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 CXGN::Transformation::Transformation;
  20 use SGN::Model::Cvterm;
  21 use CXGN::Location::LocationLookup;
  22 use CXGN::List;
  23 use CXGN::Stock::Status;
  24
  25 use File::Basename qw | basename dirname|;
  26 use File::Copy;
  27 use File::Slurp;
  28 use File::Spec::Functions;
  29 use Digest::MD5;
  30 use File::Path qw(make_path);
  31 use File::Spec::Functions qw / catfile catdir/;
  32
  33 use LWP::UserAgent;
  34 use LWP::Simple;
  35 use HTML::Entities;
  36 use URI::Encode qw(uri_encode uri_decode);
  37 use Tie::UrlEncoder; our(%urlencode);
  38
  39
  40 BEGIN { extends 'Catalyst::Controller::REST' }
  41
  42 __PACKAGE__->config(
  43     default   => 'application/json',
  44     stash_key => 'rest',
  45     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  46    );
  47
  48
  49 sub create_tracking_activity_project : Path('/ajax/tracking_activity/create_tracking_activity_project') : ActionClass('REST'){ }
  50
  51 sub create_tracking_activity_project_POST : Args(0) {
  52     my $self = shift;
  53     my $c = shift;
  54     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  55     my $dbh = $c->dbc->dbh;
  56     my $project_name = $c->req->param("project_name");
  57     my $activity_type = $c->req->param("activity_type");
  58     my $breeding_program_id = $c->req->param("breeding_program");
  59     my $project_location = $c->req->param("project_location");
  60     my $year = $c->req->param("year");
  61     my $project_description = $c->req->param("project_description");
  62
  63     my $user = $c->user();
  64     if (!$user) {
  65         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
  66         return;
  67     }
  68
  69     if (!($user->has_role('submitter') or $user->has_role('curator'))) {
  70         $c->stash->{rest} = { error => "You do not have sufficient privileges to create tracking activity project." };
  71         return;
  72     }
  73
  74     my $program_name = $schema->resultset('Project::Project')->find({project_id => $breeding_program_id})->name();
  75     my @user_roles = $c->user->roles();
  76     my %has_roles = ();
  77     map { $has_roles{$_} = 1; } @user_roles;
  78
  79     if (! ( (exists($has_roles{$program_name}) && exists($has_roles{submitter})) || exists($has_roles{curator}))) {
  80         $c->stash->{rest} = { error => "You need to be either a curator, or a submitter associated with breeding program $program_name to add tracking project." };
  81         return;
  82     }
  83
  84     my $user_id = $c->user()->get_object()->get_sp_person_id();
  85
  86     my $geolocation_lookup = CXGN::Location::LocationLookup->new(schema =>$schema);
  87     $geolocation_lookup->set_location_name($project_location);
  88     if(!$geolocation_lookup->get_geolocation()){
  89         $c->stash->{rest}={error => "Location not found"};
  90         return;
  91     }
  92
  93     my $return;
  94     eval{
  95         my $add_activity_project = CXGN::TrackingActivity::AddActivityProject->new({
  96             bcs_schema => $schema,
  97             dbh => $dbh,
  98             breeding_program_id => $breeding_program_id,
  99             year => $year,
 100             project_description => $project_description,
 101             activity_project_name => $project_name,
 102             activity_type => $activity_type,
 103             nd_geolocation_id => $geolocation_lookup->get_geolocation()->nd_geolocation_id(),
 104             owner_id => $user_id
 105         });
 106
 107         $return = $add_activity_project->save_activity_project();
 108     };
 109
 110     if (!$return){
 111         $c->stash->{rest} = {error => "Error saving project",};
 112         return;
 113     }
 114
 115     if ($return->{error}){
 116         $c->stash->{rest} = {error => $return->{error}};
 117         return;
 118     }
 119
 120     if ($@) {
 121         $c->stash->{rest} = {error => $@};
 122         return;
 123     } else {
 124         $c->stash->{rest} = {success => 1};
 125     }
 126
 127
 128 }
 129
 130
 131 sub generate_tracking_identifiers : Path('/ajax/tracking_activity/generate_tracking_identifiers') : ActionClass('REST'){ }
 132
 133 sub generate_tracking_identifiers_POST : Args(0) {
 134     my $self = shift;
 135     my $c = shift;
 136     my $project_name = $c->req->param("project_name");
 137     my $list_id = $c->req->param("list_id");
 138     my $program_name = $c->req->param("program_name");
 139
 140     if (!$c->user()) {
 141         $c->stash->{rest} = { error => "You must be logged in to generate tracking identifiers." };
 142         return;
 143     }
 144     if (!($c->user()->has_role('submitter') or $c->user()->has_role('curator'))) {
