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