@rcsb/rcsb-saguaro-app 6.3.7-dev-js-seqcoord.14 → 6.3.7-react-downgrade.0

package/lib/commonjs/RcsbGraphQL/RcsbQueryAnnotations.js

@@ -1,9 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbQueryGroupAnnotations = exports.RcsbQueryGroupAnnotationsSumary = exports.RcsbQueryAnnotations = void 0;
+exports.RcsbQueryGroupAnnotations = exports.RcsbQueryAnnotations = void 0;
 const tslib_1 = require("tslib");
 const QueryAnnotations_graphql_1 = tslib_1.__importDefault(require("../RcsbQueries/Borrego/QueryAnnotations.graphql"));
-const QueryGroupAnnotationsSummary_graphql_1 = tslib_1.__importDefault(require("../RcsbQueries/Borrego/QueryGroupAnnotationsSummary.graphql"));
 const QueryGroupAnnotations_graphql_1 = tslib_1.__importDefault(require("../RcsbQueries/Borrego/QueryGroupAnnotations.graphql"));
 class RcsbQueryAnnotations {
     constructor(getClient) {
@@ -12,7 +11,13 @@ class RcsbQueryAnnotations {
     request(requestConfig) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             try {
-                const annotationsResponse = yield this.getClient().request(requestConfig, QueryAnnotations_graphql_1.default);
+                const annotationsResponse = yield this.getClient().request({
+                    queryId: requestConfig.queryId,
+                    reference: requestConfig.reference,
+                    sources: requestConfig.sources,
+                    filters: requestConfig.filters,
+                    range: requestConfig.range
+                }, QueryAnnotations_graphql_1.default);
                 return annotationsResponse.annotations;
             }
             catch (error) {
@@ -23,24 +28,6 @@ class RcsbQueryAnnotations {
     }
 }
 exports.RcsbQueryAnnotations = RcsbQueryAnnotations;
-class RcsbQueryGroupAnnotationsSumary {
-    constructor(getClient) {
-        this.getClient = getClient;
-    }
-    request(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            try {
-                const annotationsResponse = yield this.getClient().request(requestConfig, QueryGroupAnnotationsSummary_graphql_1.default);
-                return annotationsResponse.group_annotations_summary;
-            }
-            catch (error) {
-                console.error(error);
-                throw error;
-            }
-        });
-    }
-}
-exports.RcsbQueryGroupAnnotationsSumary = RcsbQueryGroupAnnotationsSumary;
 class RcsbQueryGroupAnnotations {
     constructor(getClient) {
         this.getClient = getClient;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartLayout.d.ts

@@ -1,4 +1,4 @@
-import React, { ReactNode } from "react";
+import React from "react";
 import { RcsbChartInterface } from "../../../RcsbSeacrh/FacetTools";
 export type ChartMapType = Map<string, RcsbChartInterface[]>;
 export interface RcsbChartLayoutInterface {
@@ -6,6 +6,6 @@ export interface RcsbChartLayoutInterface {
     chartMap: ChartMapType;
 }
 export declare class GroupChartLayout extends React.Component<RcsbChartLayoutInterface, {}> {
-    render(): ReactNode;
+    render(): JSX.Element;
     private renderCell;
 }

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbGroupChartComponent.d.ts

@@ -1,4 +1,4 @@
-import React, { ReactNode } from "react";
+import React from "react";
 import { ChartMapType } from "./GroupChartLayout";
 import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
 import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
@@ -16,7 +16,7 @@ interface RcsbGroupChartState {
 }
 export declare class RcsbGroupChartComponent extends React.Component<RcsbGroupChartInterface, RcsbGroupChartState> {
     componentDidMount(): Promise<void>;
-    render(): ReactNode;
+    render(): JSX.Element;
     private updateState;
 }
 export {};

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbStatsChartComponent.d.ts

@@ -1,4 +1,4 @@
-import React, { ReactNode } from "react";
+import React from "react";
 import { FacetStoreInterface } from "../../../RcsbSeacrh/FacetStore/FacetStoreInterface";
 import { BucketFacet } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchResultInterface";
 import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
@@ -13,7 +13,7 @@ interface RcsbStatsChartState {
 }
 export declare class RcsbStatsChartComponent extends React.Component<RcsbStatsChartInterface, RcsbStatsChartState> {
     componentDidMount(): Promise<void>;
-    render(): ReactNode;
+    render(): JSX.Element;
     private updateState;
 }
 export {};

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/Components/Slider.d.ts

@@ -9,8 +9,8 @@ export interface SliderInterface {
     displayNumber?(x: number): string;
 }
 export declare class Slider extends React.Component<SliderInterface> {
-    render(): ReactNode;
+    render(): JSX.Element;
     private slide;
     private displayNumber;
 }
-export declare function actionIcon(action: SlideAction): ReactNode;
+export declare function actionIcon(action: SlideAction): JSX.Element;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMemberItem.js

