[WIP] Support Regulatory Fusions

client/src/app/generated/server.model.graphql

@@ -5026,6 +5026,7 @@ type Fusion implements Commentable & EventOriginObject & EventSubject & Flaggabl
   link: String!
   name: String!
   openRevisionCount: Int!
+  regulatoryFusionType: RegulatoryFusionType
 
   """
   List and filter revisions.
@@ -5221,11 +5222,17 @@ input FusionPartnerInput {
   The status of the fusion partner
   """
   partnerStatus: FusionPartnerStatus!
+
+  """
+  If the fusion partner status is set to regulatory, what type of regulatory fusion is it?
+  """
+  regulatoryFusionType: RegulatoryFusionType
 }
 
 enum FusionPartnerStatus {
   KNOWN
   MULTIPLE
+  REGULATORY
   UNKNOWN
 }
 
@@ -9804,6 +9811,35 @@ enum ReferenceBuild {
   NCBI36
 }
 
+enum RegulatoryFusionType {
+  REG_ATTENUATOR
+  REG_CAAT_SIGNAL
+  REG_DNASE_I_HYPERSENSITIVE_SITE
+  REG_ENHANCER
+  REG_ENHANCER_BLOCKING_ELEMENT
+  REG_GC_SIGNAL
+  REG_IMPRINTING_CONTROL_REGION
+  REG_INSULATOR
+  REG_LOCUS_CONTROL_REGION
+  REG_MATRIX_ATTACHMENT_REGION
+  REG_MINUS_10_SIGNAL
+  REG_MINUS_35_SIGNAL
+  REG_OTHER
+  REG_POLYA_SIGNAL_SEQUENCE
+  REG_PROMOTER
+  REG_RECODING_STIMULATORY_REGION
+  REG_RECOMBINATION_ENHANCER
+  REG_REPLICATION_REGULATORY_REGION
+  REG_RESPONSE_ELEMENT
+  REG_RIBOSOME_BINDING_SITE
+  REG_RIBOSWITCH
+  REG_SILENCER
+  REG_TATA_BOX
+  REG_TERMINATOR
+  REG_TRANSCRIPTIONAL_CIS_REGULATORY_REGION
+  REG_UORF
+}
+
 type RejectRevisionsActivity implements ActivityInterface {
   createdAt: ISO8601DateTime!
   events: [Event!]!

client/src/app/generated/server.schema.json

@@ -23867,6 +23867,18 @@
               "isDeprecated": false,
               "deprecationReason": null
             },
+            {
+              "name": "regulatoryFusionType",
+              "description": null,
+              "args": [],
+              "type": {
+                "kind": "ENUM",
+                "name": "RegulatoryFusionType",
+                "ofType": null
+              },
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
             {
               "name": "revisions",
               "description": "List and filter revisions.",
@@ -24516,6 +24528,18 @@
               "defaultValue": null,
               "isDeprecated": false,
               "deprecationReason": null
+            },
+            {
+              "name": "regulatoryFusionType",
+              "description": "If the fusion partner status is set to regulatory, what type of regulatory fusion is it?",
+              "type": {
+                "kind": "ENUM",
+                "name": "RegulatoryFusionType",
+                "ofType": null
+              },
+              "defaultValue": null,
+              "isDeprecated": false,
+              "deprecationReason": null
             }
           ],
           "interfaces": null,
@@ -24547,6 +24571,12 @@
               "description": null,
               "isDeprecated": false,
               "deprecationReason": null
+            },
+            {
+              "name": "REGULATORY",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
             }
           ],
           "possibleTypes": null
@@ -44531,6 +44561,173 @@
           ],
           "possibleTypes": null
         },
+        {
+          "kind": "ENUM",
+          "name": "RegulatoryFusionType",
+          "description": null,
+          "fields": null,
+          "inputFields": null,
+          "interfaces": null,
+          "enumValues": [
+            {
+              "name": "REG_ATTENUATOR",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_CAAT_SIGNAL",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_DNASE_I_HYPERSENSITIVE_SITE",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_ENHANCER",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_ENHANCER_BLOCKING_ELEMENT",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_GC_SIGNAL",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_IMPRINTING_CONTROL_REGION",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_INSULATOR",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_LOCUS_CONTROL_REGION",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_MATRIX_ATTACHMENT_REGION",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_MINUS_35_SIGNAL",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_MINUS_10_SIGNAL",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_POLYA_SIGNAL_SEQUENCE",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_PROMOTER",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_RECODING_STIMULATORY_REGION",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_RECOMBINATION_ENHANCER",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_REPLICATION_REGULATORY_REGION",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_RESPONSE_ELEMENT",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_RIBOSOME_BINDING_SITE",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_RIBOSWITCH",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_SILENCER",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_TATA_BOX",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_TERMINATOR",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_TRANSCRIPTIONAL_CIS_REGULATORY_REGION",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_UORF",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "REG_OTHER",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            }
+          ],
+          "possibleTypes": null
+        },
         {
           "kind": "OBJECT",
           "name": "RejectRevisionsActivity",

server/app/graphql/mutations/create_fusion_feature.rb

@@ -36,14 +36,22 @@ def ready?(organization_id: nil, five_prime_gene:, three_prime_gene:,**kwargs)
 
