lib/CXGN/BrAPI/v2/References.pm

   1 package CXGN::BrAPI::v2::References;
   2
   3 use Moose;
   4 use Data::Dumper;
   5 use CXGN::BrAPI::Pagination;
   6 use CXGN::BrAPI::JSONResponse;
   7 use JSON;
   8
   9 extends 'CXGN::BrAPI::v2::Common';
  10
  11 sub search {
  12         my $self = shift;
  13         my $inputs = shift;
  14         my $schema = $self->bcs_schema();
  15     my $status = $self->status;
  16         my $page_size = $self->page_size;
  17         my $page = $self->page;
  18
  19     my $referenceset_ids = $inputs->{referenceSetDbId} || ($inputs->{referenceSetDbIds} || ());
  20     my $reference_ids = $inputs->{referenceDbId} || ($inputs->{referenceDbIds} || ());
  21     my $accession = $inputs->{accession} || ($inputs->{accessions} || ());
  22     my $is_derived = $inputs->{isDerived} || ($inputs->{isDerived} || ());
  23     my $md5checksum = $inputs->{md5checksum} || ($inputs->{md5checksums} || ());
  24     my $max_length = $inputs->{maxLength} || ($inputs->{maxLength} || ());
  25     my $min_length = $inputs->{minLength} || ($inputs->{minLength} || ());
  26
  27     if ($md5checksum || $accession || $is_derived ){
  28         push @$status, { 'error' => 'The following parameters search are not implemented: md5checksum, accession, isDerived' };
  29     }
  30
  31         my @data;
  32         my $counter = 0;
  33         my $where_clause = "";
  34     my %reference_sets;
  35
  36     my $vcf_map_details_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'vcf_map_details', 'protocol_property')->cvterm_id();
  37
  38     if ($referenceset_ids && scalar(@$referenceset_ids)>0) {
  39         my $protocol_sql = join ("," , @$referenceset_ids);
  40         $where_clause = "AND nd_protocolprop.nd_protocol_id in ($protocol_sql)";
  41     }
  42
  43         my $subquery = "SELECT distinct value->'reference_genome_name', value->'species_name', nd_protocol_id, value->'header_information_lines' from nd_protocolprop where type_id = $vcf_map_details_cvterm_id $where_clause";
  44
  45     my $h = $schema->storage->dbh()->prepare($subquery);
  46     $h->execute();
  47
  48     my $start_index = $page*$page_size;
  49     my $end_index = $page*$page_size + $page_size - 1;
  50
  51     while (my ($referenceset, $species, $protocol, $header ) = $h->fetchrow_array()) {
  52         $referenceset =~ s/"//g;
  53         $species =~ s/"//g;
  54         $protocol =~ s/"//g;
  55         my $source;
  56
  57         my $head = decode_json $header;
  58
  59         foreach (@{$head}){
  60             $source = $1 if ($_ =~ /##source=(\w+)/);
  61         }
  62
  63         foreach (@{$head}){
  64             my $referenceName = $1 if ($_ =~ /##contig=<ID=(\w+)/) ;
  65             my $length = $1 if ($_ =~ /,length=(\d+)/) ;
  66             my $md5 = $1 if ($_ =~ /,md5=(\w+)/) ;
  67             if ( $md5checksum && $md5 && ! grep { $_ eq $md5 } @{$md5checksum}  ) { next; }
  68             if ( $referenceName && $reference_ids && ! grep { $_ eq $referenceName } @{$reference_ids} ) { next; }
  69             if ( $max_length && $length && $max_length->[0] < $length + 0 ) { next; }
  70             if ( $min_length && $length && $min_length->[0] > $length + 0 ) { next; }
  71
  72             if($referenceName){
  73                 if ($counter >= $start_index && $counter <= $end_index) {
  74                     push @data, {
  75                         additionalInfo => {},
  76                         isDerived => JSON::false,
  77                         length => $length + 0,
  78                         md5checksum => $md5,
  79                         referenceSetDbId => qq|$protocol|,
  80                         referenceSetName => $referenceset,
  81                         referenceDbId => qq|$referenceName|,
  82                         referenceName => qq|$referenceName|,
  83                         sourceAccessions => undef,
  84                         sourceDivergence => undef,
  85                         sourceURI => undef,
  86                         species => {
  87                             term => $species,
  88                             termURI => undef
  89                         }
  90                     };
  91                 }
  92                 $counter++;
  93             }
  94         }
  95     }
  96
  97     my %result = (data=>\@data);
  98     my @data_files;
  99     my $pagination = CXGN::BrAPI::Pagination->pagination_response($counter,$page_size,$page);
 100     return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'References result constructed');
 101 }
 102
 103 sub detail {
 104     my $self = shift;
 105     my $reference_ids = shift;
 106     my $schema = $self->bcs_schema();
 107     my $page_size = $self->page_size;
 108     my $page = $self->page;
 109
 110     my @data;
 111     my $counter = 0;
 112     my $where_clause;
 113     my %reference_sets;
 114
 115     my $vcf_map_details_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'vcf_map_details', 'protocol_property')->cvterm_id();
 116
 117     my $subquery = "SELECT distinct value->'reference_genome_name', value->'species_name', nd_protocol_id, value->'header_information_lines' from nd_protocolprop where type_id = $vcf_map_details_cvterm_id $where_clause";
 118
 119     my $h = $schema->storage->dbh()->prepare($subquery);
 120     $h->execute();
 121
 122     while (my ($referenceset, $species, $protocol, $header ) = $h->fetchrow_array()) {
 123         $referenceset =~ s/"//g;
 124         $species =~ s/"//g;
 125         $protocol =~ s/"//g;
 126         my $source;
 127
 128         my $head = decode_json $header;
 129
 130         foreach (@{$head}){
 131             $source = $1 if ($_ =~ /##source=(\w+)/);
 132         }
 133
 134         foreach (@{$head}){
 135             my $referenceName = $1 if ($_ =~ /##contig=<ID=(\w+)/) ;
 136             my $length = $1 if ($_ =~ /,length=(\d+)/) ;
 137             my $md5 = $1 if ($_ =~ /,md5=(\w+)/) ;
 138
 139             if($referenceName  && $reference_ids eq $referenceName ){
 140                 push @data, {
 141                     additionalInfo => {},
 142                     isDerived => JSON::false,
 143                     length => $length + 0,
 144                     md5checksum => $md5,
 145                     referenceSetDbId => qq|$protocol|,
 146                     referenceSetName => $referenceset,
 147                     referenceDbId => qq|$referenceName|,
 148                     referenceName => qq|$referenceName|,
 149                     sourceAccessions => undef,
 150                     sourceDivergence => undef,
 151                     sourceURI => undef,
 152                     species => {
 153                         term => $species,
 154                         termURI => undef
 155                     }
 156                 };
 157                 $counter++;
 158             }
 159         }
 160     }
 161
 162
 163     my $status = $self->status;
 164
 165     my %result = (data=>\@data);
 166     my @data_files;
 167     my $pagination = CXGN::BrAPI::Pagination->pagination_response($counter,$page_size,$page);
 168     return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'References result constructed');
 169 }
 170
 171 1;