MultipleEntryPropertyCollector includes polymer entity prd ids

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [6.0.1] - 2023-11-27
+### Improvement
+- `MultipleEntryPropertyCollector` includes polymer entity prd ids
+
 ## [6.0.0] - 2023-11-22
 ### Breaking changes
 - Types are not anymore exposed from `build/src`

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rcsb/rcsb-saguaro-app",
-  "version": "6.0.0",
+  "version": "6.0.1",
   "description": "RCSB 1D Saguaro Web App",
   "main": "build/app.js",
   "files": [

src/RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector.ts

@@ -1,34 +1,39 @@
 import {rcsbClient, RcsbClient} from "../../RcsbGraphQL/RcsbClient";
-import {CoreEntry, QueryEntriesArgs} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import {
+    CoreEntry,
+    CorePolymerEntity,
+    QueryEntriesArgs
+} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
 import {StructureDeterminationMethodology} from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
 import {Assertions} from "../../RcsbUtils/Helpers/Assertions";
 import assertDefined = Assertions.assertDefined;
 import assertElementListDefined = Assertions.assertElementListDefined;
 
-export interface EntryPropertyIntreface {
+export interface EntryPropertyInterface {
     rcsbId: string;
     entryId: string;
     experimentalMethod: string;
     resolution?: number;
     name: string;
     taxNames: Array<string>;
     entryMolecularWeight?: number;
-    description:Array<string>;
+    description: Array<string>;
     entityToInstance: Map<string,Array<string>>;
     structureDeterminationMethodology: StructureDeterminationMethodology;
     nonPolymerEntityToInstance: Map<string,Array<string>>;
     instanceToOperator: Map<string,Map<string,Array<string>>>;
+    entityToPrd: Map<string,string>;
 }
 
 export class MultipleEntryPropertyCollector {
     private readonly rcsbFvQuery: RcsbClient = rcsbClient;
 
-    public async collect(requestConfig: QueryEntriesArgs): Promise<Array<EntryPropertyIntreface>> {
+    public async collect(requestConfig: QueryEntriesArgs): Promise<Array<EntryPropertyInterface>> {
         const result: Array<CoreEntry> = await this.rcsbFvQuery.requestMultipleEntriesProperties(requestConfig);
         return result.map(r=>MultipleEntryPropertyCollector.getEntryProperties(r));
     }
 
-    private static getEntryProperties(r:CoreEntry): EntryPropertyIntreface{
+    private static getEntryProperties(r:CoreEntry): EntryPropertyInterface{
         return {
             rcsbId: r.rcsb_id,
             entryId: r.rcsb_id,
@@ -43,7 +48,8 @@ export class MultipleEntryPropertyCollector {
             structureDeterminationMethodology: r.rcsb_entry_info.structure_determination_methodology as StructureDeterminationMethodology,
             nonPolymerEntityToInstance: r.nonpolymer_entities?.map(pe=>([pe?.rcsb_id, pe?.nonpolymer_entity_instances?.map(pei=>pei?.rcsb_id)] as [string,string[]]))
                 .reduce((r:Map<string, string[]>,x:[string, string[]])=>r.set(x[0],x[1]),new Map<string, string[]>()) ?? new Map<string, string[]>(),
-            instanceToOperator: MultipleEntryPropertyCollector.instanceToOperator(r)
+            instanceToOperator: MultipleEntryPropertyCollector.instanceToOperator(r),
+            entityToPrd: r.polymer_entities?.filter((pe): pe is CorePolymerEntity => typeof pe != "undefined").map( pe=> [pe?.rcsb_id ?? "", pe?.entity_poly?.rcsb_prd_id ?? ""]).reduce((map, pair)=>map.set(pair[0],pair[1]), new Map<string,string>()) ?? new Map()
         };
     }
 

src/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainObservedAlignmentTrackFactory.ts

