lib/SGN/Controller/AJAX/TrackingActivity.pm

   1
   2 package SGN::Controller::AJAX::TrackingActivity;
   3
   4 use Moose;
   5 use CXGN::Stock::Order;
   6 use CXGN::Stock::OrderBatch;
   7 use Data::Dumper;
   8 use JSON;
   9 use DateTime;
  10 use CXGN::People::Person;
  11 use CXGN::Contact;
  12 use CXGN::Trial::Download;
  13 use CXGN::TrackingActivity::AddTrackingIdentifier;
  14 use CXGN::TrackingActivity::ActivityInfo;
  15 use CXGN::TrackingActivity::AddActivityProject;
  16 use CXGN::TrackingActivity::ActivityProject;
  17 use CXGN::TrackingActivity::TrackingIdentifier;
  18 use CXGN::Transformation::CreateAutogeneratedNames;
  19 use SGN::Model::Cvterm;
  20 use CXGN::Location::LocationLookup;
  21 use CXGN::List;
  22 use CXGN::Stock::Status;
  23
  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 File::Path qw(make_path);
  30 use File::Spec::Functions qw / catfile catdir/;
  31
  32 use LWP::UserAgent;
  33 use LWP::Simple;
  34 use HTML::Entities;
  35 use URI::Encode qw(uri_encode uri_decode);
  36 use Tie::UrlEncoder; our(%urlencode);
  37
  38
  39 BEGIN { extends 'Catalyst::Controller::REST' }
  40
  41 __PACKAGE__->config(
  42     default   => 'application/json',
  43     stash_key => 'rest',
  44     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  45    );
  46
  47
  48 sub create_tracking_activity_project : Path('/ajax/tracking_activity/create_tracking_activity_project') : ActionClass('REST'){ }
  49
  50 sub create_tracking_activity_project_POST : Args(0) {
  51     my $self = shift;
  52     my $c = shift;
  53
  54     my $user = $c->user();
  55     if (!$user) {
  56         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
  57         return;
  58     }
  59
  60     if (!($user->has_role('submitter') or $user->has_role('curator'))) {
  61         $c->stash->{rest} = { error => "You do not have sufficient privileges to create tracking activity project." };
  62         return;
  63     }
  64
  65     my $user_id = $c->user()->get_object()->get_sp_person_id();
  66     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  67     my $dbh = $c->dbc->dbh;
  68
  69     my $project_name = $c->req->param("project_name");
  70     my $activity_type = $c->req->param("activity_type");
  71     my $breeding_program_id = $c->req->param("breeding_program");
  72     my $project_location = $c->req->param("project_location");
  73     my $year = $c->req->param("year");
  74     my $project_description = $c->req->param("project_description");
  75
  76     my $geolocation_lookup = CXGN::Location::LocationLookup->new(schema =>$schema);
  77     $geolocation_lookup->set_location_name($project_location);
  78     if(!$geolocation_lookup->get_geolocation()){
  79         $c->stash->{rest}={error => "Location not found"};
  80         return;
  81     }
  82
  83     my $return;
  84     eval{
  85         my $add_activity_project = CXGN::TrackingActivity::AddActivityProject->new({
  86             bcs_schema => $schema,
  87             dbh => $dbh,
  88             breeding_program_id => $breeding_program_id,
  89             year => $year,
  90             project_description => $project_description,
  91             activity_project_name => $project_name,
  92             activity_type => $activity_type,
  93             nd_geolocation_id => $geolocation_lookup->get_geolocation()->nd_geolocation_id(),
  94             owner_id => $user_id
  95         });
  96
  97         $return = $add_activity_project->save_activity_project();
  98     };
  99
 100     if (!$return){
 101         $c->stash->{rest} = {error => "Error saving project",};
 102         return;
 103     }
 104
 105     if ($return->{error}){
 106         $c->stash->{rest} = {error => $return->{error}};
 107         return;
 108     }
 109
 110     if ($@) {
 111         $c->stash->{rest} = {error => $@};
 112         return;
 113     } else {
 114         $c->stash->{rest} = {success => 1};
 115     }
 116
 117
 118 }
 119
 120
 121 sub generate_tracking_identifiers : Path('/ajax/tracking_activity/generate_tracking_identifiers') : ActionClass('REST'){ }
 122
 123 sub generate_tracking_identifiers_POST : Args(0) {
 124     my $self = shift;
 125     my $c = shift;
 126
 127     if (!$c->user()) {
 128         $c->stash->{rest} = { error => "You must be logged in to generate tracking identifiers." };
