Merge branch 'devel' into david_misc

Changes

@@ -1,5 +1,16 @@
 {{$NEXT}}
 
+0.272     2014-12-04 07:18:46 Europe/London
+
+0.272     2014-12-03 16:04:43 Europe/London
+
+    Bugfix: recovery class foreign key added to correct column
+    Update interface for crispr es qc, allow validation of qc run.
+
+0.271     2014-12-03 07:42:17 Europe/London
+
+    Update Legacy Cre KnockIn report
+
 0.270     2014-11-21 15:05:18 Europe/London
 
     QcRunSummary report gene symbols and support for crispr qc

ddl/versions/78/fixtures.sql

@@ -0,0 +1 @@
+INSERT INTO schema_versions(version) VALUES (78);

ddl/versions/78/up.sql

@@ -0,0 +1,2 @@
+ALTER TABLE projects ADD CONSTRAINT projects_recovery_class_fkey FOREIGN KEY (recovery_class) REFERENCES project_recovery_class(id);
+ALTER TABLE projects DROP CONSTRAINT projects_recovery_comment_fkey;

ddl/versions/79/audit-up.sql

@@ -0,0 +1,2 @@
+ALTER TABLE audit.crispr_es_qc_wells ADD COLUMN variant_size INT;
+ALTER TABLE audit.crispr_es_qc_runs ADD COLUMN validated BOOLEAN;

ddl/versions/79/fixtures.sql

@@ -0,0 +1,2 @@
+INSERT INTO schema_versions(version) VALUES (79);
+INSERT INTO crispr_damage_types( id, description ) VALUES ( 'no-call', 'No automatic damage type call could be made' );

ddl/versions/79/up.sql

@@ -0,0 +1,2 @@
+ALTER TABLE crispr_es_qc_wells ADD COLUMN variant_size INT;
+ALTER TABLE crispr_es_qc_runs ADD COLUMN validated BOOLEAN DEFAULT FALSE;

lib/LIMS2/Model/Plugin/CrisprEsQc.pm

@@ -4,6 +4,7 @@ use strict;
 use warnings FATAL => 'all';
 
 use Moose::Role;
+use DDP;
 use namespace::autoclean;
 
 requires qw( schema check_params throw retrieve log trace );
@@ -57,6 +58,9 @@ sub pspec_create_crispr_es_qc_well {
         vcf_file            => { validate => 'non_empty_string', optional => 1 },
         crispr_es_qc_run_id => { validate => 'non_empty_string' },
         species             => { validate => 'existing_species' },
+        crispr_damage_type  => { validate => 'existing_crispr_damage_type', optional => 1, rename => 'crispr_damage_type_id' },
+        variant_size        => { validate => 'integer', optional => 1 },
+        accepted            => { validate => 'boolean', optional => 1 },
     };
 }
 
@@ -70,6 +74,19 @@ sub create_crispr_es_qc_well {
 
     my $validated_params = $self->check_params( $params, $self->pspec_create_crispr_es_qc_well );
 
+    # if the qc well has been marked accepted run this logic
+    if ( $validated_params->{accepted} ) {
+        my $well = $self->retrieve_well( { id => $validated_params->{well_id} } );
+        # only mark qc accepted if the linked well is not already accepted in another run
+        if ( $well->accepted ) {
+            delete $validated_params->{accepted};
+        }
+        # mark the linked well accepted
+        else {
+            $well->update( { accepted => 1 } );
+        }
+    }
+
     my $species = delete $validated_params->{species};
     if ( $validated_params->{crispr_chr_name} ) {
         my $chr_name = delete $validated_params->{crispr_chr_name};
@@ -154,10 +171,33 @@ sub retrieve_crispr_es_qc_run {
     return $self->retrieve( CrisprEsQcRuns => $validated_params );
 }
 
-sub pspec_update_crispr_well_damage {
+=head2 validate_crispr_es_qc_run
+
+Update a crispr es qc run plus all of its wells to validated.
+
+=cut
+sub validate_crispr_es_qc_run {
+    my ( $self, $params ) = @_;
+
+    my $crispr_es_qc_run = $self->retrieve_crispr_es_qc_run( $params );
+    $crispr_es_qc_run->update( { validated => 1 } );
+
+    $self->log->info( 'Validated crispr es qc run ' . $crispr_es_qc_run->id );
+
+    return;
+}
+
+sub pspec_update_crispr_es_qc_well {
     return {
         id          => { validate => 'integer' },
-        damage_type => { validate => 'existing_crispr_damage_type', optional => 1 },
+        damage_type => {
+            validate => 'existing_crispr_damage_type',
+            optional => 1,
+            rename   => 'crispr_damage_type_id'
+            },
+        variant_size => { validate => 'integer', optional => 1 },
+        accepted     => { validate => 'boolean_string', optional => 1 },
+        MISSING_OPTIONAL_VALID => 1,
     };
 }
 
