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From: <em...@us...> - 2013-09-09 13:18:13
|
Revision: 25291
http://sourceforge.net/p/gmod/svn/25291
Author: emmert
Date: 2013-09-09 13:17:56 +0000 (Mon, 09 Sep 2013)
Log Message:
-----------
Added documentation to new tables and made some minor formatting changes where neccesary for consistency.
Modified Paths:
--------------
schema/trunk/chado/modules/library/library.sql
schema/trunk/chado/modules/organism/organism.sql
schema/trunk/chado/modules/phenotype/phenotype.sql
Modified: schema/trunk/chado/modules/library/library.sql
===================================================================
--- schema/trunk/chado/modules/library/library.sql 2013-07-26 17:23:56 UTC (rev 25290)
+++ schema/trunk/chado/modules/library/library.sql 2013-09-09 13:17:56 UTC (rev 25291)
@@ -35,8 +35,7 @@
create index library_idx2 on library (type_id);
create index library_idx3 on library (uniquename);
-COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links
-to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"';
+COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"';
-- ================================================
@@ -60,9 +59,13 @@
create index library_synonym_idx2 on library_synonym (library_id);
create index library_synonym_idx3 on library_synonym (pub_id);
+COMMENT ON TABLE library_synonym IS 'Linking table between library and synonym.';
+
COMMENT ON COLUMN library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.';
+
COMMENT ON COLUMN library_synonym.pub_id IS 'The pub_id link is for
relating the usage of a given synonym to the publication in which it was used.';
+
COMMENT ON COLUMN library_synonym.is_internal IS 'Typically a synonym
exists so that somebody querying the database with an obsolete name
can find the object they are looking for under its current name. If
@@ -85,7 +88,9 @@
create index library_pub_idx1 on library_pub (library_id);
create index library_pub_idx2 on library_pub (pub_id);
+COMMENT ON TABLE library_pub IS 'Attribution for a library.';
+
-- ================================================
-- TABLE: libraryprop
-- ================================================
@@ -104,7 +109,9 @@
create index libraryprop_idx1 on libraryprop (library_id);
create index libraryprop_idx2 on libraryprop (type_id);
+COMMENT ON TABLE libraryprop IS 'Tag-value properties - follows standard chado model.';
+
-- ================================================
-- TABLE: libraryprop_pub
-- ================================================
@@ -121,7 +128,9 @@
create index libraryprop_pub_idx1 on libraryprop_pub (libraryprop_id);
create index libraryprop_pub_idx2 on libraryprop_pub (pub_id);
+COMMENT ON TABLE libraryprop_pub IS 'Attribution for libraryprop.';
+
-- ================================================
-- TABLE: library_cvterm
-- ================================================
@@ -180,7 +189,9 @@
create index library_dbxref_idx1 on library_dbxref (library_id);
create index library_dbxref_idx2 on library_dbxref (dbxref_id);
+COMMENT ON TABLE library_dbxref IS 'Links a library to dbxrefs.';
+
-- ================================================
-- TABLE: library_expression
-- ================================================
@@ -200,7 +211,9 @@
create index library_expression_idx2 on library_expression (expression_id);
create index library_expression_idx3 on library_expression (pub_id);
+COMMENT ON TABLE library_expression IS 'Links a library to expression statements.';
+
-- ================================================
-- TABLE: library_expressionprop
-- ================================================
@@ -219,7 +232,9 @@
create index library_expressionprop_idx1 on library_expressionprop (library_expression_id);
create index library_expressionprop_idx2 on library_expressionprop (type_id);
+COMMENT ON TABLE library_expressionprop IS 'Attributes of a library_expression relationship.';
+
-- ================================================
-- TABLE: library_featureprop
-- ================================================
@@ -238,7 +253,9 @@
create index library_featureprop_idx1 on library_featureprop (library_feature_id);
create index library_featureprop_idx2 on library_featureprop (type_id);
+COMMENT ON TABLE library_featureprop IS 'Attributes of a library_feature relationship.';
+
-- ================================================
-- TABLE: library_interaction
-- ================================================
@@ -258,7 +275,9 @@
create index library_interaction_idx2 on library_interaction (library_id);
create index library_interaction_idx3 on library_interaction (pub_id);
+COMMENT ON TABLE library_interaction IS 'Links a library to an interaction.';
+
-- ================================================
-- TABLE: library_relationship
-- ================================================
@@ -278,7 +297,9 @@
create index library_relationship_idx2 on library_relationship (object_id);
create index library_relationship_idx3 on library_relationship (type_id);
+COMMENT ON TABLE library_relationship IS 'Relationships between libraries.';
+
-- ================================================
-- TABLE: library_relationship_pub
-- ================================================
@@ -295,7 +316,9 @@
create index library_relationship_pub_idx1 on library_relationship_pub (library_relationship_id);
create index library_relationship_pub_idx2 on library_relationship_pub (pub_id);
+COMMENT ON TABLE library_relationship_pub IS 'Provenance of library_relationship.';
+
-- ================================================
-- TABLE: library_strain
-- ================================================
@@ -311,3 +334,5 @@
);
create index library_strain_idx1 on library_strain (library_id);
create index library_strain_idx2 on library_strain (strain_id);
+
+COMMENT ON TABLE library_strain IS 'Links a library to a strain.';
Modified: schema/trunk/chado/modules/organism/organism.sql
===================================================================
--- schema/trunk/chado/modules/organism/organism.sql 2013-07-26 17:23:56 UTC (rev 25290)
+++ schema/trunk/chado/modules/organism/organism.sql 2013-09-09 13:17:56 UTC (rev 25291)
@@ -56,7 +56,9 @@
create index organism_dbxref_idx1 on organism_dbxref (organism_id);
create index organism_dbxref_idx2 on organism_dbxref (dbxref_id);
+COMMENT ON TABLE library_dbxref IS 'Links a library to dbxrefs.';
+
-- ================================================
-- TABLE: organismprop
-- ================================================
@@ -118,7 +120,9 @@
create index organism_pub_idx1 on organism_pub (organism_id);
create index organism_pub_idx2 on organism_pub (pub_id);
+COMMENT ON TABLE organism_pub IS 'Attribution for organism.';
+
-- ================================================
-- TABLE: organism_cvterm
-- ================================================
@@ -374,11 +378,13 @@
create index strain_dbxref_idx1 on strain_dbxref (strain_id);
create index strain_dbxref_idx2 on strain_dbxref (dbxref_id);
+COMMENT ON TABLE strain_dbxref IS 'Links a strain to dbxrefs. This is for secondary identifiers; primary identifiers should use strain.dbxref_id.';
--- ================================================
--- TABLE: strain_pub
--- ================================================
+-- ================================================
+-- TABLE: strain_pub
+-- ================================================
+
drop table strain_pub cascade;
create table strain_pub (
strain_pub_id serial not null,
@@ -392,7 +398,9 @@
create index strain_pub_idx1 on strain_pub (strain_id);
create index strain_pub_idx2 on strain_pub (pub_id);
+COMMENT ON TABLE strain_pub IS 'Provenance. Linking table between strains and publications that mention them.';
+
-- ================================================
-- TABLE: strain_synonym
-- ================================================
Modified: schema/trunk/chado/modules/phenotype/phenotype.sql
===================================================================
--- schema/trunk/chado/modules/phenotype/phenotype.sql 2013-07-26 17:23:56 UTC (rev 25290)
+++ schema/trunk/chado/modules/phenotype/phenotype.sql 2013-09-09 13:17:56 UTC (rev 25291)
@@ -45,6 +45,7 @@
COMMENT ON COLUMN phenotype.cvalue_id IS 'Phenotype attribute value (state).';
COMMENT ON COLUMN phenotype.assay_id IS 'Evidence type.';
+
-- ================================================
-- TABLE: phenotype_cvterm
-- ================================================
@@ -62,8 +63,9 @@
CREATE INDEX phenotype_cvterm_idx1 ON phenotype_cvterm (phenotype_id);
CREATE INDEX phenotype_cvterm_idx2 ON phenotype_cvterm (cvterm_id);
-COMMENT ON TABLE phenotype_cvterm IS NULL;
+COMMENT ON TABLE phenotype_cvterm IS 'phenotype to cvterm associations.';
+
-- ================================================
-- TABLE: feature_phenotype
-- ================================================
@@ -80,9 +82,12 @@
CREATE INDEX feature_phenotype_idx1 ON feature_phenotype (feature_id);
CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id);
-COMMENT ON TABLE feature_phenotype IS NULL;
+COMMENT ON TABLE feature_phenotype IS 'Linking table between features and phenotypes.';
+-- ================================================
+-- TABLE: phenotypeprop
+-- ================================================
create table phenotypeprop (
phenotypeprop_id serial not null,
@@ -98,8 +103,4 @@
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.';
+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...> - 2013-07-26 17:24:10
|
Revision: 25290
http://sourceforge.net/p/gmod/svn/25290
Author: scottcain
Date: 2013-07-26 17:23:56 +0000 (Fri, 26 Jul 2013)
Log Message:
-----------
added a warning message for the GFF bulk loader if part_of isn't found and a minor doc fix for UPGRADE.txt.
Modified Paths:
--------------
schema/trunk/chado/Changes
schema/trunk/chado/UPGRADE.txt
schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2013-07-16 17:49:23 UTC (rev 25289)
+++ schema/trunk/chado/Changes 2013-07-26 17:23:56 UTC (rev 25290)
@@ -1,4 +1,5 @@
Version 1.24 Mon Mar 4 17:18:47 EST 2013
+* Added a warning message for the GFF bulk loader if part_of isn't found.
* Fixed ncbi_taxonomy loader to load entire NCBI taxonomy (Naama)
* Patched gmod_bulk_load_gff3.pl (provided by Alexie P) to fix the
"orgainism from data" option.
