@rcsb/rcsb-saguaro-app 6.0.0-development.1 → 6.0.0-development.2

package/lib/RcsbChartWeb/AbsractChartComponent.d.ts

@@ -0,0 +1,21 @@
+import { ChartObjectInterface } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface";
+import React from "react";
+import { ChartInterface, ChartState } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartComponent";
+interface AbstractChartInterface extends Omit<ChartInterface, "chartComponentImplementation" | "dataProvider"> {
+    attributeName: string;
+}
+interface AbstractChartState extends Partial<ChartState> {
+    data: ChartObjectInterface[][];
+}
+export declare abstract class AbstractChartComponent extends React.Component<AbstractChartInterface, AbstractChartState> {
+    private asyncSubscription;
+    private subscription;
+    readonly state: AbstractChartState;
+    componentDidMount(): void;
+    componentWillUnmount(): void;
+    private unsubscribe;
+    private subscribe;
+    private updateChartMap;
+    private asyncUpdate;
+}
+export {};

package/lib/RcsbChartWeb/AbsractChartComponent.js

@@ -0,0 +1,48 @@
+import { asyncScheduler } from "rxjs";
+import React from "react";
+import { SearchQueryContextManager } from "../RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/SearchQueryContextManager";
+export class AbstractChartComponent extends React.Component {
+    constructor() {
+        super(...arguments);
+        this.state = {
+            data: this.props.data,
+            chartConfig: this.props.chartConfig
+        };
+    }
+    componentDidMount() {
+        this.subscribe();
+    }
+    componentWillUnmount() {
+        this.unsubscribe();
+    }
+    unsubscribe() {
+        var _a, _b;
+        (_b = (_a = this.subscription) === null || _a === void 0 ? void 0 : _a.unsubscribe) === null || _b === void 0 ? void 0 : _b.call(_a);
+    }
+    subscribe() {
+        this.subscription = SearchQueryContextManager.dataSubscription((o) => {
+            this.updateChartMap(o);
+        });
+    }
+    updateChartMap(sqData) {
+        if (!sqData.chartMap)
+            return;
+        if (this.props.attributeName === sqData.attributeName) {
+            this.asyncUpdate(sqData);
+        }
+        else {
+            this.asyncUpdate(sqData, 10);
+        }
+    }
+    asyncUpdate(sqData, x) {
+        var _a;
+        (_a = this.asyncSubscription) === null || _a === void 0 ? void 0 : _a.unsubscribe();
+        this.asyncSubscription = asyncScheduler.schedule(() => {
+            const data = sqData.chartMap.get(this.props.attributeName);
+            if (data)
+                this.setState({
+                    data
+                });
+        }, x);
+    }
+}

package/lib/RcsbChartWeb/BarChartComponent.d.ts

@@ -0,0 +1,4 @@
+import { AbstractChartComponent } from "./AbsractChartComponent";
+export declare class BarChartComponent extends AbstractChartComponent {
+    render(): import("react/jsx-runtime").JSX.Element;
+}

package/lib/RcsbChartWeb/BarChartComponent.js

@@ -0,0 +1,10 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { AbstractChartComponent } from "./AbsractChartComponent";
+import { ChartComponent } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartComponent";
+import { BarChartDataProvider } from "@rcsb/rcsb-charts/lib/RcsbChartDataProvider/BarChartDataProvider";
+import { ChartJsBarComponent } from "@rcsb/rcsb-charts/lib/RcsbChartImplementations/ChatJsImplementations/ChartJsBarComponent";
+export class BarChartComponent extends AbstractChartComponent {
+    render() {
+        return (_jsx(ChartComponent, { data: this.state.data, chartComponentImplementation: ChartJsBarComponent, dataProvider: new BarChartDataProvider(), chartConfig: this.props.chartConfig }));
+    }
+}

package/lib/RcsbChartWeb/HistogramChartComponent.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+import { AbstractChartComponent } from "./AbsractChartComponent";
+export declare class HistogramChartComponent extends AbstractChartComponent {
+    render(): JSX.Element;
+}

