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From: <sco...@us...> - 2012-02-28 21:26:33
|
Revision: 25255 http://gmod.svn.sourceforge.net/gmod/?rev=25255&view=rev Author: scottcain Date: 2012-02-28 21:26:20 +0000 (Tue, 28 Feb 2012) Log Message: ----------- Changed all perl script #! lines to use "/usr/bin/env perl" instead of the mishmash that was being used in various scripts. Modified Paths: -------------- schema/trunk/chado/Changes schema/trunk/chado/bin/chado-build-schema.pl schema/trunk/chado/bin/chado-fix-flybase-instance.pl schema/trunk/chado/bin/create-bridge-sql.pl schema/trunk/chado/bin/create-so-bridge.pl schema/trunk/chado/bin/ddltrans schema/trunk/chado/bin/gencode2sql.pl schema/trunk/chado/bin/gmod_add_organism.pl schema/trunk/chado/bin/gmod_apollo_triggers.pl schema/trunk/chado/bin/gmod_bulk_load_pubmed.pl schema/trunk/chado/bin/gmod_chado_properties.pl schema/trunk/chado/bin/gmod_dump_gff3.pl schema/trunk/chado/bin/gmod_extract_dbxref_from_gff.pl schema/trunk/chado/bin/gmod_fasta2gff3.pl schema/trunk/chado/bin/gmod_gff3_preprocessor.pl schema/trunk/chado/bin/gmod_make_cvtermpath.pl schema/trunk/chado/bin/gmod_make_gff_from_dbxref.pl schema/trunk/chado/bin/gmod_materialize_gbrowse_views.pl schema/trunk/chado/bin/gmod_materialized_view_tool.pl schema/trunk/chado/bin/gmod_sort_gff3.pl schema/trunk/chado/bin/gmod_update_chado.pl schema/trunk/chado/bin/interactions2SIF.pl schema/trunk/chado/bin/load_ncbi_taxonomy.pl schema/trunk/chado/bin/load_taxonomy_cvterms.pl schema/trunk/chado/bin/make_cvtermpath.pl schema/trunk/chado/bin/make_partial_indexes.pl schema/trunk/chado/bin/pg2cdbi.pl schema/trunk/chado/bin/pg2cdbi_viaTT.pl schema/trunk/chado/bin/pg2diagram.pl schema/trunk/chado/bin/pg2graphviz.pl schema/trunk/chado/bin/pg2graphviz_svg.pl schema/trunk/chado/bin/pg2html.pl schema/trunk/chado/bin/test_load.pl schema/trunk/chado/bin/ucsc_genes2gff.pl schema/trunk/chado/bin/ucsc_snp2gff.pl schema/trunk/chado/cas-utils/cgi-bin/apollo_request_region.pl schema/trunk/chado/cas-utils/cgi-bin/upload_game.pl schema/trunk/chado/chaos-xml/bin/cx-chadoxml2chaos.pl schema/trunk/chado/chaos-xml/bin/cx-chaos-report.pl schema/trunk/chado/chaos-xml/bin/cx-download-enscore.pl schema/trunk/chado/chaos-xml/bin/cx-enscore2chaos.pl schema/trunk/chado/chaos-xml/bin/cx-genbank2chaos.pl schema/trunk/chado/load/bin/load_affymetrix.pl schema/trunk/chado/load/bin/load_affyxls.pl schema/trunk/chado/load/bin/load_taxonomy.pl schema/trunk/chado/load/bin/new_gff_loader.pl schema/trunk/chado/modules/audit/make_audit_ddl schema/trunk/chado/modules/bin/makedep.pl schema/trunk/chado/modules/bin/mk.pl schema/trunk/chado/modules/cv/bridges/bin/create-bridge-sql.pl schema/trunk/chado/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl schema/trunk/chado/modules/sequence/bdgp/bin/create-so-layer.pl schema/trunk/chado/modules/sequence/bridges/bin/create-sofa-bridge.pl schema/trunk/chado/schemas/generate_diff_dirs.pl schema/trunk/chado/soi/cgi/get_xml.pl schema/trunk/chado/soi/scripts/dump_fasta.pl schema/trunk/chado/soi/scripts/dump_segment.pl schema/trunk/chado/soi/scripts/generegion.pl schema/trunk/chado/soi/t/t_soi_parse_intersect schema/trunk/chado/src/test/perl/scripts/add-implicit-loc.pl schema/trunk/chado/src/test/perl/scripts/fgraph.pl Modified: schema/trunk/chado/Changes =================================================================== --- schema/trunk/chado/Changes 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/Changes 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,6 +1,8 @@ Version 1.23 Thu Dec 1 14:45:22 EST 2011 * Added $VERSION to Bio::GMOD::DB::Config so that when installing Bio::DB::Das::Chado it would be happy. +* Changed all perl script #! lines to use /usr/bin/env perl instead of the +mishmash that was being used in various scripts. Version 1.22 Thu Nov 17 12:48:10 EST 2011 * Created a script to automatically create the schemas dirs for a release and Modified: schema/trunk/chado/bin/chado-build-schema.pl =================================================================== --- schema/trunk/chado/bin/chado-build-schema.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/chado-build-schema.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,6 +1,7 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Data::Stag; use FileHandle; use Getopt::Long; Modified: schema/trunk/chado/bin/chado-fix-flybase-instance.pl =================================================================== --- schema/trunk/chado/bin/chado-fix-flybase-instance.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/chado-fix-flybase-instance.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,6 +1,7 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use DBIx::DBStag; use Getopt::Long; Modified: schema/trunk/chado/bin/create-bridge-sql.pl =================================================================== --- schema/trunk/chado/bin/create-bridge-sql.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/create-bridge-sql.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,8 +1,9 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl # usage docs at end of file use strict; +use warnings; use Data::Stag; my %relation_type_h = (); Modified: schema/trunk/chado/bin/create-so-bridge.pl =================================================================== --- schema/trunk/chado/bin/create-so-bridge.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/create-so-bridge.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,6 +1,7 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Carp; use DBI; Modified: schema/trunk/chado/bin/ddltrans =================================================================== --- schema/trunk/chado/bin/ddltrans 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/ddltrans 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/env perl # DDLTRANS: Transform sql schema definitions into various useful formats. # (DDL=data definition language, the schema defining subset of SQL -- create table, etc.) Modified: schema/trunk/chado/bin/gencode2sql.pl =================================================================== --- schema/trunk/chado/bin/gencode2sql.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gencode2sql.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,6 +1,7 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl #This is old code and hasn't been tested! use strict; +use warnings; my @nucs = qw(T C A G); my $x = 0; Modified: schema/trunk/chado/bin/gmod_add_organism.pl =================================================================== --- schema/trunk/chado/bin/gmod_add_organism.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_add_organism.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Getopt::Long; #use lib '/home/cain/cvs_stuff/schema/chado/lib'; Modified: schema/trunk/chado/bin/gmod_apollo_triggers.pl =================================================================== --- schema/trunk/chado/bin/gmod_apollo_triggers.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_apollo_triggers.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; Modified: schema/trunk/chado/bin/gmod_bulk_load_pubmed.pl =================================================================== --- schema/trunk/chado/bin/gmod_bulk_load_pubmed.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_bulk_load_pubmed.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -91,8 +91,9 @@ =cut -#! /usr/bin/perl +#! /usr/bin/env perl use strict; +use warnings; use Bio::GMOD::Config; Modified: schema/trunk/chado/bin/gmod_chado_properties.pl =================================================================== --- schema/trunk/chado/bin/gmod_chado_properties.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_chado_properties.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Getopt::Long; #use lib '/home/cain/cvs_stuff/schema/chado/lib'; Modified: schema/trunk/chado/bin/gmod_dump_gff3.pl =================================================================== --- schema/trunk/chado/bin/gmod_dump_gff3.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_dump_gff3.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use DBI; use Bio::GMOD::Config; Modified: schema/trunk/chado/bin/gmod_extract_dbxref_from_gff.pl =================================================================== --- schema/trunk/chado/bin/gmod_extract_dbxref_from_gff.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_extract_dbxref_from_gff.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use strict; use warnings; use URI::Escape; Modified: schema/trunk/chado/bin/gmod_fasta2gff3.pl =================================================================== --- schema/trunk/chado/bin/gmod_fasta2gff3.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_fasta2gff3.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Getopt::Long; use Bio::DB::Fasta; Modified: schema/trunk/chado/bin/gmod_gff3_preprocessor.pl =================================================================== --- schema/trunk/chado/bin/gmod_gff3_preprocessor.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_gff3_preprocessor.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Bio::FeatureIO; use Getopt::Long; Modified: schema/trunk/chado/bin/gmod_make_cvtermpath.pl =================================================================== --- schema/trunk/chado/bin/gmod_make_cvtermpath.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_make_cvtermpath.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl =pod Modified: schema/trunk/chado/bin/gmod_make_gff_from_dbxref.pl =================================================================== --- schema/trunk/chado/bin/gmod_make_gff_from_dbxref.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_make_gff_from_dbxref.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use strict; use warnings; Modified: schema/trunk/chado/bin/gmod_materialize_gbrowse_views.pl =================================================================== --- schema/trunk/chado/bin/gmod_materialize_gbrowse_views.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_materialize_gbrowse_views.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Getopt::Long; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; Modified: schema/trunk/chado/bin/gmod_materialized_view_tool.pl =================================================================== --- schema/trunk/chado/bin/gmod_materialized_view_tool.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_materialized_view_tool.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,6 +1,7 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use strict; +use warnings; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; Modified: schema/trunk/chado/bin/gmod_sort_gff3.pl =================================================================== --- schema/trunk/chado/bin/gmod_sort_gff3.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_sort_gff3.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Getopt::Long; Modified: schema/trunk/chado/bin/gmod_update_chado.pl =================================================================== --- schema/trunk/chado/bin/gmod_update_chado.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/gmod_update_chado.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Getopt::Long; #use lib '/home/cain/cvs_stuff/schema/chado/lib'; Modified: schema/trunk/chado/bin/interactions2SIF.pl =================================================================== --- schema/trunk/chado/bin/interactions2SIF.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/interactions2SIF.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use DBI; use Bio::GMOD::Config; Modified: schema/trunk/chado/bin/load_ncbi_taxonomy.pl =================================================================== --- schema/trunk/chado/bin/load_ncbi_taxonomy.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/load_ncbi_taxonomy.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -138,7 +138,7 @@ =cut -#! /usr/bin/perl +#! /usr/bin/env perl use strict; Modified: schema/trunk/chado/bin/load_taxonomy_cvterms.pl =================================================================== --- schema/trunk/chado/bin/load_taxonomy_cvterms.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/load_taxonomy_cvterms.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -49,7 +49,7 @@ =cut -#!/usr/bin/perl +#!/usr/bin/env perl use strict; use Bio::GMOD::Config; Modified: schema/trunk/chado/bin/make_cvtermpath.pl =================================================================== --- schema/trunk/chado/bin/make_cvtermpath.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/make_cvtermpath.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl # assumes empty password--that should be fixed Modified: schema/trunk/chado/bin/make_partial_indexes.pl =================================================================== --- schema/trunk/chado/bin/make_partial_indexes.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/make_partial_indexes.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use DBI; Modified: schema/trunk/chado/bin/pg2cdbi.pl =================================================================== --- schema/trunk/chado/bin/pg2cdbi.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/pg2cdbi.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl # vim: set ft=perl ts=2 expandtab: use strict; Modified: schema/trunk/chado/bin/pg2cdbi_viaTT.pl =================================================================== --- schema/trunk/chado/bin/pg2cdbi_viaTT.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/pg2cdbi_viaTT.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl # vim: set ft=perl ts=2 expandtab: use strict; Modified: schema/trunk/chado/bin/pg2diagram.pl =================================================================== --- schema/trunk/chado/bin/pg2diagram.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/pg2diagram.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use SQL::Translator; use Data::Dumper; Modified: schema/trunk/chado/bin/pg2graphviz.pl =================================================================== --- schema/trunk/chado/bin/pg2graphviz.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/pg2graphviz.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use SQL::Translator; use Data::Dumper; Modified: schema/trunk/chado/bin/pg2graphviz_svg.pl =================================================================== --- schema/trunk/chado/bin/pg2graphviz_svg.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/pg2graphviz_svg.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use SQL::Translator; use Data::Dumper; Modified: schema/trunk/chado/bin/pg2html.pl =================================================================== --- schema/trunk/chado/bin/pg2html.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/pg2html.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use SQL::Translator; use Data::Dumper; Modified: schema/trunk/chado/bin/test_load.pl =================================================================== --- schema/trunk/chado/bin/test_load.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/test_load.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl # # A simple script to create the Chado database and tables. Modified: schema/trunk/chado/bin/ucsc_genes2gff.pl =================================================================== --- schema/trunk/chado/bin/ucsc_genes2gff.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/ucsc_genes2gff.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl # convert UCSC gene files into GFF3 data Modified: schema/trunk/chado/bin/ucsc_snp2gff.pl =================================================================== --- schema/trunk/chado/bin/ucsc_snp2gff.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/bin/ucsc_snp2gff.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl # convert UCSC gene files into GFF3 data Modified: schema/trunk/chado/cas-utils/cgi-bin/apollo_request_region.pl =================================================================== --- schema/trunk/chado/cas-utils/cgi-bin/apollo_request_region.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/cas-utils/cgi-bin/apollo_request_region.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use warnings; use strict; Modified: schema/trunk/chado/cas-utils/cgi-bin/upload_game.pl =================================================================== --- schema/trunk/chado/cas-utils/cgi-bin/upload_game.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/cas-utils/cgi-bin/upload_game.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use strict; use warnings; use Time::HiRes qw/gettimeofday/; Modified: schema/trunk/chado/chaos-xml/bin/cx-chadoxml2chaos.pl =================================================================== --- schema/trunk/chado/chaos-xml/bin/cx-chadoxml2chaos.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/chaos-xml/bin/cx-chadoxml2chaos.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Getopt::Long; use FileHandle; Modified: schema/trunk/chado/chaos-xml/bin/cx-chaos-report.pl =================================================================== --- schema/trunk/chado/chaos-xml/bin/cx-chaos-report.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/chaos-xml/bin/cx-chaos-report.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Getopt::Long; use Bio::Chaos::ChaosGraph; Modified: schema/trunk/chado/chaos-xml/bin/cx-download-enscore.pl =================================================================== --- schema/trunk/chado/chaos-xml/bin/cx-download-enscore.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/chaos-xml/bin/cx-download-enscore.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,6 +1,7 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Getopt::Long; use File::Glob ':glob'; Modified: schema/trunk/chado/chaos-xml/bin/cx-enscore2chaos.pl =================================================================== --- schema/trunk/chado/chaos-xml/bin/cx-enscore2chaos.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/chaos-xml/bin/cx-enscore2chaos.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Bio::Chaos::ChaosGraph; use Bio::Chaos::FeatureUtil qw(:all); Modified: schema/trunk/chado/chaos-xml/bin/cx-genbank2chaos.pl =================================================================== --- schema/trunk/chado/chaos-xml/bin/cx-genbank2chaos.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/chaos-xml/bin/cx-genbank2chaos.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Bio::Chaos::ChaosGraph; use Bio::SeqIO; Modified: schema/trunk/chado/load/bin/load_affymetrix.pl =================================================================== --- schema/trunk/chado/load/bin/load_affymetrix.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/load/bin/load_affymetrix.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use strict; use lib 'lib'; Modified: schema/trunk/chado/load/bin/load_affyxls.pl =================================================================== --- schema/trunk/chado/load/bin/load_affyxls.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/load/bin/load_affyxls.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl package Bio::Chado::CDBI::Affymetrixdchip; use lib 'lib'; Modified: schema/trunk/chado/load/bin/load_taxonomy.pl =================================================================== --- schema/trunk/chado/load/bin/load_taxonomy.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/load/bin/load_taxonomy.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl #$Id: load_taxonomy.pl,v 1.1 2006-04-17 05:22:22 allenday Exp $ #download from ftp://ftp.ncbi.nih.gov/pub/taxonomy/ use strict; Modified: schema/trunk/chado/load/bin/new_gff_loader.pl =================================================================== --- schema/trunk/chado/load/bin/new_gff_loader.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/load/bin/new_gff_loader.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Bio::Tools::GFF; use Bio::SeqIO; use Getopt::Long; Modified: schema/trunk/chado/modules/audit/make_audit_ddl =================================================================== --- schema/trunk/chado/modules/audit/make_audit_ddl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/modules/audit/make_audit_ddl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl # # make_audit_ddl # Modified: schema/trunk/chado/modules/bin/makedep.pl =================================================================== --- schema/trunk/chado/modules/bin/makedep.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/modules/bin/makedep.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl # # (c) Hilmar Lapp, hlapp at gmx.net, 2007. # @@ -6,6 +6,7 @@ # as Perl itself. Consult the Perl Artistic License. use strict; +use warnings; use Getopt::Long; ################################################################# Modified: schema/trunk/chado/modules/bin/mk.pl =================================================================== --- schema/trunk/chado/modules/bin/mk.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/modules/bin/mk.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/env perl foreach $f (@ARGV) { open(F,$f) || die("no $f"); Modified: schema/trunk/chado/modules/cv/bridges/bin/create-bridge-sql.pl =================================================================== --- schema/trunk/chado/modules/cv/bridges/bin/create-bridge-sql.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/modules/cv/bridges/bin/create-bridge-sql.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,6 +1,7 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Data::Stag; my %relation_type_h = (); Modified: schema/trunk/chado/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl =================================================================== --- schema/trunk/chado/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,5 +1,6 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; open ONTO, "ad_hoc_cv" or die "couldn't open ad_hoc_cv:$!\n"; open INSERTS, ">cv_inserts.sql" or die "couldn't open cv_inserts.sql: $!\n"; Modified: schema/trunk/chado/modules/sequence/bdgp/bin/create-so-layer.pl =================================================================== --- schema/trunk/chado/modules/sequence/bdgp/bin/create-so-layer.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/modules/sequence/bdgp/bin/create-so-layer.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,6 +1,7 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Carp; use DBI; Modified: schema/trunk/chado/modules/sequence/bridges/bin/create-sofa-bridge.pl =================================================================== --- schema/trunk/chado/modules/sequence/bridges/bin/create-sofa-bridge.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/modules/sequence/bridges/bin/create-sofa-bridge.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,6 +1,7 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl use strict; +use warnings; use Carp; use DBI; Modified: schema/trunk/chado/schemas/generate_diff_dirs.pl =================================================================== --- schema/trunk/chado/schemas/generate_diff_dirs.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/schemas/generate_diff_dirs.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use strict; use warnings; use Scalar::Util qw(looks_like_number); Modified: schema/trunk/chado/soi/cgi/get_xml.pl =================================================================== --- schema/trunk/chado/soi/cgi/get_xml.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/soi/cgi/get_xml.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/env perl BEGIN{ eval{do "config.pl"}; Modified: schema/trunk/chado/soi/scripts/dump_fasta.pl =================================================================== --- schema/trunk/chado/soi/scripts/dump_fasta.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/soi/scripts/dump_fasta.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/env perl # generegion_soi.pl Modified: schema/trunk/chado/soi/scripts/dump_segment.pl =================================================================== --- schema/trunk/chado/soi/scripts/dump_segment.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/soi/scripts/dump_segment.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/env perl use FindBin qw($RealBin); use lib (($ENV{SOI_ROOT}) || Modified: schema/trunk/chado/soi/scripts/generegion.pl =================================================================== --- schema/trunk/chado/soi/scripts/generegion.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/soi/scripts/generegion.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/env perl # generegion_soi.pl Modified: schema/trunk/chado/soi/t/t_soi_parse_intersect =================================================================== --- schema/trunk/chado/soi/t/t_soi_parse_intersect 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/soi/t/t_soi_parse_intersect 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl use lib "../"; BEGIN { @@ -11,6 +11,7 @@ } use strict; +use warnings; use XML::Parser::PerlSAX; use SOI::SOIHandler; use IO; Modified: schema/trunk/chado/src/test/perl/scripts/add-implicit-loc.pl =================================================================== --- schema/trunk/chado/src/test/perl/scripts/add-implicit-loc.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/src/test/perl/scripts/add-implicit-loc.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/env perl use XML::NestArray qw(:all); use XML::NestArray::ITextParser; use XML::NestArray::Base; @@ -6,6 +6,7 @@ use FileHandle; use strict; +use warnings; use Data::Dumper; my $nudata = Node([]); Modified: schema/trunk/chado/src/test/perl/scripts/fgraph.pl =================================================================== --- schema/trunk/chado/src/test/perl/scripts/fgraph.pl 2012-02-28 16:47:44 UTC (rev 25254) +++ schema/trunk/chado/src/test/perl/scripts/fgraph.pl 2012-02-28 21:26:20 UTC (rev 25255) @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/env perl use GraphViz; use XML::NestArray qw(:all); @@ -7,6 +7,7 @@ use FileHandle; use strict; +use warnings; use Data::Dumper; my @valid_fmts = qw(png gd pic ps gd mif pcl gd2 jpeg vrml svg); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2012-02-28 16:48:02
