapsCorrespondence.pm | 50 ++- lib/SGN/Schema/TempMapCorrespondence.pm | 98 +++-- lib/SGN/Schema/TempMarkerCorrespondence.pm | 75 +++- lib/SGN/Schema/TigrtcIndex.pm | 49 ++- lib/SGN/Schema/TigrtcMembership.pm | 103 ++++-- lib/SGN/Schema/TigrtcTracking.pm | 103 ++++-- lib/SGN/Schema/TmMarker.pm | 218 +++++++---- lib/SGN/Schema/TmMarkersSequence.pm | 107 +++--- lib/SGN/Schema/TrimFeature.pm | 126 ++++--- lib/SGN/Schema/TrimFeatureType.pm | 48 ++- lib/SGN/Schema/Type.pm | 60 ++- lib/SGN/Schema/Unigene.pm | 205 +++++++++-- lib/SGN/Schema/UnigeneBuild.pm | 295 +++++++++++---- lib/SGN/Schema/UnigeneConsensi.pm | 72 +++- lib/SGN/Schema/UnigeneMember.pm | 213 +++++++---- 113 files changed, 11807 insertions(+), 4770 deletions(-) rewrite lib/SGN/Schema/AnnotationTargetType.pm (64%) rewrite lib/SGN/Schema/Author.pm (61%) rewrite lib/SGN/Schema/BlastDb.pm (64%) rewrite lib/SGN/Schema/BlastDefline.pm (66%) rewrite lib/SGN/Schema/BlastHit.pm (66%) rewrite lib/SGN/Schema/BlastTarget.pm (65%) rewrite lib/SGN/Schema/Cd.pm (70%) create mode 100644 lib/SGN/Schema/CommonNameprop.pm rewrite lib/SGN/Schema/CosMarker.pm (77%) rewrite lib/SGN/Schema/CosiiOrtholog.pm (66%) rewrite lib/SGN/Schema/DeprecatedMap.pm (60%) rewrite lib/SGN/Schema/Domain.pm (60%) rewrite lib/SGN/Schema/DomainMatch.pm (63%) create mode 100644 lib/SGN/Schema/EstMappedByClone.pm rewrite lib/SGN/Schema/Facility.pm (71%) rewrite lib/SGN/Schema/FamilyBuild.pm (62%) rewrite lib/SGN/Schema/FamilyMember.pm (64%) rewrite lib/SGN/Schema/FamilyTree.pm (64%) rewrite lib/SGN/Schema/FishFile.pm (61%) rewrite lib/SGN/Schema/FishKaryotypeConstant.pm (64%) rewrite lib/SGN/Schema/FishKaryotypeConstantsOld.pm (65%) rewrite lib/SGN/Schema/FishResult.pm (63%) rewrite lib/SGN/Schema/FishResultComposite.pm (73%) create mode 100644 lib/SGN/Schema/FishResultImage.pm rewrite lib/SGN/Schema/GroupLinkage.pm (63%) rewrite lib/SGN/Schema/IdLinkage.pm (64%) rewrite lib/SGN/Schema/IlInfo.pm (76%) rewrite lib/SGN/Schema/Library.pm (73%) rewrite lib/SGN/Schema/LocType.pm (63%) rewrite lib/SGN/Schema/ManualAnnotation.pm (65%) create mode 100644 lib/SGN/Schema/MarkerAlias.pm rewrite lib/SGN/Schema/MarkerCollectible.pm (61%) rewrite lib/SGN/Schema/MarkerToMap.pm (76%) rewrite lib/SGN/Schema/Microarray.pm (68%) rewrite lib/SGN/Schema/Misc.pm (64%) create mode 100644 lib/SGN/Schema/Organismgroup.pm create mode 100644 lib/SGN/Schema/OrganismgroupMember.pm rewrite lib/SGN/Schema/PMarker.pm (65%) create mode 100644 lib/SGN/Schema/PcrExperimentSequence.pm rewrite lib/SGN/Schema/PrimerUnigeneMatch.pm (67%) rewrite lib/SGN/Schema/QcReport.pm (72%) rewrite lib/SGN/Schema/RflpMarker.pm (66%) rewrite lib/SGN/Schema/Seqread.pm (65%) create mode 100644 lib/SGN/Schema/Snp.pm create mode 100644 lib/SGN/Schema/SnpFile.pm create mode 100644 lib/SGN/Schema/Snpprop.pm rewrite lib/SGN/Schema/Ssr.pm (69%) create mode 100644 lib/SGN/Schema/SsrPrimerUnigeneMatches.pm rewrite lib/SGN/Schema/SsrRepeat.pm (69%) rewrite lib/SGN/Schema/SubmitUser.pm (74%) rewrite lib/SGN/Schema/TigrtcMembership.pm (60%) rewrite lib/SGN/Schema/TigrtcTracking.pm (60%) rewrite lib/SGN/Schema/TmMarker.pm (68%) rewrite lib/SGN/Schema/TmMarkersSequence.pm (63%) rewrite lib/SGN/Schema/TrimFeature.pm (67%) rewrite lib/SGN/Schema/UnigeneMember.pm (61%) diff --git a/lib/SGN/Schema.pm b/lib/SGN/Schema.pm index 1489562..5b8e411 100644 --- a/lib/SGN/Schema.pm +++ b/lib/SGN/Schema.pm @@ -1,5 +1,8 @@ package SGN::Schema; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; @@ -8,8 +11,8 @@ use base 'DBIx::Class::Schema'; __PACKAGE__->load_classes; -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Aj9dpiwQwtY4XWsXAgEjPg +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:VQdWWO0hj5kKE21DngHpYQ # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Accession.pm b/lib/SGN/Schema/Accession.pm index 59d44ad..9e71e47 100644 --- a/lib/SGN/Schema/Accession.pm +++ b/lib/SGN/Schema/Accession.pm @@ -1,88 +1,203 @@ package SGN::Schema::Accession; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Accession + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("accession"); + +=head1 ACCESSORS + +=head2 accession_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'accession_accession_id_seq' + +=head2 organism_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 common_name + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 accession_name_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 chado_organism_id + + data_type: 'integer' + is_nullable: 1 + +=head2 stock_id + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "accession_id", { - data_type => "integer", - default_value => "nextval('accession_accession_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "accession_accession_id_seq", }, "organism_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "common_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, + { data_type => "varchar", is_nullable => 1, size => 80 }, "accession_name_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "chado_organism_id", + { data_type => "integer", is_nullable => 1 }, + "stock_id", + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("accession_id"); __PACKAGE__->add_unique_constraint("unique_accession_name", ["accession_name_id"]); + +=head1 RELATIONS + +=head2 organism + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "organism", "SGN::Schema::Organism", { organism_id => "organism_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 accession_name + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "accession_name", "SGN::Schema::AccessionName", { accession_name_id => "accession_name_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 accession_names + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "accession_names", "SGN::Schema::AccessionName", { "foreign.accession_id" => "self.accession_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 map_ancestors + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "map_ancestors", "SGN::Schema::Map", { "foreign.ancestor" => "self.accession_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 map_parent_2s + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "map_parent_2s", "SGN::Schema::Map", { "foreign.parent_2" => "self.accession_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 map_parent_1s + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "map_parent_1s", "SGN::Schema::Map", { "foreign.parent_1" => "self.accession_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 pcr_exp_accessions + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "pcr_exp_accessions", "SGN::Schema::PcrExpAccession", { "foreign.accession_id" => "self.accession_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:PpupFuImZrTs71w3q/kLvw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:838fnA2hrzzcn5PKEGLZRA # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/AccessionName.pm b/lib/SGN/Schema/AccessionName.pm index b2b5c81..d699353 100644 --- a/lib/SGN/Schema/AccessionName.pm +++ b/lib/SGN/Schema/AccessionName.pm @@ -1,53 +1,100 @@ package SGN::Schema::AccessionName; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::AccessionName + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("accession_names"); + +=head1 ACCESSORS + +=head2 accession_name_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'accession_names_accession_name_id_seq' + +=head2 accession_name + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 accession_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "accession_name_id", { - data_type => "bigint", - default_value => "nextval('accession_names_accession_name_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "accession_names_accession_name_id_seq", }, "accession_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, + { data_type => "varchar", is_nullable => 1, size => 255 }, "accession_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, ); __PACKAGE__->set_primary_key("accession_name_id"); + +=head1 RELATIONS + +=head2 accession + +Type: might_have + +Related object: L + +=cut + __PACKAGE__->might_have( "accession", "SGN::Schema::Accession", { "foreign.accession_name_id" => "self.accession_name_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 accession + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "accession", "SGN::Schema::Accession", { accession_id => "accession_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:G9e5N3E4Irk71oOf99ETXg +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:AWnIAIDyVrbybKPzRs9kKQ # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/AnnotationTargetType.pm b/lib/SGN/Schema/AnnotationTargetType.pm dissimilarity index 64% index 410a196..533c1c9 100644 --- a/lib/SGN/Schema/AnnotationTargetType.pm +++ b/lib/SGN/Schema/AnnotationTargetType.pm @@ -1,56 +1,80 @@ -package SGN::Schema::AnnotationTargetType; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("annotation_target_type"); -__PACKAGE__->add_columns( - "annotation_target_type_id", - { - data_type => "bigint", - default_value => "nextval('annotation_target_type_annotation_target_type_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 8, - }, - "type_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 25, - }, - "type_description", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 250, - }, - "table_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 250, - }, - "index_field_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 250, - }, -); -__PACKAGE__->set_primary_key("annotation_target_type_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:VZTFOr/UFqbpEMKJI1xlzg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::AnnotationTargetType; + +# 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 + +SGN::Schema::AnnotationTargetType + +=cut + +__PACKAGE__->table("annotation_target_type"); + +=head1 ACCESSORS + +=head2 annotation_target_type_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'annotation_target_type_annotation_target_type_id_seq' + +=head2 type_name + + data_type: 'varchar' + is_nullable: 1 + size: 25 + +=head2 type_description + + data_type: 'varchar' + is_nullable: 1 + size: 250 + +=head2 table_name + + data_type: 'varchar' + is_nullable: 1 + size: 250 + +=head2 index_field_name + + data_type: 'varchar' + is_nullable: 1 + size: 250 + +=cut + +__PACKAGE__->add_columns( + "annotation_target_type_id", + { + data_type => "bigint", + is_auto_increment => 1, + is_nullable => 0, + sequence => "annotation_target_type_annotation_target_type_id_seq", + }, + "type_name", + { data_type => "varchar", is_nullable => 1, size => 25 }, + "type_description", + { data_type => "varchar", is_nullable => 1, size => 250 }, + "table_name", + { data_type => "varchar", is_nullable => 1, size => 250 }, + "index_field_name", + { data_type => "varchar", is_nullable => 1, size => 250 }, +); +__PACKAGE__->set_primary_key("annotation_target_type_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Bjf4bx76aEIipEgUK70buw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Author.pm b/lib/SGN/Schema/Author.pm dissimilarity index 61% index 59709a1..1353bf7 100644 --- a/lib/SGN/Schema/Author.pm +++ b/lib/SGN/Schema/Author.pm @@ -1,42 +1,62 @@ -package SGN::Schema::Author; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("authors"); -__PACKAGE__->add_columns( - "author_id", - { - data_type => "integer", - default_value => "nextval('authors_author_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "name", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "institution", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("author_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:+WmxBrPrgo37jUNNMJ0dmw - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::Author; + +# 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 + +SGN::Schema::Author + +=cut + +__PACKAGE__->table("authors"); + +=head1 ACCESSORS + +=head2 author_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'authors_author_id_seq' + +=head2 name + + data_type: 'text' + is_nullable: 1 + +=head2 institution + + data_type: 'text' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "author_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "authors_author_id_seq", + }, + "name", + { data_type => "text", is_nullable => 1 }, + "institution", + { data_type => "text", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("author_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:fA2/6P0m0s2ItG4IkmiJ9g + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/BlastAnnotation.pm b/lib/SGN/Schema/BlastAnnotation.pm index 0a232e1..8c5074e 100644 --- a/lib/SGN/Schema/BlastAnnotation.pm +++ b/lib/SGN/Schema/BlastAnnotation.pm @@ -1,69 +1,146 @@ package SGN::Schema::BlastAnnotation; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::BlastAnnotation + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("blast_annotations"); + +=head1 ACCESSORS + +=head2 blast_annotation_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'blast_annotations_blast_annotation_id_seq' + +=head2 apply_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 apply_type + + data_type: 'integer' + is_nullable: 1 + +=head2 blast_target_id + + data_type: 'integer' + is_nullable: 1 + +=head2 n_hits + + data_type: 'integer' + is_nullable: 1 + +=head2 hits_stored + + data_type: 'integer' + is_nullable: 1 + +=head2 last_updated + + data_type: 'integer' + is_nullable: 1 + +=head2 host + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 pid + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "blast_annotation_id", { - data_type => "integer", - default_value => "nextval('blast_annotations_blast_annotation_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "blast_annotations_blast_annotation_id_seq", }, "apply_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "apply_type", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "blast_target_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "n_hits", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "hits_stored", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "last_updated", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "host", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, + { data_type => "varchar", is_nullable => 1, size => 20 }, "pid", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("blast_annotation_id"); __PACKAGE__->add_unique_constraint( "blast_annotations_apply_id_blast_target_id_uq", ["apply_id", "blast_target_id"], ); + +=head1 RELATIONS + +=head2 apply + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "apply", "SGN::Schema::Unigene", { unigene_id => "apply_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 blast_hits + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "blast_hits", "SGN::Schema::BlastHit", { "foreign.blast_annotation_id" => "self.blast_annotation_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:c25ns20ozFJhtQvjZZXq3Q +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:43aWHj56ncTWYbyZmIAs4Q # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/BlastDb.pm b/lib/SGN/Schema/BlastDb.pm dissimilarity index 64% index aeaed21..8a0a709 100644 --- a/lib/SGN/Schema/BlastDb.pm +++ b/lib/SGN/Schema/BlastDb.pm @@ -1,118 +1,191 @@ -package SGN::Schema::BlastDb; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("blast_db"); -__PACKAGE__->add_columns( - "blast_db_id", - { - data_type => "integer", - default_value => "nextval('blast_db_blast_db_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "file_base", - { - data_type => "character varying", - default_value => undef, - is_nullable => 0, - size => 120, - }, - "title", - { - data_type => "character varying", - default_value => undef, - is_nullable => 0, - size => 80, - }, - "type", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "source_url", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "lookup_url", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "update_freq", - { - data_type => "character varying", - default_value => "'monthly'::character varying", - is_nullable => 0, - size => 80, - }, - "info_url", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "index_seqs", - { - data_type => "boolean", - default_value => "false", - is_nullable => 0, - size => 1, - }, - "blast_db_group_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, - "web_interface_visible", - { - data_type => "boolean", - default_value => "false", - is_nullable => 1, - size => 1, - }, - "description", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("blast_db_id"); -__PACKAGE__->add_unique_constraint("blast_db_file_base_key", ["file_base"]); -__PACKAGE__->belongs_to( - "blast_db_group", - "SGN::Schema::BlastDbGroup", - { blast_db_group_id => "blast_db_group_id" }, - { join_type => "LEFT" }, -); -__PACKAGE__->has_many( - "unigene_builds", - "SGN::Schema::UnigeneBuild", - { "foreign.blast_db_id" => "self.blast_db_id" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:dgwbxWK+Txu+tex3qf0BFg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::BlastDb; + +# 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 + +SGN::Schema::BlastDb + +=head1 DESCRIPTION + +This table holds metadata about the BLAST databases that we keep in stock. + +=cut + +__PACKAGE__->table("blast_db"); + +=head1 ACCESSORS + +=head2 blast_db_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'blast_db_blast_db_id_seq' + +=head2 file_base + + data_type: 'varchar' + is_nullable: 0 + size: 120 + +the basename of the blast db files, relative to the root of the databases repository. A blast DB is usually composed of 3 files, all with a given basename, and with the extensions .[pn]in, .[pn]sq, and .[pn]hr. + +=head2 title + + data_type: 'varchar' + is_nullable: 0 + size: 80 + +=head2 type + + data_type: 'varchar' + is_nullable: 0 + size: 80 + +=head2 source_url + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 lookup_url + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 update_freq + + data_type: 'varchar' + default_value: 'monthly' + is_nullable: 0 + size: 80 + +=head2 info_url + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 index_seqs + + data_type: 'boolean' + default_value: true + is_nullable: 0 + +corresponds to formatdb -o option. Set true if formatdb should be given a '-o T'. This is used only if you later want to fetch specific sequences out of this blast db. + +=head2 blast_db_group_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +blast_db_group this belongs to, for displaying on web + +=head2 web_interface_visible + + data_type: 'boolean' + default_value: false + is_nullable: 1 + +whether this blast DB is available for BLASTing via web interfaces + +=head2 description + + data_type: 'text' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "blast_db_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "blast_db_blast_db_id_seq", + }, + "file_base", + { data_type => "varchar", is_nullable => 0, size => 120 }, + "title", + { data_type => "varchar", is_nullable => 0, size => 80 }, + "type", + { data_type => "varchar", is_nullable => 0, size => 80 }, + "source_url", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "lookup_url", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "update_freq", + { + data_type => "varchar", + default_value => "monthly", + is_nullable => 0, + size => 80, + }, + "info_url", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "index_seqs", + { data_type => "boolean", default_value => \"true", is_nullable => 0 }, + "blast_db_group_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "web_interface_visible", + { data_type => "boolean", default_value => \"false", is_nullable => 1 }, + "description", + { data_type => "text", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("blast_db_id"); +__PACKAGE__->add_unique_constraint("blast_db_file_base_key", ["file_base"]); + +=head1 RELATIONS + +=head2 blast_db_group + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "blast_db_group", + "SGN::Schema::BlastDbGroup", + { blast_db_group_id => "blast_db_group_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 unigenes_build + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "unigenes_build", + "SGN::Schema::UnigeneBuild", + { "foreign.blast_db_id" => "self.blast_db_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:CtJt3leN5YsnLZmy0I1YFw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/BlastDbGroup.pm b/lib/SGN/Schema/BlastDbGroup.pm index 0f96c55..1789a1f 100644 --- a/lib/SGN/Schema/BlastDbGroup.pm +++ b/lib/SGN/Schema/BlastDbGroup.pm @@ -1,41 +1,79 @@ package SGN::Schema::BlastDbGroup; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::BlastDbGroup + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("blast_db_group"); + +=head1 ACCESSORS + +=head2 blast_db_group_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'blast_db_group_blast_db_group_id_seq' + +=head2 name + + data_type: 'varchar' + is_nullable: 1 + size: 50 + +=head2 ordinal + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "blast_db_group_id", { - data_type => "integer", - default_value => "nextval('blast_db_group_blast_db_group_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "blast_db_group_blast_db_group_id_seq", }, "name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 50, - }, + { data_type => "varchar", is_nullable => 1, size => 50 }, "ordinal", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("blast_db_group_id"); + +=head1 RELATIONS + +=head2 blast_dbs + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "blast_dbs", "SGN::Schema::BlastDb", { "foreign.blast_db_group_id" => "self.blast_db_group_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:6C3I38meStK8O5wEoU2A9A +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:aH2DxlwsJstedBgQOG01rQ # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/BlastDefline.pm b/lib/SGN/Schema/BlastDefline.pm dissimilarity index 66% index 6665a33..4d56ea2 100644 --- a/lib/SGN/Schema/BlastDefline.pm +++ b/lib/SGN/Schema/BlastDefline.pm @@ -1,58 +1,84 @@ -package SGN::Schema::BlastDefline; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("blast_defline"); -__PACKAGE__->add_columns( - "defline_id", - { - data_type => "integer", - default_value => "nextval('blast_defline_defline_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "blast_target_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "target_db_id", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "defline", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "defline_fulltext", - { - data_type => "tsvector", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "identifier_defline_fulltext", - { - data_type => "tsvector", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("defline_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:8yU0F15zAHGCgzzTxjqR3A - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::BlastDefline; + +# 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 + +SGN::Schema::BlastDefline + +=cut + +__PACKAGE__->table("blast_defline"); + +=head1 ACCESSORS + +=head2 defline_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'blast_defline_defline_id_seq' + +=head2 blast_target_id + + data_type: 'integer' + is_nullable: 1 + +=head2 target_db_id + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 defline + + data_type: 'text' + is_nullable: 1 + +=head2 defline_fulltext + + data_type: 'tsvector' + is_nullable: 1 + +=head2 identifier_defline_fulltext + + data_type: 'tsvector' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "defline_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "blast_defline_defline_id_seq", + }, + "blast_target_id", + { data_type => "integer", is_nullable => 1 }, + "target_db_id", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "defline", + { data_type => "text", is_nullable => 1 }, + "defline_fulltext", + { data_type => "tsvector", is_nullable => 1 }, + "identifier_defline_fulltext", + { data_type => "tsvector", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("defline_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:c3T+el9V3/ziJEFzPnmUUg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/BlastHit.pm b/lib/SGN/Schema/BlastHit.pm dissimilarity index 66% index 179544a..564f4dc 100644 --- a/lib/SGN/Schema/BlastHit.pm +++ b/lib/SGN/Schema/BlastHit.pm @@ -1,76 +1,128 @@ -package SGN::Schema::BlastHit; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("blast_hits"); -__PACKAGE__->add_columns( - "blast_hit_id", - { - data_type => "integer", - default_value => "nextval('blast_hits_blast_hit_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "blast_annotation_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, - "target_db_id", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "evalue", - { - data_type => "double precision", - default_value => undef, - is_nullable => 1, - size => 8, - }, - "score", - { - data_type => "double precision", - default_value => undef, - is_nullable => 1, - size => 8, - }, - "identity_percentage", - { - data_type => "double precision", - default_value => undef, - is_nullable => 1, - size => 8, - }, - "apply_start", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "apply_end", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "defline_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, -); -__PACKAGE__->set_primary_key("blast_hit_id"); -__PACKAGE__->belongs_to( - "blast_annotation", - "SGN::Schema::BlastAnnotation", - { blast_annotation_id => "blast_annotation_id" }, - { join_type => "LEFT" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:QKBiP2cK+zwhJ7uLGcmmiQ - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::BlastHit; + +# 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 + +SGN::Schema::BlastHit + +=cut + +__PACKAGE__->table("blast_hits"); + +=head1 ACCESSORS + +=head2 blast_hit_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'blast_hits_blast_hit_id_seq' + +=head2 blast_annotation_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 target_db_id + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 evalue + + data_type: 'double precision' + is_nullable: 1 + +=head2 score + + data_type: 'double precision' + is_nullable: 1 + +=head2 identity_percentage + + data_type: 'double precision' + is_nullable: 1 + +=head2 apply_start + + data_type: 'bigint' + is_nullable: 1 + +=head2 apply_end + + data_type: 'bigint' + is_nullable: 1 + +=head2 defline_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "blast_hit_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "blast_hits_blast_hit_id_seq", + }, + "blast_annotation_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "target_db_id", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "evalue", + { data_type => "double precision", is_nullable => 1 }, + "score", + { data_type => "double precision", is_nullable => 1 }, + "identity_percentage", + { data_type => "double precision", is_nullable => 1 }, + "apply_start", + { data_type => "bigint", is_nullable => 1 }, + "apply_end", + { data_type => "bigint", is_nullable => 1 }, + "defline_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("blast_hit_id"); + +=head1 RELATIONS + +=head2 blast_annotation + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "blast_annotation", + "SGN::Schema::BlastAnnotation", + { blast_annotation_id => "blast_annotation_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:oIds6hCNHjaKMqpIqLeoAQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/BlastTarget.pm b/lib/SGN/Schema/BlastTarget.pm dissimilarity index 65% index b746b68..456b9ae 100644 --- a/lib/SGN/Schema/BlastTarget.pm +++ b/lib/SGN/Schema/BlastTarget.pm @@ -1,51 +1,79 @@ -package SGN::Schema::BlastTarget; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("blast_targets"); -__PACKAGE__->add_columns( - "blast_target_id", - { - data_type => "integer", - default_value => "nextval('blast_targets_blast_target_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "blast_program", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 7, - }, - "db_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "db_path", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "local_copy_timestamp", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, -); -__PACKAGE__->set_primary_key("blast_target_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:J/73wB//mUYLUj1wybSdhw - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::BlastTarget; + +# 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 + +SGN::Schema::BlastTarget + +=cut + +__PACKAGE__->table("blast_targets"); + +=head1 ACCESSORS + +=head2 blast_target_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'blast_targets_blast_target_id_seq' + +=head2 blast_program + + data_type: 'varchar' + is_nullable: 1 + size: 7 + +=head2 db_name + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 db_path + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 local_copy_timestamp + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "blast_target_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "blast_targets_blast_target_id_seq", + }, + "blast_program", + { data_type => "varchar", is_nullable => 1, size => 7 }, + "db_name", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "db_path", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "local_copy_timestamp", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("blast_target_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:vAn2GVNUrs9RPpEzKHuf+Q + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Cd.pm b/lib/SGN/Schema/Cd.pm dissimilarity index 70% index 3d3d0b9..4e2d586 100644 --- a/lib/SGN/Schema/Cd.pm +++ b/lib/SGN/Schema/Cd.pm @@ -1,108 +1,187 @@ -package SGN::Schema::Cd; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("cds"); -__PACKAGE__->add_columns( - "cds_id", - { - data_type => "bigint", - default_value => "nextval('cds_cds_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 8, - }, - "unigene_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, - "seq_text", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "seq_edits", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "protein_seq", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "begin", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "end", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "forward_reverse", - { - data_type => "character", - default_value => undef, - is_nullable => 1, - size => 1, - }, - "run_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "score", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "method", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, - "frame", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 2, - }, - "preferred", - { data_type => "boolean", default_value => undef, is_nullable => 1, size => 1 }, - "cds_seq", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "protein_feature_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, -); -__PACKAGE__->set_primary_key("cds_id"); -__PACKAGE__->belongs_to( - "unigene", - "SGN::Schema::Unigene", - { unigene_id => "unigene_id" }, - { join_type => "LEFT" }, -); -__PACKAGE__->has_many( - "domain_matches", - "SGN::Schema::DomainMatch", - { "foreign.cds_id" => "self.cds_id" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:wh6CiS4uWY0VfH0yTtoUyQ - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::Cd; + +# 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 + +SGN::Schema::Cd + +=cut + +__PACKAGE__->table("cds"); + +=head1 ACCESSORS + +=head2 cds_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'cds_cds_id_seq' + +=head2 unigene_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 seq_text + + data_type: 'text' + is_nullable: 1 + +=head2 seq_edits + + data_type: 'text' + is_nullable: 1 + +=head2 protein_seq + + data_type: 'text' + is_nullable: 1 + +=head2 begin + + data_type: 'integer' + is_nullable: 1 + +=head2 end + + data_type: 'integer' + is_nullable: 1 + +=head2 forward_reverse + + data_type: 'char' + is_nullable: 1 + size: 1 + +=head2 run_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 score + + data_type: 'integer' + is_nullable: 1 + +=head2 method + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 frame + + data_type: 'varchar' + is_nullable: 1 + size: 2 + +=head2 preferred + + data_type: 'boolean' + is_nullable: 1 + +=head2 cds_seq + + data_type: 'text' + is_nullable: 1 + +=head2 protein_feature_id + + data_type: 'bigint' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "cds_id", + { + data_type => "bigint", + is_auto_increment => 1, + is_nullable => 0, + sequence => "cds_cds_id_seq", + }, + "unigene_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "seq_text", + { data_type => "text", is_nullable => 1 }, + "seq_edits", + { data_type => "text", is_nullable => 1 }, + "protein_seq", + { data_type => "text", is_nullable => 1 }, + "begin", + { data_type => "integer", is_nullable => 1 }, + "end", + { data_type => "integer", is_nullable => 1 }, + "forward_reverse", + { data_type => "char", is_nullable => 1, size => 1 }, + "run_id", + { data_type => "bigint", is_nullable => 1 }, + "score", + { data_type => "integer", is_nullable => 1 }, + "method", + { data_type => "varchar", is_nullable => 1, size => 20 }, + "frame", + { data_type => "varchar", is_nullable => 1, size => 2 }, + "preferred", + { data_type => "boolean", is_nullable => 1 }, + "cds_seq", + { data_type => "text", is_nullable => 1 }, + "protein_feature_id", + { data_type => "bigint", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("cds_id"); + +=head1 RELATIONS + +=head2 unigene + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "unigene", + "SGN::Schema::Unigene", + { unigene_id => "unigene_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 domain_matches + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "domain_matches", + "SGN::Schema::DomainMatch", + { "foreign.cds_id" => "self.cds_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:U8lI8JoWcDtZrDhqgQ/yLg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Clone.pm b/lib/SGN/Schema/Clone.pm index e5b19ff..0df7a69 100644 --- a/lib/SGN/Schema/Clone.pm +++ b/lib/SGN/Schema/Clone.pm @@ -1,57 +1,109 @@ package SGN::Schema::Clone; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Clone + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("clone"); + +=head1 ACCESSORS + +=head2 clone_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'clone_clone_id_seq' + +=head2 library_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 clone_name + + data_type: 'varchar' + is_nullable: 1 + size: 50 + +=head2 clone_group_id + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "clone_id", { - data_type => "integer", - default_value => "nextval('clone_clone_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "clone_clone_id_seq", }, "library_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "clone_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 50, - }, + { data_type => "varchar", is_nullable => 1, size => 50 }, "clone_group_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("clone_id"); __PACKAGE__->add_unique_constraint("clone_name_library_id_unique", ["clone_name", "library_id"]); __PACKAGE__->add_unique_constraint("library_id_clone_name_key", ["library_id", "clone_name"]); + +=head1 RELATIONS + +=head2 library + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "library", "SGN::Schema::Library", { library_id => "library_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 seqreads + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "seqreads", "SGN::Schema::Seqread", { "foreign.clone_id" => "self.clone_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:WutXkVOk1ZLogdSm2dveXA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:qHcI1QlJSTctgHcs6FedCg # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/CloningVector.pm b/lib/SGN/Schema/CloningVector.pm index 716c19f..352334e 100644 --- a/lib/SGN/Schema/CloningVector.pm +++ b/lib/SGN/Schema/CloningVector.pm @@ -1,42 +1,63 @@ package SGN::Schema::CloningVector; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::CloningVector + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("cloning_vector"); + +=head1 ACCESSORS + +=head2 cloning_vector_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'cloning_vector_cloning_vector_id_seq' + +=head2 