Add allele loading for JSON importing

Refs #1779

lib/Canto/Curs/AlleleManager.pm

@@ -207,4 +207,39 @@ sub allele_from_json
   return $schema->create_with_type('Allele', \%create_args);
 }
 
+=head2 create_simple_allele
+
+ Usage   : my $allele = $allele_manager->create_simple_allele(...);
+ Function: Create an Allele object given some allele properties and a gene
+ Args    : $primary_identifier - the primary key in the database
+           $allele_type
+           $name
+           $description
+           $expression
+           $gene - a Gene object
+ Returns : the new Allele
+
+=cut
+
+sub create_simple_allele
+{
+  my $self = shift;
+
+  my $primary_identifier = shift;
+  my $allele_type = shift;
+  my $name = shift;
+  my $description = shift;
+  my $gene = shift;
+
+  my %create_args = (
+    primary_identifier => $primary_identifier,
+    type => $allele_type,
+    name => $name || undef,
+    description => $description || undef,
+    gene => $gene->gene_id(),
+  );
+
+  return $self->curs_schema()->create_with_type('Allele', \%create_args);
+}
+
 1;

lib/Canto/Track/LoadUtil.pm

@@ -50,6 +50,8 @@ use feature qw(state);
 use Package::Alias PubmedUtil => 'Canto::Track::PubmedUtil';
 
 use Canto::Curs::GeneManager;
+use Canto::Curs::AlleleManager;
+use Canto::Curs::GenotypeManager;
 
 use Canto::Track;
 
@@ -858,8 +860,14 @@ sub create_sessions_from_json
     my ($curs, $cursdb) =
       Canto::Track::create_curs($config, $self->schema(), $pub, $connect_options);
 
-    my $gene_manager = Canto::Curs::GeneManager->new(config => $config,
-                                                     curs_schema => $cursdb);
+    push @results, [$curs, $cursdb];
+
+    my $allele_manager =
+      Canto::Curs::AlleleManager->new(config => $config, curs_schema => $cursdb);
+    my $genotype_manager =
+      Canto::Curs::GenotypeManager->new(config => $config, curs_schema => $cursdb);
+    my $gene_manager =
+      Canto::Curs::GeneManager->new(config => $config, curs_schema => $cursdb);
 
     $curator_manager->set_curator($curs->curs_key(), $curator_email_address);
 
@@ -871,12 +879,43 @@ sub create_sessions_from_json
     print "created session: ", $curs->curs_key(), " pub: ", $pub->uniquename(),
       " for: $curator_email_address\n";
 
+    my %db_genes = ();
+
     for my $gene_uniquename (@{$session_data->{genes}}) {
       my $lookup_result = $gene_lookup->lookup([$gene_uniquename]);
-      $gene_manager->create_genes_from_lookup($lookup_result);
+      my %result = $gene_manager->create_genes_from_lookup($lookup_result);
+      while (my ($result_uniquename, $result_gene) = each %result) {
+        $db_genes{$result_uniquename} = $result_gene;
+      }
     }
-  }
 
+    my $alleles = $session_data->{alleles};
+
+    if ($alleles) {
+      while (my ($allele_uniquename, $allele_details) = each %$alleles) {
+        my $allele_gene_uniquename = $allele_details->{gene};
+        if (!defined $allele_gene_uniquename) {
+          die qq|no "gene" field in details for $allele_uniquename in $pub_uniquename|;
+        }
+        my $gene = $db_genes{$allele_gene_uniquename};
+        if (!defined $gene) {
+          die qq|no gene the session for $allele_uniquename in $pub_uniquename|;
+        }
+
+        my $type = $allele_details->{allele_type} || 'other';
+        my $name = $allele_details->{allele_name} || undef;
+        my $description = $allele_details->{allele_description} || undef;
+        my @args = ($allele_uniquename, $type, $name, $description, $gene);
+
+        my @alleles_for_make_genotype =
+          $allele_manager->create_simple_allele(@args);
+
+        $genotype_manager->make_genotype(undef, undef, \@alleles_for_make_genotype,
+                                         $gene->organism()->taxonid(),
+                                         "genotype-$allele_uniquename");
+      }
+    }
+  }
 
   return @results;
 }

t/60_load_util.t

@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use Test::More tests => 4;
+use Test::More tests => 10;
 use Test::Exception;
 
 use Canto::TestUtil;
@@ -31,6 +31,24 @@ my $gene_load = Canto::Track::GeneLoad->new(organism => $fly, schema => $schema)
 $gene_load->create_gene('FBgn0004107', 'Dmel\Cdk2', [], 'Cyclin-dependent kinase 2');
 $gene_load->create_gene('FBgn0016131', 'Dmel\Cdk4', [], 'Cyclin-dependent kinase 4');
 my $test_json_file = $test_util->root_dir() . '/t/data/sessions_from_json_test.json';
-my ($curs, $cursdb, $person) =
+my @created_sessions =
   $load_util->create_sessions_from_json($config, $test_json_file,
                                         'test.user@3926fef56bb23eb871ee91dc2e3fdd7c46ef1385.org');
+
+is (@created_sessions, 1);
+
+my ($created_curs, $created_cursdb) = @{$created_sessions[0]};
+
+my $FBal0119310_allele =
+  $created_cursdb->resultset('Allele')->find({ primary_identifier => "FBal0119310" });
+
+ok (defined $FBal0119310_allele);
+
+is($FBal0119310_allele->type(), 'other');
+is($FBal0119310_allele->name(), 'Dmel\Cdk2_UAS.Tag:MYC');
+is($FBal0119310_allele->description(), 'description of FBal0119310');
+
+my $genotype_FBal0119310 =
+  $created_cursdb->resultset('Genotype')->find({ identifier => "genotype-FBal0119310" });
+
+is(($genotype_FBal0119310->alleles()->all())[0]->name(), 'Dmel\Cdk2_UAS.Tag:MYC');

t/data/sessions_from_json_test.json

@@ -8,7 +8,7 @@
         "gene": "FBgn0004107",
         "allele_type": "other",
         "allele_name": "Dmel\\Cdk2_UAS.Tag:MYC",
-        "allele_description": null
+        "allele_description": "description of FBal0119310"
       },
       "FBal0064432": {
         "gene": "FBgn0016131",