Menu
▾
▴
gmod-schema-cmts
|
From: <nm...@us...> - 2012-01-24 19:16:31
|
Revision: 25253
http://gmod.svn.sourceforge.net/gmod/?rev=25253&view=rev
Author: nm249
Date: 2012-01-24 19:16:18 +0000 (Tue, 24 Jan 2012)
Log Message:
-----------
no need for dbh. Autocommit should be on, and use schema transaction
Modified Paths:
--------------
schema/trunk/chado/bin/gmod_load_cvterms.pl
Modified: schema/trunk/chado/bin/gmod_load_cvterms.pl
===================================================================
--- schema/trunk/chado/bin/gmod_load_cvterms.pl 2011-12-01 19:46:55 UTC (rev 25252)
+++ schema/trunk/chado/bin/gmod_load_cvterms.pl 2012-01-24 19:16:18 UTC (rev 25253)
@@ -156,6 +156,7 @@
use Bio::GMOD::DB::Config;
use Bio::Chado::Schema;
+use Try::Tiny;
our ($opt_d, $opt_h, $opt_H, $opt_F, $opt_n, $opt_D, $opt_v, $opt_t,
$opt_u, $opt_o, $opt_p, $opt_r, $opt_g, $opt_s);
@@ -203,12 +204,10 @@
$dsn .= ";host=$dbhost";
$dsn .= ";port=$port";
-my $schema= Bio::Chado::Schema->connect($dsn, $user, $pass||'', { AutoCommit=>0 });
+my $schema= Bio::Chado::Schema->connect($dsn, $user, $pass||'');
-my $dbh=$schema->storage->dbh();
+if (!$schema) { die "No schema is avaiable! \n"; }
-if (!$schema || !$dbh) { die "No schema or dbh is avaiable! \n"; }
-
#######################
my $error = 0; # keep track of input errors (in command line switches).
@@ -251,42 +250,43 @@
push @onts, $ont;
}
message("Default namespace is " . $default_ont->name . " \n" , 1);
+
my $default_cv= $schema->resultset('Cv::Cv')->find_or_create( { name => $default_ont->name } , { key => 'cv_c1' }, );
foreach my $new_ont(@onts) {
- my $new_ont_name=$new_ont->name();
- message("....found namespace '$new_ont_name' \n", 1);
+ my $coderef = sub {
+ my $new_ont_name=$new_ont->name();
+ message("....found namespace '$new_ont_name' \n", 1);
- if ($opt_n && ( $opt_n ne $new_ont_name) ) {
- message ("$opt_n: skipping to next ontology..\n",1);
- next ();
- }
- my $rel_cv;
- #check if relationship ontology is already loaded:
- if ($new_ont_name ne 'relationship') {
- $rel_cv= $schema->resultset("Cv::Cv")->find_or_create( { name => 'relationship' } , { key => 'cv_c1' }, );
- my @rel= $schema->resultset("Cv::Cvterm")->search(
- { cv_id => $rel_cv->get_column('cv_id'),
- is_relationshiptype => 1,
- });
- if (!@rel) {
- warn "Relationship ontology must be loaded first!!\n" ;
- exit(0);
+ if ($opt_n && ( $opt_n ne $new_ont_name) ) {
+ message ("$opt_n: skipping to next ontology..\n",1);
+ next ();
}
- }
- ####add Typedef parsing to obo.pm!###
- ####store a new cv if the ontology namespace does not exist
- my $cv= $schema->resultset('Cv::Cv')->find_or_create( { name => $new_ont_name } , { key => 'cv_c1' }, );
+ my $rel_cv;
+ #check if relationship ontology is already loaded:
+ if ($new_ont_name ne 'relationship') {
+ $rel_cv= $schema->resultset("Cv::Cv")->find_or_create( { name => 'relationship' } , { key => 'cv_c1' }, );
+ my @rel= $schema->resultset("Cv::Cvterm")->search(
+ { cv_id => $rel_cv->get_column('cv_id'),
+ is_relationshiptype => 1,
+ });
+ if (!@rel) {
+ warn "Relationship ontology must be loaded first!!\n" ;
+ exit(0);
+ }
+ }
+ ####add Typedef parsing to obo.pm!###
+ ####store a new cv if the ontology namespace does not exist
+ my $cv= $schema->resultset('Cv::Cv')->find_or_create( { name => $new_ont_name } , { key => 'cv_c1' }, );
- print STDERR "cv_id = ".($cv->get_column('cv_id') )."\n";
- print STDERR "Updating an ontology in the database...\n";
- my $db_ont = $cv;
- my $ontology_name=$db_ont->get_column('name');
- message("Ontology name: ".($db_ont->name())."\n", 1);
- my %file_relationships = (); # relationships currently defined in the file
- my %db_relationships = ();
-
- eval {
+ print STDERR "cv_id = ".($cv->get_column('cv_id') )."\n";
+ print STDERR "Updating an ontology in the database...\n";
+ my $db_ont = $cv;
+ my $ontology_name=$db_ont->get_column('name');
+ message("Ontology name: ".($db_ont->name())."\n", 1);
+ my %file_relationships = (); # relationships currently defined in the file
+ my %db_relationships = ();
+ ######
my $db = $schema->resultset("General::Db")->find_or_create(
{ name => $opt_s }, { key => 'db_c1' }, );
@@ -395,7 +395,7 @@
$db_index{$k}->set_column(name => $name );
$db_index{$k}->set_column( definition => $file_index{$k}->definition() );
$db_index{$k}->set_column(is_obsolete => $file_index{$k}->is_obsolete() );
-
+
#changing the name of obsolete terms to "$name (obsolete $db:$accession)"
#to avoid violating the cvterm unique constaint (name, cv_id, is_obsolete)
if ($db_index{$k}->is_obsolete() ) {
@@ -476,9 +476,9 @@
my %file_secondary_ids = ();
foreach my $i ($file_index{$k}->get_secondary_ids()) {
+ $i = substr($i, 0, 255); #dbxref.accession is varchar(255) maybe it needs to be text?
$file_secondary_ids{uc($i)}=1;
message("adding secondary id $i to the database...\n");
-
$db_index{$k}->add_secondary_dbxref($i);
}
#########
@@ -638,7 +638,7 @@
print STDERR "\n";
#####################################
my $r_count = 0;
- RELATIONSHIP: foreach my $r (keys(%file_relationships)) {
+ RELATIONSHIP: foreach my $r (keys(%file_relationships)) {
$r_count++;
if (!exists($db_relationships{$r})) {
if ($opt_v) { print STDERR "Novel relationship: $r\n"; }
@@ -737,25 +737,23 @@
);
}
}
- }
+ }
message($ontology_name." : ". scalar(@novel_relationships)." novel relationships among ".(scalar(keys(%file_relationships)))." were found and stored.\n", 1);
- };
- if ($@ || ($opt_t)) {
- message( "Either running as trial mode (-t) or AN ERROR OCCURRED: $@\n",1);
- $dbh->rollback();
- exit(0);
- }
- else {
+ if ($opt_t) {
+ die "TEST RUN! rolling back\n";
+ }
+ };
+
+ try {
+ $schema->txn_do($coderef);
message("Committing! \n If you are using cvtermpath you should now run gmod_make_cvtermpath.pl . See the perldoc for more info. \n\n", 1);
- $dbh->commit();
+ } catch {
+ # Transaction failed
+ die "An error occured! Rolling back! " . $_ . "\n";
}
}
-print STDERR "Done.\n";
-
-
-
sub recursive_children {
my $ont = shift;
my $node = shift;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <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 {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
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);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
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);
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
Thanks for helping keep SourceForge clean.
X