lib/SGN/Controller/Analysis.pm

   1
   2 package SGN::Controller::Analysis;
   3
   4 use Moose;
   5 use URI::FromHash 'uri';
   6 use Data::Dumper;
   7
   8 BEGIN { extends 'Catalyst::Controller' };
   9
  10 sub view_analyses :Path('/analyses') Args(0) {
  11     my $self = shift;
  12     my $c = shift;
  13
  14     my $user_id;
  15     if ($c->user()) {
  16         $user_id = $c->user->get_object()->get_sp_person_id();
  17     }
  18     if (!$user_id) {
  19         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
  20     }
  21
  22     my $schema = $c->dbic_schema("Bio::Chado::Schema", undef, $user_id);
  23
  24     $c->stash->{template} = '/analyses/index.mas';
  25 }
  26
  27 sub analysis_detail :Path('/analyses') Args(1) {
  28     my $self = shift;
  29     my $c = shift;
  30     my $analysis_id = shift;
  31     my $user = $c->user();
  32
  33     my $user_id;
  34     if ($c->user()) {
  35         $user_id = $c->user->get_object()->get_sp_person_id();
  36     }
  37     if (!$user_id) {
  38         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
  39         $c->detach();
  40     }
  41
  42     my $bcs_schema = $c->dbic_schema("Bio::Chado::Schema", undef, $user_id);
  43     print STDERR "Viewing analysis with id $analysis_id\n";
  44
  45     my $a = CXGN::Analysis->new({
  46         bcs_schema => $bcs_schema,
  47         people_schema => $c->dbic_schema("CXGN::People::Schema", undef, $user_id),
  48         metadata_schema => $c->dbic_schema("CXGN::Metadata::Schema", undef, $user_id),
  49         phenome_schema => $c->dbic_schema("CXGN::Phenome::Schema", undef, $user_id),
  50         trial_id => $analysis_id,
  51     });
  52
  53     if (! $a) {
  54         $c->stash->{template} = '/generic_message.mas';
  55         $c->stash->{message} = 'The requested analysis ID does not exist in the database.';
  56         return;
  57     }
  58
  59     $c->stash->{analysis_id} = $analysis_id;
  60     $c->stash->{analysis_name} = $a->name();
  61     $c->stash->{analysis_description} = $a->description();
  62     $c->stash->{breeding_program_name} = $a->get_breeding_program();
  63     $c->stash->{breeding_program_id} = $bcs_schema->resultset("Project::Project")->find({name=>$a->get_breeding_program()})->project_id();
  64     $c->stash->{year} = $a->get_year();
  65     $c->stash->{trial_stock_type} = 'accession';
  66     $c->stash->{trial_phenotype_stock_type} = 'analysis_instance';
  67     $c->stash->{has_col_and_row_numbers} = $a->has_col_and_row_numbers();
  68     $c->stash->{identifier_prefix} = $c->config->{identifier_prefix};
  69     $c->stash->{analysis_metadata} = $a->metadata();
  70     $c->stash->{user_can_modify} = $user->check_roles("submitter") || $user->check_roles("curator");
  71     $c->stash->{template} = '/analyses/detail.mas';
  72 }
  73
  74 sub analysis_model_detail :Path('/analyses_model') Args(1) {
  75     my $self = shift;
  76     my $c = shift;
  77     my $model_id = shift;
  78
  79     my $user_id;
  80     if ($c->user()) {
  81         $user_id = $c->user->get_object()->get_sp_person_id();
  82     }
  83     if (!$user_id) {
  84         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
  85         $c->detach();
  86     }
  87
  88     my $bcs_schema = $c->dbic_schema("Bio::Chado::Schema", undef, $user_id);
  89     print STDERR "Viewing analysis model with id $model_id\n";
  90
  91     my $m = CXGN::AnalysisModel::GetModel->new({
  92         bcs_schema=>$bcs_schema,
  93         metadata_schema=>$c->dbic_schema("CXGN::Metadata::Schema", undef, $user_id),
  94         phenome_schema=>$c->dbic_schema("CXGN::Phenome::Schema", undef, $user_id),
  95         nd_protocol_id=>$model_id
  96     });
  97     my $saved_model_object = $m->get_model();
  98     #print STDERR Dumper $saved_model_object;
  99
 100     if (!$saved_model_object->{model_id}) {
 101         $c->stash->{template} = '/generic_message.mas';
 102         $c->stash->{message} = 'The requested model ID does not exist in the database.';
 103         return;
 104     }
 105
 106     $c->stash->{model_id} = $saved_model_object->{model_id};
 107     $c->stash->{model_name} = $saved_model_object->{model_name};
 108     $c->stash->{model_description} = $saved_model_object->{model_description};
 109     $c->stash->{model_properties} = $saved_model_object->{model_properties};
 110     $c->stash->{model_file_ids} = $saved_model_object->{model_file_ids};
 111     $c->stash->{model_type_name} = $saved_model_object->{model_type_name};
 112     $c->stash->{model_files} = $saved_model_object->{model_files};
 113     $c->stash->{identifier_prefix} = $c->config->{identifier_prefix}."_Model_";
 114     $c->stash->{template} = '/analyses/model_detail.mas';
 115 }
 116
 117 1;
 118