Merge pull request #1145 from griffithlab/civicpy

Change top level genes/fusions/factors resolver to add configurable status filter
griffithlab · Oct 30, 2024 · e8bb009 · e8bb009
2 parents fdc1a01 + 7286038
commit e8bb009
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Showing 11 changed files with 197 additions and 152 deletions.
diff --git a/...omponents/molecular-profiles/molecular-profiles-menu/molecular-profiles-menu.component.ts b/...omponents/molecular-profiles/molecular-profiles-menu/molecular-profiles-menu.component.ts
@@ -7,7 +7,7 @@ import {
   MolecularProfileConnection,
   MolecularProfileMenuQueryVariables,
   MolecularProfileMenuGQL,
-  MolecularProfileDisplayFilter,
+  AssociatedEvidenceStatusFilter,
 } from '@app/generated/civic.apollo'
 import { map, debounceTime, filter, startWith } from 'rxjs/operators'
 import { Observable, Subject } from 'rxjs'
@@ -32,8 +32,8 @@ export class CvcMolecularProfilesMenuComponent implements OnInit {
   loading$?: Observable<boolean>;
 
   mpNameFilter: Maybe<string>
-  statusFilter: MolecularProfileDisplayFilter =
-    MolecularProfileDisplayFilter.All
+  statusFilter: AssociatedEvidenceStatusFilter =
+    AssociatedEvidenceStatusFilter.All
 
   private debouncedQuery = new Subject<void>()
   private result$!: Observable<ApolloQueryResult<MolecularProfileMenuQuery>>
@@ -91,7 +91,7 @@ export class CvcMolecularProfilesMenuComponent implements OnInit {
     this.debouncedQuery.next()
   }
 
-  onMolecularProfileStatusFilterChanged(filter: MolecularProfileDisplayFilter) {
+  onMolecularProfileStatusFilterChanged(filter: AssociatedEvidenceStatusFilter) {
     this.queryRef$.refetch({
       first: this.pageSize,
       evidenceStatusFilter: filter

diff --git a/...src/app/components/molecular-profiles/molecular-profiles-menu/molecular-profiles-menu.gql b/...src/app/components/molecular-profiles/molecular-profiles-menu/molecular-profiles-menu.gql
@@ -6,7 +6,7 @@ query MolecularProfileMenu(
   $last: Int
   $before: String
   $after: String
-  $evidenceStatusFilter: MolecularProfileDisplayFilter
+  $evidenceStatusFilter: AssociatedEvidenceStatusFilter
 ) {
   molecularProfiles(
     geneId: $geneId

diff --git a/client/src/app/generated/civic.apollo.ts b/client/src/app/generated/civic.apollo.ts
@@ -490,6 +490,17 @@ export enum AssertionType {
   Prognostic = 'PROGNOSTIC'
 }
 
+export enum AssociatedEvidenceStatusFilter {
+  /** Apply no status filter to an entity in order to display all entities regardless of attached evidence status. */
+  All = 'ALL',
+  /** Apply filter to an entity to display only those which have at least one accepted associated evidence item. */
+  WithAccepted = 'WITH_ACCEPTED',
+  /** Apply filter to an entity to display only those which have at least one accepted or submitted associated evidence item. */
+  WithAcceptedOrSubmitted = 'WITH_ACCEPTED_OR_SUBMITTED',
+  /** Apply filter to an entity to display only those which have at least one submitted associated evidence item. */
+  WithSubmitted = 'WITH_SUBMITTED'
+}
+
 export enum BooleanOperator {
   And = 'AND',
   Or = 'OR'
@@ -3965,17 +3976,6 @@ export enum MolecularProfileDeprecationReasonMutationInput {
   Other = 'OTHER'
 }
 
-export enum MolecularProfileDisplayFilter {
-  /** Display all molecular profiles regardless of attached evidence status. */
-  All = 'ALL',
-  /** Display only molecular profiles which have at least one accepted evidence item. */
-  WithAccepted = 'WITH_ACCEPTED',
-  /** Display only molecular profiles which have evidence in either an accepted or submitted state. */
-  WithAcceptedOrSubmitted = 'WITH_ACCEPTED_OR_SUBMITTED',
-  /** Display molecular profiles which have at least one submitted evidence item. */
-  WithSubmitted = 'WITH_SUBMITTED'
-}
-
 /** An edge in a connection. */
 export type MolecularProfileEdge = {
   __typename: 'MolecularProfileEdge';
@@ -5280,6 +5280,7 @@ export type QueryFactorArgs = {
 export type QueryFactorsArgs = {
   after?: InputMaybe<Scalars['String']['input']>;
   before?: InputMaybe<Scalars['String']['input']>;
+  evidenceStatusFilter?: InputMaybe<AssociatedEvidenceStatusFilter>;
   first?: InputMaybe<Scalars['Int']['input']>;
   last?: InputMaybe<Scalars['Int']['input']>;
   name?: InputMaybe<Array<Scalars['String']['input']>>;
@@ -5324,8 +5325,7 @@ export type QueryFusionArgs = {
 export type QueryFusionsArgs = {
   after?: InputMaybe<Scalars['String']['input']>;
   before?: InputMaybe<Scalars['String']['input']>;
-  entrezIds?: InputMaybe<Array<Scalars['Int']['input']>>;
-  entrezSymbols?: InputMaybe<Array<Scalars['String']['input']>>;
+  evidenceStatusFilter?: InputMaybe<AssociatedEvidenceStatusFilter>;
   first?: InputMaybe<Scalars['Int']['input']>;
   genePartnerId?: InputMaybe<Scalars['Int']['input']>;
   last?: InputMaybe<Scalars['Int']['input']>;
@@ -5343,6 +5343,7 @@ export type QueryGenesArgs = {
   before?: InputMaybe<Scalars['String']['input']>;
   entrezIds?: InputMaybe<Array<Scalars['Int']['input']>>;
   entrezSymbols?: InputMaybe<Array<Scalars['String']['input']>>;
+  evidenceStatusFilter?: InputMaybe<AssociatedEvidenceStatusFilter>;
   first?: InputMaybe<Scalars['Int']['input']>;
   last?: InputMaybe<Scalars['Int']['input']>;
 };
@@ -5357,7 +5358,7 @@ export type QueryMolecularProfilesArgs = {
   after?: InputMaybe<Scalars['String']['input']>;
   alleleRegistryId?: InputMaybe<Scalars['String']['input']>;
   before?: InputMaybe<Scalars['String']['input']>;
-  evidenceStatusFilter?: InputMaybe<MolecularProfileDisplayFilter>;
+  evidenceStatusFilter?: InputMaybe<AssociatedEvidenceStatusFilter>;
   featureId?: InputMaybe<Scalars['Int']['input']>;
   first?: InputMaybe<Scalars['Int']['input']>;
   geneId?: InputMaybe<Scalars['Int']['input']>;
@@ -8287,7 +8288,7 @@ export type MolecularProfileMenuQueryVariables = Exact<{
   last?: InputMaybe<Scalars['Int']['input']>;
   before?: InputMaybe<Scalars['String']['input']>;
   after?: InputMaybe<Scalars['String']['input']>;
-  evidenceStatusFilter?: InputMaybe<MolecularProfileDisplayFilter>;
+  evidenceStatusFilter?: InputMaybe<AssociatedEvidenceStatusFilter>;
 }>;
 