package/lib/RcsbChartWeb/HistogramChartComponent.js

@@ -0,0 +1,10 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { AbstractChartComponent } from "./AbsractChartComponent";
+import { ChartComponent } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartComponent";
+import { HistogramChartDataProvider } from "@rcsb/rcsb-charts/lib/RcsbChartDataProvider/HistogramChartDataProvider";
+import { ChartJsHistogramComponent } from "@rcsb/rcsb-charts/lib/RcsbChartImplementations/ChatJsImplementations/ChartJsHistogramComponent";
+export class HistogramChartComponent extends AbstractChartComponent {
+    render() {
+        return (_jsx(ChartComponent, { data: this.state.data.map(d => d.map(d => { var _a, _b; return (Object.assign(Object.assign({}, d), { label: (parseFloat(d.label.toString()) + ((_b = (_a = this.props.chartConfig) === null || _a === void 0 ? void 0 : _a.histogramBinIncrement) !== null && _b !== void 0 ? _b : 0) * 0.5) })); })), chartComponentImplementation: ChartJsHistogramComponent, dataProvider: new HistogramChartDataProvider(), chartConfig: this.props.chartConfig }));
+    }
+}

package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollector.d.ts

@@ -0,0 +1,17 @@
+import { AlignmentCollectConfig, AlignmentCollectorInterface } from "./AlignmentCollectorInterface";
+import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare class AlignmentCollector implements AlignmentCollectorInterface {
+    private requestStatus;
+    readonly rcsbFvQuery: RcsbClient;
+    private readonly targetsSubject;
+    private alignmentResponse;
+    private readonly alignmentResponseSubject;
+    private readonly alignmentLengthSubject;
+    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
+    getTargets(): Promise<Array<string>>;
+    getAlignment(): Promise<AlignmentResponse>;
+    getAlignmentLength(): Promise<number>;
+    requestAlignment(requestConfig: AlignmentCollectConfig): Promise<AlignmentResponse>;
+    private complete;
+}

package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollector.js

@@ -0,0 +1,104 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { Subject } from "rxjs";
+import { ObservableHelper } from "../../RcsbUtils/Helpers/ObservableHelper";
+import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
+var assertElementListDefined = Assertions.assertElementListDefined;
+export class AlignmentCollector {
+    constructor() {
+        this.requestStatus = "complete";
+        this.rcsbFvQuery = rcsbClient;
+        this.targetsSubject = new Subject();
+        this.alignmentResponseSubject = new Subject();
+        this.alignmentLengthSubject = new Subject();
+    }
+    collect(requestConfig, filter) {
+        var _a, _b, _c, _d, _e, _f;
+        return __awaiter(this, void 0, void 0, function* () {
+            this.requestStatus = "pending";
+            this.alignmentResponse = yield this.requestAlignment(requestConfig);
+            const targetAlignment = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignment) !== null && _b !== void 0 ? _b : (_e = (_d = (_c = this.alignmentResponse) === null || _c === void 0 ? void 0 : _c.target_alignment_subset) === null || _d === void 0 ? void 0 : _d.edges) === null || _e === void 0 ? void 0 : _e.map(e => e === null || e === void 0 ? void 0 : e.node);
+            if (targetAlignment) {
+                assertElementListDefined(targetAlignment);
+                this.alignmentResponse.target_alignment = !filter ? targetAlignment : targetAlignment === null || targetAlignment === void 0 ? void 0 : targetAlignment.filter(ta => { var _a; return filter.includes((_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "not-included"); });
+            }
+            this.alignmentResponse = typeof ((_f = requestConfig.externalTrackBuilder) === null || _f === void 0 ? void 0 : _f.filterAlignments) === "function" ? yield requestConfig.externalTrackBuilder.filterAlignments({ alignments: this.alignmentResponse }) : this.alignmentResponse;
+            this.complete();
+            return this.alignmentResponse;
+        });
+    }
+    getTargets() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                var _a, _b;
+                if (this.requestStatus === "complete") {
+                    const targetIds = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignment) === null || _b === void 0 ? void 0 : _b.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
+                    assertElementListDefined(targetIds);
+                    resolve(targetIds);
+                }
+                else {
+                    ObservableHelper.oneTimeSubscription(resolve, this.targetsSubject);
+                }
+            });
+        });
+    }
+    getAlignment() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                if (this.requestStatus === "complete") {
+                    resolve(this.alignmentResponse);
+                }
+                else {
+                    ObservableHelper.oneTimeSubscription(resolve, this.alignmentResponseSubject);
+                }
+            });
+        });
+    }
+    getAlignmentLength() {
+        return new Promise((resolve, reject) => {
+            var _a, _b, _c;
+            if (this.requestStatus === "complete") {
+                resolve((_c = ((_b = (_a = this.alignmentResponse.query_sequence) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : this.alignmentResponse.alignment_length)) !== null && _c !== void 0 ? _c : -1);
+            }
+            else {
+                ObservableHelper.oneTimeSubscription(resolve, this.alignmentLengthSubject);
+            }
+        });
+    }
+    requestAlignment(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            this.requestStatus = "pending";
+            if (requestConfig.queryId) {
+                return yield this.rcsbFvQuery.requestAlignment({
+                    queryId: requestConfig.queryId,
+                    from: requestConfig.from,
+                    to: requestConfig.to
+                });
+            }
+            else {
+                if (requestConfig.group && requestConfig.page) {
+                    return yield this.rcsbFvQuery.requestGroupAlignment({
+                        group: requestConfig.group,
+                        groupId: requestConfig.groupId,
+                        page: requestConfig.page,
+                        excludeLogo: requestConfig.excludeLogo,
+                        filter: requestConfig.filter
+                    });
+                }
+                else {
+                    return {};
+                }
+            }
+        });
+    }
+    complete() {
+        var _a, _b, _c, _d, _e;
+        this.requestStatus = "complete";
+        const targetIds = (_b = (_a = this.alignmentResponse.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id)) !== null && _b !== void 0 ? _b : [];
+        assertElementListDefined(targetIds);
+        this.targetsSubject.next(targetIds);
+        this.alignmentResponseSubject.next(this.alignmentResponse);
+        this.alignmentLengthSubject.next((_e = ((_d = (_c = this.alignmentResponse.query_sequence) === null || _c === void 0 ? void 0 : _c.length) !== null && _d !== void 0 ? _d : this.alignmentResponse.alignment_length)) !== null && _e !== void 0 ? _e : -1);
+        console.info("Alignment Processing Complete");
+    }
+}

