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

ddl/versions/83/up.sql

@@ -3,3 +3,4 @@ ALTER TABLE designs ADD foreign key (nonsense_design_crispr_id) references crisp
 
 ALTER TABLE crisprs ADD COLUMN nonsense_crispr_original_crispr_id INT;
 ALTER TABLE crisprs ADD foreign key (nonsense_crispr_original_crispr_id) references crisprs(id);
+

ddl/versions/84/fixtures.sql

@@ -0,0 +1 @@
+INSERT INTO schema_versions(version) VALUES (84);

ddl/versions/84/up.sql

@@ -0,0 +1,3 @@
+alter table crispr_primers drop constraint "crispr_id and primer name must be unique";
+alter table crispr_primers drop constraint "crispr_pair_id and primer name must be unique";
+alter table crispr_primers drop constraint "crispr_group_id and and primer_name must be unique";

lib/LIMS2/Model/Plugin/Primer.pm

@@ -34,16 +34,90 @@ sub retrieve_crispr_primer {
     return $crispr_primer;
 }
 
+# Retrieve only the crispr primer where the is_rejected flag is not set to true
+# There should be only one of these but this is constrained in the model
+# rather than the database so it may not always be the case
+sub retrieve_current_crispr_primer{
+    my ( $self, $params ) = @_;
+
+    my $validated_params = $self->check_params( $params, $self->pspec_retrieve_crispr_primer );
+
+    my %params = slice_def $validated_params,
+            qw( crispr_id crispr_pair_id crispr_group_id primer_name );
+
+    $params{is_rejected} = [0, undef];
+
+    my $crispr_primer = $self->retrieve(
+        CrisprPrimer => \%params,
+    );
+
+    return $crispr_primer;
+
+}
+
+sub pspec_create_primer_common {
+    return {
+        primer_seq      => { validate => 'dna_seq' },
+        tm              => { validate => 'numeric', optional => 1 },
+        gc_content      => { validate => 'numeric', optional => 1 },
+        locus           => { validate => 'hashref' },
+        overwrite       => { validate => 'boolean', optional => 1, default => 0 },
+        check_for_rejection => { validate => 'boolean', optional => 1, default => 0 },
+    };
+}
+
+# pspec_create_genotyping_primer already exists in WebApp Common hence slightly odd name here
+sub pspec_create_genotyping_primer_lims2{
+    my $common = pspec_create_primer_common;
+    return {
+        %$common,
+        design_id       => { validate => 'integer' },
+        primer_name     => { validate => 'existing_genotyping_primer_type' }
+    };
+}
+
+=head2 create_genotyping_primer
+
+Like create_crispr_primer.. but for genotyping primers which are linked to a design
+
+=cut
+sub create_genotyping_primer{
+    my ($self, $params) = @_;
+
+    my $validated_params = $self->check_params( $params, $self->pspec_create_genotyping_primer_lims2 );
+
+    my $ready_to_create = $self->_handle_existing_primers('GenotypingPrimer', $validated_params);
+
+    my $primer;
+    if($ready_to_create){
+        $primer = $self->schema->resultset('GenotypingPrimer')->create({
+            genotyping_primer_type_id => $validated_params->{primer_name},
+            seq                       => $validated_params->{primer_seq},
+            slice_def(
+                $validated_params,
+                qw( design_id tm gc_content )
+            )
+        });
+
+        $self->log->debug( 'Create primer ' . $primer->id );
+
+        my $locus_params = $validated_params->{locus};
+        $locus_params->{genotyping_primer_id} = $primer->id;
+        $self->create_genotyping_primer_locus( $locus_params, $primer );
+    }
+
+    return $primer;
+}
+
 sub pspec_create_crispr_primer {
+    my $common = pspec_create_primer_common;
     return {
+        %$common,
         crispr_id       => { validate => 'integer', optional => 1 },
         crispr_pair_id  => { validate => 'integer', optional => 1 },
         crispr_group_id => { validate => 'integer', optional => 1 },
         primer_name     => { validate => 'existing_crispr_primer_type' },
-        primer_seq      => { validate => 'dna_seq' },
-        tm              => { validate => 'numeric', optional => 1 },
-        gc_content      => { validate => 'numeric', optional => 1 },
-        locus           => { validate => 'hashref' },
+
         REQUIRE_SOME    => { single_pair_or_group_crispr_id =>
                 [ 1, qw( crispr_id crispr_pair_id crispr_group_id ) ] },
     };
@@ -54,27 +128,105 @@ sub pspec_create_crispr_primer {
 Create a crispr primer record, along with its locus.
 First check to see crispr does not already have primer of same type.
 