|
Revision: 25254 http://gmod.svn.sourceforge.net/gmod/?rev=25254&view=rev Author: scottcain Date: 2012-02-28 16:47:44 +0000 (Tue, 28 Feb 2012) Log Message: ----------- adding Bio::Chado::Schema to the prereqs Modified Paths: -------------- schema/trunk/chado/INSTALL.Chado Modified: schema/trunk/chado/INSTALL.Chado =================================================================== --- schema/trunk/chado/INSTALL.Chado 2012-01-24 19:16:18 UTC (rev 25253) +++ schema/trunk/chado/INSTALL.Chado 2012-02-28 16:47:44 UTC (rev 25254) @@ -17,7 +17,7 @@ - PostgreSQL -Currently GMOD developers are using 8.1 or better (PostgreSQL 8.4 has not +Currently GMOD developers are using 8.1 or better (PostgreSQL 9 has not been tested). Items to do with Postgres to make it ready to go: @@ -172,7 +172,7 @@ * XML::Simple (Chado) * LWP (Chado) * Template (Chado) - * Log::Log4perl (Chado) + * Bio::Chado::Schema (Chado) INSTALL THE CHADO SCHEMA This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nm...@us...> - 2012-01-24 19:16:31
|
Revision: 25253 http://gmod.svn.sourceforge.net/gmod/?rev=25253&view=rev Author: nm249 Date: 2012-01-24 19:16:18 +0000 (Tue, 24 Jan 2012) Log Message: ----------- no need for dbh. Autocommit should be on, and use schema transaction Modified Paths: -------------- schema/trunk/chado/bin/gmod_load_cvterms.pl Modified: schema/trunk/chado/bin/gmod_load_cvterms.pl =================================================================== --- schema/trunk/chado/bin/gmod_load_cvterms.pl 2011-12-01 19:46:55 UTC (rev 25252) +++ schema/trunk/chado/bin/gmod_load_cvterms.pl 2012-01-24 19:16:18 UTC (rev 25253) @@ -156,6 +156,7 @@ use Bio::GMOD::DB::Config; use Bio::Chado::Schema; +use Try::Tiny; our ($opt_d, $opt_h, $opt_H, $opt_F, $opt_n, $opt_D, $opt_v, $opt_t, $opt_u, $opt_o, $opt_p, $opt_r, $opt_g, $opt_s); @@ -203,12 +204,10 @@ $dsn .= ";host=$dbhost"; $dsn .= ";port=$port"; -my $schema= Bio::Chado::Schema->connect($dsn, $user, $pass||'', { AutoCommit=>0 }); +my $schema= Bio::Chado::Schema->connect($dsn, $user, $pass||''); -my $dbh=$schema->storage->dbh(); +if (!$schema) { die "No schema is avaiable! \n"; } -if (!$schema || !$dbh) { die "No schema or dbh is avaiable! \n"; } - ####################### my $error = 0; # keep track of input errors (in command line switches). @@ -251,42 +250,43 @@ push @onts, $ont; } message("Default namespace is " . $default_ont->name . " \n" , 1); + my $default_cv= $schema->resultset('Cv::Cv')->find_or_create( { name => $default_ont->name } , { key => 'cv_c1' }, ); foreach my $new_ont(@onts) { - my $new_ont_name=$new_ont->name(); - message("....found namespace '$new_ont_name' \n", 1); + my $coderef = sub { + my $new_ont_name=$new_ont->name(); + message("....found namespace '$new_ont_name' \n", 1); - if ($opt_n && ( $opt_n ne $new_ont_name) ) { - message ("$opt_n: skipping to next ontology..\n",1); - next (); - } - my $rel_cv; - #check if relationship ontology is already loaded: - if ($new_ont_name ne 'relationship') { - $rel_cv= $schema->resultset("Cv::Cv")->find_or_create( { name => 'relationship' } , { key => 'cv_c1' }, ); - my @rel= $schema->resultset("Cv::Cvterm")->search( - { cv_id => $rel_cv->get_column('cv_id'), - is_relationshiptype => 1, - }); - if (!@rel) { - warn "Relationship ontology must be loaded first!!\n" ; - exit(0); + if ($opt_n && ( $opt_n ne $new_ont_name) ) { + message ("$opt_n: skipping to next ontology..\n",1); + next (); } - } - ####add Typedef parsing to obo.pm!### - ####store a new cv if the ontology namespace does not exist - my $cv= $schema->resultset('Cv::Cv')->find_or_create( { name => $new_ont_name } , { key => 'cv_c1' }, ); + my $rel_cv; + #check if relationship ontology is already loaded: + if ($new_ont_name ne 'relationship') { + $rel_cv= $schema->resultset("Cv::Cv")->find_or_create( { name => 'relationship' } , { key => 'cv_c1' }, ); + my @rel= $schema->resultset("Cv::Cvterm")->search( + { cv_id => $rel_cv->get_column('cv_id'), + is_relationshiptype => 1, + }); + if (!@rel) { + warn "Relationship ontology must be loaded first!!\n" ; + exit(0); + } + } + ####add Typedef parsing to obo.pm!### + ####store a new cv if the ontology namespace does not exist + my $cv= $schema->resultset('Cv::Cv')->find_or_create( { name => $new_ont_name } , { key => 'cv_c1' }, ); - print STDERR "cv_id = ".($cv->get_column('cv_id') )."\n"; - print STDERR "Updating an ontology in the database...\n"; - my $db_ont = $cv; - my $ontology_name=$db_ont->get_column('name'); - message("Ontology name: ".($db_ont->name())."\n", 1); - my %file_relationships = (); # relationships currently defined in the file - my %db_relationships = (); - - eval { + print STDERR "cv_id = ".($cv->get_column('cv_id') )."\n"; + print STDERR "Updating an ontology in the database...\n"; + my $db_ont = $cv; + my $ontology_name=$db_ont->get_column('name'); + message("Ontology name: ".($db_ont->name())."\n", 1); + my %file_relationships = (); # relationships currently defined in the file + my %db_relationships = (); + ###### my $db = $schema->resultset("General::Db")->find_or_create( { name => $opt_s }, { key => 'db_c1' }, ); @@ -395,7 +395,7 @@ $db_index{$k}->set_column(name => $name ); $db_index{$k}->set_column( definition => $file_index{$k}->definition() ); $db_index{$k}->set_column(is_obsolete => $file_index{$k}->is_obsolete() ); - + #changing the name of obsolete terms to "$name (obsolete $db:$accession)" #to avoid violating the cvterm unique constaint (name, cv_id, is_obsolete) if ($db_index{$k}->is_obsolete() ) { @@ -476,9 +476,9 @@ my %file_secondary_ids = (); foreach my $i ($file_index{$k}->get_secondary_ids()) { + $i = substr($i, 0, 255); #dbxref.accession is varchar(255) maybe it needs to be text? $file_secondary_ids{uc($i)}=1; message("adding secondary id $i to the database...\n"); - $db_index{$k}->add_secondary_dbxref($i); } ######### @@ -638,7 +638,7 @@ print STDERR "\n"; ##################################### my $r_count = 0; - RELATIONSHIP: foreach my $r (keys(%file_relationships)) { + RELATIONSHIP: foreach my $r (keys(%file_relationships)) { $r_count++; if (!exists($db_relationships{$r})) { if ($opt_v) { print STDERR "Novel relationship: $r\n"; } @@ -737,25 +737,23 @@ ); } } - } + } message($ontology_name." : ". scalar(@novel_relationships)." novel relationships among ".(scalar(keys(%file_relationships)))." were found and stored.\n", 1); - }; - if ($@ || ($opt_t)) { - message( "Either running as trial mode (-t) or AN ERROR OCCURRED: $@\n",1); - $dbh->rollback(); - exit(0); - } - else { + if ($opt_t) { + die "TEST RUN! rolling back\n"; + } + }; + + try { + $schema->txn_do($coderef); message("Committing! \n If you are using cvtermpath you should now run gmod_make_cvtermpath.pl . See the perldoc for more info. \n\n", 1); - $dbh->commit(); + } catch { + # Transaction failed + die "An error occured! Rolling back! " . $_ . "\n"; } } -print STDERR "Done.\n"; - - - sub recursive_children { my $ont = shift; my $node = shift; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-12-01 19:47:10
|
Revision: 25252 http://gmod.svn.sourceforge.net/gmod/?rev=25252&view=rev Author: scottcain Date: 2011-12-01 19:46:55 +0000 (Thu, 01 Dec 2011) Log Message: ----------- bumping the version and adding $VERSION to Bio::GMOD::DB::Config. Modified Paths: -------------- schema/trunk/chado/Changes schema/trunk/chado/MANIFEST schema/trunk/chado/Makefile.PL schema/trunk/chado/lib/Bio/GMOD/DB/Config.pm schema/trunk/chado/load/Build.PL Added Paths: ----------- schema/trunk/chado/schemas/1-1.23/ schema/trunk/chado/schemas/1-1.23/diff.sql schema/trunk/chado/schemas/1.1-1.23/ schema/trunk/chado/schemas/1.1-1.23/diff.sql schema/trunk/chado/schemas/1.11-1.23/ schema/trunk/chado/schemas/1.11-1.23/diff.sql schema/trunk/chado/schemas/1.2-1.23/ schema/trunk/chado/schemas/1.2-1.23/diff.sql schema/trunk/chado/schemas/1.21-1.23/ schema/trunk/chado/schemas/1.21-1.23/diff.sql schema/trunk/chado/schemas/1.22-1.23/ schema/trunk/chado/schemas/1.22-1.23/diff.sql schema/trunk/chado/schemas/1.23/ schema/trunk/chado/schemas/1.23/default_schema.sql Modified: schema/trunk/chado/Changes =================================================================== --- schema/trunk/chado/Changes 2011-11-17 19:25:12 UTC (rev 25251) +++ schema/trunk/chado/Changes 2011-12-01 19:46:55 UTC (rev 25252) @@ -1,4 +1,8 @@ -Version 1.11 Thu Nov 17 12:48:10 EST 2011 +Version 1.23 Thu Dec 1 14:45:22 EST 2011 +* Added $VERSION to Bio::GMOD::DB::Config so that when installing +Bio::DB::Das::Chado it would be happy. + +Version 1.22 Thu Nov 17 12:48:10 EST 2011 * Created a script to automatically create the schemas dirs for a release and add them to the manifest. Modified: schema/trunk/chado/MANIFEST =================================================================== --- schema/trunk/chado/MANIFEST 2011-11-17 19:25:12 UTC (rev 25251) +++ schema/trunk/chado/MANIFEST 2011-12-01 19:46:55 UTC (rev 25252) @@ -353,3 +353,10 @@ schemas/1.11-1.22/diff.sql schemas/1.2-1.22/diff.sql schemas/1.21-1.22/diff.sql +#the following added by generate_diff_dirs.pl +schemas/1-1.23/diff.sql +schemas/1.1-1.23/diff.sql +schemas/1.11-1.23/diff.sql +schemas/1.2-1.23/diff.sql +schemas/1.21-1.23/diff.sql +schemas/1.22-1.23/diff.sql Modified: schema/trunk/chado/Makefile.PL =================================================================== --- schema/trunk/chado/Makefile.PL 2011-11-17 19:25:12 UTC (rev 25251) +++ schema/trunk/chado/Makefile.PL 2011-12-01 19:46:55 UTC (rev 25252) @@ -50,7 +50,7 @@ use Template; use Module::Build; -my $VERSION = 1.22; +my $VERSION = 1.23; my %args = ( DBDRIVER => { Modified: schema/trunk/chado/lib/Bio/GMOD/DB/Config.pm =================================================================== --- schema/trunk/chado/lib/Bio/GMOD/DB/Config.pm 2011-11-17 19:25:12 UTC (rev 25251) +++ schema/trunk/chado/lib/Bio/GMOD/DB/Config.pm 2011-12-01 19:46:55 UTC (rev 25252) @@ -33,6 +33,7 @@ use vars '@ISA'; use base qw/ Bio::GMOD::Config /; +my $VERSION = 1.23; =head2 new Modified: schema/trunk/chado/load/Build.PL =================================================================== --- schema/trunk/chado/load/Build.PL 2011-11-17 19:25:12 UTC (rev 25251) +++ schema/trunk/chado/load/Build.PL 2011-12-01 19:46:55 UTC (rev 25252) @@ -3,7 +3,7 @@ use Bio::Chado::Builder; use Data::Dumper; -my $VERSION = 1.22; +my $VERSION = 1.23; my $conf = shift; my $m = Bio::Chado::Builder->new( dist_name => 'Chado', Added: schema/trunk/chado/schemas/1-1.23/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.1-1.23/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.11-1.23/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.2-1.23/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.21-1.23/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.22-1.23/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.23/default_schema.sql =================================================================== --- schema/trunk/chado/schemas/1.23/default_schema.sql (rev 0) +++ schema/trunk/chado/schemas/1.23/default_schema.sql 2011-12-01 19:46:55 UTC (rev 25252) @@ -0,0 +1,41889 @@ +-- $Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $ +-- ========================================== +-- Chado general module +-- +-- ================================================ +-- TABLE: tableinfo +-- ================================================ + +create table tableinfo ( + tableinfo_id serial not null, + primary key (tableinfo_id), + name varchar(30) not null, + primary_key_column varchar(30) null, + is_view int not null default 0, + view_on_table_id int null, + superclass_table_id int null, + is_updateable int not null default 1, + modification_date date not null default now(), + constraint tableinfo_c1 unique (name) +); + +COMMENT ON TABLE tableinfo IS NULL; + +-- ================================================ +-- TABLE: db +-- ================================================ + +create table db ( + db_id serial not null, + primary key (db_id), + name varchar(255) not null, +-- contact_id int, +-- foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, + description varchar(255) null, + urlprefix varchar(255) null, + url varchar(255) null, + constraint db_c1 unique (name) +); + +COMMENT ON TABLE db IS 'A database authority. Typical databases in +bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority +is generally known by this shortened form, which is unique within the +bioinformatics and biomedical realm. To Do - add support for URIs, +URNs (e.g. LSIDs). We can do this by treating the URL as a URI - +however, some applications may expect this to be resolvable - to be +decided.'; + +-- ================================================ +-- TABLE: dbxref +-- ================================================ + +create table dbxref ( + dbxref_id serial not null, + primary key (dbxref_id), + db_id int not null, + foreign key (db_id) references db (db_id) on delete cascade INITIALLY DEFERRED, + accession varchar(255) not null, + version varchar(255) not null default '', + description text, + constraint dbxref_c1 unique (db_id,accession,version) +); +create index dbxref_idx1 on dbxref (db_id); +create index dbxref_idx2 on dbxref (accession); +create index dbxref_idx3 on dbxref (version); + +COMMENT ON TABLE dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table <T>_dbxref). A dbxref is generally written as <DB>:<ACCESSION> or as <DB>:<ACCESSION>:<VERSION>.'; + +COMMENT ON COLUMN dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.'; + +CREATE VIEW db_dbxref_count AS + SELECT db.name,count(*) AS num_dbxrefs FROM db INNER JOIN dbxref USING (db_id) GROUP BY db.name; +COMMENT ON VIEW db_dbxref_count IS 'per-db dbxref counts'; + +CREATE OR REPLACE FUNCTION store_db (VARCHAR) + RETURNS INT AS +'DECLARE + v_name ALIAS FOR $1; + + v_db_id INTEGER; + BEGIN + SELECT INTO v_db_id db_id + FROM db + WHERE name=v_name; + IF NOT FOUND THEN + INSERT INTO db + (name) + VALUES + (v_name); + RETURN currval(''db_db_id_seq''); + END IF; + RETURN v_db_id; + END; +' LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION store_dbxref (VARCHAR,VARCHAR) + RETURNS INT AS +'DECLARE + v_dbname ALIAS FOR $1; + v_accession ALIAS FOR $2; + + v_db_id INTEGER; + v_dbxref_id INTEGER; + BEGIN + SELECT INTO v_db_id + store_db(v_dbname); + SELECT INTO v_dbxref_id dbxref_id + FROM dbxref + WHERE db_id=v_db_id AND + accession=v_accession; + IF NOT FOUND THEN + INSERT INTO dbxref + (db_id,accession) + VALUES + (v_db_id,v_accession); + RETURN currval(''dbxref_dbxref_id_seq''); + END IF; + RETURN v_dbxref_id; + END; +' LANGUAGE 'plpgsql'; + +-- $Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $ +-- ========================================== +-- Chado cv module +-- +-- ================================================================= +-- Dependencies: +-- +-- :import dbxref from general +-- ================================================================= + +-- ================================================ +-- TABLE: cv +-- ================================================ +create table cv ( + cv_id serial not null, + primary key (cv_id), + name varchar(255) not null, + definition text, + constraint cv_c1 unique (name) +); + +COMMENT ON TABLE cv IS 'A controlled vocabulary or ontology. A cv is +composed of cvterms (AKA terms, classes, types, universals - relations +and properties are also stored in cvterm) and the relationships +between them.'; + +COMMENT ON COLUMN cv.name IS 'The name of the ontology. This +corresponds to the obo-format -namespace-. cv names uniquely identify +the cv. In OBO file format, the cv.name is known as the namespace.'; + +COMMENT ON COLUMN cv.definition IS 'A text description of the criteria for +membership of this ontology.'; + +-- ================================================ +-- TABLE: cvterm +-- ================================================ +create table cvterm ( + cvterm_id serial not null, + primary key (cvterm_id), + cv_id int not null, + foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, + name varchar(1024) not null, + definition text, + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, + is_obsolete int not null default 0, + is_relationshiptype int not null default 0, + constraint cvterm_c1 unique (name,cv_id,is_obsolete), + constraint cvterm_c2 unique (dbxref_id) +); +create index cvterm_idx1 on cvterm (cv_id); +create index cvterm_idx2 on cvterm (name); +create index cvterm_idx3 on cvterm (dbxref_id); + +COMMENT ON TABLE cvterm IS 'A term, class, universal or type within an +ontology or controlled vocabulary. This table is also used for +relations and properties. cvterms constitute nodes in the graph +defined by the collection of cvterms and cvterm_relationships.'; + +COMMENT ON COLUMN cvterm.cv_id IS 'The cv or ontology or namespace to which +this cvterm belongs.'; + +COMMENT ON COLUMN cvterm.name IS 'A concise human-readable name or +label for the cvterm. Uniquely identifies a cvterm within a cv.'; + +COMMENT ON COLUMN cvterm.definition IS 'A human-readable text +definition.'; + +COMMENT ON COLUMN cvterm.dbxref_id IS 'Primary identifier dbxref - The +unique global OBO identifier for this cvterm. Note that a cvterm may +have multiple secondary dbxrefs - see also table: cvterm_dbxref.'; + +COMMENT ON COLUMN cvterm.is_obsolete IS 'Boolean 0=false,1=true; see +GO documentation for details of obsoletion. Note that two terms with +different primary dbxrefs may exist if one is obsolete.'; + +COMMENT ON COLUMN cvterm.is_relationshiptype IS 'Boolean +0=false,1=true relations or relationship types (also known as Typedefs +in OBO format, or as properties or slots) form a cv/ontology in +themselves. We use this flag to indicate whether this cvterm is an +actual term/class/universal or a relation. Relations may be drawn from +the OBO Relations ontology, but are not exclusively drawn from there.'; + +COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in +different contexts; for example "chromosome" in SO and GO. A name +should be unique within an ontology or cv. A name may exist twice in a +cv, in both obsolete and non-obsolete forms - these will be for +different cvterms with different OBO identifiers; so GO documentation +for more details on obsoletion. Note that occasionally multiple +obsolete terms with the same name will exist in the same cv. If this +is a possibility for the ontology under consideration (e.g. GO) then the +ID should be appended to the name to ensure uniqueness.'; + +COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.'; + +-- ================================================ +-- TABLE: cvterm_relationship +-- ================================================ +create table cvterm_relationship ( + cvterm_relationship_id serial not null, + primary key (cvterm_relationship_id), + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + subject_id int not null, + foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + object_id int not null, + foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + constraint cvterm_relationship_c1 unique (subject_id,object_id,type_id) +); +create index cvterm_relationship_idx1 on cvterm_relationship (type_id); +create index cvterm_relationship_idx2 on cvterm_relationship (subject_id); +create index cvterm_relationship_idx3 on cvterm_relationship (object_id); + +COMMENT ON TABLE cvterm_relationship IS 'A relationship linking two +cvterms. Each cvterm_relationship constitutes an edge in the graph +defined by the collection of cvterms and cvterm_relationships. The +meaning of the cvterm_relationship depends on the definition of the +cvterm R refered to by type_id. However, in general the definitions +are such that the statement "all SUBJs REL some OBJ" is true. The +cvterm_relationship statement is about the subject, not the +object. For example "insect wing part_of thorax".'; + +COMMENT ON COLUMN cvterm_relationship.subject_id IS 'The subject of +the subj-predicate-obj sentence. The cvterm_relationship is about the +subject. In a graph, this typically corresponds to the child node.'; + +COMMENT ON COLUMN cvterm_relationship.object_id IS 'The object of the +subj-predicate-obj sentence. The cvterm_relationship refers to the +object. In a graph, this typically corresponds to the parent node.'; + +COMMENT ON COLUMN cvterm_relationship.type_id IS 'The nature of the +relationship between subject and object. Note that relations are also +housed in the cvterm table, typically from the OBO relationship +ontology, although other relationship types are allowed.'; + +-- ================================================ +-- TABLE: cvtermpath +-- ================================================ +create table cvtermpath ( + cvtermpath_id serial not null, + primary key (cvtermpath_id), + type_id int, + foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, + subject_id int not null, + foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + object_id int not null, + foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + cv_id int not null, + foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, + pathdistance int, + constraint cvtermpath_c1 unique (subject_id,object_id,type_id,pathdistance) +); +create index cvtermpath_idx1 on cvtermpath (type_id); +create index cvtermpath_idx2 on cvtermpath (subject_id); +create index cvtermpath_idx3 on cvtermpath (object_id); +create index cvtermpath_idx4 on cvtermpath (cv_id); + +COMMENT ON TABLE cvtermpath IS 'The reflexive transitive closure of +the cvterm_relationship relation.'; + +COMMENT ON COLUMN cvtermpath.type_id IS 'The relationship type that +this is a closure over. If null, then this is a closure over ALL +relationship types. If non-null, then this references a relationship +cvterm - note that the closure will apply to both this relationship +AND the OBO_REL:is_a (subclass) relationship.'; + +COMMENT ON COLUMN cvtermpath.cv_id IS 'Closures will mostly be within +one cv. If the closure of a relationship traverses a cv, then this +refers to the cv of the object_id cvterm.'; + +COMMENT ON COLUMN cvtermpath.pathdistance IS 'The number of steps +required to get from the subject cvterm to the object cvterm, counting +from zero (reflexive relationship).'; + +-- ================================================ +-- TABLE: cvtermsynonym +-- ================================================ +create table cvtermsynonym ( + cvtermsynonym_id serial not null, + primary key (cvtermsynonym_id), + cvterm_id int not null, + foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + synonym varchar(1024) not null, + type_id int, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + constraint cvtermsynonym_c1 unique (cvterm_id,synonym) +); +create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id); + +COMMENT ON TABLE cvtermsynonym IS 'A cvterm actually represents a +distinct class or concept. A concept can be refered to by different +phrases or names. In addition to the primary name (cvterm.name) there +can be a number of alternative aliases or synonyms. For example, "T +cell" as a