package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface.d.ts

@@ -0,0 +1,29 @@
+import { AlignmentResponse, QueryAlignmentArgs, SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { RcsbQueryGroupAlignmentArguments } from "../../RcsbGraphQL/RcsbQueryAlignment";
+import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
+interface CommonAlignmentInterface {
+    externalTrackBuilder?: ExternalTrackBuilderInterface;
+    filterByTargetContains?: string;
+    dynamicDisplay?: boolean;
+    excludeAlignmentLinks?: boolean;
+    fitTitleWidth?: boolean;
+    excludeFirstRowLink?: boolean;
+}
+type QueryAlignmentArgsTypes = {
+    [K in keyof QueryAlignmentArgs]: NonNullable<QueryAlignmentArgs[K]>;
+};
+export interface CollectAlignmentInterface extends QueryAlignmentArgsTypes, CommonAlignmentInterface {
+}
+export interface CollectGroupAlignmentInterface extends RcsbQueryGroupAlignmentArguments, CommonAlignmentInterface {
+    sequencePrefix: string;
+    from?: SequenceReference;
+    to?: SequenceReference;
+}
+export type AlignmentCollectConfig = Partial<CollectAlignmentInterface & CollectGroupAlignmentInterface>;
+export interface AlignmentCollectorInterface {
+    getTargets(): Promise<Array<string>>;
+    getAlignment(): Promise<AlignmentResponse>;
+    getAlignmentLength(): Promise<number>;
+    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
+}
+export {};

package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface.js

@@ -0,0 +1 @@
+export {};

package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollector.d.ts

@@ -0,0 +1,16 @@
+import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { AnnotationRequestContext, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";
+export declare class AnnotationCollector implements AnnotationCollectorInterface {
+    readonly rcsbFvQuery: RcsbClient;
+    private requestStatus;
+    private rawFeatures;
+    private annotationFeatures;
+    private readonly rawFeaturesSubject;
+    private readonly annotationFeaturesSubject;
+    collect(requestConfig: AnnotationRequestContext): Promise<Array<AnnotationFeatures>>;
+    getFeatures(): Promise<Array<Feature>>;
+    getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
+    private requestAnnotations;
+    private complete;
+}