     #check that partner status matches gene_id presence
     [five_prime_gene, three_prime_gene].each do |gene_input|
-      if gene_input.gene_id.present? && gene_input.partner_status != 'known'
-        raise GraphQL::ExecutionError, "Partner status needs to be 'known' if a gene_id is set"
+      if gene_input.gene_id.present? && (gene_input.partner_status != 'known' || gene_input.partner_status != 'regulatory')
+        raise GraphQL::ExecutionError, "Partner status needs to be 'known' or 'regulatory' if a gene_id is set"
       end
-      if gene_input.gene_id.blank? && gene_input.partner_status == 'known'
-        raise GraphQL::ExecutionError, "Partner status can't be 'known' if a gene_id is not set"
+      if gene_input.gene_id.blank? && (gene_input.partner_status == 'known' && gene_input.partner_status != 'regulatory')
+        raise GraphQL::ExecutionError, "Partner status can't be 'known' or 'regulatory' if a gene_id is not set"
       end
     end
 
+    #check that maximum one gene has regulatory_fusion_type set
+    if five_prime_gene.partner_status == 'regulatory' && three_prime_gene.partner_status == 'regulatory'
+      raise GraphQL::ExecutionError, "Only one Fusion partner can be marked 'regulatory'"
+    end
+    if five_prime_gene.regulatory_fusion_type.present? && three_prime_gene.regulatory_fusion_type.present?
+      raise GraphQL::ExecutionError, "Only one Fusion partner can have a regulatory fusion type set."
+    end
+
     return true
   end
 
@@ -54,12 +62,16 @@ def authorized?(organization_id: nil, **kwargs)
 
   def resolve(five_prime_gene:, three_prime_gene:, organization_id: nil)
 
+    #only one can be set
+    regulatory_fusion_type = five_prime_partner_status.regulatory_fusion_type || three_prime_partner_status.regulatory_fusion_type
+
     existing_feature_instance = Features::Fusion
       .find_by(
         five_prime_gene_id: five_prime_gene.gene_id,
         three_prime_gene_id: three_prime_gene.gene_id,
         five_prime_partner_status: five_prime_gene.partner_status,
         three_prime_partner_status: three_prime_gene.partner_status,
+        regulatory_fusion_type: regulatory_fusion_type
       )
 
     if existing_feature_instance.present?
@@ -74,6 +86,7 @@ def resolve(five_prime_gene:, three_prime_gene:, organization_id: nil)
         three_prime_gene_id: three_prime_gene.gene_id,
         five_prime_partner_status: five_prime_gene.partner_status,
         three_prime_partner_status: three_prime_gene.partner_status,
+        regulatory_fusion_type: regulatory_fusion_type,
         originating_user: context[:current_user],
         organization_id: organization_id,
       )

server/app/graphql/types/entities/fusion_type.rb

@@ -7,6 +7,8 @@ class FusionType < Types::Entities::FeatureType
     field :five_prime_partner_status, Types::Fusion::FusionPartnerStatus, null: false
     field :three_prime_partner_status, Types::Fusion::FusionPartnerStatus, null: false
 
+    field :regulatory_fusion_type, Types::Fusion::RegulatoryFusionTypeType, null: true
+
     def five_prime_gene
       Loaders::AssociationLoader.for(Features::Fusion, :five_prime_gene).load(object)
     end

server/app/graphql/types/fusion/fusion_partner_input_type.rb

@@ -6,5 +6,7 @@ class FusionPartnerInputType < Types::BaseInputObject
       description: 'The status of the fusion partner'
     argument :gene_id, Int, required: false,
       description: 'The CIViC gene ID of the partner, if known'
+    argument :regulatory_fusion_type, Types::Fusion::RegulatoryFusionTypeType, required: false,
+      description: "If the fusion partner status is set to regulatory, what type of regulatory fusion is it?"
   end
 end

server/app/graphql/types/fusion/fusion_partner_status.rb

@@ -3,5 +3,6 @@ class FusionPartnerStatus < Types::BaseEnum
     value 'KNOWN', value: 'known'
     value 'UNKNOWN', value: 'unknown'
     value 'MULTIPLE', value: 'multiple'
+    value 'REGULATORY', value: 'regulatory'
   end
 end

server/app/graphql/types/fusion/regulatory_fusion_type_type.rb

@@ -0,0 +1,7 @@
+module Types::Fusion
+  class RegulatoryFusionTypeType < Types::BaseEnum
+    Constants::REGULATORY_FUSION_ENUM_TYPES.each do |(name, _)|
+      value name.upcase, value: name
+    end
+  end
+end