synonym for "T lymphocyte".'; + +COMMENT ON COLUMN cvtermsynonym.type_id IS 'A synonym can be exact, +narrower, or broader than.'; + + +-- ================================================ +-- TABLE: cvterm_dbxref +-- ================================================ +create table cvterm_dbxref ( + cvterm_dbxref_id serial not null, + primary key (cvterm_dbxref_id), + cvterm_id int not null, + foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, + is_for_definition int not null default 0, + constraint cvterm_dbxref_c1 unique (cvterm_id,dbxref_id) +); +create index cvterm_dbxref_idx1 on cvterm_dbxref (cvterm_id); +create index cvterm_dbxref_idx2 on cvterm_dbxref (dbxref_id); + +COMMENT ON TABLE cvterm_dbxref IS 'In addition to the primary +identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary +identifiers/dbxrefs, which may refer to records in external +databases. The exact semantics of cvterm_dbxref are not fixed. For +example: the dbxref could be a pubmed ID that is pertinent to the +cvterm, or it could be an equivalent or similar term in another +ontology. For example, GO cvterms are typically linked to InterPro +IDs, even though the nature of the relationship between them is +largely one of statistical association. The dbxref may be have data +records attached in the same database instance, or it could be a +"hanging" dbxref pointing to some external database. NOTE: If the +desired objective is to link two cvterms together, and the nature of +the relation is known and holds for all instances of the subject +cvterm then consider instead using cvterm_relationship together with a +well-defined relation.'; + +COMMENT ON COLUMN cvterm_dbxref.is_for_definition IS 'A +cvterm.definition should be supported by one or more references. If +this column is true, the dbxref is not for a term in an external database - +it is a dbxref for provenance information for the definition.'; + + +-- ================================================ +-- TABLE: cvtermprop +-- ================================================ +create table cvtermprop ( + cvtermprop_id serial not null, + primary key (cvtermprop_id), + cvterm_id int not null, + foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade, + value text not null default '', + rank int not null default 0, + + unique(cvterm_id, type_id, value, rank) +); +create index cvtermprop_idx1 on cvtermprop (cvterm_id); +create index cvtermprop_idx2 on cvtermprop (type_id); + +COMMENT ON TABLE cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.'; + +COMMENT ON COLUMN cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; + +COMMENT ON COLUMN cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; + +COMMENT ON COLUMN cvtermprop.rank IS 'Property-Value ordering. Any +cvterm can have multiple values for any particular property type - +these are ordered in a list using rank, counting from zero. For +properties that are single-valued rather than multi-valued, the +default 0 value should be used.'; + + +-- ================================================ +-- TABLE: dbxrefprop +-- ================================================ +create table dbxrefprop ( + dbxrefprop_id serial not null, + primary key (dbxrefprop_id), + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, + value text not null default '', + rank int not null default 0, + constraint dbxrefprop_c1 unique (dbxref_id,type_id,rank) +); +create index dbxrefprop_idx1 on dbxrefprop (dbxref_id); +create index dbxrefprop_idx2 on dbxrefprop (type_id); + +COMMENT ON TABLE dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.'; + + +-- ================================================ +-- TABLE: cvprop +-- ================================================ +create table cvprop ( + cvprop_id serial not null, + primary key (cvprop_id), + cv_id int not null, + foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, + value text, + rank int not null default 0, + constraint cvprop_c1 unique (cv_id,type_id,rank) +); + +COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; + +COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; +COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; + +COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any +cv can have multiple values for any particular property type - +these are ordered in a list using rank, counting from zero. For +properties that are single-valued rather than multi-valued, the +default 0 value should be used.'; + +-- ================================================ +-- TABLE: chadoprop +-- ================================================ +create table chadoprop ( + chadoprop_id serial not null, + primary key (chadoprop_id), + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, + value text, + rank int not null default 0, + constraint chadoprop_c1 unique (type_id,rank) +); + +COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; + +COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; +COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; + +COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any +cv can have multiple values for any particular property type - +these are ordered in a list using rank, counting from zero. For +properties that are single-valued rather than multi-valued, the +default 0 value should be used.'; + +CREATE OR REPLACE VIEW cv_root AS + SELECT + cv_id, + cvterm_id AS root_cvterm_id + FROM cvterm + WHERE + cvterm_id NOT IN ( SELECT subject_id FROM cvterm_relationship) AND + is_obsolete=0; + +COMMENT ON VIEW cv_root IS 'the roots of a cv are the set of terms +which have no parents (terms that are not the subject of a +relation). Most cvs will have a single root, some may have >1. All +will have at least 1'; + +CREATE OR REPLACE VIEW cv_leaf AS + SELECT + cv_id, + cvterm_id + FROM cvterm + WHERE + cvterm_id NOT IN ( SELECT object_id FROM cvterm_relationship); + +COMMENT ON VIEW cv_leaf IS 'the leaves of a cv are the set of terms +which have no children (terms that are not the object of a +relation). All cvs will have at least 1 leaf'; + +CREATE OR REPLACE VIEW common_ancestor_cvterm AS + SELECT + p1.subject_id AS cvterm1_id, + p2.subject_id AS cvterm2_id, + p1.object_id AS ancestor_cvterm_id, + p1.pathdistance AS pathdistance1, + p2.pathdistance AS pathdistance2, + p1.pathdistance + p2.pathdistance + AS total_pathdistance + FROM + cvtermpath AS p1, + cvtermpath AS p2 + WHERE + p1.object_id = p2.object_id; + +COMMENT ON VIEW common_ancestor_cvterm IS 'The common ancestor of any +two terms is the intersection of both terms ancestors. Two terms can +have multiple common ancestors. Use total_pathdistance to get the +least common ancestor'; + +CREATE OR REPLACE VIEW common_descendant_cvterm AS + SELECT + p1.object_id AS cvterm1_id, + p2.object_id AS cvterm2_id, + p1.subject_id AS ancestor_cvterm_id, + p1.pathdistance AS pathdistance1, + p2.pathdistance AS pathdistance2, + p1.pathdistance + p2.pathdistance + AS total_pathdistance + FROM + cvtermpath AS p1, + cvtermpath AS p2 + WHERE + p1.subject_id = p2.subject_id; + +COMMENT ON VIEW common_descendant_cvterm IS 'The common descendant of +any two terms is the intersection of both terms descendants. Two terms +can have multiple common descendants. Use total_pathdistance to get +the least common ancestor'; + +CREATE OR REPLACE VIEW stats_paths_to_root AS + SELECT + subject_id AS cvterm_id, + count(DISTINCT cvtermpath_id) AS total_paths, + avg(pathdistance) AS avg_distance, + min(pathdistance) AS min_distance, + max(pathdistance) AS max_distance + FROM cvtermpath INNER JOIN cv_root ON (object_id=root_cvterm_id) + GROUP BY cvterm_id; + +COMMENT ON VIEW stats_paths_to_root IS 'per-cvterm statistics on its +placement in the DAG relative to the root. There may be multiple paths +from any term to the root. This gives the total number of paths, and +the average minimum and maximum distances. Here distance is defined by +cvtermpath.pathdistance'; +CREATE VIEW cv_cvterm_count AS + SELECT cv.name,count(*) AS num_terms_excl_obs FROM cv INNER JOIN cvterm USING (cv_id) WHERE is_obsolete=0 GROUP BY cv.name; +COMMENT ON VIEW cv_cvterm_count IS 'per-cv terms counts (excludes obsoletes)'; + +CREATE VIEW cv_cvterm_count_with_obs AS + SELECT cv.name,count(*) AS num_terms_incl_obs FROM cv INNER JOIN cvterm USING (cv_id) GROUP BY cv.name; +COMMENT ON VIEW cv_cvterm_count_with_obs IS 'per-cv terms counts (includes obsoletes)'; + +CREATE VIEW cv_link_count AS + SELECT cv.name AS cv_name, + relation.name AS relation_name, + relation_cv.name AS relation_cv_name, + count(*) AS num_links + FROM cv + INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) + INNER JOIN cvterm_relationship ON (cvterm.cvterm_id=subject_id) + INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) + INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) + GROUP BY cv.name,relation.name,relation_cv.name; + +COMMENT ON VIEW cv_link_count IS 'per-cv summary of number of +links (cvterm_relationships) broken down by +relationship_type. num_links is the total # of links of the specified +type in which the subject_id of the link is in the named cv'; + +CREATE VIEW cv_path_count AS + SELECT cv.name AS cv_name, + relation.name AS relation_name, + relation_cv.name AS relation_cv_name, + count(*) AS num_paths + FROM cv + INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) + INNER JOIN cvtermpath ON (cvterm.cvterm_id=subject_id) + INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) + INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) + GROUP BY cv.name,relation.name,relation_cv.name; + +COMMENT ON VIEW cv_path_count IS 'per-cv summary of number of +paths (cvtermpaths) broken down by relationship_type. num_paths is the +total # of paths of the specified type in which the subject_id of the +path is in the named cv. See also: cv_distinct_relations'; + +CREATE OR REPLACE FUNCTION _get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + root alias for $1; + cterm cvtermpath%ROWTYPE; + cterm2 cvtermpath%ROWTYPE; +BEGIN + + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP + RETURN NEXT cterm; + FOR cterm2 IN SELECT * FROM _get_all_subject_ids(cterm.subject_id) LOOP + RETURN NEXT cterm2; + END LOOP; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +---arg: parent term id +---return: all children term id and their parent term id with relationship type id +CREATE OR REPLACE FUNCTION get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + root alias for $1; + cterm cvtermpath%ROWTYPE; + exist_c int; +BEGIN + + SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = root and pathdistance <= 0; + IF (exist_c > 0) THEN + FOR cterm IN SELECT * FROM cvtermpath WHERE object_id = root and pathdistance > 0 LOOP + RETURN NEXT cterm; + END LOOP; + ELSE + FOR cterm IN SELECT * FROM _get_all_subject_ids(root) LOOP + RETURN NEXT cterm; + END LOOP; + END IF; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION get_graph_below(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + root alias for $1; + cterm cvtermpath%ROWTYPE; + cterm2 cvtermpath%ROWTYPE; + +BEGIN + + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP + RETURN NEXT cterm; + FOR cterm2 IN SELECT * FROM get_all_subject_ids(cterm.subject_id) LOOP + RETURN NEXT cterm2; + END LOOP; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + + +CREATE OR REPLACE FUNCTION get_graph_above(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + leaf alias for $1; + cterm cvtermpath%ROWTYPE; + cterm2 cvtermpath%ROWTYPE; + +BEGIN + + FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP + RETURN NEXT cterm; + FOR cterm2 IN SELECT * FROM get_all_object_ids(cterm.object_id) LOOP + RETURN NEXT cterm2; + END LOOP; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION _get_all_object_ids(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + leaf alias for $1; + cterm cvtermpath%ROWTYPE; + cterm2 cvtermpath%ROWTYPE; +BEGIN + + FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP + RETURN NEXT cterm; + FOR cterm2 IN SELECT * FROM _get_all_object_ids(cterm.object_id) LOOP + RETURN NEXT cterm2; + END LOOP; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +---arg: child term id +---return: all parent term id and their childrent term id with relationship type id +CREATE OR REPLACE FUNCTION get_all_object_ids(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + leaf alias for $1; + cterm cvtermpath%ROWTYPE; + exist_c int; +BEGIN + + + SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = leaf and pathdistance <= 0; + IF (exist_c > 0) THEN + FOR cterm IN SELECT * FROM cvtermpath WHERE subject_id = leaf AND pathdistance > 0 LOOP + RETURN NEXT cterm; + END LOOP; + ELSE + FOR cterm IN SELECT * FROM _get_all_object_ids(leaf) LOOP + RETURN NEXT cterm; + END LOOP; + END IF; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +---arg: sql statement which must be in the form of select cvterm_id from ... +---return: a set of cvterm ids that includes what is in sql statement and their children (subject ids) +CREATE OR REPLACE FUNCTION get_it_sub_cvterm_ids(text) RETURNS SETOF cvterm AS +' +DECLARE + query alias for $1; + cterm cvterm%ROWTYPE; + cterm2 cvterm%ROWTYPE; +BEGIN + FOR cterm IN EXECUTE query LOOP + RETURN NEXT cterm; + FOR cterm2 IN SELECT subject_id as cvterm_id FROM get_all_subject_ids(cterm.cvterm_id) LOOP + RETURN NEXT cterm2; + END LOOP; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; +--- example: select * from fill_cvtermpath(7); where 7 is cv_id for an ontology +--- fill path from the node to its children and their children +CREATE OR REPLACE FUNCTION _fill_cvtermpath4node(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS +' +DECLARE + origin alias for $1; + child_id alias for $2; + cvid alias for $3; + typeid alias for $4; + depth alias for $5; + cterm cvterm_relationship%ROWTYPE; + exist_c int; + +BEGIN + + --- RAISE NOTICE ''depth=% root=%'', depth,child_id; + --- not check type_id as it may be null and not very meaningful in cvtermpath when pathdistance > 1 + SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; + + IF (exist_c = 0) THEN + INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); + END IF; + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP + PERFORM _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); + END LOOP; + RETURN 1; +END; +' +LANGUAGE 'plpgsql'; + + +CREATE OR REPLACE FUNCTION _fill_cvtermpath4root(INTEGER, INTEGER) RETURNS INTEGER AS +' +DECLARE + rootid alias for $1; + cvid alias for $2; + ttype int; + cterm cvterm_relationship%ROWTYPE; + child cvterm_relationship%ROWTYPE; + +BEGIN + + SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); + PERFORM _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0); + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP + PERFORM _fill_cvtermpath4root(cterm.subject_id, cvid); + -- RAISE NOTICE ''DONE for term, %'', cterm.subject_id; + END LOOP; + RETURN 1; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION fill_cvtermpath(INTEGER) RETURNS INTEGER AS +' +DECLARE + cvid alias for $1; + root cvterm%ROWTYPE; + +BEGIN + + DELETE FROM cvtermpath WHERE cv_id = cvid; + + FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP + PERFORM _fill_cvtermpath4root(root.cvterm_id, root.cv_id); + END LOOP; + RETURN 1; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION fill_cvtermpath(cv.name%TYPE) RETURNS INTEGER AS +' +DECLARE + cvname alias for $1; + cv_id int; + rtn int; +BEGIN + + SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; + SELECT INTO rtn fill_cvtermpath(cv_id); + RETURN rtn; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION _fill_cvtermpath4node2detect_cycle(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS +' +DECLARE + origin alias for $1; + child_id alias for $2; + cvid alias for $3; + typeid alias for $4; + depth alias for $5; + cterm cvterm_relationship%ROWTYPE; + exist_c int; + ccount int; + ecount int; + rtn int; +BEGIN + + EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id = ''|| origin || '' AND p2.subject_id = '' || child_id || ''AND '' || depth || ''> 0''; + GET DIAGNOSTICS ccount = ROW_COUNT; + IF (ccount > 0) THEN + --RAISE EXCEPTION ''FOUND CYCLE: node % on cycle path'',origin; + RETURN origin; + END IF; + + EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND '' || origin || ''<>'' || child_id; + GET DIAGNOSTICS ecount = ROW_COUNT; + IF (ecount > 0) THEN + --RAISE NOTICE ''FOUND TWICE (node), will check root obj % subj %'',origin, child_id; + SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(child_id, cvid); + IF (rtn > 0) THEN + RETURN rtn; + END IF; + END IF; + + EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND pathdistance = '' || depth; + GET DIAGNOSTICS exist_c = ROW_COUNT; + IF (exist_c = 0) THEN + EXECUTE ''INSERT INTO tmpcvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES('' || origin || '', '' || child_id || '', '' || cvid || '', '' || typeid || '', '' || depth || '')''; + END IF; + + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP + --RAISE NOTICE ''DOING for node, % %'', origin, cterm.subject_id; + SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); + IF (rtn > 0) THEN + RETURN rtn; + END IF; + END LOOP; + RETURN 0; +END; +' +LANGUAGE 'plpgsql'; + + +CREATE OR REPLACE FUNCTION _fill_cvtermpath4root2detect_cycle(INTEGER, INTEGER) RETURNS INTEGER AS +' +DECLARE + rootid alias for $1; + cvid alias for $2; + ttype int; + ccount int; + cterm cvterm_relationship%ROWTYPE; + child cvterm_relationship%ROWTYPE; + rtn int; +BEGIN + + SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); + SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, rootid, cvid, ttype, 0); + IF (rtn > 0) THEN + RETURN rtn; + END IF; + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP + EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id='' || rootid || '' AND p1.subject_id='' || cterm.subject_id; + GET DIAGNOSTICS ccount = ROW_COUNT; + IF (ccount > 0) THEN + --RAISE NOTICE ''FOUND TWICE (root), will check root obj % subj %'',rootid,cterm.subject_id; + SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, cterm.subject_id, cvid, ttype, 0); + IF (rtn > 0) THEN + RETURN rtn; + END IF; + ELSE + SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(cterm.subject_id, cvid); + IF (rtn > 0) THEN + RETURN rtn; + END IF; + END IF; + END LOOP; + RETURN 0; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER, INTEGER) RETURNS INTEGER AS +' +DECLARE + cvid alias for $1; + rootid alias for $2; + rtn int; +BEGIN + + CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); + CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); + + SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(rootid, cvid); + IF (rtn > 0) THEN + DROP TABLE tmpcvtermpath; + RETURN rtn; + END IF; + DROP TABLE tmpcvtermpath; + RETURN 0; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION get_cycle_cvterm_ids(INTEGER) RETURNS SETOF INTEGER AS +' +DECLARE + cvid alias for $1; + root cvterm%ROWTYPE; + rtn int; +BEGIN + + + FOR root IN SELECT DISTINCT t.* from cvterm t WHERE cv_id = cvid LOOP + SELECT INTO rtn get_cycle_cvterm_id(cvid,root.cvterm_id); + IF (rtn > 0) THEN + RETURN NEXT rtn; + END IF; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER) RETURNS INTEGER AS +' +DECLARE + cvid alias for $1; + root cvterm%ROWTYPE; + rtn int; +BEGIN + + CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); + CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); + + FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP + SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(root.cvterm_id, root.cv_id); + IF (rtn > 0) THEN + DROP TABLE tmpcvtermpath; + RETURN rtn; + END IF; + END LOOP; + DROP TABLE tmpcvtermpath; + RETURN 0; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(cv.name%TYPE) RETURNS INTEGER AS +' +DECLARE + cvname alias for $1; + cv_id int; + rtn int; +BEGIN + + SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; + SELECT INTO rtn get_cycle_cvterm_id(cv_id); + + RETURN rtn; +END; +' +LANGUAGE 'plpgsql'; +-- $Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $ +-- ========================================== +-- Chado pub module +-- +-- ================================================================= +-- Dependencies: +-- +-- :import cvterm from cv +-- :import dbxref from general +-- ================================================================= + +-- ================================================ +-- TABLE: pub +-- ================================================ + +create table pub ( + pub_id serial not null, + primary key (pub_id), + title text, + volumetitle text, + volume varchar(255), + series_name varchar(255), + issue varchar(255), + pyear varchar(255), + pages varchar(255), + miniref varchar(255), + uniquename text not null, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + is_obsolete boolean default 'false', + publisher varchar(255), + pubplace varchar(255), + constraint pub_c1 unique (uniquename) +); +CREATE INDEX pub_idx1 ON pub (type_id); + +COMMENT ON TABLE pub IS 'A documented provenance artefact - publications, +documents, personal communication.'; +COMMENT ON COLUMN pub.title IS 'Descriptive general heading.'; +COMMENT ON COLUMN pub.volumetitle IS 'Title of part if one of a series.'; +COMMENT ON COLUMN pub.series_name IS 'Full name of (journal) series.'; +COMMENT ON COLUMN pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'; +COMMENT ON COLUMN pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.'; + +-- ================================================ +-- TABLE: pub_relationship +-- ================================================ + +create table pub_relationship ( + pub_relationship_id serial not null, + primary key (pub_relationship_id), + subject_id int not null, + foreign key (subject_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + object_id int not null, + foreign key (object_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + + constraint pub_relationship_c1 unique (subject_id,object_id,type_id) +); +create index pub_relationship_idx1 on pub_relationship (subject_id); +create index pub_relationship_idx2 on pub_relationship (object_id); +create index pub_relationship_idx3 on pub_relationship (type_id); + +COMMENT ON TABLE pub_relationship IS 'Handle relationships between +publications, e.g. when one publication makes others obsolete, when one +publication contains errata with respect to other publication(s), or +when one publication also appears in another pub.'; + +-- ================================================ +-- TABLE: pub_dbxref +-- ================================================ + +create table pub_dbxref ( + pub_dbxref_id serial not null, + primary key (pub_dbxref_id), + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, + is_current boolean not null default 'true', + constraint pub_dbxref_c1 unique (pub_id,dbxref_id) +); +create index pub_dbxref_idx1 on pub_dbxref (pub_id); +create index pub_dbxref_idx2 on pub_dbxref (dbxref_id); + +COMMENT ON TABLE pub_dbxref IS 'Handle links to repositories, +e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...'; + + +-- ================================================ +-- TABLE: pubauthor +-- ================================================ + +create table pubauthor ( + pubauthor_id serial not null, + primary key (pubauthor_id), + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + rank int not null, + editor boolean default 'false', + surname varchar(100) not null, + givennames varchar(100), + suffix varchar(100), + + constraint pubauthor_c1 unique (pub_id, rank) +); +create index pubauthor_idx2 on pubauthor (pub_id); + +COMMENT ON TABLE pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.'; +COMMENT ON COLUMN pubauthor.givennames IS 'First name, initials'; +COMMENT ON COLUMN pubauthor.suffix IS 'Jr., Sr., etc'; +COMMENT ON COLUMN pubauthor.rank IS 'Order of author in author list for this pub - order is important.'; +COMMENT ON COLUMN pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.'; + + +-- ================================================ +-- TABLE: pubprop +-- ================================================ + +create table pubprop ( + pubprop_id serial not null, + primary key (pubprop_id), + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text not null, + rank integer, + + constraint pubprop_c1 unique (pub_id,type_id,rank) +); +create index pubprop_idx1 on pubprop (pub_id); +create index pubprop_idx2 on pubprop (type_id); + +COMMENT ON TABLE pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.'; +-- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $ +-- ========================================== +-- Chado organism module +-- +-- ============ +-- DEPENDENCIES +-- ============ +-- :import cvterm