t/unit_fixture/CXGN/Uploading/Storebrapiobservations.t

   1 use strict;
   2 use warnings;
   3
   4 use lib 't/lib';
   5 use SGN::Test::Fixture;
   6 use Test::More;
   7 use Test::WWW::Mechanize;
   8 use SGN::Model::Cvterm;
   9 use Data::Dumper;
  10 use JSON;
  11 use HTTP::Request;
  12 use LWP::UserAgent;
  13
  14 my $f = SGN::Test::Fixture->new();
  15 my $schema = $f->bcs_schema;
  16
  17 my $mech = Test::WWW::Mechanize->new(timeout=>30000);
  18 my $response;
  19
  20 my $plot_id1 = $schema->resultset('Stock::Stock')->find({uniquename=>'test_trial210'})->stock_id;
  21 my $plot_id2 = $schema->resultset('Stock::Stock')->find({uniquename=>'test_trial214'})->stock_id;
  22
  23 $mech->post_ok('http://localhost:3010/brapi/v1/token', [ "username"=> "janedoe", "password"=> "secretpw", "grant_type"=> "password" ]);
  24 $response = decode_json $mech->content;
  25 print STDERR Dumper $response;
  26 is($response->{'metadata'}->{'status'}->[2]->{'message'}, 'Login Successfull');
  27 my $sgn_session_id = $response->{access_token};
  28
  29
  30 my $data = {
  31     observations => [
  32         {
  33             observationDbId => '',
  34             observationUnitDbId => $plot_id1,
  35             observationVariableDbId => '70741',
  36             collector => 'collector1',
  37             observationTimeStamp => '2015-06-16T00:53:26Z',
  38             value => '11'
  39         },
  40         {
  41             observationDbId => '',
  42             observationUnitDbId => $plot_id2,
  43             observationVariableDbId => '70773',
  44             collector => 'collector1',
  45             observationTimeStamp => '2015-06-16T00:53:26Z',
  46             value => '110'
  47         },
  48     ]
  49 };
  50 my $j = encode_json $data;
  51
  52 my $req = HTTP::Request->new( "PUT" => "http://localhost:3010/brapi/v1/observations" );
  53 $req->content_type( 'application/json' );
  54 $req->content_length(
  55     do { use bytes; length( $j ) }
  56 );
  57 $req->content( $j );
  58
  59 my $ua = LWP::UserAgent->new();
  60 my $res = $ua->request($req);
  61 $response = decode_json $res->content;
  62 print STDERR Dumper $response;
  63 is_deeply($response, {
  64           'result' => undef,
  65           'metadata' => {
  66                           'status' => [
  67                                         {
  68                                           'messageType' => 'ERROR',
  69                                           'message' => 'You must login and have permission to access this BrAPI call.'