name + + data_type: 'varchar' + is_nullable: 1 + size: 32 + +=head2 seq + + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "cloning_vector_id", { - data_type => "integer", - default_value => "nextval('cloning_vector_cloning_vector_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "cloning_vector_cloning_vector_id_seq", }, "name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 32, - }, + { data_type => "varchar", is_nullable => 1, size => 32 }, "seq", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("cloning_vector_id"); __PACKAGE__->add_unique_constraint("cloning_vector_name_key", ["name"]); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:mqLP8zODA7uf+yrH8uAiKA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:YrZRLoEggB+pEDvYt5XrSQ # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/CommonName.pm b/lib/SGN/Schema/CommonName.pm index fe20cb4..e359539 100644 --- a/lib/SGN/Schema/CommonName.pm +++ b/lib/SGN/Schema/CommonName.pm @@ -1,45 +1,88 @@ package SGN::Schema::CommonName; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::CommonName + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("common_name"); + +=head1 ACCESSORS + +=head2 common_name_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'common_name_common_name_id_seq' + +=head2 common_name + + data_type: 'varchar' + is_nullable: 0 + size: 255 + +=cut + __PACKAGE__->add_columns( "common_name_id", { - data_type => "bigint", - default_value => "nextval('common_name_common_name_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "common_name_common_name_id_seq", }, "common_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 0, - size => 255, - }, + { data_type => "varchar", is_nullable => 0, size => 255 }, ); __PACKAGE__->set_primary_key("common_name_id"); __PACKAGE__->add_unique_constraint("common_name_unique", ["common_name"]); + +=head1 RELATIONS + +=head2 common_nameprops + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "organisms", - "SGN::Schema::Organism", + "common_nameprops", + "SGN::Schema::CommonNameprop", { "foreign.common_name_id" => "self.common_name_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 organisms + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "organismprops", - "SGN::Schema::Organismprop", + "organisms", + "SGN::Schema::Organism", { "foreign.common_name_id" => "self.common_name_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:tbYoxZDGDjT/Ofi+4PbgIA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:OZwtKEhvlAoHbT+X5USNAA # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/CommonNameprop.pm b/lib/SGN/Schema/CommonNameprop.pm new file mode 100644 index 0000000..ed7c502 --- /dev/null +++ b/lib/SGN/Schema/CommonNameprop.pm @@ -0,0 +1,96 @@ +package SGN::Schema::CommonNameprop; + +# 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 + +SGN::Schema::CommonNameprop + +=cut + +__PACKAGE__->table("common_nameprop"); + +=head1 ACCESSORS + +=head2 common_nameprop_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'organismprop_organismprop_id_seq' + +=head2 common_name_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 type_id + + data_type: 'integer' + is_nullable: 0 + +=head2 value + + data_type: 'varchar' + is_nullable: 0 + size: 32 + +=head2 rank + + data_type: 'integer' + default_value: 0 + is_nullable: 0 + +=cut + +__PACKAGE__->add_columns( + "common_nameprop_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "organismprop_organismprop_id_seq", + }, + "common_name_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, + "type_id", + { data_type => "integer", is_nullable => 0 }, + "value", + { data_type => "varchar", is_nullable => 0, size => 32 }, + "rank", + { data_type => "integer", default_value => 0, is_nullable => 0 }, +); +__PACKAGE__->set_primary_key("common_nameprop_id"); + +=head1 RELATIONS + +=head2 common_name + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "common_name", + "SGN::Schema::CommonName", + { common_name_id => "common_name_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:BuIRBz+5C+oT0LP0u7coNg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/CosMarker.pm b/lib/SGN/Schema/CosMarker.pm dissimilarity index 77% index 50af8bd..b38517e 100644 --- a/lib/SGN/Schema/CosMarker.pm +++ b/lib/SGN/Schema/CosMarker.pm @@ -1,130 +1,189 @@ -package SGN::Schema::CosMarker; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("cos_markers"); -__PACKAGE__->add_columns( - "cos_marker_id", - { - data_type => "integer", - default_value => "nextval('cos_markers_cos_marker_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "marker_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_foreign_key => 1, - is_nullable => 0, - size => 8, - }, - "est_read_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, - "cos_id", - { - data_type => "character varying", - default_value => "''::character varying", - is_nullable => 0, - size => 10, - }, - "at_match", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 25, - }, - "bac_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "at_position", - { - data_type => "numeric", - default_value => undef, - is_nullable => 1, - size => "7,11", - }, - "best_gb_prot_hit", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 25, - }, - "at_evalue", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 25, - }, - "at_identities", - { - data_type => "numeric", - default_value => undef, - is_nullable => 1, - size => "3,11", - }, - "mips_cat", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 11, - }, - "description", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "comment", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "tomato_copy_number", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 11, - }, - "gbprot_evalue", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 25, - }, - "gbprot_identities", - { - data_type => "numeric", - default_value => undef, - is_nullable => 1, - size => "3,11", - }, -); -__PACKAGE__->set_primary_key("cos_marker_id"); -__PACKAGE__->belongs_to("marker", "SGN::Schema::Marker", { marker_id => "marker_id" }); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:y6I+pZU5VatEMooJfHOFHw - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::CosMarker; + +# 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 + +SGN::Schema::CosMarker + +=cut + +__PACKAGE__->table("cos_markers"); + +=head1 ACCESSORS + +=head2 cos_marker_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'cos_markers_cos_marker_id_seq' + +=head2 marker_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 est_read_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 cos_id + + data_type: 'varchar' + default_value: (empty string) + is_nullable: 0 + size: 10 + +=head2 at_match + + data_type: 'varchar' + is_nullable: 1 + size: 25 + +=head2 bac_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 at_position + + data_type: 'numeric' + is_nullable: 1 + size: [11,7] + +=head2 best_gb_prot_hit + + data_type: 'varchar' + is_nullable: 1 + size: 25 + +=head2 at_evalue + + data_type: 'varchar' + is_nullable: 1 + size: 25 + +=head2 at_identities + + data_type: 'numeric' + is_nullable: 1 + size: [11,3] + +=head2 mips_cat + + data_type: 'varchar' + is_nullable: 1 + size: 11 + +=head2 description + + data_type: 'text' + is_nullable: 1 + +=head2 comment + + data_type: 'text' + is_nullable: 1 + +=head2 tomato_copy_number + + data_type: 'varchar' + is_nullable: 1 + size: 11 + +=head2 gbprot_evalue + + data_type: 'varchar' + is_nullable: 1 + size: 25 + +=head2 gbprot_identities + + data_type: 'numeric' + is_nullable: 1 + size: [11,3] + +=cut + +__PACKAGE__->add_columns( + "cos_marker_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "cos_markers_cos_marker_id_seq", + }, + "marker_id", + { + data_type => "bigint", + default_value => "0)::bigint", + is_foreign_key => 1, + is_nullable => 0, + }, + "est_read_id", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "cos_id", + { data_type => "varchar", default_value => "", is_nullable => 0, size => 10 }, + "at_match", + { data_type => "varchar", is_nullable => 1, size => 25 }, + "bac_id", + { data_type => "bigint", is_nullable => 1 }, + "at_position", + { data_type => "numeric", is_nullable => 1, size => [11, 7] }, + "best_gb_prot_hit", + { data_type => "varchar", is_nullable => 1, size => 25 }, + "at_evalue", + { data_type => "varchar", is_nullable => 1, size => 25 }, + "at_identities", + { data_type => "numeric", is_nullable => 1, size => [11, 3] }, + "mips_cat", + { data_type => "varchar", is_nullable => 1, size => 11 }, + "description", + { data_type => "text", is_nullable => 1 }, + "comment", + { data_type => "text", is_nullable => 1 }, + "tomato_copy_number", + { data_type => "varchar", is_nullable => 1, size => 11 }, + "gbprot_evalue", + { data_type => "varchar", is_nullable => 1, size => 25 }, + "gbprot_identities", + { data_type => "numeric", is_nullable => 1, size => [11, 3] }, +); +__PACKAGE__->set_primary_key("cos_marker_id"); + +=head1 RELATIONS + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:L36UiM4d0cDlEEISeWAGhQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/CosiiOrtholog.pm b/lib/SGN/Schema/CosiiOrtholog.pm dissimilarity index 66% index 93c1379..55e9c96 100644 --- a/lib/SGN/Schema/CosiiOrtholog.pm +++ b/lib/SGN/Schema/CosiiOrtholog.pm @@ -1,76 +1,130 @@ -package SGN::Schema::CosiiOrtholog; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("cosii_ortholog"); -__PACKAGE__->add_columns( - "cosii_unigene_id", - { - data_type => "bigint", - default_value => "nextval('cosii_ortholog_cosii_unigene_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 8, - }, - "marker_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, - "unigene_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "copies", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 1, - }, - "database_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 11, - }, - "sequence_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "edited_sequence_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "peptide_sequence_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "introns", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("cosii_unigene_id"); -__PACKAGE__->belongs_to( - "marker", - "SGN::Schema::Marker", - { marker_id => "marker_id" }, - { join_type => "LEFT" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:3+cYN1Wvi8E9pql7xqxyQQ - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::CosiiOrtholog; + +# 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 + +SGN::Schema::CosiiOrtholog + +=cut + +__PACKAGE__->table("cosii_ortholog"); + +=head1 ACCESSORS + +=head2 cosii_unigene_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'cosii_ortholog_cosii_unigene_id_seq' + +=head2 marker_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 unigene_id + + data_type: 'integer' + is_nullable: 1 + +=head2 copies + + data_type: 'varchar' + is_nullable: 1 + size: 1 + +=head2 database_name + + data_type: 'varchar' + is_nullable: 1 + size: 11 + +=head2 sequence_name + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 edited_sequence_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 peptide_sequence_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 introns + + data_type: 'text' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "cosii_unigene_id", + { + data_type => "bigint", + is_auto_increment => 1, + is_nullable => 0, + sequence => "cosii_ortholog_cosii_unigene_id_seq", + }, + "marker_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "unigene_id", + { data_type => "integer", is_nullable => 1 }, + "copies", + { data_type => "varchar", is_nullable => 1, size => 1 }, + "database_name", + { data_type => "varchar", is_nullable => 1, size => 11 }, + "sequence_name", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "edited_sequence_id", + { data_type => "bigint", is_nullable => 1 }, + "peptide_sequence_id", + { data_type => "bigint", is_nullable => 1 }, + "introns", + { data_type => "text", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("cosii_unigene_id"); + +=head1 RELATIONS + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:5E/wH8hjHQqk3rLvGjTuCA + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/DeprecatedLinkageGroup.pm b/lib/SGN/Schema/DeprecatedLinkageGroup.pm index 1785228..24a17c6 100644 --- a/lib/SGN/Schema/DeprecatedLinkageGroup.pm +++ b/lib/SGN/Schema/DeprecatedLinkageGroup.pm @@ -1,55 +1,107 @@ package SGN::Schema::DeprecatedLinkageGroup; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::DeprecatedLinkageGroup + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("deprecated_linkage_groups"); + +=head1 ACCESSORS + +=head2 lg_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'deprecated_linkage_groups_lg_id_seq' + +=head2 map_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 lg_order + + data_type: 'bigint' + is_nullable: 1 + +=head2 lg_name + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=cut + __PACKAGE__->add_columns( "lg_id", { - data_type => "bigint", - default_value => "nextval('deprecated_linkage_groups_lg_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "deprecated_linkage_groups_lg_id_seq", }, "map_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "lg_order", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "lg_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, + { data_type => "varchar", is_nullable => 1, size => 255 }, ); __PACKAGE__->set_primary_key("lg_id"); + +=head1 RELATIONS + +=head2 map + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "map", "SGN::Schema::DeprecatedMap", { map_id => "map_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 deprecated_mapdatas + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "deprecated_mapdatas", "SGN::Schema::DeprecatedMapdata", { "foreign.lg_id" => "self.lg_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:IxQiafwdCA59zz8+SsrNyg +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:9dFb1FK633Dd6TcghBivCA # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/DeprecatedMap.pm b/lib/SGN/Schema/DeprecatedMap.pm dissimilarity index 60% index 838122e..44f3f20 100644 --- a/lib/SGN/Schema/DeprecatedMap.pm +++ b/lib/SGN/Schema/DeprecatedMap.pm @@ -1,141 +1,235 @@ -package SGN::Schema::DeprecatedMap; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("deprecated_maps"); -__PACKAGE__->add_columns( - "map_id", - { - data_type => "integer", - default_value => "nextval('deprecated_maps_map_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "legacy_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, - "short_name", - { - data_type => "character varying", - default_value => "''::character varying", - is_nullable => 0, - size => 50, - }, - "long_name", - { - data_type => "character varying", - default_value => "''::character varying", - is_nullable => 0, - size => 250, - }, - "number_chromosomes", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, - "default_threshold", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, - "header", - { - data_type => "text", - default_value => undef, - is_nullable => 0, - size => undef, - }, - "abstract", - { - data_type => "text", - default_value => undef, - is_nullable => 0, - size => undef, - }, - "genetic_cross", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 250, - }, - "population_type", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 250, - }, - "population_size", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "seed_available", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "seed_url", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 250, - }, - "deprecated_by", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 1, - size => 8, - }, - "map_type", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 7, - }, -); -__PACKAGE__->set_primary_key("map_id"); -__PACKAGE__->has_many( - "deprecated_linkage_groups", - "SGN::Schema::DeprecatedLinkageGroup", - { "foreign.map_id" => "self.map_id" }, -); -__PACKAGE__->has_many( - "deprecated_map_crosses", - "SGN::Schema::DeprecatedMapCross", - { "foreign.map_id" => "self.map_id" }, -); -__PACKAGE__->has_many( - "deprecated_mapdatas", - "SGN::Schema::DeprecatedMapdata", - { "foreign.map_id" => "self.map_id" }, -); -__PACKAGE__->has_many( - "fish_results", - "SGN::Schema::FishResult", - { "foreign.map_id" => "self.map_id" }, -); -__PACKAGE__->has_many( - "temp_map_correspondences", - "SGN::Schema::TempMapCorrespondence", - { "foreign.old_map_id" => "self.map_id" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:ZOA9St2Q2s4BDPphigt3FA - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::DeprecatedMap; + +# 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 + +SGN::Schema::DeprecatedMap + +=cut + +__PACKAGE__->table("deprecated_maps"); + +=head1 ACCESSORS + +=head2 map_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'deprecated_maps_map_id_seq' + +=head2 legacy_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 short_name + + data_type: 'varchar' + default_value: (empty string) + is_nullable: 0 + size: 50 + +=head2 long_name + + data_type: 'varchar' + default_value: (empty string) + is_nullable: 0 + size: 250 + +=head2 number_chromosomes + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 default_threshold + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 header + + data_type: 'text' + is_nullable: 0 + +=head2 abstract + + data_type: 'text' + is_nullable: 0 + +=head2 genetic_cross + + data_type: 'varchar' + is_nullable: 1 + size: 250 + +=head2 population_type + + data_type: 'varchar' + is_nullable: 1 + size: 250 + +=head2 population_size + + data_type: 'bigint' + is_nullable: 1 + +=head2 seed_available + + data_type: 'bigint' + is_nullable: 1 + +=head2 seed_url + + data_type: 'varchar' + is_nullable: 1 + size: 250 + +=head2 deprecated_by + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 1 + +=head2 map_type + + data_type: 'varchar' + is_nullable: 1 + size: 7 + +=cut + +__PACKAGE__->add_columns( + "map_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "deprecated_maps_map_id_seq", + }, + "legacy_id", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "short_name", + { data_type => "varchar", default_value => "", is_nullable => 0, size => 50 }, + "long_name", + { data_type => "varchar", default_value => "", is_nullable => 0, size => 250 }, + "number_chromosomes", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "default_threshold", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "header", + { data_type => "text", is_nullable => 0 }, + "abstract", + { data_type => "text", is_nullable => 0 }, + "genetic_cross", + { data_type => "varchar", is_nullable => 1, size => 250 }, + "population_type", + { data_type => "varchar", is_nullable => 1, size => 250 }, + "population_size", + { data_type => "bigint", is_nullable => 1 }, + "seed_available", + { data_type => "bigint", is_nullable => 1 }, + "seed_url", + { data_type => "varchar", is_nullable => 1, size => 250 }, + "deprecated_by", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 1 }, + "map_type", + { data_type => "varchar", is_nullable => 1, size => 7 }, +); +__PACKAGE__->set_primary_key("map_id"); + +=head1 RELATIONS + +=head2 deprecated_linkage_groups + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "deprecated_linkage_groups", + "SGN::Schema::DeprecatedLinkageGroup", + { "foreign.map_id" => "self.map_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 deprecated_map_crosses + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "deprecated_map_crosses", + "SGN::Schema::DeprecatedMapCross", + { "foreign.map_id" => "self.map_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 deprecated_mapdatas + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "deprecated_mapdatas", + "SGN::Schema::DeprecatedMapdata", + { "foreign.map_id" => "self.map_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 fish_results + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "fish_results", + "SGN::Schema::FishResult", + { "foreign.map_id" => "self.map_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 temp_map_correspondences + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "temp_map_correspondences", + "SGN::Schema::TempMapCorrespondence", + { "foreign.old_map_id" => "self.map_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Z0L3rLo7AASYJCb2N7JKKQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/DeprecatedMapCross.pm b/lib/SGN/Schema/DeprecatedMapCross.pm index d420e7a..191de2c 100644 --- a/lib/SGN/Schema/DeprecatedMapCross.pm +++ b/lib/SGN/Schema/DeprecatedMapCross.pm @@ -1,49 +1,107 @@ package SGN::Schema::DeprecatedMapCross; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::DeprecatedMapCross + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("deprecated_map_cross"); + +=head1 ACCESSORS + +=head2 map_cross_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'deprecated_map_cross_map_cross_id_seq' + +=head2 map_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 organism_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=cut + __PACKAGE__->add_columns( "map_cross_id", { - data_type => "integer", - default_value => "nextval('deprecated_map_cross_map_cross_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "deprecated_map_cross_map_cross_id_seq", }, "map_id", { - data_type => "bigint", - default_value => "(0)::bigint", + data_type => "bigint", + default_value => "0)::bigint", is_foreign_key => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, }, "organism_id", { - data_type => "bigint", - default_value => "(0)::bigint", + data_type => "bigint", + default_value => "0)::bigint", is_foreign_key => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, }, ); __PACKAGE__->set_primary_key("map_cross_id"); + +=head1 RELATIONS + +=head2 organism + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "organism", "SGN::Schema::Organism", { organism_id => "organism_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 map + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "map", + "SGN::Schema::DeprecatedMap", + { map_id => "map_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, ); -__PACKAGE__->belongs_to("map", "SGN::Schema::DeprecatedMap", { map_id => "map_id" }); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:LjKtQDgffWt7h7U8ST83Lw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:XLQADezENOFU9cyXWoYgsA # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/DeprecatedMapdata.pm b/lib/SGN/Schema/DeprecatedMapdata.pm index 5caf3a9..cbc9ab7 100644 --- a/lib/SGN/Schema/DeprecatedMapdata.pm +++ b/lib/SGN/Schema/DeprecatedMapdata.pm @@ -1,76 +1,145 @@ package SGN::Schema::DeprecatedMapdata; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::DeprecatedMapdata + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("deprecated_mapdata"); + +=head1 ACCESSORS + +=head2 loc_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'deprecated_mapdata_loc_id_seq' + +=head2 map_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 lg_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 offset + + data_type: 'numeric' + is_nullable: 1 + size: [8,5] + +=head2 loc_type + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 loc_order + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=cut + __PACKAGE__->add_columns( "loc_id", { - data_type => "integer", - default_value => "nextval('deprecated_mapdata_loc_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "deprecated_mapdata_loc_id_seq", }, "map_id", { - data_type => "bigint", - default_value => "(0)::bigint", + data_type => "bigint", + default_value => "0)::bigint", is_foreign_key => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, }, "lg_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "offset", - { - data_type => "numeric", - default_value => undef, - is_nullable => 1, - size => "5,8", - }, + { data_type => "numeric", is_nullable => 1, size => [8, 5] }, "loc_type", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, "loc_order", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, ); __PACKAGE__->set_primary_key("loc_id"); -__PACKAGE__->belongs_to("map", "SGN::Schema::DeprecatedMap", { map_id => "map_id" }); + +=head1 RELATIONS + +=head2 map + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "map", + "SGN::Schema::DeprecatedMap", + { map_id => "map_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 lg + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "lg", "SGN::Schema::DeprecatedLinkageGroup", { lg_id => "lg_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 deprecated_marker_locations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "deprecated_marker_locations", "SGN::Schema::DeprecatedMarkerLocation", { "foreign.loc_id" => "self.loc_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:h90SRjb5LA8LUlGbg0tQqg +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:orOD30Vq4ddEG6GH3KNMSw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/DeprecatedMarker.pm b/lib/SGN/Schema/DeprecatedMarker.pm index 1b25923..721e05e 100644 --- a/lib/SGN/Schema/DeprecatedMarker.pm +++ b/lib/SGN/Schema/DeprecatedMarker.pm @@ -1,62 +1,132 @@ package SGN::Schema::DeprecatedMarker; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::DeprecatedMarker + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("deprecated_markers"); + +=head1 ACCESSORS + +=head2 marker_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'deprecated_markers_marker_id_seq' + +=head2 marker_type + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 marker_name + + data_type: 'varchar' + default_value: (empty string) + is_nullable: 0 + size: 32 + +=cut + __PACKAGE__->add_columns( "marker_id", { - data_type => "integer", - default_value => "nextval('deprecated_markers_marker_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "deprecated_markers_marker_id_seq", }, "marker_type", { - data_type => "bigint", - default_value => "(0)::bigint", + data_type => "bigint", + default_value => "0)::bigint", is_foreign_key => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, }, "marker_name", - { - data_type => "character varying", - default_value => "''::character varying", - is_nullable => 0, - size => 32, - }, + { data_type => "varchar", default_value => "", is_nullable => 0, size => 32 }, ); __PACKAGE__->set_primary_key("marker_id"); + +=head1 RELATIONS + +=head2 deprecated_marker_locations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "deprecated_marker_locations", "SGN::Schema::DeprecatedMarkerLocation", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 marker_type + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "marker_type", "SGN::Schema::DeprecatedMarkerType", { marker_type_id => "marker_type" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, ); + +=head2 markers_derived_from + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "marker_derived_froms", + "markers_derived_from", "SGN::Schema::MarkerDerivedFrom", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 temp_marker_correspondences + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "temp_marker_correspondences", "SGN::Schema::TempMarkerCorrespondence", { "foreign.old_marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:iq+mw1tzL17MWwDwqZaCIQ +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:ajQ/yk/MajjbX4Bw+pLvrw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/DeprecatedMarkerConfidence.pm b/lib/SGN/Schema/DeprecatedMarkerConfidence.pm index fe73b69..c57861a 100644 --- a/lib/SGN/Schema/DeprecatedMarkerConfidence.pm +++ b/lib/SGN/Schema/DeprecatedMarkerConfidence.pm @@ -1,47 +1,95 @@ package SGN::Schema::DeprecatedMarkerConfidence; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::DeprecatedMarkerConfidence + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("deprecated_marker_confidences"); + +=head1 ACCESSORS + +=head2 confidence_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'deprecated_marker_confidences_confidence_id_seq' + +=head2 confidence_name + + data_type: 'varchar' + is_nullable: 1 + size: 16 + +=head2 legacy_conf_id + + data_type: 'bigint' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "confidence_id", { - data_type => "integer", - default_value => "nextval('deprecated_marker_confidences_confidence_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "deprecated_marker_confidences_confidence_id_seq", }, "confidence_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 16, - }, + { data_type => "varchar", is_nullable => 1, size => 16 }, "legacy_conf_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("confidence_id"); __PACKAGE__->add_unique_constraint("legacy_conf_id_unique", ["legacy_conf_id"]); + +=head1 RELATIONS + +=head2 deprecated_marker_locations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "deprecated_marker_locations", "SGN::Schema::DeprecatedMarkerLocation", { "foreign.confidence" => "self.legacy_conf_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 map_versions + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "map_versions", "SGN::Schema::MapVersion", { "foreign.default_threshold" => "self.confidence_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:IawmsThhrP8yotxukwjC5A +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:jVtQOSMFK+hZZ3sajdmzqA # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/DeprecatedMarkerLocation.pm b/lib/SGN/Schema/DeprecatedMarkerLocation.pm index e70ac03..b01e565 100644 --- a/lib/SGN/Schema/DeprecatedMarkerLocation.pm +++ b/lib/SGN/Schema/DeprecatedMarkerLocation.pm @@ -1,87 +1,160 @@ package SGN::Schema::DeprecatedMarkerLocation; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::DeprecatedMarkerLocation + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("deprecated_marker_locations"); + +=head1 ACCESSORS + +=head2 marker_location_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'deprecated_marker_locations_marker_location_id_seq' + +=head2 marker_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 loc_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 confidence + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 order_in_loc + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 location_subscript + + data_type: 'char' + is_nullable: 1 + size: 2 + +=head2 mapmaker_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=cut + __PACKAGE__->add_columns( "marker_location_id", { - data_type => "integer", - default_value => "nextval('deprecated_marker_locations_marker_location_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "deprecated_marker_locations_marker_location_id_seq", }, "marker_id", { - data_type => "bigint", - default_value => "(0)::bigint", + data_type => "bigint", + default_value => "0)::bigint", is_foreign_key => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, }, "loc_id", { - data_type => "bigint", - default_value => "(0)::bigint", + data_type => "bigint", + default_value => "0)::bigint", is_foreign_key => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, }, "confidence", { - data_type => "bigint", - default_value => "(0)::bigint", + data_type => "bigint", + default_value => "0)::bigint", is_foreign_key => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, }, "order_in_loc", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, "location_subscript", - { - data_type => "character", - default_value => undef, - is_nullable => 1, - size => 2, - }, + { data_type => "char", is_nullable => 1, size => 2 }, "mapmaker_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, ); __PACKAGE__->set_primary_key("marker_location_id"); + +=head1 RELATIONS + +=head2 loc + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "loc", "SGN::Schema::DeprecatedMapdata", { loc_id => "loc_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, ); + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "marker", "SGN::Schema::DeprecatedMarker", { marker_id => "marker_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, ); + +=head2 confidence + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "confidence", "SGN::Schema::DeprecatedMarkerConfidence", { legacy_conf_id => "confidence" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:E10c2r+ogjGVYXh/P5MTZQ +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:9egEjMuXtTqa46MzDYvChg # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/DeprecatedMarkerType.pm b/lib/SGN/Schema/DeprecatedMarkerType.pm index 7ce81f6..2de7ffe 100644 --- a/lib/SGN/Schema/DeprecatedMarkerType.pm +++ b/lib/SGN/Schema/DeprecatedMarkerType.pm @@ -1,53 +1,87 @@ package SGN::Schema::DeprecatedMarkerType; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::DeprecatedMarkerType + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("deprecated_marker_types"); + +=head1 ACCESSORS + +=head2 marker_type_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'deprecated_marker_types_marker_type_id_seq' + +=head2 type_name + + data_type: 'varchar' + is_nullable: 1 + size: 32 + +=head2 description + + data_type: 'text' + is_nullable: 1 + +=head2 marker_table + + data_type: 'varchar' + is_nullable: 1 + size: 128 + +=cut + __PACKAGE__->add_columns( "marker_type_id", { - data_type => "integer", - default_value => "nextval('deprecated_marker_types_marker_type_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "deprecated_marker_types_marker_type_id_seq", }, "type_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 32, - }, + { data_type => "varchar", is_nullable => 1, size => 32 }, "description", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "marker_table", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 128, - }, + { data_type => "varchar", is_nullable => 1, size => 128 }, ); __PACKAGE__->set_primary_key("marker_type_id"); + +=head1 RELATIONS + +=head2 deprecated_markers + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "deprecated_markers", "SGN::Schema::DeprecatedMarker", { "foreign.marker_type" => "self.marker_type_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:MEeU2MrFDDFa1DfBsXv6Mw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:32:42 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:QklUU7Zc9A2ghjKSIvJRMw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/DerivedFromSource.pm b/lib/SGN/Schema/DerivedFromSource.pm index 04d3950..ce2c3e2 100644 --- a/lib/SGN/Schema/DerivedFromSource.pm +++ b/lib/SGN/Schema/DerivedFromSource.pm @@ -1,67 +1,99 @@ package SGN::Schema::DerivedFromSource; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::DerivedFromSource + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("derived_from_source"); + +=head1 ACCESSORS + +=head2 derived_from_source_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'derived_from_source_derived_from_source_id_seq' + +=head2 source_name + + accessor: undef + data_type: 'text' + is_nullable: 1 + +=head2 source_schema + + data_type: 'text' + is_nullable: 1 + +=head2 source_table + + data_type: 'text' + is_nullable: 1 + +=head2 source_col + + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "derived_from_source_id", { - data_type => "integer", - default_value => "nextval('derived_from_source_derived_from_source_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "derived_from_source_derived_from_source_id_seq", }, "source_name", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - accessor => 'src_name', - }, + { accessor => undef, data_type => "text", is_nullable => 1 }, "source_schema", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "source_table", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "source_col", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("derived_from_source_id"); __PACKAGE__->add_unique_constraint( "derived_from_source_source_schema_key", ["source_schema", "source_table", "source_col"], ); + +=head1 RELATIONS + +=head2 markers_derived_from + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "marker_derived_froms", + "markers_derived_from", "SGN::Schema::MarkerDerivedFrom", { "foreign.derived_from_source_id" => "self.derived_from_source_id", }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:iO+7Ly1A1UJAl8Me2IPnEg +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:ruLxFFQtkZYBM0p4UbMSJw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Domain.pm