@gen3/core 0.10.44

package/dist/dts/features/filters/types.d.ts

@@ -0,0 +1,113 @@
+export interface Intersection {
+    operator: 'and';
+    operands: ReadonlyArray<Operation>;
+}
+export interface Union {
+    operator: 'or';
+    operands: ReadonlyArray<Operation>;
+}
+export interface Equals {
+    operator: '=';
+    field: string;
+    operand: number | string;
+}
+export interface NotEquals {
+    operator: '!=';
+    field: string;
+    operand: number | string;
+}
+export interface Includes {
+    operator: 'in';
+    field: string;
+    operands: ReadonlyArray<string | number>;
+}
+export interface Comparison {
+    field: string;
+    operand: string | number;
+}
+export interface LessThan extends Comparison {
+    operator: '<';
+}
+export interface LessThanOrEquals extends Comparison {
+    operator: '<=';
+}
+export interface GreaterThan extends Comparison {
+    operator: '>';
+}
+export interface GreaterThanOrEquals extends Comparison {
+    operator: '>=';
+}
+export interface Exists {
+    readonly operator: 'exists';
+    readonly field: string;
+}
+export interface Missing {
+    readonly operator: 'missing';
+    readonly field: string;
+}
+export interface ExcludeIfAny {
+    readonly operator: 'excludeifany';
+    readonly field: string;
+    readonly operands: ReadonlyArray<string | number>;
+}
+export interface Excludes {
+    readonly operator: 'excludes';
+    readonly field: string;
+    readonly operands: ReadonlyArray<string | number>;
+}
+export interface NestedFilter {
+    operator: 'nested';
+    path: string;
+    operand: Operation;
+}
+export type Operation = Intersection | Union | Includes | Equals | NotEquals | LessThan | LessThanOrEquals | GreaterThan | GreaterThanOrEquals | NestedFilter | ExcludeIfAny | Excludes;
+export type OperationWithField = Includes | Equals | NotEquals | LessThan | LessThanOrEquals | GreaterThan | GreaterThanOrEquals | ExcludeIfAny | Excludes;
+export interface FilterSet {
+    readonly root: Record<string, Operation>;
+    readonly mode: 'and' | 'or';
+}
+export interface OperationHandler<T> {
+    handleEquals: (op: Equals) => T;
+    handleNotEquals: (op: NotEquals) => T;
+    handleLessThan: (op: LessThan) => T;
+    handleLessThanOrEquals: (op: LessThanOrEquals) => T;
+    handleGreaterThan: (op: GreaterThan) => T;
+    handleGreaterThanOrEquals: (op: GreaterThanOrEquals) => T;
+    handleIncludes: (op: Includes) => T;
+    handleExcludes: (op: Excludes) => T;
+    handleExcludeIfAny: (op: ExcludeIfAny) => T;
+    handleIntersection: (op: Intersection) => T;
+    handleUnion: (op: Union) => T;
+    handleNestedFilter: (op: NestedFilter) => T;
+}
+/**
+ *  Operand types for filter operations
+ */
+export type EnumFilterValue = ReadonlyArray<string | number>;
+export type RangeFilterValue = string | number;
+export type SetFilterValue = ReadonlyArray<Operation>;
+export type FilterValue = EnumFilterValue | RangeFilterValue | SetFilterValue | undefined;
+export type FacetBucket = {
+    key: string;
+    doc_count: number;
+};
+export type HistogramBucket = {
+    key: string | [number, number];
+    count: number;
+};
+export type FacetType = 'enum' | 'exact' | 'range' | 'age' | 'year' | 'years' | 'days' | 'percent' | 'datetime' | 'toggle' | 'multiselect';
+export interface AllowableRange {
+    readonly minimum?: number;
+    readonly maximum?: number;
+}
+export interface FacetDefinition {
+    readonly description?: string;
+    readonly field: string;
+    readonly dataField: string;
+    readonly index: string;
+    readonly type: FacetType;
+    readonly range?: AllowableRange;
+    readonly hasData?: boolean;
+    readonly label?: string;
+}
+export type IndexedFilterSet = Record<string, FilterSet>;