 129         return;
 130     }
 131     if (!($c->user()->has_role('submitter') or $c->user()->has_role('curator'))) {
 132         $c->stash->{rest} = { error => "You do not have sufficient privileges to generate tracking identifiers." };
 133         return;
 134     }
 135
 136     my $user_id = $c->user()->get_object()->get_sp_person_id();
 137     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 138     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema");
 139     my $dbh = $c->dbc->dbh();
 140
 141     my $project_name = $c->req->param("project_name");
 142     my $list_id = $c->req->param("list_id");
 143     my $project_id;
 144     my $project_rs = $schema->resultset("Project::Project")->find( { name => $project_name });
 145     if (!$project_rs) {
 146         $c->stash->{rest} = { error => "Error! Project name: $project_name was not found in the database.\n" };
 147         return;
 148     } else {
 149         $project_id = $project_rs->project_id();
 150     }
 151
 152     my $activity_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 153     my $all_identifiers = $activity_project->get_project_active_identifiers();
 154     my $last_number = scalar (@$all_identifiers);
 155
 156     my $list = CXGN::List->new( { dbh=>$dbh, list_id=>$list_id });
 157     my $material_names = $list->elements();
 158
 159     my @check_identifier_names;
 160     my @tracking_identifiers;
 161     my @error_messages;
 162     foreach my $name (sort @$material_names) {
 163         $last_number++;
 164 #        my $tracking_id = $project_name.":".$name."_"."T".(sprintf "%04d", $last_number);
 165         my $tracking_id = $project_name.":".$name."_"."T".$last_number;
 166         push @tracking_identifiers, [$tracking_id, $name];
 167         push @check_identifier_names, $tracking_id;
 168     }
 169
 170     my $rs = $schema->resultset("Stock::Stock")->search({
 171         'is_obsolete' => { '!=' => 't' },
 172         'uniquename' => { -in => \@check_identifier_names }
 173     });
 174     while (my $r=$rs->next){
 175         push @error_messages, "Tracking identifier name already exists in database: ".$r->uniquename;
 176     }
 177
 178     if (scalar(@error_messages) >= 1) {
 179         $c->stash->{rest} = { error => \@error_messages};
 180         return;
 181     }
 182
 183     foreach my $identifier_info (@tracking_identifiers) {
 184         my $tracking_identifier = $identifier_info->[0];
 185         my $material = $identifier_info->[1];
 186
 187         my $tracking_obj = CXGN::TrackingActivity::AddTrackingIdentifier->new({
 188             schema => $schema,
 189             phenome_schema => $phenome_schema,
 190             tracking_identifier => $tracking_identifier,
 191             material => $material,
 192             project_id => $project_id,
 193             user_id => $user_id
 194          });
 195
 196         my $return = $tracking_obj->store();
 197         if (!$return) {
 198             $c->stash->{rest} = {error => "Error generating tracking identifier"};
 199             return;
 200         } elsif ($return->{error}) {
 201             my $error = $return->{error};
 202             $c->stash->{rest} = {error => $error};
 203             return;
 204         }
 205     }
 206
 207     $c->stash->{rest} = { success => 1};
 208
 209 }
 210
 211
 212 sub activity_info_save : Path('/ajax/tracking_activity/save') : ActionClass('REST'){ }
 213
 214 sub activity_info_save_POST : Args(0) {
 215     my $self = shift;
 216     my $c = shift;
 217
 218     if (!$c->user()) {
 219         $c->stash->{rest} = { error => "You must be logged in to add new information." };
 220         return;
 221     }
 222     if (!($c->user()->has_role('submitter') or $c->user()->has_role('curator'))) {
 223         $c->stash->{rest} = { error => "You do not have sufficient privileges to record new information." };
 224         return;
 225     }
 226
 227     my $user_id = $c->user()->get_object()->get_sp_person_id();
 228
 229     my $tracking_identifier = $c->req->param("tracking_identifier_name");
 230     my $tracking_identifier_id = $c->req->param("tracking_identifier_id");
 231     my $selected_type = $c->req->param("selected_type");
 232     my $input = $c->req->param("input");
 233     my $notes = $c->req->param("notes");