from cv +-- :import dbxref from general +-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +-- ================================================ +-- TABLE: organism +-- ================================================ + +create table organism ( + organism_id serial not null, + primary key (organism_id), + abbreviation varchar(255) null, + genus varchar(255) not null, + species varchar(255) not null, + common_name varchar(255) null, + comment text null, + constraint organism_c1 unique (genus,species) +); + +COMMENT ON TABLE organism IS 'The organismal taxonomic +classification. Note that phylogenies are represented using the +phylogeny module, and taxonomies can be represented using the cvterm +module or the phylogeny module.'; + +COMMENT ON COLUMN organism.species IS 'A type of organism is always +uniquely identified by genus and species. When mapping from the NCBI +taxonomy names.dmp file, this column must be used where it +is present, as the common_name column is not always unique (e.g. environmental +samples). If a particular strain or subspecies is to be represented, +this is appended onto the species name. Follows standard NCBI taxonomy +pattern.'; + +-- ================================================ +-- TABLE: organism_dbxref +-- ================================================ + +create table organism_dbxref ( + organism_dbxref_id serial not null, + primary key (organism_dbxref_id), + organism_id int not null, + foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, + constraint organism_dbxref_c1 unique (organism_id,dbxref_id) +); +create index organism_dbxref_idx1 on organism_dbxref (organism_id); +create index organism_dbxref_idx2 on organism_dbxref (dbxref_id); + +-- ================================================ +-- TABLE: organismprop +-- ================================================ + +create table organismprop ( + organismprop_id serial not null, + primary key (organismprop_id), + organism_id int not null, + foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank int not null default 0, + constraint organismprop_c1 unique (organism_id,type_id,rank) +); +create index organismprop_idx1 on organismprop (organism_id); +create index organismprop_idx2 on organismprop (type_id); + +COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.'; + + +CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR,VARCHAR) RETURNS INT + AS ' + SELECT organism_id + FROM organism + WHERE genus=$1 + AND species=$2 + ' LANGUAGE 'sql'; + +CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR) RETURNS INT + AS ' +SELECT organism_id + FROM organism + WHERE genus=substring($1,1,position('' '' IN $1)-1) + AND species=substring($1,position('' '' IN $1)+1) + ' LANGUAGE 'sql'; + +CREATE OR REPLACE FUNCTION get_organism_id_abbrev(VARCHAR) RETURNS INT + AS ' +SELECT organism_id + FROM organism + WHERE substr(genus,1,1)=substring($1,1,1) + AND species=substring($1,position('' '' IN $1)+1) + ' LANGUAGE 'sql'; + +CREATE OR REPLACE FUNCTION store_organism (VARCHAR,VARCHAR,VARCHAR) + RETURNS INT AS +'DECLARE + v_genus ALIAS FOR $1; + v_species ALIAS FOR $2; + v_common_name ALIAS FOR $3; + + v_organism_id INTEGER; + BEGIN + SELECT INTO v_organism_id organism_id + FROM organism + WHERE genus=v_genus AND + species=v_species; + IF NOT FOUND THEN + INSERT INTO organism + (genus,species,common_name) + VALUES + (v_genus,v_species,v_common_name); + RETURN currval(''organism_organism_id_seq''); + ELSE + UPDATE organism + SET common_name=v_common_name + WHERE organism_id = v_organism_id; + END IF; + RETURN v_organism_id; + END; +' LANGUAGE 'plpgsql'; + +-- $Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $ +-- ========================================== +-- Chado sequence module +-- +-- ================================================================= +-- Dependencies: +-- +-- :import cvterm from cv +-- :import pub from pub +-- :import organism from organism +-- :import dbxref from general +-- ================================================================= + +-- ================================================ +-- TABLE: feature +-- ================================================ + +create table feature ( + feature_id serial not null, + primary key (feature_id), + dbxref_id int, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, + organism_id int not null, + foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, + name varchar(255), + uniquename text not null, + residues text, + seqlen int, + md5checksum char(32), + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + is_analysis boolean not null default 'false', + is_obsolete boolean not null default 'false', + timeaccessioned timestamp not null default current_timestamp, + timelastmodified timestamp not null default current_timestamp, + constraint feature_c1 unique (organism_id,uniquename,type_id) +); +create sequence feature_uniquename_seq; +create index feature_name_ind1 on feature(name); +create index feature_idx1 on feature (dbxref_id); +create index feature_idx2 on feature (organism_id); +create index feature_idx3 on feature (type_id); +create index feature_idx4 on feature (uniquename); +create index feature_idx5 on feature (lower(name)); + +ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; + +COMMENT ON TABLE feature IS 'A feature is a biological sequence or a +section of a biological sequence, or a collection of such +sections. Examples include genes, exons, transcripts, regulatory +regions, polypeptides, protein domains, chromosome sequences, sequence +variations, cross-genome match regions such as hits and HSPs and so +on; see the Sequence Ontology for more. The combination of +organism_id, uniquename and type_id should be unique.'; + +COMMENT ON COLUMN feature.dbxref_id IS 'An optional primary public stable +identifier for this feature. Secondary identifiers and external +dbxrefs go in the table feature_dbxref.'; + +COMMENT ON COLUMN feature.organism_id IS 'The organism to which this feature +belongs. This column is mandatory.'; + +COMMENT ON COLUMN feature.name IS 'The optional human-readable common name for +a feature, for display purposes.'; + +COMMENT ON COLUMN feature.uniquename IS 'The unique name for a feature; may +not be necessarily be particularly human-readable, although this is +preferred. This name must be unique for this type of feature within +this organism.'; + +COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters +representing biological residues (nucleic acids, amino acids). This +column does not need to be manifested for all features; it is optional +for features such as exons where the residues can be derived from the +featureloc. It is recommended that the value for this column be +manifested for features which may may non-contiguous sublocations (e.g. +transcripts), since derivation at query time is non-trivial. For +expressed sequence, the DNA sequence should be used rather than the +RNA sequence. The default storage method for the residues column is +EXTERNAL, which will store it uncompressed to make substring operations +faster.'; + +COMMENT ON COLUMN feature.seqlen IS 'The length of the residue feature. See +column:residues. This column is partially redundant with the residues +column, and also with featureloc. This column is required because the +location may be unknown and the residue sequence may not be +manifested, yet it may be desirable to store and query the length of +the feature. The seqlen should always be manifested where the length +of the sequence is known.'; + +COMMENT ON COLUMN feature.md5checksum IS 'The 32-character checksum of the sequence, +calculated using the MD5 algorithm. This is practically guaranteed to +be unique for any feature. This column thus acts as a unique +identifier on the mathematical sequence.'; + +COMMENT ON COLUMN feature.type_id IS 'A required reference to a table:cvterm +giving the feature type. This will typically be a Sequence Ontology +identifier. This column is thus used to subclass the feature table.'; + +COMMENT ON COLUMN feature.is_analysis IS 'Boolean indicating whether this +feature is annotated or the result of an automated analysis. Analysis +results also use the companalysis module. Note that the dividing line +between analysis and annotation may be fuzzy, this should be determined on +a per-project basis in a consistent manner. One requirement is that +there should only be one non-analysis version of each wild-type gene +feature in a genome, whereas the same gene feature can be predicted +multiple times in different analyses.'; + +COMMENT ON COLUMN feature.is_obsolete IS 'Boolean indicating whether this +feature has been obsoleted. Some chado instances may choose to simply +remove the feature altogether, others may choose to keep an obsolete +row in the table.'; + +COMMENT ON COLUMN feature.timeaccessioned IS 'For handling object +accession or modification timestamps (as opposed to database auditing data, +handled elsewhere). The expectation is that these fields would be +available to software interacting with chado.'; + +COMMENT ON COLUMN feature.timelastmodified IS 'For handling object +accession or modification timestamps (as opposed to database auditing data, +handled elsewhere). The expectation is that these fields would be +available to software interacting with chado.'; + +--- COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified +--- by the combination of organism, uniquename and feature type'; + +-- ================================================ +-- TABLE: featureloc +-- ================================================ + +create table featureloc ( + featureloc_id serial not null, + primary key (featureloc_id), + feature_id int not null, + foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, + srcfeature_id int, + foreign key (srcfeature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, + fmin int, + is_fmin_partial boolean not null default 'false', + fmax int, + is_fmax_partial boolean not null default 'false', + strand smallint, + phase int, + residue_info text, + locgroup int not null default 0, + rank int not null default 0, + constraint featureloc_c1 unique (feature_id,locgroup,rank), + constraint featureloc_c2 check (fmin <= fmax) +); +create index featureloc_idx1 on featureloc (feature_id); +create index featureloc_idx2 on featureloc (srcfeature_id); +create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax); + +COMMENT ON TABLE featureloc IS 'The location of a feature relative to +another feature. Important: interbase coordinates are used. This is +vital as it allows us to represent zero-length features e.g. splice +sites, insertion points without an awkward fuzzy system. Features +typically have exactly ONE location, but this need not be the +case. Some features may not be localized (e.g. a gene that has been +characterized genetically but no sequence or molecular information is +available). Note on multiple locations: Each feature can have 0 or +more locations. Multiple locations do NOT indicate non-contiguous +locations (if a feature such as a transcript has a non-contiguous +location, then the subfeatures such as exons should always be +manifested). Instead, multiple featurelocs for a feature designate +alternate locations or grouped locations; for instance, a feature +designating a blast hit or hsp will have two locations, one on the +query feature, one on the subject feature. Features representing +sequence variation could have alternate locations instantiated on a +feature on the mutant strain. The column:rank is used to +differentiate these different locations. Reflexive locations should +never be stored - th... [truncated message content] |
From: <sco...@us...> - 2011-11-17 19:25:21
|
Revision: 25251 http://gmod.svn.sourceforge.net/gmod/?rev=25251&view=rev Author: scottcain Date: 2011-11-17 19:25:12 +0000 (Thu, 17 Nov 2011) Log Message: ----------- Tagging chado release 1.22 Added Paths: ----------- schema/tags/chado-1.22/ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-17 19:19:50
|
Revision: 25250 http://gmod.svn.sourceforge.net/gmod/?rev=25250&view=rev Author: scottcain Date: 2011-11-17 19:19:40 +0000 (Thu, 17 Nov 2011) Log Message: ----------- fixing the manifest and the diff dir generator: diretories don't go in manifest, only files do. Modified Paths: -------------- schema/trunk/chado/MANIFEST schema/trunk/chado/schemas/generate_diff_dirs.pl Modified: schema/trunk/chado/MANIFEST =================================================================== --- schema/trunk/chado/MANIFEST 2011-11-17 17:48:58 UTC (rev 25249) +++ schema/trunk/chado/MANIFEST 2011-11-17 19:19:40 UTC (rev 25250) @@ -343,22 +343,13 @@ stag-templates/README TODO UPGRADE.txt -schemas/1-1.21 schemas/1-1.21/diff.sql -schemas/1.1-1.21 schemas/1.1-1.21/diff.sql -schemas/1.11-1.21 schemas/1.11-1.21/diff.sql -schemas/1.2-1.21 schemas/1.2-1.21/diff.sql #the following added by generate_diff_dirs.pl -schemas/1-1.22 schemas/1-1.22/diff.sql -schemas/1.1-1.22 schemas/1.1-1.22/diff.sql -schemas/1.11-1.22 schemas/1.11-1.22/diff.sql -schemas/1.2-1.22 schemas/1.2-1.22/diff.sql -schemas/1.21-1.22 schemas/1.21-1.22/diff.sql Modified: schema/trunk/chado/schemas/generate_diff_dirs.pl =================================================================== --- schema/trunk/chado/schemas/generate_diff_dirs.pl 2011-11-17 17:48:58 UTC (rev 25249) +++ schema/trunk/chado/schemas/generate_diff_dirs.pl 2011-11-17 19:19:40 UTC (rev 25250) @@ -25,7 +25,7 @@ my $newdir = $dir.'-'.$VERSION; mkdir $newdir; system("touch $newdir/diff.sql"); - push @add_to_manifest, "schemas/$newdir", "schemas/$newdir/diff.sql"; + push @add_to_manifest, "schemas/$newdir/diff.sql"; system("svn add $newdir"); } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-17 17:49:07
|
Revision: 25249 http://gmod.svn.sourceforge.net/gmod/?rev=25249&view=rev Author: scottcain Date: 2011-11-17 17:48:58 +0000 (Thu, 17 Nov 2011) Log Message: ----------- version bump Modified Paths: -------------- schema/trunk/chado/Changes Modified: schema/trunk/chado/Changes =================================================================== --- schema/trunk/chado/Changes 2011-11-17 17:47:56 UTC (rev 25248) +++ schema/trunk/chado/Changes 2011-11-17 17:48:58 UTC (rev 25249) @@ -1,3 +1,7 @@ +Version 1.11 Thu Nov 17 12:48:10 EST 2011 +* Created a script to automatically create the schemas dirs for a release and +add them to the manifest. + Version 1.21 Thu Oct 20 10:52:55 EDT 2011 * Added rudimentary support for non-public schemas in Postgres, though it's only good for Tripal at the moment. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-17 17:48:05
|
Revision: 25248 http://gmod.svn.sourceforge.net/gmod/?rev=25248&view=rev Author: scottcain Date: 2011-11-17 17:47:56 +0000 (Thu, 17 Nov 2011) Log Message: ----------- bumping the version to 1.22 Modified Paths: -------------- schema/trunk/chado/Makefile.PL schema/trunk/chado/load/Build.PL Modified: schema/trunk/chado/Makefile.PL =================================================================== --- schema/trunk/chado/Makefile.PL 2011-11-17 17:47:08 UTC (rev 25247) +++ schema/trunk/chado/Makefile.PL 2011-11-17 17:47:56 UTC (rev 25248) @@ -50,7 +50,7 @@ use Template; use Module::Build; -my $VERSION = 1.21; +my $VERSION = 1.22; my %args = ( DBDRIVER => { Modified: schema/trunk/chado/load/Build.PL =================================================================== --- schema/trunk/chado/load/Build.PL 2011-11-17 17:47:08 UTC (rev 25247) +++ schema/trunk/chado/load/Build.PL 2011-11-17 17:47:56 UTC (rev 25248) @@ -3,7 +3,7 @@ use Bio::Chado::Builder; use Data::Dumper; -my $VERSION = 1.21; +my $VERSION = 1.22; my $conf = shift; my $m = Bio::Chado::Builder->new( dist_name => 'Chado', This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-17 17:47:27
|
Revision: 25247 http://gmod.svn.sourceforge.net/gmod/?rev=25247&view=rev Author: scottcain Date: 2011-11-17 17:47:08 +0000 (Thu, 17 Nov 2011) Log Message: ----------- created a script to automatically create schmema diff dirs Modified Paths: -------------- schema/trunk/chado/MANIFEST Added Paths: ----------- schema/trunk/chado/schemas/1-1.22/ schema/trunk/chado/schemas/1-1.22/diff.sql schema/trunk/chado/schemas/1.1-1.22/ schema/trunk/chado/schemas/1.1-1.22/diff.sql schema/trunk/chado/schemas/1.11-1.22/ schema/trunk/chado/schemas/1.11-1.22/diff.sql schema/trunk/chado/schemas/1.2-1.22/ schema/trunk/chado/schemas/1.2-1.22/diff.sql schema/trunk/chado/schemas/1.21-1.22/ schema/trunk/chado/schemas/1.21-1.22/diff.sql schema/trunk/chado/schemas/1.22/ schema/trunk/chado/schemas/1.22/default_schema.sql schema/trunk/chado/schemas/generate_diff_dirs.pl Modified: schema/trunk/chado/MANIFEST =================================================================== --- schema/trunk/chado/MANIFEST 2011-11-16 18:52:59 UTC (rev 25246) +++ schema/trunk/chado/MANIFEST 2011-11-17 17:47:08 UTC (rev 25247) @@ -343,3 +343,22 @@ stag-templates/README TODO UPGRADE.txt +schemas/1-1.21 +schemas/1-1.21/diff.sql +schemas/1.1-1.21 +schemas/1.1-1.21/diff.sql +schemas/1.11-1.21 +schemas/1.11-1.21/diff.sql +schemas/1.2-1.21 +schemas/1.2-1.21/diff.sql +#the following added by generate_diff_dirs.pl +schemas/1-1.22 +schemas/1-1.22/diff.sql +schemas/1.1-1.22 +schemas/1.1-1.22/diff.sql +schemas/1.11-1.22 +schemas/1.11-1.22/diff.sql +schemas/1.2-1.22 +schemas/1.2-1.22/diff.sql +schemas/1.21-1.22 +schemas/1.21-1.22/diff.sql Added: schema/trunk/chado/schemas/1-1.22/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.1-1.22/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.11-1.22/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.2-1.22/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.21-1.22/diff.sql =================================================================== Added: schema/trunk/chado/schemas/1.22/default_schema.sql =================================================================== --- schema/trunk/chado/schemas/1.22/default_schema.sql (rev 0) +++ schema/trunk/chado/schemas/1.22/default_schema.sql 2011-11-17 17:47:08 UTC (rev 25247) @@ -0,0 +1,41889 @@ +-- $Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $ +-- ========================================== +-- Chado general module +-- +-- ================================================ +-- TABLE: tableinfo +-- ================================================ + +create table tableinfo ( + tableinfo_id serial not null, + primary key (tableinfo_id), + name varchar(30) not null, + primary_key_column varchar(30) null, + is_view int not null default 0, + view_on_table_id int null, + superclass_table_id int null, + is_updateable int not null default 1, + modification_date date not null default now(), + constraint tableinfo_c1 unique (name) +); + +COMMENT ON TABLE tableinfo IS NULL; + +-- ================================================ +-- TABLE: db +-- ================================================ + +create table db ( + db_id serial not null, + primary key (db_id), + name varchar(255) not null, +-- contact_id int, +-- foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, + description varchar(255) null, + urlprefix varchar(255) null, + url varchar(255) null, + constraint db_c1 unique (name) +); + +COMMENT ON TABLE db IS 'A database authority. Typical databases in +bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority +is generally known by this shortened form, which is unique within the +bioinformatics and biomedical realm. To Do - add support for URIs, +URNs (e.g. LSIDs). We can do this by treating the URL as a URI - +however, some applications may expect this to be resolvable - to be +decided.'; + +-- ================================================ +-- TABLE: dbxref +-- ================================================ + +create table dbxref ( + dbxref_id serial not null, + primary key (dbxref_id), + db_id int not null, + foreign key (db_id) references db (db_id) on delete cascade INITIALLY DEFERRED, + accession varchar(255) not null, + version varchar(255) not null default '', + description text, + constraint dbxref_c1 unique (db_id,accession,version) +); +create index dbxref_idx1 on dbxref (db_id); +create index dbxref_idx2 on dbxref (accession); +create index dbxref_idx3 on dbxref (version); + +COMMENT ON TABLE dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table <T>_dbxref). A dbxref is generally written as <DB>:<ACCESSION> or as <DB>:<ACCESSION>:<VERSION>.'; + +COMMENT ON COLUMN dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.'; + +CREATE VIEW db_dbxref_count AS + SELECT db.name,count(*) AS num_dbxrefs FROM db INNER JOIN dbxref USING (db_id) GROUP BY db.name; +COMMENT ON VIEW db_dbxref_count IS 'per-db dbxref counts'; + +CREATE OR REPLACE FUNCTION store_db (VARCHAR) + RETURNS INT AS +'DECLARE + v_name ALIAS FOR $1; + + v_db_id INTEGER; + BEGIN + SELECT INTO v_db_id db_id + FROM db + WHERE name=v_name; + IF NOT FOUND THEN + INSERT INTO db + (name) + VALUES + (v_name); + RETURN currval(''db_db_id_seq''); + END IF; + RETURN v_db_id; + END; +' LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION store_dbxref (VARCHAR,VARCHAR) + RETURNS INT AS +'DECLARE + v_dbname ALIAS FOR $1; + v_accession ALIAS FOR $2; + + v_db_id INTEGER; + v_dbxref_id INTEGER; + BEGIN + SELECT INTO v_db_id + store_db(v_dbname); + SELECT INTO v_dbxref_id dbxref_id + FROM dbxref + WHERE db_id=v_db_id AND + accession=v_accession; + IF NOT FOUND THEN + INSERT INTO dbxref + (db_id,accession) + VALUES + (v_db_id,v_accession); + RETURN currval(''dbxref_dbxref_id_seq''); + END IF; + RETURN v_dbxref_id; + END; +' LANGUAGE 'plpgsql'; + +-- $Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $ +-- ========================================== +-- Chado cv module +-- +-- ================================================================= +-- Dependencies: +-- +-- :import dbxref from general +-- ================================================================= + +-- ================================================ +-- TABLE: cv +-- ================================================ +create table cv ( + cv_id serial not null, + primary key (cv_id), + name varchar(255) not null, + definition text, + constraint cv_c1 unique (name) +); + +COMMENT ON TABLE cv IS 'A controlled vocabulary or ontology. A cv is +composed of cvterms (AKA terms, classes, types, universals - relations +and properties are also stored in cvterm) and the relationships +between them.'; + +COMMENT ON COLUMN cv.name IS 'The name of the ontology. This +corresponds to the obo-format -namespace-. cv names uniquely identify +the cv. In OBO file format, the cv.name is known as the namespace.'; + +COMMENT ON COLUMN cv.definition IS 'A text description of the criteria for +membership of this ontology.'; + +-- ================================================ +-- TABLE: cvterm +-- ================================================ +create table cvterm ( + cvterm_id serial not null, + primary key (cvterm_id), + cv_id int not null, + foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, + name varchar(1024) not null, + definition text, + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, + is_obsolete int not null default 0, + is_relationshiptype int not null default 0, + constraint cvterm_c1 unique (name,cv_id,is_obsolete), + constraint cvterm_c2 unique (dbxref_id) +); +create index cvterm_idx1 on cvterm (cv_id); +create index cvterm_idx2 on cvterm (name); +create index cvterm_idx3 on cvterm (dbxref_id); + +COMMENT ON TABLE cvterm IS 'A term, class, universal or type within an +ontology or controlled vocabulary. This table is also used for +relations and properties. cvterms constitute nodes in the graph +defined by the collection of cvterms and cvterm_relationships.'; + +COMMENT ON COLUMN cvterm.cv_id IS 'The cv or ontology or namespace to which +this cvterm belongs.'; + +COMMENT ON COLUMN cvterm.name IS 'A concise human-readable name or +label for the cvterm. Uniquely identifies a cvterm within a cv.'; + +COMMENT ON COLUMN cvterm.definition IS 'A human-readable text +definition.'; + +COMMENT ON COLUMN cvterm.dbxref_id IS 'Primary identifier dbxref - The +unique global OBO identifier for this cvterm. Note that a cvterm may +have multiple secondary dbxrefs - see also table: cvterm_dbxref.'; + +COMMENT ON COLUMN cvterm.is_obsolete IS 'Boolean 0=false,1=true; see +GO documentation for details of obsoletion. Note that two terms with +different primary dbxrefs may exist if one is obsolete.'; + +COMMENT ON COLUMN cvterm.is_relationshiptype IS 'Boolean +0=false,1=true relations or relationship types (also known as Typedefs +in OBO format, or as properties or slots) form a cv/ontology in +themselves. We use this flag to indicate whether this cvterm is an +actual term/class/universal