Revert to previous AGM script

WormBase · Jan 6, 2025 · b6983be · b6983be
1 parent c320f4b
commit b6983be
Showing 1 changed file with 2 additions and 68 deletions.
diff --git a/scripts/AGR/curation_db_submissions/make_agr_agm_json.pl b/scripts/AGR/curation_db_submissions/make_agr_agm_json.pl
@@ -7,7 +7,7 @@
 use Const::Fast;
 
 my ($help, $debug, $test, $verbose, $store, $wormbase);
-my ($outfile, $acedbpath, $ws_version, $out_fh, $association_outfile);
+my ($outfile, $acedbpath, $ws_version, $out_fh);
 
 const my $LINKML_SCHEMA => 'v2.8.1';
 
@@ -18,7 +18,6 @@
 	    "store:s"     => \$store,
 	    "database:s"  => \$acedbpath,
 	    "outfile:s"   => \$outfile,
-	    "assoc:s"     => \$association_outfile,
             "wsversion=s" => \$ws_version
 	    );
 
@@ -38,10 +37,9 @@
 my $it = $db->fetch_many(-query => $query);
 
 $outfile = "./wormbase.agms.${ws_version}.${LINKML_SCHEMA}.json" unless defined $outfile;
-$association_outfile = "./wormbase.agm_associations.${ws_version}.${LINKML_SCHEMA}.json" unless defined $association_outfile;
 
 my @agms;
-my @agm_components;
+
 
 while (my $obj = $it->next) {
     unless ($obj->Species) {
@@ -75,31 +73,6 @@
 	data_provider_dto => $data_provider_dto_json
     };
     push @agms, $strain;
-
-    if ($obj->Variation) {
-	my @component_variations =  $obj->at('Contains.Variation');
-	for my $cv (@component_variations) {
-	    my $cv_json = {
-		agm_subject_identifier => "WB:$obj",
-		zygosity_curie => "GENO:0000137",
-		allele_identifier => "WB:" . $cv->name,
-		relation_name => "contains"
-	    };
-	    push @agm_components, $cv_json;
-	}
-    }
-    if ($obj->Transgene) {
-	my @component_transgenes =  $obj->at('Contains.Transgene');
-	for my $ct (@component_transgenes) {
-	    my $ct_json = {
-		agm_subject_identifier => "WB:$obj",
-		zygosity_curie => "GENO:0000137",
-		allele_identifier => "WB:" . $ct->name,
-		relation_name => "contains"
-	    };
-	    push @agm_components, $ct_json;
-	}
-    }
 }
 
 
@@ -139,57 +112,18 @@
 	data_provider_dto => $data_provider_dto_json
     };
     push @agms, $genotype;
-
-    if ($obj->Variation) {
-	my @component_variations =  $obj->at('Genotype_component.Variation');
-	for my $cv (@component_variations) {
-	    my $cv_json = {
-		agm_subject_identifier => "WB:$obj",
-		zygosity_curie => "GENO:0000137",
-		allele_identifier => "WB:" . $cv->name,
-		relation_name => "contains"
-	    };
-	    push @agm_components, $cv_json;
-	}
-    }
-    if ($obj->Transgene) {
-	my @component_transgenes =  $obj->at('Genotype_component.Transgene');
-	for my $ct (@component_transgenes) {
-	    my $ct_json = {
-		agm_subject_identifier => "WB:$obj",
-		zygosity_curie => "GENO:0000137",
-		allele_identifier => "WB:" . $ct->name,
-		relation_name => "contains"
-	    };
-	    push @agm_components, $ct_json;
-	}
-    }
 }
-
 my $data = {
     linkml_version => $LINKML_SCHEMA,
     alliance_member_release_version => $ws_version,
     agm_ingest_set => \@agms,
 };
 
-my $assoc_data = {
-    linkml_version => $LINKML_SCHEMA,
-    alliance_member_release_version => $ws_version,
-    agm_allele_association_ingest_set => \@agm_components
-}
-
 my $json_obj = JSON->new;
 my $string   = $json_obj->allow_nonref->canonical->pretty->encode($data);
 my $out_fh;
 open $out_fh, ">$outfile" or die "Could not open $outfile for writing\n";
 
 print $out_fh $string;
-
-my $assoc_json_obj = JSON->new;
-my $assoc_string = $assoc_json_obj->allow_nonref->canonical->pretty->encode($assoc_data);
-my $assoc_out_fh;
-open $assoc_out_fh, ">$association_outfile" or die "Could not open $association_outfile for writing\n";
-
-print $assoc_out_fh $assoc_string;
 $db->close;