arrayref constraint not needed. use well mehtods instead of ProcessGr…

…aph methods. more tests

lib/LIMS2/Model/FormValidator/Constraint.pm

@@ -381,12 +381,6 @@ sub hashref {
     }
 }
 
-sub arrayref {
-    return sub {
-        ref $_[0] eq ref [];
-    }
-}
-
 sub file_handle {
     return sub {
         my $val = shift;

lib/LIMS2/Model/Plugin/Well.pm

@@ -498,22 +498,10 @@ sub pspec_generate_eng_seq_params {
         well_id     => { validate => 'integer', rename => 'id', optional => 1 },
         cassette    => { validate => 'existing_final_cassette', optional => 1 },
         backbone    => { validate => 'existing_backbone',       optional => 1 },
-        recombinase => { validate => 'arrayref', default => [], optional => 1 },
+        recombinase => { validate => 'existing_recombinase', default => [], optional => 1 },
         targeted_trap => { validate => 'boolean', default => 0, optional => 1 },
 	}
 }
-use Data::Dumper;
-$Data::Dumper::Maxdepth=3;
-
-sub retrieve_well_design{
-	my ( $self, $well ) = @_;
-
-    my $graph = LIMS2::Model::ProcessGraph->new({ start_with => $well, type => 'ancestors' });
-    my $proc_design = $graph->find_process($well, 'process_design')
-        or die "No process_design identified for well ID ".$well->id;
-
-    return $proc_design->design->as_hash;
-}
 
 sub generate_well_eng_seq_params{
 
@@ -525,7 +513,7 @@ sub generate_well_eng_seq_params{
     $self->throw( NotFound => { entity_class => 'Well', search_params => $params })
         unless $well;
 
-    my $design = $self->retrieve_well_design( $well );
+    my $design = $well->design->as_hash;
 
     # Infer stage from plate type information
     my $plate_type_descr = $well->plate->type->description;

lib/LIMS2/Model/Util/EngSeqParams.pm

@@ -86,31 +86,29 @@ sub fetch_well_eng_seq_params{
 
 	my ($well_params, $method);
 
-	my $graph = LIMS2::Model::ProcessGraph->new({  start_with => $well, type => 'ancestors' });
-
 	# Fetch cassette etc from process graph if not user supplied
 	unless ($params->{cassette}){
-		my $process_cassette = $graph->find_process($well, 'process_cassette');
-		$params->{cassette} = $process_cassette ? $process_cassette->cassette->name
-		                                        : undef ;
+		my $cassette = $well->cassette;
+		$params->{cassette} = $cassette ? $cassette->name
+		                                : undef ;
 	}
 
 	unless (@{ $params->{recombinase} }){
-		my $process_recombinases = $graph->find_process($well, 'process_recombinases');
-		# FIXME: should these be sorted by rank?
-		my @recombinases = $process_recombinases ? map { lc $_->recombinase_id } $process_recombinases->all
-		                                         : () ;
-		$params->{recombinase} = \@recombinases;
+		$params->{recombinase} = $well->recombinases;
 	}
 
 	unless ($params->{backbone} or $params->{is_allele}){
-		my $process_backbone = $graph->find_process($well, 'process_backbone');
-		$params->{backbone} = $process_backbone ? $process_backbone->backbone->name
-		                                        : undef ;
+		my $backbone = $well->backbone;
+		$params->{backbone} = $backbone ? $backbone->name
+		                                : undef ;
 	}
 
-    # Always store recombinase
-    $well_params->{recombinase} = $params->{recombinase};
+    # Always store recombinase (in lower case)
+    my @recom = map { lc $_ } @{ $params->{recombinase} };
+    $well_params->{recombinase} = \@recom;
+
+    # We always need a cassette
+    die "No cassette found for well ".$well->id unless $params->{cassette};
 
 	my $design_type = $params->{design_type};
 
@@ -143,7 +141,8 @@ sub fetch_well_eng_seq_params{
 
 	}
 	else {
-		$well_params->{backbone}->{name} = $params->{backbone};
+		$well_params->{backbone}->{name} = $params->{backbone}
+		    or die "No backbone found for well ".$well->id;
 
 	    if ( $design_type eq 'conditional') {
 	        $method = 'conditional_vector_seq';

t/50-model-plugin-well.t

@@ -17,8 +17,21 @@ my $well_data= test_data( 'well.yaml' );
 
 note( "Testing well EngSeqParam generation");
 {
-    ok my ($method, $params) = model->generate_well_eng_seq_params({ well_id => 850 }),
-        'generate well_eng_seq_params should succeed'; 
+    throws_ok {
+    	model->generate_well_eng_seq_params({ well_id => 850 });
+    } qr/No cassette found for well/;
+
+    my %user_params = ( cassette => 'L1L2_GT2_LacZ_BSD', backbone => 'R3R4_pBR_amp', recombinase => ['Cre']);
+    ok my ($method2, $params2) = model->generate_well_eng_seq_params({ well_id => 850, %user_params }),
+        'generate well_eng_seq_params with user specified details should succeed';
+    is_deeply ($params2, test_data("well_850_user_params.yaml"),
+        'engseq params as expected for well 850 with user specified params');
+    is $method2, 'conditional_vector_seq', 'engseq method correct';    
+
+    ok my ($method3, $params3) = model->generate_well_eng_seq_params({ well_id => 848, %user_params }),
+        'generate well_eng_seq_params should succeed';
+    is_deeply ($params3, test_data('well_848.yaml'), 'engseq params as expected for well 848');
+
 }
 
 note( "Testing well creation" );

t/data/well_848.yaml

@@ -0,0 +1,20 @@
+---
+assembly: GRCm38
+backbone:
+  name: R3R4_pBR_amp
+chromosome: '9'
+d_insertion:
+  name: LoxP
+design_id: 170606
+display_id: 170606#L1L2_GT2_LacZ_BSD#R3R4_pBR_amp#cre
+five_arm_end: 20926524
+five_arm_start: 20920679
+recombinase:
+- cre
+strand: -1
+target_region_end: 20920581
+target_region_start: 20917778
+three_arm_end: 20917744
+three_arm_start: 20914201
+u_insertion:
+  name: L1L2_GT2_LacZ_BSD

t/data/well_850_user_params.yaml

@@ -0,0 +1,20 @@
+---
+assembly: GRCm38
+backbone:
+  name: R3R4_pBR_amp
+chromosome: '15'
+d_insertion:
+  name: LoxP
+design_id: 84231
+display_id: 84231#L1L2_GT2_LacZ_BSD#R3R4_pBR_amp#cre
+five_arm_end: 58122003
+five_arm_start: 58116316
+recombinase:
+- cre
+strand: -1
+target_region_end: 58116243
+target_region_start: 58115459
+three_arm_end: 58115448
+three_arm_start: 58111237
+u_insertion:
+  name: L1L2_GT2_LacZ_BSD