@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/RcsbSeacrh/FacetStore/UniprotGroupFacetStore.d.ts

@@ -1,16 +0,0 @@
-import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { FacetMemberInterface } from "./FacetMemberInterface";
-import { FacetStoreInterface } from "./FacetStoreInterface";
-declare class UniprotGroupFacetStore implements FacetStoreInterface {
-    private readonly entryFacet;
-    private readonly instanceFacet;
-    private readonly entityFacet;
-    private readonly uniprotFacet;
-    private readonly nonPolymerFacet;
-    getServices(): (Service.Text | Service.TextChem)[];
-    getFacetService(service: Service | "all"): FacetMemberInterface[];
-    readonly facetLayoutGrid: string[];
-    readonly returnType: ReturnType;
-}
-export declare const uniprotGroupFacetStore: UniprotGroupFacetStore;
-export {};

package/lib/RcsbSeacrh/FacetStore/UniprotGroupFacetStore.js

@@ -1,70 +0,0 @@
-import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { RcsbSearchMetadata } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
-import { CHEM_COMP_FACET, ENTITY_NAME_FACET, EXPERIMENTAL_METHOD_FACET, LIGAND_FACET, ORGANISM_FACET, PFAM_FACET, RELEASE_DATE_FACET, RESOLUTION_FACET, SCOP_FACET, TAXONOMY_FACET, CATH_FACET, ECOD_FACET, ENZYME_CLASS_FACET, GO_FUNCTION_FACET, GO_PROCESS_FACET, GO_COMPONENT_FACET, METHODOLOGY_FACET, TAXONOMY_COUNT_FACET, DISEASE_FACET, INTERPRO_FACET, PHENOTYPE_FACET } from "./SingleFacets";
-import { cloneDeep } from "lodash";
-class UniprotGroupFacetStore {
-    constructor() {
-        this.entryFacet = [
-            cloneDeep(EXPERIMENTAL_METHOD_FACET),
-            cloneDeep(RESOLUTION_FACET),
-            cloneDeep(METHODOLOGY_FACET),
-            cloneDeep(RELEASE_DATE_FACET),
-            cloneDeep(ENZYME_CLASS_FACET)
-        ];
-        this.instanceFacet = [
-            cloneDeep(SCOP_FACET),
-            cloneDeep(CATH_FACET),
-            cloneDeep(ECOD_FACET),
-            cloneDeep(LIGAND_FACET)
-        ];
-        this.entityFacet = [
-            cloneDeep(ORGANISM_FACET),
-            cloneDeep(TAXONOMY_FACET),
-            cloneDeep(PFAM_FACET),
-            cloneDeep(ENTITY_NAME_FACET),
-            cloneDeep(GO_FUNCTION_FACET),
-            cloneDeep(GO_PROCESS_FACET),
-            cloneDeep(GO_COMPONENT_FACET),
-            cloneDeep(TAXONOMY_COUNT_FACET)
-        ];
-        this.uniprotFacet = [
-            cloneDeep(DISEASE_FACET),
-            cloneDeep(PHENOTYPE_FACET),
-            cloneDeep(INTERPRO_FACET)
-        ];
-        this.nonPolymerFacet = [
-            cloneDeep(CHEM_COMP_FACET)
-        ];
-        this.facetLayoutGrid = [
-            RcsbSearchMetadata.RcsbAccessionInfo.DepositDate.path,
-            RcsbSearchMetadata.RcsbEntryInfo.ResolutionCombined.path, RcsbSearchMetadata.Exptl.Method.path, RcsbSearchMetadata.RcsbEntryInfo.StructureDeterminationMethodology.path,
-            RcsbSearchMetadata.ChemComp.Type.path,
-            RcsbSearchMetadata.RcsbEntitySourceOrganism.NcbiScientificName.path, RcsbSearchMetadata.RcsbEntitySourceOrganism.NcbiParentScientificName.path,
-            RcsbSearchMetadata.RcsbPolymerEntityAnnotation.Name.path, RcsbSearchMetadata.RcsbPolymerInstanceAnnotation.AnnotationLineage.Name.path
-        ];
-        this.returnType = ReturnType.PolymerEntity;
-    }
-    getServices() {
-        return [Service.Text];
-    }
-    getFacetService(service) {
-        switch (service) {
-            case Service.Text:
-                return this.entryFacet
-                    .concat(this.instanceFacet)
-                    .concat(this.entityFacet)
-                    .concat(this.uniprotFacet);
-            case Service.TextChem:
-                return this.nonPolymerFacet;
-            case "all":
-                return this.entryFacet
-                    .concat(this.instanceFacet)
-                    .concat(this.entityFacet)
-                    .concat(this.nonPolymerFacet)
-                    .concat(this.uniprotFacet);
-            default:
-                return [];
-        }
-    }
-}
-export const uniprotGroupFacetStore = new UniprotGroupFacetStore();