or a relation. Relations may be drawn from +the OBO Relations ontology, but are not exclusively drawn from there.'; + +COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in +different contexts; for example "chromosome" in SO and GO. A name +should be unique within an ontology or cv. A name may exist twice in a +cv, in both obsolete and non-obsolete forms - these will be for +different cvterms with different OBO identifiers; so GO documentation +for more details on obsoletion. Note that occasionally multiple +obsolete terms with the same name will exist in the same cv. If this +is a possibility for the ontology under consideration (e.g. GO) then the +ID should be appended to the name to ensure uniqueness.'; + +COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.'; + +-- ================================================ +-- TABLE: cvterm_relationship +-- ================================================ +create table cvterm_relationship ( + cvterm_relationship_id serial not null, + primary key (cvterm_relationship_id), + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + subject_id int not null, + foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + object_id int not null, + foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + constraint cvterm_relationship_c1 unique (subject_id,object_id,type_id) +); +create index cvterm_relationship_idx1 on cvterm_relationship (type_id); +create index cvterm_relationship_idx2 on cvterm_relationship (subject_id); +create index cvterm_relationship_idx3 on cvterm_relationship (object_id); + +COMMENT ON TABLE cvterm_relationship IS 'A relationship linking two +cvterms. Each cvterm_relationship constitutes an edge in the graph +defined by the collection of cvterms and cvterm_relationships. The +meaning of the cvterm_relationship depends on the definition of the +cvterm R refered to by type_id. However, in general the definitions +are such that the statement "all SUBJs REL some OBJ" is true. The +cvterm_relationship statement is about the subject, not the +object. For example "insect wing part_of thorax".'; + +COMMENT ON COLUMN cvterm_relationship.subject_id IS 'The subject of +the subj-predicate-obj sentence. The cvterm_relationship is about the +subject. In a graph, this typically corresponds to the child node.'; + +COMMENT ON COLUMN cvterm_relationship.object_id IS 'The object of the +subj-predicate-obj sentence. The cvterm_relationship refers to the +object. In a graph, this typically corresponds to the parent node.'; + +COMMENT ON COLUMN cvterm_relationship.type_id IS 'The nature of the +relationship between subject and object. Note that relations are also +housed in the cvterm table, typically from the OBO relationship +ontology, although other relationship types are allowed.'; + +-- ================================================ +-- TABLE: cvtermpath +-- ================================================ +create table cvtermpath ( + cvtermpath_id serial not null, + primary key (cvtermpath_id), + type_id int, + foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, + subject_id int not null, + foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + object_id int not null, + foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + cv_id int not null, + foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, + pathdistance int, + constraint cvtermpath_c1 unique (subject_id,object_id,type_id,pathdistance) +); +create index cvtermpath_idx1 on cvtermpath (type_id); +create index cvtermpath_idx2 on cvtermpath (subject_id); +create index cvtermpath_idx3 on cvtermpath (object_id); +create index cvtermpath_idx4 on cvtermpath (cv_id); + +COMMENT ON TABLE cvtermpath IS 'The reflexive transitive closure of +the cvterm_relationship relation.'; + +COMMENT ON COLUMN cvtermpath.type_id IS 'The relationship type that +this is a closure over. If null, then this is a closure over ALL +relationship types. If non-null, then this references a relationship +cvterm - note that the closure will apply to both this relationship +AND the OBO_REL:is_a (subclass) relationship.'; + +COMMENT ON COLUMN cvtermpath.cv_id IS 'Closures will mostly be within +one cv. If the closure of a relationship traverses a cv, then this +refers to the cv of the object_id cvterm.'; + +COMMENT ON COLUMN cvtermpath.pathdistance IS 'The number of steps +required to get from the subject cvterm to the object cvterm, counting +from zero (reflexive relationship).'; + +-- ================================================ +-- TABLE: cvtermsynonym +-- ================================================ +create table cvtermsynonym ( + cvtermsynonym_id serial not null, + primary key (cvtermsynonym_id), + cvterm_id int not null, + foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + synonym varchar(1024) not null, + type_id int, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + constraint cvtermsynonym_c1 unique (cvterm_id,synonym) +); +create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id); + +COMMENT ON TABLE cvtermsynonym IS 'A cvterm actually represents a +distinct class or concept. A concept can be refered to by different +phrases or names. In addition to the primary name (cvterm.name) there +can be a number of alternative aliases or synonyms. For example, "T +cell" as a synonym for "T lymphocyte".'; + +COMMENT ON COLUMN cvtermsynonym.type_id IS 'A synonym can be exact, +narrower, or broader than.'; + + +-- ================================================ +-- TABLE: cvterm_dbxref +-- ================================================ +create table cvterm_dbxref ( + cvterm_dbxref_id serial not null, + primary key (cvterm_dbxref_id), + cvterm_id int not null, + foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, + is_for_definition int not null default 0, + constraint cvterm_dbxref_c1 unique (cvterm_id,dbxref_id) +); +create index cvterm_dbxref_idx1 on cvterm_dbxref (cvterm_id); +create index cvterm_dbxref_idx2 on cvterm_dbxref (dbxref_id); + +COMMENT ON TABLE cvterm_dbxref IS 'In addition to the primary +identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary +identifiers/dbxrefs, which may refer to records in external +databases. The exact semantics of cvterm_dbxref are not fixed. For +example: the dbxref could be a pubmed ID that is pertinent to the +cvterm, or it could be an equivalent or similar term in another +ontology. For example, GO cvterms are typically linked to InterPro +IDs, even though the nature of the relationship between them is +largely one of statistical association. The dbxref may be have data +records attached in the same database instance, or it could be a +"hanging" dbxref pointing to some external database. NOTE: If the +desired objective is to link two cvterms together, and the nature of +the relation is known and holds for all instances of the subject +cvterm then consider instead using cvterm_relationship together with a +well-defined relation.'; + +COMMENT ON COLUMN cvterm_dbxref.is_for_definition IS 'A +cvterm.definition should be supported by one or more references. If +this column is true, the dbxref is not for a term in an external database - +it is a dbxref for provenance information for the definition.'; + + +-- ================================================ +-- TABLE: cvtermprop +-- ================================================ +create table cvtermprop ( + cvtermprop_id serial not null, + primary key (cvtermprop_id), + cvterm_id int not null, + foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade, + value text not null default '', + rank int not null default 0, + + unique(cvterm_id, type_id, value, rank) +); +create index cvtermprop_idx1 on cvtermprop (cvterm_id); +create index cvtermprop_idx2 on cvtermprop (type_id); + +COMMENT ON TABLE cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.'; + +COMMENT ON COLUMN cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; + +COMMENT ON COLUMN cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; + +COMMENT ON COLUMN cvtermprop.rank IS 'Property-Value ordering. Any +cvterm can have multiple values for any particular property type - +these are ordered in a list using rank, counting from zero. For +properties that are single-valued rather than multi-valued, the +default 0 value should be used.'; + + +-- ================================================ +-- TABLE: dbxrefprop +-- ================================================ +create table dbxrefprop ( + dbxrefprop_id serial not null, + primary key (dbxrefprop_id), + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, + value text not null default '', + rank int not null default 0, + constraint dbxrefprop_c1 unique (dbxref_id,type_id,rank) +); +create index dbxrefprop_idx1 on dbxrefprop (dbxref_id); +create index dbxrefprop_idx2 on dbxrefprop (type_id); + +COMMENT ON TABLE dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.'; + + +-- ================================================ +-- TABLE: cvprop +-- ================================================ +create table cvprop ( + cvprop_id serial not null, + primary key (cvprop_id), + cv_id int not null, + foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, + value text, + rank int not null default 0, + constraint cvprop_c1 unique (cv_id,type_id,rank) +); + +COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; + +COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; +COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; + +COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any +cv can have multiple values for any particular property type - +these are ordered in a list using rank, counting from zero. For +properties that are single-valued rather than multi-valued, the +default 0 value should be used.'; + +-- ================================================ +-- TABLE: chadoprop +-- ================================================ +create table chadoprop ( + chadoprop_id serial not null, + primary key (chadoprop_id), + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, + value text, + rank int not null default 0, + constraint chadoprop_c1 unique (type_id,rank) +); + +COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; + +COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; +COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; + +COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any +cv can have multiple values for any particular property type - +these are ordered in a list using rank, counting from zero. For +properties that are single-valued rather than multi-valued, the +default 0 value should be used.'; + +CREATE OR REPLACE VIEW cv_root AS + SELECT + cv_id, + cvterm_id AS root_cvterm_id + FROM cvterm + WHERE + cvterm_id NOT IN ( SELECT subject_id FROM cvterm_relationship) AND + is_obsolete=0; + +COMMENT ON VIEW cv_root IS 'the roots of a cv are the set of terms +which have no parents (terms that are not the subject of a +relation). Most cvs will have a single root, some may have >1. All +will have at least 1'; + +CREATE OR REPLACE VIEW cv_leaf AS + SELECT + cv_id, + cvterm_id + FROM cvterm + WHERE + cvterm_id NOT IN ( SELECT object_id FROM cvterm_relationship); + +COMMENT ON VIEW cv_leaf IS 'the leaves of a cv are the set of terms +which have no children (terms that are not the object of a +relation). All cvs will have at least 1 leaf'; + +CREATE OR REPLACE VIEW common_ancestor_cvterm AS + SELECT + p1.subject_id AS cvterm1_id, + p2.subject_id AS cvterm2_id, + p1.object_id AS ancestor_cvterm_id, + p1.pathdistance AS pathdistance1, + p2.pathdistance AS pathdistance2, + p1.pathdistance + p2.pathdistance + AS total_pathdistance + FROM + cvtermpath AS p1, + cvtermpath AS p2 + WHERE + p1.object_id = p2.object_id; + +COMMENT ON VIEW common_ancestor_cvterm IS 'The common ancestor of any +two terms is the intersection of both terms ancestors. Two terms can +have multiple common ancestors. Use total_pathdistance to get the +least common ancestor'; + +CREATE OR REPLACE VIEW common_descendant_cvterm AS + SELECT + p1.object_id AS cvterm1_id, + p2.object_id AS cvterm2_id, + p1.subject_id AS ancestor_cvterm_id, + p1.pathdistance AS pathdistance1, + p2.pathdistance AS pathdistance2, + p1.pathdistance + p2.pathdistance + AS total_pathdistance + FROM + cvtermpath AS p1, + cvtermpath AS p2 + WHERE + p1.subject_id = p2.subject_id; + +COMMENT ON VIEW common_descendant_cvterm IS 'The common descendant of +any two terms is the intersection of both terms descendants. Two terms +can have multiple common descendants. Use total_pathdistance to get +the least common ancestor'; + +CREATE OR REPLACE VIEW stats_paths_to_root AS + SELECT + subject_id AS cvterm_id, + count(DISTINCT cvtermpath_id) AS total_paths, + avg(pathdistance) AS avg_distance, + min(pathdistance) AS min_distance, + max(pathdistance) AS max_distance + FROM cvtermpath INNER JOIN cv_root ON (object_id=root_cvterm_id) + GROUP BY cvterm_id; + +COMMENT ON VIEW stats_paths_to_root IS 'per-cvterm statistics on its +placement in the DAG relative to the root. There may be multiple paths +from any term to the root. This gives the total number of paths, and +the average minimum and maximum distances. Here distance is defined by +cvtermpath.pathdistance'; +CREATE VIEW cv_cvterm_count AS + SELECT cv.name,count(*) AS num_terms_excl_obs FROM cv INNER JOIN cvterm USING (cv_id) WHERE is_obsolete=0 GROUP BY cv.name; +COMMENT ON VIEW cv_cvterm_count IS 'per-cv terms counts (excludes obsoletes)'; + +CREATE VIEW cv_cvterm_count_with_obs AS + SELECT cv.name,count(*) AS num_terms_incl_obs FROM cv INNER JOIN cvterm USING (cv_id) GROUP BY cv.name; +COMMENT ON VIEW cv_cvterm_count_with_obs IS 'per-cv terms counts (includes obsoletes)'; + +CREATE VIEW cv_link_count AS + SELECT cv.name AS cv_name, + relation.name AS relation_name, + relation_cv.name AS relation_cv_name, + count(*) AS num_links + FROM cv + INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) + INNER JOIN cvterm_relationship ON (cvterm.cvterm_id=subject_id) + INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) + INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) + GROUP BY cv.name,relation.name,relation_cv.name; + +COMMENT ON VIEW cv_link_count IS 'per-cv summary of number of +links (cvterm_relationships) broken down by +relationship_type. num_links is the total # of links of the specified +type in which the subject_id of the link is in the named cv'; + +CREATE VIEW cv_path_count AS + SELECT cv.name AS cv_name, + relation.name AS relation_name, + relation_cv.name AS relation_cv_name, + count(*) AS num_paths + FROM cv + INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) + INNER JOIN cvtermpath ON (cvterm.cvterm_id=subject_id) + INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) + INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) + GROUP BY cv.name,relation.name,relation_cv.name; + +COMMENT ON VIEW cv_path_count IS 'per-cv summary of number of +paths (cvtermpaths) broken down by relationship_type. num_paths is the +total # of paths of the specified type in which the subject_id of the +path is in the named cv. See also: cv_distinct_relations'; + +CREATE OR REPLACE FUNCTION _get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + root alias for $1; + cterm cvtermpath%ROWTYPE; + cterm2 cvtermpath%ROWTYPE; +BEGIN + + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP + RETURN NEXT cterm; + FOR cterm2 IN SELECT * FROM _get_all_subject_ids(cterm.subject_id) LOOP + RETURN NEXT cterm2; + END LOOP; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +---arg: parent term id +---return: all children term id and their parent term id with relationship type id +CREATE OR REPLACE FUNCTION get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + root alias for $1; + cterm cvtermpath%ROWTYPE; + exist_c int; +BEGIN + + SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = root and pathdistance <= 0; + IF (exist_c > 0) THEN + FOR cterm IN SELECT * FROM cvtermpath WHERE object_id = root and pathdistance > 0 LOOP + RETURN NEXT cterm; + END LOOP; + ELSE + FOR cterm IN SELECT * FROM _get_all_subject_ids(root) LOOP + RETURN NEXT cterm; + END LOOP; + END IF; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION get_graph_below(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + root alias for $1; + cterm cvtermpath%ROWTYPE; + cterm2 cvtermpath%ROWTYPE; + +BEGIN + + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP + RETURN NEXT cterm; + FOR cterm2 IN SELECT * FROM get_all_subject_ids(cterm.subject_id) LOOP + RETURN NEXT cterm2; + END LOOP; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + + +CREATE OR REPLACE FUNCTION get_graph_above(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + leaf alias for $1; + cterm cvtermpath%ROWTYPE; + cterm2 cvtermpath%ROWTYPE; + +BEGIN + + FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP + RETURN NEXT cterm; + FOR cterm2 IN SELECT * FROM get_all_object_ids(cterm.object_id) LOOP + RETURN NEXT cterm2; + END LOOP; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION _get_all_object_ids(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + leaf alias for $1; + cterm cvtermpath%ROWTYPE; + cterm2 cvtermpath%ROWTYPE; +BEGIN + + FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP + RETURN NEXT cterm; + FOR cterm2 IN SELECT * FROM _get_all_object_ids(cterm.object_id) LOOP + RETURN NEXT cterm2; + END LOOP; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +---arg: child term id +---return: all parent term id and their childrent term id with relationship type id +CREATE OR REPLACE FUNCTION get_all_object_ids(integer) RETURNS SETOF cvtermpath AS +' +DECLARE + leaf alias for $1; + cterm cvtermpath%ROWTYPE; + exist_c int; +BEGIN + + + SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = leaf and pathdistance <= 0; + IF (exist_c > 0) THEN + FOR cterm IN SELECT * FROM cvtermpath WHERE subject_id = leaf AND pathdistance > 0 LOOP + RETURN NEXT cterm; + END LOOP; + ELSE + FOR cterm IN SELECT * FROM _get_all_object_ids(leaf) LOOP + RETURN NEXT cterm; + END LOOP; + END IF; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +---arg: sql statement which must be in the form of select cvterm_id from ... +---return: a set of cvterm ids that includes what is in sql statement and their children (subject ids) +CREATE OR REPLACE FUNCTION get_it_sub_cvterm_ids(text) RETURNS SETOF cvterm AS +' +DECLARE + query alias for $1; + cterm cvterm%ROWTYPE; + cterm2 cvterm%ROWTYPE; +BEGIN + FOR cterm IN EXECUTE query LOOP + RETURN NEXT cterm; + FOR cterm2 IN SELECT subject_id as cvterm_id FROM get_all_subject_ids(cterm.cvterm_id) LOOP + RETURN NEXT cterm2; + END LOOP; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; +--- example: select * from fill_cvtermpath(7); where 7 is cv_id for an ontology +--- fill path from the node to its children and their children +CREATE OR REPLACE FUNCTION _fill_cvtermpath4node(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS +' +DECLARE + origin alias for $1; + child_id alias for $2; + cvid alias for $3; + typeid alias for $4; + depth alias for $5; + cterm cvterm_relationship%ROWTYPE; + exist_c int; + +BEGIN + + --- RAISE NOTICE ''depth=% root=%'', depth,child_id; + --- not check type_id as it may be null and not very meaningful in cvtermpath when pathdistance > 1 + SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; + + IF (exist_c = 0) THEN + INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); + END IF; + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP + PERFORM _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); + END LOOP; + RETURN 1; +END; +' +LANGUAGE 'plpgsql'; + + +CREATE OR REPLACE FUNCTION _fill_cvtermpath4root(INTEGER, INTEGER) RETURNS INTEGER AS +' +DECLARE + rootid alias for $1; + cvid alias for $2; + ttype int; + cterm cvterm_relationship%ROWTYPE; + child cvterm_relationship%ROWTYPE; + +BEGIN + + SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); + PERFORM _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0); + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP + PERFORM _fill_cvtermpath4root(cterm.subject_id, cvid); + -- RAISE NOTICE ''DONE for term, %'', cterm.subject_id; + END LOOP; + RETURN 1; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION fill_cvtermpath(INTEGER) RETURNS INTEGER AS +' +DECLARE + cvid alias for $1; + root cvterm%ROWTYPE; + +BEGIN + + DELETE FROM cvtermpath WHERE cv_id = cvid; + + FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP + PERFORM _fill_cvtermpath4root(root.cvterm_id, root.cv_id); + END LOOP; + RETURN 1; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION fill_cvtermpath(cv.name%TYPE) RETURNS INTEGER AS +' +DECLARE + cvname alias for $1; + cv_id int; + rtn int; +BEGIN + + SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; + SELECT INTO rtn fill_cvtermpath(cv_id); + RETURN rtn; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION _fill_cvtermpath4node2detect_cycle(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS +' +DECLARE + origin alias for $1; + child_id alias for $2; + cvid alias for $3; + typeid alias for $4; + depth alias for $5; + cterm cvterm_relationship%ROWTYPE; + exist_c int; + ccount int; + ecount int; + rtn int; +BEGIN + + EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id = ''|| origin || '' AND p2.subject_id = '' || child_id || ''AND '' || depth || ''> 0''; + GET DIAGNOSTICS ccount = ROW_COUNT; + IF (ccount > 0) THEN + --RAISE EXCEPTION ''FOUND CYCLE: node % on cycle path'',origin; + RETURN origin; + END IF; + + EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND '' || origin || ''<>'' || child_id; + GET DIAGNOSTICS ecount = ROW_COUNT; + IF (ecount > 0) THEN + --RAISE NOTICE ''FOUND TWICE (node), will check root obj % subj %'',origin, child_id; + SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(child_id, cvid); + IF (rtn > 0) THEN + RETURN rtn; + END IF; + END IF; + + EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND pathdistance = '' || depth; + GET DIAGNOSTICS exist_c = ROW_COUNT; + IF (exist_c = 0) THEN + EXECUTE ''INSERT INTO tmpcvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES('' || origin || '', '' || child_id || '', '' || cvid || '', '' || typeid || '', '' || depth || '')''; + END IF; + + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP + --RAISE NOTICE ''DOING for node, % %'', origin, cterm.subject_id; + SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); + IF (rtn > 0) THEN + RETURN rtn; + END IF; + END LOOP; + RETURN 0; +END; +' +LANGUAGE 'plpgsql'; + + +CREATE OR REPLACE FUNCTION _fill_cvtermpath4root2detect_cycle(INTEGER, INTEGER) RETURNS INTEGER AS +' +DECLARE + rootid alias for $1; + cvid alias for $2; + ttype int; + ccount int; + cterm cvterm_relationship%ROWTYPE; + child cvterm_relationship%ROWTYPE; + rtn int; +BEGIN + + SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); + SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, rootid, cvid, ttype, 0); + IF (rtn > 0) THEN + RETURN rtn; + END IF; + FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP + EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id='' || rootid || '' AND p1.subject_id='' || cterm.subject_id; + GET DIAGNOSTICS ccount = ROW_COUNT; + IF (ccount > 0) THEN + --RAISE NOTICE ''FOUND TWICE (root), will check root obj % subj %'',rootid,cterm.subject_id; + SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, cterm.subject_id, cvid, ttype, 0); + IF (rtn > 0) THEN + RETURN rtn; + END IF; + ELSE + SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(cterm.subject_id, cvid); + IF (rtn > 0) THEN + RETURN rtn; + END IF; + END IF; + END LOOP; + RETURN 0; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER, INTEGER) RETURNS INTEGER AS +' +DECLARE + cvid alias for $1; + rootid alias for $2; + rtn int; +BEGIN + + CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); + CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); + + SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(rootid, cvid); + IF (rtn > 0) THEN + DROP TABLE tmpcvtermpath; + RETURN rtn; + END IF; + DROP TABLE tmpcvtermpath; + RETURN 0; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION get_cycle_cvterm_ids(INTEGER) RETURNS SETOF INTEGER AS +' +DECLARE + cvid alias for $1; + root cvterm%ROWTYPE; + rtn int; +BEGIN + + + FOR root IN SELECT DISTINCT t.