lib/SGN/Controller/ActivityInfo.pm

   1
   2 package SGN::Controller::ActivityInfo;
   3
   4 use Moose;
   5 use URI::FromHash 'uri';
   6 use Data::Dumper;
   7 use CXGN::TrackingActivity::TrackingIdentifier;
   8 use CXGN::Stock::Status;
   9 use CXGN::People::Person;
  10 use CXGN::Transformation::Transformation;
  11 use JSON;
  12
  13 BEGIN { extends 'Catalyst::Controller'; }
  14
  15 sub activity_details :Path('/activity/details') : Args(1) {
  16     my $self = shift;
  17     my $c = shift;
  18     my $identifier_id = shift;
  19     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  20     my $dbh = $c->dbc->dbh;
  21     my $user_role;
  22
  23     if (! $c->user()) {
  24         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
  25         return;
  26     }
  27
  28     if ($c->user() && $c->user()->check_roles("curator")) {
  29         $user_role = "curator";
  30     }
  31
  32     my $tracking_identifier_obj = CXGN::TrackingActivity::TrackingIdentifier->new({schema=>$schema, dbh=>$dbh, tracking_identifier_stock_id=>$identifier_id});
  33     my $tracking_info = $tracking_identifier_obj->get_tracking_identifier_info();
  34
  35     my $identifier_name = $tracking_info->[0]->[1];
  36     my $material_id = $tracking_info->[0]->[2];
  37     my $material_name = $tracking_info->[0]->[3];
  38     my $material_type = $tracking_info->[0]->[4];
  39
  40     my $updated_status_type = $tracking_info->[0]->[7];
  41     my $completed_metadata;
  42     my $terminated_metadata;
  43     my $status_display;
  44     if ($updated_status_type eq 'terminated_metadata') {
  45         $status_display = '<span style="color:red">'.'TERMINATED'.'</span>';
  46         $terminated_metadata = 1;
  47     } elsif ($updated_status_type eq 'completed_metadata') {
  48         $status_display = '<span style="color:red">'.'COMPLETED'.'</span>';
  49         $completed_metadata = 1;
  50     }
  51
  52     my $associated_projects = $tracking_identifier_obj->get_associated_project_program();
  53     my $tracking_project_id = $associated_projects->[0]->[0];
  54     my $program_name = $associated_projects->[0]->[3];
  55     my $tracking_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $tracking_project_id);
  56     my $activity_type = $tracking_project->get_project_activity_type();
  57
  58     my $types;
  59     my $activity_type_header;
  60     if ($activity_type eq 'tissue_culture') {
  61         $types = $c->config->{tracking_tissue_culture_info};
  62         $activity_type_header = $c->config->{tracking_tissue_culture_info_header};
  63     } elsif ($activity_type eq 'transformation') {
  64         $types = $c->config->{tracking_transformation_info};
  65         $activity_type_header = $c->config->{tracking_transformation_info_header};
  66     }
  67
  68     my @type_select_options = split ',',$types;
  69     my @activity_headers = split ',',$activity_type_header;
  70
  71     my @options = ();
  72     for my $i (0 .. $#type_select_options) {
  73         push @options, [$type_select_options[$i], $activity_headers[$i]];
  74     }
  75
  76     my $updated_status_string;
  77     if ($updated_status_type) {
  78         my $updated_status = CXGN::Stock::Status->new({ bcs_schema => $schema, parent_id => $identifier_id, completed_metadata => $completed_metadata, terminated_metadata => $terminated_metadata});
  79         my $updated_status_info = $updated_status->get_status_details();
  80         my $person_id = $updated_status_info->[0];
  81         my $person= CXGN::People::Person->new($dbh, $person_id);
  82         my $person_name=$person->get_first_name()." ".$person->get_last_name();
  83         my $operator_info = "Updated by". ":"."".$person_name;
  84         my $date_info = "Updated Date". ":"."".$updated_status_info->[1];
  85         my $reason_info = "Comments". ":"."".$updated_status_info->[2];
  86         my @all_info = ($operator_info, $date_info, $reason_info);
  87         my $all_info_string = join("<br>", @all_info);
  88         $updated_status_string = '<span style="color:red">'.$all_info_string.'</span>';
  89     }
  90
  91     my $time = DateTime->now();
  92     my $timestamp = $time->ymd()."_".$time->hms();
  93     my $date = $time->ymd();
  94
  95     my $source_info_string;
  96     if ($material_type eq 'transformation') {
  97         my $transformation_obj = CXGN::Transformation::Transformation->new({schema=>$schema, dbh=>$dbh, transformation_stock_id=>$material_id});
  98         my $info = $transformation_obj->get_transformation_info();
  99         my $plant_material_name = $info->[0]->[1];
 100         my $vector_name = $info->[0]->[3];
 101         my $transformation_project_name = $associated_projects->[0]->[5];
 102         my $source_info_hash = {};
 103         $source_info_hash->{'breedingProgram'} = $program_name;
 104         $source_info_hash->{'transformationProject'} = $transformation_project_name;
 105         $source_info_hash->{'transformationID'} = $material_name;
 106         $source_info_hash->{'vectorConstruct'} = $vector_name;
 107         $source_info_hash->{'plantMaterial'} = $plant_material_name;
 108         $source_info_string = encode_json $source_info_hash;
 109     }
 110
 111     $c->stash->{identifier_id} = $identifier_id;
 112     $c->stash->{identifier_name} = $identifier_name;
 113     $c->stash->{type_select_options} = \@options;
 114     $c->stash->{activity_headers} = \@activity_headers;
 115     $c->stash->{material_name} = $material_name;
 116     $c->stash->{material_id} = $material_id;
 117     $c->stash->{material_type} = $material_type;