 234     my $record_timestamp = $c->req->param("record_timestamp");
 235     my $tracking_transformation = $c->config->{tracking_transformation};
 236
 237     if ($selected_type =~ m/number/ && !($input =~ /^\d+?$/) ) {
 238         $c->stash->{rest} = {error => "Input is not a positive integer"};
 239         return;
 240     }
 241
 242     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 243     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema");
 244     my $dbh = $c->dbc->dbh();
 245     my $number_of_transformants;
 246     if (($selected_type eq 'number_of_transformants') && $tracking_transformation) {
 247         $number_of_transformants = $input;
 248         my $tracking_identifier_obj = CXGN::TrackingActivity::TrackingIdentifier->new({schema => $schema, dbh => $dbh, tracking_identifier_stock_id => $tracking_identifier_id});
 249         my $project_and_program_info = $tracking_identifier_obj->get_associated_project_program();
 250         my $program_id = $project_and_program_info->[0]->[2];
 251         my $linked_project_id = $project_and_program_info->[0]->[4];
 252         my $autogenerated_name_prefix_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'autogenerated_name_prefix', 'project_property')->cvterm_id();
 253         my $material_of_type_id  =  SGN::Model::Cvterm->get_cvterm_row($schema, 'material_of', 'stock_relationship')->cvterm_id;
 254         if ($linked_project_id) {
 255             my $new_names_info;
 256             my $stored_prefix = $schema->resultset('Project::Projectprop')->find({ project_id => $linked_project_id, type_id => $autogenerated_name_prefix_cvterm_id});
 257             if ($stored_prefix) {
 258                 my $prefix = $stored_prefix->value();
 259                 my $autogenerated_names = CXGN::Transformation::CreateAutogeneratedNames->new({schema => $schema, dbh => $dbh, breeding_program_id => $program_id, prefix => $prefix, number_of_names => $number_of_transformants });
 260                 $new_names_info = $autogenerated_names->create_names();
 261                 print STDERR "NEW NAMES INFO=".Dumper($new_names_info)."\n";
 262                 my $new_names = $new_names_info->{'new_autogenerated_names'};
 263                 my $new_current_serial_number = $new_names_info->{'new_current_serial_number'};
 264
 265                 my $transformation_stock_id = $schema->resultset("Stock::StockRelationship")->find({object_id=>$tracking_identifier_id, type_id=>$material_of_type_id})->subject_id();
 266                 my $add_transformants = CXGN::Transformation::AddTransformant->new({
 267                     schema => $schema,
 268                     phenome_schema => $phenome_schema,
 269                     dbh => $dbh,
 270                     transformation_stock_id => $transformation_stock_id,
 271                     transformant_names => $new_names,
 272                     owner_id => $user_id,
 273                 });
 274
 275                 $add_transformants->add_transformant();
 276
 277                 my $name_metadata_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'autogenerated_name_metadata', 'project_property');
 278                 my $program = $schema->resultset('Project::Project')->find({ project_id => $program_id});
 279                 my $metadata_projectprop_rs = $program->projectprops({type_id => $name_metadata_cvterm->cvterm_id});
 280                 if ($metadata_projectprop_rs->count == 1){
 281                     my $stored_name_metadata_string = $metadata_projectprop_rs->first->value();
 282                     my $name_metadata_hash = decode_json $stored_name_metadata_string;
 283                     print STDERR "PREVIOUS METADATA =".Dumper($name_metadata_hash)."\n";
 284                     $name_metadata_hash->{$prefix}->{'current_serial_number'} = $new_current_serial_number;
 285                     my $new_name_metadata_string = encode_json $name_metadata_hash;
 286                     print STDERR "UPDATED METADATA =".Dumper($name_metadata_hash)."\n";
 287                     $metadata_projectprop_rs->first->update({value=>$new_name_metadata_string});
 288                 }
 289             }
 290         }
 291
 292     }
 293
 294     my $add_activity_info = CXGN::TrackingActivity::ActivityInfo->new({
 295         schema => $schema,
 296         tracking_identifier => $tracking_identifier,