package/lib/RcsbSeacrh/FacetTools.d.ts

@@ -1,54 +0,0 @@
-import { BucketFacet } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchResultInterface";
-import { FacetMemberInterface } from "./FacetStore/FacetMemberInterface";
-import { AttributeTextQueryParameters } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { ChartDisplayConfigInterface, ChartObjectInterface } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface";
-import { RcsbSearchAttributeType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
-export type SearchFilter = {
-    attribute: RcsbSearchAttributeType;
-    value: AttributeTextQueryParameters['value'];
-    operator: AttributeTextQueryParameters["operator"];
-    service: Service.Text | Service.TextChem;
-};
-export interface RcsbChartInterface<T = any> extends Omit<FacetMemberInterface, "id" | "facet"> {
-    data: ChartObjectInterface<T>[];
-    filters?: SearchFilter[];
-}
-export declare class FacetTools {
-    static getResultDrilldowns(facetMembers: FacetMemberInterface[], searchResultFacets: Array<BucketFacet>): Array<RcsbChartInterface>;
-    static subtractDrilldowns(partial: Array<RcsbChartInterface>, full: Array<RcsbChartInterface>): Array<RcsbChartInterface>;
-    static getFacetFromName(facetMembers: FacetMemberInterface[], name: string): FacetMemberInterface | undefined;
-    static addChartDisplayConfig(chart: RcsbChartInterface, chartDisplayConfig: Partial<ChartDisplayConfigInterface>): {
-        chartConfig: {
-            chartDisplayConfig: Partial<ChartDisplayConfigInterface>;
-            mostPopulatedGroups?: number;
-            domainMinValue?: number;
-            domainMaxValue?: number;
-            domainEmptyBins?: boolean;
-            histogramBinIncrement?: number;
-            tickIncrement?: {
-                origin: number;
-                increment: number;
-            };
-            tickFormat?: {
-                domAxis?: (x: string | number) => string;
-                imgAxis?: (x: string | number) => string;
-            };
-            axisLabel?: string;
-            barClickCallback?: import("@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface").BarClickCallbackType;
-            sort?: (b: import("@rcsb/rcsb-charts/lib/RcsbChartDataProvider/ChartDataProviderInterface").ChartDataColumnInterface, a: import("@rcsb/rcsb-charts/lib/RcsbChartDataProvider/ChartDataProviderInterface").ChartDataColumnInterface) => number;
-            tooltipText?: (a: import("@rcsb/rcsb-charts/lib/RcsbChartDataProvider/ChartDataProviderInterface").ChartDataValueInterface) => string | string[] | undefined;
-        };
-        data: ChartObjectInterface<any>[];
-        filters?: SearchFilter[];
-        title?: string | undefined;
-        attribute: RcsbSearchAttributeType;
-        attributeName: string;
-        chartType: import("@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface").ChartType;
-        facetConfig?: import("./FacetStore/FacetMemberInterface").FacetConfigInterface | undefined;
-        contentType: "date" | "number" | "string";
-    };
-    private static includeMissingFacets;
-    private static getFacetChartTypeFromAttribute;
-    private static getFacetFiltersFromName;
-}