Modified: schema/trunk/chado/UPGRADE.txt
===================================================================
--- schema/trunk/chado/UPGRADE.txt 2013-07-16 17:49:23 UTC (rev 25289)
+++ schema/trunk/chado/UPGRADE.txt 2013-07-26 17:23:56 UTC (rev 25290)
@@ -16,7 +16,7 @@
perl Makefile.PL
make
- make install
+ sudo make install
and then, rather than doing the next step (make load_schema) which would wipe
out the current database, do
Modified: schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm
===================================================================
--- schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm 2013-07-16 17:49:23 UTC (rev 25289)
+++ schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm 2013-07-26 17:23:56 UTC (rev 25290)
@@ -1506,6 +1506,9 @@
$sth->execute;
($part_of) = $sth->fetchrow_array();
+ warn "\n\nWARNING:\nUnable to find a 'part_of' term in the relationship ontology;\nIt's absense indicates that there is something really wrong with the database.\nConsider stopping and checking the state of your cvterm table.\n\n\n";
+
+
$sth = $self->dbh->prepare(
"select cvterm_id from cvterm where name = 'derives_from' and cv_id in (
SELECT cv_id FROM cv WHERE name='relationship'
@@ -3432,6 +3435,7 @@
$tuniquename = $target_id;
$name = $target_id;
}
+###FIXME: put my $tuniquename = $target_id.'_'.$self->nextfeature; in else here
$self->print_f($self->nextfeature, $self->organism_id(), $name,$tuniquename , $type, '\N','\N');
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|
|
From: <nm...@us...> - 2013-07-16 17:49:36
|
Revision: 25289
http://sourceforge.net/p/gmod/svn/25289
Author: nm249
Date: 2013-07-16 17:49:23 +0000 (Tue, 16 Jul 2013)
Log Message:
-----------
dbxref accession is varchar 255
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 2013-05-29 17:04:46 UTC (rev 25288)
+++ schema/trunk/chado/bin/gmod_load_cvterms.pl 2013-07-16 17:49:23 UTC (rev 25289)
@@ -491,7 +491,8 @@
my $def_dbxref = $dblink->database() . ':' . $dblink->primary_id();
$file_def_dbxrefs{uc($def_dbxref)}=1;
message("adding definition dbxref $def_dbxref to cvterm_dbxref\n");
- $db_index{$k}->add_secondary_dbxref($def_dbxref, 1);
+ $def_dbxref = substr($def_dbxref, 0, 255);
+ $db_index{$k}->add_secondary_dbxref($def_dbxref, 1);
}
}
}
@@ -568,12 +569,13 @@
foreach my $i ($novel_terms{$k}->get_secondary_ids()) { #store secondary ids in cvterm_dbxref
message("adding secondary dbxref '$i' to cvterm_dbxref\n");
-
+ $i = substr($i, 0, 255);
$new_term->add_secondary_dbxref($i);
}
foreach my $r ($novel_terms{$k}->get_dbxrefs() ) { #store definition's dbxrefs in cvterm_dbxref
if (!$r->database || !$r->primary_id) { next; } # skip def. dbxrefs without both db_name and accession
my $def_dbxref= $r->database() . ':' . $r->primary_id();
+ $def_dbxref = substr($def_dbxref, 0, 255);
message("adding definition dbxref $def_dbxref to cvterm_dbxref\n");
$new_term->add_secondary_dbxref($def_dbxref, 1);
}
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|
|
From: <sco...@us...> - 2013-05-29 17:04:57
|
Revision: 25288
http://gmod.svn.sourceforge.net/gmod/?rev=25288&view=rev
Author: scottcain
Date: 2013-05-29 17:04:46 +0000 (Wed, 29 May 2013)
Log Message:
-----------
added note about taxonomy loader fix
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2013-05-29 16:35:23 UTC (rev 25287)
+++ schema/trunk/chado/Changes 2013-05-29 17:04:46 UTC (rev 25288)
@@ -1,4 +1,5 @@
Version 1.24 Mon Mar 4 17:18:47 EST 2013
+* Fixed ncbi_taxonomy loader to load entire NCBI taxonomy (Naama)
* Patched gmod_bulk_load_gff3.pl (provided by Alexie P) to fix the
"orgainism from data" option.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nm...@us...> - 2013-05-29 16:35:37
|
Revision: 25287
http://gmod.svn.sourceforge.net/gmod/?rev=25287&view=rev
Author: nm249
Date: 2013-05-29 16:35:23 +0000 (Wed, 29 May 2013)
Log Message:
-----------
optional loading of entire ncbi taxonomy should work now
Modified Paths:
--------------
schema/trunk/chado/bin/load_ncbi_taxonomy.pl
Modified: schema/trunk/chado/bin/load_ncbi_taxonomy.pl
===================================================================
--- schema/trunk/chado/bin/load_ncbi_taxonomy.pl 2013-03-04 22:27:55 UTC (rev 25286)
+++ schema/trunk/chado/bin/load_ncbi_taxonomy.pl 2013-05-29 16:35:23 UTC (rev 25287)
@@ -290,68 +290,76 @@
#read in the taxonomy tree
open( NODE, "nodes.dmp" );
while ( my $line = <NODE> ) {
+ chomp $line;
my ( $id, $parent, $level ) = split /\s+\|\s+/, $line;
###message("id = $id, parent = $parent, level = $level\n",1);
- next unless $okay_level{ $level };
-
- # check for data consistency
- if ($infile) {
+ if ( !($okay_level{ $level } ) ) {
+ message("Node rank not found in the database (" . $okay_level{ $level } . "). Skipping\n");
+ next;
+ }
+ # check for data consistency
+ if ($infile) {
if ( exists $tax_file{$id} ) {
# check if the parent is in the taxfile
if ( $parent && !(exists $tax_file{ $parent } ) ) {
- message ("Parent $parent for tax_id $id does not exist in your input file ! This means $id is your root, or you need to check your input!\n",1);
+ message ("Parent $parent for tax_id '" . $id . "' does not exist in your input file ! This means $id is your root, or you need to check your input!\n",1);
}
} else{ next(); } # skip nodes not in tax_file
}
-
+
###message("STORING NODE is node hash\n",1);
- $node{ $id }{ 'parent_taxid' } = $parent;
- $node{ $id }{ 'self_taxid' } = $id;
- $node{ $id }{ 'level' } = $level;
+ $node{$id}{ 'parent_taxid' } = $parent;
+ $node{$id}{ 'self_taxid' } = $id;
+ $node{$id}{ 'level' } = $level;
}
close( NODE );
open( NAME, "names.dmp" );
while ( my $line = <NAME> ) {
- #next unless $line =~ /scientific name/;
+ chomp $line;
my ( $id, $name ) = split /\s+\|\s+/, $line;
###message("NAMES: id = $id, name = $name\n",1);
- next unless $node{ $id }; #skip nodes
+ next unless $node{$id}; #skip nodes
if ( $line =~ /scientific name/) {
###message("Storing scientific name '$name'\n",1);
- $node{ $id }{ 'name' } = $name;
- $node{ $id }{ 'name' } .= " Taxonomy:$id" if $seen{ $name }++;
+ $node{$id}{ 'name' } = $name;
+ $node{$id}{ 'name' } .= " Taxonomy:$id" if $seen{ $name }++;
} elsif ( $line =~ /common name/) { # genbank common names
- push(@{ $node{ $id }{ 'common_name' } } , $name);
+ push(@{ $node{$id}{ 'common_name' } } , $name);
push(@{ $node{$id}{ 'synonyms' } }, $name);
-
+
} elsif ( $line =~ /synonym/ ) {
push @{ $node{$id}{ 'synonyms' } }, $name;
}
+ # populate $tax_file with the ids from the names file if a filtering file is not passed
+ if (!$infile) {
+ $tax_file{$id} = $id;
+ }
+ #
}
close( NAME );
foreach my $id ( keys %node ) {
- ###message("Looking at id $id in node hash... level = " . $node{ $id }{'level'} . "\n",1);
- my $parent_taxid = $node{ $id }{ 'parent_taxid' } ;
- if (!$tax_file{$parent_taxid}) {
- message("No parent id found for species " . $node{ $id }{ 'name' } . " (id = $id) !! This means your species is the root node, or there is an error in yout input file \n", 1);
+ ##message("Looking at id '" . $id . "' in node hash... level = " . $node{$id}{'level'} . "\n",1);
+ my $parent_taxid = $node{$id}{ 'parent_taxid' } ;
+ if (!$tax_file{$parent_taxid}) {
+ message("No parent id found for species " . $node{ $id }{ 'name' } . " (id = '" . $id . "') !! This means your species is the root node, or there is an error in yout input file \n\n", 1);
}
if ( $node{ $id }{ 'level' } eq 'species' ) {
# load the genus name from the parent_taxid
if (!$tax_file{$parent_taxid}) {
- die "No parent id found for species " . $node{ $id }{ 'name' } . " (id = $id) !! Check your input file !!\n" ;
+ die "No parent id found for species " . $node{ $id }{ 'name' } . " (id = '" . $id . "') !! Check your input file !!\n" ;
}
-
+
$node{ $id }{ 'genus' } = $node{ $parent_taxid }{ 'name' };
$node{ $id }{ 'species' } = $node{ $id }{ 'name' };
###message("FOUND SPECIES: " . $node{ $id }{ 'name' } . " genus = " . $node{ $id }{ 'genus' } . "\n" , 1);
-
+
} else {
- ###message("FOUND NODE NAME: " . $node{ $node{ $id }{ 'parent_taxid' }}{ 'name' } . "( genus = " . $node{ $id }{ 'level' } . " species = " . $node{ $id }{ 'name' } . "\n",1);
-
+ ###message("FOUND NODE NAME: " . $node{ $node{ $id }{ 'parent_taxid' }}{ 'name' } . "( genus = " . $node{ $id }{ 'level' } . " species = " . $node{ $id }{ 'name' } . "\n",1);
+
$node{ $id }{ 'genus' } = $node{ $id }{ 'level' };
$node{ $id }{ 'species' } = $node{ $id }{ 'name' };
}
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|
|
From: <sco...@us...> - 2013-03-04 22:28:06
|
Revision: 25286
http://gmod.svn.sourceforge.net/gmod/?rev=25286&view=rev
Author: scottcain
Date: 2013-03-04 22:27:55 +0000 (Mon, 04 Mar 2013)
Log Message:
-----------
updating the changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2013-03-04 22:09:03 UTC (rev 25285)
+++ schema/trunk/chado/Changes 2013-03-04 22:27:55 UTC (rev 25286)
@@ -1,3 +1,7 @@
+Version 1.24 Mon Mar 4 17:18:47 EST 2013
+* Patched gmod_bulk_load_gff3.pl (provided by Alexie P) to fix the
+"orgainism from data" option.
+
Version 1.23 Thu Dec 1 14:45:22 EST 2011
* Added $VERSION to Bio::GMOD::DB::Config so that when installing
Bio::DB::Das::Chado it would be happy.
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|
|
From: <sco...@us...> - 2013-03-04 22:09:15
|
Revision: 25285
http://gmod.svn.sourceforge.net/gmod/?rev=25285&view=rev
Author: scottcain
Date: 2013-03-04 22:09:03 +0000 (Mon, 04 Mar 2013)
Log Message:
-----------
add a patch from Alexie for the organism from data functionality; not tested yet!
Modified Paths:
--------------
schema/trunk/chado/load/bin/bulk_load_gff3.PLS
Modified: schema/trunk/chado/load/bin/bulk_load_gff3.PLS
===================================================================
--- schema/trunk/chado/load/bin/bulk_load_gff3.PLS 2013-02-28 19:43:35 UTC (rev 25284)
+++ schema/trunk/chado/load/bin/bulk_load_gff3.PLS 2013-03-04 22:09:03 UTC (rev 25285)
@@ -826,7 +826,11 @@
? ($feature->annotation->get_Annotations('organism'))[0]
: '';
if($gff_organism && $gff_organism ne $chado->organism()) {
- $ORGANISM = "$gff_organism";# is it pesky bperl object?
+ #next 4 lines patch by Alexie P.