 145         $c->stash->{rest} = { error => "You do not have sufficient privileges to add tracking identifiers." };
 146         return;
 147     }
 148
 149     my @user_roles = $c->user->roles();
 150     my %has_roles = ();
 151     map { $has_roles{$_} = 1; } @user_roles;
 152
 153     if (! ( (exists($has_roles{$program_name}) && exists($has_roles{submitter})) || exists($has_roles{curator}))) {
 154         $c->stash->{rest} = { error => "You need to be either a curator, or a submitter associated with breeding program $program_name to add tracking identifiers." };
 155         return;
 156     }
 157
 158     my $user_id = $c->user()->get_object()->get_sp_person_id();
 159     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 160     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema");
 161     my $dbh = $c->dbc->dbh();
 162
 163     my $project_id;
 164     my $project_rs = $schema->resultset("Project::Project")->find( { name => $project_name });
 165     if (!$project_rs) {
 166         $c->stash->{rest} = { error => "Error! Project name: $project_name was not found in the database.\n" };
 167         return;
 168     } else {
 169         $project_id = $project_rs->project_id();
 170     }
 171
 172     my $activity_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 173     my $all_identifiers = $activity_project->get_project_active_identifiers();
 174     my $last_number = scalar (@$all_identifiers);
 175
 176     my $list = CXGN::List->new( { dbh=>$dbh, list_id=>$list_id });
 177     my $material_names = $list->elements();
 178
 179     my @check_identifier_names;
 180     my @tracking_identifiers;
 181     my @error_messages;
 182     foreach my $name (sort @$material_names) {
 183         $last_number++;
 184 #        my $tracking_id = $project_name.":".$name."_"."T".(sprintf "%04d", $last_number);
 185         my $tracking_id = $project_name.":".$name."_"."T".$last_number;
 186         push @tracking_identifiers, [$tracking_id, $name];
 187         push @check_identifier_names, $tracking_id;
 188     }
 189
 190     my $rs = $schema->resultset("Stock::Stock")->search({
 191         'is_obsolete' => { '!=' => 't' },
 192         'uniquename' => { -in => \@check_identifier_names }
 193     });
 194     while (my $r=$rs->next){
 195         push @error_messages, "Tracking identifier name already exists in database: ".$r->uniquename;
 196     }
 197
 198     if (scalar(@error_messages) >= 1) {
 199         $c->stash->{rest} = { error => \@error_messages};
 200         return;
 201     }
 202
 203     foreach my $identifier_info (@tracking_identifiers) {
 204         my $tracking_identifier = $identifier_info->[0];
 205         my $material = $identifier_info->[1];
 206
 207         my $tracking_obj = CXGN::TrackingActivity::AddTrackingIdentifier->new({
 208             schema => $schema,
 209             phenome_schema => $phenome_schema,
 210             tracking_identifier => $tracking_identifier,
 211             material => $material,
 212             project_id => $project_id,
 213             user_id => $user_id
 214          });
 215
 216         my $return = $tracking_obj->store();
 217         if (!$return) {
 218             $c->stash->{rest} = {error => "Error generating tracking identifier"};
 219             return;
 220         } elsif ($return->{error}) {
 221             my $error = $return->{error};
 222             $c->stash->{rest} = {error => $error};
 223             return;
 224         }
 225     }
 226
 227     $c->stash->{rest} = { success => 1};
 228
 229 }
 230
 231
 232 sub activity_info_save : Path('/ajax/tracking_activity/save') : ActionClass('REST'){ }
 233
 234 sub activity_info_save_POST : Args(0) {
 235     my $self = shift;
 236     my $c = shift;
 237     my $tracking_identifier = $c->req->param("tracking_identifier_name");
 238     my $tracking_identifier_id = $c->req->param("tracking_identifier_id");
 239     my $selected_type = $c->req->param("selected_type");
 240     my $input = $c->req->param("input");
 241     my $notes = $c->req->param("notes");
 242     my $record_timestamp = $c->req->param("record_timestamp");
 243     my $activity_type = $c->req->param("activity_type");
 244     my $program_name = $c->req->param("program_name");
 245     my $tracking_transformation = $c->config->{tracking_transformation};
 246
 247     if (!$c->user()) {
 248         $c->stash->{rest} = { error => "You must be logged in to add new information." };
 249         return;
 250     }
 251     if (!($c->user()->has_role('submitter') or $c->user()->has_role('curator'))) {
 252         $c->stash->{rest} = { error => "You do not have sufficient privileges to record new information." };
 253         return;
 254     }
 255
 256     my @user_roles = $c->user->roles();
 257     my %has_roles = ();
 258     map { $has_roles{$_} = 1; } @user_roles;