@@ -166,28 +206,28 @@ sub pspec_update_crispr_well_damage {
 Update the crispr_damage type value of a crispr es qc well row
 
 =cut
-sub update_crispr_well_damage {
+sub update_crispr_es_qc_well{
     my ( $self, $params ) = @_;
 
-    # to deal with user unsetting a damage type
-    delete $params->{damage_type} unless $params->{damage_type};
-
-    my $validated_params = $self->check_params( $params, $self->pspec_update_crispr_well_damage );
+    my $validated_params = $self->check_params( $params, $self->pspec_update_crispr_es_qc_well );
 
-    my $qc_well = $self->schema->resultset('CrisprEsQcWell')->find(
-        {
-            id => $validated_params->{id},
-        },
-    );
+    my $id = delete $validated_params->{id};
+    my $qc_well = $self->schema->resultset('CrisprEsQcWell')->find( { id => $id } );
     unless ( $qc_well ) {
         $self->throw(
-            NotFound => { entity_class  => 'CrisprEsQcWell', search_params => $validated_params }
-        );
+            NotFound => { entity_class => 'CrisprEsQcWell', search_params => { id => $id } } );
     }
-    my $damage_type = $validated_params->{damage_type} ? $validated_params->{damage_type} : undef;
 
-    $qc_well->update( { crispr_damage_type_id => $damage_type } );
-    $self->log->info( "Updated crispr damage type on crispr es qc well: " . $qc_well->id . ' to: ' . ( $damage_type ? $damage_type : 'unset' ) );
+    $qc_well->update( $validated_params );
+
+    $self->log->info( "Updated crispr es qc well "
+            . $qc_well->id . ' to: ' . p( $validated_params ) );
+
+    if ( exists $validated_params->{accepted} ) {
+        my $well = $qc_well->well;
+        $well->update( { accepted => $validated_params->{accepted} } );
+        $self->log->info( "Updated $well well accepted " . $validated_params->{accepted} );
+    }
 
     return $qc_well;
 }

lib/LIMS2/Model/Schema/Result/CrisprEsQcRuns.pm

@@ -73,6 +73,12 @@ __PACKAGE__->table("crispr_es_qc_runs");
   data_type: 'text'
   is_nullable: 1
 
+=head2 validated
+
+  data_type: 'boolean'
+  default_value: false
+  is_nullable: 1
+
 =cut
 
 __PACKAGE__->add_columns(
@@ -93,6 +99,8 @@ __PACKAGE__->add_columns(
   { data_type => "text", is_foreign_key => 1, is_nullable => 0 },
   "sub_project",
   { data_type => "text", is_nullable => 1 },
+  "validated",
+  { data_type => "boolean", default_value => \"false", is_nullable => 1 },
 );
 
 =head1 PRIMARY KEY
@@ -155,8 +163,8 @@ __PACKAGE__->belongs_to(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-04-16 16:43:15
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:KStXhk631rbpalREDS3uoA
+# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-12-01 11:39:17
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:A7ZSinww6G/DqZs50j+0+w
 
 sub as_hash {
   my ( $self, $options ) = @_;

lib/LIMS2/Model/Schema/Result/CrisprEsQcWell.pm

@@ -111,6 +111,11 @@ __PACKAGE__->table("crispr_es_qc_wells");
   is_foreign_key: 1
   is_nullable: 1
 
+=head2 variant_size
+
+  data_type: 'integer'
+  is_nullable: 1
+
 =cut
 
 __PACKAGE__->add_columns(
@@ -145,6 +150,8 @@ __PACKAGE__->add_columns(
   { data_type => "text", is_nullable => 1 },
   "crispr_damage_type_id",
   { data_type => "text", is_foreign_key => 1, is_nullable => 1 },
+  "variant_size",
+  { data_type => "integer", is_nullable => 1 },
 );
 