+ $ORGANISM = "$gff_organism";# is it pesky bperl object? # sadly yes
+ if (ref($gff_organism)){
+ $ORGANISM = $gff_organism->value();
+ }
warn "Organism $ORGANISM from data\n" unless($seen_organism{$ORGANISM}++);
$chado->organism($ORGANISM);
$chado->organism_id($ORGANISM) #? dont die if many orgs? auto-add *
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|
|
From: <em...@us...> - 2013-03-01 09:03:10
|
Revision: 25284
http://gmod.svn.sourceforge.net/gmod/?rev=25284&view=rev
Author: emmert
Date: 2013-02-28 19:43:35 +0000 (Thu, 28 Feb 2013)
Log Message:
-----------
Add tables to organism module: strain_phenotypeprop and strain_relationship_pub
Modified Paths:
--------------
schema/trunk/chado/modules/organism/organism.sql
Modified: schema/trunk/chado/modules/organism/organism.sql
===================================================================
--- schema/trunk/chado/modules/organism/organism.sql 2013-02-27 19:43:09 UTC (rev 25283)
+++ schema/trunk/chado/modules/organism/organism.sql 2013-02-28 19:43:35 UTC (rev 25284)
@@ -149,7 +149,7 @@
the default 0 value should be used';
---================================================
+-- ================================================
-- TABLE: organism_cvtermprop
-- ================================================
@@ -232,7 +232,7 @@
COMMENT ON TABLE strain_cvterm IS 'strain to cvterm associations. Examples: GOid';
---================================================
+-- ================================================
-- TABLE: strain_cvtermprop
-- ================================================
@@ -295,6 +295,26 @@
-- ================================================
+-- TABLE: strain_relationship_pub
+-- ================================================
+
+drop table strain_relationship_pub cascade;
+create table strain_relationship_pub (
+ strain_relationship_pub_id serial not null,
+ primary key (strain_relationship_pub_id),
+ strain_relationship_id int not null,
+ foreign key (strain_relationship_id) references strain_relationship (strain_relationship_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 strain_relationship_pub_c1 unique (strain_relationship_id,pub_id)
+);
+create index strain_relationship_pub_idx1 on strain_relationship_pub (strain_relationship_id);
+create index strain_relationship_pub_idx2 on strain_relationship_pub (pub_id);
+
+COMMENT ON TABLE strain_relationship_pub IS 'Provenance. Attach optional evidence to a strain_relationship in the form of a publication.';
+
+
+-- ================================================
-- TABLE: strainprop
-- ================================================
@@ -358,6 +378,7 @@
-- ================================================
-- TABLE: strain_pub
-- ================================================
+
drop table strain_pub cascade;
create table strain_pub (
strain_pub_id serial not null,
@@ -462,3 +483,26 @@
create index strain_phenotype_idx2 ON strain_phenotype (phenotype_id);
COMMENT on table strain_phenotype IS 'Links phenotype(s) associated with a given strain. Types may be, eg, "selected" or "unassigned".';
+
+
+-- ================================================
+-- TABLE: strain_phenotypeprop
+-- ================================================
+
+drop table strain_phenotypeprop cascade;
+create table strain_phenotypeprop (
+ strain_phenotypeprop_id serial not null,
+ primary key (strain_phenotypeprop_id),
+ strain_phenotype_id int not null,
+ foreign key (strain_phenotype_id) references strain_phenotype (strain_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 strain_phenotypeprop_c1 unique (strain_phenotype_id,type_id,rank)
+);
+create index strain_phenotypeprop_idx1 on strain_phenotypeprop (strain_phenotype_id);
+create index strain_phenotypeprop_idx2 on strain_phenotypeprop (type_id);
+
+COMMENT ON TABLE strain_phenotypeprop IS 'Attributes of a strain_phenotype relationship. Eg, a comment';
+
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|
|
From: <em...@us...> - 2013-02-27 19:52:18
|
Revision: 25283
http://gmod.svn.sourceforge.net/gmod/?rev=25283&view=rev
Author: emmert
Date: 2013-02-27 19:43:09 +0000 (Wed, 27 Feb 2013)
Log Message:
-----------
Add strain_pub table to module
Modified Paths:
--------------
schema/trunk/chado/modules/organism/organism.sql
Modified: schema/trunk/chado/modules/organism/organism.sql
===================================================================
--- schema/trunk/chado/modules/organism/organism.sql 2013-02-08 21:25:30 UTC (rev 25282)
+++ schema/trunk/chado/modules/organism/organism.sql 2013-02-27 19:43:09 UTC (rev 25283)
@@ -355,6 +355,23 @@
create index strain_dbxref_idx2 on strain_dbxref (dbxref_id);
+-- ================================================
+-- TABLE: strain_pub
+-- ================================================
+drop table strain_pub cascade;
+create table strain_pub (
+ strain_pub_id serial not null,
+ primary key (strain_pub_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ unique(strain_id,pub_id)
+);
+create index strain_pub_idx1 on strain_pub (strain_id);
+create index strain_pub_idx2 on strain_pub (pub_id);
+
+
-- ================================================
-- TABLE: strain_synonym
-- ================================================
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|
|
From: <sco...@us...> - 2013-02-01 21:04:51
|
Revision: 25281
http://gmod.svn.sourceforge.net/gmod/?rev=25281&view=rev
Author: scottcain
Date: 2013-02-01 21:04:39 +0000 (Fri, 01 Feb 2013)
Log Message:
-----------
adding back the check to keep the script from running if the owner specifically requests it not run with userdata NoCallHome:1
Modified Paths:
--------------
schema/trunk/chado/bin/GMODCallHome.pl
Modified: schema/trunk/chado/bin/GMODCallHome.pl
===================================================================
--- schema/trunk/chado/bin/GMODCallHome.pl 2013-02-01 20:07:28 UTC (rev 25280)
+++ schema/trunk/chado/bin/GMODCallHome.pl 2013-02-01 21:04:39 UTC (rev 25281)
@@ -18,7 +18,7 @@
exit 0 if (-f "$Bin/gitc_lock");
#check if user specifically doesn't want to call home
-#exit 0 if ($userdata{'NoCallHome'});
+exit 0 if ($userdata{'NoCallHome'});
my $ipaddress = $instance->publicIpv4;
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|
|
From: <sco...@us...> - 2013-02-01 20:07:39
|
Revision: 25280
http://gmod.svn.sourceforge.net/gmod/?rev=25280&view=rev
Author: scottcain
Date: 2013-02-01 20:07:28 +0000 (Fri, 01 Feb 2013)
Log Message:
-----------
Script to "call home" on a GMOD in the Cloud instance; works on Ubuntu 10.04. It's an open question as to whether it will work on 12.04.
Added Paths:
-----------
schema/trunk/chado/bin/GMODCallHome.pl
Added: schema/trunk/chado/bin/GMODCallHome.pl
===================================================================
--- schema/trunk/chado/bin/GMODCallHome.pl (rev 0)
+++ schema/trunk/chado/bin/GMODCallHome.pl 2013-02-01 20:07:28 UTC (rev 25280)
@@ -0,0 +1,47 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use VM::EC2;
+use HTTP::Request::Common;
+use LWP::UserAgent;
+use FindBin '$Bin';
+use constant REGISTRATION_SERVER
+ => 'http://modencode.oicr.on.ca/cgi-bin/gbrowse_registration';
+
+
+my $instance = VM::EC2->instance_metadata(); # should be a metadata object
+
+my $userdata = $instance->userData;
+my %userdata = map {split /\s*\:\s*/, $_ } split "\n", $userdata;
+
+#check to see if this instance all ready called
+exit 0 if (-f "$Bin/gitc_lock");
+
+#check if user specifically doesn't want to call home
+#exit 0 if ($userdata{'NoCallHome'});
+
+my $ipaddress = $instance->publicIpv4;
+
+my @callhome = ( user => "GMOD in the Cloud:".$instance->imageId.'|'.$instance->instanceType,
+ email => $userdata{email} || '',
+ org => $userdata{org} || '',
+ organism => $userdata{organism} || '',
+ site => $ipaddress
+ );
+
+print @callhome;
+
+my $ua = LWP::UserAgent->new;
+my $response = $ua->request(
+ POST(REGISTRATION_SERVER,
+ \@callhome
+ ));
+
+#to prevent the same instance from calling home more than once
+open (LOCK, ">$Bin/gitc_lock");
+print LOCK "Sending the 'call home' email. If you would like to suppress this in the\nfuture, add 'NoCallHome : 1' to the userdata when launching the instance.\n";
+
+close LOCK;
+
+exit 0;
+
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|
|
From: <em...@us...> - 2013-01-15 15:11:03
|
Revision: 25279
http://gmod.svn.sourceforge.net/gmod/?rev=25279&view=rev
Author: emmert
Date: 2013-01-15 15:10:50 +0000 (Tue, 15 Jan 2013)
Log Message:
-----------
Extensions to interaction, expression, and organism modules; extension to library module to link to these. All changes are back-compatible.
Modified Paths:
--------------
schema/trunk/chado/modules/expression/expression.sql
schema/trunk/chado/modules/interaction/interaction.sql
schema/trunk/chado/modules/library/library.sql
schema/trunk/chado/modules/organism/organism.sql
Modified: schema/trunk/chado/modules/expression/expression.sql
===================================================================
--- schema/trunk/chado/modules/expression/expression.sql 2012-12-13 19:59:18 UTC (rev 25278)
+++ schema/trunk/chado/modules/expression/expression.sql 2013-01-15 15:10:50 UTC (rev 25279)
@@ -21,11 +21,12 @@
uniquename text not null,
md5checksum character(32),
description text,
- constraint expression_c1 unique(uniquename)
+ constraint expression_c1 unique (uniquename)
);
COMMENT ON TABLE expression IS 'The expression table is essentially a bridge table.';
+
-- ================================================
-- TABLE: expression_cvterm
-- ================================================
@@ -40,12 +41,13 @@
rank int not null default 0,
cvterm_type_id int not null,
foreign key (cvterm_type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
- constraint expression_cvterm_c1 unique(expression_id,cvterm_id,cvterm_type_id)
+ constraint expression_cvterm_c1 unique (expression_id,cvterm_id,rank,cvterm_type_id)
);
create index expression_cvterm_idx1 on expression_cvterm (expression_id);
create index expression_cvterm_idx2 on expression_cvterm (cvterm_id);
create index expression_cvterm_idx3 on expression_cvterm (cvterm_type_id);
+
--================================================
-- TABLE: expression_cvtermprop
-- ================================================
@@ -112,7 +114,7 @@
foreign key (expression_id) references expression (expression_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 expression_pub_c1 unique(expression_id,pub_id)
+ constraint expression_pub_c1 unique (expression_id,pub_id)
);
create index expression_pub_idx1 on expression_pub (expression_id);
create index expression_pub_idx2 on expression_pub (pub_id);
@@ -131,7 +133,7 @@
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 feature_expression_c1 unique(expression_id,feature_id,pub_id)
+ constraint feature_expression_c1 unique (expression_id,feature_id,pub_id)
);
create index feature_expression_idx1 on feature_expression (expression_id);
create index feature_expression_idx2 on feature_expression (feature_id);
Modified: schema/trunk/chado/modules/interaction/interaction.sql
===================================================================
--- schema/trunk/chado/modules/interaction/interaction.sql 2012-12-13 19:59:18 UTC (rev 25278)
+++ schema/trunk/chado/modules/interaction/interaction.sql 2013-01-15 15:10:50 UTC (rev 25279)
@@ -24,6 +24,7 @@
-- ================================================
-- TABLE: interaction
-- ================================================
+
drop table interaction cascade;
create table interaction (
interaction_id serial NOT NULL,
@@ -34,13 +35,11 @@
on delete cascade INITIALLY DEFERRED,
description text,
is_obsolete boolean not null default false,
- constraint interaction_c1 unique(uniquename,type_id)
+ constraint interaction_c1 unique (uniquename,type_id)
);
create index interaction_idx1 on interaction (uniquename);
create index interaction_idx2 on interaction (type_id);
-grant all on interaction to public;
-grant all on interaction_interaction_id_seq to public;
-- ================================================
-- TABLE: interactionprop
@@ -61,12 +60,12 @@
create index interactionprop_idx1 on interactionprop (interaction_id);
create index interactionprop_idx2 on interactionprop (type_id);
-grant all on interactionprop to public;
-grant all on interactionprop_interactionprop_id_seq to public;
-- ================================================
-- TABLE: interactionprop_pub
-- ================================================
+
+drop table interactionprop_pub cascade;
create table interactionprop_pub (
interactionprop_pub_id serial not null,
primary key (interactionprop_pub_id),
@@ -80,9 +79,6 @@
create index interactionprop_pub_idx2 on interactionprop_pub (pub_id);
-grant all on interactionprop_pub to public;
-grant all on interactionprop_pub_interactionprop_pub_id_seq to public;
-
-- ================================================
-- TABLE: interaction_pub
-- ================================================
@@ -100,15 +96,12 @@
create index interaction_pub_idx1 on interaction_pub (interaction_id);
create index interaction_pub_idx2 on interaction_pub (pub_id);
-grant all on interaction_pub to public;
-grant all on interaction_pub_interaction_pub_id_seq to public;
-- ================================================
-- TABLE: interaction_expression
-- ================================================
drop table interaction_expression cascade;
-
create table interaction_expression (
interaction_expression_id serial not null,
primary key (interaction_expression_id),
@@ -118,14 +111,12 @@
foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
pub_id int not null,
foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
- unique(expression_id,interaction_id,pub_id)
+ constraint interaction_expression_c1 unique (expression_id,interaction_id,pub_id)
);
create index interaction_expression_idx1 on interaction_expression (expression_id);
create index interaction_expression_idx2 on interaction_expression (interaction_id);