package/lib/RcsbSeacrh/FacetTools.js

@@ -1,97 +0,0 @@
-import { cloneDeep } from "lodash";
-import { getBucketsFromFacets } from "@rcsb/rcsb-search-tools/lib/SearchParseTools/SearchFacetTools";
-export class FacetTools {
-    static getResultDrilldowns(facetMembers, searchResultFacets) {
-        const out = new Array();
-        const bucketList = getBucketsFromFacets(searchResultFacets);
-        bucketList.forEach(bucket => {
-            const facet = FacetTools.getFacetFromName(facetMembers, bucket.name);
-            if (!facet)
-                return;
-            const chart = FacetTools.getFacetChartTypeFromAttribute(facetMembers, bucket.name);
-            out.push(Object.assign(Object.assign({}, chart), { attributeName: bucket.name, attribute: facet.attribute, data: applyChartConfigToData(bucket, facet === null || facet === void 0 ? void 0 : facet.facetConfig), filters: FacetTools.getFacetFiltersFromName(facetMembers, bucket.name), contentType: facet.contentType }));
-        });
-        return out;
-    }
-    static subtractDrilldowns(partial, full) {
-        const diff = cloneDeep(full);
-        const dataMap = new Map();
-        diff.forEach(fullChart => {
-            dataMap.set(fullChart.attributeName, new Map());
-            fullChart.data.forEach(d => {
-                var _a;
-                (_a = dataMap.get(fullChart.attributeName)) === null || _a === void 0 ? void 0 : _a.set(d.label, d);
-            });
-        });
-        partial.forEach(partialChart => {
-            partialChart.data.forEach(d => {
-                var _a;
-                const data = (_a = dataMap.get(partialChart.attributeName)) === null || _a === void 0 ? void 0 : _a.get(d.label);
-                if (data)
-                    data.population -= d.population;
-            });
-        });
-        FacetTools.includeMissingFacets(partial, diff);
-        return diff;
-    }
-    static getFacetFromName(facetMembers, name) {
-        return facetMembers.find((facet) => (facet.attributeName === name));
-    }
-    static addChartDisplayConfig(chart, chartDisplayConfig) {
-        return Object.assign(Object.assign({}, chart), { chartConfig: Object.assign(Object.assign({}, chart.chartConfig), { chartDisplayConfig: chartDisplayConfig }) });
-    }
-    static includeMissingFacets(partial, full) {
-        const partialFacetNameSet = new Set(partial.map(f => f.attributeName));
-        const fullFacetNameSet = new Map(full.map(f => [f.attributeName, f]));
-        fullFacetNameSet.forEach((v, k) => {
-            if (!partialFacetNameSet.has(k)) {
-                partial.push(Object.assign(Object.assign({}, cloneDeep(v)), { data: [] }));
-            }
-        });
-    }
-    static getFacetChartTypeFromAttribute(facetMembers, attribute) {
-        const facet = facetMembers.find((facet) => (facet.attributeName === attribute));
-        if (!facet)
-            throw `Unknown facet attribute ${attribute}`;
-        return facet;
-    }
-    static getFacetFiltersFromName(facetMembers, attribute) {
-        const facet = facetMembers.find((facet) => (facet.attributeName === attribute));
-        if (!facet)
-            throw `Unknown facet attribute ${attribute}`;
-        const filters = new Array();
-        if (facet.facet.filter) {
-            filters.push(facet.facet.filter);
-        }
-        //TODO second level filters should be considered. However, when included, in some cases e.g. SCOP, the search service returns empty results
-        /*const facets = (facet.facet as TermsFacet | HistogramFacet | DateHistogramFacet | RangeFacet | DateRangeFacet | FilterFacet).facets;
-        if( facets ){
-           facets.forEach(facet=>{
-                if((facet as FilterFacet).filter ){
-                    filters.push((facet as FilterFacet).filter as FilterQueryTerminalNode);
-                }
-            })
-        }*/
-        return filters.map((f) => ({
-            operator: f.parameters.operator,
-            value: f.parameters.value,
-            attribute: f.parameters.attribute,
-            service: f.service
-        }));
-    }
-}
-function applyChartConfigToData(bucket, facetConfig) {
-    if (facetConfig === null || facetConfig === void 0 ? void 0 : facetConfig.mergeDomainMaxValue)
-        return mergeDomainMaxValue(bucket.data, facetConfig.mergeDomainMaxValue);
-    if (facetConfig === null || facetConfig === void 0 ? void 0 : facetConfig.facetTransform)
-        return facetConfig.facetTransform(bucket.data);
-    return bucket.data;
-}
-function mergeDomainMaxValue(data, domMaxValue) {
-    const n = data.filter(d => parseFloat(d.label.toString()) >= domMaxValue).reduce((prev, curr) => prev + curr.population, 0);
-    return n > 0 ? data.filter(d => parseFloat(d.label.toString()) < domMaxValue).concat({
-        population: n,
-        label: domMaxValue,
-        labelPath: [domMaxValue.toString()]
-    }) : data;
-}