package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollector.js

@@ -0,0 +1,83 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { Subject } from "rxjs";
+import { ObservableHelper } from "../../RcsbUtils/Helpers/ObservableHelper";
+export class AnnotationCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+        this.requestStatus = "complete";
+        this.rawFeaturesSubject = new Subject();
+        this.annotationFeaturesSubject = new Subject();
+    }
+    collect(requestConfig) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            this.requestStatus = "pending";
+            this.annotationFeatures = yield this.requestAnnotations(requestConfig);
+            if (typeof (requestConfig === null || requestConfig === void 0 ? void 0 : requestConfig.annotationGenerator) === "function") {
+                const generatedFeatures = yield requestConfig.annotationGenerator(this.annotationFeatures);
+                if (generatedFeatures && generatedFeatures.filter((f) => (f != null)).length > 0)
+                    this.annotationFeatures = this.annotationFeatures.concat(generatedFeatures.filter((f) => (f != null)));
+            }
+            if (typeof (requestConfig === null || requestConfig === void 0 ? void 0 : requestConfig.annotationFilter) === "function") {
+                this.annotationFeatures = yield requestConfig.annotationFilter(this.annotationFeatures);
+            }
+            if (typeof ((_a = requestConfig === null || requestConfig === void 0 ? void 0 : requestConfig.externalTrackBuilder) === null || _a === void 0 ? void 0 : _a.filterFeatures) === "function")
+                this.annotationFeatures = yield requestConfig.externalTrackBuilder.filterFeatures({ annotations: this.annotationFeatures, rcsbContext: requestConfig.rcsbContext });
+            this.rawFeatures = [].concat.apply([], this.annotationFeatures.map(af => af.features));
+            this.complete();
+            return this.annotationFeatures;
+        });
+    }
+    getFeatures() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                if (this.requestStatus === "complete") {
+                    resolve(this.rawFeatures);
+                }
+                else {
+                    ObservableHelper.oneTimeSubscription(resolve, this.rawFeaturesSubject);
+                }
+            });
+        });
+    }
+    getAnnotationFeatures() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                if (this.requestStatus === "complete") {
+                    resolve(this.annotationFeatures);
+                }
+                else {
+                    ObservableHelper.oneTimeSubscription(resolve, this.annotationFeaturesSubject);
+                }
+            });
+        });
+    }
+    requestAnnotations(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (requestConfig.queryId)
+                return yield this.rcsbFvQuery.requestRcsbPdbAnnotations({
+                    queryId: requestConfig.queryId,
+                    reference: requestConfig.reference,
+                    sources: requestConfig.sources,
+                    filters: requestConfig.filters,
+                    range: requestConfig.range
+                });
+            else if (requestConfig.group && requestConfig.groupId)
+                return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotations({
+                    group: requestConfig.group,
+                    groupId: requestConfig.groupId,
+                    sources: requestConfig.sources,
+                    filters: requestConfig.filters,
+                    histogram: requestConfig.histogram
+                });
+            throw new Error(`Annotation query error`);
+        });
+    }
+    complete() {
+        this.requestStatus = "complete";
+        this.annotationFeaturesSubject.next(this.annotationFeatures);
+        this.rawFeaturesSubject.next(this.rawFeatures);
+        console.info("Features Processing Complete");
+    }
+}

package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface.d.ts

@@ -0,0 +1,37 @@
+import { AnnotationFeatures, Feature, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FeaturePositionGaps } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager";
+import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
+import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
+import { TrackManagerInterface } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
+export type IncreaseAnnotationValueType = (feature: {
+    type: string;
+    targetId: string;
+    positionKey: string;
+    d: Feature;
+    p: FeaturePositionGaps;
+}) => number;
+export interface AnnotationProcessingInterface {
+    getAnnotationValue?: IncreaseAnnotationValueType;
+    computeAnnotationValue?: (annotationTracks: Map<string, TrackManagerInterface>) => void;
+    addTrackElementCallback?: IncreaseAnnotationValueType;
+}
+export interface CommonAnnotationInterface {
+    rcsbContext?: Partial<PolymerEntityInstanceInterface>;
+    annotationProcessing?: AnnotationProcessingInterface;
+    externalTrackBuilder?: ExternalTrackBuilderInterface;
+    annotationGenerator?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
+    annotationFilter?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
+    titleSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
+    trackTitle?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
+    typeSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
+}
+export interface AnnotationsCollectConfig extends QueryAnnotationsArgs, CommonAnnotationInterface {
+}
+export interface CollectGroupAnnotationsInterface extends QueryGroup_AnnotationsArgs, CommonAnnotationInterface {
+}
+export type AnnotationRequestContext = Partial<AnnotationsCollectConfig & CollectGroupAnnotationsInterface>;
+export interface AnnotationCollectorInterface {
+    collect(requestConfig: AnnotationsCollectConfig | CollectGroupAnnotationsInterface): Promise<Array<AnnotationFeatures>>;
+    getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
+    getFeatures(): Promise<Array<Feature>>;
+}

