t/unit_mech/AJAX/SequenceMetadata.t

   1 use strict;
   2
   3 use lib 't/lib';
   4
   5 use Test::More tests => 16;
   6
   7 use Data::Dumper;
   8 use JSON;
   9 use File::Copy;
  10
  11 use SGN::Test::Fixture;
  12 use SGN::Test::Data qw/create_test/;
  13 use SGN::Test::WWW::Mechanize;
  14 use LWP::UserAgent;
  15
  16 use SGN::Model::Cvterm;
  17 use CXGN::Genotype::SequenceMetadata;
  18
  19
  20 my $t = SGN::Test::Fixture->new();
  21 my $mech = SGN::Test::WWW::Mechanize->new;
  22 my $ua = LWP::UserAgent->new;
  23 my $schema = $t->bcs_schema;
  24 my $dbh = $mech->context->dbc->dbh;
  25
  26 my $smd = CXGN::Genotype::SequenceMetadata->new(bcs_schema => $schema);
  27 my $smd_script_dir = $t->config->{basepath} . $smd->shell_script_dir;
  28 my $test_file = $t->config->{basepath} . "/t/data/sequence_metadata/gwas_sgn.gff3";
  29
  30 my $genus_name = "SMDTest";
  31 my $species_name = "SMDtest";
  32 my $species = $genus_name . ' ' . $species_name;
  33 my ($organism_rs) = $schema->resultset("Organism::Organism")->create({genus => $genus_name, species => $species_name});
  34 my $feature_organism_id = $organism_rs->organism_id;
  35 my $feature_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'chromosome', 'sequence')->cvterm_id();
  36 my $type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'GWAS Results', 'sequence_metadata_types')->cvterm_id();
  37
  38 my $query_reference_genome_name = "Test Reference Genome";
  39 my $query_feature_name = "SMD_TEST_CHR_1A";
  40 my $query_feature_id;
  41 my $query_type_name = "GWAS Results";
  42 my $query_type_id;
  43 my $query_protocol_name = "Test Protocol";
  44 my $query_protocol_id;
  45
  46
  47 # Get features from test file
  48 my $script = $smd_script_dir . "/get_unique_features.sh";
  49 my $cmd = "bash " . $script . " \"" . $test_file . "\"";
  50 my @features = `$cmd`;
  51 chomp(@features);
  52
  53 # Add features to database
  54 foreach my $feature (@features) {
  55     if ( $feature !~ /^#/ ) {
  56         my ($feature_rs) = $schema->resultset("Sequence::Feature")->create({
  57             organism_id => $feature_organism_id,
  58             name => $feature,
  59             uniquename => $feature,
  60             type_id => $feature_type_id,
  61             is_obsolete => 'f'
  62         });
  63     }
  64 }
  65
  66 # Get attributes from test file
  67 my $attributes_script = $smd_script_dir . "/get_unique_attributes.sh";
  68 my $attributes_cmd = "bash " . $attributes_script . " \"" . $test_file . "\"";
  69 my @attributes = `$attributes_cmd`;
  70 chomp(@attributes);
  71
  72
  73
  74
  75 ##
  76 ## TEST: LOGIN
  77 ## tests = 3
  78 ##
  79 $mech->post_ok('/brapi/v1/token', [ "username"=> "janedoe", "password"=> "secretpw", "grant_type"=> "password" ], "BrAPI Login");
  80 my $response = decode_json $mech->content;
  81 is($response->{'metadata'}->{'status'}->[2]->{'message'}, 'Login Successfull', "Login Succssful");
  82 my $sgn_session_id = $response->{access_token};
  83 isnt($sgn_session_id, '', "SGN Session Token");
  84
  85
  86
  87 ##
  88 ## TEST: VERIFY GFF FILE
  89 ## tests = 2
  90 ##
  91 my %verification_body = (
  92     file => [ $test_file, 'sequence_metadata_upload' ],
  93     species => $species,
  94     "use_existing_protocol" => "false",
  95     "new_protocol_attribute_count" => scalar @attributes
  96 );
  97 my $verification_attribute_count = 1;
  98 foreach my $a (@attributes) {
  99     $verification_body{'new_protocol_attribute_key_' . $verification_attribute_count} = $a;
 100     $verification_attribute_count++;
 101 }
 102
 103 my $verification_response = $ua->post(
 104     'http://localhost:3010/ajax/sequence_metadata/file_upload_verify',
 105     Cookie => 'sgn_session_id=' . $sgn_session_id,
 106     Content_Type => 'form-data',
 107     Content => \%verification_body
 108 );
 109 my $verification_message = decode_json $verification_response->decoded_content;
 110 my $processed_file = $verification_message->{'results'}->{'processed_filepath'};
 111 is($verification_message->{'results'}->{'processed'}, 1, "Process GFF File");
 112 is($verification_message->{'results'}->{'verified'}, 1, "Verify GFF File");