  70                                         }
  71                                       ],
  72                           'datafiles' => [],
  73                           'pagination' => {
  74                                             'pageSize' => 1,
  75                                             'totalCount' => 0,
  76                                             'totalPages' => 0,
  77                                             'currentPage' => 0
  78                                           }
  79                         }
  80         });
  81
  82 my $trait_id1 = SGN::Model::Cvterm->get_cvterm_row_from_trait_name($schema, 'CO_334:0000092')->cvterm_id();
  83 my $trait_id2 = SGN::Model::Cvterm->get_cvterm_row_from_trait_name($schema, 'CO_334:0000016')->cvterm_id();
  84
  85 my $data = {
  86     access_token => $sgn_session_id,
  87     observations => [
  88         {
  89             observationDbId => '',
  90             observationUnitDbId => $plot_id1,
  91             observationVariableDbId => $trait_id1,
  92             collector => 'collector1',
  93             observationTimeStamp => '2015-06-16T00:53:26Z',
  94             value => '11'
  95         },
  96         {
  97             observationDbId => '',
  98             observationUnitDbId => $plot_id2,
  99             observationVariableDbId => $trait_id2,
 100             collector => 'collector1',
 101             observationTimeStamp => '2015-06-16T00:53:26Z',
 102             value => '110'
 103         },
 104     ]
 105 };
 106 $j = encode_json $data;
 107 $req = HTTP::Request->new( "PUT" => "http://localhost:3010/brapi/v1/observations" );
 108 $req->content_type( 'application/json' );
 109 $req->content_length(
 110     do { use bytes; length( $j ) }
 111 );
 112 $req->content( $j );
 113
 114 $ua = LWP::UserAgent->new();
 115 $res = $ua->request($req);
 116 $response = decode_json $res->content;
 117 print STDERR Dumper $response;
 118
 119 #Remove observationdbid from result because it is variable
 120 foreach (@{$response->{result}->{observations}}){
 121     delete $_->{observationDbId};
 122 }
 123
 124 is_deeply($response, {
 125           'result' => {
 126                         'observations' => [
 127                                             {
 128                                               'observationLevel' => 'plot',
 129                                               'observationTimeStamp' => '2015-06-16T00:53:26Z',
 130                                               'germplasmName' => 'test_accession3',
 131                                               'observationUnitName' => 'test_trial210',
 132                                               'uploadedBy' => 'collector1',
 133                                               'collector' => 'collector1',
 134                                               'germplasmDbId' => 38842,
 135                                               'observationUnitDbId' => 38866,
 136                                               'value' => '11',
 137                                               'observationVariableName' => 'dry matter content percentage',
 138                                               'observationVariableDbId' => '70741',
 139                                               'studyDbId' => 137,
 140                                               'externalReferences' => undef,
 141                                               'additionalInfo' => undef,
 142                                             },
 143                                             {
 144                                               'observationLevel' => 'plot',
 145                                               'observationTimeStamp' => '2015-06-16T00:53:26Z',
 146                                               'germplasmName' => 'test_accession4',
 147                                               'observationUnitName' => 'test_trial214',
 148                                               'uploadedBy' => 'collector1',
 149                                               'collector' => 'collector1',
 150                                               'germplasmDbId' => 38843,
 151                                               'observationUnitDbId' => 38870,
 152                                               'value' => '110',
 153                                               'observationVariableDbId' => '70773',
 154                                               'observationVariableName' => 'fresh shoot weight measurement in kg',
 155                                               'studyDbId' => 137,
 156                                               'externalReferences' => undef,
 157                                               'additionalInfo' => undef,
 158                                             }
 159                                           ]
 160                       },
 161           'metadata' => {
 162                           'datafiles' => [],
 163                           'status' => [
 164                                         {
 165                                           'message' => 'BrAPI base call found with page=0, pageSize=10',
 166                                           'messageType' => 'INFO'
 167                                         },
 168                                         {
 169                                           'messageType' => 'INFO',
 170                                           'message' => 'Loading CXGN::BrAPI::v1::Observations'
 171                                         },
 172                                         {
 173                                           'message' => 'Request structure is valid',
 174                                           'messageType' => 'info'
 175                                         },
 176                                         {
 177                                           'messageType' => 'info',
 178                                           'message' => 'Request data is valid'
 179                                         },
 180                                         {
 181                                           'message' => 'File for incoming brapi obserations saved in archive.',
 182                                           'messageType' => 'info'
 183                                         },
 184                                         {
 185                                           'messageType' => 'INFO',
 186                                           'message' => 'All values in your file have been successfully processed!<br><br>2 new values stored<br>0 previously stored values skipped<br>0 previously stored values overwritten<br>0 previously stored values removed<br><br>'
 187                                         }
 188                                       ],
 189                           'pagination' => {
 190                                             'totalPages' => 1,
 191                                             'totalCount' => 2,
 192                                             'pageSize' => 10,
 193                                             'currentPage' => 0
 194                                           }
 195                         }
 196         });
 197
 198 done_testing;