db/00002/PhenomeAnnotationsToStock.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  PhenomeAnnotationsToStock.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run ThisPackageName [options] -H hostname -D dbname -u username [-F]
  11
  12 this is a subclass of L<CXGN::Metadata::Dbpatch>
  13 see the perldoc of parent class for more details.
  14
  15 =head1 DESCRIPTION
  16
  17 This is a patch for loading cvterm annotation data in phenome.individual_dbxref in the stock module (stock_cvterm) and the evidence codes into stock_cvtermprop. Previous annotations loaded into stock_dbxref and stock_dbxrefprop will be deleted.
  18
  19 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  20
  21 =head1 AUTHOR
  22
  23  Naama Menda<nm249@cornell.edu>
  24
  25 =head1 COPYRIGHT & LICENSE
  26
  27 Copyright 2011 Boyce Thompson Institute for Plant Research
  28
  29 This program is free software; you can redistribute it and/or modify
  30 it under the same terms as Perl itself.
  31
  32 =cut
  33
  34
  35 package PhenomeAnnotationsToStock;
  36
  37 use Try::Tiny;
  38 use Moose;
  39 extends 'CXGN::Metadata::Dbpatch';
  40
  41 use Bio::Chado::Schema;
  42
  43 use CXGN::Phenome::Population;
  44 use CXGN::Phenome::Individual;
  45 use CXGN::Chado::Dbxref;
  46
  47 use CXGN::People::Person;
  48
  49
  50 sub init_patch {
  51     my $self=shift;
  52     my $name = __PACKAGE__;
  53     print "dbpatch name is : '" .  $name . "'\n\n";
  54     my $description = 'Loading the phenome individual annotations into stock_cvterm ';
  55     my @previous_requested_patches = ('LoadPhenomeInStock', 'AddStockCvtermProp','PopulateStockPub'); #ADD HERE
  56
  57     $self->name($name);
  58     $self->description($description);
  59     $self->prereq(\@previous_requested_patches);
  60
  61 }
  62
  63 sub patch {
  64     my $self=shift;
  65
  66     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  67
  68     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  69
  70     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } ,  { on_connect_do => ['SET search_path TO public;'], autocommit => 1 });
  71
  72 ###################################################################
  73     my $pub_curator = $schema->resultset('Pub::Pub')->find( { title => 'curator' });
  74
  75 ##################
  76     my $result = $schema->txn_do( sub {
  77         print "loading ...\n";
  78 # do this for GO, PO, SP - copy from stock_dbxref to stock cvterm, and the evidence codes copied to stock_cvtermprop.
  79         my $stockdbxrefs = $schema->resultset("General::Db")->search( {
  80             -or => [
  81                  name => 'GO',
  82                  name => 'PO',
  83                  name => 'SP',
  84                 ], } )
  85             ->search_related('dbxrefs')->search_related('stock_dbxrefs');
  86         while ( my $sd = $stockdbxrefs->next )  {
  87             # for each stock_dbxref create a stock_cvterm
  88             my $stock_cvterm = $sd->stock->find_or_create_related('stock_cvterms' , {
  89                 cvterm_id => $sd->dbxref->search_related('cvterm')->first->cvterm_id ,
  90                 pub_id => $pub_curator->pub_id  } );
  91             #print "Added cvterm for stock " . $sd->stock->name . "\n";
  92
  93             # get all the properties of the stock_dbxref , and load them into stock_cvtermprop
  94             my $dprops = $sd->search_related('stock_dbxrefprops') ;
  95           PROP: while ( my $dprop = $dprops->next )  {
  96               my $cv_name = $dprop->type->cv->name;
  97               my $type_name = $dprop->type->name;
  98               my $db_name = $dprop->type->dbxref->db->name;
  99               my $value = $dprop->value
 100                   or die "Invalid stock_dbxrefprop: ".Data::Dumper::Dumper({ $dprop->get_columns });
 101               my $rank = $dprop->rank;
 102               if ($cv_name eq 'local' ) {
 103                   # load the reference into stock_cvterm.pub_id
 104                   if ($type_name eq 'reference' ) {
 105                       my @pubs = $schema->resultset("General::Dbxref")
 106                                         ->find({ dbxref_id => $value })
 107                                         ->pubs_mm;
 108                       if( @pubs > 1 ) {
 109                           die "multiple pubs for stock_dbxrefprop ID ".$dprop->stock_dbxrefprop_id;
 110                       }
 111                       $stock_cvterm->update( { pub_id => $_->pub_id } ) for @pubs;
 112                       next PROP;
 113                   }
 114                   $stock_cvterm->create_stock_cvtermprops(
 115                       {  $type_name => $value  } , { cv_name =>'local' , autocreate=>1} ) if ( $value && $rank == 0) ;
 116                   #print "Added prop to stock_cvterm. type= $type_name , value =  $value \n";
 117               }
 118               if ($cv_name eq 'relationship' || $cv_name eq 'evidence_code' ) {
 119                   $stock_cvterm->create_stock_cvtermprops(
 120                       {  $cv_name => $dprop->type_id  } , { cv_name =>$cv_name , db_name => $db_name} ) if $value && $rank == 0 ;
 121                   #print "Added prop to stock_cvterm. type= $cv_name , value =  $type_name \n";
 122               }
 123               #delete the stock_dbxrefprop
 124               $dprop->delete
 125           }
 126             # delete the stock_dbxref
 127             $sd->delete;
 128         }
 129         if ( $self->trial ) {
 130             print "Trial mode! Rolling back transaction.\n\n";
 131             $schema->txn_rollback;
 132             return 0;
 133         } else {
 134             print "Committing.\n";
 135             return 1;
 136         }
 137     });
 138
 139     print $result ? "Patch applied successfully.\n" : "Patch not applied.\n";
 140 }
 141
 142 return 1;