package/dist/dts/features/filters/utils.d.ts

@@ -0,0 +1,26 @@
+export declare const trimFirstFieldNameToTitle: (fieldName: string, trim?: boolean) => string;
+/**
+ * Converts a filter name to a title,
+ * For example files.input.experimental_strategy will get converted to Experimental Strategy
+ * if sections == 2 then the output would be Input Experimental Strategy
+ * @param fieldName input filter expected to be: string.firstpart_secondpart
+ * @param sections number of "sections" string.string.string to got back from the end of the field
+ */
+export declare const fieldNameToTitle: (fieldName: string, sections?: number) => string;
+/**
+ * Extracts the index name from the field name
+ * @param fieldName
+ */
+export declare const extractIndexFromFullFieldName: (fieldName: string) => string;
+/**
+ * prepend the index name to the field name
+ */
+export declare const prependIndexToFieldName: (fieldName: string, index: string) => string;
+/**
+ * extract the field name from the index.field name
+ */
+export declare const extractFieldNameFromFullFieldName: (fieldName: string) => string;
+/**
+ * extract the field name and the index from the index.field name returning as a tuple
+ */
+export declare const extractIndexAndFieldNameFromFullFieldName: (fieldName: string) => [string, string];

package/dist/dts/features/gen3/gen3Api.d.ts

@@ -0,0 +1,11 @@
+import { Middleware, Reducer } from '@reduxjs/toolkit';
+/**
+ * Creates a base class core API for building other API endpoints on top of.
+ * @param reducerPath - The root key name that the other slices will be derived from
+ * @param baseQuery: - The template query which the slices will addon to
+ * @param endpoints - Base API endpoints that should exist in every slice
+ * @returns: The generated base API
+ */
+export declare const gen3Api: import("@reduxjs/toolkit/dist/query/apiTypes").Api<import("@reduxjs/toolkit/dist/query/baseQueryTypes").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query/fetchBaseQuery").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query/fetchBaseQuery").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query/fetchBaseQuery").FetchBaseQueryMeta>, {}, "gen3Services", never, keyof import("@reduxjs/toolkit/dist/query/apiTypes").ApiModules<any, any, any, any>>;
+export declare const gen3ServicesReducer: Reducer;
+export declare const gen3ServicesReducerMiddleware: Middleware;

package/dist/dts/features/gen3/index.d.ts

@@ -0,0 +1,2 @@
+import { gen3Api } from './gen3Api';
+export { gen3Api };

package/dist/dts/features/gen3Apps/Gen3App.d.ts

@@ -0,0 +1,48 @@
+import React, { ComponentType } from 'react';
+import { EntityType } from './gen3AppsSlice';
+import { AnyAction } from '@reduxjs/toolkit';
+import { Store, Action } from 'redux';
+import { DataStatus } from '../../dataAccess';
+export interface CreateGen3AppOptions {
+    readonly App: ComponentType;
+    readonly name: string;
+    readonly version: string;
+    readonly requiredEntityTypes: ReadonlyArray<EntityType>;
+}
+export declare const getGen3AppId: (name: string, version: string) => string;
+/**
+ *  TODO: can't tell what anything in this directory is doing.
+ */
+export declare const createGen3App: ({ App, name, version, requiredEntityTypes, }: CreateGen3AppOptions) => React.FC;
+export interface AppDataSelectorResponse<T> {
+    readonly data?: T;
+    readonly status: DataStatus;
+    readonly error?: string;
+}
+export interface UseAppDataResponse<T> {
+    readonly data?: T;
+    readonly error?: string;
+    readonly isUninitialized: boolean;
+    readonly isFetching: boolean;
+    readonly isSuccess: boolean;
+    readonly isError: boolean;
+}
+export interface UseAppDataHook<P, T> {
+    (...params: P[]): UseAppDataResponse<T>;
+}
+export interface CreateGEN3AppStore {
+    readonly name: string;
+    readonly version: string;
+    readonly reducers: (...args: any) => any;
+}
+export declare const createAppStore: (options: CreateGEN3AppStore) => Record<any, any>;
+export interface CreateGen3AppWithOwnStoreOptions<A extends Action = AnyAction, S = any> {
+    readonly App: ComponentType;
+    readonly id: string;
+    readonly name: string;
+    readonly version: string;
+    readonly requiredEntityTypes: ReadonlyArray<EntityType>;
+    readonly store: Store<S, A>;
+    readonly context: any;
+}
+export declare const createGen3AppWithOwnStore: <A extends Action = AnyAction, S = any>(options: CreateGen3AppWithOwnStoreOptions<A, S>) => React.ReactNode;