@@ -18,7 +18,7 @@ import {range} from "lodash";
 import {PlainAlignmentTrackFactory} from "./PlainAlignmentTrackFactory";
 import {TrackUtils} from "./Helper/TrackUtils";
 import {rcsbRequestCtxManager} from "../../../../RcsbRequest/RcsbRequestContextManager";
-import {EntryPropertyIntreface} from "../../../../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
+import {EntryPropertyInterface} from "../../../../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
 import {Assertions} from "../../../../RcsbUtils/Helpers/Assertions";
 import assertDefined = Assertions.assertDefined;
 import {TagDelimiter} from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
@@ -50,7 +50,7 @@ export class PlainObservedAlignmentTrackFactory implements TrackFactoryInterface
             return uor.target_id.split(TagDelimiter.instance)[0]
         }));
         //TODO define a Translator class for multiple entry entry data
-        const entryProperties: EntryPropertyIntreface[] = (await Promise.all<EntryPropertyIntreface[]>(Operator.arrayChunk(entryIds, 100).map(ids => rcsbRequestCtxManager.getEntryProperties(ids)))).flat();
+        const entryProperties: EntryPropertyInterface[] = (await Promise.all<EntryPropertyInterface[]>(Operator.arrayChunk(entryIds, 100).map(ids => rcsbRequestCtxManager.getEntryProperties(ids)))).flat();
         entryProperties.forEach(ep=>{
             ep.entityToInstance.forEach((instanceList,entityId)=>{
                 this.entityInstanceNumberMap.set(entityId, instanceList.length);

src/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PositionalScoreAlignmentTrackFactory.ts

@@ -20,7 +20,7 @@ import {range} from "lodash";
 import {PlainAlignmentTrackFactory} from "./PlainAlignmentTrackFactory";
 import {TrackUtils} from "./Helper/TrackUtils";
 import {rcsbRequestCtxManager} from "../../../../RcsbRequest/RcsbRequestContextManager";
-import {EntryPropertyIntreface} from "../../../../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
+import {EntryPropertyInterface} from "../../../../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
 import {Assertions} from "../../../../RcsbUtils/Helpers/Assertions";
 import assertDefined = Assertions.assertDefined;
 import {TagDelimiter} from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
@@ -65,7 +65,7 @@ export class PositionalScoreAlignmentTrackFactory implements TrackFactoryInterfa
             return uor.target_id.split(TagDelimiter.instance)[0];
         }));
         //TODO define a Translator class for multiple entry entry data
-        const entryProperties: EntryPropertyIntreface[] = (await Promise.all<EntryPropertyIntreface[]>(Operator.arrayChunk(entryIds, 100).map(ids => rcsbRequestCtxManager.getEntryProperties(ids)))).flat();
+        const entryProperties: EntryPropertyInterface[] = (await Promise.all<EntryPropertyInterface[]>(Operator.arrayChunk(entryIds, 100).map(ids => rcsbRequestCtxManager.getEntryProperties(ids)))).flat();
         entryProperties.forEach(ep=>{
             ep.entityToInstance.forEach((instanceList,entityId)=>{
                 instanceList.forEach(instanceId=>{

src/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMembersGrid.tsx

@@ -9,7 +9,7 @@ import {SearchQueryTools as SQT} from "../../../RcsbSeacrh/SearchQueryTools";
 import {RcsbSearchMetadata} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
 import {ReturnType, SortDirection} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
 import {
-    EntryPropertyIntreface
+    EntryPropertyInterface
 } from "../../../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
 import {GroupProvenanceId} from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
 import {rcsbRequestCtxManager} from "../../../RcsbRequest/RcsbRequestContextManager";
@@ -135,9 +135,9 @@ async function searchRequest(groupProvenanceId: GroupProvenanceId, groupId: stri
     });
 }
 
-function parseItems(groupProvenanceId: GroupProvenanceId, propsList:Array<EntryPropertyIntreface>|Array<PolymerEntityInterface>): Array<ItemFeaturesInterface>{
+function parseItems(groupProvenanceId: GroupProvenanceId, propsList:Array<EntryPropertyInterface>|Array<PolymerEntityInterface>): Array<ItemFeaturesInterface>{
     return groupProvenanceId === GroupProvenanceId.ProvenanceMatchingDepositGroupId ?
-        (propsList as Array<EntryPropertyIntreface>).map((o)=>({...o, molecularWeight:o.entryMolecularWeight}))
+        (propsList as Array<EntryPropertyInterface>).map((o)=>({...o, molecularWeight:o.entryMolecularWeight}))
         :
         (propsList as Array<PolymerEntityInterface>).map((o)=>(o.instances)).flat().map((o)=>({...o, molecularWeight: o.entityMolecularWeight}));
 }