@@ -7,7 +7,7 @@ const react_1 = tslib_1.__importDefault(require("react"));
 const web_resources_json_1 = tslib_1.__importDefault(require("../../../RcsbServerConfig/web.resources.json"));
 const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
 const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
-const bxs_cube_svg_1 = tslib_1.__importDefault(require("./icons/bxs-cube.svg"));
+const bxs_cube_svg_1 = tslib_1.__importDefault(require("boxicons/svg/solid/bxs-cube.svg"));
 const NA = "N/A";
 class GroupMemberItem extends react_1.default.Component {
     render() {

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMembersGrid.d.ts

@@ -1,4 +1,4 @@
-import React, { ReactNode } from "react";
+import React from "react";
 import { ItemFeaturesInterface } from "./GroupMemberItem";
 import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
 import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
@@ -15,7 +15,7 @@ interface GroupMembersGridState {
 }
 export declare class GroupMembersGrid extends React.Component<GroupMembersGridInterface, GroupMembersGridState> {
     readonly state: GroupMembersGridState;
-    render(): ReactNode;
+    render(): JSX.Element;
     componentDidMount(): Promise<void>;
     componentDidUpdate(prevProps: GroupMembersGridInterface, prevState: GroupMembersGridState, snapshot?: any): Promise<void>;
     private getMembersData;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/RcsbGroupMembersComponent.d.ts

@@ -1,4 +1,4 @@
-import React, { ReactNode } from "react";
+import React from "react";
 import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
 import { QueryResult } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchResultInterface";
 import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
@@ -18,7 +18,7 @@ export declare class RcsbGroupMembersComponent extends React.Component<RcsbGroup
     readonly state: RcsbGroupMembersState;
     readonly groupMembersDiv: string;
     constructor(props: RcsbGroupMembersInterface);
-    render(): ReactNode;
+    render(): JSX.Element;
     componentDidMount(): Promise<void>;
     componentDidUpdate(prevProps: Readonly<RcsbGroupMembersInterface>, prevState: Readonly<RcsbGroupMembersState>, snapshot?: any): Promise<void>;
     private subscribe;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/RcsbGroupSeacrhQueryComponent.d.ts

@@ -1,7 +1,6 @@
 import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
 import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { ReactNode } from "react";
 export declare class SearchQueryComponentFactory {
     private static unique;
-    static getGroupSearchComponent(groupProvenanceId: GroupProvenanceId, groupId: string, searchQuery?: SearchQuery): ReactNode;
+    static getGroupSearchComponent(groupProvenanceId: GroupProvenanceId, groupId: string, searchQuery?: SearchQuery): JSX.Element;
 }

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/RcsbResidueChartComponent.d.ts

@@ -1,4 +1,4 @@
-import React, { ReactNode } from "react";
+import React from "react";
 import { ChartMapType } from "../RcsbGroupChart/GroupChartLayout";
 import { ResidueChartInterface } from "./ResidueChartTools/ResidueChartTools";
 import { ChartDisplayConfigInterface } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface";
@@ -10,7 +10,7 @@ export declare class RcsbResidueChartComponent extends React.Component<ResidueCh
     facetLayoutGrid?: string[];
     chartDisplayConfig?: Partial<ChartDisplayConfigInterface>;
 }, RcsbResidueChartState> {
-    render(): ReactNode;
+    render(): JSX.Element;
     componentDidMount(): Promise<void>;
     private updateState;
 }

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/ResidueChartTools.js

@@ -56,7 +56,7 @@ var ResidueChartTools;
             const annotationsRequestContext = {
                 queryId: instanceId,
                 reference: GqlTypes_1.SequenceReference.PdbInstance,
-                sources: [GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.PdbInstance, GqlTypes_1.AnnotationReference.Uniprot, GqlTypes_1.AnnotationReference.PdbInterface],
+                sources: [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance, GqlTypes_1.Source.Uniprot, GqlTypes_1.Source.PdbInterface],
                 annotationGenerator: RcsbFvInterface_1.interfaceAnnotations,
                 annotationFilter: RcsbFvInterface_1.filter
             };

package/lib/commonjs/RcsbQueries/Borrego/.graphqlconfig

@@ -0,0 +1,15 @@
+{
+  "name": "Untitled GraphQL Schema",
+  "schemaPath": "schema.graphql",
+  "extensions": {
+    "endpoints": {
+      "Default GraphQL Endpoint": {
+        "url": "https://1d-coordinates.rcsb.org/graphql",
+        "headers": {
+          "user-agent": "JS GraphQL"
+        },
+        "introspect": false
+      }
+    }
+  }
+}