package/dist/dts/features/gen3Apps/gen3AppRegistry.d.ts

@@ -0,0 +1,7 @@
+/**
+ * A registry for the Gen3 Apps.
+ */
+export declare const REGISTRY: Record<string, React.ReactNode>;
+export declare const registerGen3App: (id: string, gen3App: React.ReactNode) => void;
+export declare const lookupGen3App: (id: string) => React.ReactNode;
+export declare const computeGen3AppId: (name: string, version: string) => string;

package/dist/dts/features/gen3Apps/gen3AppsSlice.d.ts

@@ -0,0 +1,19 @@
+import React from 'react';
+import { CoreState } from '../../reducers';
+export interface Gen3AppsState {
+    readonly gen3Apps: Readonly<Record<string, Gen3AppMetadata>>;
+    readonly currentAppId?: string;
+}
+export interface Gen3AppMetadata {
+    readonly id: string;
+    readonly name: string;
+    readonly version: string;
+    readonly requiredEntityTypes: ReadonlyArray<EntityType>;
+}
+export type EntityType = 'case' | 'gene' | 'ssm' | 'cnv' | 'file';
+export declare const gen3AppReducer: import("redux").Reducer<Gen3AppsState>;
+export declare const addGen3AppMetadata: import("@reduxjs/toolkit").ActionCreatorWithPayload<Gen3AppMetadata, "gen3Apps/addGen3AppMetadata">;
+export declare const selectGen3AppIds: (state: CoreState) => ReadonlyArray<string>;
+export declare const selectAllGen3AppMetadata: (state: CoreState) => ReadonlyArray<Gen3AppMetadata>;
+export declare const selectGen3AppMetadataById: (state: CoreState, appId: string) => Gen3AppMetadata;
+export declare const selectGen3AppById: (appId: string) => React.ReactNode;

package/dist/dts/features/gen3Apps/index.d.ts

@@ -0,0 +1,3 @@
+import { createGen3App, getGen3AppId } from './Gen3App';
+import { selectGen3AppMetadataById, selectGen3AppById } from './gen3AppsSlice';
+export { createGen3App, selectGen3AppMetadataById, selectGen3AppById, getGen3AppId, };

package/dist/dts/features/graphQL/graphQLSlice.d.ts

@@ -0,0 +1,12 @@
+import { JSONObject } from '../../types';
+export declare const graphQLWithTags: import("@reduxjs/toolkit/dist/query").Api<import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, import("@reduxjs/toolkit/dist/query/endpointDefinitions").UpdateDefinitions<{}, "graphQL", never>, "gen3Services", "graphQL", keyof import("@reduxjs/toolkit/dist/query").ApiModules<any, any, any, any>>;
+/**
+ * Creates a graphQLAPI for graphql queries to elasticsearch indices via guppy
+ * @see https://github.com/uc-cdis/guppy/blob/master/doc/queries.md
+ * @param query - Resolver function which configures the graphql query with graphQLParams argument
+ * @returns: A guppy search API for fetching metadata
+ */
+export declare const graphQLAPI: import("@reduxjs/toolkit/dist/query").Api<import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, import("@reduxjs/toolkit/dist/query/endpointDefinitions").UpdateDefinitions<{}, "graphQL", never> & {
+    graphQL: import("@reduxjs/toolkit/dist/query").QueryDefinition<JSONObject, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, "graphQL", JSONObject, "gen3Services">;
+}, "gen3Services", "graphQL", keyof import("@reduxjs/toolkit/dist/query").ApiModules<any, any, any, any>>;
+export declare const useGraphQLQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<JSONObject, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, "graphQL", JSONObject, "gen3Services">>;

package/dist/dts/features/graphQL/index.d.ts

@@ -0,0 +1 @@
+export * from './graphQLSlice';

