David's last commit

lib/LIMS2/Model/Plugin/AssemblyWellQc.pm

@@ -0,0 +1,21 @@
+package LIMS2::Model::Plugin::AssemblyWellQc;
+
+use strict;
+use warnings FATAL => 'all';
+use Moose::Role;
+use Hash::MoreUtils qw( slice_def );
+use Try::Tiny;
+
+requires qw( schema check_params throw retrieve log trace );
+
+=head
+
+A Catalyst plugin that provides methods for updating well_assembly_qc values
+ 
+=cut
+
+
+
+1;
+
+__END__

lib/LIMS2/Report/AssemblyPlate.pm

@@ -125,6 +125,7 @@ override _build_columns => sub {
     return [
         'Well Name', 'Design ID', 'Gene ID', 'Gene Symbol', 'Gene Sponsors',
         'Crispr ID', 'Crispr Design', 'Genoverse View', 'Genbank File',
+        'Crispr Left QC', 'Crispr Right QC', 'Vector QC',
         'Cassette', 'Cassette Resistance', 'Cassette Type', 'Backbone', #'Recombinases',
         'Crispr Vector Well(s)', 'Final Pick Well',
         'DNA Quality EGel Pass?','Sequencing QC Pass',
@@ -154,6 +155,7 @@ override iterator => sub {
         my $crispr_primers = $self->get_primers( $crispr, $genotyping_primers->{ $well_data->{design_id} } );
         my @crispr_vectors = map{ $_->{plate_name} . '_' . $_->{well_name} } @{ $well_data->{crispr_wells}{crispr_vectors} };
         my ( $genoverse_button, $crispr_designs );
+        my ( $crispr_left_qc_combo, $crispr_right_qc_combo, $vector_qc_combo );
         if ( $crispr ) {
             $genoverse_button = $self->create_button_json(
                 {   'design_id'      => $well_data->{design_id},
@@ -169,6 +171,9 @@ override iterator => sub {
                 }
             );
             $crispr_designs = join( "/", map{ $_->design_id } $crispr->crispr_designs->all );
+            $crispr_left_qc_combo = $self->create_combo_json();
+            $crispr_right_qc_combo = $self->create_combo_json();
+            $vector_qc_combo = $self->create_combo_json();
         }
 
         # build string reporting individual crispr details
@@ -191,6 +196,9 @@ override iterator => sub {
             $crispr_designs,
             $genoverse_button,
             $self->catalyst ? $self->catalyst->uri_for( '/public_reports/well_eng_seq', $well_data->{well_id} ) : '-',
+            $crispr_left_qc_combo,
+            $crispr_right_qc_combo,
+            $vector_qc_combo,
             $well_data->{cassette},
             $well_data->{cassette_resistance},
             $well_data->{cassette_promoter},

lib/LIMS2/ReportGenerator/Plate.pm

@@ -560,6 +560,14 @@ sub create_button_json {
     return $json_text;
 }
 
+sub create_combo_json {
+    my $self = shift;
+    my $params = shift;
+
+    my $json_text = 'Placeholder text';
+    return $json_text;
+}
+
 sub well_primer_bands_data {
     my ( $self, $well ) = @_;
 

lib/LIMS2/WebApp/Controller/API/AssemblyQc.pm

@@ -0,0 +1,76 @@
+package LIMS2::WebApp::Controller::API::AssemblyQc;
+use Moose;
+use namespace::autoclean;
+use Try::Tiny;
+
+BEGIN {extends 'LIMS2::Catalyst::Controller::REST'; }
+
+=head1 NAME
+
+LIMS2::WebApp::Controller::API::AssemblyQc - Catalyst Controller
+
+=head1 DESCRIPTION
+
+API methods dealing with assembly well qc
+
+=cut
+
+sub update_assembly_qc_well :Path('/api/update_qc_well') :Args(0) :ActionClass('REST') {
+}
+
+sub update_assembly_qc_well_POST {
+    my ( $self, $c ) = @_;
+
+    $c->assert_user_roles('edit');
+
+    try{
+        my $qc_well = $c->model('Golgi')->txn_do(
+            sub {
+                shift->update_assembly_qc_well( $c->request->params );
+            }
+        );
+        $self->status_ok( $c, entity => { success => 1 } );
+    }
+    catch {
+        $c->log->error( "Error updating assembly qc well value: $_" );
+        $self->status_bad_request( $c, message => "Error: $_" );
+    };
+
+    return
+}
+
+sub crispr_es_qc_run : Path( '/api/crispr_es_qc_run' ) : Args(0) :ActionClass( 'REST' ) {
+}
+
+=head2 GET /api/crispr_es_qc_run
+
+Retrieve a crispr es qc run by id
+
+=cut
+
+sub crispr_es_qc_run_GET {
+    my ( $self, $c ) = @_;
+
+    $c->assert_user_roles('read');
+
+    my $crispr_es_qc_run = $c->model( 'Golgi' )->txn_do(
+        sub {
+            shift->retrieve_crispr_es_qc_run( { id => $c->request->param( 'id' ) } );
+        }
+    );
+
+    return $self->status_ok( $c, entity => $crispr_es_qc_run );
+}
+
+=head2 POST
+
+=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;

root/site/user/report/generic_report_grid.tt

@@ -93,6 +93,35 @@
                 "id" = 1
                 "well id" = 1
                 } %]
+
+                var assembly_qc_store = Ext.create('Ext.data.store',{
+                    fields: ['call_type'],
+                    data: [
+                        {"call_type":"-"}
+                        [%- FOREACH call_type IN call_types %]
+                        ,{"call_type":"[% call_type %]"}
+                        [%- END %]
+                    ]
+                });
+
+                var assembly_qc_combo = Ext.create('Ext.form.ComboBox', {
+                    typeAhead: true,
+                    triggerAction: 'all',
+                    editable: true,
+                    store: assembly_qc_store,
+                    displayField: 'assembly_qc',
+                    listeners: {
+                        change: function (field, newValue, oldValue) {
+                            console.log('assembly qc listener');
+                            var record = grid.getSelectionMode().getSelection()[0];
+
+                            console.log("Updating " + record.data.id + " with value " + field.getValue());
+                            var newRecord = field.findRecordByValue(newValue);
+
+                            $.getJSON( "[% c.iri_for('/api/assembly_well_qc') %]", {id:record.data.id, assembly_qc:field.getValue()}, function(){record.commit();});
+                        }
+                    } 
+                });
 
             var recovery_class_store = Ext.create('Ext.data.Store',{
                 fields: ['recovery_class'],
@@ -225,6 +254,16 @@
                         }
                     },
                     [%- END %]
+
+                    [%- IF col.match( 'Crispr_.*_qc' ) %]
+                    width: 120,
+                    editor: assembly_qc_combo,
+                    [%- END %]
+
+                    [%- IF col.match( 'Vector_qc') %]
+                    width: 120,
+                    editor: assembly_qc_combo,
+                    [%- END %]
 
 
                     dataIndex: '[%- col %]'