 297         selected_type => $selected_type,
 298         input => $input,
 299         timestamp => $record_timestamp,
 300         operator_id => $user_id,
 301         notes => $notes,
 302     });
 303     my $return = $add_activity_info->add_info();
 304 #    print STDERR "ADD INFO =".Dumper ($add_activity_info->add_info())."\n";
 305
 306     if (!$return){
 307         $c->stash->{rest} = {error => "Error saving info",};
 308         return;
 309     } else {
 310         $c->stash->{rest} = $return;
 311     }
 312
 313 }
 314
 315
 316 sub get_activity_details :Path('/ajax/tracking_activity/details') :Args(1) {
 317     my $self = shift;
 318     my $c = shift;
 319     my $identifier_id = shift;
 320     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 321     my $dbh = $c->dbc->dbh;
 322
 323     my $tracking_identifier_obj = CXGN::TrackingActivity::TrackingIdentifier->new({schema=>$schema, dbh=>$dbh, tracking_identifier_stock_id=>$identifier_id});
 324     my $associated_projects = $tracking_identifier_obj->get_associated_project_program();
 325     my $tracking_project_id = $associated_projects->[0]->[0];
 326     my $tracking_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $tracking_project_id);
 327     my $activity_type = $tracking_project->get_project_activity_type();
 328
 329     my $tracking_activities;
 330     if ($activity_type eq 'tissue_culture') {
 331         $tracking_activities = $c->config->{tracking_tissue_culture_info};
 332     } elsif ($activity_type eq 'transformation') {
 333         $tracking_activities = $c->config->{tracking_transformation_info};
 334     }
 335
 336     my @details;
 337     my @activity_types = split ',',$tracking_activities;
 338
 339     my $tracking_data_json_cvterm_id  =  SGN::Model::Cvterm->get_cvterm_row($schema, 'tracking_tissue_culture_json', 'stock_property')->cvterm_id();
 340     my $activity_info_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $identifier_id, type_id => $tracking_data_json_cvterm_id});
 341     if ($activity_info_rs) {
 342         my $activity_json = $activity_info_rs->value();
 343         my $info = JSON::Any->jsonToObj($activity_json);
 344         my %info_hash = %{$info};
 345         foreach my $type (@activity_types){
 346             my $empty_string;
 347             my @each_type_details = ();
 348             my $each_timestamp_string;
 349             my $each_type_string;
 350             if ($info_hash{$type}) {
 351                 my @each_type_details = ();
 352                 my $details = {};
 353                 my %details_hash = ();
 354                 $details = $info_hash{$type};
 355                 %details_hash = %{$details};
 356 #                print STDERR "DETAILS HASH =".Dumper(\%details_hash);
 357                 foreach my $timestamp (sort keys %details_hash) {
 358                     my @each_timestamp_details = ();
 359                     push @each_timestamp_details, "timestamp".":"."".$timestamp;
 360                     my $operator_id = $details_hash{$timestamp}{'operator_id'};
 361
 362                     my $person= CXGN::People::Person->new($dbh, $operator_id);
 363                     my $operator_name = $person->get_first_name()." ".$person->get_last_name();
 364
 365                     push @each_timestamp_details, "operator".":"."".$operator_name;
 366                     my $input = $details_hash{$timestamp}{'input'};
 367                     push @each_timestamp_details, "input".":"."".$input;
 368                     my $notes = $details_hash{$timestamp}{'notes'};
 369                     push @each_timestamp_details, "notes".":"."".$notes;
 370
 371                     push @each_timestamp_details, $empty_string;
 372
 373                     $each_timestamp_string = join("<br>", @each_timestamp_details);
 374                     push @each_type_details, $each_timestamp_string;
 375                 }
 376
 377                 $each_type_string = join("<br>", @each_type_details);
 378 #                print STDERR "EACH TYPE STRING =".Dumper($each_type_string)."\n";
 379                 push @details, $each_type_string;
 380             } else {
 381                 my $empty_string;
 382                 push @details, $empty_string;
 383             }
 384         }
 385     } else {
 386         foreach my $type (@activity_types) {
