t/unit_mech/AJAX/MarkersetAndSearch.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 CXGN::List;
   9 use CXGN::Genotype::Protocol;
  10 use Data::Dumper;
  11 use JSON;
  12
  13 local $Data::Dumper::Indent = 0;
  14
  15 my $f = SGN::Test::Fixture->new();
  16 my $schema = $f->bcs_schema;
  17 my $dbh = $schema->storage->dbh;
  18 my $people_schema = $f->people_schema;
  19
  20 my $mech = Test::WWW::Mechanize->new;
  21
  22 $mech->post_ok('http://localhost:3010/brapi/v1/token', [ "username"=> "janedoe", "password"=> "secretpw", "grant_type"=> "password" ]);
  23 my $response = decode_json $mech->content;
  24 is($response->{'metadata'}->{'status'}->[2]->{'message'}, 'Login Successfull');
  25 my $sgn_session_id = $response->{access_token};
  26
  27 my $location_rs = $schema->resultset('NaturalDiversity::NdGeolocation')->search({description => 'Cornell Biotech'});
  28 my $location_id = $location_rs->first->nd_geolocation_id;
  29
  30 my $bp_rs = $schema->resultset('Project::Project')->search({name => 'test'});
  31 my $breeding_program_id = $bp_rs->first->project_id;
  32
  33 #adding genotyping data for testing markerset and accession search
  34 my $file = $f->config->{basepath}."/t/data/genotype_data/test_genotype_upload.vcf";
  35
  36 my $ua = LWP::UserAgent->new;
  37 $response = $ua->post(
  38         'http://localhost:3010/ajax/genotype/upload',
  39         Content_Type => 'form-data',
  40         Content => [
  41             upload_genotype_vcf_file_input => [ $file, 'genotype_vcf_data_upload' ],
  42             "sgn_session_id"=>$sgn_session_id,
  43             "upload_genotypes_species_name_input"=>"Manihot esculenta",
  44             "upload_genotype_vcf_project_name"=>"test_genotype_project",
  45             "upload_genotype_location_select"=>$location_id,
  46             "upload_genotype_year_select"=>"2015",
  47             "upload_genotype_breeding_program_select"=>$breeding_program_id,
  48             "upload_genotype_vcf_observation_type"=>"accession",
  49             "upload_genotype_vcf_facility_select"=>"IGD",
  50             "upload_genotype_vcf_project_description"=>"Test uploading",
  51             "upload_genotype_vcf_protocol_name"=>"2015_genotype_protocol",
  52             "upload_genotype_vcf_include_igd_numbers"=>0,
  53             "upload_genotype_vcf_reference_genome_name"=>"Mesculenta_511_v7",
  54             "upload_genotype_add_new_accessions"=>0,
  55             "upload_genotype_accept_warnings"=>1,
  56         ]
  57     );
  58
  59 #print STDERR Dumper $response;
  60 ok($response->is_success);
  61 my $message = $response->decoded_content;
  62 my $message_hash = decode_json $message;
  63 is($message_hash->{success}, 1);
  64 ok($message_hash->{project_id});
  65 ok($message_hash->{nd_protocol_id});
  66
  67 my $protocol_id = $message_hash->{nd_protocol_id};
  68 my $project_id = $message_hash->{project_id};
  69
  70 #test adding markerset
  71 $mech->get_ok('http://localhost:3010/list/new?name=test_markerset_1&desc=test');
  72 $response = decode_json $mech->content;
  73 my $markerset_list_id = $response->{list_id};
  74 #print STDERR "MARKERSET LIST ID =".Dumper($markerset_list_id)."\n";
  75 ok($markerset_list_id);
  76
  77 $mech->get_ok('http://localhost:3010/list/item/add?list_id='.$markerset_list_id.'&element={"genotyping_protocol_name":"2015_genotype_protocol", "genotyping_protocol_id":'.$protocol_id.', "genotyping_data_type":"Dosage"}');