 113
 114
 115
 116 ##
 117 ## TEST 3: STORE GFF FILE
 118 ## tests = 2
 119 ##
 120 my %store_body = (
 121     "processed_filepath" => $processed_file,
 122     "use_existing_protocol" => "false",
 123     "new_protocol_name" => $query_protocol_name,
 124     "new_protocol_description" => "Protocol used for testing the sequence metadata storage",
 125     "new_protocol_sequence_metadata_type" => $type_id,
 126     "new_protocol_reference_genome" => $query_reference_genome_name,
 127     "new_protocol_species" => $species,
 128     "new_protocol_score_description" => "score description",
 129     "new_protocol_attribute_count" => scalar @attributes
 130 );
 131 my $store_attribute_count = 1;
 132 foreach my $a (@attributes) {
 133     $store_body{'new_protocol_attribute_key_' . $store_attribute_count} = $a;
 134     $store_attribute_count++;
 135 }
 136
 137 my $store_response = $ua->post(
 138     'http://localhost:3010/ajax/sequence_metadata/store',
 139     Cookie => 'sgn_session_id=' . $sgn_session_id,
 140     Content_Type => 'form-data',
 141     Content => \%store_body
 142 );
 143 my $store_message = decode_json $store_response->decoded_content;
 144 my $nd_protocol_id = $store_message->{'results'}->{'nd_protocol_id'};
 145 is($store_message->{'results'}->{'stored'}, 1, "Store GFF File");
 146 cmp_ok($store_message->{'results'}->{'chunks'}, 'gt', 0, "Stored Chunks");
 147
 148
 149
 150 ##
 151 ## TEST: GET FEATURES
 152 ## tests = 1
 153 ##
 154 $mech->get('/ajax/sequence_metadata/features');
 155 my $features_response = decode_json($mech->content)->{'features'};
 156 my $missing_features = 0;
 157 foreach my $ff (@features) {
 158     if ( $ff !~ /^#/ ) {
 159         my $found = 0;
 160         foreach my $rf (@$features_response) {
 161             if ( $rf->{'feature_name'} eq $ff ) {
 162                 $found = 1;
 163                 if ( $ff eq $query_feature_name ) {
 164                     $query_feature_id = $rf->{'feature_id'};
 165                 }
 166             }
 167         }
 168         if ( !$found ) {
 169             $missing_features++;
 170         }
 171     }
 172 }
 173 is($missing_features, 0, "Stored and Retrieved Features");
 174
 175
 176
 177 ##
 178 ## TEST: GET DATA TYPES
 179 ## tests = 1
 180 ##
 181 $mech->get('/ajax/sequence_metadata/types');
 182 my $types_response = decode_json($mech->content)->{'types'};
 183 foreach my $type (@$types_response) {
 184     if ( $type->{'type_name'} eq $query_type_name ) {
 185         $query_type_id = $type->{'type_id'};
 186     }
 187 }
 188 cmp_ok(scalar @$types_response, 'gt', 0, "Retrieved Data Types");
 189
 190
 191
 192 ##
 193 ## TEST: GET PROTOCOLS
 194 ## tests = 1
 195 ##
 196 $mech->get('/ajax/sequence_metadata/protocols');
 197 my $protocols_response = decode_json($mech->content)->{'protocols'};
 198 my $found_protocol = 0;
 199 foreach my $protocol (@$protocols_response) {
 200     if ( $protocol->{'nd_protocol_name'} eq $query_protocol_name ) {
 201         if ( $protocol->{'nd_protocol_id'} == $nd_protocol_id ) {
 202             $found_protocol = 1;
 203             $query_protocol_id = $protocol->{'nd_protocol_id'};
 204         }
 205     }
 206 }
 207 is($found_protocol, 1, "Stored and Retrieved Protocol");
 208
 209
 210
 211 ##
 212 ## TEST: QUERY
 213 ## tests = 6
 214 ##
 215 isnt($query_feature_id, undef, "Query Feature ID Defined");
 216 isnt($query_type_id, undef, "Query Type ID Defined");
 217 isnt($query_protocol_id, undef, "Query Protocol ID Defined");
 218
 219 my $params = "feature_id=$query_feature_id&type_id=$query_type_id&nd_protocol_id=$query_protocol_id&";
 220 $params .= "reference_genome=$query_reference_genome_name&start=20000000&end=22000000&";
 221 $params .= "attribute=score|$query_protocol_id|gt|0.03,Locus|$query_protocol_id|eq|TraesCS1A02G038400";
 222
 223 # JSON Format
 224 $mech->get("/ajax/sequence_metadata/query?$params&format=JSON");
 225 my $json_response = decode_json($mech->content);
 226 is_deeply($json_response, {
 227     'results' => [
 228         {
 229             'start' => 21040550,
 230             'featureprop_json_id' => 1,
 231             'type_id' => $query_type_id,