b/lib/SGN/Schema/Domain.pm dissimilarity index 60% index 9bac0dc..2a139d4 100644 --- a/lib/SGN/Schema/Domain.pm +++ b/lib/SGN/Schema/Domain.pm @@ -1,74 +1,136 @@ -package SGN::Schema::Domain; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("domain"); -__PACKAGE__->add_columns( - "domain_id", - { - data_type => "bigint", - default_value => "nextval('domain_domain_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 8, - }, - "method_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "domain_accession", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, - "description", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "interpro_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "description_fulltext", - { - data_type => "tsvector", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "dbxref_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "metadata_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, -); -__PACKAGE__->set_primary_key("domain_id"); -__PACKAGE__->belongs_to( - "metadata", - "SGN::Schema::Metadata", - { metadata_id => "metadata_id" }, - { join_type => "LEFT" }, -); -__PACKAGE__->has_many( - "domain_matches", - "SGN::Schema::DomainMatch", - { "foreign.domain_id" => "self.domain_id" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:K5I03ILpPrUzILGjyYY77A - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::Domain; + +# 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 + +SGN::Schema::Domain + +=cut + +__PACKAGE__->table("domain"); + +=head1 ACCESSORS + +=head2 domain_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'domain_domain_id_seq' + +=head2 method_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 domain_accession + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 description + + data_type: 'text' + is_nullable: 1 + +=head2 interpro_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 description_fulltext + + data_type: 'tsvector' + is_nullable: 1 + +=head2 dbxref_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 metadata_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "domain_id", + { + data_type => "bigint", + is_auto_increment => 1, + is_nullable => 0, + sequence => "domain_domain_id_seq", + }, + "method_id", + { data_type => "bigint", is_nullable => 1 }, + "domain_accession", + { data_type => "varchar", is_nullable => 1, size => 20 }, + "description", + { data_type => "text", is_nullable => 1 }, + "interpro_id", + { data_type => "bigint", is_nullable => 1 }, + "description_fulltext", + { data_type => "tsvector", is_nullable => 1 }, + "dbxref_id", + { data_type => "bigint", is_nullable => 1 }, + "metadata_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("domain_id"); + +=head1 RELATIONS + +=head2 metadata + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "metadata", + "SGN::Schema::Metadata", + { metadata_id => "metadata_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 domain_matches + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "domain_matches", + "SGN::Schema::DomainMatch", + { "foreign.domain_id" => "self.domain_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:+6BgaigBWwHVaAw929m+tQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/DomainMatch.pm b/lib/SGN/Schema/DomainMatch.pm dissimilarity index 63% index 8153560..f9daa42 100644 --- a/lib/SGN/Schema/DomainMatch.pm +++ b/lib/SGN/Schema/DomainMatch.pm @@ -1,92 +1,178 @@ -package SGN::Schema::DomainMatch; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("domain_match"); -__PACKAGE__->add_columns( - "domain_match_id", - { - data_type => "bigint", - default_value => "nextval('domain_match_domain_match_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 8, - }, - "cds_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, - "unigene_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "domain_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, - "match_begin", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "match_end", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "e_value", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 10, - }, - "hit_status", - { - data_type => "character", - default_value => undef, - is_nullable => 1, - size => 1, - }, - "run_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "metadata_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, -); -__PACKAGE__->set_primary_key("domain_match_id"); -__PACKAGE__->belongs_to( - "metadata", - "SGN::Schema::Metadata", - { metadata_id => "metadata_id" }, - { join_type => "LEFT" }, -); -__PACKAGE__->belongs_to( - "domain", - "SGN::Schema::Domain", - { domain_id => "domain_id" }, - { join_type => "LEFT" }, -); -__PACKAGE__->belongs_to( - "cd", - "SGN::Schema::Cd", - { cds_id => "cds_id" }, - { join_type => "LEFT" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:LknuRUb+6qXkKJRrgEi5bg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::DomainMatch; + +# 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 + +SGN::Schema::DomainMatch + +=cut + +__PACKAGE__->table("domain_match"); + +=head1 ACCESSORS + +=head2 domain_match_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'domain_match_domain_match_id_seq' + +=head2 cds_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 unigene_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 domain_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 match_begin + + data_type: 'integer' + is_nullable: 1 + +=head2 match_end + + data_type: 'integer' + is_nullable: 1 + +=head2 e_value + + data_type: 'varchar' + is_nullable: 1 + size: 10 + +=head2 hit_status + + data_type: 'char' + is_nullable: 1 + size: 1 + +=head2 run_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 metadata_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "domain_match_id", + { + data_type => "bigint", + is_auto_increment => 1, + is_nullable => 0, + sequence => "domain_match_domain_match_id_seq", + }, + "cds_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "unigene_id", + { data_type => "bigint", is_nullable => 1 }, + "domain_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "match_begin", + { data_type => "integer", is_nullable => 1 }, + "match_end", + { data_type => "integer", is_nullable => 1 }, + "e_value", + { data_type => "varchar", is_nullable => 1, size => 10 }, + "hit_status", + { data_type => "char", is_nullable => 1, size => 1 }, + "run_id", + { data_type => "bigint", is_nullable => 1 }, + "metadata_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("domain_match_id"); + +=head1 RELATIONS + +=head2 metadata + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "metadata", + "SGN::Schema::Metadata", + { metadata_id => "metadata_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 domain + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "domain", + "SGN::Schema::Domain", + { domain_id => "domain_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 cd + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "cd", + "SGN::Schema::Cd", + { cds_id => "cds_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:0wucSV8vE26N2AjTvcBIzw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Enzyme.pm b/lib/SGN/Schema/Enzyme.pm index 0df26ae..a765806 100644 --- a/lib/SGN/Schema/Enzyme.pm +++ b/lib/SGN/Schema/Enzyme.pm @@ -1,40 +1,73 @@ package SGN::Schema::Enzyme; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Enzyme + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("enzymes"); + +=head1 ACCESSORS + +=head2 enzyme_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'enzymes_enzyme_id_seq' + +=head2 enzyme_name + + data_type: 'varchar' + is_nullable: 1 + size: 32 + +=cut + __PACKAGE__->add_columns( "enzyme_id", { - data_type => "integer", - default_value => "nextval('enzymes_enzyme_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "enzymes_enzyme_id_seq", }, "enzyme_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 32, - }, + { data_type => "varchar", is_nullable => 1, size => 32 }, ); __PACKAGE__->set_primary_key("enzyme_id"); __PACKAGE__->add_unique_constraint("enzymes_enzyme_name_key", ["enzyme_name"]); + +=head1 RELATIONS + +=head2 pcr_products + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "pcr_products", "SGN::Schema::PcrProduct", { "foreign.enzyme_id" => "self.enzyme_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:JeQmHKNgqLPrUL0vYl0gRQ +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:7LZeXCaVkuG7Yq8TRquAHw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/EnzymeRestrictionSite.pm b/lib/SGN/Schema/EnzymeRestrictionSite.pm index 695ff74..d945a2e 100644 --- a/lib/SGN/Schema/EnzymeRestrictionSite.pm +++ b/lib/SGN/Schema/EnzymeRestrictionSite.pm @@ -1,36 +1,61 @@ package SGN::Schema::EnzymeRestrictionSite; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::EnzymeRestrictionSite + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("enzyme_restriction_sites"); + +=head1 ACCESSORS + +=head2 enzyme_id + + data_type: 'integer' + is_nullable: 1 + +=head2 restriction_site + + data_type: 'text' + is_nullable: 1 + +=head2 enzyme_restriction_sites_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'enzyme_restriction_sites_enzyme_restriction_sites_id_seq' + +=cut + __PACKAGE__->add_columns( "enzyme_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "restriction_site", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "enzyme_restriction_sites_id", { - data_type => "integer", - default_value => "nextval('enzyme_restriction_sites_enzyme_restriction_sites_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "enzyme_restriction_sites_enzyme_restriction_sites_id_seq", }, ); __PACKAGE__->set_primary_key("enzyme_restriction_sites_id"); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:NCE8PNR5UyuHqK/wsXFMHw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:SYxEfX3A5/LD9KaY5DERug # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Est.pm b/lib/SGN/Schema/Est.pm index 7b0bab6..41400e2 100644 --- a/lib/SGN/Schema/Est.pm +++ b/lib/SGN/Schema/Est.pm @@ -1,96 +1,193 @@ package SGN::Schema::Est; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Est + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("est"); + +=head1 ACCESSORS + +=head2 est_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'est_est_id_seq' + +=head2 read_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 version + + data_type: 'integer' + is_nullable: 1 + +=head2 basecaller + + data_type: 'varchar' + is_nullable: 1 + size: 40 + +=head2 seq + + data_type: 'text' + is_nullable: 1 + +=head2 qscore + + data_type: 'text' + is_nullable: 1 + +=head2 call_positions + + data_type: 'text' + is_nullable: 1 + +=head2 status + + data_type: 'integer' + is_nullable: 1 + +=head2 flags + + data_type: 'bigint' + is_nullable: 1 + +=head2 date + + data_type: 'date' + is_nullable: 1 + +=head2 genbank_submission_date + + data_type: 'date' + is_nullable: 1 + +=head2 genbank_confirmed + + data_type: 'boolean' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "est_id", { - data_type => "integer", - default_value => "nextval('est_est_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "est_est_id_seq", }, "read_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "version", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "basecaller", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 40, - }, + { data_type => "varchar", is_nullable => 1, size => 40 }, "seq", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "qscore", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "call_positions", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "status", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "flags", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "date", - { data_type => "date", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "date", is_nullable => 1 }, "genbank_submission_date", - { data_type => "date", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "date", is_nullable => 1 }, "genbank_confirmed", - { data_type => "boolean", default_value => undef, is_nullable => 1, size => 1 }, + { data_type => "boolean", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("est_id"); + +=head1 RELATIONS + +=head2 read + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "read", "SGN::Schema::Seqread", { read_id => "read_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 est_dbxrefs + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "est_dbxrefs", "SGN::Schema::EstDbxref", { "foreign.est_id" => "self.est_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 qc_report + +Type: might_have + +Related object: L + +=cut + __PACKAGE__->might_have( "qc_report", "SGN::Schema::QcReport", { "foreign.est_id" => "self.est_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 unigene_members + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "unigene_members", "SGN::Schema::UnigeneMember", { "foreign.est_id" => "self.est_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:/9dRnSHAEUwZAT6rU6Fl8Q +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:DeimiLHdVqQ+IoBlB+xxog sub hqi_seq { my ( $self ) = @_; diff --git a/lib/SGN/Schema/EstDbxref.pm b/lib/SGN/Schema/EstDbxref.pm index 94d2e08..ac2d30a 100644 --- a/lib/SGN/Schema/EstDbxref.pm +++ b/lib/SGN/Schema/EstDbxref.pm @@ -1,39 +1,80 @@ package SGN::Schema::EstDbxref; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::EstDbxref + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("est_dbxref"); + +=head1 ACCESSORS + +=head2 est_dbxref_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'est_dbxref_est_dbxref_id_seq' + +=head2 est_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 dbxref_id + + data_type: 'integer' + is_nullable: 0 + +=cut + __PACKAGE__->add_columns( "est_dbxref_id", { - data_type => "integer", - default_value => "nextval('est_dbxref_est_dbxref_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "est_dbxref_est_dbxref_id_seq", }, "est_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, "dbxref_id", - { data_type => "integer", default_value => undef, is_nullable => 0, size => 4 }, + { data_type => "integer", is_nullable => 0 }, ); __PACKAGE__->set_primary_key("est_dbxref_id"); __PACKAGE__->add_unique_constraint("est_dbxref_est_id_key", ["est_id", "dbxref_id"]); -__PACKAGE__->belongs_to("est", "SGN::Schema::Est", { est_id => "est_id" }); + +=head1 RELATIONS + +=head2 est + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "est", + "SGN::Schema::Est", + { est_id => "est_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:KSmD9wFQDRyRFOJbg0Bvfw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:yyhJ86bEnQ+gyZW2jwkD6A # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/EstMappedByClone.pm b/lib/SGN/Schema/EstMappedByClone.pm new file mode 100644 index 0000000..ddd414e --- /dev/null +++ b/lib/SGN/Schema/EstMappedByClone.pm @@ -0,0 +1,85 @@ +package SGN::Schema::EstMappedByClone; + +# 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 + +SGN::Schema::EstMappedByClone + +=cut + +__PACKAGE__->table("ests_mapped_by_clone"); + +=head1 ACCESSORS + +=head2 embc_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'ests_mapped_by_clone_embc_id_seq' + +=head2 marker_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 clone_id + + data_type: 'bigint' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "embc_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "ests_mapped_by_clone_embc_id_seq", + }, + "marker_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "clone_id", + { data_type => "bigint", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("embc_id"); + +=head1 RELATIONS + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:PC0s36N6gQ0VsLP00ZBreQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/ExperimentType.pm b/lib/SGN/Schema/ExperimentType.pm index 2fa0387..7650c79 100644 --- a/lib/SGN/Schema/ExperimentType.pm +++ b/lib/SGN/Schema/ExperimentType.pm @@ -1,46 +1,79 @@ package SGN::Schema::ExperimentType; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::ExperimentType + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("experiment_type"); + +=head1 ACCESSORS + +=head2 experiment_type_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'experiment_type_experiment_type_id_seq' + +=head2 name + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 description + + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "experiment_type_id", { - data_type => "bigint", - default_value => "nextval('experiment_type_experiment_type_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "experiment_type_experiment_type_id_seq", }, "name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, + { data_type => "varchar", is_nullable => 1, size => 255 }, "description", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("experiment_type_id"); + +=head1 RELATIONS + +=head2 pcr_experiments + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "pcr_experiments", "SGN::Schema::PcrExperiment", { "foreign.experiment_type_id" => "self.experiment_type_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:dTcoOxFqZW86L0MPWpZ3uA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:M6VKiqWKu+9a/dtKynIa4Q # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Facility.pm b/lib/SGN/Schema/Facility.pm dissimilarity index 71% index c5a36bb..17e67b2 100644 --- a/lib/SGN/Schema/Facility.pm +++ b/lib/SGN/Schema/Facility.pm @@ -1,114 +1,164 @@ -package SGN::Schema::Facility; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("facility"); -__PACKAGE__->add_columns( - "facility_id", - { - data_type => "integer", - default_value => "nextval('facility_facility_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "submit_user_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "facility_moniker", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, - "facility_shortname", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 12, - }, - "facility_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "facility_contact", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "facility_address", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "funding_agency", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "funding_comment", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "sequencing_primers", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "machine", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 40, - }, - "chemistry", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 40, - }, - "attribution_display", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "sp_person_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, -); -__PACKAGE__->set_primary_key("facility_id"); -__PACKAGE__->has_many( - "seqreads", - "SGN::Schema::Seqread", - { "foreign.facility_id" => "self.facility_id" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:T/2zUyjpP6CvfX69ixSiuQ - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::Facility; + +# 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 + +SGN::Schema::Facility + +=cut + +__PACKAGE__->table("facility"); + +=head1 ACCESSORS + +=head2 facility_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'facility_facility_id_seq' + +=head2 submit_user_id + + data_type: 'integer' + is_nullable: 1 + +=head2 facility_moniker + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 facility_shortname + + data_type: 'varchar' + is_nullable: 1 + size: 12 + +=head2 facility_name + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 facility_contact + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 facility_address + + data_type: 'text' + is_nullable: 1 + +=head2 funding_agency + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 funding_comment + + data_type: 'text' + is_nullable: 1 + +=head2 sequencing_primers + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 machine + + data_type: 'varchar' + is_nullable: 1 + size: 40 + +=head2 chemistry + + data_type: 'varchar' + is_nullable: 1 + size: 40 + +=head2 attribution_display + + data_type: 'text' + is_nullable: 1 + +=head2 sp_person_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "facility_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "facility_facility_id_seq", + }, + "submit_user_id", + { data_type => "integer", is_nullable => 1 }, + "facility_moniker", + { data_type => "varchar", is_nullable => 1, size => 20 }, + "facility_shortname", + { data_type => "varchar", is_nullable => 1, size => 12 }, + "facility_name", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "facility_contact", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "facility_address", + { data_type => "text", is_nullable => 1 }, + "funding_agency", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "funding_comment", + { data_type => "text", is_nullable => 1 }, + "sequencing_primers", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "machine", + { data_type => "varchar", is_nullable => 1, size => 40 }, + "chemistry", + { data_type => "varchar", is_nullable => 1, size => 40 }, + "attribution_display", + { data_type => "text", is_nullable => 1 }, + "sp_person_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("facility_id"); + +=head1 RELATIONS + +=head2 seqreads + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "seqreads", + "SGN::Schema::Seqread", + { "foreign.facility_id" => "self.facility_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:XLirPpQidO8sVoh61D2sjg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Family.pm b/lib/SGN/Schema/Family.pm index d047516..e4602ca 100644 --- a/lib/SGN/Schema/Family.pm +++ b/lib/SGN/Schema/Family.pm @@ -1,80 +1,166 @@ package SGN::Schema::Family; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Family + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("family"); + +=head1 ACCESSORS + +=head2 family_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'family_family_id_seq' + +=head2 family_build_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 family_annotation + + data_type: 'text' + is_nullable: 1 + +=head2 tree_log_file_location + + data_type: 'text' + is_nullable: 1 + original: {data_type => "varchar"} + +=head2 tree_file_location + + data_type: 'text' + is_nullable: 1 + original: {data_type => "varchar"} + +=head2 tree_taxa_number + + data_type: 'integer' + is_nullable: 1 + +=head2 tree_overlap_length + + data_type: 'integer' + is_nullable: 1 + +=head2 family_nr + + data_type: 'integer' + is_nullable: 1 + +=head2 member_count + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "family_id", { - data_type => "bigint", - default_value => "nextval('family_family_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "family_family_id_seq", }, "family_build_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "family_annotation", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "tree_log_file_location", { - data_type => "character varying", - default_value => undef, + data_type => "text", is_nullable => 1, - size => undef, + original => { data_type => "varchar" }, }, "tree_file_location", { - data_type => "character varying", - default_value => undef, + data_type => "text", is_nullable => 1, - size => undef, + original => { data_type => "varchar" }, }, "tree_taxa_number", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "tree_overlap_length", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "family_nr", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "member_count", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("family_id"); + +=head1 RELATIONS + +=head2 family_build + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "family_build", "SGN::Schema::FamilyBuild", { family_build_id => "family_build_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 family_members + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "family_members", "SGN::Schema::FamilyMember", { "foreign.family_id" => "self.family_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 family_trees + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "family_trees", "SGN::Schema::FamilyTree", { "foreign.family_id" => "self.family_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:rkeY5UCmUyMW1xuxxozDAA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:b0V0phWXlABHu1CSjK8XfA # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/FamilyBuild.pm b/lib/SGN/Schema/FamilyBuild.pm dissimilarity index 62% index d362337..3d19483 100644 --- a/lib/SGN/Schema/FamilyBuild.pm +++ b/lib/SGN/Schema/FamilyBuild.pm @@ -1,58 +1,107 @@ -package SGN::Schema::FamilyBuild; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("family_build"); -__PACKAGE__->add_columns( - "family_build_id", - { - data_type => "bigint", - default_value => "nextval('family_build_family_build_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 8, - }, - "group_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "build_nr", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "i_value", - { - data_type => "double precision", - default_value => undef, - is_nullable => 1, - size => 8, - }, - "build_date", - { - data_type => "timestamp without time zone", - default_value => "('now'::text)::timestamp(6) with time zone", - is_nullable => 0, - size => 8, - }, - "status", - { - data_type => "character", - default_value => "'C'::bpchar", - is_nullable => 1, - size => 1, - }, -); -__PACKAGE__->set_primary_key("family_build_id"); -__PACKAGE__->has_many( - "families", - "SGN::Schema::Family", - { "foreign.family_build_id" => "self.family_build_id" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:7wifZAmGXzBAUd7SfYY/ag - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::FamilyBuild; + +# 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 + +SGN::Schema::FamilyBuild + +=cut + +__PACKAGE__->table("family_build"); + +=head1 ACCESSORS + +=head2 family_build_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'family_build_family_build_id_seq' + +=head2 group_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 build_nr + + data_type: 'bigint' + is_nullable: 1 + +=head2 i_value + + data_type: 'double precision' + is_nullable: 1 + +=head2 build_date + + data_type: 'timestamp' + default_value: ('now'::text)::timestamp(6) with time zone + is_nullable: 0 + +=head2 status + + data_type: 'char' + default_value: 'C' + is_nullable: 1 + size: 1 + +=cut + +__PACKAGE__->add_columns( + "family_build_id", + { + data_type => "bigint", + is_auto_increment => 1, + is_nullable => 0, + sequence => "family_build_family_build_id_seq", + }, + "group_id", + { data_type => "bigint", is_nullable => 1 }, + "build_nr", + { data_type => "bigint", is_nullable => 1 }, + "i_value", + { data_type => "double precision", is_nullable => 1 }, + "build_date", + { + data_type => "timestamp", + default_value => \"('now'::text)::timestamp(6) with time zone", + is_nullable => 0, + }, + "status", + { data_type => "char", default_value => "C", is_nullable => 1, size => 1 }, +); +__PACKAGE__->set_primary_key("family_build_id"); + +=head1 RELATIONS + +=head2 families + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "families", + "SGN::Schema::Family", + { "foreign.family_build_id" => "self.family_build_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:QaGnsmu4vvcnLGzPzibWjg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/FamilyMember.pm b/lib/SGN/Schema/FamilyMember.pm dissimilarity index 64% index e948149..6ae2582 100644 --- a/lib/SGN/Schema/FamilyMember.pm +++ b/lib/SGN/Schema/FamilyMember.pm @@ -1,67 +1,115 @@ -package SGN::Schema::FamilyMember; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("family_member"); -__PACKAGE__->add_columns( - "family_member_id", - { - data_type => "bigint", - default_value => "nextval('family_member_family_member_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 8, - }, - "cds_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "organism_group_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "family_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, - "database_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, - "sequence_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 50, - }, - "alignment_seq", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("family_member_id"); -__PACKAGE__->belongs_to( - "family", - "SGN::Schema::Family", - { family_id => "family_id" }, - { join_type => "LEFT" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:/Pw0xdFCdtj0+afRDX811Q - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::FamilyMember; + +# 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 + +SGN::Schema::FamilyMember + +=cut + +__PACKAGE__->table("family_member"); + +=head1 ACCESSORS + +=head2 family_member_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'family_member_family_member_id_seq' + +=head2 cds_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 organism_group_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 family_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 database_name + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 sequence_name + + data_type: 'varchar' + is_nullable: 1 + size: 50 + +=head2 alignment_seq + + data_type: 'text' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "family_member_id", + { + data_type => "bigint", + is_auto_increment => 1, + is_nullable => 0, + sequence => "family_member_family_member_id_seq", + }, + "cds_id", + { data_type => "bigint", is_nullable => 1 }, + "organism_group_id", + { data_type => "bigint", is_nullable => 1 }, + "family_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "database_name", + { data_type => "varchar", is_nullable => 1, size => 20 }, + "sequence_name", + { data_type => "varchar", is_nullable => 1, size => 50 }, + "alignment_seq", + { data_type => "text", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("family_member_id"); + +=head1 RELATIONS + +=head2 family + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "family", + "SGN::Schema::Family", + { family_id => "family_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:EwK2XAL/yXMUV8rOpDh0VA + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/FamilyTree.pm b/lib/SGN/Schema/FamilyTree.pm dissimilarity index 64% index ab6bac8..9918f78 100644 --- a/lib/SGN/Schema/FamilyTree.pm +++ b/lib/SGN/Schema/FamilyTree.pm @@ -1,53 +1,104 @@ -package SGN::Schema::FamilyTree; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("family_tree"); -__PACKAGE__->add_columns( - "family_tree_id", - { - data_type => "integer", - default_value => "nextval('family_tree_family_tree_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "family_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, - "tree_nr", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "newick_cds", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "newick_unigene", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("family_tree_id"); -__PACKAGE__->belongs_to("family", "SGN::Schema::Family", { family_id => "family_id" }); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:96Pb3uKjjqxmmtCCzval2Q - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::FamilyTree; + +# 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 + +SGN::Schema::FamilyTree + +=cut + +__PACKAGE__->table("family_tree"); + +=head1 ACCESSORS + +=head2 family_tree_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'family_tree_family_tree_id_seq' + +=head2 family_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 tree_nr + + data_type: 'integer' + is_nullable: 1 + +=head2 newick_cds + + data_type: 'text' + is_nullable: 1 + original: {data_type => "varchar"} + +=head2 newick_unigene + + data_type: 'text' + is_nullable: 1 + original: {data_type => "varchar"} + +=cut + +__PACKAGE__->add_columns( + "family_tree_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "family_tree_family_tree_id_seq", + }, + "family_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, + "tree_nr", + { data_type => "integer", is_nullable => 1 }, + "newick_cds", + { + data_type => "text", + is_nullable => 1, + original => { data_type => "varchar" }, + }, + "newick_unigene", + { + data_type => "text", + is_nullable => 1, + original => { data_type => "varchar" }, + }, +); +__PACKAGE__->set_primary_key("family_tree_id"); + +=head1 RELATIONS + +=head2 family + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "family", + "SGN::Schema::Family", + { family_id => "family_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:olyNyjmYqt3GuL+Ry+I+qg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/FishChromatinDensityConstant.pm b/lib/SGN/Schema/FishChromatinDensityConstant.pm index 5a47a71..54bfe10 100644 --- a/lib/SGN/Schema/FishChromatinDensityConstant.pm +++ b/lib/SGN/Schema/FishChromatinDensityConstant.pm @@ -1,28 +1,49 @@ package SGN::Schema::FishChromatinDensityConstant; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::FishChromatinDensityConstant + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("fish_chromatin_density_constants"); + +=head1 ACCESSORS + +=head2 arm + + data_type: 'varchar' + default_value: 'E' + is_nullable: 0 + size: 1 + +=head2 density + + data_type: 'real' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "arm", - { - data_type => "character varying", - default_value => "'E'::character varying", - is_nullable => 0, - size => 1, - }, + { data_type => "varchar", default_value => "E", is_nullable => 0, size => 1 }, "density", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "real", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("arm"); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:dVbgqT3zCORAdxZMrBfn9g +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:ACCZqFUM8p3nR/j4MmmhqA # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/FishExperimenter.pm b/lib/SGN/Schema/FishExperimenter.pm index 2aafff8..b286167 100644 --- a/lib/SGN/Schema/FishExperimenter.pm +++ b/lib/SGN/Schema/FishExperimenter.pm @@ -1,40 +1,73 @@ package SGN::Schema::FishExperimenter; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::FishExperimenter + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("fish_experimenter"); + +=head1 ACCESSORS + +=head2 fish_experimenter_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'fish_experimenter_fish_experimenter_id_seq' + +=head2 fish_experimenter_name + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=cut + __PACKAGE__->add_columns( "fish_experimenter_id", { - data_type => "integer", - default_value => "nextval('fish_experimenter_fish_experimenter_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "fish_experimenter_fish_experimenter_id_seq", }, "fish_experimenter_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, + { data_type => "varchar", is_nullable => 1, size => 20 }, ); __PACKAGE__->set_primary_key("fish_experimenter_id"); __PACKAGE__->add_unique_constraint("fish_expermenter_name_uniq", ["fish_experimenter_name"]); + +=head1 RELATIONS + +=head2 fish_results + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "fish_results", "SGN::Schema::FishResult", { "foreign.fish_experimenter_id" => "self.fish_experimenter_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:ocoSQMPPyQCzpoTisbvC0g +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:HqAPxapG9dVDcUi2WIPIWA # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/FishFile.pm b/lib/SGN/Schema/FishFile.pm dissimilarity index 61% index b667f86..dd4ca93 100644 --- a/lib/SGN/Schema/FishFile.pm +++ b/lib/SGN/Schema/FishFile.pm @@ -1,42 +1,64 @@ -package SGN::Schema::FishFile; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("fish_file"); -__PACKAGE__->add_columns( - "fish_file_id", - { - data_type => "bigint", - default_value => "nextval('fish_file_fish_file_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 8, - }, - "filename", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "fish_result_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, -); -__PACKAGE__->set_primary_key("fish_file_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:r8PqTUqIYaUIWKv0E6nrVQ - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::FishFile; + +# 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 + +SGN::Schema::FishFile + +=cut + +__PACKAGE__->table("fish_file"); + +=head1 ACCESSORS + +=head2 fish_file_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'fish_file_fish_file_id_seq' + +=head2 filename + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 fish_result_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=cut + +__PACKAGE__->add_columns( + "fish_file_id", + { + data_type => "bigint", + is_auto_increment => 1, + is_nullable => 0, + sequence => "fish_file_fish_file_id_seq", + }, + "filename", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "fish_result_id", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, +); +__PACKAGE__->set_primary_key("fish_file_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:wFX+WY6+MP6TSA2Sh9nboA + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/FishImage.pm b/lib/SGN/Schema/FishImage.pm index 39aecb1..23ee0f6 100644 --- a/lib/SGN/Schema/FishImage.pm +++ b/lib/SGN/Schema/FishImage.pm @@ -1,30 +1,57 @@ package SGN::Schema::FishImage; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::FishImage + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("fish_image"); + +=head1 ACCESSORS + +=head2 fish_image_id + + data_type: 'integer' + default_value: 0 + is_nullable: 0 + +=head2 filename + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 fish_result_id + + data_type: 'integer' + default_value: 0 + is_nullable: 0 + +=cut + __PACKAGE__->add_columns( "fish_image_id", - { data_type => "integer", default_value => 0, is_nullable => 0, size => 4 }, + { data_type => "integer", default_value => 0, is_nullable => 0 }, "filename", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, + { data_type => "varchar", is_nullable => 1, size => 255 }, "fish_result_id", - { data_type => "integer", default_value => 0, is_nullable => 0, size => 4 }, + { data_type => "integer", default_value => 0, is_nullable => 0 }, ); __PACKAGE__->set_primary_key("fish_image_id"); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Ouk79KO/gIA1Lu8jVnGk9Q +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:xu/8TWncnO9lYh3PlaG8Iw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/FishKaryotypeConstant.pm b/lib/SGN/Schema/FishKaryotypeConstant.pm dissimilarity index 64% index 32a0c75..f00fca6 100644 --- a/lib/SGN/Schema/FishKaryotypeConstant.pm +++ b/lib/SGN/Schema/FishKaryotypeConstant.pm @@ -1,57 +1,79 @@ -package SGN::Schema::FishKaryotypeConstant; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("fish_karyotype_constants"); -__PACKAGE__->add_columns( - "fish_experimenter_id", - { data_type => "integer", default_value => undef, is_nullable => 0, size => 4 }, - "chromo_num", - { - data_type => "smallint", - default_value => undef, - is_nullable => 0, - size => 2, - }, - "chromo_arm", - { - data_type => "text", - default_value => undef, - is_nullable => 0, - size => undef, - }, - "arm_length", - { - data_type => "numeric", - default_value => undef, - is_nullable => 0, - size => "2,5", - }, - "arm_eu_length", - { - data_type => "numeric", - default_value => undef, - is_nullable => 0, - size => "2,5", - }, - "arm_het_length", - { - data_type => "numeric", - default_value => undef, - is_nullable => 0, - size => "2,5", - }, -); -__PACKAGE__->set_primary_key("fish_experimenter_id", "chromo_num", "chromo_arm"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:ttvFJoD3qnIp1c2pkWH+vQ - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::FishKaryotypeConstant; + +# 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 + +SGN::Schema::FishKaryotypeConstant + +=cut + +__PACKAGE__->table("fish_karyotype_constants"); + +=head1 ACCESSORS + +=head2 fish_experimenter_id + + data_type: 'integer' + is_nullable: 0 + +=head2 chromo_num + + data_type: 'smallint' + is_nullable: 0 + +=head2 chromo_arm + + data_type: 'text' + is_nullable: 0 + +=head2 arm_length + + data_type: 'numeric' + is_nullable: 0 + size: [5,2] + +=head2 arm_eu_length + + data_type: 'numeric' + is_nullable: 0 + size: [5,2] + +=head2 arm_het_length + + data_type: 'numeric' + is_nullable: 0 + size: [5,2] + +=cut + +__PACKAGE__->add_columns( + "fish_experimenter_id", + { data_type => "integer", is_nullable => 0 }, + "chromo_num", + { data_type => "smallint", is_nullable => 0 }, + "chromo_arm", + { data_type => "text", is_nullable => 0 }, + "arm_length", + { data_type => "numeric", is_nullable => 0, size => [5, 2] }, + "arm_eu_length", + { data_type => "numeric", is_nullable => 0, size => [5, 2] }, + "arm_het_length", + { data_type => "numeric", is_nullable => 0, size => [5, 2] }, +); +__PACKAGE__->set_primary_key("fish_experimenter_id", "chromo_num", "chromo_arm"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:YQHAN1Jx5OvUQ6YPNWTlnQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/FishKaryotypeConstantsOld.pm b/lib/SGN/Schema/FishKaryotypeConstantsOld.pm dissimilarity index 65% index 14e455a..f14996a 100644 --- a/lib/SGN/Schema/FishKaryotypeConstantsOld.pm +++ b/lib/SGN/Schema/FishKaryotypeConstantsOld.pm @@ -1,43 +1,102 @@ -package SGN::Schema::FishKaryotypeConstantsOld; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("fish_karyotype_constants_old"); -__PACKAGE__->add_columns( - "chromo_num", - { - data_type => "smallint", - default_value => "(0)::smallint", - is_nullable => 0, - size => 2, - }, - "chromo_length", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "chromo_arm_ratio", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "short_arm_length", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "short_arm_eu_length", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "short_arm_het_length", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "long_arm_length", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "long_arm_eu_length", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "long_arm_het_length", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, -); -__PACKAGE__->set_primary_key("chromo_num"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:WfE8usSbJsTs11/oxc5Ajg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::FishKaryotypeConstantsOld; + +# 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 + +SGN::Schema::FishKaryotypeConstantsOld + +=cut + +__PACKAGE__->table("fish_karyotype_constants_old"); + +=head1 ACCESSORS + +=head2 chromo_num + + data_type: 'smallint' + default_value: '0)::smallint' + is_nullable: 0 + +=head2 chromo_length + + data_type: 'real' + is_nullable: 1 + +=head2 chromo_arm_ratio + + data_type: 'real' + is_nullable: 1 + +=head2 short_arm_length + + data_type: 'real' + is_nullable: 1 + +=head2 short_arm_eu_length + + data_type: 'real' + is_nullable: 1 + +=head2 short_arm_het_length + + data_type: 'real' + is_nullable: 1 + +=head2 long_arm_length + + data_type: 'real' + is_nullable: 1 + +=head2 long_arm_eu_length + + data_type: 'real' + is_nullable: 1 + +=head2 long_arm_het_length + + data_type: 'real' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "chromo_num", + { + data_type => "smallint", + default_value => "0)::smallint", + is_nullable => 0, + }, + "chromo_length", + { data_type => "real", is_nullable => 1 }, + "chromo_arm_ratio", + { data_type => "real", is_nullable => 1 }, + "short_arm_length", + { data_type => "real", is_nullable => 1 }, + "short_arm_eu_length", + { data_type => "real", is_nullable => 1 }, + "short_arm_het_length", + { data_type => "real", is_nullable => 1 }, + "long_arm_length", + { data_type => "real", is_nullable => 1 }, + "long_arm_eu_length", + { data_type => "real", is_nullable => 1 }, + "long_arm_het_length", + { data_type => "real", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("chromo_num"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:MWu9so2oKdhOIqWNeg9h0g + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/FishResult.pm b/lib/SGN/Schema/FishResult.pm dissimilarity index 63% index ded702f..07abdc4 100644 --- a/lib/SGN/Schema/FishResult.pm +++ b/lib/SGN/Schema/FishResult.pm @@ -1,88 +1,167 @@ -package SGN::Schema::FishResult; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("fish_result"); -__PACKAGE__->add_columns( - "fish_result_id", - { - data_type => "bigint", - default_value => "nextval('fish_result_fish_result_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 8, - }, - "map_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 8, - }, - "fish_experimenter_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, - "experiment_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 0, - size => 10, - }, - "clone_id", - { data_type => "bigint", default_value => undef, is_nullable => 0, size => 8 }, - "chromo_num", - { - data_type => "smallint", - default_value => undef, - is_nullable => 0, - size => 2, - }, - "chromo_arm", - { - data_type => "character varying", - default_value => undef, - is_nullable => 0, - size => 1, - }, - "percent_from_centromere", - { data_type => "real", default_value => undef, is_nullable => 0, size => 4 }, - "experiment_group", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 12, - }, - "attribution_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, -); -__PACKAGE__->set_primary_key("fish_result_id"); -__PACKAGE__->add_unique_constraint( - "fish_result_fish_experimenter_clone_id_experiment_name", - ["fish_experimenter_id", "clone_id", "experiment_name"], -); -__PACKAGE__->belongs_to( - "fish_experimenter", - "SGN::Schema::FishExperimenter", - { fish_experimenter_id => "fish_experimenter_id" }, -); -__PACKAGE__->belongs_to("map", "SGN::Schema::DeprecatedMap", { map_id => "map_id" }); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:u6gmDcAvOElivbc5PM6u9A - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::FishResult; + +# 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 + +SGN::Schema::FishResult + +=cut + +__PACKAGE__->table("fish_result"); + +=head1 ACCESSORS + +=head2 fish_result_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'fish_result_fish_result_id_seq' + +=head2 map_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 fish_experimenter_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 experiment_name + + data_type: 'varchar' + is_nullable: 0 + size: 10 + +=head2 clone_id + + data_type: 'bigint' + is_nullable: 0 + +=head2 chromo_num + + data_type: 'smallint' + is_nullable: 0 + +=head2 chromo_arm + + data_type: 'varchar' + is_nullable: 0 + size: 1 + +=head2 percent_from_centromere + + data_type: 'real' + is_nullable: 0 + +=head2 experiment_group + + data_type: 'varchar' + is_nullable: 1 + size: 12 + +=head2 attribution_id + + data_type: 'bigint' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "fish_result_id", + { + data_type => "bigint", + is_auto_increment => 1, + is_nullable => 0, + sequence => "fish_result_fish_result_id_seq", + }, + "map_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 }, + "fish_experimenter_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, + "experiment_name", + { data_type => "varchar", is_nullable => 0, size => 10 }, + "clone_id", + { data_type => "bigint", is_nullable => 0 }, + "chromo_num", + { data_type => "smallint", is_nullable => 0 }, + "chromo_arm", + { data_type => "varchar", is_nullable => 0, size => 1 }, + "percent_from_centromere", + { data_type => "real", is_nullable => 0 }, + "experiment_group", + { data_type => "varchar", is_nullable => 1, size => 12 }, + "attribution_id", + { data_type => "bigint", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("fish_result_id"); +__PACKAGE__->add_unique_constraint( + "fish_result_fish_experimenter_clone_id_experiment_name", + ["fish_experimenter_id", "clone_id", "experiment_name"], +); + +=head1 RELATIONS + +=head2 fish_experimenter + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "fish_experimenter", + "SGN::Schema::FishExperimenter", + { fish_experimenter_id => "fish_experimenter_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 map + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "map", + "SGN::Schema::DeprecatedMap", + { map_id => "map_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 fish_result_images + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "fish_result_images", + "SGN::Schema::FishResultImage", + { "foreign.fish_result_id" => "self.fish_result_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:3Qs/Qm/jdBZo2BRoSH9EGg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/FishResultComposite.pm b/lib/SGN/Schema/FishResultComposite.pm dissimilarity index 73% index 47a4b38..4b5b6b2 100644 --- a/lib/SGN/Schema/FishResultComposite.pm +++ b/lib/SGN/Schema/FishResultComposite.pm @@ -1,97 +1,160 @@ -package SGN::Schema::FishResultComposite; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("fish_result_composite"); -__PACKAGE__->add_columns( - "fish_result_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, - "map_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, - "fish_experimenter_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "experiment_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 10, - }, - "clone_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, - "chromo_num", - { - data_type => "smallint", - default_value => "(0)::smallint", - is_nullable => 0, - size => 2, - }, - "chromo_arm", - { - data_type => "character varying", - default_value => "'P'::character varying", - is_nullable => 0, - size => 1, - }, - "percent_from_centromere", - { - data_type => "real", - default_value => "(0)::real", - is_nullable => 0, - size => 4, - }, - "het_or_eu", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 1, - }, - "um_from_centromere", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "um_from_arm_end", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "um_from_arm_border", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "mbp_from_arm_end", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "mbp_from_centromere", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "mbp_from_arm_border", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "experiment_group", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 12, - }, -); -__PACKAGE__->set_primary_key("fish_result_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Dqjpbir9VTv1xIIPs8nYkw - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::FishResultComposite; + +# 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 + +SGN::Schema::FishResultComposite + +=cut + +__PACKAGE__->table("fish_result_composite"); + +=head1 ACCESSORS + +=head2 fish_result_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 map_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 fish_experimenter_id + + data_type: 'integer' + is_nullable: 1 + +=head2 experiment_name + + data_type: 'varchar' + is_nullable: 1 + size: 10 + +=head2 clone_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 chromo_num + + data_type: 'smallint' + default_value: '0)::smallint' + is_nullable: 0 + +=head2 chromo_arm + + data_type: 'varchar' + default_value: 'P' + is_nullable: 0 + size: 1 + +=head2 percent_from_centromere + + data_type: 'real' + default_value: '0)::real' + is_nullable: 0 + +=head2 het_or_eu + + data_type: 'varchar' + is_nullable: 1 + size: 1 + +=head2 um_from_centromere + + data_type: 'real' + is_nullable: 1 + +=head2 um_from_arm_end + + data_type: 'real' + is_nullable: 1 + +=head2 um_from_arm_border + + data_type: 'real' + is_nullable: 1 + +=head2 mbp_from_arm_end + + data_type: 'real' + is_nullable: 1 + +=head2 mbp_from_centromere + + data_type: 'real' + is_nullable: 1 + +=head2 mbp_from_arm_border + + data_type: 'real' + is_nullable: 1 + +=head2 experiment_group + + data_type: 'varchar' + is_nullable: 1 + size: 12 + +=cut + +__PACKAGE__->add_columns( + "fish_result_id", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "map_id", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "fish_experimenter_id", + { data_type => "integer", is_nullable => 1 }, + "experiment_name", + { data_type => "varchar", is_nullable => 1, size => 10 }, + "clone_id", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "chromo_num", + { + data_type => "smallint", + default_value => "0)::smallint", + is_nullable => 0, + }, + "chromo_arm", + { data_type => "varchar", default_value => "P", is_nullable => 0, size => 1 }, + "percent_from_centromere", + { data_type => "real", default_value => "0)::real", is_nullable => 0 }, + "het_or_eu", + { data_type => "varchar", is_nullable => 1, size => 1 }, + "um_from_centromere", + { data_type => "real", is_nullable => 1 }, + "um_from_arm_end", + { data_type => "real", is_nullable => 1 }, + "um_from_arm_border", + { data_type => "real", is_nullable => 1 }, + "mbp_from_arm_end", + { data_type => "real", is_nullable => 1 }, + "mbp_from_centromere", + { data_type => "real", is_nullable => 1 }, + "mbp_from_arm_border", + { data_type => "real", is_nullable => 1 }, + "experiment_group", + { data_type => "varchar", is_nullable => 1, size => 12 }, +); +__PACKAGE__->set_primary_key("fish_result_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:nJPjSahTyJeD1dzWQt2KLg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/FishResultImage.pm b/lib/SGN/Schema/FishResultImage.pm new file mode 100644 index 0000000..4fdf4df --- /dev/null +++ b/lib/SGN/Schema/FishResultImage.pm @@ -0,0 +1,85 @@ +package SGN::Schema::FishResultImage; + +# 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 + +SGN::Schema::FishResultImage + +=cut + +__PACKAGE__->table("fish_result_image"); + +=head1 ACCESSORS + +=head2 fish_result_image_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'fish_result_image_fish_result_image_id_seq' + +=head2 image_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 fish_result_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "fish_result_image_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "fish_result_image_fish_result_image_id_seq", + }, + "image_id", + { data_type => "bigint", is_nullable => 1 }, + "fish_result_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("fish_result_image_id"); + +=head1 RELATIONS + +=head2 fish_result + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "fish_result", + "SGN::Schema::FishResult", + { fish_result_id => "fish_result_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:L5lujszy4fNROQMVyCqPqw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Go.pm b/lib/SGN/Schema/Go.pm index d1dddd1..78fdba2 100644 --- a/lib/SGN/Schema/Go.pm +++ b/lib/SGN/Schema/Go.pm @@ -1,54 +1,87 @@ package SGN::Schema::Go; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Go + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("go"); + +=head1 ACCESSORS + +=head2 go_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'go_go_id_seq' + +=head2 go_accession + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 description + + data_type: 'text' + is_nullable: 1 + +=head2 description_fulltext + + data_type: 'tsvector' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "go_id", { - data_type => "bigint", - default_value => "nextval('go_go_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "go_go_id_seq", }, "go_accession", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, + { data_type => "varchar", is_nullable => 1, size => 20 }, "description", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "description_fulltext", - { - data_type => "tsvector", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "tsvector", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("go_id"); __PACKAGE__->add_unique_constraint("go_go_accession_key", ["go_accession"]); + +=head1 RELATIONS + +=head2 interpros_go + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "interpro_goes", + "interpros_go", "SGN::Schema::InterproGo", { "foreign.go_accession" => "self.go_accession" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:oO8KY9cre9CuhJK8J/FkWA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:XuyLAWBLxoap9z3FlcVShQ # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Group.pm b/lib/SGN/Schema/Group.pm index 781173c..405d215 100644 --- a/lib/SGN/Schema/Group.pm +++ b/lib/SGN/Schema/Group.pm @@ -1,41 +1,78 @@ package SGN::Schema::Group; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Group + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("groups"); + +=head1 ACCESSORS + +=head2 group_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'groups_group_id_seq' + +=head2 type + + data_type: 'integer' + is_nullable: 1 + +=head2 comment + + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "group_id", { - data_type => "integer", - default_value => "nextval('groups_group_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "groups_group_id_seq", }, "type", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "comment", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("group_id"); + +=head1 RELATIONS + +=head2 unigenes_build + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "unigene_builds", + "unigenes_build", "SGN::Schema::UnigeneBuild", { "foreign.organism_group_id" => "self.group_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:yOXQC5bAqXvLNXXk/+buAQ +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:hLfMQICZ6B5wCnRaeNh3Ag # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/GroupLinkage.pm b/lib/SGN/Schema/GroupLinkage.pm dissimilarity index 63% index 3ad533b..8502d3f 100644 --- a/lib/SGN/Schema/GroupLinkage.pm +++ b/lib/SGN/Schema/GroupLinkage.pm @@ -1,41 +1,76 @@ -package SGN::Schema::GroupLinkage; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("group_linkage"); -__PACKAGE__->add_columns( - "group_linkage_id", - { - data_type => "integer", - default_value => "nextval('group_linkage_group_linkage_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "group_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "member_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "member_type", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "member_value", - { - data_type => "bytea", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("group_linkage_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:x7MyQMDgy4P+S5MdYUYXqg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::GroupLinkage; + +# 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 + +SGN::Schema::GroupLinkage + +=cut + +__PACKAGE__->table("group_linkage"); + +=head1 ACCESSORS + +=head2 group_linkage_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'group_linkage_group_linkage_id_seq' + +=head2 group_id + + data_type: 'integer' + is_nullable: 1 + +=head2 member_id + + data_type: 'integer' + is_nullable: 1 + +=head2 member_type + + data_type: 'bigint' + is_nullable: 1 + +=head2 member_value + + data_type: 'bytea' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "group_linkage_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "group_linkage_group_linkage_id_seq", + }, + "group_id", + { data_type => "integer", is_nullable => 1 }, + "member_id", + { data_type => "integer", is_nullable => 1 }, + "member_type", + { data_type => "bigint", is_nullable => 1 }, + "member_value", + { data_type => "bytea", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("group_linkage_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:wRthsfk+3dZbyhxvnSULVw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/IdLinkage.pm b/lib/SGN/Schema/IdLinkage.pm dissimilarity index 64% index 852c3bf..8ad3a07 100644 --- a/lib/SGN/Schema/IdLinkage.pm +++ b/lib/SGN/Schema/IdLinkage.pm @@ -1,41 +1,77 @@ -package SGN::Schema::IdLinkage; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("id_linkage"); -__PACKAGE__->add_columns( - "id_linkage_id", - { - data_type => "integer", - default_value => "nextval('id_linkage_id_linkage_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "link_id", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "link_id_type", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "internal_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "internal_id_type", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, -); -__PACKAGE__->set_primary_key("id_linkage_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:oYcL2G3WGqzmIF85gIz0uQ - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::IdLinkage; + +# 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 + +SGN::Schema::IdLinkage + +=cut + +__PACKAGE__->table("id_linkage"); + +=head1 ACCESSORS + +=head2 id_linkage_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'id_linkage_id_linkage_id_seq' + +=head2 link_id + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 link_id_type + + data_type: 'integer' + is_nullable: 1 + +=head2 internal_id + + data_type: 'integer' + is_nullable: 1 + +=head2 internal_id_type + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "id_linkage_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "id_linkage_id_linkage_id_seq", + }, + "link_id", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "link_id_type", + { data_type => "integer", is_nullable => 1 }, + "internal_id", + { data_type => "integer", is_nullable => 1 }, + "internal_id_type", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("id_linkage_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:3lxwVVcsl6z0eWnMu9HAZQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/IlInfo.pm b/lib/SGN/Schema/IlInfo.pm dissimilarity index 76% index 8446618..d7663f2 100644 --- a/lib/SGN/Schema/IlInfo.pm +++ b/lib/SGN/Schema/IlInfo.pm @@ -1,71 +1,113 @@ -package SGN::Schema::IlInfo; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("il_info"); -__PACKAGE__->add_columns( - "ns_marker_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "sn_marker_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "map_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "map_version_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "population_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "ns_position", - { - data_type => "numeric", - default_value => undef, - is_nullable => 1, - size => "5,8", - }, - "sn_position", - { - data_type => "numeric", - default_value => undef, - is_nullable => 1, - size => "5,8", - }, - "name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 100, - }, - "ns_alias", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "sn_alias", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "lg_name", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Y2aYOpBgSIUTs+CFBn4Z2A - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::IlInfo; + +# 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 + +SGN::Schema::IlInfo + +=cut + +__PACKAGE__->table("il_info"); + +=head1 ACCESSORS + +=head2 ns_marker_id + + data_type: 'integer' + is_nullable: 1 + +=head2 sn_marker_id + + data_type: 'integer' + is_nullable: 1 + +=head2 map_id + + data_type: 'integer' + is_nullable: 1 + +=head2 map_version_id + + data_type: 'integer' + is_nullable: 1 + +=head2 population_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 ns_position + + data_type: 'numeric' + is_nullable: 1 + size: [8,5] + +=head2 sn_position + + data_type: 'numeric' + is_nullable: 1 + size: [8,5] + +=head2 name + + data_type: 'varchar' + is_nullable: 1 + size: 100 + +=head2 ns_alias + + data_type: 'text' + is_nullable: 1 + +=head2 sn_alias + + data_type: 'text' + is_nullable: 1 + +=head2 lg_name + + data_type: 'text' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "ns_marker_id", + { data_type => "integer", is_nullable => 1 }, + "sn_marker_id", + { data_type => "integer", is_nullable => 1 }, + "map_id", + { data_type => "integer", is_nullable => 1 }, + "map_version_id", + { data_type => "integer", is_nullable => 1 }, + "population_id", + { data_type => "bigint", is_nullable => 1 }, + "ns_position", + { data_type => "numeric", is_nullable => 1, size => [8, 5] }, + "sn_position", + { data_type => "numeric", is_nullable => 1, size => [8, 5] }, + "name", + { data_type => "varchar", is_nullable => 1, size => 100 }, + "ns_alias", + { data_type => "text", is_nullable => 1 }, + "sn_alias", + { data_type => "text", is_nullable => 1 }, + "lg_name", + { data_type => "text", is_nullable => 1 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:bolPyJfTePfg3/kyvYUg/g + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Interpro.pm b/lib/SGN/Schema/Interpro.pm index 34dacd8..af5ac25 100644 --- a/lib/SGN/Schema/Interpro.pm +++ b/lib/SGN/Schema/Interpro.pm @@ -1,54 +1,87 @@ package SGN::Schema::Interpro; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Interpro + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("interpro"); + +=head1 ACCESSORS + +=head2 interpro_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'interpro_interpro_id_seq' + +=head2 interpro_accession + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 description + + data_type: 'text' + is_nullable: 1 + +=head2 description_fulltext + + data_type: 'tsvector' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "interpro_id", { - data_type => "bigint", - default_value => "nextval('interpro_interpro_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "interpro_interpro_id_seq", }, "interpro_accession", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, + { data_type => "varchar", is_nullable => 1, size => 20 }, "description", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "description_fulltext", - { - data_type => "tsvector", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "tsvector", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("interpro_id"); __PACKAGE__->add_unique_constraint("interpro_interpro_accession_key", ["interpro_accession"]); + +=head1 RELATIONS + +=head2 interpros_go + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "interpro_goes", + "interpros_go", "SGN::Schema::InterproGo", { "foreign.interpro_accession" => "self.interpro_accession" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:eOKpm49x0BGacxaavYLf2Q +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:goZBzUs2dp7PRwn/DDOY0A # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/InterproGo.pm b/lib/SGN/Schema/InterproGo.pm index bc75c17..a5f4f07 100644 --- a/lib/SGN/Schema/InterproGo.pm +++ b/lib/SGN/Schema/InterproGo.pm @@ -1,55 +1,107 @@ package SGN::Schema::InterproGo; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::InterproGo + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("interpro_go"); + +=head1 ACCESSORS + +=head2 interpro_go_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'interpro_go_interpro_go_id_seq' + +=head2 interpro_accession + + data_type: 'varchar' + is_foreign_key: 1 + is_nullable: 1 + size: 20 + +=head2 go_accession + + data_type: 'varchar' + is_foreign_key: 1 + is_nullable: 1 + size: 20 + +=cut + __PACKAGE__->add_columns( "interpro_go_id", { - data_type => "bigint", - default_value => "nextval('interpro_go_interpro_go_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "interpro_go_interpro_go_id_seq", }, "interpro_accession", - { - data_type => "character varying", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 20, - }, + { data_type => "varchar", is_foreign_key => 1, is_nullable => 1, size => 20 }, "go_accession", - { - data_type => "character varying", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 20, - }, + { data_type => "varchar", is_foreign_key => 1, is_nullable => 1, size => 20 }, ); __PACKAGE__->set_primary_key("interpro_go_id"); + +=head1 RELATIONS + +=head2 go_accession + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "go_accession", "SGN::Schema::Go", { go_accession => "go_accession" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 interpro_accession + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "interpro_accession", "SGN::Schema::Interpro", { interpro_accession => "interpro_accession" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:DY8Jg7Fa9DNO0wrdyZ6MGw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:xsDCm4apdwyu7QR/kIlmJg # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Library.pm b/lib/SGN/Schema/Library.pm dissimilarity index 73% index ba27518..5cec04c 100644 --- a/lib/SGN/Schema/Library.pm +++ b/lib/SGN/Schema/Library.pm @@ -1,191 +1,291 @@ -package SGN::Schema::Library; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("library"); -__PACKAGE__->add_columns( - "library_id", - { - data_type => "integer", - default_value => "nextval('library_library_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "type", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, - "submit_user_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "library_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "library_shortname", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 16, - }, - "authors", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "organism_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "cultivar", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "accession", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "tissue", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "development_stage", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "treatment_conditions", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "cloning_host", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "vector", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "rs1", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 12, - }, - "rs2", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 12, - }, - "cloning_kit", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "comments", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "contact_information", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "order_routing_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "sp_person_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "forward_adapter", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "reverse_adapter", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "obsolete", - { data_type => "boolean", default_value => undef, is_nullable => 1, size => 1 }, - "modified_date", - { - data_type => "timestamp with time zone", - default_value => undef, - is_nullable => 1, - size => 8, - }, - "create_date", - { - data_type => "timestamp with time zone", - default_value => undef, - is_nullable => 1, - size => 8, - }, -); -__PACKAGE__->set_primary_key("library_id"); -__PACKAGE__->add_unique_constraint("library_shortname_idx", ["library_shortname"]); -__PACKAGE__->has_many( - "clones", - "SGN::Schema::Clone", - { "foreign.library_id" => "self.library_id" }, -); -__PACKAGE__->belongs_to( - "type", - "SGN::Schema::Type", - { type_id => "type" }, - { join_type => "LEFT" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:vuUbthf1WddZqGJ3Vhpz2w - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::Library; + +# 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 + +SGN::Schema::Library + +=cut + +__PACKAGE__->table("library"); + +=head1 ACCESSORS + +=head2 library_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'library_library_id_seq' + +=head2 type + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 submit_user_id + + data_type: 'integer' + is_nullable: 1 + +=head2 library_name + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 library_shortname + + data_type: 'varchar' + is_nullable: 1 + size: 16 + +=head2 authors + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 organism_id + + data_type: 'integer' + is_nullable: 1 + +=head2 cultivar + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 accession + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 tissue + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 development_stage + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 treatment_conditions + + data_type: 'text' + is_nullable: 1 + +=head2 cloning_host + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 vector + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 rs1 + + data_type: 'varchar' + is_nullable: 1 + size: 12 + +=head2 rs2 + + data_type: 'varchar' + is_nullable: 1 + size: 12 + +=head2 cloning_kit + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 comments + + data_type: 'text' + is_nullable: 1 + +=head2 contact_information + + data_type: 'text' + is_nullable: 1 + +=head2 order_routing_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 sp_person_id + + data_type: 'integer' + is_nullable: 1 + +=head2 forward_adapter + + data_type: 'text' + is_nullable: 1 + original: {data_type => "varchar"} + +=head2 reverse_adapter + + data_type: 'text' + is_nullable: 1 + original: {data_type => "varchar"} + +=head2 obsolete + + data_type: 