  78 $response = decode_json $mech->content;
  79 is($response->[0],'SUCCESS');
  80
  81 $mech->get_ok('http://localhost:3010/list/item/add?list_id='.$markerset_list_id.'&element={"marker_name":"S1_21597", "allele_dosage":"0"}');
  82 $response = decode_json $mech->content;
  83 is($response->[0],'SUCCESS');
  84
  85 $mech->get_ok('http://localhost:3010/list/new?name=test_markerset_2&desc=test');
  86 $response = decode_json $mech->content;
  87 my $markerset2_list_id = $response->{list_id};
  88 #print STDERR "MARKERSET LIST ID =".Dumper($markerset_list_id)."\n";
  89 ok($markerset2_list_id);
  90
  91 $mech->get_ok('http://localhost:3010/list/item/add?list_id='.$markerset2_list_id.'&element={"genotyping_protocol_name":"2015_genotype_protocol", "genotyping_protocol_id":'.$protocol_id.', "genotyping_data_type":"SNP"}');
  92 $response = decode_json $mech->content;
  93 is($response->[0],'SUCCESS');
  94
  95 $mech->get_ok('http://localhost:3010/list/item/add?list_id='.$markerset2_list_id.'&element={"marker_name":"S1_21597","allele1":"G","allele2":"G"}');
  96 $response = decode_json $mech->content;
  97 is($response->[0],'SUCCESS');
  98
  99 #create a list of accessions
 100 $mech->get_ok('http://localhost:3010/list/new?name=accession_list_1&desc=test');
 101 $response = decode_json $mech->content;
 102 my $accession_list_id = $response->{list_id};
 103 #print STDERR "ACCESSION LIST ID =".Dumper($accession_list_id)."\n";
 104 ok($accession_list_id);
 105
 106 my @accessions = qw(UG120001 UG120002 UG120003 UG120004 UG120005 UG120006 UG120007 UG120008 UG120009 UG120010 UG120011 UG120012 UG120013 UG120014 UG120015 UG120016 UG120017 UG120018 UG120019 UG120020 UG120021);
 107
 108 my $accession_list = CXGN::List->new( { dbh=>$dbh, list_id => $accession_list_id });
 109 my $response = $accession_list->add_bulk(\@accessions);
 110 is($response->{'count'},21);
 111
 112 #test searching accessions with dosage
 113 $mech->get_ok('http://localhost:3010/ajax/search/search_stocks_using_markerset?stock_list_id='.$accession_list_id.'&markerset_id='.$markerset_list_id);
 114 $response = decode_json $mech->content;
 115 #print STDERR "RESPONSE 4=".Dumper($response)."\n";
 116 my %result_hash1 = %{$response};
 117 my $selected_accessions_dosage = $result_hash1{'data'};
 118 my $number_of_accessions_dosage = scalar@$selected_accessions_dosage;
 119 is($number_of_accessions_dosage,16);
 120
 121 #test searching accessions with snp
 122 $mech->get_ok('http://localhost:3010/ajax/search/search_stocks_using_markerset?stock_list_id='.$accession_list_id.'&markerset_id='.$markerset2_list_id);
 123 $response = decode_json $mech->content;
 124 #print STDERR "RESPONSE 4=".Dumper($response)."\n";
 125 my %result_hash2 = %{$response};
 126 my $selected_accessions_snp = $result_hash2{'data'};
 127 my $number_of_accessions_snp = scalar@$selected_accessions_snp;
 128 is($number_of_accessions_snp,14);
 129
 130 # Delete genotype protocol after testing
 131 $mech->get("/ajax/genotyping_protocol/delete/$protocol_id");
 132 $response = decode_json $mech->content;
 133 is($response->{'success'}, 1);
 134
 135 #Delete created list
 136 CXGN::List::delete_list($schema->storage->dbh, $markerset_list_id);
 137 CXGN::List::delete_list($schema->storage->dbh, $markerset2_list_id);
 138 CXGN::List::delete_list($schema->storage->dbh, $accession_list_id);
 139 $schema->resultset("Project::Project")->find({project_id=>$project_id})->delete();
 140
 141 $f->clean_up_db();
 142
 143 done_testing();