+To overwrite the existing primer use overwrite = 1
+To check if this primer seq has previously been rejected before creating it
+use check_for_rejection = 1
+
+You should run this in a txn_do
+
 =cut
 sub create_crispr_primer {
     my ( $self, $params ) = @_;
 
     my $validated_params = $self->check_params( $params, $self->pspec_create_crispr_primer );
 
-    my $crispr_primer = $self->schema->resultset('CrisprPrimer')->create(
-        {   slice_def(
+    my $ready_to_create = $self->_handle_existing_primers('CrisprPrimer', $validated_params);
+
+    my $crispr_primer;
+    if($ready_to_create){
+        $crispr_primer = $self->schema->resultset('CrisprPrimer')->create({
+            slice_def(
                 $validated_params,
                 qw( crispr_id crispr_pair_id crispr_group_id
                     primer_seq primer_name tm gc_content
                     )
             )
-        }
+        });
+
+        $self->log->debug( 'Create crispr primer ' . $crispr_primer->id );
+
+        my $locus_params = $validated_params->{locus};
+        $locus_params->{crispr_oligo_id} = $crispr_primer->id;
+        $self->create_crispr_primer_locus( $locus_params, $crispr_primer );
+    }
+
+    return $crispr_primer;
+}
+
+# Decide how to handle existing CrisprPrimers or GenotypingPrimers using common logic
+# and overwrite/check_for_rejection flag parameters
+sub _handle_existing_primers{
+    my ($self, $resultset, $validated_params) = @_;
+    my $ready_to_create = 0;
+
+    my %search_params = slice_def( $validated_params,
+        qw( crispr_id crispr_pair_id crispr_group_id design_id primer_name)
     );
-    $self->log->debug( 'Create crispr primer ' . $crispr_primer->id );
 
-    my $locus_params = $validated_params->{locus};
-    $locus_params->{crispr_oligo_id} = $crispr_primer->id;
-    $self->create_crispr_primer_locus( $locus_params, $crispr_primer );
+    # Bit of a hack because primer_name in CrisprPrimer == genotyping_primer_type_id in GenotypingPrimer
+    if($resultset eq 'GenotypingPrimer'){
+        $search_params{genotyping_primer_type_id} = $search_params{primer_name};
+        delete $search_params{primer_name};
+    }
+
+    my @existing_primers = $self->schema->resultset($resultset)->search(\%search_params)->all;
+    my %rejected_seqs;
+    my @current_primers;
+    foreach my $existing (@existing_primers){
+        if($existing->is_rejected){
+            my $seq = uc($existing->primer_seq);
+            $rejected_seqs{$seq} = 1;
+        }
+        else{
+            push @current_primers, $existing;
+        }
+    }
+
+    if(@current_primers){
+        $self->log->debug("Existing $resultset found");
+        unless($validated_params->{overwrite}){
+            $self->throw( Validation => 'Primer '.$validated_params->{primer_name}.' already exists' );
+        }
 
+        if($validated_params->{check_for_rejection}){
+            $self->_check_for_rejection($validated_params->{primer_seq}, \%rejected_seqs);
+        }
+
+        # If method has not died yet it is time to remove existing and create new primer
+        foreach my $existing (@current_primers){
+            $self->log->debug('Deleting existing primer '.$existing->id);
+            $existing->delete;
+        }
+        $ready_to_create = 1;
+    }
+    else{
+        if($validated_params->{check_for_rejection}){
+            $self->_check_for_rejection($validated_params->{primer_seq}, \%rejected_seqs);
+        }
+
+        # If method has not died we can go ahead and create the primer
+        $ready_to_create = 1;
+    }
+    return $ready_to_create;
+}
+
+sub _check_for_rejection{
+    my ($self, $seq, $rejected_seqs) = @_;
+    $seq = uc($seq);
+    $self->log->debug('Checking if new primer seq has previously been rejected');
+    if($rejected_seqs->{$seq}){
+        $self->throw( Validation => "Primer with sequence $seq has previously been rejected" );
+    }
     return;
 }
 
@@ -119,6 +271,46 @@ sub create_crispr_primer_locus {
     return $crispr_primer_locus;
 }
 
