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::Location::LocationLookup;
  33 use CXGN::Stock::StockLookup;
  34 use CXGN::UploadFile;
  35 use CXGN::Fieldbook::TraitInfo;
  36 use CXGN::Fieldbook::DownloadTrial;
  37 use SGN::Model::Cvterm;
  38 use CXGN::List;
  39 use CXGN::List::Validate;
  40 use CXGN::List::Transform;
  41 use Data::Dumper;
  42
  43 BEGIN { extends 'Catalyst::Controller::REST' }
  44
  45 __PACKAGE__->config(
  46     default   => 'application/json',
  47     stash_key => 'rest',
  48     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  49    );
  50
  51
  52 sub create_fieldbook_from_trial : Path('/ajax/fieldbook/create') : ActionClass('REST') { }
  53
  54 sub create_fieldbook_from_trial_POST : Args(0) {
  55   my ($self, $c) = @_;
  56   my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  57   my $trial_id = $c->req->param('trial_id');
  58   my $data_level = $c->req->param('data_level') || 'plots';
  59   my $treatment_project_ids = $c->req->param('treatment_project_id') ? [$c->req->param('treatment_project_id')] : [];
  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             $c->stash->{rest} = {error =>  "Trial does not have plant entries. You must first create plant entries." };
  85             return;
  86         }
  87     }
  88     if ($data_level eq 'subplots' || $data_level eq 'plants_subplots') {
  89         my $trial = CXGN::Trial->new( { bcs_schema => $schema, trial_id => $trial_id });
  90         if (!$trial->has_subplot_entries()) {
  91             $c->stash->{rest} = {error =>  "Trial does not have subplot entries." };
  92             return;
  93         }
  94     }
  95
  96     my $selected_columns = $c->req->param('selected_columns') ? decode_json $c->req->param('selected_columns') : {};
  97     my $selected_trait_list_id = $c->req->param('trait_list');
  98     my @selected_traits;
  99     my @trait_list;
 100     if ($selected_trait_list_id){
 101         my $list = CXGN::List->new({ dbh => $c->dbc->dbh, list_id => $selected_trait_list_id });
 102         @trait_list = @{$list->elements()};
 103         my $validator = CXGN::List::Validate->new();
 104         my @absent_traits = @{$validator->validate($schema, 'traits', \@trait_list)->{'missing'}};
 105         if (scalar(@absent_traits)>0){
 106             $c->stash->{rest} = {error =>  "Trait list is not valid because of these terms: ".join ',',@absent_traits };
 107             $c->detach();
 108         }
 109         my $lt = CXGN::List::Transform->new();
 110         @selected_traits = @{$lt->transform($schema, "traits_2_trait_ids", \@trait_list)->{transform}};
 111     }
 112
 113   my $dir = $c->tempfiles_subdir('/other');
 114   my $tempfile = $c->config->{basepath}."/".$c->tempfile( TEMPLATE => 'other/excelXXXX');
 115
 116     my $create_fieldbook = CXGN::Fieldbook::DownloadTrial->new({
 117         bcs_schema => $schema,
 118         metadata_schema => $metadata_schema,
 119         phenome_schema => $phenome_schema,
 120         trial_id => $trial_id,
 121         tempfile => $tempfile,
 122         archive_path => $c->config->{archive_path},
 123         user_id => $c->user()->get_object()->get_sp_person_id(),
 124         user_name => $c->user()->get_object()->get_username(),
 125         data_level => $data_level,
 126         treatment_project_ids => $treatment_project_ids,
 127         selected_columns => $selected_columns,
 128         selected_trait_ids => \@selected_traits,
 129         selected_trait_names => \@trait_list
 130     });
 131
 132     my $create_fieldbook_return = $create_fieldbook->download();
 133     my $error;
 134     if ($create_fieldbook_return->{'error_messages'}){
 135         $error = join ',', @{$create_fieldbook_return->{'error_messages'}};
 136     }
 137
 138     $c->stash->{rest} = {
 139         error_string => $error,
 140         success => 1,
 141         result => $create_fieldbook_return->{'result'},
 142         file => $create_fieldbook_return->{'file'},
 143         file_id => $create_fieldbook_return->{'file_id'},
 144     };
 145 }
 146
 147 sub create_trait_file_for_field_book : Path('/ajax/fieldbook/traitfile/create') : ActionClass('REST') { }
 148
 149 sub create_trait_file_for_field_book_POST : Args(0) {
 150   my ($self, $c) = @_;
 151
 152   if (!$c->user()) {
 153     $c->stash->{rest} = {error => "You need to be logged in to create a field book" };
 154     return;
 155   }
 156   if (!any { $_ eq "curator" || $_ eq "submitter" } ($c->user()->roles)  ) {
 157     $c->stash->{rest} = {error =>  "You have insufficient privileges to create a field book." };
 158     return;
 159   }
 160
 161   my @trait_list;
 162   my $trait_file_name = $c->req->param('trait_file_name');
 163   my $user_id = $c->user()->get_object()->get_sp_person_id();