 259
 260     if (! ( (exists($has_roles{$program_name}) && exists($has_roles{submitter})) || exists($has_roles{curator}))) {
 261         $c->stash->{rest} = { error => "You need to be either a curator, or a submitter associated with breeding program $program_name to record new information." };
 262         return;
 263     }
 264
 265     my $user_id = $c->user()->get_object()->get_sp_person_id();
 266
 267     if ($selected_type =~ m/number/ && !($input =~ /^\d+?$/) ) {
 268         $c->stash->{rest} = {error => "Input is not a positive integer"};
 269         return;
 270     }
 271
 272     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 273     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema");
 274     my $dbh = $c->dbc->dbh();
 275     my $number_of_transformants;
 276     if (($selected_type eq 'number_of_transformants') && $tracking_transformation) {
 277         $number_of_transformants = $input;
 278         my $tracking_identifier_obj = CXGN::TrackingActivity::TrackingIdentifier->new({schema => $schema, dbh => $dbh, tracking_identifier_stock_id => $tracking_identifier_id});
 279         my $project_and_program_info = $tracking_identifier_obj->get_associated_project_program();
 280         my $program_id = $project_and_program_info->[0]->[2];
 281         my $linked_project_id = $project_and_program_info->[0]->[4];
 282         my $autogenerated_name_prefix_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'autogenerated_name_prefix', 'project_property')->cvterm_id();
 283         my $material_of_type_id  =  SGN::Model::Cvterm->get_cvterm_row($schema, 'material_of', 'stock_relationship')->cvterm_id;
 284
 285         if ($linked_project_id) {
 286             my $new_names_info;
 287             my $stored_prefix = $schema->resultset('Project::Projectprop')->find({ project_id => $linked_project_id, type_id => $autogenerated_name_prefix_cvterm_id});
 288             if (!$stored_prefix) {
 289                 $c->stash->{rest} = {error => "Please set up prefix for autogenerated names for this transformation project before using tracking tool"};
 290                 return;
 291             } else {
 292                 my $prefix = $stored_prefix->value();
 293                 my $autogenerated_names = CXGN::Transformation::CreateAutogeneratedNames->new({schema => $schema, dbh => $dbh, breeding_program_id => $program_id, prefix => $prefix, number_of_names => $number_of_transformants });
 294                 my $return = $autogenerated_names->create_names();
 295                 if (!$return){
 296                     $c->stash->{rest} = {error => "Error generating transformant names"};
 297                     return;
 298                 } elsif ($return->{error}) {
 299                     $c->stash->{rest} = {error => $return->{error}};
 300                     return;
 301                 }
 302
 303                 $new_names_info = $return->{new_names};
 304                 my $new_names = $new_names_info->{'new_autogenerated_names'};
 305                 my $new_last_serial_number = $new_names_info->{'new_last_serial_number'};
 306
 307                 my $transformation_stock_id = $schema->resultset("Stock::StockRelationship")->find({object_id=>$tracking_identifier_id, type_id=>$material_of_type_id})->subject_id();
 308                 my $add_transformants = CXGN::Transformation::AddTransformant->new({
 309                     schema => $schema,
 310                     phenome_schema => $phenome_schema,
 311                     dbh => $dbh,
 312                     transformation_stock_id => $transformation_stock_id,
 313                     transformant_names => $new_names,
 314                     owner_id => $user_id,
 315                 });
 316
 317                 $add_transformants->add_transformant();
 318
 319                 my $name_metadata_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'autogenerated_name_metadata', 'project_property');
 320                 my $program = $schema->resultset('Project::Project')->find({ project_id => $program_id});
 321                 my $metadata_projectprop_rs = $program->projectprops({type_id => $name_metadata_cvterm->cvterm_id});
 322                 if ($metadata_projectprop_rs->count == 1){
 323                     my $stored_name_metadata_string = $metadata_projectprop_rs->first->value();
 324                     my $name_metadata_hash = decode_json $stored_name_metadata_string;
 325                     $name_metadata_hash->{$prefix}->{'last_serial_number'} = $new_last_serial_number;
 326                     my $new_name_metadata_string = encode_json $name_metadata_hash;
 327                     $metadata_projectprop_rs->first->update({value=>$new_name_metadata_string});
 328                 }
 329             }
