Added the ability to upload well dna status data while ignoring water…

… only wells not represented in LIMS2

lib/LIMS2/Model/Plugin/Well.pm

@@ -246,22 +246,39 @@ sub pspec_create_well_dna_status {
 
 sub create_well_dna_status {
     my ( $self, $params ) = @_;
-
     my $validated_params = $self->check_params( $params, $self->pspec_create_well_dna_status );
 
-    my $well = $self->retrieve_well( { slice_def $validated_params, qw( id plate_name well_name ) } );
+    my $well;
+    my $dna_status;
+    # If the well does not exist on the target plate, we assume that the well in the spreadsheet is
+    # empty (water or buffer solution only). These wells are not recorded in LIMS2 as it is not
+    # possible to parent empty wells.
+    # DJP-S 6/3/13
+    #
+    try {
+        $well = $self->retrieve_well( { slice_def $validated_params, qw( id plate_name well_name ) } );
+    }
+    catch {
+        # If the well doesn't exist make it undef and carry on
+        $well = undef;
+    };
 
     #will need to provide some method of changing the dna status level on a well
-    if ( my $dna_status = $well->well_dna_status ) {
-        $self->throw( Validation => "Well $well already has a dna status of "
-                . ( $dna_status->pass == 1 ? 'pass' : 'fail' )
+    if ( $well ) {
+        if ( $dna_status = $well->well_dna_status ) {
+            $self->throw( Validation => "Well $well already has a dna status of "
+                    . ( $dna_status->pass == 1 ? 'pass' : 'fail' )
+            );
+        }
+
+        $dna_status = $well->create_related(
+            well_dna_status => { slice_def $validated_params, qw( pass comment_text created_by_id created_at ) }
         );
+        $self->log->debug( 'Well DNA status set to ' . $dna_status->pass . ' for well  ' . $dna_status->well_id );
+    }
+    else {
+        $dna_status = undef;
     }
-
-    my $dna_status = $well->create_related(
-        well_dna_status => { slice_def $validated_params, qw( pass comment_text created_by_id created_at ) }
-    );
-    $self->log->debug( 'Well DNA status set to ' . $dna_status->pass . ' for well  ' . $dna_status->well_id );
 
     return $dna_status;
 }

lib/LIMS2/Model/Util/DataUpload.pm

@@ -31,6 +31,7 @@ sub pspec__check_dna_status {
 sub upload_plate_dna_status {
     my ( $model, $params ) = @_;
     my @success_message;
+    my @failure_message;
 
     my $data = parse_csv_file( $params->{csv_fh} );
 
@@ -47,11 +48,19 @@ sub upload_plate_dna_status {
             }
         );
 
-        push @success_message,
-            $dna_status->well->name . ' - ' . ( $dna_status->pass == 1 ? 'pass' : 'fail' );
+        if ( $dna_status ) {
+            push @success_message,
+                $dna_status->well->name . ' - ' . ( $dna_status->pass == 1 ? 'pass' : 'fail' );
+        }
+        else {
+            # Some of the wells in the input were not present in LIMS2
+            push @failure_message,
+                $validated_params->{'well_name'} . ' - well not available in LIMS2';
+        }
     }
 
-    return \@success_message;
+    push my @returned_messages, ( @failure_message, @success_message );
+    return \@returned_messages;
 }
 
 sub check_plate_type {

t/80-dna_status_upload.t

@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/env perl -d
 
 use strict;
 use warnings FATAL => 'all';
@@ -109,4 +109,37 @@ my $mech = mech();
     } 'delete dna status data';
 }
 
+{
+    note( 'Test uploading of empty wells not represented in LIMS2' );
+
+    my $plate_data = test_data( 'dna_status.yaml' );
+    ok my $dna_plate = model->create_plate( $plate_data->{'dna_plate_create_params'} ),
+        'dna plate creation succeeded';
+    my $dna_status_update = model->create_well_dna_status ( $plate_data->{'create_well_dna_status_params'} );
+    ok  (! $dna_status_update ,
+        'dna status update for empty (non-existent LIMS2) well was handled correctly');
+    my $test_file = File::Temp->new or die('Could not create temp test file ' . $!);
+    $test_file->print("well_name,dna_status_result,comments\n"
+                      . "A03,pass,this is a comment");
+    $test_file->seek( 0, 0 );
+    $mech->get_ok('/user/dna_status_update');
+    $mech->title_is('DNA Status Update');
+    ok my $res = $mech->submit_form(
+        form_id => 'dna_status_update',
+        fields  => {
+            plate_name => 'DUMMY01',
+            datafile   => $test_file->filename
+        },
+        button  => 'update_dna_status'
+    ), 'submit form with valid parameters';
+
+    ok $res->is_success, '...response is_success';
+    is $res->base->path, '/user/dna_status_update', '... stays on same page';
+    like $res->content, qr/Uploaded dna status information onto plate DUMMY01/ ,
+        '...page has success message';
+    like $res->content, qr/A03 - well not available in LIMS2/,
+        '...well A03 not available in LIMS2 -- reported correctly';
+
+
+}
 done_testing;

t/data/dna_status.yaml

@@ -0,0 +1,29 @@
+---
+dna_plate_create_params:
+    name: DUMMY01
+    species: Mouse
+    type: DNA
+    description: DNA_test
+    created_by: test_user@example.org
+    comments:
+        - comment_text: This test plate is not based on real data
+          created_by: test_user@example.org
+    wells:
+        - well_name: A01
+          process_type: dna_prep
+          parent_plate: MOHFAS0001_A
+          parent_well: A01
+        - well_name: B01
+          process_type: dna_prep
+          parent_plate: MOHFAS0001_A
+          parent_well: B02
+        - well_name: C01
+          process_type: dna_prep
+          parent_plate: MOHFAS0001_A
+          parent_well: C03
+create_well_dna_status_params:
+        plate_name:  DUMMY01
+        well_name: A02
+        pass: true
+        created_by: test_user@example.org
+