'boolean' + is_nullable: 1 + +=head2 modified_date + + data_type: 'timestamp with time zone' + is_nullable: 1 + +=head2 create_date + + data_type: 'timestamp with time zone' + is_nullable: 1 + +=head2 chado_organism_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "library_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "library_library_id_seq", + }, + "type", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "submit_user_id", + { data_type => "integer", is_nullable => 1 }, + "library_name", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "library_shortname", + { data_type => "varchar", is_nullable => 1, size => 16 }, + "authors", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "organism_id", + { data_type => "integer", is_nullable => 1 }, + "cultivar", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "accession", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "tissue", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "development_stage", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "treatment_conditions", + { data_type => "text", is_nullable => 1 }, + "cloning_host", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "vector", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "rs1", + { data_type => "varchar", is_nullable => 1, size => 12 }, + "rs2", + { data_type => "varchar", is_nullable => 1, size => 12 }, + "cloning_kit", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "comments", + { data_type => "text", is_nullable => 1 }, + "contact_information", + { data_type => "text", is_nullable => 1 }, + "order_routing_id", + { data_type => "bigint", is_nullable => 1 }, + "sp_person_id", + { data_type => "integer", is_nullable => 1 }, + "forward_adapter", + { + data_type => "text", + is_nullable => 1, + original => { data_type => "varchar" }, + }, + "reverse_adapter", + { + data_type => "text", + is_nullable => 1, + original => { data_type => "varchar" }, + }, + "obsolete", + { data_type => "boolean", is_nullable => 1 }, + "modified_date", + { data_type => "timestamp with time zone", is_nullable => 1 }, + "create_date", + { data_type => "timestamp with time zone", is_nullable => 1 }, + "chado_organism_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("library_id"); +__PACKAGE__->add_unique_constraint("library_shortname_idx", ["library_shortname"]); + +=head1 RELATIONS + +=head2 clones + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "clones", + "SGN::Schema::Clone", + { "foreign.library_id" => "self.library_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 type + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "type", + "SGN::Schema::Type", + { type_id => "type" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:mEVMxr8tPb/rp+t5593leg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/LinkageGroup.pm b/lib/SGN/Schema/LinkageGroup.pm index da01a53..29def20 100644 --- a/lib/SGN/Schema/LinkageGroup.pm +++ b/lib/SGN/Schema/LinkageGroup.pm @@ -1,54 +1,79 @@ package SGN::Schema::LinkageGroup; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::LinkageGroup + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("linkage_group"); + +=head1 ACCESSORS + +=head2 lg_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'linkage_group_lg_id_seq' + +=head2 map_version_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 lg_order + + data_type: 'integer' + is_nullable: 0 + +=head2 lg_name + + data_type: 'text' + is_nullable: 1 + +=head2 north_location_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 south_location_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "lg_id", { - data_type => "integer", - default_value => "nextval('linkage_group_lg_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "linkage_group_lg_id_seq", }, "map_version_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "lg_order", - { data_type => "integer", default_value => undef, is_nullable => 0, size => 4 }, + { data_type => "integer", is_nullable => 0 }, "lg_name", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "north_location_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "south_location_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, ); __PACKAGE__->set_primary_key("lg_id"); __PACKAGE__->add_unique_constraint( @@ -59,33 +84,87 @@ __PACKAGE__->add_unique_constraint( "linkage_group_map_version_id_key1", ["map_version_id", "lg_name"], ); + +=head1 RELATIONS + +=head2 north_location + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "north_location", "SGN::Schema::MarkerLocation", { location_id => "north_location_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 map_version + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "map_version", "SGN::Schema::MapVersion", { map_version_id => "map_version_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 south_location + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "south_location", "SGN::Schema::MarkerLocation", { location_id => "south_location_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 marker_locations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "marker_locations", "SGN::Schema::MarkerLocation", { "foreign.lg_id" => "self.lg_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:kh9JvYZOT21+HyY29JBGdA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:AeXr/gcdemGIXiaObXaycw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/LocType.pm b/lib/SGN/Schema/LocType.pm dissimilarity index 63% index 63bac49..011fbdc 100644 --- a/lib/SGN/Schema/LocType.pm +++ b/lib/SGN/Schema/LocType.pm @@ -1,42 +1,66 @@ -package SGN::Schema::LocType; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("loc_types"); -__PACKAGE__->add_columns( - "loc_type_id", - { - data_type => "integer", - default_value => "nextval('loc_types_loc_type_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "type_code", - { - data_type => "character varying", - default_value => "''::character varying", - is_nullable => 0, - size => 10, - }, - "type_name", - { - data_type => "character varying", - default_value => "''::character varying", - is_nullable => 0, - size => 12, - }, -); -__PACKAGE__->set_primary_key("loc_type_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:RCbTZwAvN7ne+jOqxcgqvQ - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::LocType; + +# 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 + +SGN::Schema::LocType + +=cut + +__PACKAGE__->table("loc_types"); + +=head1 ACCESSORS + +=head2 loc_type_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'loc_types_loc_type_id_seq' + +=head2 type_code + + data_type: 'varchar' + default_value: (empty string) + is_nullable: 0 + size: 10 + +=head2 type_name + + data_type: 'varchar' + default_value: (empty string) + is_nullable: 0 + size: 12 + +=cut + +__PACKAGE__->add_columns( + "loc_type_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "loc_types_loc_type_id_seq", + }, + "type_code", + { data_type => "varchar", default_value => "", is_nullable => 0, size => 10 }, + "type_name", + { data_type => "varchar", default_value => "", is_nullable => 0, size => 12 }, +); +__PACKAGE__->set_primary_key("loc_type_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:n2Sy/U9Sb8EDwZZ1HUnpPg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/ManualAnnotation.pm b/lib/SGN/Schema/ManualAnnotation.pm dissimilarity index 65% index 470de6a..9e50ca6 100644 --- a/lib/SGN/Schema/ManualAnnotation.pm +++ b/lib/SGN/Schema/ManualAnnotation.pm @@ -1,52 +1,97 @@ -package SGN::Schema::ManualAnnotation; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("manual_annotations"); -__PACKAGE__->add_columns( - "manual_annotations_id", - { - data_type => "bigint", - default_value => "nextval('manual_annotations_manual_annotations_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 8, - }, - "annotation_target_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "annotation_target_type_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "annotation_text", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "author_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "date_entered", - { data_type => "date", default_value => undef, is_nullable => 1, size => 4 }, - "last_modified", - { data_type => "date", default_value => undef, is_nullable => 1, size => 4 }, - "annotation_text_fulltext", - { - data_type => "tsvector", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("manual_annotations_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:K8QGDYaUCQtnVbQ9FY22QQ - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::ManualAnnotation; + +# 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 + +SGN::Schema::ManualAnnotation + +=cut + +__PACKAGE__->table("manual_annotations"); + +=head1 ACCESSORS + +=head2 manual_annotations_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'manual_annotations_manual_annotations_id_seq' + +=head2 annotation_target_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 annotation_target_type_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 annotation_text + + data_type: 'text' + is_nullable: 1 + +=head2 author_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 date_entered + + data_type: 'date' + is_nullable: 1 + +=head2 last_modified + + data_type: 'date' + is_nullable: 1 + +=head2 annotation_text_fulltext + + data_type: 'tsvector' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "manual_annotations_id", + { + data_type => "bigint", + is_auto_increment => 1, + is_nullable => 0, + sequence => "manual_annotations_manual_annotations_id_seq", + }, + "annotation_target_id", + { data_type => "bigint", is_nullable => 1 }, + "annotation_target_type_id", + { data_type => "bigint", is_nullable => 1 }, + "annotation_text", + { data_type => "text", is_nullable => 1 }, + "author_id", + { data_type => "bigint", is_nullable => 1 }, + "date_entered", + { data_type => "date", is_nullable => 1 }, + "last_modified", + { data_type => "date", is_nullable => 1 }, + "annotation_text_fulltext", + { data_type => "tsvector", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("manual_annotations_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Gcxm7n7LvfxTdi36jg+9Gg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/ManualCensorReason.pm b/lib/SGN/Schema/ManualCensorReason.pm index 6a043e8..d3a43ea 100644 --- a/lib/SGN/Schema/ManualCensorReason.pm +++ b/lib/SGN/Schema/ManualCensorReason.pm @@ -1,34 +1,54 @@ package SGN::Schema::ManualCensorReason; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::ManualCensorReason + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("manual_censor_reasons"); + +=head1 ACCESSORS + +=head2 censor_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'manual_censor_reasons_censor_id_seq' + +=head2 reason + + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "censor_id", { - data_type => "integer", - default_value => "nextval('manual_censor_reasons_censor_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "manual_censor_reasons_censor_id_seq", }, "reason", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("censor_id"); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:SX8GxhPLUj0Es62m0H+1Mg +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Q79FT+pen42efio+jHsBHQ # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Map.pm b/lib/SGN/Schema/Map.pm index 3945e93..ad7566f 100644 --- a/lib/SGN/Schema/Map.pm +++ b/lib/SGN/Schema/Map.pm @@ -1,114 +1,227 @@ package SGN::Schema::Map; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Map + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("map"); + +=head1 ACCESSORS + +=head2 map_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'map_map_id_seq' + +=head2 short_name + + data_type: 'text' + is_nullable: 0 + +=head2 long_name + + data_type: 'text' + is_nullable: 1 + +=head2 abstract + + data_type: 'text' + is_nullable: 1 + +=head2 map_type + + data_type: 'text' + is_nullable: 1 + +=head2 parent_1 + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 parent_2 + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 units + + data_type: 'text' + default_value: 'cM' + is_nullable: 1 + +=head2 ancestor + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 population_id + + data_type: 'integer' + is_nullable: 1 + +=head2 parent1_stock_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 parent2_stock_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 population_stock_id + + data_type: 'bigint' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "map_id", { - data_type => "integer", - default_value => "nextval('map_map_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "map_map_id_seq", }, "short_name", - { - data_type => "text", - default_value => undef, - is_nullable => 0, - size => undef, - }, + { data_type => "text", is_nullable => 0 }, "long_name", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "abstract", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "map_type", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "parent_1", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "parent_2", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "units", - { - data_type => "text", - default_value => "'cM'::text", - is_nullable => 1, - size => undef, - }, + { data_type => "text", default_value => "cM", is_nullable => 1 }, "ancestor", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "population_id", + { data_type => "integer", is_nullable => 1 }, + "parent1_stock_id", + { data_type => "bigint", is_nullable => 1 }, + "parent2_stock_id", + { data_type => "bigint", is_nullable => 1 }, + "population_stock_id", + { data_type => "bigint", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("map_id"); + +=head1 RELATIONS + +=head2 ancestor + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "ancestor", "SGN::Schema::Accession", { accession_id => "ancestor" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 parent_2 + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "parent_2", "SGN::Schema::Accession", { accession_id => "parent_2" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 parent_1 + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "parent_1", "SGN::Schema::Accession", { accession_id => "parent_1" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 map_versions + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "map_versions", "SGN::Schema::MapVersion", { "foreign.map_id" => "self.map_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 pcr_experiments + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "pcr_experiments", "SGN::Schema::PcrExperiment", { "foreign.map_id" => "self.map_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:VAbpsHO3jE5BVJ77K8dd5Q +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:AYZYWOx5WJ4XydpNX0pWIw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/MapVersion.pm b/lib/SGN/Schema/MapVersion.pm index 4717ae8..e9eb274 100644 --- a/lib/SGN/Schema/MapVersion.pm +++ b/lib/SGN/Schema/MapVersion.pm @@ -1,78 +1,185 @@ package SGN::Schema::MapVersion; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::MapVersion + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("map_version"); + +=head1 ACCESSORS + +=head2 map_version_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'map_version_map_version_id_seq' + +=head2 map_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 date_loaded + + data_type: 'date' + is_nullable: 1 + +=head2 current_version + + data_type: 'boolean' + is_nullable: 1 + +=head2 default_threshold + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 has_il + + data_type: 'boolean' + is_nullable: 1 + +=head2 has_physical + + data_type: 'boolean' + is_nullable: 1 + +=head2 metadata_id + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "map_version_id", { - data_type => "integer", - default_value => "nextval('map_version_map_version_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "map_version_map_version_id_seq", }, "map_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "date_loaded", - { data_type => "date", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "date", is_nullable => 1 }, "current_version", - { data_type => "boolean", default_value => undef, is_nullable => 1, size => 1 }, + { data_type => "boolean", is_nullable => 1 }, "default_threshold", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "has_il", - { data_type => "boolean", default_value => undef, is_nullable => 1, size => 1 }, + { data_type => "boolean", is_nullable => 1 }, "has_physical", - { data_type => "boolean", default_value => undef, is_nullable => 1, size => 1 }, + { data_type => "boolean", is_nullable => 1 }, + "metadata_id", + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("map_version_id"); + +=head1 RELATIONS + +=head2 linkage_groups + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "linkage_groups", "SGN::Schema::LinkageGroup", { "foreign.map_version_id" => "self.map_version_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 map + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "map", "SGN::Schema::Map", { map_id => "map_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 default_threshold + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "default_threshold", "SGN::Schema::DeprecatedMarkerConfidence", { confidence_id => "default_threshold" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 marker_locations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "marker_locations", "SGN::Schema::MarkerLocation", { "foreign.map_version_id" => "self.map_version_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 temp_map_correspondences + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "temp_map_correspondences", "SGN::Schema::TempMapCorrespondence", { "foreign.map_version_id" => "self.map_version_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:pmMIeYu513Kw/Cu3g6n72w +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:8cm9eQqw3sOvPHi6hveD2A # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Marker.pm b/lib/SGN/Schema/Marker.pm index fc42555..2730bfd 100644 --- a/lib/SGN/Schema/Marker.pm +++ b/lib/SGN/Schema/Marker.pm @@ -1,94 +1,266 @@ package SGN::Schema::Marker; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Marker + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("marker"); + +=head1 ACCESSORS + +=head2 marker_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'marker_marker_id_seq' + +=head2 dummy_field + + data_type: 'boolean' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "marker_id", { - data_type => "integer", - default_value => "nextval('marker_marker_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "marker_marker_id_seq", }, "dummy_field", - { data_type => "boolean", default_value => undef, is_nullable => 1, size => 1 }, + { data_type => "boolean", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("marker_id"); + +=head1 RELATIONS + +=head2 cosii_orthologs + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "cosii_orthologs", "SGN::Schema::CosiiOrtholog", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 cos_markers + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "cos_markers", "SGN::Schema::CosMarker", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 ests_mapped_by_clone + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "ests_mapped_by_clones", - "SGN::Schema::EstsMappedByClone", + "ests_mapped_by_clone", + "SGN::Schema::EstMappedByClone", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 marker_aliases + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "marker_alias", - "SGN::Schema::MarkerAlia", + "marker_aliases", + "SGN::Schema::MarkerAlias", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 marker_collectibles + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "marker_collectibles", "SGN::Schema::MarkerCollectible", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 marker_experiments + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "marker_experiments", "SGN::Schema::MarkerExperiment", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 pcr_experiments + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "pcr_experiments", "SGN::Schema::PcrExperiment", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 p_markers + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "p_markers", "SGN::Schema::PMarker", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 primer_unigene_matches + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "primer_unigene_matches", "SGN::Schema::PrimerUnigeneMatch", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 rflp_markers + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "rflp_markers", "SGN::Schema::RflpMarker", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 snps + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "snps", + "SGN::Schema::Snp", + { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 ssrs + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "ssrs", "SGN::Schema::Ssr", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 ssr_repeats + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "ssr_repeats", "SGN::Schema::SsrRepeat", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 tm_markers + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "tm_markers", "SGN::Schema::TmMarker", { "foreign.marker_id" => "self.marker_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:V5P7TW1z/mtDGvIGRG0rfw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:TcM/fzk1Rzekob/ZX5Q3pg # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/MarkerAlias.pm b/lib/SGN/Schema/MarkerAlias.pm new file mode 100644 index 0000000..09e3d5b --- /dev/null +++ b/lib/SGN/Schema/MarkerAlias.pm @@ -0,0 +1,89 @@ +package SGN::Schema::MarkerAlias; + +# 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 + +SGN::Schema::MarkerAlias + +=cut + +__PACKAGE__->table("marker_alias"); + +=head1 ACCESSORS + +=head2 alias_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'marker_alias_alias_id_seq' + +=head2 alias + + data_type: 'text' + is_nullable: 0 + +=head2 marker_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 preferred + + data_type: 'boolean' + default_value: true + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "alias_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "marker_alias_alias_id_seq", + }, + "alias", + { data_type => "text", is_nullable => 0 }, + "marker_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, + "preferred", + { data_type => "boolean", default_value => \"true", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("alias_id"); +__PACKAGE__->add_unique_constraint("marker_alias_alias_key", ["alias"]); + +=head1 RELATIONS + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:E+03TkLOicO7zNp3CmApfA + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/MarkerCollectible.pm b/lib/SGN/Schema/MarkerCollectible.pm dissimilarity index 61% index 43e943b..99f454d 100644 --- a/lib/SGN/Schema/MarkerCollectible.pm +++ b/lib/SGN/Schema/MarkerCollectible.pm @@ -1,47 +1,97 @@ -package SGN::Schema::MarkerCollectible; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("marker_collectible"); -__PACKAGE__->add_columns( - "marker_collectible_dummy_id", - { - data_type => "integer", - default_value => "nextval('marker_collectible_marker_collectible_dummy_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "marker_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, - "mc_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, -); -__PACKAGE__->set_primary_key("marker_collectible_dummy_id"); -__PACKAGE__->add_unique_constraint("marker_collectible_marker_id_key", ["marker_id", "mc_id"]); -__PACKAGE__->belongs_to("mc", "SGN::Schema::MarkerCollection", { mc_id => "mc_id" }); -__PACKAGE__->belongs_to("marker", "SGN::Schema::Marker", { marker_id => "marker_id" }); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:EtUEbTiZ2cwlutSGJD/rrw - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::MarkerCollectible; + +# 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 + +SGN::Schema::MarkerCollectible + +=cut + +__PACKAGE__->table("marker_collectible"); + +=head1 ACCESSORS + +=head2 marker_collectible_dummy_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'marker_collectible_marker_collectible_dummy_id_seq' + +=head2 marker_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 mc_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=cut + +__PACKAGE__->add_columns( + "marker_collectible_dummy_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "marker_collectible_marker_collectible_dummy_id_seq", + }, + "marker_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, + "mc_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, +); +__PACKAGE__->set_primary_key("marker_collectible_dummy_id"); +__PACKAGE__->add_unique_constraint("marker_collectible_marker_id_key", ["marker_id", "mc_id"]); + +=head1 RELATIONS + +=head2 mc + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "mc", + "SGN::Schema::MarkerCollection", + { mc_id => "mc_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Jx+9+xVR4fa6jp7x3Q6hZg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/MarkerCollection.pm b/lib/SGN/Schema/MarkerCollection.pm index 7fcb32a..9b145bd 100644 --- a/lib/SGN/Schema/MarkerCollection.pm +++ b/lib/SGN/Schema/MarkerCollection.pm @@ -1,47 +1,79 @@ package SGN::Schema::MarkerCollection; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::MarkerCollection + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("marker_collection"); + +=head1 ACCESSORS + +=head2 mc_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'marker_collection_mc_id_seq' + +=head2 mc_name + + data_type: 'text' + is_nullable: 0 + +=head2 mc_description + + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "mc_id", { - data_type => "integer", - default_value => "nextval('marker_collection_mc_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "marker_collection_mc_id_seq", }, "mc_name", - { - data_type => "text", - default_value => undef, - is_nullable => 0, - size => undef, - }, + { data_type => "text", is_nullable => 0 }, "mc_description", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("mc_id"); __PACKAGE__->add_unique_constraint("marker_collection_mc_name_key", ["mc_name"]); + +=head1 RELATIONS + +=head2 marker_collectibles + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "marker_collectibles", "SGN::Schema::MarkerCollectible", { "foreign.mc_id" => "self.mc_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:YALcddlZMO4e8TJX9om2ow +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:ZLN5hiKV+Bxhzzzdbeq75Q # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/MarkerConfidence.pm b/lib/SGN/Schema/MarkerConfidence.pm index 54884cd..b656e41 100644 --- a/lib/SGN/Schema/MarkerConfidence.pm +++ b/lib/SGN/Schema/MarkerConfidence.pm @@ -1,40 +1,72 @@ package SGN::Schema::MarkerConfidence; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::MarkerConfidence + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("marker_confidence"); + +=head1 ACCESSORS + +=head2 confidence_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'marker_confidence_confidence_id_seq' + +=head2 confidence_name + + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "confidence_id", { - data_type => "integer", - default_value => "nextval('marker_confidence_confidence_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "marker_confidence_confidence_id_seq", }, "confidence_name", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("confidence_id"); __PACKAGE__->add_unique_constraint("marker_confidence_confidence_name_key", ["confidence_name"]); + +=head1 RELATIONS + +=head2 marker_locations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "marker_locations", "SGN::Schema::MarkerLocation", { "foreign.confidence_id" => "self.confidence_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:PLEAad4zj+tcQotey4ZxWQ +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:roKn9U2mzGcfcoxTGgFjuw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/MarkerDerivedFrom.pm b/lib/SGN/Schema/MarkerDerivedFrom.pm index 656fd43..f4b379a 100644 --- a/lib/SGN/Schema/MarkerDerivedFrom.pm +++ b/lib/SGN/Schema/MarkerDerivedFrom.pm @@ -1,57 +1,112 @@ package SGN::Schema::MarkerDerivedFrom; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::MarkerDerivedFrom + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("marker_derived_from"); + +=head1 ACCESSORS + +=head2 marker_derived_dummy_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'marker_derived_from_marker_derived_dummy_id_seq' + +=head2 marker_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 derived_from_source_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 id_in_source + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "marker_derived_dummy_id", { - data_type => "integer", - default_value => "nextval('marker_derived_from_marker_derived_dummy_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "marker_derived_from_marker_derived_dummy_id_seq", }, "marker_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "derived_from_source_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "id_in_source", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("marker_derived_dummy_id"); + +=head1 RELATIONS + +=head2 derived_from_source + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "derived_from_source", "SGN::Schema::DerivedFromSource", { "derived_from_source_id" => "derived_from_source_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "marker", "SGN::Schema::DeprecatedMarker", { marker_id => "marker_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:r92tl5lsU17+QAaDcwDA+A +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:V85eQuoqWZtVfXXxk2r19g # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/MarkerExperiment.pm b/lib/SGN/Schema/MarkerExperiment.pm index bcda715..123aace 100644 --- a/lib/SGN/Schema/MarkerExperiment.pm +++ b/lib/SGN/Schema/MarkerExperiment.pm @@ -1,94 +1,172 @@ package SGN::Schema::MarkerExperiment; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::MarkerExperiment + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("marker_experiment"); + +=head1 ACCESSORS + +=head2 marker_experiment_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'marker_experiment_marker_experiment_id_seq' + +=head2 marker_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 pcr_experiment_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 rflp_experiment_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 location_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 protocol + + data_type: 'text' + is_nullable: 0 + +=cut + __PACKAGE__->add_columns( "marker_experiment_id", { - data_type => "integer", - default_value => "nextval('marker_experiment_marker_experiment_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "marker_experiment_marker_experiment_id_seq", }, "marker_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "pcr_experiment_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "rflp_experiment_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "location_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "protocol", - { - data_type => "text", - default_value => undef, - is_nullable => 0, - size => undef, - }, + { data_type => "text", is_nullable => 0 }, ); __PACKAGE__->set_primary_key("marker_experiment_id"); __PACKAGE__->add_unique_constraint( "marker_experiment_pcr_experiment_id_key", ["pcr_experiment_id", "rflp_experiment_id", "location_id"], ); + +=head1 RELATIONS + +=head2 pcr_experiment + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "pcr_experiment", "SGN::Schema::PcrExperiment", { pcr_experiment_id => "pcr_experiment_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 location + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "location", "SGN::Schema::MarkerLocation", { location_id => "location_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 rflp_experiment + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "rflp_experiment", "SGN::Schema::RflpMarker", { rflp_id => "rflp_experiment_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "marker", "SGN::Schema::Marker", { marker_id => "marker_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Kyh1yEJMn3Hy5Y5Ezh9rsA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:LACXBxVUAZwsF+fcMy8Y3g # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/MarkerLocation.pm b/lib/SGN/Schema/MarkerLocation.pm index 233f3da..de8e0c2 100644 --- a/lib/SGN/Schema/MarkerLocation.pm +++ b/lib/SGN/Schema/MarkerLocation.pm @@ -1,91 +1,195 @@ package SGN::Schema::MarkerLocation; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::MarkerLocation + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("marker_location"); + +=head1 ACCESSORS + +=head2 location_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'marker_location_location_id_seq' + +=head2 lg_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 map_version_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 position + + data_type: 'numeric' + is_nullable: 0 + size: [9,6] + +=head2 confidence_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 subscript + + data_type: 'char' + is_nullable: 1 + size: 1 + +=head2 position_north + + data_type: 'numeric' + is_nullable: 1 + size: [8,5] + +=head2 position_south + + data_type: 'numeric' + is_nullable: 1 + size: [8,5] + +=cut + __PACKAGE__->add_columns( "location_id", { - data_type => "integer", - default_value => "nextval('marker_location_location_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "marker_location_location_id_seq", }, "lg_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, "map_version_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, "position", - { - data_type => "numeric", - default_value => undef, - is_nullable => 0, - size => "5,8", - }, + { data_type => "numeric", is_nullable => 0, size => [9, 6] }, "confidence_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, "subscript", - { - data_type => "character", - default_value => undef, - is_nullable => 1, - size => 1, - }, + { data_type => "char", is_nullable => 1, size => 1 }, + "position_north", + { data_type => "numeric", is_nullable => 1, size => [8, 5] }, + "position_south", + { data_type => "numeric", is_nullable => 1, size => [8, 5] }, ); __PACKAGE__->set_primary_key("location_id"); + +=head1 RELATIONS + +=head2 linkage_group_north_locations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "linkage_group_north_location_ids", + "linkage_group_north_locations", "SGN::Schema::LinkageGroup", { "foreign.north_location_id" => "self.location_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 linkage_group_south_locations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "linkage_group_south_location_ids", + "linkage_group_south_locations", "SGN::Schema::LinkageGroup", { "foreign.south_location_id" => "self.location_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 marker_experiments + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "marker_experiments", "SGN::Schema::MarkerExperiment", { "foreign.location_id" => "self.location_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 lg + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "lg", + "SGN::Schema::LinkageGroup", + { lg_id => "lg_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, ); -__PACKAGE__->belongs_to("lg", "SGN::Schema::LinkageGroup", { lg_id => "lg_id" }); + +=head2 confidence + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "confidence", "SGN::Schema::MarkerConfidence", { confidence_id => "confidence_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, ); + +=head2 map_version + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "map_version", "SGN::Schema::MapVersion", { map_version_id => "map_version_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:hU7wmPdERZMKq01VIQMbXw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:2P4PX4+ciHl38fLPp715fQ # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/MarkerToMap.pm b/lib/SGN/Schema/MarkerToMap.pm dissimilarity index 76% index 476ba19..365b1df 100644 --- a/lib/SGN/Schema/MarkerToMap.pm +++ b/lib/SGN/Schema/MarkerToMap.pm @@ -1,65 +1,126 @@ -package