lib/SGN/Controller/AJAX/Cross/CrossingExperiment.pm

   1 =head1 NAME
   2
   3 SGN::Controller::AJAX::Cross::CrossingExperiment - a REST controller class to provide
   4 functions related to crossing experiment
   5
   6 =head1 DESCRIPTION
   7
   8
   9 =head1 AUTHOR
  10
  11 Titima Tantikanjana <tt15@cornell.edu>
  12
  13 =cut
  14
  15 package SGN::Controller::AJAX::Cross::CrossingExperiment;
  16 use Moose;
  17 use Try::Tiny;
  18 use DateTime;
  19 use Time::HiRes qw(time);
  20 use POSIX qw(strftime);
  21 use Data::Dumper;
  22 use File::Basename qw | basename dirname|;
  23 use File::Copy;
  24 use File::Slurp;
  25 use File::Spec::Functions;
  26 use Digest::MD5;
  27 use List::MoreUtils qw /any /;
  28 use List::MoreUtils 'none';
  29 use Bio::GeneticRelationships::Pedigree;
  30 use Bio::GeneticRelationships::Individual;
  31 use CXGN::UploadFile;
  32 use CXGN::Pedigree::ParseUpload;
  33 use CXGN::List::Validate;
  34 use CXGN::List;
  35 use CXGN::Pedigree::TargetNumbers;
  36 use Carp;
  37 use File::Path qw(make_path);
  38 use File::Spec::Functions qw / catfile catdir/;
  39 use CXGN::Cross;
  40 use JSON;
  41 use SGN::Model::Cvterm;
  42 use Tie::UrlEncoder; our(%urlencode);
  43 use LWP::UserAgent;
  44 use URI::Encode qw(uri_encode uri_decode);
  45 use Sort::Key::Natural qw(natsort);
  46 BEGIN { extends 'Catalyst::Controller::REST' }
  47
  48 __PACKAGE__->config(
  49     default   => 'application/json',
  50     stash_key => 'rest',
  51     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON'  },
  52 );
  53
  54 sub upload_target_numbers : Path('/ajax/crossing_experiment/upload_target_numbers') : ActionClass('REST'){ }
  55
  56 sub upload_target_numbers_POST : Args(0) {
  57     my $self = shift;
  58     my $c = shift;
  59     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  60     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
  61     my $dbh = $c->dbc->dbh;
  62     my $target_numbers_experiment_id = $c->req->param('target_numbers_experiment_id');
  63     my $upload = $c->req->upload('target_numbers_file');
  64     my $parser;
  65     my $parsed_data;
  66     my $upload_original_name = $upload->filename();
  67     my $upload_tempfile = $upload->tempname;
  68     my $subdirectory = "target_numbers_upload";
  69     my $archived_filename_with_path;
  70     my $md5;
  71     my $validate_file;
  72     my $parsed_file;
  73     my $parse_errors;
  74     my %parsed_data;
  75     my $time = DateTime->now();
  76     my $timestamp = $time->ymd()."_".$time->hms();
  77     my $user_role;
  78     my $user_id;
  79     my $user_name;
  80     my $owner_name;
  81     my $session_id = $c->req->param("sgn_session_id");
  82     my @error_messages;
  83
  84     if ($session_id){
  85         my $dbh = $c->dbc->dbh;
  86         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
  87         if (!$user_info[0]){
  88             $c->stash->{rest} = {error=>'You must be logged in to upload target numbers!'};
  89             $c->detach();
  90         }
  91         $user_id = $user_info[0];
  92         $user_role = $user_info[1];
  93         my $p = CXGN::People::Person->new($dbh, $user_id);
  94         $user_name = $p->get_username;
  95     } else {
  96         if (!$c->user){
  97             $c->stash->{rest} = {error=>'You must be logged in to upload intercross data!'};
  98             $c->detach();
  99         }
 100         $user_id = $c->user()->get_object()->get_sp_person_id();
 101         $user_name = $c->user()->get_object()->get_username();
 102         $user_role = $c->user->get_object->get_user_type();
 103     }
 104
 105     if (($user_role ne 'curator') && ($user_role ne 'submitter')) {
 106         $c->stash->{rest} = {error=>'Only a submitter or a curator can upload target numbers of seed/progenies'};
 107         $c->detach();
 108     }
 109
 110     my $uploader = CXGN::UploadFile->new({
 111         tempfile => $upload_tempfile,
 112         subdirectory => $subdirectory,
 113         archive_path => $c->config->{archive_path},
 114         archive_filename => $upload_original_name,
 115         timestamp => $timestamp,
 116         user_id => $user_id,
 117         user_role => $user_role
 118     });
 119
 120         ## Store uploaded temporary file in arhive
 121     $archived_filename_with_path = $uploader->archive();
 122     $md5 = $uploader->get_md5($archived_filename_with_path);
 123     if (!$archived_filename_with_path) {