 330         }
 331     }
 332
 333     my $add_activity_info = CXGN::TrackingActivity::ActivityInfo->new({
 334         schema => $schema,
 335         tracking_identifier => $tracking_identifier,
 336         selected_type => $selected_type,
 337         input => $input,
 338         timestamp => $record_timestamp,
 339         operator_id => $user_id,
 340         notes => $notes,
 341         activity_type => $activity_type
 342     });
 343     my $return = $add_activity_info->add_info();
 344
 345     if (!$return){
 346         $c->stash->{rest} = {error => "Error saving info",};
 347         return;
 348     } else {
 349         $c->stash->{rest} = $return;
 350     }
 351
 352 }
 353
 354
 355 sub get_activity_details :Path('/ajax/tracking_activity/details') :Args(1) {
 356     my $self = shift;
 357     my $c = shift;
 358     my $identifier_id = shift;
 359     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 360     my $dbh = $c->dbc->dbh;
 361
 362     my $tracking_identifier_obj = CXGN::TrackingActivity::TrackingIdentifier->new({schema=>$schema, dbh=>$dbh, tracking_identifier_stock_id=>$identifier_id});
 363     my $associated_projects = $tracking_identifier_obj->get_associated_project_program();
 364     my $tracking_project_id = $associated_projects->[0]->[0];
 365     my $tracking_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $tracking_project_id);
 366     my $activity_type = $tracking_project->get_project_activity_type();
 367
 368
 369     my $tracking_activities;
 370     my $tracking_data_json_cvterm_id;
 371     if ($activity_type eq 'tissue_culture') {
 372         $tracking_activities = $c->config->{tracking_tissue_culture_info};
 373     } elsif ($activity_type eq 'transformation') {
 374         $tracking_activities = $c->config->{tracking_transformation_info};
 375     }
 376
 377     my @details;
 378     my @activity_types = split ',',$tracking_activities;
 379
 380     my $tracking_identifier_info = $tracking_identifier_obj->get_tracking_identifier_info();
 381     my $tracking_identifier_stockprop = $tracking_identifier_info->[0]->[5];
 382
 383     if ($tracking_identifier_stockprop) {
 384         my $info = JSON::Any->jsonToObj($tracking_identifier_stockprop);
 385         my %info_hash = %{$info};
 386         foreach my $type (@activity_types){
 387             my $empty_string;
 388             my @each_type_details = ();
 389             my $each_timestamp_string;
 390             my $each_type_string;
 391             if ($info_hash{$type}) {
 392                 my @each_type_details = ();
 393                 my $details = {};
 394                 my %details_hash = ();
 395                 $details = $info_hash{$type};
 396                 %details_hash = %{$details};
 397                 foreach my $timestamp (sort keys %details_hash) {
 398                     my @each_timestamp_details = ();
 399                     push @each_timestamp_details, "timestamp".":"."".$timestamp;
 400                     my $operator_id = $details_hash{$timestamp}{'operator_id'};
 401
 402                     my $person= CXGN::People::Person->new($dbh, $operator_id);
 403                     my $operator_name = $person->get_first_name()." ".$person->get_last_name();
 404
 405                     push @each_timestamp_details, "operator".":"."".$operator_name;
 406                     my $input = $details_hash{$timestamp}{'input'};
 407                     push @each_timestamp_details, "input".":"."".$input;
 408                     my $notes = $details_hash{$timestamp}{'notes'};
 409                     push @each_timestamp_details, "notes".":"."".$notes;
 410
 411                     push @each_timestamp_details, $empty_string;
 412
 413                     $each_timestamp_string = join("<br>", @each_timestamp_details);
 414                     push @each_type_details, $each_timestamp_string;
 415                 }
 416
 417                 $each_type_string = join("<br>", @each_type_details);
 418 #                print STDERR "EACH TYPE STRING =".Dumper($each_type_string)."\n";
 419                 push @details, $each_type_string;
 420             } else {
 421                 my $empty_string;
 422                 push @details, $empty_string;
 423             }
 424         }
 425     } else {
 426         foreach my $type (@activity_types) {
 427             push @details, 'NA';
 428         }
 429     }
 430
 431     my @all_details;
 432     push @all_details, [@details];
 433
 434     $c->stash->{rest} = { data => \@all_details };
 435
 436 }
 437
 438
 439 sub get_activity_summary :Path('/ajax/tracking_activity/summary') :Args(1) {
 440     my $self = shift;
 441     my $c = shift;
 442     my $identifier_id = shift;
 443     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 444     my $dbh = $c->dbc->dbh;
