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[Gmod-schema-cmts] SF.net SVN: gmod:[25258] schema/trunk/chado/bin/gmod_make_cvtermpath.pl
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From: <nm...@us...> - 2012-03-09 20:29:13
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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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