 124         $c->stash->{rest} = {error => "Could not save file $upload_original_name in archive",};
 125         return;
 126     }
 127     unlink $upload_tempfile;
 128
 129     #parse uploaded file with appropriate plugin
 130     $parser = CXGN::Pedigree::ParseUpload->new(chado_schema => $schema, filename => $archived_filename_with_path);
 131     $parser->load_plugin('TargetNumbersExcel');
 132     $parsed_data = $parser->parse();
 133     #print STDERR "PARSED DATA =". Dumper($parsed_data)."\n";
 134     if (!$parsed_data){
 135         my $return_error = '';
 136         my $parse_errors;
 137         if (!$parser->has_parse_errors() ){
 138             $c->stash->{rest} = {error_string => "Could not get parsing errors"};
 139         } else {
 140             $parse_errors = $parser->get_parse_errors();
 141             #print STDERR Dumper $parse_errors;
 142             foreach my $error_string (@{$parse_errors->{'error_messages'}}){
 143                 $return_error .= $error_string."<br>";
 144             }
 145         }
 146         $c->stash->{rest} = {error_string => $return_error};
 147         $c->detach();
 148     }
 149
 150     if ($parsed_data){
 151
 152         my $md_row = $metadata_schema->resultset("MdMetadata")->create({create_person_id => $user_id});
 153         $md_row->insert();
 154         my $upload_file = CXGN::UploadFile->new();
 155         my $md5 = $upload_file->get_md5($archived_filename_with_path);
 156         my $md5checksum = $md5->hexdigest();
 157         my $file_row = $metadata_schema->resultset("MdFiles")->create({
 158             basename => basename($archived_filename_with_path),
 159             dirname => dirname($archived_filename_with_path),
 160             filetype => 'target_numbers_upload',
 161             md5checksum => $md5checksum,
 162             metadata_id => $md_row->metadata_id(),
 163         });
 164         my $file_id = $file_row->file_id();
 165         my %target_numbers = %{$parsed_data};
 166
 167 #        print STDERR "UPLOAD TARGET NUMBERS=".Dumper(\%target_numbers)."\n";
 168         my $targets = CXGN::Pedigree::TargetNumbers->new({ chado_schema => $schema, crossing_experiment_id => $target_numbers_experiment_id, target_numbers => \%target_numbers });
 169         $targets->store();
 170     }
 171
 172
 173     $c->stash->{rest} = {success => "1",};
 174 }
 175
 176
 177 sub record_target_numbers_using_lists : Path('/ajax/crossing_experiment/record_target_numbers') : ActionClass('REST') { }
 178
 179 sub record_target_numbers_using_lists_POST : Args(0) {
 180     my $self = shift;
 181     my $c = shift;
 182     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 183     my $crossing_experiment_id = $c->req->param('crossing_experiment_id');
 184     my $number_of_seeds = decode_json $c->req->param('number_of_seeds');
 185     my $number_of_progenies = decode_json $c->req->param('number_of_progenies');
 186
 187     my %target_numbers_hash;
 188     foreach my$seed_info_hash (@$number_of_seeds) {
 189         $target_numbers_hash{$seed_info_hash->{female_name}}{$seed_info_hash->{male_name}}{'target_number_of_seeds'} = $seed_info_hash->{number_of_seeds};
 190     }
 191
 192     foreach my$progeny_info_hash (@$number_of_progenies) {
 193         $target_numbers_hash{$progeny_info_hash->{female_name}}{$progeny_info_hash->{male_name}}{'target_number_of_progenies'} = $progeny_info_hash->{number_of_progenies};
 194     }
 195
 196     print STDERR "TARGET NUMBERS HASH =".Dumper(\%target_numbers_hash)."\n";
 197     my $targets = CXGN::Pedigree::TargetNumbers->new({ chado_schema => $schema, crossing_experiment_id => $crossing_experiment_id, target_numbers => \%target_numbers_hash });
 198     $targets->store();
 199
 200     $c->stash->{rest} = {success => "1",};
 201
 202 }
 203
 204 sub get_target_numbers_and_progress :Path('/ajax/crossing_experiment/target_numbers_and_progress') Args(1) {
 205     my $self = shift;
 206     my $c = shift;
 207     my $crossing_experiment_id = shift;
 208     my $schema = $c->dbic_schema("Bio::Chado::Schema");
 209
 210     my $target_numbers = CXGN::Pedigree::TargetNumbers->new({ chado_schema => $schema, crossing_experiment_id => $crossing_experiment_id});
 211     my $target_info = $target_numbers->get_target_numbers_and_progress();
 212 #    print STDERR "AJAX TARGET NUMBERS =".Dumper($target_info)."\n";
 213
 214
 215     $c->stash->{rest} = { data => $target_info };
 216
 217 }
 218
 219
 220 1;