lib/CXGN/Population.pm

   1
   2 package CXGN::Population;
   3
   4 use Moose;
   5 use SGN::Model::Cvterm;
   6 use Data::Dumper;
   7 use JSON;
   8
   9 extends 'CXGN::Stock';
  10
  11 has 'population_stock_id' => (isa => 'Maybe[Int]',
  12     is => 'rw',
  13 );
  14
  15 has 'population_name' => (isa => 'Maybe[Str]',
  16     is => 'rw',
  17 );
  18
  19 has 'accession_members' => (isa => 'ArrayRef',
  20     is => 'rw',
  21 );
  22
  23 has 'stock_relationship_id' => (isa => 'Maybe[Int]',
  24     is => 'rw',
  25 );
  26
  27
  28
  29 sub BUILD {
  30     my $self = shift;
  31     my $args = shift;
  32
  33     my $schema = $args->{schema};
  34     my $population_id = $args->{population_stock_id};
  35
  36     $self->stock_id($population_id);
  37
  38     my $accession_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id();
  39     my $population_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'population', 'stock_type')->cvterm_id();
  40     my $member_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'member_of', 'stock_relationship')->cvterm_id();
  41
  42     my $row = $schema->resultset("Stock::Stock")->find( { stock_id => $population_id, type_id => $population_cvterm_id });
  43
  44     if ($row) {
  45         my $name = $row->uniquename();
  46         $self->population_name($name);
  47         $self->population_stock_id($population_id);
  48
  49     }
  50
  51     my $accession_members = $self->get_accession_members();
  52     print STDERR Dumper($accession_members);
  53
  54     if ($accession_members) {
  55         $self->accession_members($accession_members);
  56     }
  57
  58 }
  59
  60
  61 sub get_accession_members {
  62     my $self = shift;
  63     my $schema = $self->schema;
  64     my $population_id = $self->population_stock_id;
  65
  66     my $member_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "member_of", "stock_relationship")->cvterm_id();
  67     my $accession_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "accession", "stock_type")->cvterm_id();
  68
  69     my $q = "SELECT member.stock_id, member.uniquename
  70         FROM stock
  71         JOIN stock_relationship ON (stock_relationship.object_id = stock.stock_id) AND stock_relationship.type_id = ?
  72         JOIN stock AS member ON (stock_relationship.subject_id = member.stock_id) AND member.type_id = ?
  73         WHERE stock.stock_id = ?";
  74
  75      my $h = $schema->storage->dbh()->prepare($q);
  76      $h->execute($member_of_type_id, $accession_type_id, $population_id);
  77      my @accession_members = ();
  78      while (my ($stock_id, $stock_name) = $h->fetchrow_array()){
  79          push @accession_members, [$stock_id, $stock_name]
  80      }
  81
  82      return \@accession_members;
  83 }
  84
  85
  86 sub delete_population {
  87     my $self = shift;
  88     my $dbh = $self->schema()->storage()->dbh();
  89     my $schema = $self->schema();
  90     my $population_id = $self->population_stock_id();
  91
  92     eval {
  93         $dbh->begin_work();
  94
  95         my $population_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "population", "stock_type")->cvterm_id();
  96         my $male_parent_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "male_parent", "stock_relationship")->cvterm_id();
  97
  98         my $male_parent_rs = $schema->resultset("Stock::StockRelationship")->search({subject_id => $population_id, type_id => $male_parent_type_id});
  99         if ($male_parent_rs->count > 0){
 100             print STDERR "Population has associated cross or pedigree. Cannot delete.\n";
 101             die "Population has associated cross or pedigree: Cannot delete.\n";
 102         }
 103
 104         #checking if the stock id has population stock type
 105         my $population_rs = $schema->resultset("Stock::Stock")->find ({stock_id => $population_id, type_id => $population_type_id});
 106         if (!$population_rs) {
 107             print STDERR "This stock id is not a population. Cannot delete.\n";
 108                 die "This stock id is not a population. Cannot delete.\n";
 109         }
 110
 111         my $q = "delete from phenome.stock_owner where stock_id = ?";
 112             my $h = $dbh->prepare($q);
 113             $h->execute($population_id);
 114
 115             my $q2 = "delete from stock where stock.stock_id = ? and stock.type_id = ?";
 116             my $h2 = $dbh->prepare($q2);
 117             $h2->execute($population_id, $population_type_id);
 118     };
 119
 120
 121     if ($@) {
 122             print STDERR "An error occurred while deleting population id ".$population_id."$@\n";
 123             $dbh->rollback();
 124             return $@;
 125     } else {
 126             $dbh->commit();
 127             return 0;
 128     }
 129 }
 130
 131
 132 sub delete_population_member {
 133     my $self = shift;
 134     my $dbh = $self->schema()->storage()->dbh();
 135     my $schema = $self->schema();
 136     my $stock_relationship_id = $self->stock_relationship_id();
 137
 138     eval {
 139         $dbh->begin_work();
 140
 141         my $population_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "population", "stock_type")->cvterm_id();
 142         my $male_parent_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "male_parent", "stock_relationship")->cvterm_id();
 143         my $member_of_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "member_of", "stock_relationship")->cvterm_id();
 144
 145         my $population_id;
 146         my $population_member_rs = $schema->resultset("Stock::StockRelationship")->find({stock_relationship_id => $stock_relationship_id, type_id => $member_of_type_id});
 147         if (!$population_member_rs) {
 148             print STDERR "This accession is not a population member. Cannot delete.\n";
 149                 die "This accession is not a population memeber. Cannot delete.\n";
 150         } else {
 151             $population_id = $population_member_rs->object_id();
 152             my $population_rs = $schema->resultset("Stock::Stock")->find ({stock_id => $population_id, type_id => $population_type_id});
 153             if (!$population_rs) {
 154                 print STDERR "This stock id is not a population. Cannot delete.\n";
 155                 die "This stock is not a population. Cannot delete.\n";
 156             } else {
 157                 my $male_parent_rs = $schema->resultset("Stock::StockRelationship")->search({subject_id => $population_id, type_id => $male_parent_type_id});
 158                 if ($male_parent_rs->count > 0){
 159                     print STDERR "Population has associated cross or pedigree. Cannot delete population member.\n";
 160                     die "Population has associated cross or pedigree: Cannot delete population member.\n";
 161                 }
 162             }
 163         }
 164
 165         $population_member_rs->delete;
 166     };
 167
 168     if ($@) {
 169             print STDERR "An error occurred while deleting accession member "."$@\n";
 170             $dbh->rollback();
 171             return $@;
 172     } else {
 173             $dbh->commit();
 174             return 0;
 175     }
 176 }
 177
 178
 179
 180
 181 1;