lib/solGS/queryJobs.pm

   1 package solGS::queryJobs;
   2
   3
   4 use Moose;
   5 use namespace::autoclean;
   6
   7 use CXGN::Tools::Run;
   8 use File::Spec::Functions qw / catfile catdir/;
   9 use File::Temp qw / tempfile tempdir /;
  10 use File::Slurp qw /write_file read_file/;
  11 use Try::Tiny;
  12 use Storable qw/ nstore retrieve /;
  13 use solGS::AnalysisReport;
  14 use Carp qw/ carp confess croak /;
  15
  16 use SGN::Model::solGS::solGS;
  17 use SGN::Controller::solGS::solGS;
  18 use SGN::Controller::solGS::List;
  19 use Data::Dumper;
  20 use Bio::Chado::Schema;
  21 use CXGN::People::Schema;
  22
  23 with 'MooseX::Getopt';
  24 with 'MooseX::Runnable';
  25
  26
  27 has 'data_type' => (
  28     is       => 'ro',
  29     isa      => 'Str',
  30     required => 1,
  31     );
  32
  33 has 'dbname' => (isa => 'Str',
  34 is=>'rw',
  35 required=> 1
  36
  37 );
  38
  39 has 'dbhost' => (isa => 'Str',
  40 is=>'rw',
  41 required=> 1
  42
  43 );
  44
  45 has 'dbport' => (isa => 'Int',
  46 is=>'rw',
  47 default => 5432
  48
  49 );
  50
  51 has 'dbpass' => (isa => 'Str',
  52 is=>'rw',
  53 required=> 1
  54
  55 );
  56
  57 has 'dbuser' => (isa => 'Str',
  58 is=>'rw',
  59 required=> 1
  60
  61 );
  62
  63 has 'population_type' => (
  64     is       => 'ro',
  65     isa      => 'Str',
  66     required => 1,
  67     );
  68
  69 has 'args_file' => (
  70      is       => 'ro',
  71      isa      => 'Str',
  72      required => 1,
  73
  74     );
  75
  76 has 'check_data_exists' => (
  77     is => 'ro',
  78     isa => 'Num',
  79     required => 0,
  80     );
  81
  82
  83 sub run {
  84     my $self = shift;
  85
  86     if  ($self->population_type =~ /trial/) {
  87         if ($self->data_type =~ /phenotype/) {
  88             $self->trial_phenotype_data();
  89         } elsif ($self->data_type =~ /genotype/) {
  90             $self->trial_genotype_data();
  91         }
  92     } elsif ($self->population_type =~ /list/) {
  93
  94         if ($self->data_type =~ /phenotype/) {
  95             $self->plots_list_phenotype_data();
  96         } elsif ($self->data_type =~ /genotype/) {
  97             $self->genotypes_list_genotype_data();
  98         }
  99     } elsif ($self->population_type =~ /dataset/) {
 100
 101         if ($self->data_type =~ /phenotype/) {
 102             $self->plots_list_phenotype_data();
 103         } elsif ($self->data_type =~ /genotype/) {
 104             $self->dataset_genotype_data();
 105         }
 106     }
 107
 108 }
 109
 110 sub get_args {
 111         my $self = shift;
 112         return retrieve($self->args_file);
 113 }
 114
 115
 116 sub trial_genotype_data {
 117     my $self = shift;
 118
 119     my $args  = $self->get_args();
 120     my $geno_file  = $args->{genotype_file};
 121
 122     my $model = $self->get_model();
 123
 124     my $search_obj = $model->genotype_data($args);
 125     $self->write_geno_data($search_obj, $geno_file);
 126
 127 }
 128
 129
 130 sub write_geno_data {
 131     my ($self, $search_obj, $file) = @_;
 132
 133     my $exists = $self->check_data_exists;
 134     my $count = 1;
 135     my $marker_headers;
 136
 137     my $model = $self->get_model();
 138     my $add_headers = 1;
 139     while (my $geno = $search_obj->get_next_genotype_info())
 140     {
 141         my $geno_data;
 142
 143         if ($count == 1)
 144         {
 145             my $geno_hash = $geno->{selected_genotype_hash};
 146             $marker_headers = $model->get_dataset_markers($geno_hash);
 147         }  else {
 148             $add_headers = 0;
 149         }
 150
 151         $geno_data  = $model->structure_genotype_data($geno, $marker_headers, $add_headers);
 152         write_file($file, {append => 1, binmode => ':utf8'}, $$geno_data);
 153
 154         $count++;
 155         if ($self->check_data_exists)
 156         {
 157             last if $$geno_data;
 158         }
 159     }
 160
 161 }
 162
 163
 164 sub trial_phenotype_data {
 165     my $self = shift;
 166
 167     my $args  =  $self->get_args();
 168