create index interaction_expression_idx3 on interaction_expression (pub_id);
-grant all on interaction_expression to public;
-grant all on interaction_expression_interaction_expression_id_seq to public;
--================================================
-- TABLE: interaction_expressionprop
@@ -141,22 +132,17 @@
foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value text null,
rank int not null default 0,
- unique (interaction_expression_id,type_id,rank)
+ constraint interaction_expressionprop_c1 unique (interaction_expression_id,type_id,rank)
);
-
-
create index interaction_expressionprop_idx1 on interaction_expressionprop (interaction_expression_id);
create index interaction_expressionprop_idx2 on interaction_expressionprop (type_id);
-grant all on interaction_expressionprop to public;
-grant all on interaction_expressionprop_interaction_expressionprop_id_seq to public;
-- ================================================
-- TABLE: interaction_cvterm
-- ================================================
drop table interaction_cvterm cascade;
-
create table interaction_cvterm (
interaction_cvterm_id serial not null,
primary key (interaction_cvterm_id),
@@ -164,20 +150,17 @@
foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
cvterm_id int not null,
foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
- unique(interaction_id,cvterm_id)
+ constraint interaction_cvterm_c1 unique (interaction_id,cvterm_id)
);
create index interaction_cvterm_idx1 on interaction_cvterm (interaction_id);
create index interaction_cvterm_idx2 on interaction_cvterm (cvterm_id);
-create index interaction_cvterm_idx3 on interaction_cvterm (pub_id);
-grant all on interaction_cvterm to public;
-grant all on interaction_cvterm_interaction_cvterm_id_seq to public;
--================================================
-- TABLE: interaction_cvtermprop
-- ================================================
-drop table interaction_cvtermprop;
+drop table interaction_cvtermprop cascade;
create table interaction_cvtermprop (
interaction_cvtermprop_id serial not null,
primary key (interaction_cvtermprop_id),
@@ -187,42 +170,13 @@
foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value text null,
rank int not null default 0,
- unique (interaction_cvterm_id,type_id,rank)
+ constraint interaction_cvtermprop_c1 unique (interaction_cvterm_id,type_id,rank)
);
-
-
create index interaction_cvtermprop_idx1 on interaction_cvtermprop (interaction_cvterm_id);
create index interaction_cvtermprop_idx2 on interaction_cvtermprop (type_id);
-grant all on interaction_cvtermprop to public;
-grant all on interaction_cvtermprop_interaction_cvtermprop_id_seq to public;
-
-- ================================================
--- TABLE: library_interaction
--- ================================================
-
-drop table library_interaction cascade;
-
-create table library_interaction (
- library_interaction_id serial not null,
- primary key (library_interaction_id),
- interaction_id int not null,
- foreign key (interaction_id) references interaction (interaction_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,
- unique(interaction_id,library_id,pub_id)
-);
-create index library_interaction_idx1 on library_interaction (interaction_id);
-create index library_interaction_idx2 on library_interaction (library_id);
-create index library_interaction_idx3 on library_interaction (pub_id);
-
-grant all on library_interaction to public;
-grant all on library_interaction_library_interaction_id_seq to public;
-
--- ================================================
-- TABLE: feature_interaction
-- ================================================
@@ -237,18 +191,16 @@
role_id int not null,
foreign key (role_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
rank int not null default 0,
- unique(feature_id,interaction_id, role_id)
+ constraint feature_interaction_c1 unique (feature_id,interaction_id, role_id)
);
create index feature_interaction_idx1 on feature_interaction (feature_id);
create index feature_interaction_idx2 on feature_interaction (interaction_id);
create index feature_interaction_idx3 on feature_interaction (role_id);
-grant all on feature_interaction to public;
-grant all on feature_interaction_feature_interaction_id_seq to public;
-
-- ? do we want to add rank to the unique key ? thinking stochiometry issues
-- and might we have one form modified and not another ? may be too much
+
-- ================================================
-- TABLE: feature_interactionprop
-- ================================================
@@ -268,8 +220,6 @@
create index feature_interactionprop_idx1 on feature_interactionprop (feature_interaction_id);
create index feature_interactionprop_idx2 on feature_interactionprop (type_id);
-grant all on feature_interactionprop to public;
-grant all on feature_interactionprop_feature_interactionprop_id_seq to public;
-- ================================================
-- TABLE: feature_interaction_pub
@@ -288,15 +238,12 @@
create index feature_interaction_pub_idx1 on feature_interaction_pub (feature_interaction_id);
create index feature_interaction_pub_idx2 on feature_interaction_pub (pub_id);
-grant all on feature_interaction_pub to public;
-grant all on feature_interaction_pub_feature_interaction_pub_id_seq to public;
-- ================================================
-- TABLE: interaction_cell_line
-- ================================================
drop table interaction_cell_line cascade;
-
create table interaction_cell_line (
interaction_cell_line_id serial not null,
primary key (interaction_cell_line_id),
@@ -306,11 +253,43 @@
foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
pub_id int not null,
foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
- unique(cell_line_id,interaction_id,pub_id)
+ constraint interaction_cell_line_c1 unique (cell_line_id,interaction_id,pub_id)
);
create index interaction_cell_line_idx1 on interaction_cell_line (cell_line_id);
create index interaction_cell_line_idx2 on interaction_cell_line (interaction_id);
create index interaction_cell_line_idx3 on interaction_cell_line (pub_id);
-grant all on interaction_cell_line to public;
-grant all on interaction_cell_line_interaction_cell_line_id_seq to public;
+
+-- ================================================
+-- TABLE: interaction_group
+-- ================================================
+
+drop table interaction_group cascade;
+create table interaction_group (
+ interaction_group_id serial not null,
+ primary key (interaction_group_id),
+ uniquename text NOT NULL,
+ is_obsolete boolean not null default false,
+ description text,
+ constraint interaction_group_c1 unique (uniquename)
+);
+create index interaction_group_idx1 on interaction_group (uniquename);
+
+
+-- ================================================
+-- TABLE: interaction_group_feature_interaction
+-- ================================================
+
+drop table interaction_group_feature_interaction cascade;
+create table interaction_group_feature_interaction (
+ interaction_group_feature_interaction_id serial not null,
+ primary key (interaction_group_feature_interaction_id),
+ interaction_group_id int not null,
+ foreign key (interaction_group_id) references interaction_group (interaction_group_id) on delete cascade INITIALLY DEFERRED,
+ feature_interaction_id int not null,
+ foreign key (feature_interaction_id) references feature_interaction (feature_interaction_id) on delete cascade INITIALLY DEFERRED,
+ rank int not null default 0,
+ constraint interaction_group_feature_interaction_c1 unique (interaction_group_id,feature_interaction_id,rank)
+);
+create index interaction_group_feature_interaction_idx1 on interaction_group_feature_interaction (interaction_group_id);
+create index interaction_group_feature_interaction_idx2 on interaction_group_feature_interaction (feature_interaction_id);
Modified: schema/trunk/chado/modules/library/library.sql
===================================================================
--- schema/trunk/chado/modules/library/library.sql 2012-12-13 19:59:18 UTC (rev 25278)
+++ schema/trunk/chado/modules/library/library.sql 2013-01-15 15:10:50 UTC (rev 25279)
@@ -7,6 +7,9 @@
-- :import cvterm from cv
-- :import pub from pub
-- :import organism from organism
+-- :import expression from expression
+-- :import interaction from interaction
+-- :import strain from strain
-- =================================================================
-- ================================================
@@ -178,6 +181,133 @@
create index library_dbxref_idx2 on library_dbxref (dbxref_id);
+-- ================================================
+-- TABLE: library_expression
+-- ================================================
+create table library_expression (
+ library_expression_id serial not null,
+ primary key (library_expression_id),
+ library_id int not null,
+ foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ expression_id int not null,
+ foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id),
+ constraint library_expression_c1 unique (library_id,expression_id)
+);
+create index library_expression_idx1 on library_expression (library_id);
+create index library_expression_idx2 on library_expression (expression_id);
+create index library_expression_idx3 on library_expression (pub_id);
+-- ================================================
+-- TABLE: library_expressionprop
+-- ================================================
+
+create table library_expressionprop (
+ library_expressionprop_id serial not null,
+ primary key (library_expressionprop_id),
+ library_expression_id int not null,
+ foreign key (library_expression_id) references library_expression (library_expression_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id),
+ value text null,
+ rank int not null default 0,
+ constraint library_expressionprop_c1 unique (library_expression_id,type_id,rank)
+);
+create index library_expressionprop_idx1 on library_expressionprop (library_expression_id);
+create index library_expressionprop_idx2 on library_expressionprop (type_id);
+
+
+-- ================================================
+-- TABLE: library_featureprop
+-- ================================================
+
+create table library_featureprop (
+ library_featureprop_id serial not null,
+ primary key (library_featureprop_id),
+ library_feature_id int not null,
+ foreign key (library_feature_id) references library_feature (library_feature_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id),
+ value text null,
+ rank int not null default 0,
+ constraint library_featureprop_c1 unique (library_feature_id,type_id,rank)
+);
+create index library_featureprop_idx1 on library_featureprop (library_feature_id);
+create index library_featureprop_idx2 on library_featureprop (type_id);
+
+
+-- ================================================
+-- TABLE: library_interaction
+-- ================================================
+
+create table library_interaction (
+ library_interaction_id serial not null,
+ primary key (library_interaction_id),
+ library_id int not null,
+ foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id),
+ constraint library_interaction_c1 unique (interaction_id,library_id,pub_id)
+);
+create index library_interaction_idx1 on library_interaction (interaction_id);
+create index library_interaction_idx2 on library_interaction (library_id);
+create index library_interaction_idx3 on library_interaction (pub_id);
+
+
+-- ================================================
+-- TABLE: library_relationship
+-- ================================================
+
+create table library_relationship (
+ library_relationship_id serial not null,
+ primary key (library_relationship_id),
+ subject_id int not null,
+ foreign key (subject_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ object_id int not null,
+ foreign key (object_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id),
+ constraint library_relationship_c1 unique (subject_id,object_id,type_id)
+);
+create index library_relationship_idx1 on library_relationship (subject_id);
+create index library_relationship_idx2 on library_relationship (object_id);
+create index library_relationship_idx3 on library_relationship (type_id);
+
+
+-- ================================================
+-- TABLE: library_relationship_pub
+-- ================================================
+
+create table library_relationship_pub (
+ library_relationship_pub_id serial not null,
+ primary key (library_relationship_pub_id),
+ library_relationship_id int not null,
+ foreign key (library_relationship_id) references library_relationship (library_relationship_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id),
+ constraint library_relationship_pub_c1 unique (library_relationship_id,pub_id)
+);
+create index library_relationship_pub_idx1 on library_relationship_pub (library_relationship_id);
+create index library_relationship_pub_idx2 on library_relationship_pub (pub_id);
+
+
+-- ================================================
+-- TABLE: library_strain
+-- ================================================
+
+create table library_strain (
+ library_strain_id serial not null,
+ primary key (library_strain_id),
+ library_id int not null,
+ foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ constraint library_strain_c1 unique (library_id,strain_id)
+);
+create index library_strain_idx1 on library_strain (library_id);
+create index library_strain_idx2 on library_strain (strain_id);
Modified: schema/trunk/chado/modules/organism/organism.sql
===================================================================
--- schema/trunk/chado/modules/organism/organism.sql 2012-12-13 19:59:18 UTC (rev 25278)
+++ schema/trunk/chado/modules/organism/organism.sql 2013-01-15 15:10:50 UTC (rev 25279)
@@ -1,4 +1,4 @@
--- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $
+-- $Id: organism.sql,v 1.19 2007/04/01 18:45:41 briano Exp $
-- ==========================================
-- Chado organism module
--
@@ -13,6 +13,7 @@
-- TABLE: organism
