lib/SGN/Controller/AJAX/FieldBook.pm

   1
   2 =head1 NAME
   3
   4 SGN::Controller::AJAX::FieldBook - a REST controller class to provide the
   5 backend for field book operations
   6
   7 =head1 DESCRIPTION
   8
   9 Creating and viewing trials
  10
  11 =head1 AUTHOR
  12
  13 Jeremy Edwards <jde22@cornell.edu>
  14
  15 =cut
  16
  17 package SGN::Controller::AJAX::FieldBook;
  18
  19 use Moose;
  20 use List::MoreUtils qw /any /;
  21 use Scalar::Util qw(looks_like_number);
  22 use DateTime;
  23 use Try::Tiny;
  24 use File::Basename qw | basename dirname|;
  25 use File::Copy;
  26 use File::Slurp;
  27 use File::Spec::Functions;
  28 use Digest::MD5;
  29 use JSON -support_by_pp;
  30 use Spreadsheet::WriteExcel;
  31 use SGN::View::Trial qw/design_layout_view design_info_view/;
  32 use CXGN::Phenotypes::ParseUpload;
  33 use CXGN::Phenotypes::StorePhenotypes;
  34 use CXGN::Trial::TrialLayout;
  35 use CXGN::Location::LocationLookup;
  36 use CXGN::Stock::StockLookup;
  37 use CXGN::UploadFile;
  38 use CXGN::Fieldbook::TraitInfo;
  39 use CXGN::Fieldbook::DownloadTrial;
  40 use SGN::Model::Cvterm;
  41
  42 #use Data::Dumper;
  43
  44 BEGIN { extends 'Catalyst::Controller::REST' }
  45
  46 __PACKAGE__->config(
  47     default   => 'application/json',
  48     stash_key => 'rest',
  49     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  50    );
  51
  52
  53 sub create_fieldbook_from_trial : Path('/ajax/fieldbook/create') : ActionClass('REST') { }
  54
  55 sub create_fieldbook_from_trial_POST : Args(0) {
  56   my ($self, $c) = @_;
  57   my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  58   my $trial_id = $c->req->param('trial_id');
  59   my $data_level = $c->req->param('data_level') || 'plots';
  60   my $metadata_schema = $c->dbic_schema('CXGN::Metadata::Schema');
  61   my $phenome_schema = $c->dbic_schema('CXGN::Phenome::Schema');
  62
  63   chomp($trial_id);
  64   if (!$c->user()) {
  65     $c->stash->{rest} = {error => "You need to be logged in to create a field book" };
  66     return;
  67   }
  68   if (!any { $_ eq "curator" || $_ eq "submitter" } ($c->user()->roles)  ) {
  69     $c->stash->{rest} = {error =>  "You have insufficient privileges to create a field book." };
  70     return;
  71   }
  72   if (!$trial_id) {
  73     $c->stash->{rest} = {error =>  "No trial ID supplied." };
  74     return;
  75   }
  76   my $trial = $schema->resultset('Project::Project')->find({project_id => $trial_id});
  77   if (!$trial) {
  78     $c->stash->{rest} = {error =>  "Trial does not exist with id $trial_id." };
  79     return;
  80   }
  81     if ($data_level eq 'plants') {
  82         my $trial = CXGN::Trial->new( { bcs_schema => $schema, trial_id => $trial_id });
  83         if (!$trial->has_plant_entries()){
  84             $c->stash->{rest} = {error =>  "Trial does not have plant entries. You must first create plant entries." };
  85             return;
  86         }
  87     }
  88
  89   my $dir = $c->tempfiles_subdir('/other');
  90   my $tempfile = $c->config->{basepath}."/".$c->tempfile( TEMPLATE => 'other/excelXXXX');
  91
  92     my $create_fieldbook = CXGN::Fieldbook::DownloadTrial->new({
  93         bcs_schema => $schema,
  94         metadata_schema => $metadata_schema,
  95         phenome_schema => $phenome_schema,
  96         trial_id => $trial_id,
  97         tempfile => $tempfile,
  98         archive_path => $c->config->{archive_path},
  99         user_id => $c->user()->get_object()->get_sp_person_id(),
 100         user_name => $c->user()->get_object()->get_username(),
 101         data_level => $data_level,
 102     });
 103
 104     my $create_fieldbook_return = $create_fieldbook->download();
 105
 106     $c->stash->{rest} = {
 107         error_string => $create_fieldbook_return->{'error_messages'},
 108         success => 1,
 109         result => $create_fieldbook_return->{'result'},
 110         file => $create_fieldbook_return->{'file'},
 111     };
 112 }
 113
 114 sub create_trait_file_for_field_book : Path('/ajax/fieldbook/traitfile/create') : ActionClass('REST') { }
 115
 116 sub create_trait_file_for_field_book_POST : Args(0) {
 117   my ($self, $c) = @_;
 118
 119   if (!$c->user()) {
 120     $c->stash->{rest} = {error => "You need to be logged in to create a field book" };
 121     return;
 122   }
 123   if (!any { $_ eq "curator" || $_ eq "submitter" } ($c->user()->roles)  ) {