 445
 446     my $tracking_identifier_obj = CXGN::TrackingActivity::TrackingIdentifier->new({schema=>$schema, dbh=>$dbh, tracking_identifier_stock_id=>$identifier_id});
 447     my $associated_projects = $tracking_identifier_obj->get_associated_project_program();
 448     my $tracking_project_id = $associated_projects->[0]->[0];
 449     my $tracking_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $tracking_project_id);
 450     my $activity_type = $tracking_project->get_project_activity_type();
 451
 452     my $tracking_activities;
 453     my $tracking_data_json_cvterm_id;
 454     if ($activity_type eq 'tissue_culture') {
 455         $tracking_activities = $c->config->{tracking_tissue_culture_info};
 456     } elsif ($activity_type eq 'transformation') {
 457         $tracking_activities = $c->config->{tracking_transformation_info};
 458     }
 459
 460     my @summary = ();
 461     my @activity_types = split ',',$tracking_activities;
 462
 463     my $tracking_identifier_info = $tracking_identifier_obj->get_tracking_identifier_info();
 464     my $tracking_identifier_stockprop = $tracking_identifier_info->[0]->[5];
 465     my $material_stock_type = $tracking_identifier_info->[0]->[4];
 466     my $material_stock_id = $tracking_identifier_info->[0]->[2];
 467
 468     my $obsoleted_transformant_count;
 469     if ($material_stock_type eq 'transformation') {
 470         my $transformation_obj = CXGN::Transformation::Transformation->new({schema=>$schema, dbh=>$dbh, transformation_stock_id=>$material_stock_id});
 471         my $obsoleted_transformants = $transformation_obj->get_obsoleted_transformants();
 472         if ($obsoleted_transformants) {
 473             $obsoleted_transformant_count = scalar @$obsoleted_transformants;
 474         }
 475     }
 476
 477     if ($tracking_identifier_stockprop) {
 478         my $info = JSON::Any->jsonToObj($tracking_identifier_stockprop);
 479         my %info_hash = %{$info};
 480         foreach my $type (@activity_types){
 481             my $input = '';
 482             my $empty_string;
 483             my @each_type_details = ();
 484             my $each_timestamp_string;
 485             my $each_type_string;
 486             if ($info_hash{$type}) {
 487                 my $details = {};
 488                 my %details_hash = ();
 489                 $details = $info_hash{$type};
 490                 %details_hash = %{$details};
 491
 492                 if (($type =~ m/number/) || ($type =~ m/count/)) {
 493                     $input = 0;
 494                     foreach my $key (keys %details_hash) {
 495                         $input += $details_hash{$key}{'input'};
 496                     }
 497
 498                     if (($type eq 'number_of_transformants') && ($obsoleted_transformant_count >= 1)) {
 499                         my @details = ();
 500                         my $generated_count = 'Selected'. ":"." ".$input;
 501                         my $obsoleted_count = 'Obsoleted'. ":"." ".$obsoleted_transformant_count;
 502                         my $current_number = 'Current Number'. ":"." ".($input-=$obsoleted_transformant_count);
 503                         push @details, ($generated_count, $obsoleted_count, $current_number);
 504                         my $details_string = join("<br>", @details);
 505                         push @summary, $details_string;
 506                     } else {
 507                         push @summary, $input;
 508                     }
 509                 } elsif ($type =~ m/date/) {
 510                     foreach my $key (keys %details_hash) {
 511                         $input = $details_hash{$key}{'input'};
 512                     }
 513                     push @summary, $input;
 514                 }
 515             } else {
 516                 push @summary, $input;
 517             }
 518         }
 519     } else {
 520         foreach my $type (@activity_types) {
 521             push @summary, 'NA';
 522         }
 523     }
 524
 525     my @all_summary;
 526     push @all_summary, [@summary];
 527
 528     $c->stash->{rest} = { data => \@all_summary };
 529
 530 }
 531
 532 sub get_project_active_identifiers :Path('/ajax/tracking_activity/project_active_identifiers') :Args(1) {
 533     my $self = shift;
 534     my $c = shift;
 535     my $project_id = shift;
 536     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 537
 538     my $tracking_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 539     my $activity_type = $tracking_project->get_project_activity_type();
 540
 541     my $tracking_activities;
 542     if ($activity_type eq 'tissue_culture') {
 543         $tracking_activities = $c->config->{tracking_tissue_culture_info};