 387             push @details, 'NA';
 388         }
 389     }
 390
 391     my @all_details;
 392     push @all_details, [@details];
 393
 394 #    print STDERR "ALL DETAILS =".Dumper(\@all_details)."\n";
 395
 396     $c->stash->{rest} = { data => \@all_details };
 397
 398 }
 399
 400
 401 sub get_activity_summary :Path('/ajax/tracking_activity/summary') :Args(1) {
 402     my $self = shift;
 403     my $c = shift;
 404     my $identifier_id = shift;
 405     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 406     my $dbh = $c->dbc->dbh;
 407
 408     my $tracking_identifier_obj = CXGN::TrackingActivity::TrackingIdentifier->new({schema=>$schema, dbh=>$dbh, tracking_identifier_stock_id=>$identifier_id});
 409     my $associated_projects = $tracking_identifier_obj->get_associated_project_program();
 410     my $tracking_project_id = $associated_projects->[0]->[0];
 411     my $tracking_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $tracking_project_id);
 412     my $activity_type = $tracking_project->get_project_activity_type();
 413
 414     my $tracking_activities;
 415     if ($activity_type eq 'tissue_culture') {
 416         $tracking_activities = $c->config->{tracking_tissue_culture_info};
 417     } elsif ($activity_type eq 'transformation') {
 418         $tracking_activities = $c->config->{tracking_transformation_info};
 419     }
 420
 421     my @summary = ();
 422     my @activity_types = split ',',$tracking_activities;
 423
 424     my $tracking_data_json_cvterm_id  =  SGN::Model::Cvterm->get_cvterm_row($schema, 'tracking_tissue_culture_json', 'stock_property')->cvterm_id();
 425     my $activity_info_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $identifier_id, type_id => $tracking_data_json_cvterm_id});
 426     if ($activity_info_rs) {
 427         my $activity_json = $activity_info_rs->value();
 428         my $info = JSON::Any->jsonToObj($activity_json);
 429         my %info_hash = %{$info};
 430         foreach my $type (@activity_types){
 431             my $input = '';
 432             my $empty_string;
 433             my @each_type_details = ();
 434             my $each_timestamp_string;
 435             my $each_type_string;
 436             if ($info_hash{$type}) {
 437                 my $details = {};
 438                 my %details_hash = ();
 439                 $details = $info_hash{$type};
 440                 %details_hash = %{$details};
 441
 442                 if (($type =~ m/number/) || ($type =~ m/count/)) {
 443                     $input = 0;
 444                     foreach my $key (keys %details_hash) {
 445                         $input += $details_hash{$key}{'input'};
 446                     }
 447                     push @summary, $input;
 448                 } elsif ($type =~ m/date/) {
 449                     foreach my $key (keys %details_hash) {
 450                         $input = $details_hash{$key}{'input'};
 451                     }
 452                     push @summary, $input;
 453                 }
 454             } else {
 455                 push @summary, $input;
 456             }
 457         }
 458     } else {
 459         foreach my $type (@activity_types) {
 460             push @summary, 'NA';
 461         }
 462     }
 463
 464     my @all_summary;
 465     push @all_summary, [@summary];
 466
 467     $c->stash->{rest} = { data => \@all_summary };
 468
 469 }
 470
 471 sub get_project_active_identifiers :Path('/ajax/tracking_activity/project_active_identifiers') :Args(1) {
 472     my $self = shift;
 473     my $c = shift;
 474     my $project_id = shift;
 475     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 476
 477     my $tracking_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 478     my $activity_type = $tracking_project->get_project_activity_type();
 479
 480     my $tracking_activities;
 481     if ($activity_type eq 'tissue_culture') {
 482         $tracking_activities = $c->config->{tracking_tissue_culture_info};
 483     } elsif ($activity_type eq 'transformation') {
 484         $tracking_activities = $c->config->{tracking_transformation_info};
 485     }
 486
 487     my @activity_types = split ',',$tracking_activities;
 488     my $transformation_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation", 'stock_type')->cvterm_id();
 489