-- ================================================
+drop table organism cascade;
create table organism (
organism_id serial not null,
primary key (organism_id),
@@ -37,10 +38,12 @@
this is appended onto the species name. Follows standard NCBI taxonomy
pattern.';
+
-- ================================================
-- TABLE: organism_dbxref
-- ================================================
+drop table organism_dbxref cascade;
create table organism_dbxref (
organism_dbxref_id serial not null,
primary key (organism_dbxref_id),
@@ -53,10 +56,12 @@
create index organism_dbxref_idx1 on organism_dbxref (organism_id);
create index organism_dbxref_idx2 on organism_dbxref (dbxref_id);
+
-- ================================================
-- TABLE: organismprop
-- ================================================
+drop table organismprop cascade;
create table organismprop (
organismprop_id serial not null,
primary key (organismprop_id),
@@ -73,3 +78,370 @@
COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.';
+
+-- ================================================
+-- TABLE: organismprop_pub
+-- ================================================
+
+drop table organismprop_pub cascade;
+create table organismprop_pub (
+ organismprop_pub_id serial not null,
+ primary key (organismprop_pub_id),
+ organismprop_id int not null,
+ foreign key (organismprop_id) references organismprop (organismprop_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint organismprop_pub_c1 unique (organismprop_id,pub_id)
+);
+create index organismprop_pub_idx1 on organismprop_pub (organismprop_id);
+create index organismprop_pub_idx2 on organismprop_pub (pub_id);
+
+COMMENT ON TABLE organismprop_pub IS 'Attribution for organismprop.';
+
+
+-- ================================================
+-- TABLE: organism_pub
+-- ================================================
+
+drop table organism_pub cascade;
+create table organism_pub (
+ organism_pub_id serial not null,
+ primary key (organism_pub_id),
+ organism_id int not null,
+ foreign key (organism_id) references organism (organism_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 organism_pub_c1 unique (organism_id,pub_id)
+);
+create index organism_pub_idx1 on organism_pub (organism_id);
+create index organism_pub_idx2 on organism_pub (pub_id);
+
+
+-- ================================================
+-- TABLE: organism_cvterm
+-- ================================================
+
+drop table organism_cvterm cascade;
+create table organism_cvterm (
+ organism_cvterm_id serial not null,
+ primary key (organism_cvterm_id),
+ organism_id int not null,
+ foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY
+DEFERRED,
+ cvterm_id int not null,
+ foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ rank int not null default 0,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint organism_cvterm_c1 unique(organism_id,cvterm_id,pub_id)
+);
+create index organism_cvterm_idx1 on organism_cvterm (organism_id);
+create index organism_cvterm_idx2 on organism_cvterm (cvterm_id);
+
+COMMENT ON TABLE organism_cvterm IS 'organism to cvterm associations. Examples: taxonomic name';
+
+COMMENT ON COLUMN organism_cvterm.rank IS 'Property-Value
+ordering. Any organism_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: organism_cvtermprop
+-- ================================================
+
+drop table organism_cvtermprop cascade;
+create table organism_cvtermprop (
+ organism_cvtermprop_id serial not null,
+ primary key (organism_cvtermprop_id),
+ organism_cvterm_id int not null,
+ foreign key (organism_cvterm_id) references organism_cvterm (organism_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 organism_cvtermprop_c1 unique (organism_cvterm_id,type_id,rank)
+);
+create index organism_cvtermprop_idx1 on organism_cvtermprop (organism_cvterm_id);
+create index organism_cvtermprop_idx2 on organism_cvtermprop (type_id);
+
+COMMENT ON TABLE organism_cvtermprop IS 'Extensible properties for
+organism to cvterm associations. Examples: qualifiers';
+
+COMMENT ON COLUMN organism_cvtermprop.type_id IS 'The name of the
+property/slot is a cvterm. The meaning of the property is defined in
+that cvterm. ';
+
+COMMENT ON COLUMN organism_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 organism_cvtermprop.rank IS 'Property-Value
+ordering. Any organism_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: strain
+-- ================================================
+
+drop table strain cascade;
+create table strain (
+ strain_id serial not null,
+ primary key (strain_id),
+ name varchar(255) null,
+ uniquename text not null,
+ organism_id int not null,
+ foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED,
+ dbxref_id int null,
+ foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED,
+ is_obsolete boolean not null default 'false',
+ constraint strain_c1 unique (organism_id, uniquename)
+);
+
+create index strain_idx1 on strain (uniquename);
+create index strain_idx2 on strain (name);
+
+COMMENT ON TABLE strain IS 'A characterized strain of a given organism.';
+
+
+-- ================================================
+-- TABLE: strain_cvterm
+-- ================================================
+
+drop table strain_cvterm cascade;
+create table strain_cvterm (
+ strain_cvterm_id serial not null,
+ primary key (strain_cvterm_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_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,
+ constraint strain_cvterm_c1 unique(strain_id,cvterm_id,pub_id)
+);
+create index strain_cvterm_idx1 on strain_cvterm (strain_id);
+create index strain_cvterm_idx2 on strain_cvterm (cvterm_id);
+
+COMMENT ON TABLE strain_cvterm IS 'strain to cvterm associations. Examples: GOid';
+
+--================================================
+-- TABLE: strain_cvtermprop
+-- ================================================
+
+drop table strain_cvtermprop cascade;
+create table strain_cvtermprop (
+ strain_cvtermprop_id serial not null,
+ primary key (strain_cvtermprop_id),
+ strain_cvterm_id int not null,
+ foreign key (strain_cvterm_id) references strain_cvterm (strain_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 strain_cvtermprop_c1 unique (strain_cvterm_id,type_id,rank)
+);
+create index strain_cvtermprop_idx1 on strain_cvtermprop (strain_cvterm_id);
+create index strain_cvtermprop_idx2 on strain_cvtermprop (type_id);
+
+COMMENT ON TABLE strain_cvtermprop IS 'Extensible properties for
+strain to cvterm associations. Examples: qualifiers';
+
+COMMENT ON COLUMN strain_cvtermprop.type_id IS 'The name of the
+property/slot is a cvterm. The meaning of the property is defined in
+that cvterm. ';
+
+COMMENT ON COLUMN strain_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 strain_cvtermprop.rank IS 'Property-Value
+ordering. Any strain_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: strain_relationship
+-- ================================================
+
+drop table strain_relationship cascade;
+create table strain_relationship (
+ strain_relationship_id serial not null,
+ primary key (strain_relationship_id),
+ subject_id int not null,
+ foreign key (subject_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ object_id int not null,
+ foreign key (object_id) references strain (strain_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 strain_relationship_c1 unique (subject_id, object_id, type_id, rank)
+);
+create index strain_relationship_idx1 on strain_relationship (subject_id);
+create index strain_relationship_idx2 on strain_relationship (object_id);
+
+COMMENT ON TABLE strain_relationship IS 'Relationships between strains, eg, progenitor.';
+
+
+-- ================================================
+-- TABLE: strainprop
+-- ================================================
+
+drop table strainprop cascade;
+create table strainprop (
+ strainprop_id serial not null,
+ primary key (strainprop_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_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 strainprop_c1 unique (strain_id, type_id, rank)
+);
+create index strainprop_idx1 on strainprop (strain_id);
+create index strainprop_idx2 on strainprop (type_id);
+
+COMMENT ON TABLE strainprop IS 'Attributes of a given strain';
+
+
+-- ================================================
+-- TABLE: strainprop_pub
+-- ================================================
+
+drop table strainprop_pub cascade;
+create table strainprop_pub (
+ strainprop_pub_id serial not null,
+ primary key (strainprop_pub_id),
+ strainprop_id int not null,
+ foreign key (strainprop_id) references strainprop (strainprop_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 strainprop_pub_c1 unique (strainprop_id,pub_id)
+);
+create index strainprop_pub_idx1 on strainprop_pub (strainprop_id);
+create index strainprop_pub_idx2 on strainprop_pub (pub_id);
+
+COMMENT ON TABLE strainprop_pub IS 'Provenance. Any strainprop assignment can optionally be supported by a publication.';
+
+
+-- ================================================
+-- TABLE: strain_dbxref
+-- ================================================
+
+drop table strain_dbxref cascade;
+create table strain_dbxref (
+ strain_dbxref_id serial not null,
+ primary key (strain_dbxref_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_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 strain_dbxref_c1 unique (strain_id,dbxref_id)
+);
+create index strain_dbxref_idx1 on strain_dbxref (strain_id);
+create index strain_dbxref_idx2 on strain_dbxref (dbxref_id);
+
+
+-- ================================================
+-- TABLE: strain_synonym
+-- ================================================
+
+drop table strain_synonym cascade;
+create table strain_synonym (
+ strain_synonym_id serial not null,
+ primary key (strain_synonym_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_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 strain_synonym_c1 unique (synonym_id,strain_id,pub_id)
+);
+create index strain_synonym_idx1 on strain_synonym (synonym_id);
+create index strain_synonym_idx2 on strain_synonym (strain_id);
+create index strain_synonym_idx3 on strain_synonym (pub_id);
+
+COMMENT ON TABLE strain_synonym IS 'Linking table between strain and synonym.';
+
+
+-- ================================================
+-- TABLE: strain_feature
+-- ================================================
+
+drop table strain_feature cascade;
+create table strain_feature (
+ strain_feature_id serial not null,
+ primary key (strain_feature_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_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 strain_feature_c1 unique (strain_id,feature_id,pub_id)
+);
+create index strain_feature_idx1 on strain_feature (strain_id);
+create index strain_feature_idx2 on strain_feature (feature_id);
+
+COMMENT ON TABLE strain_feature IS 'strain_feature links a strain to features associated with the strain. Type may
+be, eg, "homozygous" or "heterozygous".';
+
+
+-- ================================================
+-- TABLE: strain_featureprop
+-- ================================================
+
+drop table strain_featureprop cascade;
+create table strain_featureprop (
+ strain_featureprop_id serial not null,
+ primary key (strain_featureprop_id),
+ strain_feature_id int not null,
+ foreign key (strain_feature_id) references strain_feature (strain_feature_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 strain_featureprop_c1 unique (strain_feature_id,type_id,rank)
+);
+create index strain_featureprop_idx1 on strain_featureprop (strain_feature_id);
+create index strain_featureprop_idx2 on strain_featureprop (type_id);
+
+COMMENT ON TABLE strain_featureprop IS 'Attributes of a strain_feature relationship. Eg, a comment';
+
+
+-- ================================================
+-- TABLE: strain_phenotype
+-- ================================================
+
+drop table strain_phenotype cascade;
+create table strain_phenotype (
+ strain_phenotype_id SERIAL NOT NULL,
+ primary key (strain_phenotype_id),
+ strain_id INT NOT NULL,
+ foreign key (strain_id) references strain (strain_id) on delete cascade,
+ phenotype_id INT NOT NULL,
+ foreign key (phenotype_id) references phenotype (phenotype_id) on delete cascade,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint strain_phenotype_c1 unique (strain_id,phenotype_id,pub_id)
+);
+create index strain_phenotype_idx1 ON strain_phenotype (strain_id);
+create index strain_phenotype_idx2 ON strain_phenotype (phenotype_id);
+
+COMMENT on table strain_phenotype IS 'Links phenotype(s) associated with a given strain. Types may be, eg, "selected" or "unassigned".';
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sco...@us...> - 2012-12-13 19:59:26
|
Revision: 25278
http://gmod.svn.sourceforge.net/gmod/?rev=25278&view=rev
Author: scottcain
Date: 2012-12-13 19:59:18 +0000 (Thu, 13 Dec 2012)
Log Message:
-----------
chado release 1.23
Added Paths:
-----------
schema/tags/chado-1.23/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sco...@us...> - 2012-12-11 17:25:49
|
Revision: 25277
http://gmod.svn.sourceforge.net/gmod/?rev=25277&view=rev
Author: scottcain
Date: 2012-12-11 17:25:38 +0000 (Tue, 11 Dec 2012)
Log Message:
-----------
Modified Makefile.PL so that if using PREFIX it won't stomp on the
GMOD_ROOT envirnment variable (that is, everything goes in PREFIX, except what
goes in GMOD_ROOT).
Modified Paths:
--------------
schema/trunk/chado/Changes
schema/trunk/chado/Makefile.PL
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2012-11-08 09:48:15 UTC (rev 25276)
+++ schema/trunk/chado/Changes 2012-12-11 17:25:38 UTC (rev 25277)
@@ -5,6 +5,9 @@
mishmash that was being used in various scripts.
* Fixed the GFF3 preprocessor so that if an insert into the sorting table fails,
the script will die to avoid losing GFF lines in the resulting file.
+* Modified Makefile.PL so that if using PREFIX it won't stomp on the
+GMOD_ROOT envirnment variable (that is, everything goes in PREFIX, except what
+goes in GMOD_ROOT).
