lib/CXGN/Onto.pm

   1 package CXGN::Onto;
   2
   3 use Moose;
   4 use Moose::Util::TypeConstraints;
   5 use Data::Dumper;
   6 use JSON::Any;
   7 use Try::Tiny;
   8 use Bio::Chado::Schema;
   9 use SGN::Model::Cvterm;
  10
  11 has 'schema' => (
  12     isa => 'Bio::Chado::Schema',
  13     is => 'rw',
  14     required => 1
  15     );
  16
  17 =head2 get_terms
  18
  19 parameters: namespace
  20
  21 returns: terms in namespace
  22
  23 Side Effects: none
  24
  25 =cut
  26
  27 sub get_terms {
  28       my $self = shift;
  29       my $cv_id = shift;
  30
  31       my $query = "SELECT cvterm_id, (((cvterm.name::text || '|'::text) || db.name::text) || ':'::text) || dbxref.accession::text AS name
  32                   FROM cvterm
  33                   JOIN dbxref USING(dbxref_id)
  34                   JOIN db USING(db_id)
  35                   LEFT JOIN cvterm_relationship is_subject ON cvterm.cvterm_id = is_subject.subject_id
  36                   LEFT JOIN cvterm_relationship is_object ON cvterm.cvterm_id = is_object.object_id
  37                   WHERE cv_id = ? AND is_object.object_id IS NULL AND is_subject.subject_id IS NOT NULL
  38                   GROUP BY 1,2
  39                   ORDER BY 2,1";
  40
  41       my $h = $self->schema->storage->dbh->prepare($query);
  42       $h->execute($cv_id);
  43
  44       my @results;
  45       while (my ($id, $name) = $h->fetchrow_array()) {
  46         push @results, [$id, $name];
  47       }
  48
  49       return @results;
  50 }
  51
  52 sub get_root_nodes {
  53       my $self = shift;
  54       my $cv_type = shift;
  55
  56       my $query = "SELECT cv.cv_id, (((db.name::text || ':'::text) || dbxref.accession::text) || ' '::text) || cvterm.name AS name
  57                     FROM cv
  58                     JOIN cvprop ON(cv.cv_id = cvprop.cv_id AND cvprop.type_id IN (SELECT cvterm_id from cvterm where cvterm.name = ?))
  59                     JOIN cvterm on(cvprop.cv_id = cvterm.cv_id)
  60                     JOIN dbxref USING(dbxref_id)
  61                     JOIN db USING(db_id)
  62                     LEFT JOIN cvterm_relationship ON(cvterm.cvterm_id=cvterm_relationship.subject_id)
  63                     WHERE cvterm_relationship.subject_id IS NULL AND cvterm.is_obsolete= 0 AND cvterm.is_relationshiptype = 0";
  64
  65       my $h = $self->schema->storage->dbh->prepare($query);
  66       $h->execute($cv_type);
  67
  68       my @results;
  69       while (my ($id, $name) = $h->fetchrow_array()) {
  70         push @results, [$id, $name];
  71       }
  72
  73       return @results;
  74 }
  75
  76
  77 sub store_composed_term {
  78     my $self = shift;
  79     my $new_trait_names = shift;
  80
  81     my $schema = $self->schema();
  82     my $dbh = $schema->storage->dbh;
  83
  84     my @new_terms;
  85     foreach my $name (sort keys %$new_trait_names){
  86         my $ids = $new_trait_names->{$name};
  87         my @component_ids = split ',', $ids;
  88
  89         if (scalar(@component_ids)<2){
  90             die "Should not save postcomposed term with less than 2 components\n";
  91         }
  92
  93         my $existing_trait_id = SGN::Model::Cvterm->get_trait_from_exact_components($schema, \@component_ids);
  94         if ($existing_trait_id) {
  95             print STDERR "Skipping: This trait already exists $name with the following component_ids".Dumper(\@component_ids)."\n";
  96             next;
  97         }
  98
  99         my $db = $schema->resultset("General::Db")->find_or_create({ name => 'COMP' });
 100         my $cv= $schema->resultset('Cv::Cv')->find_or_create( { name => 'composed_trait' });
 101
 102         my $accession_query = "SELECT nextval('composed_trait_ids')";
 103         my $h = $dbh->prepare($accession_query);
 104         $h->execute();
 105         my $accession = $h->fetchrow_array();
 106
 107       my $new_term_dbxref =  $schema->resultset("General::Dbxref")->create(
 108       {   db_id     => $db->get_column('db_id'),
 109                       accession => sprintf("%07d",$accession)
 110                   });
 111
 112       my $parent_term= $schema->resultset("Cv::Cvterm")->find(
 113         { cv_id  =>$cv->cv_id(),
 114           name   => 'Composed traits',
 115       });
 116
 117     #print STDERR "Parent cvterm_id = " . $parent_term->cvterm_id();
 118
 119     my $new_term = $schema->resultset('Cv::Cvterm')->find({ name=>$name });
 120     if ($new_term){
 121         print STDERR "Cvterm with name $name already exists... so components must be new\n";
 122     } else {
 123         $new_term= $schema->resultset("Cv::Cvterm")->create({
 124             cv_id  =>$cv->cv_id(),
 125             name   => $name,
 126             dbxref_id  => $new_term_dbxref-> dbxref_id()
 127         });
 128     }
 129
 130
 131     #print STDERR "New term cvterm_id = " . $new_term->cvterm_id();
 132
 133         my $contains_relationship = $schema->resultset("Cv::Cvterm")->find({ name => 'contains' });
 134         my $variable_relationship = $schema->resultset("Cv::Cvterm")->find({ name => 'VARIABLE_OF' });
 135
 136         my $variable_rel = $schema->resultset('Cv::CvtermRelationship')->create({
 137             subject_id => $new_term->cvterm_id(),
 138             object_id  => $parent_term->cvterm_id(),
 139             type_id    => $variable_relationship->cvterm_id()
 140         });
 141
 142         foreach my $component_id (@component_ids) {
 143             my $contains_rel = $schema->resultset('Cv::CvtermRelationship')->create({
 144                 subject_id => $component_id,
 145                 object_id  => $new_term->cvterm_id(),
 146                 type_id    => $contains_relationship->cvterm_id()
 147             });
 148         }
 149
 150         push @new_terms, [$new_term->cvterm_id, $new_term->name().'|COMP:'.sprintf("%07d",$accession)];
 151     }
 152
 153     #Takes long on cassavabase.. instead the materialized view is refreshed automatically in a background ajax process.
 154     #my $refresh1 = "REFRESH MATERIALIZED VIEW traits";
 155     #my $h = $dbh->prepare($refresh1);
 156     #$h->execute();
 157
 158     #my $refresh2 = "REFRESH MATERIALIZED VIEW trait_componentsXtraits";
 159     #$h = $dbh->prepare($refresh2);
 160     #$h->execute();
 161
 162     return \@new_terms;
 163 }
 164
 165
 166 1;