Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel

htgt · Sep 10, 2014 · 0f976e4 · 0f976e4
2 parents 4406679 + 186392a
commit 0f976e4
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Showing 11 changed files with 335 additions and 4 deletions.
diff --git a/Changes b/Changes
@@ -1,5 +1,9 @@
 {{$NEXT}}
 
+0.238     2014-09-10 09:25:52 Europe/London
+
+    Added Project Efforts, under the Genes tab
+
 0.237     2014-09-02 14:50:23 Europe/London
 
     Add interface to link crispr groups to designs

diff --git a/ddl/versions/72/audit-up.sql b/ddl/versions/72/audit-up.sql
@@ -0,0 +1 @@
+ALTER TABLE audit.projects ADD COLUMN effort_concluded BOOLEAN NOT NULL DEFAULT FALSE;
diff --git a/ddl/versions/72/fixtures.sql b/ddl/versions/72/fixtures.sql
@@ -0,0 +1 @@
+INSERT INTO schema_versions(version) VALUES (72);
diff --git a/ddl/versions/72/up.sql b/ddl/versions/72/up.sql
@@ -0,0 +1 @@
+ALTER TABLE projects ADD COLUMN effort_concluded BOOLEAN NOT NULL DEFAULT FALSE;
diff --git a/lib/LIMS2/Model/Plugin/Project.pm b/lib/LIMS2/Model/Plugin/Project.pm
@@ -0,0 +1,67 @@
+package LIMS2::Model::Plugin::Project;
+
+use strict;
+use warnings FATAL => 'all';
+
+use Moose::Role;
+use Hash::MoreUtils qw( slice slice_def );
+use TryCatch;
+use LIMS2::Exception;
+use namespace::autoclean;
+
+requires qw( schema check_params throw retrieve log trace );
+
+
+
+sub pspec_retrieve_project {
+    return {
+        sponsor_id           => { validate => 'non_empty_string' },
+        gene_id              => { validate => 'non_empty_string' },
+        targeting_type       => { validate => 'non_empty_string' },
+        species_id           => { validate => 'existing_species' },
+    };
+}
+
+sub retrieve_project {
+    my ( $self, $params ) = @_;
+
+    my $validated_params = $self->check_params( $params, $self->pspec_retrieve_project );
+
+    my $project = $self->retrieve( Project => { slice_def $validated_params, qw( id sponsor_id gene_id targeting_type species_id ) } );
+
+    return $project;
+}
+
+sub pspec_retrieve_project_by_id {
+    return {
+        id => { validate => 'integer' },
+    };
+}
+
+sub retrieve_project_by_id {
+    my ( $self, $params ) = @_;
+
+    my $validated_params = $self->check_params( $params, $self->pspec_retrieve_project_by_id );
+
+    my $project = $self->retrieve( Project => { slice_def $validated_params, qw( id sponsor_id gene_id targeting_type species_id ) } );
+
+    return $project;
+}
+
+sub toggle_concluded_flag {
+    my ( $self, $params ) = @_;
+
+    my $project = $self->retrieve_project_by_id($params);
+
+    if ($project->effort_concluded) {
+        $project->update( { effort_concluded => 0 } );
+    } else {
+        $project->update( { effort_concluded => 1 } );
+    };
+
+    return $project;
+}
+
+1;
+
+__END__
diff --git a/lib/LIMS2/Model/Schema/Result/Project.pm b/lib/LIMS2/Model/Schema/Result/Project.pm
@@ -77,6 +77,12 @@ __PACKAGE__->table("projects");
   data_type: 'integer'
   is_nullable: 1
 
+=head2 effort_concluded
+
+  data_type: 'boolean'
+  default_value: false
+  is_nullable: 0
+
 =cut
 
 __PACKAGE__->add_columns(
@@ -99,6 +105,8 @@ __PACKAGE__->add_columns(
   { data_type => "text", is_nullable => 1 },
   "htgt_project_id",
   { data_type => "integer", is_nullable => 1 },
+  "effort_concluded",
+  { data_type => "boolean", default_value => \"false", is_nullable => 0 },
 );
 