package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface.js

@@ -0,0 +1 @@
+export {};

package/lib/RcsbCollectTools/DataCollectors/AssemblyInterfacesCollector.d.ts

@@ -0,0 +1,9 @@
+import { QueryAssembliesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+export interface AssemblyInterfacesInterface {
+    rcsbId: string;
+    interfaceIds: Array<string>;
+}
+export declare class AssemblyInterfacesCollector {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: QueryAssembliesArgs): Promise<Array<AssemblyInterfacesInterface>>;
+}

package/lib/RcsbCollectTools/DataCollectors/AssemblyInterfacesCollector.js

@@ -0,0 +1,31 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
+var assertDefined = Assertions.assertDefined;
+export class AssemblyInterfacesCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+    }
+    collect(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const result = yield this.rcsbFvQuery.requestAssemblyInterfaces(requestConfig);
+                return result.map(r => parseAssemblyInterfaces(r));
+            }
+            catch (error) {
+                console.log(error);
+                throw error;
+            }
+        });
+    }
+}
+function parseAssemblyInterfaces(assemblyInterfaces) {
+    var _a, _b;
+    return {
+        rcsbId: assemblyInterfaces.rcsb_id,
+        interfaceIds: (_b = (_a = assemblyInterfaces.interfaces) === null || _a === void 0 ? void 0 : _a.map(i => {
+            assertDefined(i === null || i === void 0 ? void 0 : i.rcsb_id);
+            return i.rcsb_id;
+        })) !== null && _b !== void 0 ? _b : []
+    };
+}

package/lib/RcsbCollectTools/DataCollectors/DataCollectorInterface.d.ts

@@ -0,0 +1,7 @@
+export type DataCollectorArgsType<K extends string> = Record<K, string | Array<string>>;
+export interface MultipleDocumentPropertyCollectorInterface<K extends string, T> {
+    collect(args: DataCollectorArgsType<K>): Promise<Array<T>>;
+}
+export interface SingleDocumentPropertyCollectorInterface<K extends string, T> {
+    collect(args: DataCollectorArgsType<K>): Promise<T>;
+}

package/lib/RcsbCollectTools/DataCollectors/DataCollectorInterface.js

@@ -0,0 +1 @@
+export {};

package/lib/RcsbCollectTools/DataCollectors/EntryAssembliesCollector.d.ts

@@ -0,0 +1,10 @@
+import { QueryEntryArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
+export declare class EntryAssembliesCollector {
+    private readonly rcsbFvQuery;
+    static readonly modelKey: string;
+    collect(requestConfig: QueryEntryArgs): Promise<Map<string, Array<PolymerEntityInstanceInterface>>>;
+    private static getEntryAssemblies;
+    private static parsePolymerEntityInstances;
+    private static parsePolymerEntityAssemblies;
+}