 544     } elsif ($activity_type eq 'transformation') {
 545         $tracking_activities = $c->config->{tracking_transformation_info};
 546     }
 547
 548     my @activity_types = split ',',$tracking_activities;
 549     my $transformation_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation", 'stock_type')->cvterm_id();
 550
 551     my $activity_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 552     my $all_identifier_info = $activity_project->get_project_active_identifiers();
 553     my @all_identifiers;
 554     foreach my $identifier_info (@$all_identifier_info) {
 555         my @row = ();
 556         my $identifier_id = $identifier_info->[0];
 557         my $identifier_name = $identifier_info->[1];
 558         push @row, qq{<a href="/activity/details/$identifier_id">$identifier_name</a>};
 559
 560         my $material_id = $identifier_info->[2];
 561         my $material_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $material_id });
 562         my $material_stock_type_id = $material_rs->type_id;
 563         my $material_name = $identifier_info->[3];
 564         if ($material_stock_type_id == $transformation_type_id) {
 565             push @row, qq{<a href="/transformation/$material_id">$material_name</a>}
 566         } else {
 567             push @row, qq{<a href="/stock/$material_id/view">$material_name</a>};
 568         }
 569         my $progress = $identifier_info->[5];
 570         if ($progress) {
 571             my $progress_ref = JSON::Any->jsonToObj($progress);
 572             my %progress_hash = %{$progress_ref};
 573             foreach my $type (@activity_types){
 574                 my $input = '';
 575                 if ($progress_hash{$type}) {
 576                     my $details = {};
 577                     my %details_hash = ();
 578                     $details = $progress_hash{$type};
 579                     %details_hash = %{$details};
 580
 581                     if (($type =~ m/number/) || ($type =~ m/count/)) {
 582                         $input = 0;
 583                         foreach my $key (keys %details_hash) {
 584                             $input += $details_hash{$key}{'input'};
 585                         }
 586                         push @row, $input;
 587                     } elsif ($type =~ m/date/) {
 588                         foreach my $key (keys %details_hash) {
 589                             $input = $details_hash{$key}{'input'};
 590                         }
 591                         push @row, $input;
 592                     }
 593                 } else {
 594                     push @row, $input;
 595                 }
 596             }
 597         } else {
 598             foreach my $type (@activity_types) {
 599                 push @row, '';
 600             }
 601         }
 602         push @row, $identifier_name;
 603         push @all_identifiers,[@row];
 604     }
 605
 606     $c->stash->{rest} = { data => \@all_identifiers };
 607
 608 }
 609
 610
 611 sub get_project_active_identifier_names :Path('/ajax/tracking_activity/project_active_identifier_names') :Args(1) {
 612     my $self = shift;
 613     my $c = shift;
 614     my $project_id = shift;
 615     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 616
 617     my $activity_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 618     my $all_identifier_info = $activity_project->get_project_active_identifiers();
 619     my @identifier_names;
 620     foreach my $identifier_info (@$all_identifier_info) {
 621         push @identifier_names, $identifier_info->[1];
 622     }
 623
 624     $c->stash->{rest} = { data => \@identifier_names };
 625
 626 }
 627
 628
 629 sub update_status : Path('/ajax/tracking_activity/update_status') : ActionClass('REST'){ }
 630
 631 sub update_status_POST : Args(0) {
 632     my $self = shift;
 633     my $c = shift;
 634     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 635     my $dbh = $c->dbc->dbh();
 636     my $identifier_id = $c->req->param("identifier_id");
 637     my $status_type = $c->req->param("status_type");
 638     my $comments = $c->req->param("comments");
 639     my $material_id = $c->req->param("material_id");
 640     my $program_name = $c->req->param("program_name");
 641     my $time = DateTime->now();
 642     my $update_date = $time->ymd();
 643     my @stocks_to_update;
 644
 645     if (!$c->user()){
 646         $c->stash->{rest} = { error_string => "You must be logged in to update status" };
 647         return;
 648     }
 649     if (!$c->user()->check_roles("curator")) {
 650         $c->stash->{rest} = { error_string => "You do not have the correct role to update status. Please contact us." };
 651         return;
 652     }
 653
 654     my @user_roles = $c->user->roles();
 655     my %has_roles = ();