 =head1 PRIMARY KEY
@@ -232,8 +239,8 @@ __PACKAGE__->belongs_to(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-10-27 09:07:15
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:ZqMaBc51jDRz1dseBj+8Ig
+# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-12-03 11:52:40
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:HLxWkhqfpzrHco4xOT7tdQ
 
 use JSON;
 use List::Util qw ( min max );
@@ -367,6 +374,7 @@ sub format_well_data {
         rev_read                => $self->rev_read,
         damage_type             => $self->crispr_damage_type_id,
         vep_output              => $json->{vep_output},
+        variant_size            => $self->variant_size,
     };
 }
 

lib/LIMS2/Model/Schema/Result/Project.pm

@@ -86,12 +86,12 @@ __PACKAGE__->table("projects");
 =head2 recovery_class
 
   data_type: 'text'
+  is_foreign_key: 1
   is_nullable: 1
 
 =head2 recovery_comment
 
   data_type: 'text'
-  is_foreign_key: 1
   is_nullable: 1
 
 =head2 priority
@@ -124,9 +124,9 @@ __PACKAGE__->add_columns(
   "effort_concluded",
   { data_type => "boolean", default_value => \"false", is_nullable => 0 },
   "recovery_class",
-  { data_type => "text", is_nullable => 1 },
-  "recovery_comment",
   { data_type => "text", is_foreign_key => 1, is_nullable => 1 },
+  "recovery_comment",
+  { data_type => "text", is_nullable => 1 },
   "priority",
   { data_type => "text", is_nullable => 1 },
 );
@@ -183,7 +183,7 @@ __PACKAGE__->has_many(
   { cascade_copy => 0, cascade_delete => 0 },
 );
 
-=head2 recovery_comment
+=head2 recovery_class
 
 Type: belongs_to
 
@@ -192,9 +192,9 @@ Related object: L<LIMS2::Model::Schema::Result::ProjectRecoveryClass>
 =cut
 
 __PACKAGE__->belongs_to(
-  "recovery_comment",
+  "recovery_class",
   "LIMS2::Model::Schema::Result::ProjectRecoveryClass",
-  { id => "recovery_comment" },
+  { id => "recovery_class" },
   {
     is_deferrable => 1,
     join_type     => "LEFT",
@@ -218,8 +218,9 @@ __PACKAGE__->belongs_to(
   { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
 );
 
-# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-10-14 11:17:00
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:djydxXiT/U9oK3BE/QW9iw
+
+# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-12-03 15:40:30
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:gp9bd7euuZta5rwWDBvWUQ
 
 sub as_hash {
     my $self = shift;

lib/LIMS2/Model/Schema/Result/ProjectRecoveryClass.pm

@@ -83,12 +83,13 @@ Related object: L<LIMS2::Model::Schema::Result::Project>
 __PACKAGE__->has_many(
   "projects",
   "LIMS2::Model::Schema::Result::Project",
-  { "foreign.recovery_comment" => "self.id" },
+  { "foreign.recovery_class" => "self.id" },
   { cascade_copy => 0, cascade_delete => 0 },
 );
 
-# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-10-14 14:05:24
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:SANap7GZzTCDqebVX8hgAw
+
+# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-12-03 15:40:30
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:WWpruQh1u9fbedff6V50mg
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration
 __PACKAGE__->meta->make_immutable;

lib/LIMS2/Model/Schema/Result/QcEngSeq.pm

@@ -170,5 +170,13 @@ sub design_id {
     return $eng_seq_params->{design_id};
 }
 
+sub crispr_id {
+    my $self = shift;
+
+    my $eng_seq_params = decode_json( $self->params );
+
+    return $eng_seq_params->{crispr_id};
+}
+
 __PACKAGE__->meta->make_immutable;
 1;

lib/LIMS2/Model/Schema/Result/QcTemplateWell.pm

@@ -250,5 +250,11 @@ sub design_id {
     return $self->qc_eng_seq->design_id;
 }
 
+sub crispr_id {
+    my $self = shift;
+
+    return $self->qc_eng_seq->crispr_id;
+}
+
 __PACKAGE__->meta->make_immutable;
 1;

lib/LIMS2/Model/Util/CrisprESQC.pm

@@ -694,8 +694,14 @@ sub build_qc_data {
         $qc_data{crispr_chr_name} = $crispr->chr_name;
     }
 
-    if ( $analyser && $analyser->vcf_file_target_region ) {
-        $qc_data{vcf_file} = $analyser->vcf_file_target_region->slurp;
+    if ( $analyser ) {
+        $qc_data{vcf_file} = $analyser->vcf_file_target_region->slurp if $analyser->vcf_file_target_region;
+        $qc_data{variant_size} = $analyser->variant_size if $analyser->variant_size;
+        if ( $analyser->variant_type ) {
+            $qc_data{crispr_damage_type} = $analyser->variant_type;
+            # if a variant type other can no-call has been made then mark well accepted
+            $qc_data{accepted} = 1 if $analyser->variant_type ne 'no-call';
+        }
     }
 
     if ( exists $well_reads->{forward} ) {