package/lib/RcsbCollectTools/DataCollectors/EntryAssembliesCollector.js

@@ -0,0 +1,92 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
+var assertElementListDefined = Assertions.assertElementListDefined;
+var assertDefined = Assertions.assertDefined;
+export class EntryAssembliesCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+    }
+    collect(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const coreEntry = yield this.rcsbFvQuery.requestEntityInstances(requestConfig);
+                return EntryAssembliesCollector.getEntryAssemblies(coreEntry);
+            }
+            catch (error) {
+                console.log(error);
+                throw error;
+            }
+        });
+    }
+    static getEntryAssemblies(entry) {
+        const out = new Map();
+        out.set(EntryAssembliesCollector.modelKey, new Array());
+        const asymInstanceMap = new Map();
+        if ((entry === null || entry === void 0 ? void 0 : entry.polymer_entities) instanceof Array) {
+            entry.polymer_entities.forEach(entity => {
+                if ((entity === null || entity === void 0 ? void 0 : entity.polymer_entity_instances) && Array.isArray(entity === null || entity === void 0 ? void 0 : entity.polymer_entity_instances)) {
+                    assertElementListDefined(entity.polymer_entity_instances);
+                    EntryAssembliesCollector.parsePolymerEntityInstances(entity.polymer_entity_instances, asymInstanceMap, out);
+                }
+            });
+        }
+        if ((entry === null || entry === void 0 ? void 0 : entry.assemblies) instanceof Array) {
+            entry.assemblies.forEach(assembly => {
+                if (assembly)
+                    EntryAssembliesCollector.parsePolymerEntityAssemblies(assembly, asymInstanceMap, out);
+            });
+        }
+        return out;
+    }
+    static parsePolymerEntityInstances(polymerEntityInstances, asymInstanceMap, out) {
+        polymerEntityInstances.forEach(instance => {
+            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p, _q, _r, _s, _t, _u, _v, _w, _x, _y, _z, _0, _1, _2, _3;
+            const taxIds = new Set();
+            if (((_a = instance === null || instance === void 0 ? void 0 : instance.polymer_entity) === null || _a === void 0 ? void 0 : _a.rcsb_entity_source_organism) instanceof Array)
+                instance.polymer_entity.rcsb_entity_source_organism.forEach(sO => {
+                    if (typeof (sO === null || sO === void 0 ? void 0 : sO.ncbi_scientific_name) === "string" && sO.ncbi_scientific_name.length > 0)
+                        taxIds.add(sO.ncbi_scientific_name);
+                });
+            const o = instance.rcsb_polymer_entity_instance_container_identifiers;
+            assertDefined(o), assertDefined(o === null || o === void 0 ? void 0 : o.entry_id), assertDefined(o === null || o === void 0 ? void 0 : o.entity_id), assertDefined(o === null || o === void 0 ? void 0 : o.entity_id), assertDefined(o === null || o === void 0 ? void 0 : o.asym_id), assertDefined(o === null || o === void 0 ? void 0 : o.auth_asym_id), assertElementListDefined(o === null || o === void 0 ? void 0 : o.auth_to_entity_poly_seq_mapping);
+            assertDefined((_c = (_b = instance.polymer_entity) === null || _b === void 0 ? void 0 : _b.entity_poly) === null || _c === void 0 ? void 0 : _c.rcsb_sample_sequence_length);
+            assertDefined((_d = instance.polymer_entity.entry) === null || _d === void 0 ? void 0 : _d.rcsb_entry_info.structure_determination_methodology);
+            const d = {
+                rcsbId: instance.rcsb_id,
+                entryId: o.entry_id,
+                entityId: o.entity_id,
+                asymId: o.asym_id,
+                authId: o.auth_asym_id,
+                authResId: o.auth_to_entity_poly_seq_mapping,
+                name: (_m = ((_j = (_h = (_g = (_f = (_e = instance.polymer_entity) === null || _e === void 0 ? void 0 : _e.rcsb_polymer_entity) === null || _f === void 0 ? void 0 : _f.rcsb_polymer_name_combined) === null || _g === void 0 ? void 0 : _g.names) === null || _h === void 0 ? void 0 : _h.join(", ")) !== null && _j !== void 0 ? _j : (_l = (_k = instance.polymer_entity) === null || _k === void 0 ? void 0 : _k.rcsb_polymer_entity) === null || _l === void 0 ? void 0 : _l.pdbx_description)) !== null && _m !== void 0 ? _m : "NA",
+                taxNames: Array.from(taxIds),
+                experimentalMethod: (_q = (_p = (_o = instance.polymer_entity) === null || _o === void 0 ? void 0 : _o.entry) === null || _p === void 0 ? void 0 : _p.rcsb_entry_info.experimental_method) !== null && _q !== void 0 ? _q : "NA",
+                resolution: (_u = (_t = (_s = (_r = instance.polymer_entity) === null || _r === void 0 ? void 0 : _r.entry) === null || _s === void 0 ? void 0 : _s.rcsb_entry_info.resolution_combined) === null || _t === void 0 ? void 0 : _t[0]) !== null && _u !== void 0 ? _u : undefined,
+                sequenceLength: (_w = (_v = instance.polymer_entity) === null || _v === void 0 ? void 0 : _v.entity_poly) === null || _w === void 0 ? void 0 : _w.rcsb_sample_sequence_length,
+                entityMolecularWeight: (_y = (_x = instance.polymer_entity.rcsb_polymer_entity) === null || _x === void 0 ? void 0 : _x.formula_weight) !== null && _y !== void 0 ? _y : undefined,
+                entryMolecularWeight: (_0 = (_z = instance.polymer_entity.entry) === null || _z === void 0 ? void 0 : _z.rcsb_entry_info.molecular_weight) !== null && _0 !== void 0 ? _0 : undefined,
+                structureDeterminationMethodology: instance.polymer_entity.entry.rcsb_entry_info.structure_determination_methodology
+            };
+            (_1 = out.get(EntryAssembliesCollector.modelKey)) === null || _1 === void 0 ? void 0 : _1.push(d);
+            if ((_2 = instance === null || instance === void 0 ? void 0 : instance.rcsb_polymer_entity_instance_container_identifiers) === null || _2 === void 0 ? void 0 : _2.asym_id)
+                asymInstanceMap.set((_3 = instance === null || instance === void 0 ? void 0 : instance.rcsb_polymer_entity_instance_container_identifiers) === null || _3 === void 0 ? void 0 : _3.asym_id, d);
+        });
+    }
+    static parsePolymerEntityAssemblies(assembly, asymInstanceMap, out) {
+        var _a;
+        out.set(assembly.rcsb_assembly_container_identifiers.assembly_id, new Array());
+        (_a = assembly.pdbx_struct_assembly_gen) === null || _a === void 0 ? void 0 : _a.forEach(assemblyGen => {
+            var _a;
+            (_a = assemblyGen === null || assemblyGen === void 0 ? void 0 : assemblyGen.asym_id_list) === null || _a === void 0 ? void 0 : _a.forEach(asymId => {
+                var _a;
+                if (!asymId)
+                    return;
+                const o = asymInstanceMap.get(asymId);
+                if (o)
+                    (_a = out.get(assembly.rcsb_assembly_container_identifiers.assembly_id)) === null || _a === void 0 ? void 0 : _a.push(o);
+            });
+        });
+    }
+}
+EntryAssembliesCollector.modelKey = "Model";

