App-Mimosa

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Build.PL  view on Meta::CPAN

        'Catalyst::Plugin::Session'                    => 0,
        'Catalyst::Plugin::Session::Store::FastMmap'   => 0,
        'Catalyst::Plugin::Session::State::Cookie'     => 0,
        'Catalyst::Plugin::Static::Simple'             => 0,
        'Catalyst::Runtime'                            => '5.80029',
        'Catalyst::View::Bio::SeqIO'                   => 0,
        'Catalyst::View::Email'                        => 0,
        'Catalyst::View::HTML::Mason'                  => 0,
        'Class::Accessor::Fast'                        => 0,
        'Config::JFDI'                                 => 0,
        'DateTime'                                     => 0,
        'Digest::SHA1'                                 => 0,
        'DBIx::Class'                                  => '0.08127',
        'File::Temp'                                   => 0,
        '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',

META.json  view on Meta::CPAN

            "Catalyst::Plugin::Session::State::Cookie" : 0,
            "Catalyst::Plugin::Session::Store::FastMmap" : 0,
            "Catalyst::Plugin::Static::Simple" : 0,
            "Catalyst::Runtime" : "5.80029",
            "Catalyst::View::Bio::SeqIO" : 0,
            "Catalyst::View::Email" : 0,
            "Catalyst::View::HTML::Mason" : 0,
            "Class::Accessor::Fast" : 0,
            "Config::JFDI" : 0,
            "DBIx::Class" : "0.08127",
            "DateTime" : 0,
            "Digest::SHA1" : 0,
            "File::Slurp" : "9999.15",
            "File::Temp" : 0,
            "HTML::Entities" : 0,
            "IO::String" : 0,
            "IPC::Cmd" : "0.70",
            "IPC::Run" : 0,
            "IPC::System::Simple" : 0,
            "JSON::Any" : "1.25",
            "Moose" : "1.19",

META.yml  view on Meta::CPAN

  Catalyst::Plugin::Session::State::Cookie: 0
  Catalyst::Plugin::Session::Store::FastMmap: 0
  Catalyst::Plugin::Static::Simple: 0
  Catalyst::Runtime: 5.80029
  Catalyst::View::Bio::SeqIO: 0
  Catalyst::View::Email: 0
  Catalyst::View::HTML::Mason: 0
  Class::Accessor::Fast: 0
  Config::JFDI: 0
  DBIx::Class: 0.08127
  DateTime: 0
  Digest::SHA1: 0
  File::Slurp: 9999.15
  File::Temp: 0
  HTML::Entities: 0
  IO::String: 0
  IPC::Cmd: 0.70
  IPC::Run: 0
  IPC::System::Simple: 0
  JSON::Any: 1.25
  Moose: 1.19

Makefile.PL  view on Meta::CPAN

                   'Catalyst::Plugin::Session::Store::FastMmap' => 0,
                   'Catalyst::Plugin::Static::Simple' => 0,
                   'Catalyst::Runtime' => '5.80029',
                   'Catalyst::Test' => 0,
                   'Catalyst::View::Bio::SeqIO' => 0,
                   'Catalyst::View::Email' => 0,
                   'Catalyst::View::HTML::Mason' => 0,
                   'Class::Accessor::Fast' => 0,
                   'Config::JFDI' => 0,
                   'DBIx::Class' => '0.08127',
                   'DateTime' => 0,
                   'Digest::SHA1' => 0,
                   'File::Slurp' => '9999.15',
                   'File::Temp' => 0,
                   'HTML::Entities' => 0,
                   'HTML::Lint' => 0,
                   'HTML::Tagset' => '3.20',
                   'IO::String' => 0,
                   'IPC::Cmd' => '0.70',
                   'IPC::Run' => 0,
                   'IPC::System::Simple' => 0,

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

use Path::Class;

use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;
use File::Spec::Functions;
use Bio::GMOD::Blast::Graph;

use App::Mimosa::Job;
use App::Mimosa::Database;
use Try::Tiny;
use DateTime;
use HTML::Entities;
use Digest::SHA1 qw/sha1_hex/;
#use Carp::Always;
use Cwd;

BEGIN { extends 'Catalyst::Controller' }
with 'Catalyst::Component::ApplicationAttribute';

#
# Sets the actions in this controller to be registered with no prefix

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

        alphabet               => $c->stash->{alphabet} || 'nucleotide',
        output_file            => "$output_file",
        input_file             => "$input_file",
        alignment_view         => $alignment_view,
            map { $_ => $c->req->param($_) || '' }
            qw/ program maxhits output_graphs evalue matrix /,
    );

    # Regardless of it working, the job is now complete
    my $rs   = $c->model('BCS')->resultset('Mimosa::Job');
    $rs->search( { mimosa_job_id => $j->job_id } )->update( { end_time => DateTime->now } );

    my $error = $j->run;
    if ($error) {
        ( $c->stash->{error} = $error ) =~ s!\n!<br />!g;
        $c->detach( $error =~ /Could not calculate ungapped/i ? '/input_error' : '/error' );
    } else {

        # stat the output file before opening it in hopes of avoiding
        # some kind of bizarre race condition i've been seeing in
        # which the file doesn't appear to be visible yet to the web

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

        uploads => $c->req->uploads,
        #TODO: add the user - user   => $c->user,
    };

    my $rs = $c->model('BCS')->resultset('Mimosa::Job');
    my $jobs = $rs->search( { sha1 => $sha1 } );
    if ($jobs->count == 0) { # not a duplicate job, proceed
        my $job = $rs->create({
            sha1       => $sha1,
            user       => $c->user_exists ? $c->user->get('username') : 'anonymous',
            start_time => DateTime->now(),
        });
        $c->stash->{job_id} = $job->mimosa_job_id();
    } else { # this is a duplicate, check if it is still running and notify user appropriately
        my $job = $jobs->single;
        my ($start,$end) = ($job->start_time, $job->end_time);
        my $jid          = $job->mimosa_job_id;
        my $user         = $job->user;
        # TODO: add more info to the error message
        if( $end ) { # already finished
            $c->stash->{job_id} = $jid;

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

package App::Mimosa::Schema::BCS::Result::Mimosa::Job;
use strict;
use warnings;

use base 'DBIx::Class::Core';

__PACKAGE__->load_components(qw/InflateColumn::DateTime/);


=head1 NAME

App::Mimosa::Schema::BCS::Result::Mimosa::Job - Mimosa Job

=head1 COLUMNS

=cut