 490     my $activity_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 491     my $all_identifier_info = $activity_project->get_project_active_identifiers();
 492     my @all_identifiers;
 493     foreach my $identifier_info (@$all_identifier_info) {
 494         my @row = ();
 495         my $identifier_id = $identifier_info->[0];
 496         my $identifier_name = $identifier_info->[1];
 497         push @row, qq{<a href="/activity/details/$identifier_id">$identifier_name</a>};
 498
 499         my $material_id = $identifier_info->[2];
 500         my $material_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $material_id });
 501         my $material_stock_type_id = $material_rs->type_id;
 502         my $material_name = $identifier_info->[3];
 503         if ($material_stock_type_id == $transformation_type_id) {
 504             push @row, qq{<a href="/transformation/$material_id">$material_name</a>}
 505         } else {
 506             push @row, qq{<a href="/stock/$material_id/view">$material_name</a>};
 507         }
 508         my $progress = $identifier_info->[5];
 509         if ($progress) {
 510             my $progress_ref = JSON::Any->jsonToObj($progress);
 511             my %progress_hash = %{$progress_ref};
 512             foreach my $type (@activity_types){
 513                 my $input = '';
 514                 if ($progress_hash{$type}) {
 515                     my $details = {};
 516                     my %details_hash = ();
 517                     $details = $progress_hash{$type};
 518                     %details_hash = %{$details};
 519
 520                     if (($type =~ m/number/) || ($type =~ m/count/)) {
 521                         $input = 0;
 522                         foreach my $key (keys %details_hash) {
 523                             $input += $details_hash{$key}{'input'};
 524                         }
 525                         push @row, $input;
 526                     } elsif ($type =~ m/date/) {
 527                         foreach my $key (keys %details_hash) {
 528                             $input = $details_hash{$key}{'input'};
 529                         }
 530                         push @row, $input;
 531                     }
 532                 } else {
 533                     push @row, $input;
 534                 }
 535             }
 536         } else {
 537             foreach my $type (@activity_types) {
 538                 push @row, '';
 539             }
 540         }
 541         push @row, $identifier_name;
 542         push @all_identifiers,[@row];
 543     }
 544
 545     $c->stash->{rest} = { data => \@all_identifiers };
 546
 547 }
 548
 549
 550 sub get_project_active_identifier_names :Path('/ajax/tracking_activity/project_active_identifier_names') :Args(1) {
 551     my $self = shift;
 552     my $c = shift;
 553     my $project_id = shift;
 554     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 555
 556     my $activity_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 557     my $all_identifier_info = $activity_project->get_project_active_identifiers();
 558     my @identifier_names;
 559     foreach my $identifier_info (@$all_identifier_info) {
 560         push @identifier_names, $identifier_info->[1];
 561     }
 562
 563     $c->stash->{rest} = { data => \@identifier_names };
 564
 565 }
 566
 567
 568 sub update_status : Path('/ajax/tracking_activity/update_status') : ActionClass('REST'){ }
 569
 570 sub update_status_POST : Args(0) {
 571     my $self = shift;
 572     my $c = shift;
 573     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 574     my $dbh = $c->dbc->dbh();
 575     my $identifier_id = $c->req->param("identifier_id");
 576     my $status_type = $c->req->param("status_type");
 577     my $comments = $c->req->param("comments");
 578     my $material_id = $c->req->param("material_id");
 579     my $time = DateTime->now();
 580     my $update_date = $time->ymd();
 581     my @stocks_to_update;
 582
 583     if (!$c->user()){
 584         $c->stash->{rest} = { error_string => "You must be logged in to update status" };
 585         return;
 586     }
 587     if (!$c->user()->check_roles("curator")) {
 588         $c->stash->{rest} = { error_string => "You do not have the correct role to update status. Please contact us." };
 589         return;
 590     }