 232             'end' => 21040550,
 233             'type_name' => $query_type_name,
 234             'nd_protocol_id' => $query_protocol_id,
 235             'attributes' => {
 236                     'qvalue' => '0.0455793811186712',
 237                     'Variable' => 'CO_321:0001138',
 238                     'zvalue' => '3.3484904423247',
 239                     'ID' => 'Ex_c64327_523',
 240                     'Trait' => 'SDS sedimentation',
 241                     'Locus' => 'TraesCS1A02G038400',
 242                     'Population' => 'TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon',
 243                     'pvalue' => '0.000812530833156448'
 244                 },
 245             'feature_id' => $query_feature_id,
 246             'nd_protocol_name' => $query_protocol_name,
 247             'feature_name' => $query_feature_name,
 248             'score' => '0.0455793811186712',
 249             'links' => {}
 250         }
 251     ]
 252 }, 'Query JSON Response');
 253
 254
 255 # GA4GH Format
 256 $mech->get("/ajax/sequence_metadata/query?$params&format=GA4GH");
 257 my $ga4gh_response = decode_json($mech->content);
 258 is_deeply($ga4gh_response, {
 259     'features' => [
 260         {
 261             'end' => 21040550,
 262             'feature_set_id' => $query_protocol_id,
 263             'reference_name' => $query_feature_name,
 264             'parent_id' => $query_feature_id,
 265             'start' => 21040550,
 266             'attributes' => {
 267                 'Population' => [
 268                     'TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon'
 269                 ],
 270                 'pvalue' => [
 271                     '0.000812530833156448'
 272                 ],
 273                 'zvalue' => [
 274                     '3.3484904423247'
 275                 ],
 276                 'Locus' => [
 277                     'TraesCS1A02G038400'
 278                 ],
 279                 'bb_metadata' => {
 280                     'type_name' => [
 281                         'GWAS Results'
 282                     ],
 283                     'type_id' => [
 284                         $query_type_id
 285                     ],
 286                     'nd_protocol_id' => [
 287                         $query_protocol_id
 288                     ],
 289                     'nd_protocol_name' => [
 290                         $query_protocol_name
 291                     ]
 292                 },
 293                 'ID' => [
 294                     'Ex_c64327_523'
 295                 ],
 296                 'Variable' => [
 297                     'CO_321:0001138'
 298                 ],
 299                 'Trait' => [
 300                     'SDS sedimentation'
 301                 ],
 302                 'score' => [
 303                     '0.0455793811186712'
 304                 ],
 305                 'qvalue' => [
 306                     '0.0455793811186712'
 307                 ]
 308             },
 309             'id' => '1.0'
 310         }
 311     ]
 312 }, "Query GA4GH Response");
 313
 314 # GFF Format
 315 $mech->get("/ajax/sequence_metadata/query?$params&format=gff");
 316 my $gff_response = $mech->content;
 317 like(
 318     $gff_response,
 319     qr/$query_feature_name\t\.\t\.\t21040550\t21040550\t0\.0455793811186712\t\.\t\.\t.*/,
 320     "Query GFF Response"
 321 );
 322
 323
 324
 325 ##
 326 ## CLEANUP
 327 ##
 328
 329 # Remove the SMD feature props
 330 $dbh->do("DELETE FROM public.featureprop_json WHERE nd_protocol_id = ?", undef, $nd_protocol_id);
 331
 332 # Remove the features
 333 foreach my $feature (@features) {
 334     if ( $feature !~ /^#/ ) {
 335         $dbh->do("DELETE FROM public.feature WHERE uniquename = ?", undef, $feature);
 336     }
 337 }
 338
 339 # Delete test organism
 340 $organism_rs->delete();
 341
 342 # Remove the SMD nd_protocol
 343 $dbh->do("DELETE FROM public.nd_protocolprop WHERE nd_protocol_id = ?", undef, $nd_protocol_id);
 344 $dbh->do("DELETE FROM public.nd_protocol WHERE nd_protocol_id = ?", undef, $nd_protocol_id);
 345
 346
 347
 348
 349 done_testing();