 =head1 PRIMARY KEY
@@ -169,8 +177,24 @@ __PACKAGE__->belongs_to(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-02-07 16:49:17
+# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-09-02 15:28:38
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:NWx1GMZQcu6KlFq2s3dSaA
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:E+p0emXyULopBYB1vFws9A
+
+
+sub as_hash {
+    my $self = shift;
+
+    return {
+          "id"                => $self->id,
+          "sponsor_id"        => $self->sponsor_id,
+          "allele_request"    => $self->allele_request,
+          "gene_id"           => $self->gene_id,
+          "targeting_type"    => $self->targeting_type,
+          "species_id"        => $self->species_id,
+          "htgt_project_id"   => $self->htgt_project_id,
+          "effort_concluded"  => $self->effort_concluded,
+    }
+}
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration

diff --git a/lib/LIMS2/WebApp/Controller/API/Project.pm b/lib/LIMS2/WebApp/Controller/API/Project.pm
@@ -0,0 +1,43 @@
+package LIMS2::WebApp::Controller::API::Project;
+use Moose;
+use Hash::MoreUtils qw( slice_def );
+use namespace::autoclean;
+
+BEGIN {extends 'LIMS2::Catalyst::Controller::REST'; }
+
+sub project : Path( '/api/project' ) : Args(0) : ActionClass( 'REST' ) {
+}
+
+sub project_GET{
+    my ( $self, $c ) = @_;
+
+    $c->assert_user_roles('read');
+
+    my $project = $c->model( 'Golgi' )->txn_do(
+        sub {
+            shift->retrieve_project_by_id( { id => $c->request->param( 'id' ) } );
+        }
+    );
+
+    return $self->status_ok( $c, entity => $project->as_hash );
+}
+
+sub project_toggle : Path( '/api/project_toggle' ) : Args(0) : ActionClass( 'REST' ) {
+}
+
+sub project_toggle_GET{
+    my ( $self, $c ) = @_;
+
+    $c->assert_user_roles('read');
+
+    my $project = $c->model( 'Golgi' )->txn_do(
+        sub {
+            shift->toggle_concluded_flag( { id => $c->request->param( 'id' ) } );
+        }
+    );
+
+    return $self->status_ok( $c, entity => $project->as_hash );
+}
+
+
+1;
diff --git a/lib/LIMS2/WebApp/Controller/User/Projects.pm b/lib/LIMS2/WebApp/Controller/User/Projects.pm
@@ -0,0 +1,112 @@
+package LIMS2::WebApp::Controller::User::Projects;
+use Moose;
+use LIMS2::WebApp::Pageset;
+use namespace::autoclean;
+
+BEGIN {extends 'Catalyst::Controller'; }
+
+=head1 NAME
+
+LIMS2::WebApp::Controller::User::Projects - Catalyst Controller
+
+=head1 DESCRIPTION
+
+Catalyst Controller.
+
+=head1 METHODS
+
+=cut
+
+
+=head2 index
+
+=cut
+
+sub index :Path( '/user/projects' ) :Args(0) {
+    my ( $self, $c ) = @_;
+
+    $c->assert_user_roles('read');
+
+    my $params = $c->request->params;
+
+    my $species_id = $c->session->{selected_species};
+
+    my @sponsors_rs =  $c->model('Golgi')->schema->resultset('Project')->search( {
+            species_id  => $species_id
+        },{
+            columns     => [ qw/sponsor_id/ ],
+            distinct    => 1
+        }
+    );
+
+    my @sponsors =  map { $_->sponsor_id } @sponsors_rs;
+
+    my $columns = ['id', 'gene_id', 'gene_symbol', 'sponsor', 'targeting type', 'concluded?'];
+
+    my $sel_sponsor;
+
+    $c->stash(
+        sponsor_id => [ map { $_->sponsor_id } @sponsors_rs ],
+        effort_concluded => ['true', 'false'],
+        title           => 'Project Efforts',
+        columns         => $columns,
+        sel_sponsor      => $sel_sponsor,
+    );
+
+
+    return unless ( $params->{filter} || $params->{show_all} );
+
+    if ($params->{show_all}) {
+        $params->{sponsor_id} = '';
+    }
+
+    my $search = {
+        species_id => $species_id,
+    };
+
+    if ($params->{sponsor_id}) {
+        $search->{sponsor_id} = $params->{sponsor_id};
+        $sel_sponsor = $params->{sponsor_id};
+    }
+
+    my @projects_rs =  $c->model('Golgi')->schema->resultset('Project')->search( $search );
+
+
+    my @project_genes = map { [
+        $_->id,
+        $_->gene_id,
+        $c->model('Golgi')->find_gene( { species => $species_id, search_term => $_->gene_id } )->{gene_symbol},
+        $_->sponsor_id,
+        $_->targeting_type,
+        $_->effort_concluded
+    ] } @projects_rs;
+
+
+    $c->stash(
+        sponsor_id => [ map { $_->sponsor_id } @sponsors_rs ],
+        effort_concluded => ['true', 'false'],
+        title           => 'Project Efforts',
+        columns         => $columns,
+        data            => \@project_genes,
+        get_grid        => 1,
+        sel_sponsor      => $sel_sponsor,
+    );
+
+    return;
+}
+
+
+=head1 AUTHOR
+
+Team 87
+
+=head1 LICENSE
+
+This library is free software. You can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+__PACKAGE__->meta->make_immutable;
+
+1;
diff --git a/root/lib/navigation.tt b/root/lib/navigation.tt
@@ -20,6 +20,9 @@
             <li>
               <a href="[% c.uri_for( '/user/sponsor_report' ) %]">Sponsor Report</a>
             </li>
+            <li>
+              <a href="[% c.uri_for( '/user/projects' ) %]">Project Efforts</a>
+            </li>
           </ul>
         </li>
 

