lib/CXGN/Trial.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Trial - factory object for project entries (phenotyping trials, genotyping trials, crossing trials, and analyses
   5
   6 =head1 DESCRIPTION
   7
   8 my $trial = CXGN::Trial->new( { bcs_schema => $schema, ... , trial_id => $trial_id });
   9
  10 If $trial_id is a phenotyping trial, the type of object returned will be CXGN::PhenotypingTrial.
  11
  12 =head1 AUTHOR
  13
  14 Lukas Mueller <lam87@cornell.edu>
  15
  16 =head1 METHODS
  17
  18 =cut
  19
  20 package CXGN::Trial;
  21
  22 use Moose;
  23 use Data::Dumper;
  24 use Try::Tiny;
  25 use Data::Dumper;
  26 use CXGN::Trial::Folder;
  27 use CXGN::Trial::TrialLayout;
  28 use CXGN::Trial::TrialLayoutDownload;
  29 use SGN::Model::Cvterm;
  30 use Time::Piece;
  31 use Time::Seconds;
  32 use CXGN::Calendar;
  33 use JSON;
  34 use File::Basename qw | basename dirname|;
  35
  36 =head1 NAME
  37
  38
  39 =head1 DESCRIPTION
  40
  41 If $trial_id is a genotyping trial, the type of object returned will be CXGN::GenotypingTrial.
  42
  43 If $trial_id is a crossing trial, the type of object returned will be CXGN::CrossingTrial.
  44
  45 If $trial_id is an analysis, the type of object returned will be CXGN::Analysis.
  46
  47 (you get the idea).
  48
  49 Inheritance structure of Trial objects:
  50
  51 CXGN::Trial - Factory object (for backwards compatibility)
  52
  53 CXGN::Project
  54 |
  55 ---CXGN::PhenotypingTrial
  56 |  |
  57 |  ---CXGN::GenotypingTrial
  58 |  |
  59 |  ---CXGN::CrossingTrial
  60 |
  61 ---CXGN::Analysis
  62
  63 =head1 AUTHOR
  64
  65 Lukas Mueller <lam87@cornell.edu>
  66
  67 Based on work by the entire group :-)
  68
  69 =cut
  70
  71 package CXGN::Trial;
  72
  73 use CXGN::PhenotypingTrial;
  74 use CXGN::GenotypingTrial;
  75 use CXGN::CrossingTrial;
  76 use CXGN::Analysis;
  77 use CXGN::SamplingTrial;
  78 use CXGN::ManagementFactor;
  79 use CXGN::GenotypeDataProject;
  80 use CXGN::AerialImagingEventBandProject;
  81 use CXGN::AerialImagingEventProject;
  82 use Data::Dumper;
  83
  84 sub new {
  85     my $class = shift;
  86     my $args = shift;
  87     my $schema = $args->{bcs_schema};
  88     my $trial_id = $args->{trial_id};
  89
  90     my $trial_rs = $schema->resultset("Project::Projectprop")->search( { project_id => $trial_id },{ join => 'type' });
  91
  92     if ($trial_id && $trial_rs->count() == 0) {
  93         return CXGN::PhenotypingTrial->new($args);
  94     }
  95
  96     my $object;
  97     while (my $trial_row = $trial_rs->next()) {
  98         my $name = $trial_row->type()->name();
  99         my $val = $trial_row->value();
 100         # print STDERR Dumper [$name, $val];
 101         if ($val eq "genotyping_plate") {
 102             return CXGN::GenotypingTrial->new($args);
 103         }
 104         elsif ($name eq "crossing_trial") {
 105             return CXGN::CrossingTrial->new($args);
 106         }
 107         elsif ($name eq "analysis") {
 108             return CXGN::Analysis->new($args);
 109         }
 110         elsif ($val eq "treatment") {
 111             return CXGN::ManagementFactor->new($args);
 112         }
 113         elsif ($val eq "sampling_trial") {
 114             return CXGN::SamplingTrial->new($args);
 115         }
 116         elsif (($val eq "genotype_data_project") || ($val eq "pcr_genotype_data_project")) {
 117             return CXGN::GenotypeDataProject->new($args);
 118         }
 119         elsif ($val eq "drone_run") {
 120             return CXGN::AerialImagingEventProject->new($args);
 121         }
 122         elsif ($val eq "drone_run_band") {
 123             return CXGN::AerialImagingEventBandProject->new($args);
 124         }
 125         else {
 126             $object = CXGN::PhenotypingTrial->new($args);
 127         }
 128     }
 129     return $object;
 130 }
 131
 132 =head2 class method get_all_locations()
 133
 134  Usage:        my $locations = CXGN::Trial::get_all_locations($schema)
 135  Desc:
 136  Ret:
 137  Args:
 138  Side Effects:
 139  Example:
 140
 141 =cut
 142
 143 sub get_all_locations {
 144     my $schema = shift;
 145         my $location_id = shift;
 146     my @locations;
 147
 148         my %search_params;
 149         if ($location_id){
 150                 $search_params{'nd_geolocation_id'} = $location_id;
