App-Mimosa

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Build.PL  view on Meta::CPAN

        'File::Slurp'                                  => '9999.15',
        'HTML::Entities'                               => 0,
        'IPC::Cmd'                                     => '0.70',
        'IPC::Run'                                     => 0,
        'IPC::System::Simple'                          => 0,
        'IO::String'                                   => 0,
        'JSON::Any'                                    => '1.25',
        'Moose'                                        => '1.19',
        'Set::Scalar'                                  => 0,
        'SQL::Translator'                              => '0.11007',
        'namespace::autoclean'                         => 0,
        'Path::Class'                                  => 0,
        'YAML'                                         => 0,
    },
    add_to_cleanup      => [ 'mimosa.db', 'mimosa_test.db', catfile(qw/examples data .mimosa_cache*/),
                              catfile(qr/t data .mimosa_cache*/), catfile(qw/t var BCS.db/)  ],
    create_makefile_pl  => 'traditional',
    meta_merge     => {
        resources => {
            repository  => 'http://github.com/gmod/mimosa/tree/master'
        },

META.json  view on Meta::CPAN

            "IPC::Run" : 0,
            "IPC::System::Simple" : 0,
            "JSON::Any" : "1.25",
            "Moose" : "1.19",
            "Path::Class" : 0,
            "SQL::Translator" : "0.11007",
            "Set::Scalar" : 0,
            "YAML" : 0,
            "aliased" : 0,
            "autodie" : "2.00",
            "namespace::autoclean" : 0
         }
      }
   },
   "provides" : {
      "App::Mimosa" : {
         "file" : "lib/App/Mimosa.pm",
         "version" : "0.02"
      },
      "App::Mimosa::Aligner" : {
         "file" : "lib/App/Mimosa/Aligner.pm",

META.yml  view on Meta::CPAN

  IPC::Run: 0
  IPC::System::Simple: 0
  JSON::Any: 1.25
  Moose: 1.19
  Path::Class: 0
  SQL::Translator: 0.11007
  Set::Scalar: 0
  YAML: 0
  aliased: 0
  autodie: 2.00
  namespace::autoclean: 0
resources:
  license: http://dev.perl.org/licenses/
  repository: http://github.com/gmod/mimosa/tree/master
version: 0.02

Makefile.PL  view on Meta::CPAN

                   'Path::Class' => 0,
                   'SQL::Translator' => '0.11007',
                   'Set::Scalar' => 0,
                   'Test::DBIx::Class' => 0,
                   'Test::JSON' => '0.11',
                   'Test::Most' => 0,
                   'Test::WWW::Mechanize::Catalyst' => '0.56',
                   'YAML' => 0,
                   'aliased' => 0,
                   'autodie' => '2.00',
                   'namespace::autoclean' => 0
                 },
  'INSTALLDIRS' => 'site',
  'EXE_FILES' => [],
  'PL_FILES' => {},
  'test' => {
              'TESTS' => 't/*.t t/var/*.t t/data/*.t t/data/extra/*.t t/integration/*.t t/lib/*.t t/lib/App/*.t t/lib/App/Mimosa/*.t t/lib/App/Mimosa/Test/*.t t/etc/*.t'
            }
)
;

lib/App/Mimosa.pm  view on Meta::CPAN

package App::Mimosa;
use Moose;
use namespace::autoclean;

use Catalyst::Runtime 5.80;

# Set flags and add plugins for the application
#
#         -Debug: activates the debug mode for very useful log messages
#   ConfigLoader: will load the configuration from a Config::General file in the
#                 application's home directory
# Static::Simple: will serve static files from the application's root
#                 directory

lib/App/Mimosa/Controller/Auth.pm  view on Meta::CPAN

package App::Mimosa::Controller::Auth;
use Moose;
use namespace::autoclean;

BEGIN { extends 'Catalyst::Controller' }

sub authentication :Path('/authenticate') {
    my ( $self, $c ) = @_;

    my $user     = $c->req->params->{user};
    my $password = $c->req->params->{password};

    if ( $user && $password ) {

lib/App/Mimosa/Controller/JSON.pm  view on Meta::CPAN

package App::Mimosa::Controller::JSON;
use Moose;
use Bio::Chado::Schema;
use File::Spec::Functions;
use Set::Scalar;
use Digest::SHA1 'sha1_hex';
use App::Mimosa::Util qw/slurp/;

use namespace::autoclean;

BEGIN { extends 'Catalyst::Controller::REST' }

__PACKAGE__->config(
    default   => 'application/json',
    stash_key => 'rest',
    'map' => {
        # Work around an ExtJS bug that sends the wrong content-type
        'text/html'        => 'JSON',
    }

lib/App/Mimosa/Controller/Root.pm  view on Meta::CPAN

package App::Mimosa::Controller::Root;
use Moose;
use namespace::autoclean;
use autodie qw/:all/;

use App::Mimosa::Util qw/slurp/;
use File::Slurp qw/write_file/;
use File::Temp qw/tempfile/;
use IO::String;
use File::Spec::Functions;

use Storable 'freeze';
use Digest::SHA1 'sha1_hex';

lib/App/Mimosa/Controller/Sequence.pm  view on Meta::CPAN

package App::Mimosa::Controller::Sequence;
use Moose;
use Bio::Chado::Schema;
use File::Spec::Functions;
use App::Mimosa::Database;
use JSON::Any;
use Data::Dumper;
use namespace::autoclean;

BEGIN { extends 'Catalyst::Controller' };

sub sequence_sha1 :Path("/api/sequence/sha1/") :Args(2) {
    my ( $self, $c, $composite_sha1, $name ) = @_;
    my $bcs = $c->model('BCS');

    $name =~ s/\.txt$//g;
    $name =~ s/\.fasta$//g;

lib/App/Mimosa/Database.pm  view on Meta::CPAN

package App::Mimosa::Database;
use Moose;
use namespace::autoclean;
use Moose::Util::TypeConstraints;
use Cwd;

use File::Spec::Functions;
use File::Basename;
use autodie ':all';

use Bio::BLAST::Database;
#use Carp::Always;

lib/App/Mimosa/Job.pm  view on Meta::CPAN

package App::Mimosa::Job;
use Moose;
use namespace::autoclean;
use autodie ':all';

use Bio::SeqIO;
use Moose::Util::TypeConstraints;
use Bio::BLAST::Database;
use File::Spec::Functions;

use IPC::Run qw/timeout/;

# Good breakdown of commandline flags

lib/App/Mimosa/View/SeqIO.pm  view on Meta::CPAN

package App::Mimosa::View::SeqIO;
use Moose;
use Bio::Chado::Schema;
use File::Spec::Functions;
use App::Mimosa::Database;
use JSON::Any;

use namespace::autoclean;

BEGIN { extends 'Catalyst::View::Bio::SeqIO' };

__PACKAGE__->config(
    default_seqio_args => {
        -width => 80,
    },
    default_format       => 'fasta',
    default_content_type => 'text/plain',
    content_type_map     => {