From 04d4846eadff4c553440b9b1a7e2689ca5a36403 Mon Sep 17 00:00:00 2001
From: mueller <lam87@cornell.edu>
Date: Tue, 26 Oct 2010 16:02:45 -0400
Subject: [PATCH] fixing and adapting test for ajax image function

---
 lib/SGN/Controller/#Feature.pm# | 220 ++++++++++++++++++++++++++++++++++++++++
 t/image/ajax.t                  |  15 +--
 2 files changed, 228 insertions(+), 7 deletions(-)
 create mode 100644 lib/SGN/Controller/#Feature.pm#

diff --git a/lib/SGN/Controller/#Feature.pm# b/lib/SGN/Controller/#Feature.pm#
new file mode 100644
index 000000000..4737e7b5a
--- /dev/null
+++ b/lib/SGN/Controller/#Feature.pm#
@@ -0,0 +1,220 @@
+package SGN::Controller::Feature;
+
+=head1 NAME
+
+SGN::Controller::Feature - Catalyst controller for pages dealing with features
+
+=cut
+
+use Moose;
+use namespace::autoclean;
+
+use HTML::FormFu;
+use URI::FromHash 'uri';
+use YAML::Any;
+use SGN::View::Feature qw/feature_link/;
+
+has 'schema' => (
+is => 'rw',
+isa => 'DBIx::Class::Schema',
+required => 0,
+);
+
+has 'default_page_size' => (
+is => 'ro',
+default => 20,
+);
+
+
+BEGIN { extends 'Catalyst::Controller' }
+with 'Catalyst::Component::ApplicationAttribute';
+
+sub delegate_component
+{
+    my ($self, $c, $matching_features) = @_;
+    my $feature   = $matching_features->next;
+    my @children  = $feature->child_features;
+    my @parents   = $feature->parent_features;
+    my $type_name = $feature->type->name;
+    my $template  = "/feature/dhandler";
+
+    $c->stash->{feature}  = $feature;
+    $c->stash->{children} = \@children;
+    $c->stash->{parents}  = \@parents;
+
+    if ($c->view('Mason')->component_exists("/feature/$type_name.mas")) {
+        $template         = "/feature/$type_name.mas";
+        $c->stash->{type} = $type_name;
+    }
+    $c->stash->{template} = $template;
+}
+
+sub validate
+{
+    my ($self, $c,$matching_features,$key, $val) = @_;
+    my $count = $matching_features->count;
+#   EVIL HACK: We need a disambiguation process
+#   $c->throw( message => "too many features where $key='$val'") if $count > 1;
+    $c->throw( message => "feature with $key = '$val' not found") if $count < 1;
+}
+
+sub view_name :Path('/feature/view/name') Args(1) {
+    my ( $self, $c, $feature_name ) = @_;
+    $self->schema( $c->dbic_schema('Bio::Chado::Schema','sgn_chado') );
+    $self->_view_feature($c, 'name', $feature_name);
+}
+
+sub _validate_pair {
+    my ($self,$c,$key,$value) = @_;
+    $c->throw( message => "$value is not a valid value for $key" )
+        if ($key =~ m/_id$/ and $value !~ m/\d+/);
+}
+
+sub _view_feature {
+    my ($self, $c, $key, $value) = @_;
+
+    $self->_validate_pair($c,$key,$value);
+    my $matching_features = $self->schema
+                                ->resultset('Sequence::Feature')
+                                ->search({ $key => $value });
+
+    $self->validate($c, $matching_features, $key => $value);
+    $self->delegate_component($c, $matching_features);
+}
+
+sub view_id :Path('/feature/view/id') Args(1) {
+    my ( $self, $c, $feature_id ) = @_;
+    $self->schema( $c->dbic_schema('Bio::Chado::Schema','sgn_chado') );
+    $self->_view_feature($c, 'feature_id', $feature_id);
+}
+
+sub search :Path('/feature/search') Args(0) {
+    my ( $self, $c ) = @_;
+    $self->schema( $c->dbic_schema('Bio::Chado::Schema','sgn_chado') );
+
+    my $req = $c->req;
+    my $form = $self->_build_form;
+
+    $form->process( $req );
+
+    my $results;
+    if( $form->submitted_and_valid ) {
+        $results = $self->_make_feature_search_rs( $c, $form );
+    }
+
+    $c->forward_to_mason_view(
+        '/feature/search.mas',
+        form => $form,
+        results => $results,
+        pagination_link_maker => sub {
+            return uri( query => { %{$form->params}, page => shift } );
+        },
+    );
+}
+
+
+sub _build_form {