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/Makefile.PL
===================================================================
--- schema/trunk/chado/Makefile.PL 2012-11-08 09:48:15 UTC (rev 25276)
+++ schema/trunk/chado/Makefile.PL 2012-12-11 17:25:38 UTC (rev 25277)
@@ -206,7 +206,7 @@
@ARGV = ();
push @ARGV, "PREFIX=$opts{PREFIX}" if $opts{PREFIX};
push @ARGV, "INSTALL_BASE=$opts{INSTALL_BASE}" if $opts{INSTALL_BASE};
-$O{'GMOD_ROOT'} = $opts{PREFIX} if $opts{PREFIX};
+$O{'GMOD_ROOT'} = $opts{PREFIX} if ($opts{PREFIX} and !$ENV{GMOD_ROOT});
push @ARGV, "INSTALLSITEMAN1DIR=$opts{INSTALLSITEMAN1DIR}" if $opts{INSTALLSITEMAN1DIR};
push @ARGV, "INSTALLSITEMAN3DIR=$opts{INSTALLSITEMAN3DIR}" if $opts{INSTALLSITEMAN3DIR};
push @ARGV, "LIB=$opts{LIB}" if $opts{LIB};
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rb...@us...> - 2012-08-01 14:11:59
|
Revision: 25268
http://gmod.svn.sourceforge.net/gmod/?rev=25268&view=rev
Author: rbuels
Date: 2012-08-01 14:11:46 +0000 (Wed, 01 Aug 2012)
Log Message:
-----------
correct spelling error
Modified Paths:
--------------
schema/trunk/chado/chado-module-metadata.xml
Modified: schema/trunk/chado/chado-module-metadata.xml
===================================================================
--- schema/trunk/chado/chado-module-metadata.xml 2012-07-24 19:07:50 UTC (rev 25267)
+++ schema/trunk/chado/chado-module-metadata.xml 2012-08-01 14:11:46 UTC (rev 25268)
@@ -556,8 +556,8 @@
<status code='beta'>
</status>
<description>
- A collection of bridge codes that have multiple dependancies
- so they don't happily go where is most obvious
+ A collection of bridge codes that have multiple dependencies
+ so they don't happily go where is most obvious.
</description>
<component id='gff-bridge' type='bridge'>
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|
|
From: <nm...@us...> - 2012-07-24 19:15:02
|
Revision: 25267
http://gmod.svn.sourceforge.net/gmod/?rev=25267&view=rev
Author: nm249
Date: 2012-07-24 19:07:50 +0000 (Tue, 24 Jul 2012)
Log Message:
-----------
messed up secondary dbxrefs are causing loading failure
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 2012-06-12 11:36:58 UTC (rev 25266)
+++ schema/trunk/chado/bin/gmod_load_cvterms.pl 2012-07-24 19:07:50 UTC (rev 25267)
@@ -572,6 +572,7 @@
$new_term->add_secondary_dbxref($i);
}
foreach my $r ($novel_terms{$k}->get_dbxrefs() ) { #store definition's dbxrefs in cvterm_dbxref
+ if (!$r->database || !$r->primary_id) { next; } # skip def. dbxrefs without both db_name and accession
my $def_dbxref= $r->database() . ':' . $r->primary_id();
message("adding definition dbxref $def_dbxref to cvterm_dbxref\n");
$new_term->add_secondary_dbxref($def_dbxref, 1);
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|
From: <rb...@us...> - 2012-04-06 18:05:31
|
Revision: 25264
http://gmod.svn.sourceforge.net/gmod/?rev=25264&view=rev
Author: rbuels
Date: 2012-04-06 18:05:19 +0000 (Fri, 06 Apr 2012)
Log Message:
-----------
added doc header to project module
Modified Paths:
--------------
schema/trunk/chado/modules/project/project.sql
Modified: schema/trunk/chado/modules/project/project.sql
===================================================================
--- schema/trunk/chado/modules/project/project.sql 2012-04-06 18:03:43 UTC (rev 25263)
+++ schema/trunk/chado/modules/project/project.sql 2012-04-06 18:05:19 UTC (rev 25264)
@@ -1,3 +1,8 @@
+-- ==========================================
+-- Chado project module. Used primarily by other Chado modules to
+-- group experiments, stocks, and so forth that are associated with
+-- eachother administratively or organizationally.
+--
-- =================================================================
-- Dependencies:
--
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|
|
From: <rb...@us...> - 2012-04-06 18:03:56
|
Revision: 25263
http://gmod.svn.sourceforge.net/gmod/?rev=25263&view=rev
Author: rbuels
Date: 2012-04-06 18:03:43 +0000 (Fri, 06 Apr 2012)
Log Message:
-----------
add more comments in the property module
Modified Paths:
--------------
schema/trunk/chado/modules/project/project.sql
Modified: schema/trunk/chado/modules/project/project.sql
===================================================================
--- schema/trunk/chado/modules/project/project.sql 2012-03-29 16:23:06 UTC (rev 25262)
+++ schema/trunk/chado/modules/project/project.sql 2012-04-06 18:03:43 UTC (rev 25263)
@@ -12,14 +12,17 @@
-- ================================================
create table project (
- project_id serial not null,
+ 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;
+COMMENT ON TABLE project IS
+'A project is some kind of planned endeavor. Used primarily by other
+Chado modules to group experiments, stocks, and so forth that are
+associated with eachother administratively or organizationally.';
-- ================================================
-- TABLE: projectprop
@@ -36,6 +39,8 @@
rank integer not null default 0,
CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank)
);
+COMMENT ON TABLE project IS
+'Standard Chado flexible property table for projects.';
-- ================================================
-- TABLE: project_relationship
@@ -52,10 +57,14 @@
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".';
+COMMENT ON TABLE project_relationship IS
+'Linking table for relating projects to each other. For example, a
+given project could be composed of several smaller subprojects';
+COMMENT ON COLUMN project_relationship.type_id IS
+'The cvterm type of the relationship being stated, such as "part of".';
+
create table project_pub (
project_pub_id serial not null,
primary key (project_pub_id),
@@ -68,7 +77,7 @@
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)';
+COMMENT ON TABLE project_pub IS 'Linking table for associating projects and publications.';
create table project_contact (
@@ -83,4 +92,4 @@
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)';
+COMMENT ON TABLE project_contact IS 'Linking table for associating projects and contacts.';
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|
|
From: <sco...@us...> - 2012-03-29 16:23:25
|
Revision: 25262
http://gmod.svn.sourceforge.net/gmod/?rev=25262&view=rev
Author: scottcain
Date: 2012-03-29 16:23:06 +0000 (Thu, 29 Mar 2012)
Log Message:
-----------
commiting Dave's/FlyBase's interaction module
Added Paths:
-----------
schema/trunk/chado/modules/interaction/
schema/trunk/chado/modules/interaction/interaction.sql
Added: schema/trunk/chado/modules/interaction/interaction.sql
===================================================================
--- schema/trunk/chado/modules/interaction/interaction.sql (rev 0)
+++ schema/trunk/chado/modules/interaction/interaction.sql 2012-03-29 16:23:06 UTC (rev 25262)
@@ -0,0 +1,316 @@
+
+
+-- ==========================================
+-- Chado interaction module
+--
+-- ==========================================
+-- NOTES:
+--
+-- Designed to represent various types of interactions
+-- initially to be deployed for physical interactions (protein-protein)
+-- between n number of chado features
+--
+-- prop and pub tables follow usual chado conventions
+--
+-- table:interaction serves as a coalescing table for all aspects of the interaction
+-- a uniquename and link to a cvterm for the type of interaction are stored here
+--
+-- table:feature_interaction links features to the interaction
+-- a cvterm_id for the role that the feature is playing in the interaction
+-- must be specified (eg. prey, bait, evidence_for)
+-- rank may be used to order interacting features in an interaction
+--
+
+-- ================================================
+-- TABLE: interaction
+-- ================================================
+drop table interaction cascade;
+create table interaction (
+ interaction_id serial NOT NULL,
+ primary key (interaction_id),
+ uniquename text NOT NULL,
+ type_id int NOT NULL,
+ foreign key (type_id) references cvterm (cvterm_id)
+ on delete cascade INITIALLY DEFERRED,
+ description text,
+ is_obsolete boolean not null default false,
+ constraint interaction_c1 unique(uniquename,type_id)
+);
+create index interaction_idx1 on interaction (uniquename);
+create index interaction_idx2 on interaction (type_id);
+
+grant all on interaction to public;
+grant all on interaction_interaction_id_seq to public;
+
+-- ================================================
+-- TABLE: interactionprop
+-- ================================================
+
+drop table interactionprop cascade;
+create table interactionprop (
+ interactionprop_id serial not null,
+ primary key (interactionprop_id),
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_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 interactionprop_c1 unique (interaction_id,type_id,rank)
+);
+create index interactionprop_idx1 on interactionprop (interaction_id);
+create index interactionprop_idx2 on interactionprop (type_id);
+
+grant all on interactionprop to public;
+grant all on interactionprop_interactionprop_id_seq to public;
+
+-- ================================================
+-- TABLE: interactionprop_pub
+-- ================================================
+create table interactionprop_pub (
+ interactionprop_pub_id serial not null,
+ primary key (interactionprop_pub_id),
+ interactionprop_id int not null,
+ foreign key (interactionprop_id) references interactionprop (interactionprop_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 interactionprop_pub_c1 unique (interactionprop_id,pub_id)
+);
+create index interactionprop_pub_idx1 on interactionprop_pub (interactionprop_id);
+create index interactionprop_pub_idx2 on interactionprop_pub (pub_id);
+
+
+grant all on interactionprop_pub to public;
+grant all on interactionprop_pub_interactionprop_pub_id_seq to public;
+
+-- ================================================
+-- TABLE: interaction_pub
+-- ================================================
+
+drop table interaction_pub cascade;
+create table interaction_pub (
+ interaction_pub_id serial not null,
+ primary key (interaction_pub_id),
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_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 interaction_pub_c1 unique(interaction_id,pub_id)
+);
+create index interaction_pub_idx1 on interaction_pub (interaction_id);
+create index interaction_pub_idx2 on interaction_pub (pub_id);
+
+grant all on interaction_pub to public;
+grant all on interaction_pub_interaction_pub_id_seq to public;
+
+-- ================================================
+-- TABLE: interaction_expression
+-- ================================================
+
+drop table interaction_expression cascade;
+
+create table interaction_expression (
+ interaction_expression_id serial not null,
+ primary key (interaction_expression_id),
+ expression_id int not null,
+ foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED,
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ unique(expression_id,interaction_id,pub_id)
+);
+create index interaction_expression_idx1 on interaction_expression (expression_id);
+create index interaction_expression_idx2 on interaction_expression (interaction_id);
+create index interaction_expression_idx3 on interaction_expression (pub_id);
+
+grant all on interaction_expression to public;
+grant all on interaction_expression_interaction_expression_id_seq to public;