package/dist/dts/features/guppy/conversion.d.ts

@@ -0,0 +1,23 @@
+import { JSONArray, JSONObject } from '../../types';
+import { FILE_DELIMITERS } from '../../constants';
+import { UnparseConfig } from 'papaparse';
+/**
+ * Flattens a deep nested JSON object skipping
+ * the first level to avoid potentially flattening
+ * non-nested data.
+ * @param {JSON} json
+ */
+export declare function flattenJson(json: JSONObject): JSONArray;
+/**
+ * Converts JSON based on a config.
+ * @param {JSON} json
+ * @param {Object} config
+ */
+export declare function conversion(json: JSONArray, config: UnparseConfig): Promise<string>;
+/**
+ * Converts JSON to a specified file format.
+ * Defaults to JSON if file format is not supported.
+ * @param {JSON} json
+ * @param {string} format
+ */
+export declare function jsonToFormat(json: JSONObject, format: keyof typeof FILE_DELIMITERS): Promise<string | JSONObject>;

package/dist/dts/features/guppy/guppyApi.d.ts

@@ -0,0 +1,41 @@
+import type { Middleware, Reducer } from '@reduxjs/toolkit';
+import { JSONObject } from '../../types';
+export interface guppyFetchError {
+    readonly url: string;
+    readonly status: number;
+    readonly statusText: string;
+    readonly text: string;
+    readonly variables?: Record<string, any>;
+}
+export interface guppyApiSliceRequest {
+    readonly query: string;
+    readonly variables?: Record<string, unknown>;
+}
+export interface guppyApiResponse<H = JSONObject> {
+    readonly data: H;
+    readonly errors: Record<string, string>;
+}
+export interface SortOption {
+    field: string;
+    order: string;
+}
+export interface TablePageOffsetProps {
+    readonly pageSize?: number;
+    readonly offset?: number;
+    readonly sorts?: Array<SortOption>;
+    readonly searchTerm?: string;
+}
+/**
+ * Creates a base class core API for guppy API calls.
+ * @returns: guppy core API with guppyAPIFetch base query
+ */
+export declare const guppyApi: import("@reduxjs/toolkit/dist/query").Api<(query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, {}, "guppy", never, keyof import("@reduxjs/toolkit/dist/query").ApiModules<any, any, any, any>>;
+export declare const guppyAPISliceMiddleware: Middleware;
+export declare const guppyApiSliceReducerPath: string;
+export declare const guppyApiReducer: Reducer;

package/dist/dts/features/guppy/guppyDownloadSlice.d.ts

@@ -0,0 +1,21 @@
+import { GQLFilter } from '../filters';
+import { BaseGuppyDataRequest, GuppyDownloadDataParams } from './types';
+export interface GuppyDownloadDataQueryParams extends BaseGuppyDataRequest {
+    filter: GQLFilter;
+}
+interface DownloadRequestStatus {
+    readonly status: string;
+    readonly message: string;
+}
+/**
+ * Creates a Guppy API for fetching bulk (> 10K rows) elasticsearch data
+ * @see https://github.com/uc-cdis/guppy/blob/master/doc/download.md
+ * @param endpoints - Resolver function which configures the query with
+ * type, filter, accessibility, fields, and sort arguments
+ * @returns: A guppy download API for fetching bulk metadata
+ */
+export declare const downloadRequestApi: import("@reduxjs/toolkit/dist/query").Api<import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, {
+    downloadFromGuppy: import("@reduxjs/toolkit/dist/query").MutationDefinition<GuppyDownloadDataParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, DownloadRequestStatus, "gen3Services">;
+}, "gen3Services", never, keyof import("@reduxjs/toolkit/dist/query").ApiModules<any, any, any, any>>;
+export declare const useDownloadFromGuppyMutation: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseMutation<import("@reduxjs/toolkit/dist/query").MutationDefinition<GuppyDownloadDataParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, DownloadRequestStatus, "gen3Services">>;
+export {};

