App-Mimosa

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t/005_submit_route.t  view on Meta::CPAN

use strict;
use warnings;
use Test::Most tests => 25;

use lib 't/lib';
use App::Mimosa::Test;
use App::Mimosa::Util qw/clean_up_indices/;
use Test::DBIx::Class;

use File::Slurp qw/slurp/;
use HTTP::Request::Common;
use File::Spec::Functions;
#use Carp::Always;

fixtures_ok 'basic_ss';

{
    my $seq = slurp(catfile(qw/t data blastdb_test.nucleotide.seq/));
    my $response = request POST '/submit', [
                    program                => 'tblastx',
                    sequence_input_file    => '',

t/009_download_raw.t  view on Meta::CPAN

use Test::Most tests => 5;
use strict;
use warnings;

use lib 't/lib';
use App::Mimosa::Test;

use File::Slurp qw/slurp/;
use HTTP::Request::Common;
use File::Spec::Functions;
use Test::DBIx::Class;

fixtures_ok 'basic_job';

{
    my $response = request GET '/api/report/raw/42', [
    ];
    is($response->code, 400, 'Downloading the raw report of an invalid Job id should fail');
    like($response->content,qr/does not exist/);

t/010_post_index.t  view on Meta::CPAN

use Test::Most tests => 3;
use strict;
use warnings;

use lib 't/lib';
use App::Mimosa::Test;
use Test::DBIx::Class;

use File::Slurp qw/slurp/;
use HTTP::Request::Common;
use File::Spec::Functions;
use HTML::Entities;

fixtures_ok 'basic_ss';

my $seq = slurp(catfile(qw/t data blastdb_test.nucleotide.seq/));
my $eseq = encode_entities($seq);
{
    my $response = request POST '/', [
                    sequence_input         => $seq,

t/010_submit_invalid.t  view on Meta::CPAN

use Test::Most tests => 3;
use Modern::Perl;

use lib 't/lib';
use App::Mimosa::Test;
use Test::DBIx::Class;

use File::Slurp qw/slurp/;
use HTTP::Request::Common;
use File::Spec::Functions;

fixtures_ok 'basic_ss';

{
    my $seq = <<SEQ;
> guano pie
ATIUSADHJKSHDJHSDFKJSDHFKJSDHFKJSDHFKJSDHFKJSDH
SEQ
    my $f = sub {

t/011_config_min_seq_length.t  view on Meta::CPAN

BEGIN {
    $ENV{CATALYST_CONFIG_LOCAL_SUFFIX} = 'testing2';

}

use lib 't/lib';
use App::Mimosa::Test;
use Test::DBIx::Class;

use File::Slurp qw/slurp/;
use HTTP::Request::Common;
use File::Spec::Functions;

fixtures_ok 'basic_ss';

my $response = request POST '/submit', [
                program                 => 'blastn',
                sequence                => ">fasta title\nabitsmall",
                maxhits                 => 100,
                matrix                  => 'BLOSUM62',
                evalue                  => 0.1,

t/014_submit_multiple_sequence_sets.t  view on Meta::CPAN

use Test::Most tests => 7;
use strict;
use warnings;

use lib 't/lib';
use App::Mimosa::Test;
use Test::DBIx::Class;

use File::Slurp qw/slurp/;
use HTTP::Request::Common;
use File::Spec::Functions;
#use Carp::Always;
use Data::Dumper;

fixtures_ok 'basic_ss';

BEGIN {
    # This is the SHA1 of the composition of the FASTA for mimosa_sequence_set_id's 1 and 2
    # We unconditionally remove it so that we always test the creation of it
    unlink catfile( app->config->{sequence_data_dir}, ".mimosa_cache_ebe9f24f7c4bd899d31a058a703045ed4d9678c8.seq" );

t/020_auth.t  view on Meta::CPAN

BEGIN {
    $ENV{CATALYST_CONFIG_LOCAL_SUFFIX} = 'testing_auth';
}

use lib 't/lib';
use App::Mimosa::Test;
use Test::DBIx::Class;

use File::Slurp qw/slurp/;
use HTTP::Request::Common;
use File::Spec::Functions;
#use Carp::Always;

fixtures_ok 'basic_ss';

{
    my $response = request GET '/';
    like($response->content,qr/Login/, 'index page is a login if allow_anonymous=0');
}

t/025_sequence_api.t  view on Meta::CPAN

use Test::Most tests => 17;
use strict;
use warnings;

use lib 't/lib';
use App::Mimosa::Test;
use Test::DBIx::Class;
use HTTP::Request::Common;
use File::Spec::Functions;
use File::Slurp qw/slurp/;
use Test::JSON;

fixtures_ok 'basic_ss';

# we need to generate a report first, so our db gets indexed

my $seq = slurp(catfile(qw/t data blastdb_test.nucleotide.seq/));
my $response = request POST '/submit', [

t/026_abs_path_data_dir.t  view on Meta::CPAN

use warnings;

BEGIN {
    $ENV{CATALYST_CONFIG_LOCAL_SUFFIX} = 'testing_abs_path_data_dir';
}

use lib 't/lib';
use App::Mimosa::Test;
use Test::DBIx::Class;
use Test::JSON;
use HTTP::Request::Common;
use File::Spec::Functions;

my $r    = request('/api/grid/json.json?blarg=poop');
my $json = $r->content;
is_valid_json( $json, 'it returns valid JSON') or diag $json;
is_json($json, <<JSON, 'got the JSON we expected');
{"rows":[{"mimosa_sequence_set_id":1,"name":"chupacabra_dna.seq","description":null,"alphabet":"nucleotide"}],"total":0}
JSON

t/030_download_html_report.t  view on Meta::CPAN

use Test::Most tests => 7;
use strict;
use warnings;

use lib 't/lib';
use App::Mimosa::Test;

use File::Slurp qw/slurp/;
use HTTP::Request::Common;
use File::Spec::Functions;
use Test::DBIx::Class;

fixtures_ok 'basic_job';

{
    my $response = request GET '/api/report/raw/42', [
    ];
    is($response->code, 400, 'Downloading the raw report of an invalid Job id should fail');
    like($response->content,qr/does not exist/);