remove rejected EIDs and Assertions from MP relations by default

griffithlab · Aug 13, 2024 · 121df39 · 121df39
1 parent f637997
commit 121df39
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Showing 4 changed files with 57 additions and 8 deletions.
diff --git a/client/src/app/generated/server.model.graphql b/client/src/app/generated/server.model.graphql
@@ -5682,6 +5682,7 @@ type MolecularProfile implements Commentable & EventOriginObject & EventSubject
     Returns the first _n_ elements from the list.
     """
     first: Int
+    includeRejected: Boolean
 
     """
     Returns the last _n_ elements from the list.
@@ -5798,6 +5799,7 @@ type MolecularProfile implements Commentable & EventOriginObject & EventSubject
     Returns the first _n_ elements from the list.
     """
     first: Int
+    includeRejected: Boolean
 
     """
     Returns the last _n_ elements from the list.

diff --git a/client/src/app/generated/server.schema.json b/client/src/app/generated/server.schema.json
@@ -27074,6 +27074,18 @@
                   "defaultValue": null,
                   "isDeprecated": false,
                   "deprecationReason": null
+                },
+                {
+                  "name": "includeRejected",
+                  "description": null,
+                  "type": {
+                    "kind": "SCALAR",
+                    "name": "Boolean",
+                    "ofType": null
+                  },
+                  "defaultValue": null,
+                  "isDeprecated": false,
+                  "deprecationReason": null
                 }
               ],
               "type": {
@@ -27497,6 +27509,18 @@
                   "defaultValue": null,
                   "isDeprecated": false,
                   "deprecationReason": null
+                },
+                {
+                  "name": "includeRejected",
+                  "description": null,
+                  "type": {
+                    "kind": "SCALAR",
+                    "name": "Boolean",
+                    "ofType": null
+                  },
+                  "defaultValue": null,
+                  "isDeprecated": false,
+                  "deprecationReason": null
                 }
               ],
               "type": {

diff --git a/server/app/graphql/types/entities/molecular_profile_type.rb b/server/app/graphql/types/entities/molecular_profile_type.rb
@@ -15,10 +15,17 @@ class MolecularProfileType < Types::BaseObject
       description: 'The profile name with its constituent parts as objects, suitable for building tags.'
     field :variants, [Types::Interfaces::VariantInterface], null: false,
       description: 'The collection of variants included in this molecular profile. Please note the name for their relation to each other.'
-    field :assertions, Types::Entities::AssertionType.connection_type, null: false,
-      description: 'The collection of assertions associated with this molecular profile.'
-    field :evidence_items, Types::Entities::EvidenceItemType.connection_type, null: false,
-      description: 'The collection of evidence items associated with this molecular profile.'
+
+    field :assertions, Types::Entities::AssertionType.connection_type, null: false do
+      description 'The collection of assertions associated with this molecular profile.'
+      argument :include_rejected, Boolean, required: false
+    end
+
+    field :evidence_items, Types::Entities::EvidenceItemType.connection_type, null: false do
+      description 'The collection of evidence items associated with this molecular profile.'
+      argument :include_rejected, Boolean, required: false
+    end
+
     field :sources, [Types::Entities::SourceType], null: false
     field :description, String, null: true
     field :molecular_profile_aliases, [String], null: false
@@ -77,12 +84,20 @@ def complex_molecular_profile_creation_activity
       Loaders::AssociationLoader.for(MolecularProfile, :complex_molecular_profile_creation_activity).load(object)
     end
 
-    def assertions
-      Loaders::AssociationLoader.for(MolecularProfile, :assertions).load(object)
+    def assertions(include_rejected: false)
+      if include_rejected
+        Loaders::AssociationLoader.for(MolecularProfile, :assertions).load(object)
+      else
+        Loaders::AssociationLoader.for(MolecularProfile, :submitted_and_accepted_assertions).load(object)
+      end
     end
 
-    def evidence_items
-      Loaders::AssociationLoader.for(MolecularProfile, :evidence_items).load(object)
+    def evidence_items(include_rejected: false)
+      if include_rejected
+        Loaders::AssociationLoader.for(MolecularProfile, :evidence_items).load(object)
+      else
+        Loaders::AssociationLoader.for(MolecularProfile, :submitted_and_accepted_evidence_items).load(object)
+      end
     end
 
     def sources

diff --git a/server/app/models/molecular_profile.rb b/server/app/models/molecular_profile.rb
@@ -9,7 +9,15 @@ class MolecularProfile < ActiveRecord::Base
   has_and_belongs_to_many :variants
   has_and_belongs_to_many :sources
   has_many :assertions
+  has_many :submitted_and_accepted_assertions,
+    ->() { where.not(status: 'rejected') },
+    class_name: 'Assertion'
+
   has_many :evidence_items
+  has_many :submitted_and_accepted_evidence_items,
+    ->() { where.not(status: 'rejected') },
+    class_name: 'EvidenceItem'
+
   has_one :evidence_items_by_status
   has_one :evidence_items_by_type
   has_and_belongs_to_many :molecular_profile_aliases, join_table: :molecular_profile_aliases_molecular_profiles