 124     $c->stash->{rest} = {error =>  "You have insufficient privileges to create a field book." };
 125     return;
 126   }
 127
 128   my @trait_list;
 129   my $trait_file_name = $c->req->param('trait_file_name');
 130   my $user_id = $c->user()->get_object()->get_sp_person_id();
 131   my $user_name = $c->user()->get_object()->get_username();
 132   my $time = DateTime->now();
 133   my $timestamp = $time->ymd()."_".$time->hms();
 134   my $subdirectory_name = "tablet_trait_files";
 135   my $archived_file_name = catfile($user_id, $subdirectory_name,$timestamp."_".$trait_file_name.".trt");
 136   my $archive_path = $c->config->{archive_path};
 137   my $file_destination =  catfile($archive_path, $archived_file_name);
 138
 139   if ($c->req->param('trait_list')) {
 140     @trait_list = @{_parse_list_from_json($c->req->param('trait_list'))};
 141   }
 142
 143   if (!-d $archive_path) {
 144     mkdir $archive_path;
 145   }
 146
 147   if (! -d catfile($archive_path, $user_id)) {
 148     mkdir (catfile($archive_path, $user_id));
 149   }
 150
 151   if (! -d catfile($archive_path, $user_id,$subdirectory_name)) {
 152     mkdir (catfile($archive_path, $user_id, $subdirectory_name));
 153   }
 154
 155   open FILE, ">$file_destination" or die $!;
 156   my $chado_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 157   print FILE "trait,format,defaultValue,minimum,maximum,details,categories,isVisible,realPosition\n";
 158   my $order = 1;
 159
 160   foreach my $term (@trait_list) {
 161
 162       my ($trait_name, $full_cvterm_accession) = split (/\|/, $term);
 163       my ( $db_name , $accession ) = split (/:/ , $full_cvterm_accession);
 164
 165       $accession =~ s/\s+$//;
 166       $accession =~ s/^\s+//;
 167       $db_name =~ s/\s+$//;
 168       $db_name =~ s/^\s+//;
 169
 170       print STDERR "traitname: $term | accession: $accession \n";
 171
 172       #get trait info
 173
 174       my $trait_info_lookup = CXGN::Fieldbook::TraitInfo
 175           ->new({
 176               chado_schema    => $chado_schema,
 177               db_name         => $db_name,
 178               trait_accession => $accession,
 179                 });
 180       my $trait_info_string = $trait_info_lookup->get_trait_info($trait_name);
 181
 182       #return error if not $trait_info_string;
 183       #print line with trait info
 184       #print FILE "$trait_name:$db_name:$accession,text,,,,,,TRUE,$order\n";
 185       print FILE "\"$trait_name|$db_name:$accession\",$trait_info_string,\"TRUE\",\"$order\"\n";
 186       $order++;
 187   }
 188
 189   close FILE;
 190
 191   open(my $F, "<", $file_destination) || die "Can't open file ";
 192   binmode $F;
 193   my $md5 = Digest::MD5->new();
 194   $md5->addfile($F);
 195   close($F);
 196
 197   my $metadata_schema = $c->dbic_schema('CXGN::Metadata::Schema');
 198
 199   my $md_row = $metadata_schema->resultset("MdMetadata")->create({
 200                                                                   create_person_id => $user_id,
 201                                                                  });
 202   $md_row->insert();
 203
 204   my $file_row = $metadata_schema->resultset("MdFiles")->create({
 205                                                                      basename => basename($file_destination),
 206                                                                      dirname => dirname($file_destination),
 207                                                                      filetype => 'tablet trait file',
 208                                                                      md5checksum => $md5->hexdigest(),
 209                                                                      metadata_id => $md_row->metadata_id(),
 210                                                                     });
 211   $file_row->insert();
 212
 213   $c->stash->{rest} = {success => "1",};
 214
 215 }
 216
 217
 218 sub _parse_list_from_json {
 219   my $list_json = shift;
 220   my $json = new JSON;
 221   if ($list_json) {
 222     my $decoded_list = $json->allow_nonref->utf8->relaxed->escape_slash->loose->allow_singlequote->allow_barekey->decode($list_json);
 223     #my $decoded_list = decode_json($list_json);
 224     my @array_of_list_items = @{$decoded_list};
 225     return \@array_of_list_items;
 226   }
 227   else {
 228     return;
 229   }
 230 }
 231
 232
 233 1;