+
+--================================================
+-- TABLE: interaction_expressionprop
+-- ================================================
+
+drop table interaction_expressionprop;
+create table interaction_expressionprop (
+ interaction_expressionprop_id serial not null,
+ primary key (interaction_expressionprop_id),
+ interaction_expression_id int not null,
+ foreign key (interaction_expression_id) references interaction_expression (interaction_expression_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,
+ unique (interaction_expression_id,type_id,rank)
+);
+
+
+create index interaction_expressionprop_idx1 on interaction_expressionprop (interaction_expression_id);
+create index interaction_expressionprop_idx2 on interaction_expressionprop (type_id);
+
+grant all on interaction_expressionprop to public;
+grant all on interaction_expressionprop_interaction_expressionprop_id_seq to public;
+
+-- ================================================
+-- TABLE: interaction_cvterm
+-- ================================================
+
+drop table interaction_cvterm cascade;
+
+create table interaction_cvterm (
+ interaction_cvterm_id serial not null,
+ primary key (interaction_cvterm_id),
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ cvterm_id int not null,
+ foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ unique(interaction_id,cvterm_id)
+);
+create index interaction_cvterm_idx1 on interaction_cvterm (interaction_id);
+create index interaction_cvterm_idx2 on interaction_cvterm (cvterm_id);
+create index interaction_cvterm_idx3 on interaction_cvterm (pub_id);
+
+grant all on interaction_cvterm to public;
+grant all on interaction_cvterm_interaction_cvterm_id_seq to public;
+
+--================================================
+-- TABLE: interaction_cvtermprop
+-- ================================================
+
+drop table interaction_cvtermprop;
+create table interaction_cvtermprop (
+ interaction_cvtermprop_id serial not null,
+ primary key (interaction_cvtermprop_id),
+ interaction_cvterm_id int not null,
+ foreign key (interaction_cvterm_id) references interaction_cvterm (interaction_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,
+ unique (interaction_cvterm_id,type_id,rank)
+);
+
+
+create index interaction_cvtermprop_idx1 on interaction_cvtermprop (interaction_cvterm_id);
+create index interaction_cvtermprop_idx2 on interaction_cvtermprop (type_id);
+
+grant all on interaction_cvtermprop to public;
+grant all on interaction_cvtermprop_interaction_cvtermprop_id_seq to public;
+
+
+-- ================================================
+-- TABLE: library_interaction
+-- ================================================
+
+drop table library_interaction cascade;
+
+create table library_interaction (
+ library_interaction_id serial not null,
+ primary key (library_interaction_id),
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_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,
+ unique(interaction_id,library_id,pub_id)
+);
+create index library_interaction_idx1 on library_interaction (interaction_id);
+create index library_interaction_idx2 on library_interaction (library_id);
+create index library_interaction_idx3 on library_interaction (pub_id);
+
+grant all on library_interaction to public;
+grant all on library_interaction_library_interaction_id_seq to public;
+
+-- ================================================
+-- TABLE: feature_interaction
+-- ================================================
+
+drop table feature_interaction cascade;
+create table feature_interaction (
+ feature_interaction_id serial not null,
+ primary key (feature_interaction_id),
+ feature_id int not null,
+ foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED,
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ role_id int not null,
+ foreign key (role_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ rank int not null default 0,
+ unique(feature_id,interaction_id, role_id)
+);
+create index feature_interaction_idx1 on feature_interaction (feature_id);
+create index feature_interaction_idx2 on feature_interaction (interaction_id);
+create index feature_interaction_idx3 on feature_interaction (role_id);
+
+grant all on feature_interaction to public;
+grant all on feature_interaction_feature_interaction_id_seq to public;
+
+-- ? do we want to add rank to the unique key ? thinking stochiometry issues
+-- and might we have one form modified and not another ? may be too much
+
+-- ================================================
+-- TABLE: feature_interactionprop
+-- ================================================
+
+drop table feature_interactionprop cascade;
+create table feature_interactionprop (
+ feature_interactionprop_id serial not null,
+ primary key (feature_interactionprop_id),
+ feature_interaction_id int not null,
+ foreign key (feature_interaction_id) references feature_interaction (feature_interaction_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 feature_interactionprop_c1 unique (feature_interaction_id,type_id,rank)
+);
+create index feature_interactionprop_idx1 on feature_interactionprop (feature_interaction_id);
+create index feature_interactionprop_idx2 on feature_interactionprop (type_id);
+
+grant all on feature_interactionprop to public;
+grant all on feature_interactionprop_feature_interactionprop_id_seq to public;
+
+-- ================================================
+-- TABLE: feature_interaction_pub
+-- ================================================
+
+drop table feature_interaction_pub cascade;
+create table feature_interaction_pub (
+ feature_interaction_pub_id serial not null,
+ primary key (feature_interaction_pub_id),
+ feature_interaction_id int not null,
+ foreign key (feature_interaction_id) references feature_interaction (feature_interaction_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 feature_interaction_pub_c1 unique(feature_interaction_id,pub_id)
+);
+create index feature_interaction_pub_idx1 on feature_interaction_pub (feature_interaction_id);
+create index feature_interaction_pub_idx2 on feature_interaction_pub (pub_id);
+
+grant all on feature_interaction_pub to public;
+grant all on feature_interaction_pub_feature_interaction_pub_id_seq to public;
+
+-- ================================================
+-- TABLE: interaction_cell_line
+-- ================================================
+
+drop table interaction_cell_line cascade;
+
+create table interaction_cell_line (
+ interaction_cell_line_id serial not null,
+ primary key (interaction_cell_line_id),
+ cell_line_id int not null,
+ foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED,
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ unique(cell_line_id,interaction_id,pub_id)
+);
+create index interaction_cell_line_idx1 on interaction_cell_line (cell_line_id);
+create index interaction_cell_line_idx2 on interaction_cell_line (interaction_id);
+create index interaction_cell_line_idx3 on interaction_cell_line (pub_id);
+
+grant all on interaction_cell_line to public;
+grant all on interaction_cell_line_interaction_cell_line_id_seq to public;
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|
|
From: <sco...@us...> - 2012-03-14 02:34:12
|
Revision: 25261
http://gmod.svn.sourceforge.net/gmod/?rev=25261&view=rev
Author: scottcain
Date: 2012-03-14 02:33:59 +0000 (Wed, 14 Mar 2012)
Log Message:
-----------
quoting the password so special characters will be protected. Thanks to Hans Kraus for pointing it out.
Modified Paths:
--------------
schema/trunk/chado/lib/Bio/Chado/Builder.pm
Modified: schema/trunk/chado/lib/Bio/Chado/Builder.pm
===================================================================
--- schema/trunk/chado/lib/Bio/Chado/Builder.pm 2012-03-13 18:41:31 UTC (rev 25260)
+++ schema/trunk/chado/lib/Bio/Chado/Builder.pm 2012-03-14 02:33:59 UTC (rev 25261)
@@ -352,7 +352,7 @@
# loading chadoxml
my $stag_string = "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'";
$stag_string .= " --user $db_user " if $db_user;
- $stag_string .= " --password $db_pass " if $db_pass;
+ $stag_string .= " --password '$db_pass' " if $db_pass;
$sys_call = join( ' ',
$stag_string,
catfile( $conf->{'path'}{'data'}, $file->{'local'}.'xml')
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|
|
From: <sco...@us...> - 2012-03-13 18:41:55
|
Revision: 25260
http://gmod.svn.sourceforge.net/gmod/?rev=25260&view=rev
Author: scottcain
Date: 2012-03-13 18:41:31 +0000 (Tue, 13 Mar 2012)
Log Message:
-----------
updating changes
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2012-03-13 18:26:05 UTC (rev 25259)
+++ schema/trunk/chado/Changes 2012-03-13 18:41:31 UTC (rev 25260)
@@ -3,6 +3,8 @@
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.
+* Fixed the GFF3 preprocessor so that if an insert into the sorting table fails,
+the script will die to avoid losing GFF lines in the resulting file.
Version 1.22 Thu Nov 17 12:48:10 EST 2011
* Created a script to automatically create the schemas dirs for a release and
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|
|
From: <sco...@us...> - 2012-03-13 18:26:24
|
Revision: 25259
http://gmod.svn.sourceforge.net/gmod/?rev=25259&view=rev
Author: scottcain
Date: 2012-03-13 18:26:05 +0000 (Tue, 13 Mar 2012)
Log Message:
-----------
making the GFF sorter die if it fails to insert a line (so it won't be lost from the resulting sorted GFF).
Modified Paths:
--------------
schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm
Modified: schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm
===================================================================
--- schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm 2012-03-09 20:29:01 UTC (rev 25258)
+++ schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm 2012-03-13 18:26:05 UTC (rev 25259)
@@ -4688,7 +4688,7 @@
refseq varchar(4000),
id varchar(4000),
parent varchar(4000),
- gffline varchar(4000),
+ gffline varchar(8000),
row_id serial not null,
primary key(row_id)
) ");
@@ -4720,7 +4720,8 @@
my $self = shift;
my ($refseq, $id, $parent, $line) = @_;
$self->{'queries'}{'insert_gff_sort_tmp'}->execute(
- $refseq, $id, $parent, $line);
+ $refseq, $id, $parent, $line)
+ or die "Inserting into the sort table failed:$!,\nProbably due to this line: $line\n";
return;
}
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|
|
From: <nm...@us...> - 2012-03-09 20:29:13
|
Revision: 25258
http://gmod.svn.sourceforge.net/gmod/?rev=25258&view=rev
Author: nm249
Date: 2012-03-09 20:29:01 +0000 (Fri, 09 Mar 2012)
Log Message:
-----------
wrapped code in a transaction
Modified Paths:
--------------
schema/trunk/chado/bin/gmod_make_cvtermpath.pl
Modified: schema/trunk/chado/bin/gmod_make_cvtermpath.pl
===================================================================
--- schema/trunk/chado/bin/gmod_make_cvtermpath.pl 2012-03-09 18:51:04 UTC (rev 25257)
+++ schema/trunk/chado/bin/gmod_make_cvtermpath.pl 2012-03-09 20:29:01 UTC (rev 25258)
@@ -99,6 +99,7 @@
use Bio::GMOD::Config;
use Bio::GMOD::DB::Config;
use Getopt::Std;
+use Try::Tiny;
our ($opt_H, $opt_D, $opt_v, $opt_t, $opt_g, $opt_p, $opt_d, $opt_u, $opt_c, $opt_o);
@@ -146,7 +147,7 @@
$dsn .= ";host=$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 $db=$schema->storage->dbh();
@@ -219,9 +220,9 @@
%sot = ();