package/lib/RcsbSeacrh/SearchQueryTools.d.ts

@@ -1,17 +0,0 @@
-import { LogicalOperator, ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { RcsbSearchAttributeType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
-import { AttributeTextQueryParameters, ResultsContentType, SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { FacetStoreInterface } from "./FacetStore/FacetStoreInterface";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { SearchQueryType } from "@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryInterfaces";
-export declare namespace SearchQueryTools {
-    function searchGroupQuery(groupProvenance: GroupProvenanceId, groupId: string, service?: Service.Text | Service.TextChem): SearchQueryType;
-    function addGroupNodeToSearchQuery(groupProvenanceId: GroupProvenanceId, groupId: string, searchQuery: SearchQueryType, service?: Service.Text | Service.TextChem): SearchQueryType;
-    function buildNodeSearchQuery(node: SearchQueryType, searchQuery: SearchQueryType, returnType: ReturnType, resultsContentType: ResultsContentType, logicalOperator?: LogicalOperator): SearchQuery;
-    function buildSearchQuery(searchQuery: SearchQueryType, returnType: ReturnType): SearchQuery;
-    function addNewNodeToAttributeSearchQuery(attribute: RcsbSearchAttributeType, value: AttributeTextQueryParameters['value'], operator: AttributeTextQueryParameters["operator"], searchQuery: SearchQueryType, service: Service.Text | Service.TextChem, negation?: boolean): SearchQueryType;
-    function searchAttributeQuery(attribute: RcsbSearchAttributeType, value: AttributeTextQueryParameters['value'], operator: AttributeTextQueryParameters["operator"], service: Service.Text | Service.TextChem, negation?: boolean): SearchQueryType;
-    function addNodeToSearchQuery(node: SearchQueryType, searchQuery: SearchQueryType, logicalOperator?: LogicalOperator): SearchQueryType;
-    function getFacetStoreFromGroupProvenance(groupProvenanceId: GroupProvenanceId): FacetStoreInterface;
-    function searchContentType(searchQuery?: SearchQuery): ResultsContentType;
-}