 656     map { $has_roles{$_} = 1; } @user_roles;
 657
 658     if (! ( (exists($has_roles{$program_name}) && exists($has_roles{submitter})) || exists($has_roles{curator}))) {
 659         $c->stash->{rest} = { error => "You need to be either a curator, or a submitter associated with breeding program $program_name to update status." };
 660         return;
 661     }
 662
 663     my $user_id = $c->user()->get_object()->get_sp_person_id();
 664
 665     my $tracking_identifier_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "tracking_identifier", 'stock_type')->cvterm_id();
 666     my $transformation_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation", 'stock_type')->cvterm_id();
 667
 668     my $identifier_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $identifier_id, type_id => $tracking_identifier_type_id });
 669     if (!$identifier_rs) {
 670         $c->stash->{rest} = { error_string => 'Error. No tracking identifier entry found in the database.' };
 671             return;
 672     } else {
 673         push @stocks_to_update, $identifier_id;
 674     }
 675
 676     my $material_stock_type_id;
 677     my $material_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $material_id });
 678     if (!$material_rs) {
 679         $c->stash->{rest} = { error_string => 'Error. No material entry found in the database.' };
 680         return;
 681     } else {
 682        $material_stock_type_id = $material_rs->type_id;
 683     }
 684
 685     if ($material_stock_type_id == $transformation_type_id) {
 686         push @stocks_to_update, $material_id;
 687     }
 688
 689     my $completed_metadata;
 690     my $terminated_metadata;
 691     if ($status_type eq 'completed') {
 692         $completed_metadata = 1;
 693     } elsif ($status_type eq 'terminated') {
 694         $terminated_metadata = 1;
 695     }
 696
 697     foreach my $stock_id (@stocks_to_update) {
 698         my $update_status = CXGN::Stock::Status->new({
 699             bcs_schema => $schema,
 700             parent_id => $stock_id,
 701             person_id => $user_id,
 702             update_date => $update_date,
 703             comments => $comments,
 704             completed_metadata => $completed_metadata,
 705             terminated_metadata => $terminated_metadata
 706         });
 707
 708         $update_status->store();
 709
 710         if (!$update_status->store()){
 711             $c->stash->{rest} = {error_string => "Error updating status"};
 712             return;
 713         }
 714     }
 715
 716     $c->stash->{rest} = {success => "1",};
 717
 718 }
 719
 720 sub reverse_status : Path('/ajax/tracking_activity/reverse_status') : ActionClass('REST'){ }
 721
 722 sub reverse_status_POST : Args(0) {
 723     my $self = shift;
 724     my $c = shift;
 725     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 726     my $dbh = $c->dbc->dbh();
 727     my $identifier_id = $c->req->param("identifier_id");
 728     my $updated_status_type = $c->req->param("updated_status_type");
 729     my $material_id = $c->req->param("material_id");
 730     my $program_name = $c->req->param("program_name");
 731
 732     if (!$c->user()){
 733         $c->stash->{rest} = { error_string => "You must be logged in to reverse status of this tracking identifier" };
 734         return;
 735     }
 736     if (!$c->user()->check_roles("curator")) {
 737         $c->stash->{rest} = { error_string => "You do not have the correct role to reverse status of this tracking identifier. Please contact us." };
 738         return;
 739     }
 740
 741     my @user_roles = $c->user->roles();
 742     my %has_roles = ();
 743     map { $has_roles{$_} = 1; } @user_roles;
 744
 745     if (! ( (exists($has_roles{$program_name}) && exists($has_roles{submitter})) || exists($has_roles{curator}))) {
 746         $c->stash->{rest} = { error => "You need to be either a curator, or a submitter associated with breeding program $program_name to update status." };
 747         return;
 748     }
 749
 750     my $user_id = $c->user()->get_object()->get_sp_person_id();
 751
 752     my $status_type_id;
 753     if ($updated_status_type) {
 754         $status_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, $updated_status_type, 'stock_property')->cvterm_id();
 755         my $status_stockprop_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $identifier_id, type_id => $status_type_id});
 756
 757         if (defined $status_stockprop_rs->stockprop_id) {
 758             $status_stockprop_rs->delete();
 759         }
 760     }
 761
 762     my $material_stock_type_id;
 763     my $material_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $material_id });
 764     if (!$material_rs) {
 765         $c->stash->{rest} = { error_string => 'Error. No material entry found in the database.' };