 591
 592     my $user_id = $c->user()->get_object()->get_sp_person_id();
 593
 594     my $tracking_identifier_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "tracking_identifier", 'stock_type')->cvterm_id();
 595     my $transformation_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation", 'stock_type')->cvterm_id();
 596
 597     my $identifier_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $identifier_id, type_id => $tracking_identifier_type_id });
 598     if (!$identifier_rs) {
 599         $c->stash->{rest} = { error_string => 'Error. No tracking identifier entry found in the database.' };
 600             return;
 601     } else {
 602         push @stocks_to_update, $identifier_id;
 603     }
 604
 605     my $material_stock_type_id;
 606     my $material_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $material_id });
 607     if (!$material_rs) {
 608         $c->stash->{rest} = { error_string => 'Error. No material entry found in the database.' };
 609         return;
 610     } else {
 611        $material_stock_type_id = $material_rs->type_id;
 612     }
 613
 614     if ($material_stock_type_id == $transformation_type_id) {
 615         push @stocks_to_update, $material_id;
 616     }
 617
 618     my $completed_metadata;
 619     my $terminated_metadata;
 620     if ($status_type eq 'completed') {
 621         $completed_metadata = 1;
 622     } elsif ($status_type eq 'terminated') {
 623         $terminated_metadata = 1;
 624     }
 625
 626     foreach my $stock_id (@stocks_to_update) {
 627         my $update_status = CXGN::Stock::Status->new({
 628             bcs_schema => $schema,
 629             parent_id => $stock_id,
 630             person_id => $user_id,
 631             update_date => $update_date,
 632             comments => $comments,
 633             completed_metadata => $completed_metadata,
 634             terminated_metadata => $terminated_metadata
 635         });
 636
 637         $update_status->store();
 638
 639         if (!$update_status->store()){
 640             $c->stash->{rest} = {error_string => "Error updating status"};
 641             return;
 642         }
 643     }
 644
 645     $c->stash->{rest} = {success => "1",};
 646
 647 }
 648
 649 sub reverse_status : Path('/ajax/tracking_activity/reverse_status') : ActionClass('REST'){ }
 650
 651 sub reverse_status_POST : Args(0) {
 652     my $self = shift;
 653     my $c = shift;
 654     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 655     my $dbh = $c->dbc->dbh();
 656     my $identifier_id = $c->req->param("identifier_id");
 657     my $updated_status_type = $c->req->param("updated_status_type");
 658     my $material_id = $c->req->param("material_id");
 659
 660     if (!$c->user()){
 661         $c->stash->{rest} = { error_string => "You must be logged in to reverse status of this tracking identifier" };
 662         return;
 663     }
 664     if (!$c->user()->check_roles("curator")) {
 665         $c->stash->{rest} = { error_string => "You do not have the correct role to reverse status of this tracking identifier. Please contact us." };
 666         return;
 667     }
 668
 669     my $user_id = $c->user()->get_object()->get_sp_person_id();
 670
 671     my $status_type_id;
 672     if ($updated_status_type) {
 673         $status_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, $updated_status_type, 'stock_property')->cvterm_id();
 674         my $status_stockprop_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $identifier_id, type_id => $status_type_id});
 675
 676         if (defined $status_stockprop_rs->stockprop_id) {
 677             $status_stockprop_rs->delete();
 678         }
 679     }
 680
 681     my $material_stock_type_id;
 682     my $material_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $material_id });
 683     if (!$material_rs) {
 684         $c->stash->{rest} = { error_string => 'Error. No material entry found in the database.' };
 685         return;
 686     } else {
 687        $material_stock_type_id = $material_rs->type_id;
 688     }
 689
 690     my $transformation_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation", 'stock_type')->cvterm_id();
 691
 692     if ($material_stock_type_id == $transformation_type_id) {
 693         if ($status_type_id) {