package/lib/RcsbSeacrh/SearchQueryTools.js

@@ -1,114 +0,0 @@
-import { LogicalOperator, RelevanceScoreRankingOption, ScoringStrategy, Service, SortDirection, Type } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { RcsbSearchMetadata } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
-import { cloneDeep } from 'lodash';
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { buildAttributeQuery, buildRequestFromCombinedSearchQuery, buildRequestFromSearchQuery } from "@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryTools";
-import { depositionGroupFacetStore } from "./FacetStore/DepositionGroupFacetStore";
-import { sequenceGroupFacetStore } from "./FacetStore/SequenceGroupFacetStore";
-import { uniprotGroupFacetStore } from "./FacetStore/UniprotGroupFacetStore";
-export var SearchQueryTools;
-(function (SearchQueryTools) {
-    function searchGroupQuery(groupProvenance, groupId, service) {
-        const groupSearchAttr = getSearchAttribute(groupProvenance);
-        return buildAttributeQuery({
-            attribute: groupSearchAttr.path,
-            value: groupId,
-            operator: groupSearchAttr.operator.ExactMatch,
-            service: service !== null && service !== void 0 ? service : Service.Text
-        });
-    }
-    SearchQueryTools.searchGroupQuery = searchGroupQuery;
-    function addGroupNodeToSearchQuery(groupProvenanceId, groupId, searchQuery, service) {
-        return addNodeToSearchQuery(searchGroupQuery(groupProvenanceId, groupId, service), searchQuery);
-    }
-    SearchQueryTools.addGroupNodeToSearchQuery = addGroupNodeToSearchQuery;
-    function buildNodeSearchQuery(node, searchQuery, returnType, resultsContentType, logicalOperator = LogicalOperator.And) {
-        return buildRequestFromCombinedSearchQuery(searchQuery, node, returnType, logicalOperator, {
-            paginate: {
-                start: 0,
-                rows: 25
-            },
-            scoring_strategy: ScoringStrategy.Combined,
-            sort: [
-                {
-                    sort_by: RelevanceScoreRankingOption.Score,
-                    direction: SortDirection.Desc
-                }
-            ],
-            results_content_type: resultsContentType
-        });
-    }
-    SearchQueryTools.buildNodeSearchQuery = buildNodeSearchQuery;
-    function buildSearchQuery(searchQuery, returnType) {
-        return buildRequestFromSearchQuery(searchQuery, returnType, {
-            paginate: {
-                start: 0,
-                rows: 25
-            },
-            scoring_strategy: ScoringStrategy.Combined,
-            sort: [
-                {
-                    sort_by: RelevanceScoreRankingOption.Score,
-                    direction: SortDirection.Desc
-                }
-            ]
-        });
-    }
-    SearchQueryTools.buildSearchQuery = buildSearchQuery;
-    function addNewNodeToAttributeSearchQuery(attribute, value, operator, searchQuery, service, negation = false) {
-        return addNodeToSearchQuery(searchAttributeQuery(attribute, value, operator, service, negation), searchQuery);
-    }
-    SearchQueryTools.addNewNodeToAttributeSearchQuery = addNewNodeToAttributeSearchQuery;
-    function searchAttributeQuery(attribute, value, operator, service, negation = false) {
-        return buildAttributeQuery({
-            attribute,
-            value,
-            operator,
-            service,
-            negation
-        });
-    }
-    SearchQueryTools.searchAttributeQuery = searchAttributeQuery;
-    function addNodeToSearchQuery(node, searchQuery, logicalOperator = LogicalOperator.And) {
-        if (searchQuery.type === Type.Group && searchQuery.logical_operator === logicalOperator) {
-            const query = cloneDeep(searchQuery);
-            query.nodes.push(node);
-            return query;
-        }
-        return {
-            type: Type.Group,
-            logical_operator: logicalOperator,
-            nodes: [
-                searchQuery,
-                node
-            ]
-        };
-    }
-    SearchQueryTools.addNodeToSearchQuery = addNodeToSearchQuery;
-    function getFacetStoreFromGroupProvenance(groupProvenanceId) {
-        switch (groupProvenanceId) {
-            case GroupProvenanceId.ProvenanceMatchingDepositGroupId:
-                return depositionGroupFacetStore;
-            case GroupProvenanceId.ProvenanceSequenceIdentity:
-                return sequenceGroupFacetStore;
-            case GroupProvenanceId.ProvenanceMatchingUniprotAccession:
-                return uniprotGroupFacetStore;
-        }
-    }
-    SearchQueryTools.getFacetStoreFromGroupProvenance = getFacetStoreFromGroupProvenance;
-    function searchContentType(searchQuery) {
-        var _a, _b;
-        return (_b = (_a = searchQuery === null || searchQuery === void 0 ? void 0 : searchQuery.request_options) === null || _a === void 0 ? void 0 : _a.results_content_type) !== null && _b !== void 0 ? _b : ["computational", "experimental"];
-    }
-    SearchQueryTools.searchContentType = searchContentType;
-    function getSearchAttribute(groupProvenanceId) {
-        switch (groupProvenanceId) {
-            case GroupProvenanceId.ProvenanceMatchingDepositGroupId:
-                return RcsbSearchMetadata.RcsbEntryGroupMembership.GroupId;
-            case GroupProvenanceId.ProvenanceSequenceIdentity:
-                return RcsbSearchMetadata.RcsbPolymerEntityGroupMembership.GroupId;
-            case GroupProvenanceId.ProvenanceMatchingUniprotAccession:
-                return RcsbSearchMetadata.RcsbPolymerEntityGroupMembership.GroupId;
-        }
-    }
-})(SearchQueryTools || (SearchQueryTools = {}));