SGN::Schema::MarkerToMap; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("marker_to_map"); -__PACKAGE__->add_columns( - "marker_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "protocol", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "location_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "lg_name", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "lg_order", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "position", - { - data_type => "numeric", - default_value => undef, - is_nullable => 1, - size => "5,8", - }, - "confidence_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "subscript", - { - data_type => "character", - default_value => undef, - is_nullable => 1, - size => 1, - }, - "map_version_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "map_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "parent_1", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "parent_2", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "current_version", - { data_type => "boolean", default_value => undef, is_nullable => 1, size => 1 }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:EhyPmMx26Gdh59ZgLYvItg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::MarkerToMap; + +# 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 + +SGN::Schema::MarkerToMap + +=cut + +__PACKAGE__->table("marker_to_map"); + +=head1 ACCESSORS + +=head2 marker_id + + data_type: 'integer' + is_nullable: 1 + +=head2 protocol + + data_type: 'text' + is_nullable: 1 + +=head2 location_id + + data_type: 'integer' + is_nullable: 1 + +=head2 lg_name + + data_type: 'text' + is_nullable: 1 + +=head2 lg_order + + data_type: 'integer' + is_nullable: 1 + +=head2 position + + data_type: 'numeric' + is_nullable: 1 + size: [9,6] + +=head2 confidence_id + + data_type: 'integer' + is_nullable: 1 + +=head2 subscript + + data_type: 'char' + is_nullable: 1 + size: 1 + +=head2 map_version_id + + data_type: 'integer' + is_nullable: 1 + +=head2 map_id + + data_type: 'integer' + is_nullable: 1 + +=head2 parent_1 + + data_type: 'integer' + is_nullable: 1 + +=head2 parent_2 + + data_type: 'integer' + is_nullable: 1 + +=head2 current_version + + data_type: 'boolean' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "marker_id", + { data_type => "integer", is_nullable => 1 }, + "protocol", + { data_type => "text", is_nullable => 1 }, + "location_id", + { data_type => "integer", is_nullable => 1 }, + "lg_name", + { data_type => "text", is_nullable => 1 }, + "lg_order", + { data_type => "integer", is_nullable => 1 }, + "position", + { data_type => "numeric", is_nullable => 1, size => [9, 6] }, + "confidence_id", + { data_type => "integer", is_nullable => 1 }, + "subscript", + { data_type => "char", is_nullable => 1, size => 1 }, + "map_version_id", + { data_type => "integer", is_nullable => 1 }, + "map_id", + { data_type => "integer", is_nullable => 1 }, + "parent_1", + { data_type => "integer", is_nullable => 1 }, + "parent_2", + { data_type => "integer", is_nullable => 1 }, + "current_version", + { data_type => "boolean", is_nullable => 1 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:DRojZP1ZUqn3TBUzFAH+/w + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Metadata.pm b/lib/SGN/Schema/Metadata.pm index aca1ccf..296105e 100644 --- a/lib/SGN/Schema/Metadata.pm +++ b/lib/SGN/Schema/Metadata.pm @@ -1,66 +1,137 @@ package SGN::Schema::Metadata; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Metadata + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("metadata"); + +=head1 ACCESSORS + +=head2 metadata_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'metadata_metadata_id_seq' + +=head2 create_date + + data_type: 'timestamp with time zone' + default_value: current_timestamp + is_nullable: 1 + original: {default_value => \"now()"} + +=head2 create_person_id + + data_type: 'integer' + is_nullable: 0 + +=head2 modified_date + + data_type: 'timestamp with time zone' + is_nullable: 1 + +=head2 modified_person_id + + data_type: 'integer' + is_nullable: 1 + +=head2 previous_metadata_id + + data_type: 'integer' + is_nullable: 1 + +=head2 obsolete + + data_type: 'integer' + default_value: 0 + is_nullable: 1 + +=head2 obsolete_note + + data_type: 'varchar' + is_nullable: 1 + size: 250 + +=cut + __PACKAGE__->add_columns( "metadata_id", { - data_type => "bigint", - default_value => "nextval('metadata_metadata_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "metadata_metadata_id_seq", }, "create_date", { - data_type => "timestamp with time zone", - default_value => "now()", - is_nullable => 1, - size => 8, + data_type => "timestamp with time zone", + default_value => \"current_timestamp", + is_nullable => 1, + original => { default_value => \"now()" }, }, "create_person_id", - { data_type => "integer", default_value => undef, is_nullable => 0, size => 4 }, + { data_type => "integer", is_nullable => 0 }, "modified_date", - { - data_type => "timestamp with time zone", - default_value => undef, - is_nullable => 1, - size => 8, - }, + { data_type => "timestamp with time zone", is_nullable => 1 }, "modified_person_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "previous_metadata_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "obsolete", - { data_type => "integer", default_value => 0, is_nullable => 1, size => 4 }, + { data_type => "integer", default_value => 0, is_nullable => 1 }, "obsolete_note", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 250, - }, + { data_type => "varchar", is_nullable => 1, size => 250 }, ); __PACKAGE__->set_primary_key("metadata_id"); + +=head1 RELATIONS + +=head2 domains + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "domains", "SGN::Schema::Domain", { "foreign.metadata_id" => "self.metadata_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 domain_matches + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "domain_matches", "SGN::Schema::DomainMatch", { "foreign.metadata_id" => "self.metadata_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:4TPwTAwr+QSPbKsSYw2VDQ +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:BLIbTLwRw2MATmnZ/869rA # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Microarray.pm b/lib/SGN/Schema/Microarray.pm dissimilarity index 68% index f6581b9..a5f924d 100644 --- a/lib/SGN/Schema/Microarray.pm +++ b/lib/SGN/Schema/Microarray.pm @@ -1,55 +1,93 @@ -package SGN::Schema::Microarray; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("microarray"); -__PACKAGE__->add_columns( - "microarray_id", - { - data_type => "integer", - default_value => "nextval('microarray_microarray_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "chip_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "release", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "version", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "spot_id", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, - "content_specific_tag", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 40, - }, - "clone_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, -); -__PACKAGE__->set_primary_key("microarray_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:a52LI50lO2DcJ5YYwI/Xqg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::Microarray; + +# 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 + +SGN::Schema::Microarray + +=cut + +__PACKAGE__->table("microarray"); + +=head1 ACCESSORS + +=head2 microarray_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'microarray_microarray_id_seq' + +=head2 chip_name + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 release + + data_type: 'bigint' + is_nullable: 1 + +=head2 version + + data_type: 'bigint' + is_nullable: 1 + +=head2 spot_id + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 content_specific_tag + + data_type: 'varchar' + is_nullable: 1 + size: 40 + +=head2 clone_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "microarray_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "microarray_microarray_id_seq", + }, + "chip_name", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "release", + { data_type => "bigint", is_nullable => 1 }, + "version", + { data_type => "bigint", is_nullable => 1 }, + "spot_id", + { data_type => "varchar", is_nullable => 1, size => 20 }, + "content_specific_tag", + { data_type => "varchar", is_nullable => 1, size => 40 }, + "clone_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("microarray_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:D7MV8jLQPry3+egSyEAinA + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Misc.pm b/lib/SGN/Schema/Misc.pm dissimilarity index 64% index a9caf41..5b474aa 100644 --- a/lib/SGN/Schema/Misc.pm +++ b/lib/SGN/Schema/Misc.pm @@ -1,44 +1,69 @@ -package SGN::Schema::Misc; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("misc"); -__PACKAGE__->add_columns( - "misc_unique_id", - { - data_type => "integer", - default_value => "nextval('misc_misc_unique_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "misc_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "name", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "value", - { - data_type => "bytea", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("misc_unique_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:GdAgcG0jEjfTEGFmBJnCYg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::Misc; + +# 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 + +SGN::Schema::Misc + +=cut + +__PACKAGE__->table("misc"); + +=head1 ACCESSORS + +=head2 misc_unique_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'misc_misc_unique_id_seq' + +=head2 misc_id + + data_type: 'integer' + is_nullable: 1 + +=head2 name + + data_type: 'text' + is_nullable: 1 + +=head2 value + + data_type: 'bytea' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "misc_unique_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "misc_misc_unique_id_seq", + }, + "misc_id", + { data_type => "integer", is_nullable => 1 }, + "name", + { data_type => "text", is_nullable => 1 }, + "value", + { data_type => "bytea", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("misc_unique_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:oYvzANrnfJnxudkR0KNN6g + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Organism.pm b/lib/SGN/Schema/Organism.pm index 5585ef7..213372f 100644 --- a/lib/SGN/Schema/Organism.pm +++ b/lib/SGN/Schema/Organism.pm @@ -1,158 +1,282 @@ package SGN::Schema::Organism; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Organism + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("organism"); + +=head1 ACCESSORS + +=head2 organism_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'organism_organism_id_seq' + +=head2 organism_name + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 common_name_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 organism_descrip + + data_type: 'text' + is_nullable: 1 + +=head2 specie_tax + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 genus_tax + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 subfamily_tax + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 family_tax + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 order_tax + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 chr_n_gnmc + + data_type: 'integer' + is_nullable: 1 + +=head2 polypl_gnmc + + data_type: 'varchar' + is_nullable: 1 + size: 50 + +=head2 genom_size_gnmc + + data_type: 'varchar' + is_nullable: 1 + size: 50 + +=head2 genom_proj_gnmc + + data_type: 'text' + is_nullable: 1 + +=head2 est_attribution_tqmc + + data_type: 'text' + is_nullable: 1 + +=head2 chado_organism_id + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "organism_id", { - data_type => "integer", - default_value => "nextval('organism_organism_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "organism_organism_id_seq", }, "organism_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, + { data_type => "varchar", is_nullable => 1, size => 80 }, "common_name_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 }, "organism_descrip", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "specie_tax", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, + { data_type => "varchar", is_nullable => 1, size => 80 }, "genus_tax", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "subfamily_tax", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "family_tax", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "order_tax", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "chr_n_gnmc", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "polypl_gnmc", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 50, - }, + { data_type => "varchar", is_nullable => 1, size => 50 }, "genom_size_gnmc", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 50, - }, + { data_type => "varchar", is_nullable => 1, size => 50 }, "genom_proj_gnmc", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "est_attribution_tqmc", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, + "chado_organism_id", + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("organism_id"); __PACKAGE__->add_unique_constraint("unique_organism_name", ["organism_name"]); + +=head1 RELATIONS + +=head2 accessions + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "accessions", "SGN::Schema::Accession", { "foreign.organism_id" => "self.organism_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 deprecated_map_crosses + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "deprecated_map_crosses", "SGN::Schema::DeprecatedMapCross", { "foreign.organism_id" => "self.organism_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 order_tax + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "order_tax", "SGN::Schema::Taxonomy", { tax_id => "order_tax" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 family_tax + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "family_tax", "SGN::Schema::Taxonomy", { tax_id => "family_tax" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 genus_tax + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "genus_tax", "SGN::Schema::Taxonomy", { tax_id => "genus_tax" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 subfamily_tax + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "subfamily_tax", "SGN::Schema::Taxonomy", { tax_id => "subfamily_tax" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 common_name + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "common_name", "SGN::Schema::CommonName", { common_name_id => "common_name_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:hIsxt1nQ/SSj6bkmAl7lzg +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:P659Eo8bylRSynQff1O2mg # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Organismgroup.pm b/lib/SGN/Schema/Organismgroup.pm new file mode 100644 index 0000000..88f4264 --- /dev/null +++ b/lib/SGN/Schema/Organismgroup.pm @@ -0,0 +1,81 @@ +package SGN::Schema::Organismgroup; + +# 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 + +SGN::Schema::Organismgroup + +=cut + +__PACKAGE__->table("organismgroup"); + +=head1 ACCESSORS + +=head2 organismgroup_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'organismgroup_organismgroup_id_seq' + +=head2 name + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 type + + data_type: 'varchar' + is_nullable: 1 + size: 32 + +=cut + +__PACKAGE__->add_columns( + "organismgroup_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "organismgroup_organismgroup_id_seq", + }, + "name", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "type", + { data_type => "varchar", is_nullable => 1, size => 32 }, +); +__PACKAGE__->set_primary_key("organismgroup_id"); + +=head1 RELATIONS + +=head2 organismgroup_members + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "organismgroup_members", + "SGN::Schema::OrganismgroupMember", + { "foreign.organismgroup_id" => "self.organismgroup_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:QLDS19A29tivXEZCMuRwTQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/OrganismgroupMember.pm b/lib/SGN/Schema/OrganismgroupMember.pm new file mode 100644 index 0000000..681e3e8 --- /dev/null +++ b/lib/SGN/Schema/OrganismgroupMember.pm @@ -0,0 +1,85 @@ +package SGN::Schema::OrganismgroupMember; + +# 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 + +SGN::Schema::OrganismgroupMember + +=cut + +__PACKAGE__->table("organismgroup_member"); + +=head1 ACCESSORS + +=head2 organismgroup_member_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'organismgroup_member_organismgroup_member_id_seq' + +=head2 organismgroup_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 organism_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "organismgroup_member_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "organismgroup_member_organismgroup_member_id_seq", + }, + "organismgroup_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "organism_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("organismgroup_member_id"); + +=head1 RELATIONS + +=head2 organismgroup + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "organismgroup", + "SGN::Schema::Organismgroup", + { organismgroup_id => "organismgroup_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:iQB7M/6+aoBB0vMOkJfWZQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/PMarker.pm b/lib/SGN/Schema/PMarker.pm dissimilarity index 65% index 0400d11..ec0ce4a 100644 --- a/lib/SGN/Schema/PMarker.pm +++ b/lib/SGN/Schema/PMarker.pm @@ -1,51 +1,95 @@ -package SGN::Schema::PMarker; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("p_markers"); -__PACKAGE__->add_columns( - "pid", - { - data_type => "integer", - default_value => "nextval('p_markers_pid_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "marker_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_foreign_key => 1, - is_nullable => 0, - size => 8, - }, - "est_clone_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, - "p_mrkr_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 32, - }, -); -__PACKAGE__->set_primary_key("pid"); -__PACKAGE__->belongs_to("marker", "SGN::Schema::Marker", { marker_id => "marker_id" }); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:d9ZOQdC7WHhe7efaAvMTkA - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::PMarker; + +# 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 + +SGN::Schema::PMarker + +=cut + +__PACKAGE__->table("p_markers"); + +=head1 ACCESSORS + +=head2 pid + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'p_markers_pid_seq' + +=head2 marker_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 est_clone_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 p_mrkr_name + + data_type: 'varchar' + is_nullable: 1 + size: 32 + +=cut + +__PACKAGE__->add_columns( + "pid", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "p_markers_pid_seq", + }, + "marker_id", + { + data_type => "bigint", + default_value => "0)::bigint", + is_foreign_key => 1, + is_nullable => 0, + }, + "est_clone_id", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "p_mrkr_name", + { data_type => "varchar", is_nullable => 1, size => 32 }, +); +__PACKAGE__->set_primary_key("pid"); + +=head1 RELATIONS + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:LWa69DPqnjvcUKQ9kGXTnw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/PcrExpAccession.pm b/lib/SGN/Schema/PcrExpAccession.pm index 23c0f0b..b571b14 100644 --- a/lib/SGN/Schema/PcrExpAccession.pm +++ b/lib/SGN/Schema/PcrExpAccession.pm @@ -1,60 +1,127 @@ package SGN::Schema::PcrExpAccession; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::PcrExpAccession + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("pcr_exp_accession"); + +=head1 ACCESSORS + +=head2 pcr_exp_accession_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'pcr_exp_accession_pcr_exp_accession_id_seq' + +=head2 pcr_experiment_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 accession_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 stock_id + + data_type: 'bigint' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "pcr_exp_accession_id", { - data_type => "bigint", - default_value => "nextval('pcr_exp_accession_pcr_exp_accession_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "pcr_exp_accession_pcr_exp_accession_id_seq", }, "pcr_experiment_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "accession_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "stock_id", + { data_type => "bigint", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("pcr_exp_accession_id"); + +=head1 RELATIONS + +=head2 accession + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "accession", "SGN::Schema::Accession", { accession_id => "accession_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 pcr_experiment + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "pcr_experiment", "SGN::Schema::PcrExperiment", { pcr_experiment_id => "pcr_experiment_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 pcr_products + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "pcr_products", "SGN::Schema::PcrProduct", { "foreign.pcr_exp_accession_id" => "self.pcr_exp_accession_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:TDBVF7I+OjYXTIA7nhqBsg +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Y3RZikf9JL4YQNNoTtAMuw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/PcrExperiment.pm b/lib/SGN/Schema/PcrExperiment.pm index f45baeb..6353f28 100644 --- a/lib/SGN/Schema/PcrExperiment.pm +++ b/lib/SGN/Schema/PcrExperiment.pm @@ -1,148 +1,302 @@ package SGN::Schema::PcrExperiment; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::PcrExperiment + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("pcr_experiment"); + +=head1 ACCESSORS + +=head2 pcr_experiment_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'pcr_experiment_pcr_experiment_id_seq' + +=head2 marker_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 mg_concentration + + data_type: 'real' + is_nullable: 1 + +=head2 annealing_temp + + data_type: 'bigint' + is_nullable: 1 + +=head2 primer_id_fwd + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 primer_id_rev + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 subscript + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 experiment_type_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 map_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 additional_enzymes + + data_type: 'varchar' + is_nullable: 1 + size: 1023 + +=head2 primer_type + + data_type: 'varchar' + is_nullable: 1 + size: 4 + +=head2 predicted + + data_type: 'boolean' + default_value: false + is_nullable: 1 + +=head2 primer_id_pd + + data_type: 'bigint' + is_nullable: 1 + +=head2 accession_id + + data_type: 'varchar' + is_nullable: 1 + size: 7 + +=head2 stock_id + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "pcr_experiment_id", { - data_type => "bigint", - default_value => "nextval('pcr_experiment_pcr_experiment_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "pcr_experiment_pcr_experiment_id_seq", }, "marker_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "mg_concentration", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "real", is_nullable => 1 }, "annealing_temp", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "primer_id_fwd", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "primer_id_rev", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "subscript", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, + { data_type => "varchar", is_nullable => 1, size => 255 }, "experiment_type_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "map_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "additional_enzymes", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 1023, - }, + { data_type => "varchar", is_nullable => 1, size => 1023 }, "primer_type", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 4, - }, + { data_type => "varchar", is_nullable => 1, size => 4 }, "predicted", - { - data_type => "boolean", - default_value => "false", - is_nullable => 1, - size => 1, - }, + { data_type => "boolean", default_value => \"false", is_nullable => 1 }, "primer_id_pd", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "accession_id", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 7, - }, + { data_type => "varchar", is_nullable => 1, size => 7 }, + "stock_id", + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("pcr_experiment_id"); + +=head1 RELATIONS + +=head2 marker_experiments + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "marker_experiments", "SGN::Schema::MarkerExperiment", { "foreign.pcr_experiment_id" => "self.pcr_experiment_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 pcr_exp_accessions + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "pcr_exp_accessions", "SGN::Schema::PcrExpAccession", { "foreign.pcr_experiment_id" => "self.pcr_experiment_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 map + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "map", "SGN::Schema::Map", { map_id => "map_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 primer_id_fwd + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "primer_id_fwd", "SGN::Schema::Sequence", { sequence_id => "primer_id_fwd" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "marker", "SGN::Schema::Marker", { marker_id => "marker_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 primer_id_rev + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "primer_id_rev", "SGN::Schema::Sequence", { sequence_id => "primer_id_rev" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 experiment_type + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "experiment_type", "SGN::Schema::ExperimentType", { experiment_type_id => "experiment_type_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 pcr_experiment_sequences + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "pcr_experiment_sequences", + "SGN::Schema::PcrExperimentSequence", + { "foreign.pcr_experiment_id" => "self.pcr_experiment_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:5vVVTNXG2Bvq59KwYstpNw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Czl2BcSeTOW18DpeUyqtdw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/PcrExperimentSequence.pm b/lib/SGN/Schema/PcrExperimentSequence.pm new file mode 100644 index 0000000..5e636da --- /dev/null +++ b/lib/SGN/Schema/PcrExperimentSequence.pm @@ -0,0 +1,103 @@ +package SGN::Schema::PcrExperimentSequence; + +# 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 + +SGN::Schema::PcrExperimentSequence + +=cut + +__PACKAGE__->table("pcr_experiment_sequence"); + +=head1 ACCESSORS + +=head2 pcr_experiment_sequence_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'sgn.pcr_experiment_sequence_pcr_experiment_sequence_id_seq' + +=head2 pcr_experiment_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 sequence_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 type_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "pcr_experiment_sequence_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "sgn.pcr_experiment_sequence_pcr_experiment_sequence_id_seq", + }, + "pcr_experiment_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, + "sequence_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, + "type_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("pcr_experiment_sequence_id"); + +=head1 RELATIONS + +=head2 pcr_experiment + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "pcr_experiment", + "SGN::Schema::PcrExperiment", + { pcr_experiment_id => "pcr_experiment_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 sequence + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "sequence", + "SGN::Schema::Sequence", + { sequence_id => "sequence_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:95CRo7IhbTOypksTtsBcCw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/PcrProduct.pm b/lib/SGN/Schema/PcrProduct.pm index c7aa534..235c9b7 100644 --- a/lib/SGN/Schema/PcrProduct.pm +++ b/lib/SGN/Schema/PcrProduct.pm @@ -1,48 +1,79 @@ package SGN::Schema::PcrProduct; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::PcrProduct + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("pcr_product"); + +=head1 ACCESSORS + +=head2 pcr_product_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'pcr_product_pcr_product_id_seq' + +=head2 pcr_exp_accession_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 enzyme_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 multiple_flag + + data_type: 'bigint' + is_nullable: 1 + +=head2 band_size + + data_type: 'bigint' + is_nullable: 1 + +=head2 predicted + + data_type: 'boolean' + default_value: false + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "pcr_product_id", { - data_type => "bigint", - default_value => "nextval('pcr_product_pcr_product_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "pcr_product_pcr_product_id_seq", }, "pcr_exp_accession_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "enzyme_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "multiple_flag", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "band_size", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "predicted", - { - data_type => "boolean", - default_value => "false", - is_nullable => 1, - size => 1, - }, + { data_type => "boolean", default_value => \"false", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("pcr_product_id"); __PACKAGE__->add_unique_constraint( @@ -55,22 +86,52 @@ __PACKAGE__->add_unique_constraint( "predicted", ], ); + +=head1 RELATIONS + +=head2 enzyme + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "enzyme", "SGN::Schema::Enzyme", { enzyme_id => "enzyme_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 pcr_exp_accession + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "pcr_exp_accession", "SGN::Schema::PcrExpAccession", { pcr_exp_accession_id => "pcr_exp_accession_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:yoyMxXvBqSBDOlALFXab2A +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:0+jPJ6tov5a43+Pnryom0Q # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/PrimerUnigeneMatch.pm b/lib/SGN/Schema/PrimerUnigeneMatch.pm dissimilarity index 67% index 2a92ce1..c01d0da 100644 --- a/lib/SGN/Schema/PrimerUnigeneMatch.pm +++ b/lib/SGN/Schema/PrimerUnigeneMatch.pm @@ -1,74 +1,145 @@ -package SGN::Schema::PrimerUnigeneMatch; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("primer_unigene_match"); -__PACKAGE__->add_columns( - "primer_unigene_match_id", - { - data_type => "integer", - default_value => "nextval('primer_unigene_match_primer_unigene_match_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "marker_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, - "unigene_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, - "primer_direction", - { - data_type => "smallint", - default_value => undef, - is_nullable => 1, - size => 2, - }, - "match_length", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "primer_match_start", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "primer_match_end", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "unigene_match_start", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "unigene_match_end", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "e_value", - { - data_type => "double precision", - default_value => undef, - is_nullable => 1, - size => 8, - }, -); -__PACKAGE__->set_primary_key("primer_unigene_match_id"); -__PACKAGE__->belongs_to( - "unigene", - "SGN::Schema::Unigene", - { unigene_id => "unigene_id" }, -); -__PACKAGE__->belongs_to("marker", "SGN::Schema::Marker", { marker_id => "marker_id" }); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Mhaa3OkVosYAiGnjcBjOpg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::PrimerUnigeneMatch; + +# 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 + +SGN::Schema::PrimerUnigeneMatch + +=cut + +__PACKAGE__->table("primer_unigene_match"); + +=head1 ACCESSORS + +=head2 primer_unigene_match_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'primer_unigene_match_primer_unigene_match_id_seq' + +=head2 marker_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 unigene_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 primer_direction + + data_type: 'smallint' + is_nullable: 1 + +=head2 match_length + + data_type: 'integer' + is_nullable: 1 + +=head2 primer_match_start + + data_type: 'integer' + is_nullable: 1 + +=head2 primer_match_end + + data_type: 'integer' + is_nullable: 1 + +=head2 unigene_match_start + + data_type: 'integer' + is_nullable: 1 + +=head2 unigene_match_end + + data_type: 'integer' + is_nullable: 1 + +=head2 e_value + + data_type: 'double precision' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "primer_unigene_match_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "primer_unigene_match_primer_unigene_match_id_seq", + }, + "marker_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, + "unigene_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, + "primer_direction", + { data_type => "smallint", is_nullable => 1 }, + "match_length", + { data_type => "integer", is_nullable => 1 }, + "primer_match_start", + { data_type => "integer", is_nullable => 1 }, + "primer_match_end", + { data_type => "integer", is_nullable => 1 }, + "unigene_match_start", + { data_type => "integer", is_nullable => 1 }, + "unigene_match_end", + { data_type => "integer", is_nullable => 1 }, + "e_value", + { data_type => "double precision", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("primer_unigene_match_id"); + +=head1 RELATIONS + +=head2 unigene + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "unigene", + "SGN::Schema::Unigene", + { unigene_id => "unigene_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:yQIcs4lRRMRUxq4ycH1NUQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/QcReport.pm b/lib/SGN/Schema/QcReport.pm dissimilarity index 72% index 12b911d..23d0956 100644 --- a/lib/SGN/Schema/QcReport.pm +++ b/lib/SGN/Schema/QcReport.pm @@ -1,74 +1,172 @@ -package SGN::Schema::QcReport; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("qc_report"); -__PACKAGE__->add_columns( - "qc_id", - { - data_type => "integer", - default_value => "nextval('qc_report_qc_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "est_id", - { - data_type => "integer", - default_value => 0, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, - "basecaller", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 40, - }, - "qc_status", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "vs_status", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "qstart", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "qend", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "istart", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "iend", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "hqi_start", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "hqi_length", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "entropy", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "expected_error", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "quality_trim_threshold", - { data_type => "real", default_value => undef, is_nullable => 1, size => 4 }, - "vector_tokens", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("qc_id"); -__PACKAGE__->add_unique_constraint("qc_report_est_id_key", ["est_id"]); -__PACKAGE__->belongs_to("est", "SGN::Schema::Est", { est_id => "est_id" }); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:U4A2xfcDZEcs8fJNhex8yg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::QcReport; + +# 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 + +SGN::Schema::QcReport + +=cut + +__PACKAGE__->table("qc_report"); + +=head1 ACCESSORS + +=head2 qc_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'qc_report_qc_id_seq' + +=head2 est_id + + data_type: 'integer' + default_value: 0 + is_foreign_key: 1 + is_nullable: 0 + +=head2 basecaller + + data_type: 'varchar' + is_nullable: 1 + size: 40 + +=head2 qc_status + + data_type: 'bigint' + is_nullable: 1 + +=head2 vs_status + + data_type: 'bigint' + is_nullable: 1 + +=head2 qstart + + data_type: 'bigint' + is_nullable: 1 + +=head2 qend + + data_type: 'bigint' + is_nullable: 1 + +=head2 istart + + data_type: 'bigint' + is_nullable: 1 + +=head2 iend + + data_type: 'bigint' + is_nullable: 1 + +=head2 hqi_start + + data_type: 'bigint' + is_nullable: 