+    my ($self) = @_;
+
+    my $form = HTML::FormFu->new(Load(<<EOY));
+      method: POST
+      attributes:
+        name: feature_search_form
+        id: feature_search_form
+      elements:
+          - type: Text
+            name: feature_name
+            label: Feature Name
+            size: 30
+
+          - type: Select
+            name: feature_type
+            label: Feature Type
+
+          - type: Select
+            name: organism
+            label: Organism
+
+        # hidden form values for page and page size
+          - type: Hidden
+            name: page
+            value: 1
+
+          - type: Hidden
+            name: page_size
+            default: 20
+
+          - type: Submit
+            name: submit
+EOY
+
+    # set the feature type multi-select choices from the db
+    $form->get_element({ name => 'feature_type'})->options( $self->_feature_types );
+    $form->get_element({ name => 'organism'})->options( $self->_organisms );
+
+    return $form;
+}
+
+# assembles a DBIC resultset for the search based on the submitted
+# form values
+sub _make_feature_search_rs {
+    my ( $self, $c, $form ) = @_;
+
+    my $rs = $self->schema->resultset('Sequence::Feature');
+
+    if( my $name = $form->param_value('feature_name') ) {
+        $rs = $rs->search({ 'lower(name)' => { like => '%'.lc( $name ).'%' }});
+    }
+
+    if( my $type = $form->param_value('feature_type') ) {
+        $self->_validate_pair($c,'type_id',$type);
+        $rs = $rs->search({ 'type_id' => $type });
+    }
+
+    if( my $organism = $form->param_value('organism') ) {
+        $self->_validate_pair( $c, 'organism_id', $organism );
+        $rs = $rs->search({ 'organism_id' => $organism });
+    }
+
+    # page number and page size, and order by species name
+    $rs = $rs->search( undef,
+                       { page => $form->param_value('page') || 1,
+                         rows => $form->param_value('page_size') || $self->default_page_size,
+                         order_by => 'name',
+                       },
+                     );
+
+    return $rs;
+}
+
+sub _organisms {
+    my ($self) = @_;
+    return [
+        map [ $_->organism_id, $_->species ],
+        $self->schema
+             ->resultset('Organism::Organism')
+             ->search(undef, { order_by => 'species' }),
+    ];
+}
+
+sub _feature_types {
+    my ($self) = @_;
+
+    return [
+        map [$_->cvterm_id,$_->name],
+        $self->schema
+                ->resultset('Sequence::Feature')
+                ->search_related(
+                    'type',
+                    {},
+                    { select => [qw[ cvterm_id type.name ]],
+                    group_by => [qw[ cvterm_id type.name ]],
+                    order_by => 'type.name',
+                    },
+                )
+    ];
+}
+
+__PACKAGE__->meta->make_immutable;
+1;
+
diff --git a/t/image/ajax.t b/t/image/ajax.t
index ad5de4b8d..754d9675e 100644
--- a/t/image/ajax.t
+++ b/t/image/ajax.t
@@ -1,16 +1,17 @@
 use strict;
 use warnings;
 
-use Test::More tests=>6;
-use Test::WWW::Mechanize;
+use Test::More tests=>5;
+
 use lib 't/lib';
+
+use SGN::Test::WWW::Mechanize;
 use SGN::Test;
 
-my $server = $ENV{SGN_TEST_SERVER};
 
-my $m = Test::WWW::Mechanize->new();
+my $m = SGN::Test::WWW::Mechanize->new();
 
-$m->get_ok($server."/search/direct_search.pl?search=images");
+$m->get_ok("/search/direct_search.pl?search=images");
 
 my $form = { form_number=>2,
 	     fields => { },
@@ -22,11 +23,11 @@ if ($m->content()=~/image_id=(\d+)/) {
     $image_id=$1;
 }
 		 
-$m->get_ok($server."/image/ajax/fetch_image.pl?image_id=$image_id");
+$m->get_ok("/image/ajax/fetch_image.pl?image_id=$image_id");
 
 $m->content_contains('html');
 $m->content_contains('img src');
-$m->content_contains("/$image_id");
+
 
 
 
-- 
2.11.4.GIT