Bio-WebService-LANL-SequenceLocator

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META.json  view on Meta::CPAN

            "Test::LongString" : "0",
            "Test::Pod" : "1.41"
         }
      },
      "runtime" : {
         "requires" : {
            "Data::Dumper" : "0",
            "HTML::LinkExtor" : "0",
            "HTML::TableExtract" : "0",
            "HTML::TokeParser" : "0",
            "HTTP::Request::Common" : "0",
            "LWP::Protocol::https" : "0",
            "LWP::UserAgent" : "0",
            "List::AllUtils" : "0",
            "Moo" : "0",
            "perl" : "5.018",
            "strictures" : "0"
         }
      },
      "test" : {
         "requires" : {

META.yml  view on Meta::CPAN

      Plack::Middleware::ReverseProxy: '0'
      Server::Starter: '0'
      Starlet: '0'
      Text::CSV: '0'
      Web::Simple: '0'
requires:
  Data::Dumper: '0'
  HTML::LinkExtor: '0'
  HTML::TableExtract: '0'
  HTML::TokeParser: '0'
  HTTP::Request::Common: '0'
  LWP::Protocol::https: '0'
  LWP::UserAgent: '0'
  List::AllUtils: '0'
  Moo: '0'
  perl: '5.018'
  strictures: '0'
resources:
  bugtracker: https://github.com/MullinsLab/Bio-WebService-LANL-SequenceLocator/issues
  homepage: https://indra.mullins.microbiol.washington.edu/locate-sequence/
  repository: https://github.com/MullinsLab/Bio-WebService-LANL-SequenceLocator.git

Makefile.PL  view on Meta::CPAN

  },
  "DISTNAME" => "Bio-WebService-LANL-SequenceLocator",
  "LICENSE" => "perl",
  "MIN_PERL_VERSION" => "5.018",
  "NAME" => "Bio::WebService::LANL::SequenceLocator",
  "PREREQ_PM" => {
    "Data::Dumper" => 0,
    "HTML::LinkExtor" => 0,
    "HTML::TableExtract" => 0,
    "HTML::TokeParser" => 0,
    "HTTP::Request::Common" => 0,
    "LWP::Protocol::https" => 0,
    "LWP::UserAgent" => 0,
    "List::AllUtils" => 0,
    "Moo" => 0,
    "strictures" => 0
  },
  "TEST_REQUIRES" => {
    "Test::More" => "0.88"
  },
  "VERSION" => 20170324,

Makefile.PL  view on Meta::CPAN

    "TESTS" => "t/*.t"
  }
);


my %FallbackPrereqs = (
  "Data::Dumper" => 0,
  "HTML::LinkExtor" => 0,
  "HTML::TableExtract" => 0,
  "HTML::TokeParser" => 0,
  "HTTP::Request::Common" => 0,
  "LWP::Protocol::https" => 0,
  "LWP::UserAgent" => 0,
  "List::AllUtils" => 0,
  "Moo" => 0,
  "Test::More" => "0.88",
  "strictures" => 0
);


unless ( eval { ExtUtils::MakeMaker->VERSION(6.63_03) } ) {

cpanfile  view on Meta::CPAN

requires 'perl', '5.018';

requires 'Data::Dumper';
requires 'HTML::LinkExtor';
requires 'HTML::TableExtract';
requires 'HTML::TokeParser';
requires 'HTTP::Request::Common';
requires 'LWP::UserAgent';
requires 'LWP::Protocol::https';
requires 'List::AllUtils';
requires 'Moo';
requires 'strictures';

feature 'server', 'Web API server' => sub {
    requires 'File::Share';
    requires 'IO::String';
    requires 'JSON';

lib/Bio/WebService/LANL/SequenceLocator.pm  view on Meta::CPAN

=cut

package Bio::WebService::LANL::SequenceLocator;

use Moo;
use Data::Dumper;
use HTML::LinkExtor;
use HTML::TableExtract;
use HTML::TokeParser;
use HTTP::Request::Common;
use List::AllUtils qw< pairwise part min max >;

our $VERSION = 20170324;

=head1 METHODS

=head2 new

Returns a new instance of this class.  An optional parameter C<agent_string>
should be provided to identify yourself to LANL out of politeness.  See the

xt/live.t  view on Meta::CPAN

use strict;
use warnings FATAL => 'all';
use 5.018;

use Test::More;
use Test::Deep;
use Test::LongString;
use Path::Tiny;
use JSON qw< decode_json >;
use FindBin '$RealBin';
use HTTP::Request::Common;

use_ok('Bio::WebService::LANL::SequenceLocator');
use_ok('Bio::WebService::LANL::SequenceLocator::Server');

my @tests = (
    {   name        => "mixed bases",
        sequences   => ['SLYNTVAVLYYVHQR', 'TCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGG'],
        json        => path("$RealBin/data/mixed-bases.json"),
        csv         => path("$RealBin/data/mixed-bases.csv"),
    },