package/dist/dts/features/guppy/guppySlice.d.ts

@@ -0,0 +1,120 @@
+import { SWRResponse, Fetcher } from 'swr';
+import { AggregationsData, JSONObject } from '../../types';
+import { Accessibility } from '../../constants';
+import { FilterSet } from '../filters';
+import { guppyApiSliceRequest } from './guppyApi';
+import { CoreState } from '../../reducers';
+export interface GraphQLQuery {
+    query: string;
+    variables?: Record<string, unknown>;
+}
+export declare const fetchJson: Fetcher<JSONObject, string>;
+export declare const useGetStatus: () => SWRResponse<JSONObject, Error>;
+export type AggregationResponse = Record<string, JSONObject>;
+export interface RawDataAndTotalCountsParams {
+    type: string;
+    fields: string[];
+    filters: FilterSet;
+    sort?: ReadonlyArray<Record<string, 'asc' | 'desc'>>;
+    offset?: number;
+    size?: number;
+    accessibility?: Accessibility;
+    format?: string;
+}
+interface AccessibleDataSliceParams {
+    type: string;
+    fields: ReadonlyArray<string>;
+    accessType: Accessibility;
+}
+interface QueryAggsParams {
+    type: string;
+    fields: ReadonlyArray<string>;
+    filters: FilterSet;
+    accessibility?: Accessibility;
+}
+interface QueryForSubAggsParams {
+    type: string;
+    mainField: string;
+    numericAggAsText: boolean;
+    termsFields?: ReadonlyArray<string>;
+    missingFields?: ReadonlyArray<string>;
+    gqlFilter?: FilterSet;
+    accessibility?: Accessibility;
+}
+interface QueryCountsParams {
+    type: string;
+    filters: FilterSet;
+    accessibility?: Accessibility;
+}
+interface QueryForFileCountSummaryParams {
+    type: string;
+    field: string;
+    filters: FilterSet;
+}
+export declare const rawDataQueryStrForEachField: (field: string) => string;
+export declare const useGetArrayTypes: () => import("../../types").JSONValue;
+export declare const useGetRawDataAndTotalCountsQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<RawDataAndTotalCountsParams, (query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, never, any, "guppy">>, useGetAccessibleDataQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<AccessibleDataSliceParams, (query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, never, any, "guppy">>, useGetAllFieldsForTypeQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<{
+    type: string;
+}, (query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, never, any, "guppy">>, useGetAggsQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<QueryAggsParams, (query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, never, AggregationsData, "guppy">>, useGetSubAggsQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<QueryForSubAggsParams, (query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, never, AggregationsData, "guppy">>, useGetCountsQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<QueryCountsParams, (query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, never, number, "guppy">>, useGetFieldCountSummaryQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<QueryForFileCountSummaryParams, (query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, never, Record<string, any>, "guppy">>, useGetFieldsForIndexQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<string, (query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, never, any, "guppy">>, useGeneralGQLQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<guppyApiSliceRequest, (query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, never, Record<string, unknown>, "guppy">>, useLazyGeneralGQLQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseLazyQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<guppyApiSliceRequest, (query: guppyApiSliceRequest, api: import("@reduxjs/toolkit/dist/query").BaseQueryApi) => Promise<{
+    data: any;
+    error?: undefined;
+} | {
+    error: unknown;
+    data?: undefined;
+}>, never, Record<string, unknown>, "guppy">>;
+export declare const selectAggDataForIndex: (state: CoreState, index: string, field: string) => any;
+export {};

package/dist/dts/features/guppy/index.d.ts

@@ -0,0 +1,6 @@
+export * from './guppyApi';
+export * from './guppySlice';
+import { downloadFromGuppyToBlob, downloadJSONDataFromGuppy, useGetIndexFields } from './utils';
+import { useDownloadFromGuppyMutation } from './guppyDownloadSlice';
+export * from './types';
+export { downloadFromGuppyToBlob, downloadJSONDataFromGuppy, useDownloadFromGuppyMutation, useGetIndexFields, };

package/dist/dts/features/guppy/tests/downloadFromGuppy.unit.test.d.ts

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

package/dist/dts/features/guppy/types.d.ts

@@ -0,0 +1,33 @@
+import { FilterSet } from '../filters';
+import { Accessibility } from '../../constants';
+export interface BaseGuppyDataRequest {
+    type: string;
+    accessibility?: Accessibility;
+    fields: string[];
+    sort?: string[];
+}
+export interface GuppyDownloadDataParams extends BaseGuppyDataRequest {
+    filter: FilterSet;
+    format: 'json' | 'csv' | 'tsv';
+    rootPath?: string;
+}
+export interface GuppyActionFunctionParams extends Record<string, any> {
+    type: string;
+    accessibility?: Accessibility;
+    fields: string[];
+    sort?: string[];
+    filter: FilterSet;
+}
+export interface GuppyActionParams<T extends Record<string, any>> {
+    parameters: T;
+    onStart?: () => void;
+    onDone?: (blob: Blob) => void;
+    onError?: (error: Error) => void;
+    onAbort?: () => void;
+    signal?: AbortSignal;
+}
+export interface GuppyDownloadActionFunctionParams extends GuppyDownloadDataParams {
+    filename: string;
+}
+export type GuppyActionFunction<T extends Record<string, any>> = (args: GuppyActionParams<T>) => void;
+export type DownloadFromGuppyParams = GuppyActionParams<GuppyDownloadDataParams>;