 766         return;
 767     } else {
 768        $material_stock_type_id = $material_rs->type_id;
 769     }
 770
 771     my $transformation_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation", 'stock_type')->cvterm_id();
 772
 773     if ($material_stock_type_id == $transformation_type_id) {
 774         if ($status_type_id) {
 775             my $transformation_stockprop_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $material_id, type_id => $status_type_id});
 776
 777             if (defined $transformation_stockprop_rs->stockprop_id) {
 778                 $transformation_stockprop_rs->delete();
 779             }
 780         }
 781     }
 782
 783     $c->stash->{rest} = { success => 1 };
 784
 785 }
 786
 787
 788 sub get_project_inactive_identifiers :Path('/ajax/tracking_activity/project_inactive_identifiers') :Args(1) {
 789     my $self = shift;
 790     my $c = shift;
 791     my $project_id = shift;
 792     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 793
 794     my $tracking_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 795     my $activity_type = $tracking_project->get_project_activity_type();
 796
 797     my $tracking_activities;
 798     if ($activity_type eq 'tissue_culture') {
 799         $tracking_activities = $c->config->{tracking_tissue_culture_info};
 800     } elsif ($activity_type eq 'transformation') {
 801         $tracking_activities = $c->config->{tracking_transformation_info};
 802     }
 803
 804     my @activity_types = split ',',$tracking_activities;
 805
 806     my $transformation_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation", 'stock_type')->cvterm_id();
 807
 808     my $activity_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $project_id);
 809     my $all_identifier_info = $activity_project->get_project_inactive_identifiers();
 810     my @all_identifiers;
 811     foreach my $identifier_info (@$all_identifier_info) {
 812         my @row = ();
 813         my $identifier_id = $identifier_info->[0];
 814         my $identifier_name = $identifier_info->[1];
 815         push @row, qq{<a href="/activity/details/$identifier_id">$identifier_name</a>};
 816
 817         my $status = $identifier_info->[6];
 818         if ($status eq 'terminated_metadata') {
 819             $status = '<span style="color:red">'.'TERMINATED'.'</span>';
 820         } elsif ($status eq 'completed_metadata') {
 821             $status = '<span style="color:red">'.'COMPLETED'.'</span>';
 822         }
 823         push @row, $status;
 824
 825         my $material_id = $identifier_info->[2];
 826         my $material_name = $identifier_info->[3];
 827         my $material_rs = $schema->resultset("Stock::Stock")->find( { stock_id => $material_id });
 828         my $material_stock_type_id = $material_rs->type_id;
 829         if ($material_stock_type_id == $transformation_type_id) {
 830             push @row, qq{<a href="/transformation/$material_id">$material_name</a>}
 831         } else {
 832             push @row, qq{<a href="/stock/$material_id/view">$material_name</a>};
 833         }
 834
 835         my $progress = $identifier_info->[5];
 836         if ($progress) {
 837             my $progress_ref = JSON::Any->jsonToObj($progress);
 838             my %progress_hash = %{$progress_ref};
 839             foreach my $type (@activity_types){
 840                 my $input = '';
 841                 if ($progress_hash{$type}) {
 842                     my $details = {};
 843                     my %details_hash = ();
 844                     $details = $progress_hash{$type};
 845                     %details_hash = %{$details};
 846
 847                     if (($type =~ m/number/) || ($type =~ m/count/)) {
 848                         $input = 0;
 849                         foreach my $key (keys %details_hash) {
 850                             $input += $details_hash{$key}{'input'};
 851                         }
 852                         push @row, $input;
 853                     } elsif ($type =~ m/date/) {
 854                         foreach my $key (keys %details_hash) {
 855                             $input = $details_hash{$key}{'input'};
 856                         }
 857                         push @row, $input;
 858                     }
 859                 } else {
 860                     push @row, $input;
 861                 }
 862             }
 863         } else {
 864             foreach my $type (@activity_types) {
 865                 push @row, '';
 866             }
 867         }
 868         push @row, $identifier_name;
 869         push @all_identifiers,[@row];
 870     }
 871
 872     $c->stash->{rest} = { data => \@all_identifiers };
 873
 874 }
 875
 876
 877
 878
 879 1;