* from cvterm t WHERE cv_id = cvid LOOP + SELECT INTO rtn get_cycle_cvterm_id(cvid,root.cvterm_id); + IF (rtn > 0) THEN + RETURN NEXT rtn; + END IF; + END LOOP; + RETURN; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER) RETURNS INTEGER AS +' +DECLARE + cvid alias for $1; + root cvterm%ROWTYPE; + rtn int; +BEGIN + + CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); + CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); + + FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP + SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(root.cvterm_id, root.cv_id); + IF (rtn > 0) THEN + DROP TABLE tmpcvtermpath; + RETURN rtn; + END IF; + END LOOP; + DROP TABLE tmpcvtermpath; + RETURN 0; +END; +' +LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(cv.name%TYPE) RETURNS INTEGER AS +' +DECLARE + cvname alias for $1; + cv_id int; + rtn int; +BEGIN + + SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; + SELECT INTO rtn get_cycle_cvterm_id(cv_id); + + RETURN rtn; +END; +' +LANGUAGE 'plpgsql'; +-- $Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $ +-- ========================================== +-- Chado pub module +-- +-- ================================================================= +-- Dependencies: +-- +-- :import cvterm from cv +-- :import dbxref from general +-- ================================================================= + +-- ================================================ +-- TABLE: pub +-- ================================================ + +create table pub ( + pub_id serial not null, + primary key (pub_id), + title text, + volumetitle text, + volume varchar(255), + series_name varchar(255), + issue varchar(255), + pyear varchar(255), + pages varchar(255), + miniref varchar(255), + uniquename text not null, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + is_obsolete boolean default 'false', + publisher varchar(255), + pubplace varchar(255), + constraint pub_c1 unique (uniquename) +); +CREATE INDEX pub_idx1 ON pub (type_id); + +COMMENT ON TABLE pub IS 'A documented provenance artefact - publications, +documents, personal communication.'; +COMMENT ON COLUMN pub.title IS 'Descriptive general heading.'; +COMMENT ON COLUMN pub.volumetitle IS 'Title of part if one of a series.'; +COMMENT ON COLUMN pub.series_name IS 'Full name of (journal) series.'; +COMMENT ON COLUMN pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'; +COMMENT ON COLUMN pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.'; + +-- ================================================ +-- TABLE: pub_relationship +-- ================================================ + +create table pub_relationship ( + pub_relationship_id serial not null, + primary key (pub_relationship_id), + subject_id int not null, + foreign key (subject_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + object_id int not null, + foreign key (object_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + + constraint pub_relationship_c1 unique (subject_id,object_id,type_id) +); +create index pub_relationship_idx1 on pub_relationship (subject_id); +create index pub_relationship_idx2 on pub_relationship (object_id); +create index pub_relationship_idx3 on pub_relationship (type_id); + +COMMENT ON TABLE pub_relationship IS 'Handle relationships between +publications, e.g. when one publication makes others obsolete, when one +publication contains errata with respect to other publication(s), or +when one publication also appears in another pub.'; + +-- ================================================ +-- TABLE: pub_dbxref +-- ================================================ + +create table pub_dbxref ( + pub_dbxref_id serial not null, + primary key (pub_dbxref_id), + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, + is_current boolean not null default 'true', + constraint pub_dbxref_c1 unique (pub_id,dbxref_id) +); +create index pub_dbxref_idx1 on pub_dbxref (pub_id); +create index pub_dbxref_idx2 on pub_dbxref (dbxref_id); + +COMMENT ON TABLE pub_dbxref IS 'Handle links to repositories, +e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...'; + + +-- ================================================ +-- TABLE: pubauthor +-- ================================================ + +create table pubauthor ( + pubauthor_id serial not null, + primary key (pubauthor_id), + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + rank int not null, + editor boolean default 'false', + surname varchar(100) not null, + givennames varchar(100), + suffix varchar(100), + + constraint pubauthor_c1 unique (pub_id, rank) +); +create index pubauthor_idx2 on pubauthor (pub_id); + +COMMENT ON TABLE pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.'; +COMMENT ON COLUMN pubauthor.givennames IS 'First name, initials'; +COMMENT ON COLUMN pubauthor.suffix IS 'Jr., Sr., etc'; +COMMENT ON COLUMN pubauthor.rank IS 'Order of author in author list for this pub - order is important.'; +COMMENT ON COLUMN pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.'; + + +-- ================================================ +-- TABLE: pubprop +-- ================================================ + +create table pubprop ( + pubprop_id serial not null, + primary key (pubprop_id), + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text not null, + rank integer, + + constraint pubprop_c1 unique (pub_id,type_id,rank) +); +create index pubprop_idx1 on pubprop (pub_id); +create index pubprop_idx2 on pubprop (type_id); + +COMMENT ON TABLE pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.'; +-- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $ +-- ========================================== +-- Chado organism module +-- +-- ============ +-- DEPENDENCIES +-- ============ +-- :import cvterm from cv +-- :import dbxref from general +-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +-- ================================================ +-- TABLE: organism +-- ================================================ + +create table organism ( + organism_id serial not null, + primary key (organism_id), + abbreviation varchar(255) null, + genus varchar(255) not null, + species varchar(255) not null, + common_name varchar(255) null, + comment text null, + constraint organism_c1 unique (genus,species) +); + +COMMENT ON TABLE organism IS 'The organismal taxonomic +classification. Note that phylogenies are represented using the +phylogeny module, and taxonomies can be represented using the cvterm +module or the phylogeny module.'; + +COMMENT ON COLUMN organism.species IS 'A type of organism is always +uniquely identified by genus and species. When mapping from the NCBI +taxonomy names.dmp file, this column must be used where it +is present, as the common_name column is not always unique (e.g. environmental +samples). If a particular strain or subspecies is to be represented, +this is appended onto the species name. Follows standard NCBI taxonomy +pattern.'; + +-- ================================================ +-- TABLE: organism_dbxref +-- ================================================ + +create table organism_dbxref ( + organism_dbxref_id serial not null, + primary key (organism_dbxref_id), + organism_id int not null, + foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, + constraint organism_dbxref_c1 unique (organism_id,dbxref_id) +); +create index organism_dbxref_idx1 on organism_dbxref (organism_id); +create index organism_dbxref_idx2 on organism_dbxref (dbxref_id); + +-- ================================================ +-- TABLE: organismprop +-- ================================================ + +create table organismprop ( + organismprop_id serial not null, + primary key (organismprop_id), + organism_id int not null, + foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank int not null default 0, + constraint organismprop_c1 unique (organism_id,type_id,rank) +); +create index organismprop_idx1 on organismprop (organism_id); +create index organismprop_idx2 on organismprop (type_id); + +COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.'; + + +CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR,VARCHAR) RETURNS INT + AS ' + SELECT organism_id + FROM organism + WHERE genus=$1 + AND species=$2 + ' LANGUAGE 'sql'; + +CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR) RETURNS INT + AS ' +SELECT organism_id + FROM organism + WHERE genus=substring($1,1,position('' '' IN $1)-1) + AND species=substring($1,position('' '' IN $1)+1) + ' LANGUAGE 'sql'; + +CREATE OR REPLACE FUNCTION get_organism_id_abbrev(VARCHAR) RETURNS INT + AS ' +SELECT organism_id + FROM organism + WHERE substr(genus,1,1)=substring($1,1,1) + AND species=substring($1,position('' '' IN $1)+1) + ' LANGUAGE 'sql'; + +CREATE OR REPLACE FUNCTION store_organism (VARCHAR,VARCHAR,VARCHAR) + RETURNS INT AS +'DECLARE + v_genus ALIAS FOR $1; + v_species ALIAS FOR $2; + v_common_name ALIAS FOR $3; + + v_organism_id INTEGER; + BEGIN + SELECT INTO v_organism_id organism_id + FROM organism + WHERE genus=v_genus AND + species=v_species; + IF NOT FOUND THEN + INSERT INTO organism + (genus,species,common_name) + VALUES + (v_genus,v_species,v_common_name); + RETURN currval(''organism_organism_id_seq''); + ELSE + UPDATE organism + SET common_name=v_common_name + WHERE organism_id = v_organism_id; + END IF; + RETURN v_organism_id; + END; +' LANGUAGE 'plpgsql'; + +-- $Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $ +-- ========================================== +-- Chado sequence module +-- +-- ================================================================= +-- Dependencies: +-- +-- :import cvterm from cv +-- :import pub from pub +-- :import organism from organism +-- :import dbxref from general +-- ================================================================= + +-- ================================================ +-- TABLE: feature +-- ================================================ + +create table feature ( + feature_id serial not null, + primary key (feature_id), + dbxref_id int, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, + organism_id int not null, + foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, + name varchar(255), + uniquename text not null, + residues text, + seqlen int, + md5checksum char(32), + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + is_analysis boolean not null default 'false', + is_obsolete boolean not null default 'false', + timeaccessioned timestamp not null default current_timestamp, + timelastmodified timestamp not null default current_timestamp, + constraint feature_c1 unique (organism_id,uniquename,type_id) +); +create sequence feature_uniquename_seq; +create index feature_name_ind1 on feature(name); +create index feature_idx1 on feature (dbxref_id); +create index feature_idx2 on feature (organism_id); +create index feature_idx3 on feature (type_id); +create index feature_idx4 on feature (uniquename); +create index feature_idx5 on feature (lower(name)); + +ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; + +COMMENT ON TABLE feature IS 'A feature is a biological sequence or a +section of a biological sequence, or a collection of such +sections. Examples include genes, exons, transcripts, regulatory +regions, polypeptides, protein domains, chromosome sequences, sequence +variations, cross-genome match regions such as hits and HSPs and so +on; see the Sequence Ontology for more. The combination of +organism_id, uniquename and type_id should be unique.'; + +COMMENT ON COLUMN feature.dbxref_id IS 'An optional primary public stable +identifier for this feature. Secondary identifiers and external +dbxrefs go in the table feature_dbxref.'; + +COMMENT ON COLUMN feature.organism_id IS 'The organism to which this feature +belongs. This column is mandatory.'; + +COMMENT ON COLUMN feature.name IS 'The optional human-readable common name for +a feature, for display purposes.'; + +COMMENT ON COLUMN feature.uniquename IS 'The unique name for a feature; may +not be necessarily be particularly human-readable, although this is +preferred. This name must be unique for this type of feature within +this organism.'; + +COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters +representing biological residues (nucleic acids, amino acids). This +column does not need to be manifested for all features; it is optional +for features such as exons where the residues can be derived from the +featureloc. It is recommended that the value for this column be +manifested for features which may may non-contiguous sublocations (e.g. +transcripts), since derivation at query time is non-trivial. For +expressed sequence, the DNA sequence should be used rather than the +RNA sequence. The default storage method for the residues column is +EXTERNAL, which will store it uncompressed to make substring operations +faster.'; + +COMMENT ON COLUMN feature.seqlen IS 'The length of the residue feature. See +column:residues. This column is partially redundant with the residues +column, and also with featureloc. This column is required because the +location may be unknown and the residue sequence may not be +manifested, yet it may be desirable to store and query the length of +the feature. The seqlen should always be manifested where the length +of the sequence is known.'; + +COMMENT ON COLUMN feature.md5checksum IS 'The 32-character checksum of the sequence, +calculated using the MD5 algorithm. This is practically guaranteed to +be unique for any feature. This column thus acts as a unique +identifier on the mathematical sequence.'; + +COMMENT ON COLUMN feature.type_id IS 'A required reference to a table:cvterm +giving the feature type. This will typically be a Sequence Ontology +identifier. This column is thus used to subclass the feature table.'; + +COMMENT ON COLUMN feature.is_analysis IS 'Boolean indicating whether this +feature is annotated or the result of an automated analysis. Analysis +results also use the companalysis module. Note that the dividing line +between analysis and annotation may be fuzzy, this should be determined on +a per-project basis in a consistent manner. One requirement is that +there should only be one non-analysis version of each wild-type gene +feature in a genome, whereas the same gene feature can be predicted +multiple times in different analyses.'; + +COMMENT ON COLUMN feature.is_obsolete IS 'Boolean indicating whether this +feature has been obsoleted. Some chado instances may choose to simply +remove the feature altogether, others may choose to keep an obsolete +row in the table.'; + +COMMENT ON COLUMN feature.timeaccessioned IS 'For handling object +accession or modification timestamps (as opposed to database auditing data, +handled elsewhere). The expectation is that these fields would be +available to software interacting with chado.'; + +COMMENT ON COLUMN feature.timelastmodified IS 'For handling object +accession or modification timestamps (as opposed to database auditing data, +handled elsewhere). The expectation is that these fields would be +available to software interacting with chado.'; + +--- COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified +--- by the combination of organism, uniquename and feature type'; + +-- ================================================ +-- TABLE: featureloc +-- ================================================ + +create table featureloc ( + featureloc_id serial not null, + primary key (featureloc_id), + feature_id int not null, + foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, + srcfeature_id int, + foreign key (srcfeature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, + fmin int, + is_fmin_partial boolean not null default 'false', + fmax int, + is_fmax_partial boolean not null default 'false', + strand smallint, + phase int, + residue_info text, + locgroup int not null default 0, + rank int not null default 0, + constraint featureloc_c1 unique (feature_id,locgroup,rank), + constraint featureloc_c2 check (fmin <= fmax) +); +create index featureloc_idx1 on featureloc (feature_id); +create index featureloc_idx2 on featureloc (srcfeature_id); +create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax); + +COMMENT ON TABLE featureloc IS 'The location of a feature relative to +another feature. Important: interbase coordinates are used. This is +vital as it allows us to represent zero-length features e.g. splice +sites, insertion points without an awkward fuzzy system. Features +typically have exactly ONE location, but this need not be the +case. Some features may not be localized (e.g. a gene that has been +characterized genetically but no sequence or molecular information is +available). Note on multiple locations: Each feature can have 0 or +more locations. Multiple locations do NOT indicate non-contiguous +locations (if a feature such as a transcript has a non-contiguous +location, then the subfeatures such as exons should always be +manifested). Instead, multiple featurelocs for a feature designate +alternate locations or grouped locations; for instance, a feature +designating a blast hit or hsp will have two locations, one on the +query feature, one on the subject feature. Features representing +sequence variation could have alternate locations instantiated on a +feature on the mutant strain. The column:rank is used to +differentiate these different locations. Reflexive locations should +never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.'; + +COMMENT ON COLUMN featureloc.feature_id IS 'The feature that is being located. Any feature can have zero or more featurelocs.'; + +COMMENT ON COLUMN featureloc.srcfeature_id IS 'The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.'; + +COMMENT ON COLUMN featureloc.fmin IS 'The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.'; + +COMMENT ON COLUMN featureloc.fmax IS 'The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).'; + +COMMENT ON COLUMN featureloc.strand IS 'The orientation/directionality of the +location. Should be 0, -1 or +1.'; + +COMMENT ON COLUMN featureloc.rank IS 'Used when a feature has >1 +location, otherwise the default rank 0 is used. Some features (e.g. +blast hits and HSPs) have two locations - one on the query and one on +the subject. Rank is used to differentiate these. Rank=0 is always +used for the query, Rank=1 for the subject. For multiple alignments, +assi... [truncated message content] |
From: <sco...@us...> - 2011-11-16 18:53:10
|
Revision: 25246 http://gmod.svn.sourceforge.net/gmod/?rev=25246&view=rev Author: scottcain Date: 2011-11-16 18:52:59 +0000 (Wed, 16 Nov 2011) Log Message: ----------- formatting fix Modified Paths: -------------- schema/trunk/chado/Changes Modified: schema/trunk/chado/Changes =================================================================== --- schema/trunk/chado/Changes 2011-11-15 21:19:32 UTC (rev 25245) +++ schema/trunk/chado/Changes 2011-11-16 18:52:59 UTC (rev 25246) @@ -3,8 +3,8 @@ only good for Tripal at the moment. * Fixed database initialization step "make prepdb" so that the version of the schema gets set in the chadoprop table. -* Fixed bug in gmod_chado_properties.pl that caused it to crash when updating the -schema version. +* Fixed bug in gmod_chado_properties.pl that caused it to crash when updating +the schema version. Version 1.2 Tue Aug 10 13:59:05 EDT 2010 * Added some error checking to gmod_fasta2gff3.pl (Rob) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-15 21:19:42
|
Revision: 25245 http://gmod.svn.sourceforge.net/gmod/?rev=25245&view=rev Author: scottcain Date: 2011-11-15 21:19:32 +0000 (Tue, 15 Nov 2011) Log Message: ----------- Tagging chado release 1.21 Added Paths: ----------- schema/tags/chado-1.21/ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-15 20:38:45
|
Revision: 25244 http://gmod.svn.sourceforge.net/gmod/?rev=25244&view=rev Author: scottcain Date: 2011-11-15 20:38:32 +0000 (Tue, 15 Nov 2011) Log Message: ----------- adding to changes file Modified Paths: -------------- schema/trunk/chado/Changes Modified: schema/trunk/chado/Changes =================================================================== --- schema/trunk/chado/Changes 2011-11-15 20:23:05 UTC (rev 25243) +++ schema/trunk/chado/Changes 2011-11-15 20:38:32 UTC (rev 25244) @@ -3,6 +3,8 @@ only good for Tripal at the moment. * Fixed database initialization step "make prepdb" so that the version of the schema gets set in the chadoprop table. +* Fixed bug in gmod_chado_properties.pl that caused it to crash when updating the +schema version. Version 1.2 Tue Aug 10 13:59:05 EDT 2010 * Added some error checking to gmod_fasta2gff3.pl (Rob) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-15 20:23:17
|
Revision: 25243 http://gmod.svn.sourceforge.net/gmod/?rev=25243&view=rev Author: scottcain Date: 2011-11-15 20:23:05 +0000 (Tue, 15 Nov 2011) Log Message: ----------- removing warn lines Modified Paths: -------------- schema/trunk/chado/bin/gmod_update_chado.pl Modified: schema/trunk/chado/bin/gmod_update_chado.pl =================================================================== --- schema/trunk/chado/bin/gmod_update_chado.pl 2011-11-15 20:18:38 UTC (rev 25242) +++ schema/trunk/chado/bin/gmod_update_chado.pl 2011-11-15 20:23:05 UTC (rev 25243) @@ -75,7 +75,6 @@ #build path to get updates from my $path = "$gmod_root/src/chado/schemas/$current_version-$version/diff.sql"; -warn $path; my $dbuser = $db_conf->user; my $dbport = $db_conf->port; @@ -83,7 +82,6 @@ my $dbname = $db_conf->name; my $syscommand = "cat $path | psql -U $dbuser -p $dbport -h $dbhost $dbname"; -warn $syscommand; system($syscommand) == 0 or die "failed updating database"; #now update the schema version in the chadoprop table This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-15 20:18:51
|
Revision: 25242 http://gmod.svn.sourceforge.net/gmod/?rev=25242&view=rev Author: scottcain Date: 2011-11-15 20:18:38 +0000 (Tue, 15 Nov 2011) Log Message: ----------- fixed finding the version when the chadoprop table exists but there is no data in it (bug in 1.2 release) Modified Paths: -------------- schema/trunk/chado/bin/gmod_chado_properties.pl Modified: schema/trunk/chado/bin/gmod_chado_properties.pl =================================================================== --- schema/trunk/chado/bin/gmod_chado_properties.pl 2011-11-15 19:45:24 UTC (rev 25241) +++ schema/trunk/chado/bin/gmod_chado_properties.pl 2011-11-15 20:18:38 UTC (rev 25242) @@ -170,7 +170,12 @@ my $isth = $dbh->prepare($version_query); $isth->execute(); my ($version) = $isth->fetchrow_array(); - return $version; + + return $version if defined($version); + + #if the table exists but doesn't return a version, assume 1.2 (due to bug + # in that release). + return 1.2; } #if cvprop table exists, then it's 1.11 (or 1.1, same schema) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-15 19:45:37
|
Revision: 25241 http://gmod.svn.sourceforge.net/gmod/?rev=25241&view=rev Author: scottcain Date: 2011-11-15 19:45:24 +0000 (Tue, 15 Nov 2011) Log Message: ----------- fixed the version update command to do the right thing if A) the chadoprop table exists but is empty (due to a bug in the 1.2 release), or 2) if it has a value in it already (ie, update rather than insert). It will also puke if the chadoprop table doesn't exist. Modified Paths: -------------- schema/trunk/chado/bin/gmod_chado_properties.pl Modified: schema/trunk/chado/bin/gmod_chado_properties.pl =================================================================== --- schema/trunk/chado/bin/gmod_chado_properties.pl 2011-11-15 19:16:41 UTC (rev 25240) +++ schema/trunk/chado/bin/gmod_chado_properties.pl 2011-11-15 19:45:24 UTC (rev 25241) @@ -87,6 +87,7 @@ $sth->execute(); my ($cv_id) = $sth->fetchrow_array; + my $new_chadoprop = 0; my $cvterm_id; unless ($cv_id) { #chado_properties is not available, so create it @@ -94,6 +95,7 @@ $dbh->do($cv_insert); insert_version_term($dbh); + $new_chadoprop = 1; } #check that the version term is available @@ -107,11 +109,39 @@ $sth->execute(); ($cvterm_id) = $sth->fetchrow_array; + $new_chadoprop = 1; } - my $set_query = "INSERT INTO chadoprop (type_id, value) VALUES (?,?)"; - $sth = $dbh->prepare($set_query); - $sth->execute($cvterm_id,$version) or die "database error: $!"; + #find out if there's already a version in there + # and if the chadoprop table exists + my $table_query = "SELECT 1 FROM pg_tables WHERE tablename = ?"; + $sth = $dbh->prepare($table_query); + $sth->execute('chadoprop'); + + if ($sth->fetchrow_array) { + #chadoprop table exists, so check in it for a value + my $version_query = "SELECT value FROM chadoprop WHERE type_id in (SELECT cvterm_id FROM cvterm WHERE cv_id in (SELECT cv_id FROM cv WHERE name = 'chado_properties') AND name = 'version')"; + my $isth = $dbh->prepare($version_query); + $isth->execute(); + my ($old_version) = $isth->fetchrow_array(); + + if (defined($old_version)) { + #there is a version in there, update it + my $update_query = "UPDATE chadoprop SET value = $version WHERE type_id = $cvterm_id"; + $dbh->do($update_query); + } + else { + #no version but the table exists, (assume 1.2) and insert new value + my $set_query = "INSERT INTO chadoprop (type_id, value) VALUES (?,?)"; + $sth = $dbh->prepare($set_query); + $sth->execute($cvterm_id,$version) or die "database error: $!"; + } + + } + else { + die "The chadoprop table doesn't seem to exist; perhaps there is a problem with Chado?"; + } + } else { die "$version doesn't look like a valid version number."; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-15 19:16:57