 118     $c->stash->{updated_status_type} = $updated_status_type;
 119     $c->stash->{updated_status_string} = $updated_status_string;
 120     $c->stash->{status_display} = $status_display;
 121     $c->stash->{timestamp} = $timestamp;
 122     $c->stash->{date} = $date;
 123     $c->stash->{user_role} = $user_role;
 124     $c->stash->{project_id} = $tracking_project_id;
 125     $c->stash->{activity_type} = $activity_type;
 126     $c->stash->{program_name} = $program_name;
 127     $c->stash->{source_info} = $source_info_string;
 128     $c->stash->{template} = '/tracking_activities/activity_info_details.mas';
 129
 130 }
 131
 132
 133 sub record_activity :Path('/activity/record') :Args(0) {
 134     my $self = shift;
 135     my $c = shift;
 136     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 137     my $dbh = $c->dbc->dbh;
 138
 139     my $identifier_name = $c->req->param("identifier_name");
 140
 141     if (! $c->user()) {
 142             $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 143         return;
 144     }
 145
 146     if ($c->user) {
 147         my $check_vendor_role = $c->user->check_roles('vendor');
 148         $c->stash->{check_vendor_role} = $check_vendor_role;
 149     }
 150
 151     my $identifier_id;
 152     my @options = ();
 153     my @activity_headers = ();
 154     my $material_stock_id;
 155     my $material_name;
 156     my $material_type;
 157     my $tracking_project_id;
 158     my $activity_type;
 159     my $program_name;
 160     my $source_info_string;
 161
 162     if ($identifier_name) {
 163         my $identifier_rs = $schema->resultset("Stock::Stock")->find({uniquename => $identifier_name});
 164         if (!$identifier_rs) {
 165             $c->stash->{message} = "The tracking identifier does not exist or has been deleted.";
 166             $c->stash->{template} = 'generic_message.mas';
 167             return;
 168         } else {
 169             $identifier_id = $identifier_rs->stock_id();
 170         }
 171
 172         my $tracking_identifier_obj = CXGN::TrackingActivity::TrackingIdentifier->new({schema=>$schema, dbh=>$dbh, tracking_identifier_stock_id=>$identifier_id});
 173         my $associated_projects = $tracking_identifier_obj->get_associated_project_program();
 174         $program_name = $associated_projects->[0]->[3];
 175         my $material_info = $tracking_identifier_obj->get_tracking_identifier_info();
 176         $material_stock_id = $material_info->[0]->[2];
 177         $material_name = $material_info->[0]->[3];
 178         $material_type = $material_info->[0]->[4];
 179
 180         if ($material_type eq 'transformation') {
 181             my $transformation_obj = CXGN::Transformation::Transformation->new({schema=>$schema, dbh=>$dbh, transformation_stock_id=>$material_stock_id});
 182             my $info = $transformation_obj->get_transformation_info();
 183             my $plant_material_name = $info->[0]->[1];
 184             my $vector_name = $info->[0]->[3];
 185             my $transformation_project_name = $associated_projects->[0]->[5];
 186             my $source_info_hash = {};
 187             $source_info_hash->{'breedingProgram'} = $program_name;
 188             $source_info_hash->{'transformationProject'} = $transformation_project_name;
 189             $source_info_hash->{'transformationID'} = $material_name;
 190             $source_info_hash->{'vectorConstruct'} = $vector_name;
 191             $source_info_hash->{'plantMaterial'} = $plant_material_name;
 192             $source_info_string = encode_json $source_info_hash;
 193         }
 194
 195         $tracking_project_id = $associated_projects->[0]->[0];
 196         my $tracking_project = CXGN::TrackingActivity::ActivityProject->new(bcs_schema => $schema, trial_id => $tracking_project_id);
 197         $activity_type = $tracking_project->get_project_activity_type();
 198
 199         my $types;
 200         my $activity_type_header;
 201         if ($activity_type eq 'tissue_culture') {
 202             $types = $c->config->{tracking_tissue_culture_info};
 203             $activity_type_header = $c->config->{tracking_tissue_culture_info_header};
 204         } elsif ($activity_type eq 'transformation') {
 205             $types = $c->config->{tracking_transformation_info};
 206             $activity_type_header = $c->config->{tracking_transformation_info_header};
 207         }
 208
 209         my @type_select_options = split ',',$types;
 210         @activity_headers = split ',',$activity_type_header;
 211
 212         for my $i (0 .. $#type_select_options) {
 213             push @options, [$type_select_options[$i], $activity_headers[$i]];
 214         }
 215     }
 216
 217     my $time = DateTime->now();
 218     my $timestamp = $time->ymd()."_".$time->hms();
 219     my $date = $time->ymd();
 220
 221     $c->stash->{identifier_id} = $identifier_id;
 222     $c->stash->{type_select_options} = \@options;
 223     $c->stash->{activity_headers} = \@activity_headers;
 224     $c->stash->{material_stock_id} = $material_stock_id;
 225     $c->stash->{material_name} = $material_name;
 226     $c->stash->{material_type} = $material_type;
 227     $c->stash->{timestamp} = $timestamp;
 228     $c->stash->{date} = $date;
 229     $c->stash->{project_id} = $tracking_project_id;
 230     $c->stash->{activity_type} = $activity_type;
 231     $c->stash->{program_name} = $program_name;
 232     $c->stash->{source_info} = $source_info_string;
 233     $c->stash->{template} = '/tracking_activities/record_activity.mas';
 234
 235 }
 236
 237
 238
 239 1;