Merge pull request #901 from griffithlab/allele-registry-filtering

add ability to fetch Variants and MPs using ClinGen Allele Registry ids
griffithlab · Oct 3, 2023 · 2ceae64 · 2ceae64
2 parents 4b24df1 + d2bb5a3
commit 2ceae64
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Showing 5 changed files with 47 additions and 1 deletion.
diff --git a/client/src/app/generated/server.model.graphql b/client/src/app/generated/server.model.graphql
@@ -5681,6 +5681,11 @@ type Query {
     """
     after: String
 
+    """
+    Find Molecular Profiles based on the ClinGen Allele Registry ID of one of its involed Variants
+    """
+    alleleRegistryId: String
+
     """
     Returns the elements in the list that come before the specified cursor.
     """
@@ -6250,6 +6255,11 @@ type Query {
     """
     after: String
 
+    """
+    Find a CIViC Variant based on its ClinGen Allele Registry ID
+    """
+    alleleRegistryId: String
+
     """
     Returns the elements in the list that come before the specified cursor.
     """

diff --git a/client/src/app/generated/server.schema.json b/client/src/app/generated/server.schema.json
@@ -25568,6 +25568,18 @@
                   "isDeprecated": false,
                   "deprecationReason": null
                 },
+                {
+                  "name": "alleleRegistryId",
+                  "description": "Find Molecular Profiles based on the ClinGen Allele Registry ID of one of its involed Variants",
+                  "type": {
+                    "kind": "SCALAR",
+                    "name": "String",
+                    "ofType": null
+                  },
+                  "defaultValue": null,
+                  "isDeprecated": false,
+                  "deprecationReason": null
+                },
                 {
                   "name": "after",
                   "description": "Returns the elements in the list that come after the specified cursor.",
@@ -27931,6 +27943,18 @@
                   "isDeprecated": false,
                   "deprecationReason": null
                 },
+                {
+                  "name": "alleleRegistryId",
+                  "description": "Find a CIViC Variant based on its ClinGen Allele Registry ID",
+                  "type": {
+                    "kind": "SCALAR",
+                    "name": "String",
+                    "ofType": null
+                  },
+                  "defaultValue": null,
+                  "isDeprecated": false,
+                  "deprecationReason": null
+                },
                 {
                   "name": "hasNoVariantType",
                   "description": "Return Variants lacking an assigned VariantType",

diff --git a/server/app/graphql/mutations/create_molecular_profile.rb b/server/app/graphql/mutations/create_molecular_profile.rb
@@ -19,7 +19,12 @@ def ready?(structure: )
 
     if variants.size !=  variant_ids.size
       missing = variant_ids - variants.map(&:id)
-      raise  GraphQL::ExecutionError, "Variants with ID [#{missing.join(', ')}] were not found."
+      raise GraphQL::ExecutionError, "Variants with ID [#{missing.join(', ')}] were not found."
+    end
+
+    deprecated_variants = variants.select { |v| v.deprecated? }
+    if deprecated_variants.any?
+      raise GraphQL::ExecutionError, "Variants [#{deprecated_variants.map(&:name).join(', ')}] are Deprecated and should not be used."
     end
 
     return true

diff --git a/server/app/graphql/resolvers/top_level_molecular_profiles.rb b/server/app/graphql/resolvers/top_level_molecular_profiles.rb
@@ -47,4 +47,7 @@ class Resolvers::TopLevelMolecularProfiles < GraphQL::Schema::Resolver
     scope.joins(:variants).where('variants.id = ?', value)
   end
 
+  option(:allele_registry_id, type: GraphQL::Types::String, description: 'Find Molecular Profiles based on the ClinGen Allele Registry ID of one of its involed Variants') do |scope, value|
+    scope.joins(:variants).where('variants.allele_registry_id = ?', value)
+  end
 end
diff --git a/server/app/graphql/resolvers/top_level_variants.rb b/server/app/graphql/resolvers/top_level_variants.rb
@@ -26,6 +26,10 @@ class Resolvers::TopLevelVariants < GraphQL::Schema::Resolver
     end
   end
 
+  option(:allele_registry_id, type: GraphQL::Types::String, description: 'Find a CIViC Variant based on its ClinGen Allele Registry ID') do |scope, value|
+    scope.where(allele_registry_id: value)
+  end
+
   option(:has_no_variant_type, type: GraphQL::Types::Boolean, description: "Return Variants lacking an assigned VariantType") do |scope, value|
     if(value)
       scope.left_joins(:variant_types).where(variant_types: { id: nil })