 164   my $user_name = $c->user()->get_object()->get_username();
 165   my $time = DateTime->now();
 166   my $timestamp = $time->ymd()."_".$time->hms();
 167   my $subdirectory_name = "tablet_trait_files";
 168   my $archived_file_name = catfile($user_id, $subdirectory_name,$timestamp."_".$trait_file_name.".trt");
 169   my $archive_path = $c->config->{archive_path};
 170   my $file_destination =  catfile($archive_path, $archived_file_name);
 171   my $dbh = $c->dbc->dbh();
 172   my @trait_ids = @{_parse_list_from_json($c->req->param('trait_ids'))};
 173
 174   if ($c->req->param('trait_list')) {
 175     @trait_list = @{_parse_list_from_json($c->req->param('trait_list'))};
 176   }
 177
 178   if (!-d $archive_path) {
 179     mkdir $archive_path;
 180   }
 181
 182   if (! -d catfile($archive_path, $user_id)) {
 183     mkdir (catfile($archive_path, $user_id));
 184   }
 185
 186   if (! -d catfile($archive_path, $user_id,$subdirectory_name)) {
 187     mkdir (catfile($archive_path, $user_id, $subdirectory_name));
 188   }
 189
 190   open FILE, ">$file_destination" or die $!;
 191   my $chado_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 192   print FILE "trait,format,defaultValue,minimum,maximum,details,categories,isVisible,realPosition\n";
 193   my $order = 0;
 194
 195   foreach my $term (@trait_list) {
 196       #print STDERR "term is $term\n";
 197       my @parts = split (/\|/ , $term);
 198       my ($db_name, $accession) = split ":", pop @parts;
 199       my $trait_name = join ("|", @parts);
 200       #print STDERR "trait name is $trait_name, full cvterm accession is $full_cvterm_accession\n";
 201       #my ( $db_name , $accession ) = split (/:/ , $full_cvterm_accession);
 202
 203       $accession =~ s/\s+$//;
 204       $accession =~ s/^\s+//;
 205       $db_name =~ s/\s+$//;
 206       $db_name =~ s/^\s+//;
 207
 208       my $cvterm = CXGN::Chado::Cvterm->new( $dbh, $trait_ids[$order] );
 209       my $synonym = $cvterm->get_uppercase_synonym();
 210       my $name = $synonym || $trait_name; # use uppercase synonym if defined, otherwise use full trait name
 211       $order++;
 212
 213       #get trait info
 214
 215       my $trait_info_lookup = CXGN::Fieldbook::TraitInfo
 216           ->new({
 217               chado_schema    => $chado_schema,
 218               db_name         => $db_name,
 219               trait_accession => $accession,
 220                 });
 221       my $trait_info_string = $trait_info_lookup->get_trait_info($trait_name);
 222
 223       #return error if not $trait_info_string;
 224       #print line with trait info
 225       #print FILE "$trait_name:$db_name:$accession,text,,,,,,TRUE,$order\n";
 226       print STDERR " Adding line \"$name\t\t\t|$db_name:$accession\",$trait_info_string,\"TRUE\",\"$order\" to trait file\n";
 227       print FILE "\"$name\t\t\t|$db_name:$accession\",$trait_info_string,\"TRUE\",\"$order\"\n";
 228   }
 229
 230   close FILE;
 231
 232   open(my $F, "<", $file_destination) || die "Can't open file ";
 233   binmode $F;
 234   my $md5 = Digest::MD5->new();
 235   $md5->addfile($F);
 236   close($F);
 237
 238   my $metadata_schema = $c->dbic_schema('CXGN::Metadata::Schema');
 239
 240   my $md_row = $metadata_schema->resultset("MdMetadata")->create({
 241                                                                   create_person_id => $user_id,
 242                                                                  });
 243   $md_row->insert();
 244
 245   my $file_row = $metadata_schema->resultset("MdFiles")->create({
 246                                                                      basename => basename($file_destination),
 247                                                                      dirname => dirname($file_destination),
 248                                                                      filetype => 'tablet trait file',
 249                                                                      md5checksum => $md5->hexdigest(),
 250                                                                      metadata_id => $md_row->metadata_id(),
 251                                                                     });
 252   $file_row->insert();
 253
 254   my $id = $file_row->file_id();
 255
 256   $c->stash->{rest} = {success => "1", file_id => $id, };
 257
 258 }
 259
 260
 261 sub _parse_list_from_json {
 262   my $list_json = shift;
 263   my $json = new JSON;
 264   if ($list_json) {
 265     my $decoded_list = $json->allow_nonref->utf8->relaxed->escape_slash->loose->allow_singlequote->allow_barekey->decode($list_json);
 266     #my $decoded_list = decode_json($list_json);
 267     my @array_of_list_items = @{$decoded_list};
 268     return \@array_of_list_items;
 269   }
 270   else {
 271     return;
 272   }
 273 }
 274
 275
 276 1;