package/dist/dts/features/guppy/utils.d.ts

@@ -0,0 +1,28 @@
+import { DownloadFromGuppyParams } from './types';
+/**
+ * Represents a configuration for making a fetch request.
+ *
+ * @typedef {Object} FetchConfig
+ * @property {string} method - The HTTP method to use for the request.
+ * @property {Object<string, string>} headers - The headers to include in the request.
+ * @property {string} body - The request body.
+ */
+export type FetchConfig = {
+    method: string;
+    headers: Record<string, string>;
+    body: string;
+};
+/**
+ * Downloads a file from Guppy using the provided parameters.
+ * It will optionally convert the data to the specified format.
+ *
+ * @param {DownloadFromGuppyParams} parameters - The parameters to use for the download request.
+ * @param onStart - The function to call when the download starts.
+ * @param onDone - The function to call when the download is done.
+ * @param onError - The function to call when the download fails.
+ * @param onAbort - The function to call when the download is aborted.
+ * @param signal - AbortSignal to use for the request.
+ */
+export declare const downloadFromGuppyToBlob: ({ parameters, onStart, onDone, onError, onAbort, signal, }: DownloadFromGuppyParams) => Promise<void>;
+export declare const downloadJSONDataFromGuppy: ({ parameters, onAbort, signal, }: DownloadFromGuppyParams) => Promise<any>;
+export declare const useGetIndexFields: (index: string) => any;

package/dist/dts/features/metadata/index.d.ts

@@ -0,0 +1,3 @@
+import { useGetAggMDSQuery, useGetMDSQuery, useGetTagsQuery, useGetDataQuery, useGetCrosswalkDataQuery, useLazyGetCrosswalkDataQuery, useGetIndexAggMDSQuery, type MetadataPaginationParams, type MetadataRequestParams, type MetadataResponse } from './metadataSlice';
+import { type CrosswalkEntry, type CrosswalkInfo, type IndexedMetadataFilters } from './types';
+export { type MetadataPaginationParams, type MetadataRequestParams, type MetadataResponse, type CrosswalkEntry, type CrosswalkInfo, type IndexedMetadataFilters, useGetAggMDSQuery, useGetMDSQuery, useGetTagsQuery, useGetDataQuery, useGetCrosswalkDataQuery, useLazyGetCrosswalkDataQuery, useGetIndexAggMDSQuery, };

