lib/SGN/Controller/AJAX/Analytics.pm

   1 package SGN::Controller::AJAX::Analytics;
   2
   3 use Moose;
   4
   5 use File::Slurp;
   6 use Data::Dumper;
   7 use URI::FromHash 'uri';
   8 use JSON;
   9 use CXGN::BreederSearch;
  10
  11 BEGIN { extends 'Catalyst::Controller::REST' };
  12
  13 __PACKAGE__->config(
  14     default => 'application/json',
  15     stash_key => 'rest',
  16     map => { 'application/json' => 'JSON', 'text/html' => 'JSON'  },
  17 );
  18
  19 sub list_analytics_protocols_by_user_table :Path('/ajax/analytics_protocols/by_user') Args(0) {
  20     my $self = shift;
  21     my $c = shift;
  22
  23     my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
  24     my $schema = $c->dbic_schema("Bio::Chado::Schema", undef, $sp_person_id);
  25     my $people_schema = $c->dbic_schema("CXGN::People::Schema", undef, $sp_person_id);
  26     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema", undef, $sp_person_id);
  27     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema", undef, $sp_person_id);
  28     my ($user_id, $user_name, $user_role) = _check_user_login($c);
  29     my $protocol_type = $c->req->param('analytics_protocol_type');
  30
  31     my $protocol_type_where = '';
  32     if ($protocol_type) {
  33         my $protocol_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, $protocol_type, 'protocol_type')->cvterm_id();
  34         $protocol_type_where = "nd_protocol.type_id = $protocol_type_cvterm_id AND ";
  35     }
  36
  37     my $protocolprop_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'analytics_protocol_properties', 'protocol_property')->cvterm_id();
  38
  39     my %available_types = (
  40         SGN::Model::Cvterm->get_cvterm_row($schema, 'drone_imagery_analytics_env_simulation_protocol', 'protocol_type')->cvterm_id() => 'Drone Imagery Environment Simulation'
  41     );
  42
  43     my $q = "SELECT nd_protocol.nd_protocol_id, nd_protocol.name, nd_protocol.type_id, nd_protocol.description, nd_protocol.create_date, nd_protocolprop.value
  44         FROM nd_protocol
  45         JOIN nd_protocolprop USING(nd_protocol_id)
  46         WHERE $protocol_type_where nd_protocolprop.type_id=$protocolprop_type_cvterm_id;";
  47     my $h = $schema->storage->dbh()->prepare($q);
  48     $h->execute();
  49
  50     my @table;
  51     while (my ($nd_protocol_id, $name, $type_id, $description, $create_date, $props_json) = $h->fetchrow_array()) {
  52         push @table, [
  53             '<a href="/analytics_protocols/'.$nd_protocol_id.'">'.$name."</a>",
  54             $description,
  55             $available_types{$type_id},
  56             $create_date
  57         ];
  58     }
  59
  60     #print STDERR Dumper(\@table);
  61     $c->stash->{rest} = { data => \@table };
  62 }
  63
  64 sub list_analytics_protocols_result_files :Path('/ajax/analytics_protocols/result_files') Args(0) {
  65     my $self = shift;
  66     my $c = shift;
  67
  68     my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
  69     my $schema = $c->dbic_schema("Bio::Chado::Schema", undef, $sp_person_id);
  70     my $people_schema = $c->dbic_schema("CXGN::People::Schema", undef, $sp_person_id);
  71     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema", undef, $sp_person_id);
  72     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema", undef, $sp_person_id);
  73     my ($user_id, $user_name, $user_role) = _check_user_login($c);
  74     my $analytics_protocol_id = $c->req->param('analytics_protocol_id');
  75
  76     if (!$analytics_protocol_id) {
  77         $c->stash->{rest} = { error => "No ID given!" };
  78         $c->detach();
  79     }
  80
  81     my $analytics_experiment_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'analytics_protocol_experiment', 'experiment_type')->cvterm_id();
  82
  83     my $q = "SELECT nd_protocol.nd_protocol_id, nd_protocol.name, nd_protocol.description, basename, dirname, md.file_id, md.filetype, nd_protocol.type_id, nd_experiment.type_id
  84         FROM metadata.md_files AS md
  85         JOIN metadata.md_metadata AS meta ON (md.metadata_id=meta.metadata_id)
  86         JOIN phenome.nd_experiment_md_files using(file_id)
  87         JOIN nd_experiment using(nd_experiment_id)
  88         JOIN nd_experiment_protocol using(nd_experiment_id)
  89         JOIN nd_protocol using(nd_protocol_id)
  90         WHERE nd_protocol.nd_protocol_id=$analytics_protocol_id AND nd_experiment.type_id=$analytics_experiment_type_cvterm_id;";
  91     print STDERR $q."\n";
  92     my $h = $schema->storage->dbh()->prepare($q);
  93     $h->execute();
  94     my @table;
  95     while (my ($model_id, $model_name, $model_description, $basename, $filename, $file_id, $filetype, $model_type_id, $experiment_type_id, $property_type_id, $property_value) = $h->fetchrow_array()) {
  96         # $result{$model_id}->{model_id} = $model_id;
  97         # $result{$model_id}->{model_name} = $model_name;
  98         # $result{$model_id}->{model_description} = $model_description;
  99         # $result{$model_id}->{model_type_id} = $model_type_id;
 100         # $result{$model_id}->{model_type_name} = $schema->resultset("Cv::Cvterm")->find({cvterm_id => $model_type_id })->name();
 101         # $result{$model_id}->{model_experiment_type_id} = $experiment_type_id;
 102         # $result{$model_id}->{model_files}->{$filetype} = $filename."/".$basename;
 103         # $result{$model_id}->{model_file_ids}->{$file_id} = $basename;
 104         push @table, [$basename, $filetype, "<a href='/breeders/phenotyping/download/$file_id'>Download</a>"];
 105     }
 106
 107     $c->stash->{rest} = { data => \@table };
 108 }
 109
 110 sub _check_user_login {
 111     my $c = shift;
 112     my $role_check = shift;
 113     my $user_id;
 114     my $user_name;
 115     my $user_role;
 116     my $session_id = $c->req->param("sgn_session_id");
 117
 118     if ($session_id){
 119         my $dbh = $c->dbc->dbh;
 120         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
 121         if (!$user_info[0]){
 122             $c->stash->{rest} = {error=>'You must be logged in to do this!'};
 123             $c->detach();
 124         }
 125         $user_id = $user_info[0];
 126         $user_role = $user_info[1];
 127         my $p = CXGN::People::Person->new($dbh, $user_id);
 128         $user_name = $p->get_username;
 129     } else{
 130         if (!$c->user){
 131             $c->stash->{rest} = {error=>'You must be logged in to do this!'};
 132             $c->detach();
 133         }
 134         $user_id = $c->user()->get_object()->get_sp_person_id();
 135         $user_name = $c->user()->get_object()->get_username();
 136         $user_role = $c->user->get_object->get_user_type();
 137     }
 138     if ($role_check && $user_role ne $role_check) {
 139         $c->stash->{rest} = {error=>'You must have permission to do this! Please contact us!'};
 140         $c->detach();
 141     }
 142     return ($user_id, $user_name, $user_role);
 143 }
 144
 145 1;