# this is a hash for storing the already-processed leaves for a given type term.
-our %seen ;
+our %seen ;
-
+
while(keys %leaf){
foreach my $l (keys %leaf){
foreach my $type (keys %type){
@@ -256,107 +257,106 @@
sub recurse {
my($subjects,$type,$dist) = @_;
-
+
# start with the last subject
my $subject = $subjects->[-1];
#get the parents for the subject with this type (defaults to IS_A)
my @objects = objects($subject,$type);
-
+
#if there are no parents for this path, exit the loop (and the next leaf will be sent here again)
if(!@objects){
$leaf{$subject}++ ;
return;
}
my $path;
-
+
# foreach parent construct a path with each child
foreach my $object (@objects){
- my $tdist = $dist;
- # loop through the child terms
- foreach my $s (@$subjects){
- #next if the path was seen (subject-object-type-distance)
- next if $sot{$s}{$object}{$type}{$tdist};
- if (exists($sot{$s}{$object}) && exists($sot{$object}{$s})) {
- die " YOU HAVE A CYCLE IN YOUR ONTOLOGY for $s, $object ($type, $tdist) C8-( \n" ;
- }
- $sot{$s}{$object}{$type}{$tdist}++;
-
- print $tdist,"\t"x$dist,"\t",$s,"\t" , $object,"\t" ,$type||'transitive',"\n";
-
- # if type is defined , create a path using it (see the first looping through %leaf keys)
- if($type){
-
- $path = $schema->resultset("Cv::Cvtermpath")->find_or_create(
- {
- subject_id => $s,
- object_id => $object,
- type_id => $type,
- cv_id => $cv_id,
- pathdistance => $tdist
- }, { key => 'cvtermpath_c1' } , );
- message( "Inserting ($s,$object,$type,$cv_id , $tdist) into cvtermpath...path_id = " . $path->cvtermpath_id(). "\n" );
- my $ttdist = -1 * $tdist;
+ my $coderef = sub {
+ my $tdist = $dist;
+ # loop through the child terms
+ foreach my $s (@$subjects){
+ #next if the path was seen (subject-object-type-distance)
+ next if $sot{$s}{$object}{$type}{$tdist};
+ if (exists($sot{$s}{$object}) && exists($sot{$object}{$s})) {
+ die " YOU HAVE A CYCLE IN YOUR ONTOLOGY for $s, $object ($type, $tdist) C8-( \n" ;
+ }
+ $sot{$s}{$object}{$type}{$tdist}++;
+ print $tdist,"\t"x$dist,"\t",$s,"\t" , $object,"\t" ,$type||'transitive',"\n";
- $path = $schema->resultset("Cv::Cvtermpath")->find_or_create(
- {
- subject_id => $object,
- object_id => $subject,
- type_id => $type,
- cv_id => $cv_id,
- pathdistance => $ttdist
- }, { key => 'cvtermpath_c1' } , );
- message( "Inserting ($object,$subject,$type,$cv_id , $ttdist) into cvtermpath...path_id = " . $path->cvtermpath_id() . "\n" );
- } else { # if type exists (see second looping through %leaf keys) create a path using the is_a type
- message("No type defined! Using default IS_A relationship\n");
- my $is_a = $schema->resultset("Cv::Cvterm")->search({ name => 'is_a' })->first();
+ # if type is defined , create a path using it (see the first looping through %leaf keys)
+ if($type){
+ $path = $schema->resultset("Cv::Cvtermpath")->find_or_create(
+ {
+ subject_id => $s,
+ object_id => $object,
+ type_id => $type,
+ cv_id => $cv_id,
+ pathdistance => $tdist
+ }, { key => 'cvtermpath_c1' } , );
+ message( "Inserting ($s,$object,$type,$cv_id , $tdist) into cvtermpath...path_id = " . $path->cvtermpath_id(). "\n" );
+ my $ttdist = -1 * $tdist;
- $path = $schema->resultset("Cv::Cvtermpath")->find_or_create(
- {
- subject_id => $s,
- object_id => $object,
- type_id => $is_a->cvterm_id(),
- cv_id => $cv_id,
- pathdistance => $tdist
- }, { key => 'cvtermpath_c1' } , );
- message("Inserting ($s,$object, $type, " . $is_a->cv_id() . " , $tdist) into cvtermpath...path_id = " . $path->cvtermpath_id() . "\n" );
+ $path = $schema->resultset("Cv::Cvtermpath")->find_or_create(
+ {
+ subject_id => $object,
+ object_id => $subject,
+ type_id => $type,
+ cv_id => $cv_id,
+ pathdistance => $ttdist
+ }, { key => 'cvtermpath_c1' } , );
+ message( "Inserting ($object,$subject,$type,$cv_id , $ttdist) into cvtermpath...path_id = " . $path->cvtermpath_id() . "\n" );
+ } else { # if type exists (see second looping through %leaf keys) create a path using the is_a type
+ message("No type defined! Using default IS_A relationship\n");
+ my $is_a = $schema->resultset("Cv::Cvterm")->search({ name => 'is_a' })->first();
- $path = $schema->resultset("Cv::Cvtermpath")->find_or_create(
- {
- subject_id => $object,
- object_id => $subject,
- type_id => $is_a->cvterm_id(),
- cv_id => $cv_id,
- pathdistance => -$tdist
- }, { key => 'cvtermpath_c1' } , );
- message( "Inserting ($object,$subject, " . $is_a->cvterm_id() . " ,$cv_id , -$tdist) into cvtermpath... path_id = " . $path->cvtermpath_id() . "\n" );
- }
- $tdist--;
- }
- $tdist = $dist;
- # recurse with arrayref of subjects and the object, increment the pathdistance
- recurse([@$subjects,$object],$type,$dist+1);
-
- $db->commit();
- }
-
-}
+ $path = $schema->resultset("Cv::Cvtermpath")->find_or_create(
+ {
+ subject_id => $s,
+ object_id => $object,
+ type_id => $is_a->cvterm_id(),
+ cv_id => $cv_id,
+ pathdistance => $tdist
+ }, { key => 'cvtermpath_c1' } , );
+ message("Inserting ($s,$object, $type, " . $is_a->cv_id() . " , $tdist) into cvtermpath...path_id = " . $path->cvtermpath_id() . "\n" );
+ $path = $schema->resultset("Cv::Cvtermpath")->find_or_create(
+ {
+ subject_id => $object,
+ object_id => $subject,
+ type_id => $is_a->cvterm_id(),
+ cv_id => $cv_id,
+ pathdistance => -$tdist
+ }, { key => 'cvtermpath_c1' } , );
+ message( "Inserting ($object,$subject, " . $is_a->cvterm_id() . " ,$cv_id , -$tdist) into cvtermpath... path_id = " . $path->cvtermpath_id() . "\n" );
+ }
+ $tdist--;
+ }
+ $tdist = $dist;
+ # recurse with arrayref of subjects and the object, increment the pathdistance
+ recurse([@$subjects,$object],$type,$dist+1);
+ };
+ try {
+ $schema->txn_do($coderef);
+ } catch {
+ die "An error occured. Rolling back! " . $_ . "\n\n";
+ };
+ } #object
+} #recurse
+
#-------------------
sub objects {
my($subject,$type) = @_;
-
my @cvterm_rel;
if($type){
-
+
@cvterm_rel = $schema->resultset("Cv::CvtermRelationship")->search(
{ subject_id => $subject,
type_id => $type ,
}
);
-
} else {
-
@cvterm_rel = $schema->resultset("Cv::CvtermRelationship")->search(
{ subject_id => $subject }
);
@@ -368,7 +368,6 @@
sub subjects {
my($object,$type) = @_;
-
my @cvterm_rel;
if($type){
@@ -379,7 +378,6 @@
);
} else {
-
@cvterm_rel = $schema->resultset("Cv::CvtermRelationship")->search(
{ object_id => $object }
);
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|
|
From: <nm...@us...> - 2012-03-09 18:51:18
|
Revision: 25257
http://gmod.svn.sourceforge.net/gmod/?rev=25257&view=rev
Author: nm249
Date: 2012-03-09 18:51:04 +0000 (Fri, 09 Mar 2012)
Log Message:
-----------
disabling loading of cross-ontologies relationships. Temporary solution for loading PO which has cross references among anatomy and growth stages terms
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 2012-03-06 18:54:12 UTC (rev 25256)
+++ schema/trunk/chado/bin/gmod_load_cvterms.pl 2012-03-09 18:51:04 UTC (rev 25257)
@@ -690,7 +690,7 @@
next RELATIONSHIP;
}
############################################
- push @novel_relationships, $r;
+ push @novel_relationships, $r;
my $predicate_term_name = $file_relationships{$r}->predicate_term()->name();
my $predicate_term;
@@ -729,7 +729,11 @@
}
if (!$opt_t) {
message("Storing relationship $r. type cv_id=" . $predicate_term->cv_id() ."\n" ,1);
- my $new_rel = $schema->resultset('Cv::CvtermRelationship')->create(
+ if ( $subject_term->cv_id != $object_term->cv_id ) {
+ message("Wait! subjcet term has cv namespace " . $subject_term->cv->name . " which is different from the namespace of the object term (" . $object_term->cv->name . "). Cross referencing relationships across namespaces is not supported (yet.. ) SKIPPING this relationship! \n");
+ next RELATIONSHIP;
+ }
+ my $new_rel = $schema->resultset('Cv::CvtermRelationship')->create(
{ subject_id => $subject_term->cvterm_id(),
object_id => $object_term->cvterm_id(),
type_id => $predicate_term->cvterm_id(),
@@ -744,14 +748,14 @@
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);
} catch {
# Transaction failed
die "An error occured! Rolling back! " . $_ . "\n";
- }
+ };
}
sub recursive_children {
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|
|
From: <nm...@us...> - 2012-03-06 18:54:29
|
Revision: 25256
http://gmod.svn.sourceforge.net/gmod/?rev=25256&view=rev
Author: nm249
Date: 2012-03-06 18:54:12 +0000 (Tue, 06 Mar 2012)
Log Message:
-----------
added lookup for organism by ncbi taxonomy id, since species names may change. This loader also assumes species names are unique, as used in NCBI taxonomy.
Modified Paths:
--------------
schema/trunk/chado/bin/load_ncbi_taxonomy.pl
Modified: schema/trunk/chado/bin/load_ncbi_taxonomy.pl
===================================================================
--- schema/trunk/chado/bin/load_ncbi_taxonomy.pl 2012-02-28 21:26:20 UTC (rev 25255)
+++ schema/trunk/chado/bin/load_ncbi_taxonomy.pl 2012-03-06 18:54:12 UTC (rev 25256)
@@ -53,7 +53,7 @@
http://www.ncbi.nlm.nih.gov/sites/entrez?db=Taxonomy
and search by taxid (e.g. txis4070[Subtree] )
-=item -p
+=item -n
phylotree name [optional]
@@ -80,7 +80,7 @@
driver. Override driver name in gmod_config
-=item -s
+=item -p
password. Override password in gmod_config
@@ -129,7 +129,7 @@
=head1 VERISON AND DATE
-Version 2.0, October 2009.
+Version 2.1, March 2012.
=head1 TODO
@@ -147,19 +147,19 @@
use Bio::GMOD::DB::Config;
use Bio::Chado::Schema;
-
+use Try::Tiny;
use Getopt::Std;
-our ($opt_H, $opt_D, $opt_v, $opt_t, $opt_i, $opt_p, $opt_g, $opt_u, $opt_s, $opt_d);
+our ($opt_H, $opt_D, $opt_v, $opt_t, $opt_i, $opt_p, $opt_g, $opt_u, $opt_n, $opt_d);
-getopts('H:D:i:p:g:u:s:d:tv');
+getopts('H:D:i:p:g:u:n:d:tv');
my $dbhost = $opt_H;
my $dbname = $opt_D;
my $infile = $opt_i;
-my $phylotree_name= $opt_p || 'NCBI taxonomy tree';
+my $phylotree_name= $opt_n || 'NCBI taxonomy tree';
my $user = $opt_u;
-my $pass = $opt_s;
+my $pass = $opt_p;
my $driver = $opt_d;
my $port;
@@ -196,7 +196,7 @@
$dsn .= ";host=$dbhost";
$dsn .= ";port=$port" if $port;
-$schema= Bio::Chado::Schema->connect( $dsn, $user, $pass, { AutoCommit=>0 });
+$schema= Bio::Chado::Schema->connect( $dsn, $user, $pass||'');
$dbh=$schema->storage->dbh();
@@ -377,7 +377,7 @@
my %phylonode=();
my $node_count=0;
-eval {
+my $coderef = sub {
my $root_id;
my $organism_id = $maxval{'organism'};
NODE: foreach my $id ( keys %node ) {
@@ -417,10 +417,13 @@
if (!$genus || !$species) { die "NO GENUS OR SPECIES FOUND FOR tax_id $genbank_taxon_accession! Check your input file! \n" ; }
$organism = $schema->resultset('Organism::Organism')->search(
{
- genus => { 'ilike'=> $genus },
species => {'ilike' => $species }
- })->single();
- if (!$organism) { #create a new empty row object
+ })->single; # lookup is by species only . NCBI species should be unique!
+ if (!$organism) { #maybe the organism is already loaded with the ncbi taxonomy id, but the species name has changed?
+ my $organism_dbxref = $dbxref->organism_dbxrefs->single;
+ $organism= $organism_dbxref->organism if $organism_dbxref;
+ }
+ if (!$organism) { #create a new empty row object
$organism = $schema->resultset('Organism::Organism')->new({});
$insert=1;
} else { $update = 1; }
@@ -433,12 +436,12 @@
if ($update) {
$organism->update();
message( "*Updating organism " . $organism->get_column('organism_id') . " (species=" . $organism->species . ")\n", 1);
- }
+ }
if ($insert) {
$organism->insert();
- message("New organism " . $organism->get_column('organism_id') . " (species=" . $organism->species . ")\n", 1);
+ message("New organism " . $organism->get_column('organism_id') . " (species=" . $organism->species . ")\n", 1);
}
- my $organism_id= $organism->get_column('organism_id');
+ my $organism_id= $organism->get_column('organism_id');
###########################################
#store the organism synonyms
@@ -541,13 +544,16 @@
$setright->execute($ctr++, $phylonode_id);
message( "Setting right index= $ctr for phylonode id $phylonode_id\n\n",1);
}
+ if ($opt_t) { die "TEST RUN! rolling back!\n"; }
};
+try {
+ $schema->txn_do($coderef);
+ message( "Commiting!! \n");
+ message("Inserted $node_count phylonodes. \n",1 );
-if ($@ || $opt_t) {
- $dbh->rollback();
+} catch {
+ message( "An error occured! Rolling back! \n $_ \n Resetting database sequences...\n", 1);
- message( "Rolling back! \n $@\n Resetting database sequences...\n", 1);
-
#reset sequences
foreach my $key ( keys %seq ) {
my $value= $seq{$key};
@@ -555,14 +561,8 @@
if ($maxvalue) { $dbh->do("SELECT setval ('$value', $maxvalue, true)") ; }
else { $dbh->do("SELECT setval ('$value', 1, false)"); }
}
-}else {
- message( "Commiting!! \n");
- message("Inserted $node_count phylonodes. \n",1 );
-
- $dbh->commit();
-}
+};
-
sub set_maxval {
my $key=shift;
my $id_column= $key . "_id";
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