 694             my $transformation_stockprop_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $material_id, type_id => $status_type_id});
 695
 696             if (defined $transformation_stockprop_rs->stockprop_id) {
 697                 $transformation_stockprop_rs->delete();
 698             }
 699         }
 700     }
 701
 702     $c->stash->{rest} = { success => 1 };
 703
 704 }
 705
 706
 707 sub get_project_inactive_identifiers :Path('/ajax/tracking_activity/project_inactive_identifiers') :Args(1) {
 708     my $self = shift;
 709     my $c = shift;
 710     my $project_id = shift;
 711     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 712
 713     my $tracking_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 714     my $activity_type = $tracking_project->get_project_activity_type();
 715
 716     my $tracking_activities;
 717     if ($activity_type eq 'tissue_culture') {
 718         $tracking_activities = $c->config->{tracking_tissue_culture_info};
 719     } elsif ($activity_type eq 'transformation') {
 720         $tracking_activities = $c->config->{tracking_transformation_info};
 721     }
 722
 723     my @activity_types = split ',',$tracking_activities;
 724
 725     my $transformation_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation", 'stock_type')->cvterm_id();
 726
 727     my $activity_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 728     my $all_identifier_info = $activity_project->get_project_inactive_identifiers();
 729     my @all_identifiers;
 730     foreach my $identifier_info (@$all_identifier_info) {
 731         my @row = ();
 732         my $identifier_id = $identifier_info->[0];
 733         my $identifier_name = $identifier_info->[1];
 734         push @row, qq{<a href="/activity/details/$identifier_id">$identifier_name</a>};
 735
 736         my $status = $identifier_info->[6];
 737         if ($status eq 'terminated_metadata') {
 738             $status = '<span style="color:red">'.'TERMINATED'.'</span>';
 739         } elsif ($status eq 'completed_metadata') {
 740             $status = '<span style="color:red">'.'COMPLETED'.'</span>';
 741         }
 742         push @row, $status;
 743
 744         my $material_id = $identifier_info->[2];
 745         my $material_name = $identifier_info->[3];
 746         my $material_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $material_id });
 747         my $material_stock_type_id = $material_rs->type_id;
 748         if ($material_stock_type_id == $transformation_type_id) {
 749             push @row, qq{<a href="/transformation/$material_id">$material_name</a>}
 750         } else {
 751             push @row, qq{<a href="/stock/$material_id/view">$material_name</a>};
 752         }
 753
 754         my $progress = $identifier_info->[5];
 755         if ($progress) {
 756             my $progress_ref = JSON::Any->jsonToObj($progress);
 757             my %progress_hash = %{$progress_ref};
 758             foreach my $type (@activity_types){
 759                 my $input = '';
 760                 if ($progress_hash{$type}) {
 761                     my $details = {};
 762                     my %details_hash = ();
 763                     $details = $progress_hash{$type};
 764                     %details_hash = %{$details};
 765
 766                     if (($type =~ m/number/) || ($type =~ m/count/)) {
 767                         $input = 0;
 768                         foreach my $key (keys %details_hash) {
 769                             $input += $details_hash{$key}{'input'};
 770                         }
 771                         push @row, $input;
 772                     } elsif ($type =~ m/date/) {
 773                         foreach my $key (keys %details_hash) {
 774                             $input = $details_hash{$key}{'input'};
 775                         }
 776                         push @row, $input;
 777                     }
 778                 } else {
 779                     push @row, $input;
 780                 }
 781             }
 782         } else {
 783             foreach my $type (@activity_types) {
 784                 push @row, '';
 785             }
 786         }
 787         push @row, $identifier_name;
 788         push @all_identifiers,[@row];
 789     }
 790
 791     $c->stash->{rest} = { data => \@all_identifiers };
 792
 793 }
 794
 795
 796
 797
 798 1;