package/lib/RcsbSeacrh/SearchRequestProperty.d.ts

@@ -1,17 +0,0 @@
-import { SearchRequest } from "@rcsb/rcsb-api-tools/build/RcsbSearch/SearchRequest";
-import { QueryResult } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchResultInterface";
-import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { ResultsContentType, SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { FacetType } from "./FacetStore/FacetMemberInterface";
-import { SearchQueryType } from "@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryInterfaces";
-declare class SearchRequestProperty {
-    private readonly getClient;
-    constructor(getClient: () => SearchRequest);
-    private _requestFacets;
-    requestFacets(query: SearchQueryType, facets: FacetType[], returnType: ReturnType, resultsContentType: ResultsContentType): Promise<QueryResult | null>;
-    requestMembers(query: SearchQuery): Promise<string[]>;
-    requestCount(query: SearchQuery): Promise<number>;
-    request(query: SearchQuery): Promise<QueryResult | null>;
-}
-export declare const searchRequestProperty: SearchRequestProperty;
-export {};

package/lib/RcsbSeacrh/SearchRequestProperty.js

@@ -1,70 +0,0 @@
-import { __awaiter } from "tslib";
-import { rcsbRequestClient } from "../RcsbRequest/RcsbRequestClient";
-import { SearchQueryTools as SQT } from "./SearchQueryTools";
-class SearchRequestProperty {
-    constructor(getClient) {
-        this.getClient = getClient;
-    }
-    _requestFacets(config) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const facet = config.facets.shift();
-            return yield this.getClient().request({
-                query: config.query,
-                request_options: facet ? {
-                    paginate: {
-                        start: 0,
-                        rows: 0
-                    },
-                    facets: [facet, ...config.facets],
-                    results_content_type: config.resultsContentType
-                } : {
-                    paginate: {
-                        start: 0,
-                        rows: 0
-                    },
-                    results_content_type: config.resultsContentType
-                },
-                return_type: config.returnType
-            });
-        });
-    }
-    requestFacets(query, facets, returnType, resultsContentType) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return this._requestFacets({ query: query, facets: facets, returnType: returnType, resultsContentType: resultsContentType });
-        });
-    }
-    //TODO this should be part of `SearchQueryTools`
-    requestMembers(query) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
-            return (_c = (_b = (_a = (yield this.getClient().request({
-                query: query.query,
-                request_options: {
-                    return_all_hits: true,
-                    results_content_type: SQT.searchContentType(query)
-                },
-                return_type: query.return_type
-            }))) === null || _a === void 0 ? void 0 : _a.result_set) === null || _b === void 0 ? void 0 : _b.map(item => typeof item === "string" ? item : item.identifier)) !== null && _c !== void 0 ? _c : [];
-        });
-    }
-    //TODO this should be part of `SearchQueryTools`
-    requestCount(query) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
-            return (_b = (_a = (yield this.getClient().request({
-                query: query.query,
-                request_options: {
-                    return_counts: true,
-                    results_content_type: SQT.searchContentType(query)
-                },
-                return_type: query.return_type
-            }))) === null || _a === void 0 ? void 0 : _a.total_count) !== null && _b !== void 0 ? _b : -1;
-        });
-    }
-    request(query) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return yield this.getClient().request(query);
-        });
-    }
-}
-export const searchRequestProperty = new SearchRequestProperty(() => rcsbRequestClient.arches);

package/lib/RcsbServerConfig/ServerConfig.d.ts

@@ -1 +0,0 @@
-export declare const rcsbFvWebAppPath: string;