package/lib/RcsbCollectTools/DataCollectors/GroupMemberCollector.d.ts

@@ -0,0 +1,6 @@
+import { QueryPolymer_Entity_GroupArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
+export declare class GroupMemberCollector {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: QueryPolymer_Entity_GroupArgs): Promise<Array<PolymerEntityInstanceInterface>>;
+}

package/lib/RcsbCollectTools/DataCollectors/GroupMemberCollector.js

@@ -0,0 +1,21 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { MultipleEntityInstancesCollector } from "./MultipleEntityInstancesCollector";
+export class GroupMemberCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+    }
+    collect(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const result = yield this.rcsbFvQuery.requestGroupInfo(requestConfig);
+            if (result.rcsb_group_info.group_members_granularity === "polymer_entity") {
+                const multipleEntityInstancesCollector = new MultipleEntityInstancesCollector();
+                return yield multipleEntityInstancesCollector.collect({ entity_ids: result.rcsb_group_container_identifiers.group_member_ids.filter((x) => x != null) });
+            }
+            else {
+                console.error(`Group granularity ${result.rcsb_group_info.group_members_granularity} not supported`);
+                throw new Error(`Group granularity ${result.rcsb_group_info.group_members_granularity} not supported`);
+            }
+        });
+    }
+}

package/lib/RcsbCollectTools/DataCollectors/GroupPropertyCollector.d.ts

@@ -0,0 +1,10 @@
+import { QueryPolymer_Entity_GroupArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+export interface GroupPropertyInterface {
+    groupName: string;
+    groupDescription: string;
+}
+export declare class GroupPropertyCollector {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: QueryPolymer_Entity_GroupArgs): Promise<GroupPropertyInterface>;
+    private static getGroupProperties;
+}

package/lib/RcsbCollectTools/DataCollectors/GroupPropertyCollector.js

@@ -0,0 +1,26 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+export class GroupPropertyCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+    }
+    collect(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const result = yield this.rcsbFvQuery.requestGroupInfo(requestConfig);
+                return GroupPropertyCollector.getGroupProperties(result);
+            }
+            catch (error) {
+                console.log(error);
+                throw error;
+            }
+        });
+    }
+    static getGroupProperties(r) {
+        var _a, _b;
+        return {
+            groupName: (_a = r.rcsb_group_info.group_name) !== null && _a !== void 0 ? _a : "NA",
+            groupDescription: (_b = r.rcsb_group_info.group_description) !== null && _b !== void 0 ? _b : "NA"
+        };
+    }
+}