 
@@ -14472,7 +14473,7 @@ export const BrowseMolecularProfilesDocument = gql`
     }
   }
 export const MolecularProfileMenuDocument = gql`
-    query MolecularProfileMenu($geneId: Int, $featureId: Int, $mpName: String, $first: Int, $last: Int, $before: String, $after: String, $evidenceStatusFilter: MolecularProfileDisplayFilter) {
+    query MolecularProfileMenu($geneId: Int, $featureId: Int, $mpName: String, $first: Int, $last: Int, $before: String, $after: String, $evidenceStatusFilter: AssociatedEvidenceStatusFilter) {
   molecularProfiles(
     geneId: $geneId
     featureId: $featureId

diff --git a/client/src/app/generated/server.model.graphql b/client/src/app/generated/server.model.graphql
@@ -796,6 +796,28 @@ enum AssertionType {
   PROGNOSTIC
 }
 
+enum AssociatedEvidenceStatusFilter {
+  """
+  Apply no status filter to an entity in order to display all entities regardless of attached evidence status.
+  """
+  ALL
+
+  """
+  Apply filter to an entity to display only those which have at least one accepted associated evidence item.
+  """
+  WITH_ACCEPTED
+
+  """
+  Apply filter to an entity to display only those which have at least one accepted or submitted associated evidence item.
+  """
+  WITH_ACCEPTED_OR_SUBMITTED
+
+  """
+  Apply filter to an entity to display only those which have at least one submitted associated evidence item.
+  """
+  WITH_SUBMITTED
+}
+
 enum BooleanOperator {
   AND
   OR
@@ -6978,28 +7000,6 @@ enum MolecularProfileDeprecationReasonMutationInput {
   OTHER
 }
 
-enum MolecularProfileDisplayFilter {
-  """
-  Display all molecular profiles regardless of attached evidence status.
-  """
-  ALL
-
-  """
-  Display only molecular profiles which have at least one accepted evidence item.
-  """
-  WITH_ACCEPTED
-
-  """
-  Display only molecular profiles which have evidence in either an accepted or submitted state.
-  """
-  WITH_ACCEPTED_OR_SUBMITTED
-
-  """
-  Display molecular profiles which have at least one submitted evidence item.
-  """
-  WITH_SUBMITTED
-}
-
 """
 An edge in a connection.
 """
@@ -8946,6 +8946,11 @@ type Query {
     """
     before: String
 
+    """
+    Limit factors by the status of attached evidence.
+    """
+    evidenceStatusFilter: AssociatedEvidenceStatusFilter
+
     """
     Returns the first _n_ elements from the list.
     """
@@ -9048,14 +9053,9 @@ type Query {
     before: String
 
     """
-    List of Entrez Gene IDs to return results for
+    Limit fusions by the status of attached evidence.
     """
-    entrezIds: [Int!]
-
-    """
-    List of Entrez Gene symbols to return results for
-    """
-    entrezSymbols: [String!]
+    evidenceStatusFilter: AssociatedEvidenceStatusFilter
 
     """
     Returns the first _n_ elements from the list.
@@ -9102,6 +9102,11 @@ type Query {
     """
     entrezSymbols: [String!]
 
+    """
+    Limit genes by the status of attached evidence.
+    """
+    evidenceStatusFilter: AssociatedEvidenceStatusFilter
+
     """
     Returns the first _n_ elements from the list.
     """
@@ -9140,7 +9145,7 @@ type Query {
     """
     Limit molecular profiles by the status of attached evidence.
     """
-    evidenceStatusFilter: MolecularProfileDisplayFilter
+    evidenceStatusFilter: AssociatedEvidenceStatusFilter
 
     """
     Filter molecular profiles to the CIViC ID of the feature(s) involved.