package/lib/RcsbServerConfig/ServerConfig.js

@@ -1,2 +0,0 @@
-import * as path from "path";
-export const rcsbFvWebAppPath = path.resolve(__dirname);

package/lib/RcsbServerConfig/codegen.borrego.json

@@ -1,4 +0,0 @@
-{
-    "schema": "https://1d-coordinates.rcsb.org/graphql",
-    "documents": "src/RcsbQueries/Borrego/Query*.graphql"
-}

package/lib/RcsbServerConfig/codegen.yosemite.json

@@ -1,4 +0,0 @@
-{
-    "schema": "https://data.rcsb.org/graphql",
-    "documents": "src/RcsbQueries/Yosemite/Query*.graphql"
-}

package/lib/RcsbServerConfig/web.resources.json

@@ -1,43 +0,0 @@
-{
-    "swiss_model": {
-        "url": "https://swissmodel.expasy.org/repository/uniprot/",
-        "url_suffix": ".json?provider=swissmodel"
-    },
-    "rcsb_entry": {
-        "url": "/structure/"
-    },
-    "rcsb_3d_view": {
-        "url": "/3d-view/"
-    },
-    "rcsb_ligand": {
-        "url": "/ligand/"
-    },
-    "rcsb_uniprot": {
-        "url": "/groups/sequence/polymer_entity/"
-    },
-    "rcsb_search": {
-        "url": "/search?request="
-    },
-    "uniprot": {
-        "url": "https://www.uniprot.org/uniprot/"
-    },
-    "ncbi_summary_nuccore": {
-        "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nuccore&id=",
-        "url_suffix": "&retmode=json"
-    },
-    "ncbi_summary_taxonomy": {
-        "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy&id=",
-        "url_suffix": "&retmode=json"
-    },
-    "ncbi_genome_sequence": {
-        "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&",
-        "url_suffix": "&rettype=fasta&retmode=text"
-    },
-    "rcsb_cdn": {
-        "url": "https://cdn.rcsb.org/images/structures/"
-    },
-    "1d3d-alignment": {
-        "url": "/groups/3d-sequence/polymer_entity/",
-        "url_suffix": "?request="
-    }
-}

package/lib/RcsbUtils/Groups/GroupGapLessTransformer.d.ts

@@ -1,8 +0,0 @@
-import { AlignmentResponse, AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare class GroupGapLessTransformer {
-    private readonly gapLessReference;
-    private refLength;
-    private processAlignments;
-    gapLessAlignments(alignments: AlignmentResponse): void;
-    gapLessFeatures(annotations: Array<AnnotationFeatures>): void;
-}