1 + +=head2 hqi_length + + data_type: 'bigint' + is_nullable: 1 + +=head2 entropy + + data_type: 'real' + is_nullable: 1 + +=head2 expected_error + + data_type: 'real' + is_nullable: 1 + +=head2 quality_trim_threshold + + data_type: 'real' + is_nullable: 1 + +=head2 vector_tokens + + data_type: 'text' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "qc_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "qc_report_qc_id_seq", + }, + "est_id", + { + data_type => "integer", + default_value => 0, + is_foreign_key => 1, + is_nullable => 0, + }, + "basecaller", + { data_type => "varchar", is_nullable => 1, size => 40 }, + "qc_status", + { data_type => "bigint", is_nullable => 1 }, + "vs_status", + { data_type => "bigint", is_nullable => 1 }, + "qstart", + { data_type => "bigint", is_nullable => 1 }, + "qend", + { data_type => "bigint", is_nullable => 1 }, + "istart", + { data_type => "bigint", is_nullable => 1 }, + "iend", + { data_type => "bigint", is_nullable => 1 }, + "hqi_start", + { data_type => "bigint", is_nullable => 1 }, + "hqi_length", + { data_type => "bigint", is_nullable => 1 }, + "entropy", + { data_type => "real", is_nullable => 1 }, + "expected_error", + { data_type => "real", is_nullable => 1 }, + "quality_trim_threshold", + { data_type => "real", is_nullable => 1 }, + "vector_tokens", + { data_type => "text", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("qc_id"); +__PACKAGE__->add_unique_constraint("qc_report_est_id_key", ["est_id"]); + +=head1 RELATIONS + +=head2 est + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "est", + "SGN::Schema::Est", + { est_id => "est_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:qGjD3Odu3GmEF6yX4Kcsww + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/RflpMarker.pm b/lib/SGN/Schema/RflpMarker.pm dissimilarity index 66% index 597101d..917dba2 100644 --- a/lib/SGN/Schema/RflpMarker.pm +++ b/lib/SGN/Schema/RflpMarker.pm @@ -1,133 +1,222 @@ -package SGN::Schema::RflpMarker; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("rflp_markers"); -__PACKAGE__->add_columns( - "rflp_id", - { - data_type => "integer", - default_value => "nextval('rflp_markers_rflp_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "marker_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_foreign_key => 1, - is_nullable => 0, - size => 8, - }, - "rflp_name", - { - data_type => "character varying", - default_value => "''::character varying", - is_nullable => 0, - size => 64, - }, - "library_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 64, - }, - "clone_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 16, - }, - "vector", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 32, - }, - "cutting_site", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 32, - }, - "forward_seq_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, - "reverse_seq_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, - "insert_size", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, - "drug_resistance", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 16, - }, - "marker_prefix", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 8, - }, - "marker_suffix", - { - data_type => "smallint", - default_value => undef, - is_nullable => 1, - size => 2, - }, -); -__PACKAGE__->set_primary_key("rflp_id"); -__PACKAGE__->has_many( - "marker_experiments", - "SGN::Schema::MarkerExperiment", - { "foreign.rflp_experiment_id" => "self.rflp_id" }, -); -__PACKAGE__->belongs_to( - "reverse_seq", - "SGN::Schema::RflpSequence", - { seq_id => "reverse_seq_id" }, - { join_type => "LEFT" }, -); -__PACKAGE__->belongs_to("marker", "SGN::Schema::Marker", { marker_id => "marker_id" }); -__PACKAGE__->belongs_to( - "forward_seq", - "SGN::Schema::RflpSequence", - { seq_id => "forward_seq_id" }, - { join_type => "LEFT" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:JxKKWqpAeSVS1J43w+eieA - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::RflpMarker; + +# 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 + +SGN::Schema::RflpMarker + +=cut + +__PACKAGE__->table("rflp_markers"); + +=head1 ACCESSORS + +=head2 rflp_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'rflp_markers_rflp_id_seq' + +=head2 marker_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 rflp_name + + data_type: 'varchar' + default_value: (empty string) + is_nullable: 0 + size: 64 + +=head2 library_name + + data_type: 'varchar' + is_nullable: 1 + size: 64 + +=head2 clone_name + + data_type: 'varchar' + is_nullable: 1 + size: 16 + +=head2 vector + + data_type: 'varchar' + is_nullable: 1 + size: 32 + +=head2 cutting_site + + data_type: 'varchar' + is_nullable: 1 + size: 32 + +=head2 forward_seq_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 reverse_seq_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 insert_size + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 drug_resistance + + data_type: 'varchar' + is_nullable: 1 + size: 16 + +=head2 marker_prefix + + data_type: 'varchar' + is_nullable: 1 + size: 8 + +=head2 marker_suffix + + data_type: 'smallint' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "rflp_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "rflp_markers_rflp_id_seq", + }, + "marker_id", + { + data_type => "bigint", + default_value => "0)::bigint", + is_foreign_key => 1, + is_nullable => 0, + }, + "rflp_name", + { data_type => "varchar", default_value => "", is_nullable => 0, size => 64 }, + "library_name", + { data_type => "varchar", is_nullable => 1, size => 64 }, + "clone_name", + { data_type => "varchar", is_nullable => 1, size => 16 }, + "vector", + { data_type => "varchar", is_nullable => 1, size => 32 }, + "cutting_site", + { data_type => "varchar", is_nullable => 1, size => 32 }, + "forward_seq_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "reverse_seq_id", + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, + "insert_size", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "drug_resistance", + { data_type => "varchar", is_nullable => 1, size => 16 }, + "marker_prefix", + { data_type => "varchar", is_nullable => 1, size => 8 }, + "marker_suffix", + { data_type => "smallint", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("rflp_id"); + +=head1 RELATIONS + +=head2 marker_experiments + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "marker_experiments", + "SGN::Schema::MarkerExperiment", + { "foreign.rflp_experiment_id" => "self.rflp_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 reverse_seq + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "reverse_seq", + "SGN::Schema::RflpSequence", + { seq_id => "reverse_seq_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 forward_seq + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "forward_seq", + "SGN::Schema::RflpSequence", + { seq_id => "forward_seq_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:wLUUV2wuSGLIcP3pr3Gbbw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/RflpSequence.pm b/lib/SGN/Schema/RflpSequence.pm index 0bdc36c..ce3e8e2 100644 --- a/lib/SGN/Schema/RflpSequence.pm +++ b/lib/SGN/Schema/RflpSequence.pm @@ -1,49 +1,101 @@ package SGN::Schema::RflpSequence; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::RflpSequence + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("rflp_sequences"); + +=head1 ACCESSORS + +=head2 seq_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'rflp_sequences_seq_id_seq' + +=head2 fasta_sequence + + data_type: 'text' + is_nullable: 0 + +=cut + __PACKAGE__->add_columns( "seq_id", { - data_type => "integer", - default_value => "nextval('rflp_sequences_seq_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "rflp_sequences_seq_id_seq", }, "fasta_sequence", - { - data_type => "text", - default_value => undef, - is_nullable => 0, - size => undef, - }, + { data_type => "text", is_nullable => 0 }, ); __PACKAGE__->set_primary_key("seq_id"); + +=head1 RELATIONS + +=head2 rflp_markers_reverse_seqs + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "rflp_markers_reverse_seq_ids", + "rflp_markers_reverse_seqs", "SGN::Schema::RflpMarker", { "foreign.reverse_seq_id" => "self.seq_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 rflp_markers_forward_seqs + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "rflp_markers_forward_seq_ids", + "rflp_markers_forward_seqs", "SGN::Schema::RflpMarker", { "foreign.forward_seq_id" => "self.seq_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 rflp_unigene_associations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "rflp_unigene_associations", "SGN::Schema::RflpUnigeneAssociation", { "foreign.rflp_seq_id" => "self.seq_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:F/p7mn3ehGtnjlo2jBYtGA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:87+xNwu87RpRdUP2/z7cEg # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/RflpUnigeneAssociation.pm b/lib/SGN/Schema/RflpUnigeneAssociation.pm index 941704d..74c23ea 100644 --- a/lib/SGN/Schema/RflpUnigeneAssociation.pm +++ b/lib/SGN/Schema/RflpUnigeneAssociation.pm @@ -1,68 +1,133 @@ package SGN::Schema::RflpUnigeneAssociation; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::RflpUnigeneAssociation + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("rflp_unigene_associations"); + +=head1 ACCESSORS + +=head2 rflp_unigene_assoc_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'rflp_unigene_associations_rflp_unigene_assoc_id_seq' + +=head2 rflp_seq_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 unigene_id + + data_type: 'bigint' + is_foreign_key: 1 + is_nullable: 1 + +=head2 e_val + + data_type: 'double precision' + is_nullable: 1 + +=head2 align_length + + data_type: 'bigint' + is_nullable: 1 + +=head2 query_start + + data_type: 'bigint' + is_nullable: 1 + +=head2 query_end + + data_type: 'bigint' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "rflp_unigene_assoc_id", { - data_type => "integer", - default_value => "nextval('rflp_unigene_associations_rflp_unigene_assoc_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "rflp_unigene_associations_rflp_unigene_assoc_id_seq", }, "rflp_seq_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "unigene_id", - { - data_type => "bigint", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 8, - }, + { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 }, "e_val", - { - data_type => "double precision", - default_value => undef, - is_nullable => 1, - size => 8, - }, + { data_type => "double precision", is_nullable => 1 }, "align_length", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "query_start", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "query_end", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("rflp_unigene_assoc_id"); + +=head1 RELATIONS + +=head2 unigene + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "unigene", "SGN::Schema::Unigene", { unigene_id => "unigene_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 rflp_seq + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "rflp_seq", "SGN::Schema::RflpSequence", { seq_id => "rflp_seq_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:cti2ZvC/TzakSCOwWT0bpA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:8HiLrErnVTkuUbndvyRZ9g # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Seqread.pm b/lib/SGN/Schema/Seqread.pm dissimilarity index 65% index a73b019..f5e73d3 100644 --- a/lib/SGN/Schema/Seqread.pm +++ b/lib/SGN/Schema/Seqread.pm @@ -1,104 +1,192 @@ -package SGN::Schema::Seqread; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("seqread"); -__PACKAGE__->add_columns( - "read_id", - { - data_type => "integer", - default_value => "nextval('seqread_read_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "clone_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, - "facility_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, - "submitter_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "batch_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "primer", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 50, - }, - "direction", - { - data_type => "character", - default_value => undef, - is_nullable => 1, - size => 1, - }, - "trace_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 0, - size => 50, - }, - "trace_location", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "attribution_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "date", - { - data_type => "timestamp without time zone", - default_value => "('now'::text)::timestamp(6) with time zone", - is_nullable => 0, - size => 8, - }, - "censor_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, -); -__PACKAGE__->set_primary_key("read_id"); -__PACKAGE__->has_many( - "ests", - "SGN::Schema::Est", - { "foreign.read_id" => "self.read_id" }, -); -__PACKAGE__->belongs_to( - "clone", - "SGN::Schema::Clone", - { clone_id => "clone_id" }, - { join_type => "LEFT" }, -); -__PACKAGE__->belongs_to( - "facility", - "SGN::Schema::Facility", - { facility_id => "facility_id" }, - { join_type => "LEFT" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:OK5Wvi7LzpT5n8sSpMkcww - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::Seqread; + +# 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 + +SGN::Schema::Seqread + +=cut + +__PACKAGE__->table("seqread"); + +=head1 ACCESSORS + +=head2 read_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'seqread_read_id_seq' + +=head2 clone_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 facility_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 submitter_id + + data_type: 'integer' + is_nullable: 1 + +=head2 batch_id + + data_type: 'integer' + is_nullable: 1 + +=head2 primer + + data_type: 'varchar' + is_nullable: 1 + size: 50 + +=head2 direction + + data_type: 'char' + is_nullable: 1 + size: 1 + +=head2 trace_name + + data_type: 'varchar' + is_nullable: 0 + size: 50 + +=head2 trace_location + + data_type: 'text' + is_nullable: 1 + +=head2 attribution_id + + data_type: 'integer' + is_nullable: 1 + +=head2 date + + data_type: 'timestamp' + default_value: ('now'::text)::timestamp(6) with time zone + is_nullable: 0 + +=head2 censor_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "read_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "seqread_read_id_seq", + }, + "clone_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "facility_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "submitter_id", + { data_type => "integer", is_nullable => 1 }, + "batch_id", + { data_type => "integer", is_nullable => 1 }, + "primer", + { data_type => "varchar", is_nullable => 1, size => 50 }, + "direction", + { data_type => "char", is_nullable => 1, size => 1 }, + "trace_name", + { data_type => "varchar", is_nullable => 0, size => 50 }, + "trace_location", + { data_type => "text", is_nullable => 1 }, + "attribution_id", + { data_type => "integer", is_nullable => 1 }, + "date", + { + data_type => "timestamp", + default_value => \"('now'::text)::timestamp(6) with time zone", + is_nullable => 0, + }, + "censor_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("read_id"); + +=head1 RELATIONS + +=head2 ests + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "ests", + "SGN::Schema::Est", + { "foreign.read_id" => "self.read_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 clone + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "clone", + "SGN::Schema::Clone", + { clone_id => "clone_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 facility + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "facility", + "SGN::Schema::Facility", + { facility_id => "facility_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:hwCjt/hB/1BG2Uor6qL/tA + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Sequence.pm b/lib/SGN/Schema/Sequence.pm index d0d4e25..7b62fde 100644 --- a/lib/SGN/Schema/Sequence.pm +++ b/lib/SGN/Schema/Sequence.pm @@ -1,45 +1,133 @@ package SGN::Schema::Sequence; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Sequence + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("sequence"); + +=head1 ACCESSORS + +=head2 sequence_id + + data_type: 'bigint' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'sequence_sequence_id_seq' + +=head2 sequence + + accessor: undef + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "sequence_id", { - data_type => "bigint", - default_value => "nextval('sequence_sequence_id_seq'::regclass)", + data_type => "bigint", is_auto_increment => 1, - is_nullable => 0, - size => 8, + is_nullable => 0, + sequence => "sequence_sequence_id_seq", }, "sequence", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { accessor => undef, data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("sequence_id"); __PACKAGE__->add_unique_constraint("sequence_unique", ["sequence"]); + +=head1 RELATIONS + +=head2 pcr_experiment_primer_id_fwds + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "pcr_experiment_primer_id_fwds", "SGN::Schema::PcrExperiment", { "foreign.primer_id_fwd" => "self.sequence_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 pcr_experiment_primer_id_revs + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "pcr_experiment_primer_id_revs", "SGN::Schema::PcrExperiment", { "foreign.primer_id_rev" => "self.sequence_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 pcr_experiment_sequences + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "pcr_experiment_sequences", + "SGN::Schema::PcrExperimentSequence", + { "foreign.sequence_id" => "self.sequence_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 snp_sequence_rights + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "snp_sequence_rights", + "SGN::Schema::Snp", + { "foreign.sequence_right_id" => "self.sequence_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 snp_sequences_left + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "snp_sequences_left", + "SGN::Schema::Snp", + { "foreign.sequence_left_id" => "self.sequence_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:eVs1qu+FGIECyCsPsjlZBg +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Hckpd8VYR2jFEKhM0XoAqQ # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Snp.pm b/lib/SGN/Schema/Snp.pm new file mode 100644 index 0000000..03839b6 --- /dev/null +++ b/lib/SGN/Schema/Snp.pm @@ -0,0 +1,209 @@ +package SGN::Schema::Snp; + +# 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 + +SGN::Schema::Snp + +=cut + +__PACKAGE__->table("snp"); + +=head1 ACCESSORS + +=head2 snp_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'sgn.snp_snp_id_seq' + +=head2 marker_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 reference_nucleotide + + data_type: 'varchar' + is_nullable: 1 + size: 4 + +=head2 snp_nucleotide + + data_type: 'varchar' + is_nullable: 0 + size: 4 + +=head2 confirmed + + data_type: 'boolean' + default_value: false + is_nullable: 1 + +=head2 sequence_left_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 sequence_right_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 reference_stock_id + + data_type: 'integer' + is_nullable: 1 + +=head2 stock_id + + data_type: 'integer' + is_nullable: 0 + +=head2 metadata_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "snp_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "sgn.snp_snp_id_seq", + }, + "marker_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "reference_nucleotide", + { data_type => "varchar", is_nullable => 1, size => 4 }, + "snp_nucleotide", + { data_type => "varchar", is_nullable => 0, size => 4 }, + "confirmed", + { data_type => "boolean", default_value => \"false", is_nullable => 1 }, + "sequence_left_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "sequence_right_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "reference_stock_id", + { data_type => "integer", is_nullable => 1 }, + "stock_id", + { data_type => "integer", is_nullable => 0 }, + "metadata_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("snp_id"); + +=head1 RELATIONS + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 sequence_right + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "sequence_right", + "SGN::Schema::Sequence", + { sequence_id => "sequence_right_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 sequence_left + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "sequence_left", + "SGN::Schema::Sequence", + { sequence_id => "sequence_left_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + +=head2 snp_files + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "snp_files", + "SGN::Schema::SnpFile", + { "foreign.snp_id" => "self.snp_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 snpprops + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "snpprops", + "SGN::Schema::Snpprop", + { "foreign.snp_id" => "self.snp_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:wfxYe/YDtWLO0p2PSd+akw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/SnpFile.pm b/lib/SGN/Schema/SnpFile.pm new file mode 100644 index 0000000..4cd06d3 --- /dev/null +++ b/lib/SGN/Schema/SnpFile.pm @@ -0,0 +1,80 @@ +package SGN::Schema::SnpFile; + +# 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 + +SGN::Schema::SnpFile + +=cut + +__PACKAGE__->table("snp_file"); + +=head1 ACCESSORS + +=head2 snp_file_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'sgn.snp_file_snp_file_id_seq' + +=head2 snp_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=head2 file_id + + data_type: 'integer' + is_nullable: 0 + +=cut + +__PACKAGE__->add_columns( + "snp_file_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "sgn.snp_file_snp_file_id_seq", + }, + "snp_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, + "file_id", + { data_type => "integer", is_nullable => 0 }, +); +__PACKAGE__->set_primary_key("snp_file_id"); + +=head1 RELATIONS + +=head2 snp + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "snp", + "SGN::Schema::Snp", + { snp_id => "snp_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:hflJ0div2gwrhhgfJYql5w + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Snpprop.pm b/lib/SGN/Schema/Snpprop.pm new file mode 100644 index 0000000..c5ace33 --- /dev/null +++ b/lib/SGN/Schema/Snpprop.pm @@ -0,0 +1,100 @@ +package SGN::Schema::Snpprop; + +# 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 + +SGN::Schema::Snpprop + +=cut + +__PACKAGE__->table("snpprop"); + +=head1 ACCESSORS + +=head2 snpprop_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'sgn.snpprop_snpprop_id_seq' + +=head2 snp_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 value + + data_type: 'varchar' + is_nullable: 0 + size: 255 + +=head2 rank + + data_type: 'integer' + is_nullable: 1 + +=head2 type_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "snpprop_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "sgn.snpprop_snpprop_id_seq", + }, + "snp_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "value", + { data_type => "varchar", is_nullable => 0, size => 255 }, + "rank", + { data_type => "integer", is_nullable => 1 }, + "type_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("snpprop_id"); + +=head1 RELATIONS + +=head2 snp + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "snp", + "SGN::Schema::Snp", + { snp_id => "snp_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:GGWqOxLl9yAsP+lY6vtD6A + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Ssr.pm b/lib/SGN/Schema/Ssr.pm dissimilarity index 69% index 9b20749..501914f 100644 --- a/lib/SGN/Schema/Ssr.pm +++ b/lib/SGN/Schema/Ssr.pm @@ -1,100 +1,179 @@ -package SGN::Schema::Ssr; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("ssr"); -__PACKAGE__->add_columns( - "ssr_id", - { - data_type => "integer", - default_value => "nextval('ssr_ssr_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "marker_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_foreign_key => 1, - is_nullable => 0, - size => 8, - }, - "ssr_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 10, - }, - "est_read_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "start_primer", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 100, - }, - "end_primer", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 100, - }, - "pcr_product_ln", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "tm_start_primer", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 10, - }, - "tm_end_primer", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 10, - }, - "ann_high", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 10, - }, - "ann_low", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 10, - }, -); -__PACKAGE__->set_primary_key("ssr_id"); -__PACKAGE__->belongs_to("marker", "SGN::Schema::Marker", { marker_id => "marker_id" }); -__PACKAGE__->has_many( - "ssr_primer_unigene_matches", - "SGN::Schema::SsrPrimerUnigeneMatch", - { "foreign.ssr_id" => "self.ssr_id" }, -); -__PACKAGE__->has_many( - "ssr_repeats", - "SGN::Schema::SsrRepeat", - { "foreign.ssr_id" => "self.ssr_id" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:KsqiG9Iipum6TyPnH5ZRgQ - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::Ssr; + +# 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 + +SGN::Schema::Ssr + +=cut + +__PACKAGE__->table("ssr"); + +=head1 ACCESSORS + +=head2 ssr_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'ssr_ssr_id_seq' + +=head2 marker_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 ssr_name + + data_type: 'varchar' + is_nullable: 1 + size: 10 + +=head2 est_read_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 start_primer + + data_type: 'varchar' + is_nullable: 1 + size: 100 + +=head2 end_primer + + data_type: 'varchar' + is_nullable: 1 + size: 100 + +=head2 pcr_product_ln + + data_type: 'bigint' + is_nullable: 1 + +=head2 tm_start_primer + + data_type: 'varchar' + is_nullable: 1 + size: 10 + +=head2 tm_end_primer + + data_type: 'varchar' + is_nullable: 1 + size: 10 + +=head2 ann_high + + data_type: 'varchar' + is_nullable: 1 + size: 10 + +=head2 ann_low + + data_type: 'varchar' + is_nullable: 1 + size: 10 + +=cut + +__PACKAGE__->add_columns( + "ssr_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "ssr_ssr_id_seq", + }, + "marker_id", + { + data_type => "bigint", + default_value => "0)::bigint", + is_foreign_key => 1, + is_nullable => 0, + }, + "ssr_name", + { data_type => "varchar", is_nullable => 1, size => 10 }, + "est_read_id", + { data_type => "bigint", is_nullable => 1 }, + "start_primer", + { data_type => "varchar", is_nullable => 1, size => 100 }, + "end_primer", + { data_type => "varchar", is_nullable => 1, size => 100 }, + "pcr_product_ln", + { data_type => "bigint", is_nullable => 1 }, + "tm_start_primer", + { data_type => "varchar", is_nullable => 1, size => 10 }, + "tm_end_primer", + { data_type => "varchar", is_nullable => 1, size => 10 }, + "ann_high", + { data_type => "varchar", is_nullable => 1, size => 10 }, + "ann_low", + { data_type => "varchar", is_nullable => 1, size => 10 }, +); +__PACKAGE__->set_primary_key("ssr_id"); + +=head1 RELATIONS + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 ssr_primer_unigenes_matches + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "ssr_primer_unigenes_matches", + "SGN::Schema::SsrPrimerUnigeneMatches", + { "foreign.ssr_id" => "self.ssr_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + +=head2 ssr_repeats + +Type: has_many + +Related object: L + +=cut + +__PACKAGE__->has_many( + "ssr_repeats", + "SGN::Schema::SsrRepeat", + { "foreign.ssr_id" => "self.ssr_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:TflEqlyz1y3SHhPw5I6mAw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/SsrPrimerUnigeneMatches.pm b/lib/SGN/Schema/SsrPrimerUnigeneMatches.pm new file mode 100644 index 0000000..2b82c98 --- /dev/null +++ b/lib/SGN/Schema/SsrPrimerUnigeneMatches.pm @@ -0,0 +1,169 @@ +package SGN::Schema::SsrPrimerUnigeneMatches; + +# 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 + +SGN::Schema::SsrPrimerUnigeneMatches + +=cut + +__PACKAGE__->table("ssr_primer_unigene_matches"); + +=head1 ACCESSORS + +=head2 ssr_primer_unigene_match_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'ssr_primer_unigene_matches_ssr_primer_unigene_match_id_seq' + +=head2 ssr_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 unigene_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 primer_direction + + data_type: 'smallint' + default_value: '0)::smallint' + is_nullable: 0 + +=head2 match_length + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 primer_match_start + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 primer_match_end + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 unigene_match_start + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 unigene_match_end + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 e_value + + data_type: 'varchar' + default_value: (empty string) + is_nullable: 0 + size: 32 + +=cut + +__PACKAGE__->add_columns( + "ssr_primer_unigene_match_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "ssr_primer_unigene_matches_ssr_primer_unigene_match_id_seq", + }, + "ssr_id", + { + data_type => "bigint", + default_value => "0)::bigint", + is_foreign_key => 1, + is_nullable => 0, + }, + "unigene_id", + { + data_type => "bigint", + default_value => "0)::bigint", + is_foreign_key => 1, + is_nullable => 0, + }, + "primer_direction", + { + data_type => "smallint", + default_value => "0)::smallint", + is_nullable => 0, + }, + "match_length", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "primer_match_start", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "primer_match_end", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "unigene_match_start", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "unigene_match_end", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "e_value", + { data_type => "varchar", default_value => "", is_nullable => 0, size => 32 }, +); +__PACKAGE__->set_primary_key("ssr_primer_unigene_match_id"); + +=head1 RELATIONS + +=head2 ssr + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "ssr", + "SGN::Schema::Ssr", + { ssr_id => "ssr_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 unigene + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "unigene", + "SGN::Schema::Unigene", + { unigene_id => "unigene_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:eoWeR7fnqTULb9byE5+LHQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/SsrRepeat.pm b/lib/SGN/Schema/SsrRepeat.pm dissimilarity index 69% index ed24441..e7925d6 100644 --- a/lib/SGN/Schema/SsrRepeat.pm +++ b/lib/SGN/Schema/SsrRepeat.pm @@ -1,55 +1,118 @@ -package SGN::Schema::SsrRepeat; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("ssr_repeats"); -__PACKAGE__->add_columns( - "repeat_id", - { - data_type => "integer", - default_value => "nextval('ssr_repeats_repeat_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "ssr_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_foreign_key => 1, - is_nullable => 0, - size => 8, - }, - "repeat_motif", - { - data_type => "character varying", - default_value => "''::character varying", - is_nullable => 0, - size => 32, - }, - "reapeat_nr", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "marker_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, -); -__PACKAGE__->set_primary_key("repeat_id"); -__PACKAGE__->belongs_to("ssr", "SGN::Schema::Ssr", { ssr_id => "ssr_id" }); -__PACKAGE__->belongs_to("marker", "SGN::Schema::Marker", { marker_id => "marker_id" }); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:4MvWSZHgM6TpvARIiHW7hA - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::SsrRepeat; + +# 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 + +SGN::Schema::SsrRepeat + +=cut + +__PACKAGE__->table("ssr_repeats"); + +=head1 ACCESSORS + +=head2 repeat_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'ssr_repeats_repeat_id_seq' + +=head2 ssr_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 repeat_motif + + data_type: 'varchar' + default_value: (empty string) + is_nullable: 0 + size: 32 + +=head2 reapeat_nr + + data_type: 'bigint' + is_nullable: 1 + +=head2 marker_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 0 + +=cut + +__PACKAGE__->add_columns( + "repeat_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "ssr_repeats_repeat_id_seq", + }, + "ssr_id", + { + data_type => "bigint", + default_value => "0)::bigint", + is_foreign_key => 1, + is_nullable => 0, + }, + "repeat_motif", + { data_type => "varchar", default_value => "", is_nullable => 0, size => 32 }, + "reapeat_nr", + { data_type => "bigint", is_nullable => 1 }, + "marker_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, +); +__PACKAGE__->set_primary_key("repeat_id"); + +=head1 RELATIONS + +=head2 ssr + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "ssr", + "SGN::Schema::Ssr", + { ssr_id => "ssr_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:eqJ7PQCJuJpBf57paZCwMA + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/SubmitUser.pm b/lib/SGN/Schema/SubmitUser.pm dissimilarity index 74% index 18f01c7..bdf347f 100644 --- a/lib/SGN/Schema/SubmitUser.pm +++ b/lib/SGN/Schema/SubmitUser.pm @@ -1,95 +1,133 @@ -package SGN::Schema::SubmitUser; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("submit_user"); -__PACKAGE__->add_columns( - "submit_user_id", - { - data_type => "integer", - default_value => "nextval('submit_user_submit_user_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "submit_code", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 6, - }, - "username", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, - "password", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, - "name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "email_address", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 255, - }, - "phone_number", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 20, - }, - "organization", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 80, - }, - "contact_information", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "disabled", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "confirm_code", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 16, - }, - "sp_person_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, -); -__PACKAGE__->set_primary_key("submit_user_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:kNQSsWJyZQpBdc/8gM9arw - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::SubmitUser; + +# 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 + +SGN::Schema::SubmitUser + +=cut + +__PACKAGE__->table("submit_user"); + +=head1 ACCESSORS + +=head2 submit_user_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'submit_user_submit_user_id_seq' + +=head2 submit_code + + data_type: 'varchar' + is_nullable: 1 + size: 6 + +=head2 username + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 password + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 name + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 email_address + + data_type: 'varchar' + is_nullable: 1 + size: 255 + +=head2 phone_number + + data_type: 'varchar' + is_nullable: 1 + size: 20 + +=head2 organization + + data_type: 'varchar' + is_nullable: 1 + size: 80 + +=head2 contact_information + + data_type: 'text' + is_nullable: 1 + +=head2 disabled + + data_type: 'bigint' + is_nullable: 1 + +=head2 confirm_code + + data_type: 'varchar' + is_nullable: 1 + size: 16 + +=head2 sp_person_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "submit_user_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "submit_user_submit_user_id_seq", + }, + "submit_code", + { data_type => "varchar", is_nullable => 1, size => 6 }, + "username", + { data_type => "varchar", is_nullable => 1, size => 20 }, + "password", + { data_type => "varchar", is_nullable => 1, size => 20 }, + "name", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "email_address", + { data_type => "varchar", is_nullable => 1, size => 255 }, + "phone_number", + { data_type => "varchar", is_nullable => 1, size => 20 }, + "organization", + { data_type => "varchar", is_nullable => 1, size => 80 }, + "contact_information", + { data_type => "text", is_nullable => 1 }, + "disabled", + { data_type => "bigint", is_nullable => 1 }, + "confirm_code", + { data_type => "varchar", is_nullable => 1, size => 16 }, + "sp_person_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("submit_user_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:H8ElPRe7I8jN7AiPGWYTlw + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/Taxonomy.pm b/lib/SGN/Schema/Taxonomy.pm index b9235a8..ce67c2c 100644 --- a/lib/SGN/Schema/Taxonomy.pm +++ b/lib/SGN/Schema/Taxonomy.pm @@ -1,61 +1,125 @@ package SGN::Schema::Taxonomy; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Taxonomy + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("taxonomy"); + +=head1 ACCESSORS + +=head2 tax_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'taxonomy_tax_id_seq' + +=head2 tax_name + + data_type: 'varchar' + is_nullable: 0 + size: 50 + +=head2 tax_type + + data_type: 'varchar' + is_nullable: 1 + size: 50 + +=cut + __PACKAGE__->add_columns( "tax_id", { - data_type => "integer", - default_value => "nextval('taxonomy_tax_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "taxonomy_tax_id_seq", }, "tax_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 0, - size => 50, - }, + { data_type => "varchar", is_nullable => 0, size => 50 }, "tax_type", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 50, - }, + { data_type => "varchar", is_nullable => 1, size => 50 }, ); __PACKAGE__->set_primary_key("tax_id"); + +=head1 RELATIONS + +=head2 organism_order_taxes + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "organism_order_taxes", "SGN::Schema::Organism", { "foreign.order_tax" => "self.tax_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 organism_family_taxes + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "organism_family_taxes", "SGN::Schema::Organism", { "foreign.family_tax" => "self.tax_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 organism_genus_taxes + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "organism_genus_taxes", "SGN::Schema::Organism", { "foreign.genus_tax" => "self.tax_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 organism_subfamily_taxes + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "organism_subfamily_taxes", "SGN::Schema::Organism", { "foreign.subfamily_tax" => "self.tax_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:wKYjK6ac5YuoHDMfyWHi7w +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:oDr8F1joqs5Q8VT/s0g9Ow # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/TempCapsCorrespondence.pm b/lib/SGN/Schema/TempCapsCorrespondence.pm index e8a2ed7..a57dc88 100644 --- a/lib/SGN/Schema/TempCapsCorrespondence.pm +++ b/lib/SGN/Schema/TempCapsCorrespondence.pm @@ -1,31 +1,61 @@ package SGN::Schema::TempCapsCorrespondence; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::TempCapsCorrespondence + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("temp_caps_correspondence"); + +=head1 ACCESSORS + +=head2 tcc_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'temp_caps_correspondence_tcc_id_seq' + +=head2 old_marker_id + + data_type: 'integer' + is_nullable: 1 + +=head2 new_marker_id + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "tcc_id", { - data_type => "integer", - default_value => "nextval('temp_caps_correspondence_tcc_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "temp_caps_correspondence_tcc_id_seq", }, "old_marker_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "new_marker_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("tcc_id"); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:075hFpD8CmiOz0QSbguBIw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:aXrYHcEdAAKPM42jD48IDQ # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/TempMapCorrespondence.pm b/lib/SGN/Schema/TempMapCorrespondence.pm index aaecdd8..e1763f0 100644 --- a/lib/SGN/Schema/TempMapCorrespondence.pm +++ b/lib/SGN/Schema/TempMapCorrespondence.pm @@ -1,55 +1,105 @@ package SGN::Schema::TempMapCorrespondence; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::TempMapCorrespondence + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("temp_map_correspondence"); + +=head1 ACCESSORS + +=head2 tmc_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'temp_map_correspondence_tmc_id_seq' + +=head2 old_map_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 map_version_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "tmc_id", { - data_type => "integer", - default_value => "nextval('temp_map_correspondence_tmc_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "temp_map_correspondence_tmc_id_seq", }, "old_map_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "map_version_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, ); __PACKAGE__->set_primary_key("tmc_id"); + +=head1 RELATIONS + +=head2 old_map + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "old_map", "SGN::Schema::DeprecatedMap", { map_id => "old_map_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 map_version + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "map_version", "SGN::Schema::MapVersion", { map_version_id => "map_version_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:66XjlejiVdsJ6lyxPycYuA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:mGOVLygbNyVF5q7Z0F/yfw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/TempMarkerCorrespondence.pm b/lib/SGN/Schema/TempMarkerCorrespondence.pm index f82ece0..bc92972 100644 --- a/lib/SGN/Schema/TempMarkerCorrespondence.pm +++ b/lib/SGN/Schema/TempMarkerCorrespondence.pm @@ -1,43 +1,84 @@ package SGN::Schema::TempMarkerCorrespondence; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::TempMarkerCorrespondence + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("temp_marker_correspondence"); + +=head1 ACCESSORS + +=head2 tmc_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'temp_marker_correspondence_tmc_id_seq' + +=head2 old_marker_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 new_marker_id + + data_type: 'integer' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "tmc_id", { - data_type => "integer", - default_value => "nextval('temp_marker_correspondence_tmc_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "temp_marker_correspondence_tmc_id_seq", }, "old_marker_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "new_marker_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("tmc_id"); + +=head1 RELATIONS + +=head2 old_marker + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "old_marker", "SGN::Schema::DeprecatedMarker", { marker_id => "old_marker_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:QHMHgueh9OFeL5+j4AA1mA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:jzcHg9xbTPXMZOuGDihMRw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/TigrtcIndex.pm b/lib/SGN/Schema/TigrtcIndex.pm index ca00db7..6230911 100644 --- a/lib/SGN/Schema/TigrtcIndex.pm +++ b/lib/SGN/Schema/TigrtcIndex.pm @@ -1,34 +1,55 @@ package SGN::Schema::TigrtcIndex; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::TigrtcIndex + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("tigrtc_index"); + +=head1 ACCESSORS + +=head2 tcindex_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'tigrtc_index_tcindex_id_seq' + +=head2 index_name + + data_type: 'varchar' + is_nullable: 1 + size: 40 + +=cut + __PACKAGE__->add_columns( "tcindex_id", { - data_type => "integer", - default_value => "nextval('tigrtc_index_tcindex_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "tigrtc_index_tcindex_id_seq", }, "index_name", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 40, - }, + { data_type => "varchar", is_nullable => 1, size => 40 }, ); __PACKAGE__->set_primary_key("tcindex_id"); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:WR09mxZ1fvmOYge6y21SmA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:BH9l17I5337w6Ntxj8w3pA # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/TigrtcMembership.pm b/lib/SGN/Schema/TigrtcMembership.pm dissimilarity index 60% index f160722..7da2abc 100644 --- a/lib/SGN/Schema/TigrtcMembership.pm +++ b/lib/SGN/Schema/TigrtcMembership.pm @@ -1,34 +1,69 @@ -package SGN::Schema::TigrtcMembership; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("tigrtc_membership"); -__PACKAGE__->add_columns( - "tigrtc_membership_id", - { - data_type => "integer", - default_value => "nextval('tigrtc_membership_tigrtc_membership_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "tc_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "tcindex_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "read_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, -); -__PACKAGE__->set_primary_key("tigrtc_membership_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:4dZZwVDRbldW8VXAT9IFPA - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::TigrtcMembership; + +# 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 + +SGN::Schema::TigrtcMembership + +=cut + +__PACKAGE__->table("tigrtc_membership"); + +=head1 ACCESSORS + +=head2 tigrtc_membership_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'tigrtc_membership_tigrtc_membership_id_seq' + +=head2 tc_id + + data_type: 'integer' + is_nullable: 1 + +=head2 tcindex_id + + data_type: 'integer' + is_nullable: 1 + +=head2 read_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "tigrtc_membership_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "tigrtc_membership_tigrtc_membership_id_seq", + }, + "tc_id", + { data_type => "integer", is_nullable => 1 }, + "tcindex_id", + { data_type => "integer", is_nullable => 1 }, + "read_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("tigrtc_membership_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:BD8nFBZhcQiaB2S9Ddp3fA + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/TigrtcTracking.pm b/lib/SGN/Schema/TigrtcTracking.pm dissimilarity index 60% index a38fd8f..4095843 100644 --- a/lib/SGN/Schema/TigrtcTracking.pm +++ b/lib/SGN/Schema/TigrtcTracking.pm @@ -1,34 +1,69 @@ -package SGN::Schema::TigrtcTracking; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("tigrtc_tracking"); -__PACKAGE__->add_columns( - "tigrtc_tracking_id", - { - data_type => "integer", - default_value => "nextval('tigrtc_tracking_tigrtc_tracking_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "tc_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "current_tc_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "tcindex_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, -); -__PACKAGE__->set_primary_key("tigrtc_tracking_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:4dLwJ0ZdTTQHmdD/NFQfvw - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::TigrtcTracking; + +# 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 + +SGN::Schema::TigrtcTracking + +=cut + +__PACKAGE__->table("tigrtc_tracking"); + +=head1 ACCESSORS + +=head2 tigrtc_tracking_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'tigrtc_tracking_tigrtc_tracking_id_seq' + +=head2 tc_id + + data_type: 'integer' + is_nullable: 1 + +=head2 current_tc_id + + data_type: 'integer' + is_nullable: 1 + +=head2 tcindex_id + + data_type: 'integer' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "tigrtc_tracking_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "tigrtc_tracking_tigrtc_tracking_id_seq", + }, + "tc_id", + { data_type => "integer", is_nullable => 1 }, + "current_tc_id", + { data_type => "integer", is_nullable => 1 }, + "tcindex_id", + { data_type => "integer", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("tigrtc_tracking_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:pahILAHsMh//OSGAt0TlCQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/TmMarker.pm b/lib/SGN/Schema/TmMarker.pm dissimilarity index 68% index 10f6bf3..d34d66f 100644 --- a/lib/SGN/Schema/TmMarker.pm +++ b/lib/SGN/Schema/TmMarker.pm @@ -1,69 +1,149 @@ -package SGN::Schema::TmMarker; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("tm_markers"); -__PACKAGE__->add_columns( - "tm_id", - { - data_type => "integer", - default_value => "nextval('tm_markers_tm_id_seq'::regclass)", - is_auto_increment => 1, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, - "marker_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_foreign_key => 1, - is_nullable => 0, - size => 8, - }, - "tm_name", - { - data_type => "character varying", - default_value => "''::character varying", - is_nullable => 0, - size => 32, - }, - "old_cos_id", - { - data_type => "character varying", - default_value => undef, - is_nullable => 1, - size => 32, - }, - "seq_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "est_read_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "comment", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("tm_id"); -__PACKAGE__->belongs_to("marker", "SGN::Schema::Marker", { marker_id => "marker_id" }); -__PACKAGE__->belongs_to("tm", "SGN::Schema::TmMarker", { tm_id => "tm_id" }); -__PACKAGE__->might_have( - "tm_marker", - "SGN::Schema::TmMarker", - { "foreign.tm_id" => "self.tm_id" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:4A0prP6Kf6aJYrw/xOQPWg - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::TmMarker; + +# 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 + +SGN::Schema::TmMarker + +=cut + +__PACKAGE__->table("tm_markers"); + +=head1 ACCESSORS + +=head2 tm_id + + data_type: 'integer' + is_auto_increment: 1 + is_foreign_key: 1 + is_nullable: 0 + sequence: 'tm_markers_tm_id_seq' + +=head2 marker_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_foreign_key: 1 + is_nullable: 0 + +=head2 tm_name + + data_type: 'varchar' + default_value: (empty string) + is_nullable: 0 + size: 32 + +=head2 old_cos_id + + data_type: 'varchar' + is_nullable: 1 + size: 32 + +=head2 seq_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 est_read_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 comment + + data_type: 'text' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "tm_id", + { + data_type => "integer", + is_auto_increment => 1, + is_foreign_key => 1, + is_nullable => 0, + sequence => "tm_markers_tm_id_seq", + }, + "marker_id", + { + data_type => "bigint", + default_value => "0)::bigint", + is_foreign_key => 1, + is_nullable => 0, + }, + "tm_name", + { data_type => "varchar", default_value => "", is_nullable => 0, size => 32 }, + "old_cos_id", + { data_type => "varchar", is_nullable => 1, size => 32 }, + "seq_id", + { data_type => "bigint", is_nullable => 1 }, + "est_read_id", + { data_type => "bigint", is_nullable => 1 }, + "comment", + { data_type => "text", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("tm_id"); + +=head1 RELATIONS + +=head2 marker + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "marker", + "SGN::Schema::Marker", + { marker_id => "marker_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 tm + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "tm", + "SGN::Schema::TmMarker", + { tm_id => "tm_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 tm_marker + +Type: might_have + +Related object: L + +=cut + +__PACKAGE__->might_have( + "tm_marker", + "SGN::Schema::TmMarker", + { "foreign.tm_id" => "self.tm_id" }, + { cascade_copy => 0, cascade_delete => 0 }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:BU0F27X8KB5C22+IezQUxA + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/TmMarkersSequence.pm b/lib/SGN/Schema/TmMarkersSequence.pm dissimilarity index 63% index 988a007..b97ba73 100644 --- a/lib/SGN/Schema/TmMarkersSequence.pm +++ b/lib/SGN/Schema/TmMarkersSequence.pm @@ -1,43 +1,64 @@ -package SGN::Schema::TmMarkersSequence; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("tm_markers_sequences"); -__PACKAGE__->add_columns( - "tm_marker_seq_id", - { - data_type => "bigint", - default_value => "(0)::bigint", - is_nullable => 0, - size => 8, - }, - "tm_id", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "sequence", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, - "comment", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("tm_marker_seq_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:J7ci1jsVdv+jjqL27VoojA - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::TmMarkersSequence; + +# 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 + +SGN::Schema::TmMarkersSequence + +=cut + +__PACKAGE__->table("tm_markers_sequences"); + +=head1 ACCESSORS + +=head2 tm_marker_seq_id + + data_type: 'bigint' + default_value: '0)::bigint' + is_nullable: 0 + +=head2 tm_id + + data_type: 'bigint' + is_nullable: 1 + +=head2 sequence + + accessor: undef + data_type: 'text' + is_nullable: 1 + +=head2 comment + + data_type: 'text' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "tm_marker_seq_id", + { data_type => "bigint", default_value => "0)::bigint", is_nullable => 0 }, + "tm_id", + { data_type => "bigint", is_nullable => 1 }, + "sequence", + { accessor => undef, data_type => "text", is_nullable => 1 }, + "comment", + { data_type => "text", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("tm_marker_seq_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Ur2YJs3YnkXRw4IjdqsE2Q + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/TrimFeature.pm b/lib/SGN/Schema/TrimFeature.pm dissimilarity index 67% index 7beb82c..74d11fe 100644 --- a/lib/SGN/Schema/TrimFeature.pm +++ b/lib/SGN/Schema/TrimFeature.pm @@ -1,43 +1,83 @@ -package SGN::Schema::TrimFeature; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("trim_feature"); -__PACKAGE__->add_columns( - "feature_id", - { - data_type => "integer", - default_value => "nextval('trim_feature_feature_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "est_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "start", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "end", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "type", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "value", - { - data_type => "bytea", - default_value => undef, - is_nullable => 1, - size => undef, - }, -); -__PACKAGE__->set_primary_key("feature_id"); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:PNFx1WjR7/0Uob/+OqII3g - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::TrimFeature; + +# 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 + +SGN::Schema::TrimFeature + +=cut + +__PACKAGE__->table("trim_feature"); + +=head1 ACCESSORS + +=head2 feature_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'trim_feature_feature_id_seq' + +=head2 est_id + + data_type: 'integer' + is_nullable: 1 + +=head2 start + + data_type: 'bigint' + is_nullable: 1 + +=head2 end + + data_type: 'bigint' + is_nullable: 1 + +=head2 type + + data_type: 'bigint' + is_nullable: 1 + +=head2 value + + data_type: 'bytea' + is_nullable: 1 + +=cut + +__PACKAGE__->add_columns( + "feature_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "trim_feature_feature_id_seq", + }, + "est_id", + { data_type => "integer", is_nullable => 1 }, + "start", + { data_type => "bigint", is_nullable => 1 }, + "end", + { data_type => "bigint", is_nullable => 1 }, + "type", + { data_type => "bigint", is_nullable => 1 }, + "value", + { data_type => "bytea", is_nullable => 1 }, +); +__PACKAGE__->set_primary_key("feature_id"); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Kf4D6jnlOIcrZeWLnY9jLg + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; diff --git a/lib/SGN/Schema/TrimFeatureType.pm b/lib/SGN/Schema/TrimFeatureType.pm index 86ada05..04370ac 100644 --- a/lib/SGN/Schema/TrimFeatureType.pm +++ b/lib/SGN/Schema/TrimFeatureType.pm @@ -1,34 +1,54 @@ package SGN::Schema::TrimFeatureType; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::TrimFeatureType + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("trim_feature_types"); + +=head1 ACCESSORS + +=head2 trim_type_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'trim_feature_types_trim_type_id_seq' + +=head2 comment + + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "trim_type_id", { - data_type => "integer", - default_value => "nextval('trim_feature_types_trim_type_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "trim_feature_types_trim_type_id_seq", }, "comment", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("trim_type_id"); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:hfQo0wKkSuBkdKC5dvKeaA +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:wd2zH99Ru0tHfHcUEC1ZiQ # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Type.pm b/lib/SGN/Schema/Type.pm index a12e938..f6238b5 100644 --- a/lib/SGN/Schema/Type.pm +++ b/lib/SGN/Schema/Type.pm @@ -1,39 +1,71 @@ package SGN::Schema::Type; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Type + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("types"); + +=head1 ACCESSORS + +=head2 type_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'types_type_id_seq' + +=head2 comment + + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "type_id", { - data_type => "integer", - default_value => "nextval('types_type_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "types_type_id_seq", }, "comment", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("type_id"); + +=head1 RELATIONS + +=head2 libraries + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "libraries", "SGN::Schema::Library", { "foreign.type" => "self.type_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:bTeFTSAMcuk7+ABAxsNGDw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:U/OEq1RKwfw2+Qb3jx4B9Q # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/Unigene.pm b/lib/SGN/Schema/Unigene.pm index c833f9d..dc8c67d 100644 --- a/lib/SGN/Schema/Unigene.pm +++ b/lib/SGN/Schema/Unigene.pm @@ -1,100 +1,237 @@ package SGN::Schema::Unigene; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::Unigene + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("unigene"); + +=head1 ACCESSORS + +=head2 unigene_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'unigene_unigene_id_seq' + +=head2 unigene_build_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 consensi_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 cluster_no + + data_type: 'bigint' + is_nullable: 1 + +=head2 contig_no + + data_type: 'bigint' + is_nullable: 1 + +=head2 nr_members + + data_type: 'bigint' + is_nullable: 1 + +=head2 database_name + + data_type: 'text' + default_value: 'SGN' + is_nullable: 0 + original: {data_type => "varchar"} + +=head2 sequence_name + + data_type: 'bigint' + is_nullable: 0 + +=cut + __PACKAGE__->add_columns( "unigene_id", { - data_type => "integer", - default_value => "nextval('unigene_unigene_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "unigene_unigene_id_seq", }, "unigene_build_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "consensi_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "cluster_no", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "contig_no", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "nr_members", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, + { data_type => "bigint", is_nullable => 1 }, "database_name", { - data_type => "character varying", - default_value => "'SGN'::character varying", - is_nullable => 0, - size => undef, + data_type => "text", + default_value => "SGN", + is_nullable => 0, + original => { data_type => "varchar" }, }, "sequence_name", - { data_type => "bigint", default_value => undef, is_nullable => 0, size => 8 }, + { data_type => "bigint", is_nullable => 0 }, ); __PACKAGE__->set_primary_key("unigene_id"); + +=head1 RELATIONS + +=head2 blast_annotations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "blast_annotations", "SGN::Schema::BlastAnnotation", { "foreign.apply_id" => "self.unigene_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 cds + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "cds", "SGN::Schema::Cd", { "foreign.unigene_id" => "self.unigene_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 primer_unigene_matches + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "primer_unigene_matches", "SGN::Schema::PrimerUnigeneMatch", { "foreign.unigene_id" => "self.unigene_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 rflp_unigene_associations + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "rflp_unigene_associations", "SGN::Schema::RflpUnigeneAssociation", { "foreign.unigene_id" => "self.unigene_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 ssr_primer_unigenes_matches + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "ssr_primer_unigene_matches", - "SGN::Schema::SsrPrimerUnigeneMatch", + "ssr_primer_unigenes_matches", + "SGN::Schema::SsrPrimerUnigeneMatches", { "foreign.unigene_id" => "self.unigene_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 consensi + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "consensi", "SGN::Schema::UnigeneConsensi", { consensi_id => "consensi_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 unigene_build + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "unigene_build", "SGN::Schema::UnigeneBuild", { unigene_build_id => "unigene_build_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 unigene_members + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "unigene_members", "SGN::Schema::UnigeneMember", { "foreign.unigene_id" => "self.unigene_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:/WBLY/XERG0gUSp/aJJTvw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:HYSA+SrdRkUswvQeCSfweQ use Carp (); diff --git a/lib/SGN/Schema/UnigeneBuild.pm b/lib/SGN/Schema/UnigeneBuild.pm index 3294866..35635b0 100644 --- a/lib/SGN/Schema/UnigeneBuild.pm +++ b/lib/SGN/Schema/UnigeneBuild.pm @@ -1,139 +1,300 @@ package SGN::Schema::UnigeneBuild; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::UnigeneBuild + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("unigene_build"); + +=head1 ACCESSORS + +=head2 unigene_build_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'unigene_build_unigene_build_id_seq' + +=head2 source_data_group_id + + data_type: 'integer' + is_nullable: 1 + +=head2 organism_group_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 build_nr + + data_type: 'integer' + default_value: 0 + is_nullable: 0 + +=head2 build_date + + data_type: 'date' + default_value: current_timestamp + is_nullable: 1 + original: {default_value => \"now()"} + +=head2 method_id + + data_type: 'integer' + is_nullable: 1 + +=head2 status + + data_type: 'char' + is_nullable: 1 + size: 1 + +=head2 comment + + data_type: 'text' + is_nullable: 1 + +=head2 superseding_build_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 next_build_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 latest_build_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 blast_db_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "unigene_build_id", { - data_type => "integer", - default_value => "nextval('unigene_build_unigene_build_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "unigene_build_unigene_build_id_seq", }, "source_data_group_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, + { data_type => "integer", is_nullable => 1 }, "organism_group_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "build_nr", - { data_type => "integer", default_value => 0, is_nullable => 0, size => 4 }, + { data_type => "integer", default_value => 0, is_nullable => 0 }, "build_date", - { data_type => "date", default_value => "now()", is_nullable => 1, size => 4 }, - "method_id", - { data_type => "integer", default_value => undef, is_nullable => 1, size => 4 }, - "status", { - data_type => "character", - default_value => undef, - is_nullable => 1, - size => 1, + data_type => "date", + default_value => \"current_timestamp", + is_nullable => 1, + original => { default_value => \"now()" }, }, + "method_id", + { data_type => "integer", is_nullable => 1 }, + "status", + { data_type => "char", is_nullable => 1, size => 1 }, "comment", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "superseding_build_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "next_build_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "latest_build_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, "blast_db_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, ); __PACKAGE__->set_primary_key("unigene_build_id"); + +=head1 RELATIONS + +=head2 unigenes + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "unigenes", "SGN::Schema::Unigene", { "foreign.unigene_build_id" => "self.unigene_build_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 superseding_build + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "superseding_build", "SGN::Schema::UnigeneBuild", { unigene_build_id => "superseding_build_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 unigene_build_superseding_builds + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "unigene_build_superseding_build_ids", + "unigene_build_superseding_builds", "SGN::Schema::UnigeneBuild", { "foreign.superseding_build_id" => "self.unigene_build_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 organism_group + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "organism_group", "SGN::Schema::Group", { group_id => "organism_group_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 next_build + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "next_build", "SGN::Schema::UnigeneBuild", { unigene_build_id => "next_build_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 unigene_build_next_builds + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "unigene_build_next_build_ids", + "unigene_build_next_builds", "SGN::Schema::UnigeneBuild", { "foreign.next_build_id" => "self.unigene_build_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 latest_build + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "latest_build", "SGN::Schema::UnigeneBuild", { unigene_build_id => "latest_build_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); + +=head2 unigene_build_latest_builds + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( - "unigene_build_latest_build_ids", + "unigene_build_latest_builds", "SGN::Schema::UnigeneBuild", { "foreign.latest_build_id" => "self.unigene_build_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); + +=head2 blast_db + +Type: belongs_to + +Related object: L + +=cut + __PACKAGE__->belongs_to( "blast_db", "SGN::Schema::BlastDb", { blast_db_id => "blast_db_id" }, - { join_type => "LEFT" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:mO2nyOFlE+C9IHPdBeygug +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:EsKIExQ2mGfjNs4pxg8qfw # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/UnigeneConsensi.pm b/lib/SGN/Schema/UnigeneConsensi.pm index f8647ac..66e89ce 100644 --- a/lib/SGN/Schema/UnigeneConsensi.pm +++ b/lib/SGN/Schema/UnigeneConsensi.pm @@ -1,46 +1,78 @@ package SGN::Schema::UnigeneConsensi; +# Created by DBIx::Class::Schema::Loader +# DO NOT MODIFY THE FIRST PART OF THIS FILE + use strict; use warnings; -use base 'DBIx::Class'; +use base 'DBIx::Class::Core'; + + +=head1 NAME + +SGN::Schema::UnigeneConsensi + +=cut -__PACKAGE__->load_components("Core"); __PACKAGE__->table("unigene_consensi"); + +=head1 ACCESSORS + +=head2 consensi_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'unigene_consensi_consensi_id_seq' + +=head2 seq + + data_type: 'text' + is_nullable: 1 + +=head2 qscores + + data_type: 'text' + is_nullable: 1 + +=cut + __PACKAGE__->add_columns( "consensi_id", { - data_type => "integer", - default_value => "nextval('unigene_consensi_consensi_id_seq'::regclass)", + data_type => "integer", is_auto_increment => 1, - is_nullable => 0, - size => 4, + is_nullable => 0, + sequence => "unigene_consensi_consensi_id_seq", }, "seq", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, "qscores", - { - data_type => "text", - default_value => undef, - is_nullable => 1, - size => undef, - }, + { data_type => "text", is_nullable => 1 }, ); __PACKAGE__->set_primary_key("consensi_id"); + +=head1 RELATIONS + +=head2 unigenes + +Type: has_many + +Related object: L + +=cut + __PACKAGE__->has_many( "unigenes", "SGN::Schema::Unigene", { "foreign.consensi_id" => "self.consensi_id" }, + { cascade_copy => 0, cascade_delete => 0 }, ); -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:30PBjtpFcTdZHZq9zZbYVw +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:uXwmz0s7eNMeVns4gDuI6Q # You can replace this text with custom content, and it will be preserved on regeneration diff --git a/lib/SGN/Schema/UnigeneMember.pm b/lib/SGN/Schema/UnigeneMember.pm dissimilarity index 61% index 0975ed7..4f5bb48 100644 --- a/lib/SGN/Schema/UnigeneMember.pm +++ b/lib/SGN/Schema/UnigeneMember.pm @@ -1,70 +1,143 @@ -package SGN::Schema::UnigeneMember; - -use strict; -use warnings; - -use base 'DBIx::Class'; - -__PACKAGE__->load_components("Core"); -__PACKAGE__->table("unigene_member"); -__PACKAGE__->add_columns( - "unigene_member_id", - { - data_type => "integer", - default_value => "nextval('unigene_member_unigene_member_id_seq'::regclass)", - is_auto_increment => 1, - is_nullable => 0, - size => 4, - }, - "unigene_id", - { - data_type => "integer", - default_value => 0, - is_foreign_key => 1, - is_nullable => 0, - size => 4, - }, - "est_id", - { - data_type => "integer", - default_value => undef, - is_foreign_key => 1, - is_nullable => 1, - size => 4, - }, - "start", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "stop", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "qstart", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "qend", - { data_type => "bigint", default_value => undef, is_nullable => 1, size => 8 }, - "dir", - { - data_type => "character", - default_value => undef, - is_nullable => 1, - size => 1, - }, -); -__PACKAGE__->set_primary_key("unigene_member_id"); -__PACKAGE__->belongs_to( - "unigene", - "SGN::Schema::Unigene", - { unigene_id => "unigene_id" }, -); -__PACKAGE__->belongs_to( - "est", - "SGN::Schema::Est", - { est_id => "est_id" }, - { join_type => "LEFT" }, -); - - -# Created by DBIx::Class::Schema::Loader v0.04999_07 @ 2009-09-04 13:21:55 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:uGZKXAJHQWGHbYkl4yCpZw - - -# You can replace this text with custom content, and it will be preserved on regeneration -1; +package SGN::Schema::UnigeneMember; + +# 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 + +SGN::Schema::UnigeneMember + +=cut + +__PACKAGE__->table("unigene_member"); + +=head1 ACCESSORS + +=head2 unigene_member_id + + data_type: 'integer' + is_auto_increment: 1 + is_nullable: 0 + sequence: 'unigene_member_unigene_member_id_seq' + +=head2 unigene_id + + data_type: 'integer' + default_value: 0 + is_foreign_key: 1 + is_nullable: 0 + +=head2 est_id + + data_type: 'integer' + is_foreign_key: 1 + is_nullable: 1 + +=head2 start + + data_type: 'bigint' + is_nullable: 1 + +=head2 stop + + data_type: 'bigint' + is_nullable: 1 + +=head2 qstart + + data_type: 'bigint' + is_nullable: 1 + +=head2 qend + + data_type: 'bigint' + is_nullable: 1 + +=head2 dir + + data_type: 'char' + is_nullable: 1 + size: 1 + +=cut + +__PACKAGE__->add_columns( + "unigene_member_id", + { + data_type => "integer", + is_auto_increment => 1, + is_nullable => 0, + sequence => "unigene_member_unigene_member_id_seq", + }, + "unigene_id", + { + data_type => "integer", + default_value => 0, + is_foreign_key => 1, + is_nullable => 0, + }, + "est_id", + { data_type => "integer", is_foreign_key => 1, is_nullable => 1 }, + "start", + { data_type => "bigint", is_nullable => 1 }, + "stop", + { data_type => "bigint", is_nullable => 1 }, + "qstart", + { data_type => "bigint", is_nullable => 1 }, + "qend", + { data_type => "bigint", is_nullable => 1 }, + "dir", + { data_type => "char", is_nullable => 1, size => 1 }, +); +__PACKAGE__->set_primary_key("unigene_member_id"); + +=head1 RELATIONS + +=head2 unigene + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "unigene", + "SGN::Schema::Unigene", + { unigene_id => "unigene_id" }, + { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" }, +); + +=head2 est + +Type: belongs_to + +Related object: L + +=cut + +__PACKAGE__->belongs_to( + "est", + "SGN::Schema::Est", + { est_id => "est_id" }, + { + is_deferrable => 1, + join_type => "LEFT", + on_delete => "CASCADE", + on_update => "CASCADE", + }, +); + + +# Created by DBIx::Class::Schema::Loader v0.07002 @ 2012-03-03 12:35:39 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:2oZk+NBGlTaYYsoDTPnXHQ + + +# You can replace this text with custom content, and it will be preserved on regeneration +1; -- 2.11.4.GIT