package/dist/dts/features/metadata/metadataSlice.d.ts

@@ -0,0 +1,56 @@
+import { JSONObject } from '../../types';
+import { CrosswalkInfo, IndexedMetadataFilters } from './types';
+export interface Metadata {
+    readonly entries: Array<Record<string, unknown>>;
+}
+export type CrosswalkArray = Array<CrosswalkInfo>;
+interface ToMapping {
+    id: string;
+    dataPath: string[];
+}
+interface CrossWalkParams {
+    readonly ids: string[];
+    readonly toPaths: Array<ToMapping>;
+}
+export interface MetadataResponse {
+    data: Array<JSONObject>;
+    hits: number;
+}
+export interface MetadataPaginationParams {
+    pageSize: number;
+    offset: number;
+}
+export interface MetadataRequestParams extends MetadataPaginationParams {
+    guidType: string;
+    studyField: string;
+}
+interface IndexedMetadataRequestParams extends MetadataRequestParams {
+    indexKeys: Array<string>;
+    filterEmpty?: IndexedMetadataFilters;
+}
+/**
+ * Defines metadataApi service using a base URL and expected endpoints. Derived from gen3Api core API.
+ *
+ * @param endpoints - Defines endpoints used in discovery page
+ *  @param getAggMDS - Queries aggregate metadata service
+ *    @see https://github.com/uc-cdis/metadata-service/blob/master/docs/agg_mds.md
+ *    @see https://petstore.swagger.io/?url=https://raw.githubusercontent.com/uc-cdis/metadata-service/master/docs/openapi.yaml#/Aggregate/get_aggregate_metadata_aggregate_metadata_get
+ *  @param getMDS - Queries normal metadata service
+ *    @see https://petstore.swagger.io/?url=https://raw.githubusercontent.com/uc-cdis/metadata-service/master/docs/openapi.yaml#/Query/search_metadata_metadata_get
+ *  @param getIndexAggMDS - queries the Aggregate Metadata service and returns all common passed in indexKeys
+ *  @param getTags - Probably refering to Aggregate metadata service summary statistics query
+ *    @see https://petstore.swagger.io/?url=https://raw.githubusercontent.com/uc-cdis/metadata-service/master/docs/openapi.yaml#/Aggregate/get_aggregate_tags_aggregate_tags_get
+ *  @param getData - Looks like a duplicate of getMDS handler. unused in ./frontend package
+ *  @param getCrosswalkData - Maps ids from one source to another
+ * @returns: A guppy download API for fetching bulk metadata
+ */
+export declare const metadataApi: import("@reduxjs/toolkit/dist/query").Api<import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, {
+    getAggMDS: import("@reduxjs/toolkit/dist/query").QueryDefinition<MetadataRequestParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, MetadataResponse, "gen3Services">;
+    getIndexAggMDS: import("@reduxjs/toolkit/dist/query").QueryDefinition<IndexedMetadataRequestParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, MetadataResponse, "gen3Services">;
+    getMDS: import("@reduxjs/toolkit/dist/query").QueryDefinition<MetadataRequestParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, MetadataResponse, "gen3Services">;
+    getTags: import("@reduxjs/toolkit/dist/query").QueryDefinition<string, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, Metadata, "gen3Services">;
+    getData: import("@reduxjs/toolkit/dist/query").QueryDefinition<string, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, Metadata, "gen3Services">;
+    getCrosswalkData: import("@reduxjs/toolkit/dist/query").QueryDefinition<CrossWalkParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, CrosswalkArray, "gen3Services">;
+}, "gen3Services", never, keyof import("@reduxjs/toolkit/dist/query").ApiModules<any, any, any, any>>;
+export declare const useGetAggMDSQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<MetadataRequestParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, MetadataResponse, "gen3Services">>, useGetMDSQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<MetadataRequestParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, MetadataResponse, "gen3Services">>, useGetTagsQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<string, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, Metadata, "gen3Services">>, useGetDataQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<string, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, Metadata, "gen3Services">>, useGetCrosswalkDataQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<CrossWalkParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, CrosswalkArray, "gen3Services">>, useLazyGetCrosswalkDataQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseLazyQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<CrossWalkParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, CrosswalkArray, "gen3Services">>, useGetIndexAggMDSQuery: import("@reduxjs/toolkit/dist/query/react/buildHooks").UseQuery<import("@reduxjs/toolkit/dist/query").QueryDefinition<IndexedMetadataRequestParams, import("@reduxjs/toolkit/dist/query").BaseQueryFn<string | import("@reduxjs/toolkit/dist/query").FetchArgs, unknown, import("@reduxjs/toolkit/dist/query").FetchBaseQueryError, {}, import("@reduxjs/toolkit/dist/query").FetchBaseQueryMeta>, never, MetadataResponse, "gen3Services">>;
+export {};

package/dist/dts/features/metadata/types.d.ts

@@ -0,0 +1,12 @@
+export interface CrosswalkEntry {
+    fromId: string;
+    matches: Record<string, string | undefined>;
+}
+export interface IndexedMetadataFilters {
+    limit: number;
+    keys: string[];
+}
+export interface CrosswalkInfo {
+    readonly from: string;
+    readonly to: Record<string, string>;
+}

package/dist/dts/features/modals/index.d.ts

@@ -0,0 +1,2 @@
+import { Modals, showModal, hideModal, selectCurrentModal, selectCurrentMessage } from './modalsSlice';
+export { Modals, showModal, hideModal, selectCurrentModal, selectCurrentMessage, };