App-Mimosa
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## Who is Mimosa for?
Mimosa is intended to be used by evolutionary biology researchers who do
sequence alignment against sets of nucleotide or protein data. These sets could
all be for different organisms, or all the same organism. Mimosa doesn't care.
If the data is public, Mimosa can be installed on a publicly-availabe website,
and allow sequence aligment by collaborators. If the data is pre-publication
and still actively changing, Mimosa can also be setup to only be accessed by
certain persons, either people on the local intranet, or those logging in with
a username and password.
## Why does Mimosa exist? Aren't there a lot of things that already do this?
Mimosa exists to solve the problem of making a standalone sequence alignment
web interface. All existing sequence alignment web interfaces are either tightly
coupled to legacy codebases, difficult to deploy, or just plain *unfriendly* to
end users.
Mimosa plans on being an easy-to-install standalone sequence aligner, which
can be integrated into an existing website via a REST interface.
lib/App/Mimosa.pm view on Meta::CPAN
__PACKAGE__->config(
name => 'Mimosa',
# Disable deprecated behavior needed by old applications
disable_component_resolution_regex_fallback => 1,
default_view => 'Mason',
'Plugin::Authentication' => {
default => {
credential => {
class => 'Password',
password_field => 'password',
password_type => 'clear'
},
store => {
class => 'Minimal',
users => {
petunia => {
password => "cUC598",
},
}
}
}
}
);
# Start the application
__PACKAGE__->setup();
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 ) {
if ( $c->authenticate( { username => $user,
password => $password } ) ) {
$c->forward('/show_grid');
} else {
$c->stash->{error} = 'Incorrect username/password. Please <a href="/">try again</a>.';
$c->detach('/input_error');
}
} else {
$c->stash->{error} = 'You must provide both a username and password. Please <a href="/">try again</a>.';
$c->detach('/input_error');
}
}
1;
lib/App/Mimosa/Model/BCS.pm view on Meta::CPAN
package App::Mimosa::Model::BCS;
use strict;
use base 'Catalyst::Model::DBIC::Schema';
__PACKAGE__->config(
schema_class => 'App::Mimosa::Schema::BCS',
connect_info => {
dsn => 'dbi:SQLite:mimosa.db',
user => '',
password => '',
}
);
=head1 NAME
App::Mimosa::Model::BCS - Catalyst DBIC Schema Model
=head1 SYNOPSIS
See L<App::Mimosa>
root/js/ext-3.3.1/ext-all.js view on Meta::CPAN
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views/login.mason view on Meta::CPAN
<div id="content">
<h>Login</h1>
<form action="/authenticate" method="post">
Username: <input type="text" size=20 name="user"><br/>
Password: <input type="password" size=20 name="password"><br/>
<input type="submit" value="Login">
</form>
</div>
( run in 1.158 second using v1.01-cache-2.11-cpan-49f99fa48dc )