package/lib/RcsbUtils/Groups/GroupGapLessTransformer.js

@@ -1,76 +0,0 @@
-import { Logo } from "../TrackGenerators/Logo";
-import { Assertions } from "../Helpers/Assertions";
-var assertElementListDefined = Assertions.assertElementListDefined;
-export class GroupGapLessTransformer {
-    constructor() {
-        this.gapLessReference = [];
-    }
-    processAlignments(alignment) {
-        var _a, _b;
-        if (this.gapLessReference.length > 0 || !alignment.alignment_logo)
-            return;
-        const querySequenceLogo = new Array();
-        if (alignment.alignment_length && alignment.alignment_length != ((_a = alignment.alignment_logo) === null || _a === void 0 ? void 0 : _a.length))
-            throw new Error("ERROR Alignment length and logo should match");
-        (_b = alignment.alignment_logo) === null || _b === void 0 ? void 0 : _b.forEach(al => {
-            assertElementListDefined(al);
-            querySequenceLogo.push(new Logo(al));
-        });
-        let newIndex = 1;
-        this.gapLessReference[0] = -1;
-        querySequenceLogo.forEach((sl, n) => {
-            if ((sl.get("-") / sl.total()) == 1) {
-                this.gapLessReference[n + 1] = -1;
-            }
-            else {
-                this.gapLessReference[n + 1] = newIndex++;
-            }
-        });
-        this.refLength = newIndex - 1;
-    }
-    gapLessAlignments(alignments) {
-        var _a, _b, _c, _d;
-        this.processAlignments(alignments);
-        if (this.gapLessReference.length == 0)
-            return;
-        if (alignments.target_alignment)
-            (_a = alignments.target_alignment) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
-                var _a;
-                (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.forEach(region => {
-                    if (region === null || region === void 0 ? void 0 : region.query_begin)
-                        region.query_begin = this.gapLessReference[region.query_begin];
-                    if (region === null || region === void 0 ? void 0 : region.query_end)
-                        region.query_end = this.gapLessReference[region.query_end];
-                });
-            });
-        else
-            (_c = (_b = alignments.target_alignment_subset) === null || _b === void 0 ? void 0 : _b.edges) === null || _c === void 0 ? void 0 : _c.forEach(edge => {
-                var _a, _b;
-                (_b = (_a = edge === null || edge === void 0 ? void 0 : edge.node) === null || _a === void 0 ? void 0 : _a.aligned_regions) === null || _b === void 0 ? void 0 : _b.forEach(region => {
-                    if (region === null || region === void 0 ? void 0 : region.query_begin)
-                        region.query_begin = this.gapLessReference[region.query_begin];
-                    if (region === null || region === void 0 ? void 0 : region.query_end)
-                        region.query_end = this.gapLessReference[region.query_end];
-                });
-            });
-        alignments.alignment_logo = (_d = alignments.alignment_logo) === null || _d === void 0 ? void 0 : _d.filter((al, n) => this.gapLessReference[n + 1] != -1);
-        if (alignments.alignment_length)
-            alignments.alignment_length = this.refLength;
-    }
-    gapLessFeatures(annotations) {
-        if (this.gapLessReference.length == 0)
-            return;
-        annotations.forEach(ann => {
-            var _a;
-            (_a = ann.features) === null || _a === void 0 ? void 0 : _a.forEach(feature => {
-                var _a;
-                (_a = feature === null || feature === void 0 ? void 0 : feature.feature_positions) === null || _a === void 0 ? void 0 : _a.forEach(position => {
-                    if (position === null || position === void 0 ? void 0 : position.beg_seq_id)
-                        position.beg_seq_id = this.gapLessReference[position.beg_seq_id];
-                    if (position === null || position === void 0 ? void 0 : position.end_seq_id)
-                        position.end_seq_id = this.gapLessReference[position.end_seq_id];
-                });
-            });
-        });
-    }
-}

package/lib/RcsbUtils/Groups/GroupPropertiesProvider.d.ts

@@ -1,16 +0,0 @@
-import { EntryPropertyInterface } from "../../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
-export interface GroupPropertiesProviderInterface {
-    entryProperties: Array<EntryPropertyInterface>;
-}
-interface ItemPropertyInterface {
-    objectId: string;
-    value: number | string;
-}
-export type GroupPropertyType = "experimental_method" | "resolution";
-export declare class GroupPropertiesProvider {
-    private readonly entryProperties;
-    constructor(properties: GroupPropertiesProviderInterface);
-    get(key: GroupPropertyType): ItemPropertyInterface[] | undefined;
-    private getEntryProperties;
-}
-export {};

package/lib/RcsbUtils/Groups/GroupPropertiesProvider.js

@@ -1,27 +0,0 @@
-export class GroupPropertiesProvider {
-    constructor(properties) {
-        this.entryProperties = properties.entryProperties;
-    }
-    get(key) {
-        if (key === "experimental_method" || key === "resolution") {
-            return this.getEntryProperties(key);
-        }
-    }
-    getEntryProperties(key) {
-        if (key === "experimental_method") {
-            return this.entryProperties.map(p => ({
-                objectId: p.rcsbId,
-                value: p.experimentalMethod
-            }));
-        }
-        else if (key === "resolution") {
-            return this.entryProperties.map(p => {
-                var _a;
-                return ({
-                    objectId: p.rcsbId,
-                    value: (_a = p.resolution) !== null && _a !== void 0 ? _a : "NA"
-                });
-            });
-        }
-    }
-}