 151         }
 152
 153     my $loc = $schema->resultset('NaturalDiversity::NdGeolocation')->search( \%search_params, {order_by => { -asc => 'nd_geolocation_id' }} );
 154     while (my $s = $loc->next()) {
 155         my $loc_props = $schema->resultset('NaturalDiversity::NdGeolocationprop')->search( { nd_geolocation_id => $s->nd_geolocation_id() }, {join=>'type', '+select'=>['me.value', 'type.name'], '+as'=>['value', 'cvterm_name'] } );
 156
 157                 my %attr;
 158         $attr{'geodetic datum'} = $s->geodetic_datum();
 159
 160         my $country = '';
 161         my $country_code = '';
 162         my $location_type = '';
 163         my $abbreviation = '';
 164         my $address = '';
 165
 166         while (my $sp = $loc_props->next()) {
 167             if ($sp->get_column('cvterm_name') eq 'country_name') {
 168                 $country = $sp->get_column('value');
 169             } elsif ($sp->get_column('cvterm_name') eq 'country_code') {
 170                 $country_code = $sp->get_column('value');
 171             } elsif ($sp->get_column('cvterm_name') eq 'location_type') {
 172                 $location_type = $sp->get_column('value');
 173             } elsif ($sp->get_column('cvterm_name') eq 'abbreviation') {
 174                 $abbreviation = $sp->get_column('value');
 175             } elsif ($sp->get_column('cvterm_name') eq 'geolocation address') {
 176                 $address = $sp->get_column('value');
 177             } else {
 178                 $attr{$sp->get_column('cvterm_name')} = $sp->get_column('value') ;
 179             }
 180         }
 181
 182         push @locations, [$s->nd_geolocation_id(), $s->description(), $s->latitude(), $s->longitude(), $s->altitude(), $country, $country_code, \%attr, $location_type, $abbreviation, $address],
 183     }
 184
 185     return \@locations;
 186 }
 187
 188 # CLASS METHOD!
 189
 190 =head2 class method get_all_project_types()
 191
 192  Usage:        my @cvterm_ids = CXGN::Trial::get_all_project_types($schema)
 193  Desc:
 194  Ret:
 195  Args:
 196  Side Effects:
 197  Example:
 198
 199 =cut
 200
 201 sub get_all_project_types {
 202     ##my $class = shift;
 203     my $schema = shift;
 204     my $project_type_cv_id = $schema->resultset('Cv::Cv')->find( { name => 'project_type' } )->cv_id();
 205     my $rs = $schema->resultset('Cv::Cvterm')->search( { cv_id=> $project_type_cv_id }, {order_by=>'me.cvterm_id'} );
 206     my @cvterm_ids;
 207     if ($rs->count() > 0) {
 208         @cvterm_ids = map { [ $_->cvterm_id(), $_->name(), $_->definition ] } ($rs->all());
 209     }
 210     return @cvterm_ids;
 211 }
 212
 213
 214 =head2 function get_all_phenotype_metadata($schema, $n)
 215
 216  Note:         Class method!
 217  Usage:        CXGN::Trial->get_phenotype_metadata($schema, 100);
 218  Desc:         retrieves maximally $n metadata.md_file entries for the any trial . These entries are created during StorePhenotypes.
 219  Ret:
 220  Args:
 221  Side Effects:
 222  Example:
 223
 224 =cut
 225
 226 sub get_all_phenotype_metadata {
 227     my $class = shift;
 228     my $schema = shift;
 229     my $n = shift || 200;
 230     my @file_array;
 231     my %file_info;
 232     my $q = "SELECT file_id, m.create_date, p.sp_person_id, p.username, basename, dirname, filetype FROM nd_experiment_project JOIN nd_experiment_phenotype USING(nd_experiment_id) JOIN phenome.nd_experiment_md_files ON (nd_experiment_phenotype.nd_experiment_id=nd_experiment_md_files.nd_experiment_id) LEFT JOIN metadata.md_files using(file_id) LEFT JOIN metadata.md_metadata as m using(metadata_id) LEFT JOIN sgn_people.sp_person as p ON (p.sp_person_id=m.create_person_id) WHERE m.obsolete = 0 and NOT (metadata.md_files.filetype='generated from plot from plant phenotypes') and NOT (metadata.md_files.filetype='direct phenotyping') ORDER BY file_id ASC LIMIT $n";
 233     my $h = $schema->storage()->dbh()->prepare($q);
 234     $h->execute();
 235
 236     while (my ($file_id, $create_date, $person_id, $username, $basename, $dirname, $filetype) = $h->fetchrow_array()) {
 237         $file_info{$file_id} = [$file_id, $create_date, $person_id, $username, $basename, $dirname, $filetype];
 238     }
 239     foreach (keys %file_info){
 240         push @file_array, $file_info{$_};
 241     }
 242     return \@file_array;
 243
 244 }
 245
 246 1;