src/RcsbQueries/Yosemite/QueryMultipleEntriesProperties.graphql

@@ -16,6 +16,9 @@ query multiple_entries_properties($entry_ids: [String!]!){
                 }
                 rcsb_id
             }
+            entity_poly {
+                rcsb_prd_id
+            }
         }
         nonpolymer_entities {
             rcsb_id

src/RcsbRequest/RcsbRequestContextManager.ts

@@ -16,7 +16,7 @@ import {
 } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
 import {GroupMemberCollector} from "../RcsbCollectTools/DataCollectors/GroupMemberCollector";
 import {
-    EntryPropertyIntreface,
+    EntryPropertyInterface,
     MultipleEntryPropertyCollector
 } from "../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
 import {Operator} from "../RcsbUtils/Helpers/Operator";
@@ -61,7 +61,7 @@ class RcsbRequestContextManager {
     private readonly searchRequestMap: Map<string,Promise<QueryResult|null>> = new Map<string, Promise<QueryResult|null>>();
     private readonly interfaceToInstanceMap: Map<string,Promise<InterfaceInstanceTranslate>> = new Map<string, Promise<InterfaceInstanceTranslate>>();
     private readonly assemblyInterfacesMap: Map<string,Promise<AssemblyInterfacesTranslate>> = new Map<string, Promise<AssemblyInterfacesTranslate>>();
-    private readonly entryPropertyMap: Map<string,Promise<EntryPropertyIntreface>> = new Map<string, Promise<EntryPropertyIntreface>>();
+    private readonly entryPropertyMap: Map<string,Promise<EntryPropertyInterface>> = new Map<string, Promise<EntryPropertyInterface>>();
     private readonly entityPropertyMap: Map<string,Promise<PolymerEntityInterface>> = new Map<string, Promise<PolymerEntityInterface>>();
     private readonly instanceSequenceMap: Map<string,Promise<InstanceSequenceInterface>> = new Map<string, Promise<InstanceSequenceInterface>>();
 
@@ -87,8 +87,8 @@ class RcsbRequestContextManager {
         )
     }
 
-    public async getEntryProperties(entryIds:string|Array<string>): Promise<Array<EntryPropertyIntreface>> {
-        return RRT.getMultipleObjectProperties<"entry_ids",EntryPropertyIntreface>(
+    public async getEntryProperties(entryIds:string|Array<string>): Promise<Array<EntryPropertyInterface>> {
+        return RRT.getMultipleObjectProperties<"entry_ids",EntryPropertyInterface>(
             entryIds,
             this.entryPropertyMap,
             this.multipleEntryPropertyCollector,
@@ -142,7 +142,7 @@ class RcsbRequestContextManager {
             this.groupPropertyMap,
             async ()=>{
                 const result:Array<PolymerEntityInstanceInterface> = await this.groupMemberCollector.collect(groupQuery);
-                const entriesProperties: Array<EntryPropertyIntreface> = await this.multipleEntryPropertyCollector.collect({entry_ids:Operator.uniqueValues(result.map(r=>r.entryId))})
+                const entriesProperties: Array<EntryPropertyInterface> = await this.multipleEntryPropertyCollector.collect({entry_ids:Operator.uniqueValues(result.map(r=>r.entryId))})
                 return new GroupPropertiesProvider({entryProperties: entriesProperties});
             }
         );

src/RcsbUtils/Groups/GroupPropertiesProvider.ts

@@ -1,7 +1,7 @@
-import {EntryPropertyIntreface} from "../../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
+import {EntryPropertyInterface} from "../../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
 
 export interface GroupPropertiesProviderInterface{
-    entryProperties: Array<EntryPropertyIntreface>;
+    entryProperties: Array<EntryPropertyInterface>;
 }
 
 interface ItemPropertyInterface {
@@ -13,7 +13,7 @@ export type GroupPropertyType = "experimental_method" | "resolution";
 
 export class GroupPropertiesProvider {
 
-    private readonly entryProperties: Array<EntryPropertyIntreface>;
+    private readonly entryProperties: Array<EntryPropertyInterface>;
 
     constructor(properties: GroupPropertiesProviderInterface) {
         this.entryProperties = properties.entryProperties;