diff --git a/root/site/user/projects/index.tt b/root/site/user/projects/index.tt
@@ -0,0 +1,60 @@
+
+<div class="page-header">
+  <h1>[% title %]</h1>
+</div>
+
+<form method="GET" action="[% c.uri_for( '/user/projects' ) %]" class="well">
+  <fieldset>
+    <label for="sponsor_id">Sponsor:</label>
+    <select name="sponsor_id">
+      <option[% IF ! selected_sponsor.defined %] selected="selected" [% END %]>[% sel_sponsor %]</option>
+      [%- FOR sponsor IN sponsor_id %]
+      <option[% IF sponsor == selected_sponsor %] selected="selected"[% END %]>[% sponsor %]</option>
+      [%- END %]
+    </select>
+    <button name="filter" id="filter" type="submit" value="Filter" class="btn btn-primary"><i class="icon-filter icon-white"></i>Filter</button>
+    <button name="show_all" id="show_all" type="submit" value="Show All" class="btn"><i class="icon-list-alt"></i>Show All</button>
+  </fieldset>
+    <span class="help-block">
+      You can browse for efforts and mark them as concluded by checking the box.
+    </span>
+</form>
+
+
+
+
+<div id="my_results"></div>
+
+
+[%- MACRO linkify(v) BLOCK %]
+[%- IF v.match( '^https?:' ) %]
+<a href="[% v %]">Test result</a>
+[%- ELSIF v.match( '^custom:' ) %]
+    [%- USE String%]
+    [%- v_copy = String.new( text => v ) %]
+    [%- CALL v_copy.shift('custom:') %]
+    [%- FOREACH pair_val IN v_copy.split(';') %]
+        [%- pair_string = String.new ( text => pair_val) %]
+        [%- vals = pair_string.split('=', 2) %]
+        [%- left = vals.shift %]
+        [%- right = vals.shift %]
+        [%- custom.$left = right %]
+    [%- END %]
+    [%- button_label = custom.button_label %]
+    [%- tab_target = custom.browser_target %]
+    [%- api_url = custom.api_url %]
+    [%- custom.delete( 'button_label', 'api_url') -%]
+<a class="btn btn-info btn-small" <a href="[% c.uri_for( api_url, custom ) %]" target="[% tab_target %]">[% button_label %]</a>
+[%- ELSE %]
+[%- v %]
+[%- END %]
+[%- END %]
+
+<link rel="stylesheet" type="text/css" href="[% c.uri_for('/static/extjs/resources/css/ext-all.css') %]" />
+<link rel="stylesheet" type="text/css" href="[% c.uri_for('/static/css/lims2_extjs.css') %]" />
+
+<script type="text/javascript" src="[% c.uri_for('/static/extjs/ext-all.js') %]"></script>
+
+[%- IF get_grid %]
+[% PROCESS 'user/report/generic_report_grid.tt' %]
+[%- END %]