 169     my $pheno_file  = $args->{phenotype_file};
 170     my $pop_id      = $args->{population_id};
 171     my $traits_file = $args->{traits_list_file};
 172     my $metadata_file = $args->{metadata_file};
 173
 174     my $model = $self->get_model();
 175     my $pheno_data = $model->phenotype_data($pop_id);
 176     my $metadata   = $model->trial_metadata();
 177
 178     if ($pheno_data)
 179     {
 180         my $pheno_data = SGN::Controller::solGS::solGS->format_phenotype_dataset($pheno_data, $metadata, $traits_file);
 181         write_file($pheno_file, {binmode => ':utf8'}, $pheno_data);
 182     }
 183
 184     write_file($metadata_file, {binmode => ':utf8'}, join("\t", @$metadata));
 185 }
 186
 187
 188 sub genotypes_list_genotype_data {
 189     my $self = shift;
 190         my $genotypes_ids = shift;
 191
 192     my $args =  $self->get_args();
 193     $genotypes_ids  = $args->{genotypes_ids} if !$genotypes_ids->[0];
 194
 195     my $data_dir      = $args->{data_dir};
 196     my $geno_file    = $args->{genotype_file};
 197     my $protocol_id = $args->{genotyping_protocol_id};
 198
 199     my $model = $self->get_model();
 200     my $search_obj = $model->genotypes_list_genotype_data($genotypes_ids, $protocol_id);
 201
 202     ###empty cached geno file first
 203     write_file($geno_file);
 204     $self->write_geno_data($search_obj, $geno_file);
 205
 206 }
 207
 208
 209 sub plots_list_phenotype_data {
 210     my $self= shift;
 211
 212     my $args =  $self->get_args();
 213
 214     my $list_id = $args->{list_id};
 215     my $plots_ids   = $args->{plots_ids};
 216     my $traits_file = $args->{traits_file};
 217     #my $data_dir    = $args->{data_dir};
 218     my $pheno_file  = $args->{phenotype_file};
 219     my $metadata_file = $args->{metadata_file};
 220
 221     my $model = $self->get_model();
 222     my $pheno_data = $model->plots_list_phenotype_data($plots_ids);
 223     my $metadata = $model->trial_metadata();
 224
 225     $pheno_data = SGN::Controller::solGS::solGS->format_phenotype_dataset($pheno_data, $metadata, $traits_file);
 226
 227     write_file($pheno_file, {binmode => ':utf8'}, $pheno_data);
 228     write_file($metadata_file, {binmode => ':utf8'}, join("\t", @$metadata));
 229
 230 }
 231
 232
 233 sub dataset_genotype_data {
 234     my $self = shift;
 235
 236     my $args =  $self->get_args();
 237     my $dataset_id = $args->{dataset_id};
 238         my $model = $self->get_model();
 239
 240         my $genotypes_ids = $model->get_genotypes_from_dataset ($dataset_id);
 241     # my $cnt = @$genotypes_ids;
 242         if (@{$genotypes_ids})
 243         {
 244                 $self->genotypes_list_genotype_data($genotypes_ids);
 245         }
 246         else
 247         {
 248                 my $model = $self->get_model();
 249                 my $protocol_id = $args->{genotyping_protocol_id};
 250         my $search_obj = $model->get_dataset_genotype_data($dataset_id);
 251                 my $geno_file = $args->{genotype_file};
 252         ###empty cached dataset geno file first
 253         write_file($geno_file);
 254                 $self->write_geno_data($model, $search_obj, $geno_file);
 255         }
 256
 257 }
 258
 259
 260 sub get_model {
 261     my $self = shift;
 262
 263     my $dbname = $self->dbname;
 264     my $dbhost = $self->dbhost;
 265
 266     my $dbuser = $self->dbuser;
 267     my $dbpass = $self->dbpass;
 268
 269     my $dsn = "dbi:Pg:database=$dbname;host=$dbhost";
 270
 271     my $bcs_schema = Bio::Chado::Schema->connect($dsn, $dbuser, $dbpass);
 272     my $people_schema = CXGN::People::Schema->connect($dsn,  $dbuser, $dbpass, { on_connect_do => [ 'SET search_path TO sgn_people, public, sgn' ]});
 273
 274
 275     my $model = SGN::Model::solGS::solGS->new({
 276                                                schema => $bcs_schema,
 277                        people_schema =>$people_schema });
 278
 279
 280     return $model;
 281
 282 }
 283
 284
 285
 286 __PACKAGE__->meta->make_immutable;
 287
 288
 289
 290
 291 ####
 292 1; #
 293 ####