+sub pspec_create_genotyping_primer_locus {
+    return {
+        assembly        => { validate => 'existing_assembly' },
+        chr_name        => { validate => 'existing_chromosome' },
+        chr_start       => { validate => 'integer' },
+        chr_end         => { validate => 'integer' },
+        chr_strand      => { validate => 'strand' },
+        genotyping_primer_id => { validate => 'integer' },
+    };
+}
+
+=head2 create_genotyping_primer_locus
+
+Create locus record for a genotyping primer, for a given assembly
+
+=cut
+sub create_genotyping_primer_locus {
+    my ( $self, $params, $primer ) = @_;
+
+    my $validated_params = $self->check_params( $params, $self->pspec_create_genotyping_primer_locus );
+    $self->trace( "Create genotyping primer locus", $validated_params );
+
+    $primer ||= $self->schema->resultset( 'GenotypingPrimer' )->find(
+        {
+            id => $validated_params->{genotyping_primer_id},
+        }
+    );
+
+    my $primer_locus = $primer->create_related(
+        genotyping_primer_loci => {
+            assembly_id => $validated_params->{assembly},
+            chr_id      => $self->_chr_id_for( @{$validated_params}{ 'assembly', 'chr_name' } ),
+            chr_start   => $validated_params->{chr_start},
+            chr_end     => $validated_params->{chr_end},
+            chr_strand  => $validated_params->{chr_strand}
+        }
+    );
+
+    return $primer_locus;
+}
 1;
 
 __END__

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

@@ -411,6 +411,15 @@ sub current_locus {
     return $loci;
 }
 
+sub gene_id {
+    my $self = shift;
+    my $crispr_design = $self->crispr_designs->first
+        or return;
+    my $genes = $crispr_design->design->genes
+        or return;
+    return $genes->first->gene_id;
+}
+
 sub start {
     return shift->current_locus->chr_start;
 }
@@ -427,6 +436,16 @@ sub chr_name {
     return shift->current_locus->chr->name;
 }
 
+sub default_assembly{
+    return shift->species->default_assembly;
+}
+
+# The name of the foreign key column to use when
+# linking e.g. a crispr_primer to a crispr
+sub id_column_name{
+    return 'crispr_id';
+}
+
 sub target_slice {
     my ( $self, $ensembl_util ) = @_;
 

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

@@ -266,7 +266,7 @@ sub get_crispr_primers {
 
   #return a resultset of all the relevant crispr primers
   return $self->result_source->schema->resultset('CrisprPrimer')->search(
-    { $field => $analysis_data->{crispr_id} },
+    { $field => $analysis_data->{crispr_id}, is_rejected => [0, undef] },
     { order_by => { -asc => 'me.primer_name' } }
   );
 }
@@ -415,7 +415,7 @@ sub format_alignment_strings {
 
     return { forward => 'No Read', reverse => 'No Read' } if $json->{no_reads};
     return { forward => 'No valid crispr pair', reverse => 'No valid crispr pair' } if $json->{no_crispr};
-    if ( $json->{forward_no_alignment} && $json->{forward_no_alignment} ) {
+    if ( $json->{forward_no_alignment} && $json->{reverse_no_alignment} ) {
         if ( !$self->fwd_read ) {
             return { forward => 'No Read', no_reverse_alignment => 1 };
         }

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

@@ -269,6 +269,23 @@ sub species {
     return shift->right_most_crispr->species_id;
 }
 
+# Added species_id method to CrisprPair and CrisprGroup to fetch
+# the species_id (name string) so it is equivalent to Crispr->species_id
+# (Crispr->species returns the Species object)
+sub species_id {
+    return shift->right_most_crispr->species_id;
+}
+
+sub default_assembly{
+    return shift->right_most_crispr->default_assembly;
+}
+
+# The name of the foreign key column to use when
+# linking e.g. a crispr_primer to a crispr_group
+sub id_column_name{
+    return 'crispr_group_id';
+}
+
 sub target_slice {
     my ( $self, $ensembl_util ) = @_;
 

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

@@ -230,6 +230,19 @@ sub target_slice {
     return $slice;
 }
 
+sub gene_id {
+    my $self = shift;
+    my $crispr_designs = $self->crispr_designs
+        or return;
+    my $genes = $crispr_designs->first->design->genes
+        or return;
+    return $genes->first->gene_id;
+}
+
+sub species_id {
+    return shift->right_crispr->species_id;
+}
+
 sub start {
     return shift->left_crispr_locus->chr_start;
 }
@@ -246,6 +259,16 @@ sub chr_name {
     return shift->right_crispr_locus->chr->name;
 }
 
+sub default_assembly {
+    return shift->left_crispr->default_assembly;
+}
+
+# The name of the foreign key column to use when
+# linking e.g. a crispr_primer to a crispr_pair
+sub id_column_name{
+    return 'crispr_pair_id';
+}
+
 sub is_pair { return 1; }
 
 sub is_group { return; }