|
Revision: 25240 http://gmod.svn.sourceforge.net/gmod/?rev=25240&view=rev Author: scottcain Date: 2011-11-15 19:16:41 +0000 (Tue, 15 Nov 2011) Log Message: ----------- bumping version in the Build script too Modified Paths: -------------- schema/trunk/chado/load/Build.PL Modified: schema/trunk/chado/load/Build.PL =================================================================== --- schema/trunk/chado/load/Build.PL 2011-11-15 18:51:40 UTC (rev 25239) +++ schema/trunk/chado/load/Build.PL 2011-11-15 19:16:41 UTC (rev 25240) @@ -3,7 +3,7 @@ use Bio::Chado::Builder; use Data::Dumper; -my $VERSION = 1.2; +my $VERSION = 1.21; my $conf = shift; my $m = Bio::Chado::Builder->new( dist_name => 'Chado', This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-15 18:51:56
|
Revision: 25239 http://gmod.svn.sourceforge.net/gmod/?rev=25239&view=rev Author: scottcain Date: 2011-11-15 18:51:40 +0000 (Tue, 15 Nov 2011) Log Message: ----------- adding sql diffs for new version Added Paths: ----------- schema/trunk/chado/schemas/1-1.21/ schema/trunk/chado/schemas/1-1.21/diff.sql schema/trunk/chado/schemas/1.1-1.21/ schema/trunk/chado/schemas/1.1-1.21/diff schema/trunk/chado/schemas/1.1-1.21/diff.sql schema/trunk/chado/schemas/1.11-1.21/ schema/trunk/chado/schemas/1.11-1.21/diff schema/trunk/chado/schemas/1.11-1.21/diff.sql schema/trunk/chado/schemas/1.2-1.21/ schema/trunk/chado/schemas/1.2-1.21/diff.sql schema/trunk/chado/schemas/1.21/ schema/trunk/chado/schemas/1.21/default_schema.sql Added: schema/trunk/chado/schemas/1-1.21/diff.sql =================================================================== --- schema/trunk/chado/schemas/1-1.21/diff.sql (rev 0) +++ schema/trunk/chado/schemas/1-1.21/diff.sql 2011-11-15 18:51:40 UTC (rev 25239) @@ -0,0 +1,951 @@ +--Note that the so schema is left out of this diff + +ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; + +COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters +representing biological residues (nucleic acids, amino acids). This +column does not need to be manifested for all features; it is optional +for features such as exons where the residues can be derived from the +featureloc. It is recommended that the value for this column be +manifested for features which may may non-contiguous sublocations (e.g. +transcripts), since derivation at query time is non-trivial. For +expressed sequence, the DNA sequence should be used rather than the +RNA sequence. The default storage method for the residues column is +EXTERNAL, which will store it uncompressed to make substring operations +faster.'; + +ALTER TABLE feature_synonym ALTER COLUMN is_current SET DEFAULT 'false'; + +CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS ' + DECLARE + BEGIN + /* Generate a table of shared exons */ + CREATE temporary TABLE shared_exons AS + SELECT gene.feature_id as gene_feature_id + , gene.uniquename as gene_uniquename + , transcript1.uniquename as transcript1 + , exon1.feature_id as exon1_feature_id + , exon1.uniquename as exon1_uniquename + , transcript2.uniquename as transcript2 + , exon2.feature_id as exon2_feature_id + , exon2.uniquename as exon2_uniquename + , exon1_loc.fmin /* = exon2_loc.fmin */ + , exon1_loc.fmax /* = exon2_loc.fmax */ + FROM feature gene + JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id + JOIN cv gene_type_cv USING (cv_id) + JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id + JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id + JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id + JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id + JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id + JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id + JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id + JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id + JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id + JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id + JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id + JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id + JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id + JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id + JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id + JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id + JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id + JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id + WHERE gene_type_cv.name = ''sequence'' + AND gene_type.name = ''gene'' + AND transcript1_type_cv.name = ''sequence'' + AND transcript1_type.name = ''mRNA'' + AND transcript2_type_cv.name = ''sequence'' + AND transcript2_type.name = ''mRNA'' + AND exon1_type_cv.name = ''sequence'' + AND exon1_type.name = ''exon'' + AND exon2_type_cv.name = ''sequence'' + AND exon2_type.name = ''exon'' + AND exon1.feature_id < exon2.feature_id + AND exon1_loc.rank = 0 + AND exon2_loc.rank = 0 + AND exon1_loc.fmin = exon2_loc.fmin + AND exon1_loc.fmax = exon2_loc.fmax + ; + + CREATE temporary TABLE canonical_exon_representatives AS + SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin + FROM shared_exons + GROUP BY gene_feature_id,fmin + ; + + CREATE temporary TABLE exon_replacements AS + SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id + , canonical_exon_representatives.canonical_feature_id + , canonical_exon_representatives.fmin + FROM shared_exons + JOIN canonical_exon_representatives USING (gene_feature_id) + WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id + AND shared_exons.fmin = canonical_exon_representatives.fmin + ; + UPDATE feature_relationship + SET subject_id = ( + SELECT canonical_feature_id + FROM exon_replacements + WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) + WHERE subject_id IN ( + SELECT actual_feature_id FROM exon_replacements + ); + + UPDATE feature_relationship + SET object_id = ( + SELECT canonical_feature_id + FROM exon_replacements + WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) + WHERE object_id IN ( + SELECT actual_feature_id FROM exon_replacements + ); + + UPDATE feature + SET is_obsolete = true + WHERE feature_id IN ( + SELECT actual_feature_id FROM exon_replacements + ); + END; +' LANGUAGE 'plpgsql'; + +CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' + DECLARE + parent_type ALIAS FOR $1; + exon_id int; + part_of int; + exon_type int; + strand int; + arow RECORD; + order_by varchar; + rowcount int; + exon_count int; + ordered_exons int; + transcript_id int; + transcript_row feature%ROWTYPE; + BEGIN + SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' + AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); + --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' + -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); + + --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; + + FOR transcript_row IN + SELECT * FROM feature WHERE type_id = parent_type + LOOP + transcript_id = transcript_row.feature_id; + SELECT INTO rowcount count(*) FROM feature_relationship + WHERE object_id = transcript_id + AND rank = 0; + + --Dont modify this transcript if there are already numbered exons or + --if there is only one exon + IF rowcount = 1 THEN + --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; + CONTINUE; + END IF; + --need to reverse the order if the strand is negative + SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; + IF strand > 0 THEN + order_by = ''fl.fmin''; + ELSE + order_by = ''fl.fmax desc''; + END IF; + + exon_count = 0; + FOR arow IN EXECUTE + ''SELECT fr.*, fl.fmin, fl.fmax + FROM feature_relationship fr, featureloc fl + WHERE fr.object_id = ''||transcript_id||'' + AND fr.subject_id = fl.feature_id + AND fr.type_id = ''||part_of||'' + ORDER BY ''||order_by + LOOP + --number the exons for a given transcript + UPDATE feature_relationship + SET rank = exon_count + WHERE feature_relationship_id = arow.feature_relationship_id; + exon_count = exon_count + 1; + END LOOP; + + END LOOP; + + END; +' LANGUAGE 'plpgsql'; + +ALTER TABLE analysisprop ADD COLUMN rank int not null default 0; + +CREATE TABLE analysisfeatureprop ( + analysisfeatureprop_id SERIAL PRIMARY KEY, + analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, + type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, + value TEXT, + rank INTEGER NOT NULL, + CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) +); + + +ALTER TABLE phenotype_comparison_cvterm ADD CONSTRAINT phenotype_comparison_cvterm_pub_id_fkey FOREIGN KEY (pub_id) REFERENCES pub(pub_id) ON DELETE CASCADE; + + + +create table cell_line ( + cell_line_id serial not null, + primary key (cell_line_id), + name varchar(255) null, + uniquename varchar(255) not null, + organism_id int not null, + foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, + timeaccessioned timestamp not null default current_timestamp, + timelastmodified timestamp not null default current_timestamp, + constraint cell_line_c1 unique (uniquename, organism_id) +); +grant all on cell_line to PUBLIC; + + +create table cell_line_relationship ( + cell_line_relationship_id serial not null, + primary key (cell_line_relationship_id), + subject_id int not null, + foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, + object_id int not null, + foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) +); +grant all on cell_line_relationship to PUBLIC; + + +create table cell_line_synonym ( + cell_line_synonym_id serial not null, + primary key (cell_line_synonym_id), + cell_line_id int not null, + foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, + synonym_id int not null, + foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + is_current boolean not null default 'false', + is_internal boolean not null default 'false', + constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) +); +grant all on cell_line_synonym to PUBLIC; + + +create table cell_line_cvterm ( + cell_line_cvterm_id serial not null, + primary key (cell_line_cvterm_id), + cell_line_id int not null, + foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, + cvterm_id int not null, + foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + rank int not null default 0, + constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) +); +grant all on cell_line_cvterm to PUBLIC; + + +create table cell_line_dbxref ( + cell_line_dbxref_id serial not null, + primary key (cell_line_dbxref_id), + cell_line_id int not null, + foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, + dbxref_id int not null, + foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, + is_current boolean not null default 'true', + constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) +); +grant all on cell_line_dbxref to PUBLIC; + +create table cell_lineprop ( + cell_lineprop_id serial not null, + primary key (cell_lineprop_id), + cell_line_id int not null, + foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank int not null default 0, + constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) +); +grant all on cell_lineprop to PUBLIC; + +create table cell_lineprop_pub ( + cell_lineprop_pub_id serial not null, + primary key (cell_lineprop_pub_id), + cell_lineprop_id int not null, + foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) +); +grant all on cell_lineprop_pub to PUBLIC; + +create table cell_line_feature ( + cell_line_feature_id serial not null, + primary key (cell_line_feature_id), + cell_line_id int not null, + foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, + feature_id int not null, + foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) +); +grant all on cell_line_feature to PUBLIC; + +create table cell_line_cvtermprop ( + cell_line_cvtermprop_id serial not null, + primary key (cell_line_cvtermprop_id), + cell_line_cvterm_id int not null, + foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank int not null default 0, + constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) +); +grant all on cell_line_cvtermprop to PUBLIC; + +create table cell_line_pub ( + cell_line_pub_id serial not null, + primary key (cell_line_pub_id), + cell_line_id int not null, + foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + constraint cell_line_pub_c1 unique (cell_line_id, pub_id) +); +grant all on cell_line_pub to PUBLIC; + +create table cell_line_library ( + cell_line_library_id serial not null, + primary key (cell_line_library_id), + cell_line_id int not null, + foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, + library_id int not null, + foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) +); +grant all on cell_line_library to PUBLIC; + + +CREATE OR REPLACE VIEW gff3view ( +feature_id, ref, source, type, fstart, fend, +score, strand, phase, seqlen, name, organism_id +) AS +SELECT +f.feature_id, sf.name, gffdbx.accession, cv.name, +fl.fmin+1, fl.fmax, af.significance, fl.strand, +fl.phase, f.seqlen, f.name, f.organism_id +FROM feature f +LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) +LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) +LEFT JOIN ( SELECT fd.feature_id, d.accession +FROM feature_dbxref fd +JOIN dbxref d using(dbxref_id) +JOIN db using(db_id) +WHERE db.name = 'GFF_source' +) as gffdbx +ON (f.feature_id=gffdbx.feature_id) +LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) +LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); + + +CREATE OR REPLACE VIEW all_feature_names ( + feature_id, + name, + organism_id +) AS +SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature +UNION +SELECT feature_id, name, organism_id FROM feature where name is not null +UNION +SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f + WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id +UNION +SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f + WHERE f.feature_id = fp.feature_id +UNION +SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f + WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; + +--start 1.11-1.2 diff + + create table cvprop ( + cvprop_id serial not null, + primary key (cvprop_id), + cv_id int not null, + foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, + value text, + rank int not null default 0, + constraint cvprop_c1 unique (cv_id,type_id,rank) + ); + + COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; + + COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; + COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; + + COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any + cv can have multiple values for any particular property type - + these are ordered in a list using rank, counting from zero. For + properties that are single-valued rather than multi-valued, the + default 0 value should be used.'; + + create table chadoprop ( + chadoprop_id serial not null, + primary key (chadoprop_id), + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, + value text, + rank int not null default 0, + constraint chadoprop_c1 unique (type_id,rank) + ); + + COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; + + COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; + COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; + + COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any + cv can have multiple values for any particular property type - + these are ordered in a list using rank, counting from zero. For + properties that are single-valued rather than multi-valued, the + default 0 value should be used.'; + +ALTER TABLE genetic_code.gencode_startcodon ADD CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ); + +ALTER TABLE phenotype ADD COLUMN name TEXT default null; + +ALTER TABLE genotype ADD COLUMN type_id INT NOT NULL; +ALTER TABLE genotype ADD CONSTRAINT genotype_type_id_fkey FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE; + + + create table genotypeprop ( + genotypeprop_id serial not null, + primary key (genotypeprop_id), + genotype_id int not null, + foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank int not null default 0, + constraint genotypeprop_c1 unique (genotype_id,type_id,rank) + ); + create index genotypeprop_idx1 on genotypeprop (genotype_id); + create index genotypeprop_idx2 on genotypeprop (type_id); + + CREATE TABLE projectprop ( + projectprop_id serial NOT NULL, + PRIMARY KEY (projectprop_id), + project_id integer NOT NULL, + FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, + type_id integer NOT NULL, + FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, + value text, + rank integer not null default 0, + CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) + ); + + -- ================================================ + -- TABLE: project_relationship + -- ================================================ + + CREATE TABLE project_relationship ( + project_relationship_id serial NOT NULL, + PRIMARY KEY (project_relationship_id), + subject_project_id integer NOT NULL, + FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, + object_project_id integer NOT NULL, + FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, + type_id integer NOT NULL, + FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, + CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) + ); + COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; + COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; + + + create table project_pub ( + project_pub_id serial not null, + primary key (project_pub_id), + project_id int not null, + foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + constraint project_pub_c1 unique (project_id,pub_id) + ); + create index project_pub_idx1 on project_pub (project_id); + create index project_pub_idx2 on project_pub (pub_id); + + COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; + + + create table project_contact ( + project_contact_id serial not null, + primary key (project_contact_id), + project_id int not null, + foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, + contact_id int not null, + foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, + constraint project_contact_c1 unique (project_id,contact_id) + ); + create index project_contact_idx1 on project_contact (project_id); + create index project_contact_idx2 on project_contact (contact_id); + + COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; + +ALTER TABLE stock alter organism_id drop not null; + + COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.'; + + CREATE TABLE stock_relationship_cvterm ( + stock_relationship_cvterm_id SERIAL NOT NULL, + PRIMARY KEY (stock_relationship_cvterm_id), + stock_relationship_id integer NOT NULL, + FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, + cvterm_id integer NOT NULL, + FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, + pub_id integer, + FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT + ); +COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; + + +alter table stock_cvterm add column is_not boolean not null default false; +alter table stock_cvterm add column rank integer not null default 0; +alter table stock_cvterm drop constraint stock_cvterm_c1; +alter table stock_cvterm add constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) +; + + + create table stock_cvtermprop ( + stock_cvtermprop_id serial not null, + primary key (stock_cvtermprop_id), + stock_cvterm_id int not null, + foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank int not null default 0, + constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) + ); + create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); + create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); + + COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for + stock to cvterm associations. Examples: GO evidence codes; + qualifiers; metadata such as the date on which the entry was curated + and the source of the association. See the stockprop table for + meanings of type_id, value and rank.'; + + COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the + property/slot is a cvterm. The meaning of the property is defined in + that cvterm. cvterms may come from the OBO evidence code cv.'; + + COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the + property, represented as text. Numeric values are converted to their + text representation. This is less efficient than using native database + types, but is easier to query.'; + + COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value + ordering. Any stock_cvterm can have multiple values for any particular + property type - these are ordered in a list using rank, counting from + zero. For properties that are single-valued rather than multi-valued, + the default 0 value should be used.'; + + create table stock_dbxrefprop ( + stock_dbxrefprop_id serial not null, + primary key (stock_dbxrefprop_id), + stock_dbxref_id int not null, + foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank int not null default 0, + constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) + ); + create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); + create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); + + COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of + slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to + hardcoding a list of columns in the relational schema, and is + completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for + the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; + +-- VIEW gffatts: a view to get feature attributes in a format that +-- will make it easy to convert them to GFF attributes + +CREATE OR REPLACE VIEW gffatts ( + feature_id, + type, + attribute +) AS +SELECT feature_id, 'Ontology_term' AS type, s.name AS attribute +FROM cvterm s, feature_cvterm fs +WHERE fs.cvterm_id = s.cvterm_id +UNION ALL +SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute +FROM dbxref s, feature_dbxref fs, db d +WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id +UNION ALL +SELECT feature_id, 'Alias' AS type, s.name AS attribute +FROM synonym s, feature_synonym fs +WHERE fs.synonym_id = s.synonym_id +UNION ALL +SELECT fp.feature_id,cv.name,fp.value +FROM featureprop fp, cvterm cv +WHERE fp.type_id = cv.cvterm_id +UNION ALL +SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute +FROM pub s, feature_pub fs +WHERE fs.pub_id = s.pub_id; + +CREATE OR REPLACE VIEW gff3atts ( + feature_id, + type, + attribute +) AS +SELECT feature_id, + 'Ontology_term' AS type, + CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession + WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession + ELSE CAST(db.name||':'|| dbx.accession AS varchar) + END +FROM cvterm s, dbxref dbx, feature_cvterm fs, db +WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and + db.db_id = dbx.db_id +UNION ALL +SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS +attribute +FROM dbxref s, feature_dbxref fs, db d +WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and + d.name != 'GFF_source' +UNION ALL +SELECT f.feature_id, 'Alias' AS type, s.name AS attribute +FROM synonym s, feature_synonym fs, feature f +WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and + f.name != s.name and f.uniquename != s.name +UNION ALL +SELECT fp.feature_id,cv.name,fp.value +FROM featureprop fp, cvterm cv +WHERE fp.type_id = cv.cvterm_id +UNION ALL +SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS +attribute +FROM pub s, feature_pub fs +WHERE fs.pub_id = s.pub_id +UNION ALL +SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename +as attribute +FROM feature_relationship fr, feature parent +WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id +FROM cvterm WHERE name='part_of' and cv_id in (select cv_id + FROM cv WHERE name='relationship')) +UNION ALL +SELECT fr.subject_id as feature_id, 'Derives_from' as type, +parent.uniquename as attribute +FROM feature_relationship fr, feature parent +WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id +FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id + FROM cv WHERE name='relationship')) +UNION ALL +SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 +|| ' ' || fl.fmax || ' ' || fl.strand as attribute +FROM featureloc fl, feature target +WHERE fl.srcfeature_id=target.feature_id + AND fl.rank != 0 +UNION ALL +SELECT feature_id, 'ID' as type, uniquename as attribute +FROM feature +WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') +UNION