package/lib/commonjs/RcsbQueries/Borrego/QueryAlignments.graphql

@@ -1,12 +1,12 @@
-query QueryAlignment($queryId: String!, $from: SequenceReference!, $to:SequenceReference!, $range:[Int!]){
-    alignments(
+query QueryAlignment($queryId: String!, $from: SequenceReference, $to:SequenceReference, $range:[Int]){
+    alignment(
         queryId:$queryId
         from:$from
         to:$to
         range:$range
     ){
         query_sequence
-        target_alignments {
+        target_alignment {
             target_id
             orientation
             target_sequence

package/lib/commonjs/RcsbQueries/Borrego/QueryAnnotations.graphql

@@ -1,10 +1,4 @@
-query QueryAnnotations(
-    $queryId: String!,
-    $reference: SequenceReference!,
-    $sources:[AnnotationReference!]!,
-    $range:[Int!],
-    $filters: [AnnotationFilterInput!]
-){
+query QueryAnnotations($queryId: String!, $reference: SequenceReference, $sources:[Source], $range:[Int], $filters: [FilterInput]){
     annotations(
         queryId:$queryId
         reference:$reference

package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAlignments.graphql

@@ -1,37 +1,42 @@
-query QueryGroupAlignment(
-    $group: GroupReference!,
-    $groupId: String!,
-    $filter: [String!],
-    $first: Int,
-    $after: Int
-){
-    group_alignments(
+query QueryGroupAlignment($group: GroupReference!, $groupId: String!, $filter: [String], $first: Int!, $after: String){
+    group_alignment(
         group: $group
         groupId: $groupId
         filter: $filter
     ){
         alignment_length
-        alignment_logo {
+        alignment_logo{
             symbol
             value
         }
         query_sequence
-        target_alignments(first: $first, offset: $after) {
-            target_id
-            orientation
-            target_sequence
-            coverage {
-                query_coverage
-                query_length
-                target_coverage
-                target_length
+        target_alignment_subset(first: $first, after: $after) {
+            pageInfo{
+                startCursor
+                endCursor
+                hasNextPage
+                hasPreviousPage
             }
-            aligned_regions {
-                query_begin
-                query_end
-                target_begin
-                target_end
-                exon_shift
+            edges{
+                node{
+                    target_id
+                    orientation
+                    target_sequence
+                    coverage {
+                        query_coverage
+                        query_length
+                        target_coverage
+                        target_length
+                    }
+                    aligned_regions {
+                        query_begin
+                        query_end
+                        target_begin
+                        target_end
+                        exon_shift
+                    }
+                }
+                cursor
             }
         }
     }

package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAlignmentsNoLogo.graphql

@@ -1,32 +1,38 @@
-query QueryGroupAlignmentNoLogo(
-    $group: GroupReference!,
-    $groupId: String!,
-    $filter: [String!],
-    $first: Int!,
-    $after: Int!){
-    group_alignments(
+query QueryGroupAlignmentNoLogo($group: GroupReference!, $groupId: String!, $filter: [String], $first: Int!, $after: String){
+    group_alignment(
         group: $group
         groupId: $groupId
         filter: $filter
     ){
         alignment_length
         query_sequence
-        target_alignments(first: $first, offset: $after) {
-            target_id
-            orientation
-            target_sequence
-            coverage {
-                query_coverage
-                query_length
-                target_coverage
-                target_length
+        target_alignment_subset(first: $first, after: $after) {
+            pageInfo{
+                startCursor
+                endCursor
+                hasNextPage
+                hasPreviousPage
             }
-            aligned_regions {
-                query_begin
-                query_end
-                target_begin
-                target_end
-                exon_shift
+            edges{
+                node{
+                    target_id
+                    orientation
+                    target_sequence
+                    coverage {
+                        query_coverage
+                        query_length
+                        target_coverage
+                        target_length
+                    }
+                    aligned_regions {
+                        query_begin
+                        query_end
+                        target_begin
+                        target_end
+                        exon_shift
+                    }
+                }
+                cursor
             }
         }
     }

package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAnnotations.graphql

@@ -1,14 +1,10 @@
-query QueryGroupAnnotations(
-    $group: GroupReference!,
-    $groupId: String!,
-    $sources: [AnnotationReference!]!,
-    $filters: [AnnotationFilterInput!]
-){
+query QueryGroupAnnotations($group: GroupReference!, $groupId: String!, $sources:[Source], $filters: [FilterInput], $histogram:Boolean){
     group_annotations(
         group:$group
         groupId:$groupId
         sources:$sources
         filters:$filters
+        histogram:$histogram
     ){
         source
         target_id