ALL +SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS +varchar) as attribute +FROM feature +UNION ALL +SELECT feature_id, 'Name' as type, name as attribute +FROM feature; + + +-- ================================================================= +-- Dependencies: +-- +-- :import feature from sequence +-- :import cvterm from cv +-- :import pub from pub +-- :import phenotype from phenotype +-- :import organism from organism +-- :import genotype from genetic +-- :import contact from contact +-- :import project from project +-- :import stock from stock +-- :import synonym +-- ================================================================= + + +-- this probably needs some work, depending on how cross-database we +-- want to be. In Postgres, at least, there are much better ways to +-- represent geo information. + +CREATE TABLE nd_geolocation ( + nd_geolocation_id serial PRIMARY KEY NOT NULL, + description character varying(255), + latitude real, + longitude real, + geodetic_datum character varying(32), + altitude real +); + +COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; + +COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; + + +COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; + +COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; + +COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; + +COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; + + + +CREATE TABLE nd_experiment ( + nd_experiment_id serial PRIMARY KEY NOT NULL, + nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED +); + +-- +--used to be nd_diversityexperiment_project +--then was nd_assay_project +CREATE TABLE nd_experiment_project ( + nd_experiment_project_id serial PRIMARY KEY NOT NULL, + project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, + nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED +); + + + +CREATE TABLE nd_experimentprop ( + nd_experimentprop_id serial PRIMARY KEY NOT NULL, + nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , + value text null, + rank integer NOT NULL default 0, + constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) +); + +CREATE TABLE nd_experiment_pub ( + nd_experiment_pub_id serial PRIMARY KEY not null, + nd_experiment_id int not null, + foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, + pub_id int not null, + foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, + constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) +); +create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); +create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); + +COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; + + + + +CREATE TABLE nd_geolocationprop ( + nd_geolocationprop_id serial PRIMARY KEY NOT NULL, + nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank integer NOT NULL DEFAULT 0, + constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) +); + +COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; + +COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; + +COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; + +COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; + + +CREATE TABLE nd_protocol ( + nd_protocol_id serial PRIMARY KEY NOT NULL, + name character varying(255) NOT NULL unique, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED +); + +COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; + +COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; + +CREATE TABLE nd_reagent ( + nd_reagent_id serial PRIMARY KEY NOT NULL, + name character varying(80) NOT NULL, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + feature_id integer +); + +COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; + +COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; + +COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; + +COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; + + + +CREATE TABLE nd_protocol_reagent ( + nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, + nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, + reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED +); + + +CREATE TABLE nd_protocolprop ( + nd_protocolprop_id serial PRIMARY KEY NOT NULL, + nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank integer DEFAULT 0 NOT NULL, + constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) +); + +COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; + +COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; + +COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; + +COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; + +COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; + + + +CREATE TABLE nd_experiment_stock ( + nd_experiment_stock_id serial PRIMARY KEY NOT NULL, + nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, + stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED +); + +COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; + + +COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; + + +CREATE TABLE nd_experiment_protocol ( + nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, + nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, + nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED +); + +COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; + + +CREATE TABLE nd_experiment_phenotype ( + nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, + nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, + phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, + constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) +); + +COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; + +CREATE TABLE nd_experiment_genotype ( + nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, + nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, + genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , + constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) +); + +COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; + + +CREATE TABLE nd_reagent_relationship ( + nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, + subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, + object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED +); + +COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; + +COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; + +COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; + +COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; + + +CREATE TABLE nd_reagentprop ( + nd_reagentprop_id serial PRIMARY KEY NOT NULL, + nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank integer DEFAULT 0 NOT NULL, + constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) +); + +CREATE TABLE nd_experiment_stockprop ( + nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, + nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, + type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank integer DEFAULT 0 NOT NULL, + constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) +); + +COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; + +COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; + +COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; + +COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; + +COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; + + +CREATE TABLE nd_experiment_stock_dbxref ( + nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, + nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, + dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED +); + +COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; + + + +CREATE TABLE nd_experiment_dbxref ( + nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, + nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, + dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED +); + +COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; + + +CREATE TABLE nd_experiment_contact ( + nd_experiment_contact_id serial PRIMARY KEY NOT NULL, + nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, + contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED +); Added: schema/trunk/chado/schemas/1.1-1.21/diff =================================================================== --- schema/trunk/chado/schemas/1.1-1.21/diff (rev 0) +++ schema/trunk/chado/schemas/1.1-1.21/diff 2011-11-15 18:51:40 UTC (rev 25239) @@ -0,0 +1,11106 @@ +69a70,82 +> -- ================================================ +> -- TABLE: project +> -- ================================================ +> +> create table project ( +> project_id serial not null, +> primary key (project_id), +> name varchar(255) not null, +> description varchar(255) not null, +> constraint project_c1 unique (name) +> ); +> +> COMMENT ON TABLE project IS NULL; +409,458d421 +< -- ================================================ +< -- TABLE: cvprop +< -- ================================================ +< create table cvprop ( +< cvprop_id serial not null, +< primary key (cvprop_id), +< cv_id int not null, +< foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, +< type_id int not null, +< foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, +< value text, +< rank int not null default 0, +< constraint cvprop_c1 unique (cv_id,type_id,rank) +< ); +< +< COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; +< +< COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; +< COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; +< +< COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any +< cv can have multiple values for any particular property type - +< these are ordered in a list using rank, counting from zero. For +< properties that are single-valued rather than multi-valued, the +< default 0 value should be used.'; +< +< -- ================================================ +< -- TABLE: chadoprop +< -- ================================================ +< create table chadoprop ( +< chadoprop_id serial not null, +< primary key (chadoprop_id), +< type_id int not null, +< foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, +< value text, +< rank int not null default 0, +< constraint chadoprop_c1 unique (type_id,rank) +< ); +< +< COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; +< +< COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; +< COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; +< +< COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any +< cv can have multiple values for any particular property type - +< these are ordered in a list using rank, counting from zero. For +< properties that are single-valued rather than multi-valued, the +< default 0 value should be used.'; +< +1927,1928c1890 +< aa CHAR(1) NOT NULL, +< CONSTRAINT gencode_codon_unique UNIQUE( gencode_id, codon ) +--- +> aa CHAR(1) NOT NULL +1934,1935c1896 +< codon CHAR(3), +< CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ) +--- +> codon CHAR(3) +2463c2424 @@ Diff output truncated at 100000 characters. @@ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-15 18:23:14
|
Revision: 25238 http://gmod.svn.sourceforge.net/gmod/?rev=25238&view=rev Author: scottcain Date: 2011-11-15 18:22:56 +0000 (Tue, 15 Nov 2011) Log Message: ----------- removing "use lib" lines that refer to my home directories Modified Paths: -------------- schema/trunk/chado/bin/gmod_add_organism.pl schema/trunk/chado/bin/gmod_chado_properties.pl schema/trunk/chado/bin/gmod_gff3_preprocessor.pl schema/trunk/chado/bin/gmod_update_chado.pl schema/trunk/chado/load/bin/bulk_load_gff3.PLS schema/trunk/chado/load/bin/load_gff3.PLS Modified: schema/trunk/chado/bin/gmod_add_organism.pl =================================================================== --- schema/trunk/chado/bin/gmod_add_organism.pl 2011-11-14 19:53:26 UTC (rev 25237) +++ schema/trunk/chado/bin/gmod_add_organism.pl 2011-11-15 18:22:56 UTC (rev 25238) @@ -2,8 +2,8 @@ use strict; use Getopt::Long; -use lib '/home/cain/cvs_stuff/schema/chado/lib'; -use lib '/home/scott/cvs_stuff/schema/chado/lib'; +#use lib '/home/cain/cvs_stuff/schema/chado/lib'; +#use lib '/home/scott/cvs_stuff/schema/chado/lib'; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Bio::Chado::Schema; Modified: schema/trunk/chado/bin/gmod_chado_properties.pl =================================================================== --- schema/trunk/chado/bin/gmod_chado_properties.pl 2011-11-14 19:53:26 UTC (rev 25237) +++ schema/trunk/chado/bin/gmod_chado_properties.pl 2011-11-15 18:22:56 UTC (rev 25238) @@ -2,8 +2,8 @@ use strict; use Getopt::Long; -use lib '/home/cain/cvs_stuff/schema/chado/lib'; -use lib '/home/scott/cvs_stuff/schema/chado/lib'; +#use lib '/home/cain/cvs_stuff/schema/chado/lib'; +#use lib '/home/scott/cvs_stuff/schema/chado/lib'; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use ExtUtils::MakeMaker; #to get prompt Modified: schema/trunk/chado/bin/gmod_gff3_preprocessor.pl =================================================================== --- schema/trunk/chado/bin/gmod_gff3_preprocessor.pl 2011-11-14 19:53:26 UTC (rev 25237) +++ schema/trunk/chado/bin/gmod_gff3_preprocessor.pl 2011-11-15 18:22:56 UTC (rev 25238) @@ -4,8 +4,8 @@ use Bio::FeatureIO; use Getopt::Long; use FileHandle; -use lib '/home/cain/cvs_stuff/schema/chado/lib'; -use lib '/home/scott/cvs_stuff/schema/chado/lib'; +#use lib '/home/cain/cvs_stuff/schema/chado/lib'; +#use lib '/home/scott/cvs_stuff/schema/chado/lib'; use Bio::GMOD::DB::Adapter; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; Modified: schema/trunk/chado/bin/gmod_update_chado.pl =================================================================== --- schema/trunk/chado/bin/gmod_update_chado.pl 2011-11-14 19:53:26 UTC (rev 25237) +++ schema/trunk/chado/bin/gmod_update_chado.pl 2011-11-15 18:22:56 UTC (rev 25238) @@ -2,8 +2,8 @@ use strict; use Getopt::Long; -use lib '/home/cain/cvs_stuff/schema/chado/lib'; -use lib '/home/scott/cvs_stuff/schema/chado/lib'; +#use lib '/home/cain/cvs_stuff/schema/chado/lib'; +#use lib '/home/scott/cvs_stuff/schema/chado/lib'; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use ExtUtils::MakeMaker; #to get prompt Modified: schema/trunk/chado/load/bin/bulk_load_gff3.PLS =================================================================== --- schema/trunk/chado/load/bin/bulk_load_gff3.PLS 2011-11-14 19:53:26 UTC (rev 25237) +++ schema/trunk/chado/load/bin/bulk_load_gff3.PLS 2011-11-15 18:22:56 UTC (rev 25238) @@ -34,7 +34,7 @@ use strict; use warnings; -use lib '/Users/cain/cvs_stuff/schema/trunk/chado/lib'; +#use lib '/Users/cain/cvs_stuff/schema/trunk/chado/lib'; use Bio::FeatureIO; use Bio::SeqIO; use Getopt::Long; Modified: schema/trunk/chado/load/bin/load_gff3.PLS =================================================================== --- schema/trunk/chado/load/bin/load_gff3.PLS 2011-11-14 19:53:26 UTC (rev 25237) +++ schema/trunk/chado/load/bin/load_gff3.PLS 2011-11-15 18:22:56 UTC (rev 25238) @@ -34,7 +34,7 @@ print OUT <<'!NO!SUBS!'; use strict; use warnings; -use lib '/Users/cain/cvs_stuff/schema/trunk/chado/lib'; +#use lib '/Users/cain/cvs_stuff/schema/trunk/chado/lib'; use Bio::Tools::GFF; use Bio::SeqIO; use Bio::Chado::AutoDBI; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-11-14 19:53:38
|
Revision: 25237 http://gmod.svn.sourceforge.net/gmod/?rev=25237&view=rev Author: scottcain Date: 2011-11-14 19:53:26 +0000 (Mon, 14 Nov 2011) Log Message: ----------- Fixed database initialization step "make prepdb" so that the version of the schema gets set in the chadoprop table. Modified Paths: -------------- schema/trunk/chado/Changes schema/trunk/chado/lib/Bio/Chado/Builder.pm Modified: schema/trunk/chado/Changes =================================================================== --- schema/trunk/chado/Changes 2011-11-14 17:07:28 UTC (rev 25236) +++ schema/trunk/chado/Changes 2011-11-14 19:53:26 UTC (rev 25237) @@ -1,6 +1,8 @@ Version 1.21 Thu Oct 20 10:52:55 EDT 2011 * Added rudimentary support for non-public schemas in Postgres, though it's only good for Tripal at the moment. +* Fixed database initialization step "make prepdb" so that the version of the +schema gets set in the chadoprop table. Version 1.2 Tue Aug 10 13:59:05 EDT 2010 * Added some error checking to gmod_fasta2gff3.pl (Rob) Modified: schema/trunk/chado/lib/Bio/Chado/Builder.pm =================================================================== --- schema/trunk/chado/lib/Bio/Chado/Builder.pm 2011-11-14 17:07:28 UTC (rev 25236) +++ schema/trunk/chado/lib/Bio/Chado/Builder.pm 2011-11-14 19:53:26 UTC (rev 25237) @@ -100,6 +100,9 @@ } } + #set the chado schema version in the database + system("gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version"); + } =head2 ACTION_update This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nm...@us...> - 2011-11-07 17:16:30
|
Revision: 25231 http://gmod.svn.sourceforge.net/gmod/?rev=25231&view=rev Author: nm249 Date: 2011-11-07 17:16:17 +0000 (Mon, 07 Nov 2011) Log Message: ----------- new standard phenotypeprop table Modified Paths: -------------- schema/trunk/chado/modules/phenotype/phenotype.sql Modified: schema/trunk/chado/modules/phenotype/phenotype.sql =================================================================== --- schema/trunk/chado/modules/phenotype/phenotype.sql 2011-11-01 16:15:52 UTC (rev 25230) +++ schema/trunk/chado/modules/phenotype/phenotype.sql 2011-11-07 17:16:17 UTC (rev 25231) @@ -81,3 +81,25 @@ CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id); COMMENT ON TABLE feature_phenotype IS NULL; + + + +create table phenotypeprop ( + phenotypeprop_id serial not null, + primary key (phenotypeprop_id), + phenotype_id int not null, + foreign key (phenotype_id) references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, + type_id int not null, + foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, + value text null, + rank int not null default 0, + constraint phenotypeprop_c1 unique (phenotype_id,type_id,rank) +); +create index phenotypeprop_idx1 on phenotypeprop (phenotype_id); +create index phenotypeprop_idx2 on phenotypeprop (type_id); + +COMMENT ON TABLE phenotypeprop IS 'A phenotype can have any number of +slot-value property tags attached to it. This is an alternative to +hardcoding a list of columns in the relational schema, and is +completely extensible. There is a unique constraint, phenotypeprop_c1, for +the combination of phenotype_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-10-20 16:04:06
|
Revision: 25228 http://gmod.svn.sourceforge.net/gmod/?rev=25228&view=rev Author: scottcain Date: 2011-10-20 16:03:56 +0000 (Thu, 20 Oct 2011) Log Message: ----------- adding the ability for the mat view tool to work in non-public schemas Modified Paths: -------------- schema/trunk/chado/bin/gmod_materialized_view_tool.pl Modified: schema/trunk/chado/bin/gmod_materialized_view_tool.pl =================================================================== --- schema/trunk/chado/bin/gmod_materialized_view_tool.pl 2011-10-20 14:53:51 UTC (rev 25227) +++ schema/trunk/chado/bin/gmod_materialized_view_tool.pl 2011-10-20 16:03:56 UTC (rev 25228) @@ -228,6 +228,7 @@ my $gmod_conf = Bio::GMOD::Config->new(); my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE ); +$SCHEMA = $db_conf->schema || $SCHEMA; my $dbh = $db_conf->dbh; $dbh->{AutoCommit} = 0; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-10-20 14:53:58
|
Revision: 25227 http://gmod.svn.sourceforge.net/gmod/?rev=25227&view=rev Author: scottcain Date: 2011-10-20 14:53:51 +0000 (Thu, 20 Oct 2011) Log Message: ----------- updating Changes file Modified Paths: -------------- schema/trunk/chado/Changes Modified: schema/trunk/chado/Changes =================================================================== --- schema/trunk/chado/Changes 2011-10-20 14:52:33 UTC (rev 25226) +++ schema/trunk/chado/Changes 2011-10-20 14:53:51 UTC (rev 25227) @@ -1,3 +1,7 @@ +Version 1.21 Thu Oct 20 10:52:55 EDT 2011 +* Added rudimentary support for non-public schemas in Postgres, though it's +only good for Tripal at the moment. + Version 1.2 Tue Aug 10 13:59:05 EDT 2010 * Added some error checking to gmod_fasta2gff3.pl (Rob) * Updated Bio::Chado::Builder to detect recent versions of go-perl. They This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-10-20 14:52:42
|
Revision: 25226 http://gmod.svn.sourceforge.net/gmod/?rev=25226&view=rev Author: scottcain Date: 2011-10-20 14:52:33 +0000 (Thu, 20 Oct 2011) Log Message: ----------- adding rudimentary support for non-public schema (really only good for Tripal at the moment) Modified Paths: -------------- schema/trunk/chado/Makefile.PL schema/trunk/chado/install_util/conf_install.PLS Modified: schema/trunk/chado/Makefile.PL =================================================================== --- schema/trunk/chado/Makefile.PL 2011-10-20 13:23:05 UTC (rev 25225) +++ schema/trunk/chado/Makefile.PL 2011-10-20 14:52:33 UTC (rev 25226) @@ -50,7 +50,7 @@ use Template; use Module::Build; -my $VERSION = 1.2; +my $VERSION = 1.21; my %args = ( DBDRIVER => { @@ -84,6 +84,9 @@ DEFAULT => { default => 'y' }, + SCHEMA => { + default => 'public' + }, ); my %env2arg = ( @@ -237,7 +240,7 @@ # Now figure out where the values are coming from -- build.conf, # command-line, or prompt(). # -my ( $DBDRIVER, $DBNAME, $DBUSER, $DBPASS, $DBHOST, $DBPORT, +my ( $DBDRIVER, $DBNAME, $DBUSER, $DBPASS, $DBHOST, $DBPORT,$SCHEMA, $SQLFILES, $EXTERNAL_DDL, $LOCAL_TMP, $DBORGANISM, $APOLLO, $DEFAULT); $O{'SIMPLE'} = prompt( @@ -263,6 +266,7 @@ $DBORGANISM=$conf{'DBORGANISM'}|| ''; $APOLLO = $conf{'APOLLP'} || ''; $DEFAULT = $conf{'DEFAULT'} || ''; + $SCHEMA = $conf{'SCHEMA'} || ''; } elsif ( $opts{'DEFAULTS'} ) { $DBDRIVER = $args{'DBDRIVER'}{'default'}; @@ -275,6 +279,7 @@ $DBORGANISM=$args{'DBORGANISM'}{'default'}; $APOLLO = $args{'APOLLO'}{'default'}; $DEFAULT = $args{'DEFAULT'}{'default'}; + $SCHEMA = $args{'SCHEMA'}{'default'}; } elsif ( %opts ) { $DBDRIVER = $opts{'DBDRIVER'} || ''; @@ -287,6 +292,7 @@ $DBORGANISM=$opts{'DBORGANISM'}|| ''; $APOLLO = $opts{'APOLLO'} || ''; $DEFAULT = $opts{'DEFAULT'} || ''; + $SCHEMA = $opts{'SCHEMA'} || ''; } if ( !$opts{'DEFAULTS'} && !$opts{'RECONFIGURE'} ) { @@ -329,6 +335,10 @@ $conf{'DBPORT'} || $args{'DBPORT'}{'default'} ); + $SCHEMA ||= prompt( 'What schema will Chado reside in?', + $conf{'SCHEMA'} || $args{'SCHEMA'}{'default'} + ); + $LOCAL_TMP ||= prompt( 'Where shall downloaded ontologies go?', $conf{'LOCAL_TMP'} || $args{'LOCAL_TMP'}{'default'} ); @@ -388,6 +398,7 @@ " DBPASS=$DBPASS", " DBHOST=$DBHOST", " DBPORT=$DBPORT", + " SCHEMA=$SCHEMA", " LOCAL_TMP=$LOCAL_TMP", " DBORGANISM=$DBORGANISM", " DEFAULT=$DEFAULT", @@ -410,6 +421,7 @@ $conf{'LIB'} = $opts{'LIB'}; $conf{'DEFAULT'} = $DEFAULT; $conf{'VERSION'} = $VERSION; + $conf{'SCHEMA'} = $SCHEMA; print CONF map { "$_=$conf{ $_ }\n" } keys %conf; close CONF or die "Can't write file '$build_config': $!\n"; Modified: schema/trunk/chado/install_util/conf_install.PLS =================================================================== --- schema/trunk/chado/install_util/conf_install.PLS 2011-10-20 13:23:05 UTC (rev 25225) +++ schema/trunk/chado/install_util/conf_install.PLS 2011-10-20 14:52:33 UTC (rev 25226) @@ -54,7 +54,7 @@ while (<LOCALCONF>) { chomp; my ($key, $value) = split /=/; - if ($key =~ /^DB/ or $key eq 'DEFAULT') { + if ($key =~ /^DB/ or $key eq 'DEFAULT' or $key eq 'SCHEMA') { $confitems{$key} = $value; } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-10-20 13:23:18
|
Revision: 25225 http://gmod.svn.sourceforge.net/gmod/?rev=25225&view=rev Author: scottcain Date: 2011-10-20 13:23:05 +0000 (Thu, 20 Oct 2011) Log Message: ----------- adding a new method to return the schema Modified Paths: -------------- schema/trunk/chado/lib/Bio/GMOD/DB/Config.pm Modified: schema/trunk/chado/lib/Bio/GMOD/DB/Config.pm =================================================================== --- schema/trunk/chado/lib/Bio/GMOD/DB/Config.pm 2011-10-19 22:29:48 UTC (rev 25224) +++ schema/trunk/chado/lib/Bio/GMOD/DB/Config.pm 2011-10-20 13:23:05 UTC (rev 25225) @@ -177,6 +177,22 @@ shift->get_tag_value('SQLFILE'); } +=head2 schema + + Title : schema + Usage : $schema = $dbconf->schema(); + Function: Returns the schema chado resides in (usually public) + Returns : see above + Args : none + Status : Public + +=cut + +sub schema { + shift->get_tag_value('SCHEMA'); +} + + =head2 organism Title : organism This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-09-21 17:26:47
|
Revision: 25202 http://gmod.svn.sourceforge.net/gmod/?rev=25202&view=rev Author: scottcain Date: 2011-09-21 17:26:35 +0000 (Wed, 21 Sep 2011) Log Message: ----------- tagging 1.2 release Added Paths: ----------- schema/tags/chado-1.2/ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |