@oceanum/datamesh 0.1.0

package/README.md

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+# datamesh
+
+This library was generated with [Nx](https://nx.dev).
+
+## Building
+
+Run `nx build datamesh` to build the library.
+
+## Running unit tests
+
+Run `nx test datamesh` to execute the unit tests via [Vitest](https://vitest.dev/).

package/dist/index.d.ts

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+export * from "./lib/connector";
+export * from "./lib/datasource";
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

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package/dist/lib/connector.d.ts

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+import { Datasource } from "./datasource";
+import { IQuery } from "./query";
+import { Dataset, DatameshStore } from "./datamodel";
+/**
+ * Datamesh connector class.
+ *
+ * All datamesh operations are methods of this class.
+ */
+declare class Connector {
+    private _token;
+    private _proto;
+    private _host;
+    private _authHeaders;
+    private _gateway;
+    /**
+     * Datamesh connector constructor
+     *
+     * @param token - Your datamesh access token. Defaults to environment variable DATAMESH_TOKEN if defined else $DATAMESH_TOKEN
+     * @param service - URL of datamesh service. Defaults to environment variable DATAMESH_SERVICE or "https://datamesh.oceanum.io".
+     * @param gateway - URL of gateway service. Defaults to "https://gateway.<datamesh_service_domain>".
+     * @param user - Organisation user name for the datamesh connection. Defaults to None.
+     *
+     * @throws {Error} - If a valid token is not provided.
+     */
+    constructor(token?: string, service?: string, gateway?: string);
+    /**
+     * Get datamesh host.
+     *
+     * @returns The datamesh server host.
+     */
+    get host(): string;
+    /**
+     * Check the status of the metadata server.
+     *
+     * @returns True if the metadata server is up, false otherwise.
+     */
+    status(): Promise<boolean>;
+    /**
+     * Validate response from server.
+     *
+     * @param response - The response object to validate.
+     * @throws {Error} - If the response contains an error status code.
+     */
+    private validateResponse;
+    /**
+     * Request metadata from datamesh.
+     *
+     * @param datasourceId - The ID of the datasource to request.
+     * @param params - Additional parameters for the request.
+     * @returns The response from the server.
+     */
+    private metadataRequest;
+    /**
+     * Request data from datamesh.
+     *
+     * @param datasourceId - The ID of the datasource to request.
+     * @param dataFormat - The format of the requested data. Defaults to "application/json".
+     * @param cache - Whether to cache the response. Defaults to false.
+     * @returns The path to the cached file.
+     */
+    dataRequest(datasourceId: string, dataFormat?: string): Promise<Blob>;
+    /**
+     * Stage a query to the datamesh.
+     *
+     * @param query - The query to stage.
+     * @returns The staged response.
+     */
+    private stageRequest;
+    /**
+     * Execute a query to the datamesh.
+     *
+     * @param query - The query to execute.
+     * @param useDask - Whether to use Dask for execution. Defaults to false.
+     * @param cacheTimeout - The cache timeout for the query. Defaults to 0.
+     * @returns The response from the server.
+     */
+    query(query: IQuery): Promise<Dataset<DatameshStore> | null>;
+    /**
+     * Get a datasource instance from the datamesh.
+     *
+     * @param datasourceId - Unique datasource ID.
+     * @returns The datasource instance.
+     * @throws {Error} - If the datasource cannot be found or is not authorized.
+     */
+    getDatasource(datasourceId: string): Promise<Datasource>;
+    /**
+     * Load a datasource into the work environment.
+     *
+     * @param datasourceId - Unique datasource ID.
+     * @param parameters - Additional datasource parameters.
+     * @param useDask - Whether to use Dask for loading. Defaults to false.
+     * @returns The datasource container.
+     */
+    loadDatasource(datasourceId: string, parameters?: Record<string, string | number>): Promise<Dataset<DatameshStore> | null>;
+}
+export default Connector;
+//# sourceMappingURL=connector.d.ts.map

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package/dist/lib/datamodel.d.ts

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+import { CachedHTTPStore } from "./zarr";
+import * as zarr from "@zarrita/core";
+import { DataType, Listable, Location } from "@zarrita/core";
+import { Mutable, AsyncReadable } from "@zarrita/storage";
+import { Slice } from "@zarrita/indexing";
+import { Schema } from "./datasource";
+declare type ATypedArray = Int8Array | Int16Array | Int32Array | Uint8Array | Uint16Array | Uint32Array | Float32Array | Float64Array;
+declare type Scalar = string | number | boolean;
+declare type NDArray = Scalar[] | Scalar[][] | Scalar[][][] | Scalar[][][][] | ATypedArray[] | ATypedArray[][] | ATypedArray[][][] | ATypedArray[][][][];
+declare type Data = NDArray | ATypedArray | Scalar;
+/**
+ * Represents a data variable.
+ */
+export declare type DataVariable = {
+    /**
+     * Attributes of the variable.
+     */
+    attrs: Record<string, string | unknown>;
+    /**
+     * Dimensions of the variable
+     *  */
+    dims: string[];
+    /**
+     * Datatype of the variable.
+     */
+    dtype?: string;
+    /**
+     * Data associated with the variable.
+     */
+    data?: Data;
+};
+export declare type DatameshStore = Location<Listable<AsyncReadable>>;
+export declare type TempStore = Location<Mutable>;
+/**
+ * Represents a data variable within a dataset.
+ */
+export declare class DataVar<DType extends DataType, S extends TempStore | DatameshStore> {
+    /**
+     * Creates an instance of DataVar.
+     * @param id - The identifier for the data variable.
+     * @param dims - The dimensions associated with the data variable.
+     * @param attrs - The attributes of the data variable, represented as a record of key-value pairs.
+     * @param arr - The zarr array associated with the data variable.
+     */
+    id: string;
+    dims: string[];
+    attrs: Record<string, unknown>;
+    arr: S extends TempStore ? zarr.Array<DType, Mutable> : zarr.Array<DType, AsyncReadable>;
+    constructor(id: string, dims: string[], attrs: Record<string, unknown>, arr: S extends TempStore ? zarr.Array<DType, Mutable> : zarr.Array<DType, AsyncReadable>);
+    /**
+     * Retrieves the data from the zarr array. If the data is already cached, it returns the cached data.
+     * @param slice - Optional slice parameters to retrieve specific data from the zarr array.
+     * @returns A promise that resolves to the data of the zarr array.
+     */
+    get(slice?: (null | Slice | number)[] | null | undefined): Promise<Data>;
+}
+/**
+ * Represents a dataset with dimensions, data variables, and attributes.
+ * Implements the DatasetApi interface.
+ */
+export declare class Dataset<S extends DatameshStore | TempStore> {
+    /**
+     * Creates an instance of Dataset.
+     * @param dims - The dimensions of the dataset.
+     * @param data_vars - The data variables of the dataset.
+     * @param attrs - The attributes of the dataset.
+     * @param root - The root group of the dataset.
+     */
+    dims: Record<string, number>;
+    data_vars: S extends TempStore ? Record<string, DataVar<DataType, TempStore>> : Record<string, DataVar<DataType, DatameshStore>>;
+    attrs: Record<string, unknown>;
+    root: S;
+    constructor(dims: Record<string, number>, data_vars: S extends TempStore ? Record<string, DataVar<DataType, TempStore>> : Record<string, DataVar<DataType, DatameshStore>>, attrs: Record<string, unknown>, root: S);
+    /**
+     * Creates a Dataset instance from a Zarr store.
+     * @param gateway - The URL of the datamesh gateway.
+     * @param authHeaders - The authentication headers.
+     * @param parameters - Optional parameters for the request.
+     * @param chunks - Optional chunking strategy.
+     * @param downsample - Optional downsampling strategy.
+     * @returns A promise that resolves to a Dataset instance.
+     */
+    static zarr(url: string, authHeaders: Record<string, string>, parameters?: Record<string, string | number>, chunks?: string, downsample?: Record<string, number>): Promise<Dataset<zarr.Location<zarr.Listable<CachedHTTPStore>>>>;
+    /**
+     * Initializes an in memory Dataset instance from a data object.
+     * @param datasource - An object containing id, dimensions, data variables, and attributes.
+     */
+    static init(datasource: Schema): Promise<void>;
+    /**
+     * Converts the data variables into a dataframe format.
+     *
+     * @returns {Promise<Record<string, unknown>[]>} A promise that resolves to an array of records,
+     * where each record represents a row in the dataframe.
+     *
+     * @remarks
+     * This method iterates over the data variables, retrieves their dimensions and data,
+     * and then flattens the data into a dataframe structure.
+     *
+     * @example
+     * ```typescript
+     * const dataframe = await instance.to_dataframe();
+     * console.log(dataframe);
+     * ```
+     */
+    to_dataframe(): Promise<Record<string, unknown>[]>;
+    /**
+     * Asynchronously assigns data to a variable in the dataset.
+     *
+     * @param varid - The identifier for the variable.
+     * @param dims - An array of dimension names corresponding to the data.
+     * @param data - The data to be assigned, which can be a multi-dimensional array.
+     * @param attrs - Optional. A record of attributes to be associated with the variable.
+     * @param dtype - The data type of the variable.
+     * @param chunks - Optional. An array specifying the chunk sizes for the data.
+     
+     * @returns A promise that resolves when the data has been successfully assigned.
+     * @throws Will throw an error if the shape of the data does not match the provided dimensions.
+     * @throws Will throw an error if an existing dimension size does not match the new data.
+     */
+    assign(varid: string, dims: string[], data: Data, attrs?: Record<string, unknown>, chunks?: number[]): Promise<void>;
+}
+export {};
+//# sourceMappingURL=datamodel.d.ts.map

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package/dist/lib/datasource.d.ts

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+import { Geometry } from "geojson";
+import dayjs from "dayjs";
+import duration from "dayjs/plugin/duration";
+import { DataVariable } from "./datamodel";
+/**
+ * Represents a data variable.
+ */
+declare enum Coordinate {
+    "Station" = "s",
+    "Ensemble" = "e",
+    "Raster band" = "b",
+    "Category" = "c",
+    "Quantile" = "q",
+    "Season" = "n",
+    "Month" = "m",
+    "Time" = "t",
+    "Vertical coordinate" = "z",
+    "Horizontal northerly" = "y",
+    "Horizontal easterly" = "x",
+    "Geometry" = "g",
+    "Frequency" = "f",
+    "Direction" = "d",
+    "Coordinate_i" = "i",
+    "Coordinate_j" = "j",
+    "Coordinate_k" = "k"
+}
+declare type Coordinates = {
+    [key in Coordinate]?: string;
+};
+/**
+ * Represents the schema of a data source.
+ */
+export declare type Schema = {
+    /**
+     * Attributes of the schema.
+     */
+    attrs?: Record<string, string | number>;
+    /**
+     * Dimensions of the schema.
+     */
+    dims: Record<string, number>;
+    /**
+     * Coordinates of the schema.
+     */
+    coords?: Record<string, DataVariable>;
+    /**
+     * Data variables of the schema.
+     */
+    data_vars: Record<string, DataVariable>;
+};
+/**
+ * Represents a data source.
+ */
+export declare type Datasource = {
+    /**
+     * Unique identifier for the data source.
+     */
+    id: string;
+    /**
+     * Name of the data source.
+     */
+    name: string;
+    /**
+     * Description of the data source.
+     */
+    description?: string;
+    /**
+     * Parameters associated with the data source.
+     */
+    parameters?: Record<string, unknown>;
+    /**
+     * Geometric representation of the data source.
+     */
+    geom?: Geometry;
+    /**
+     * Start time for the data source.
+     */
+    tstart?: dayjs.Dayjs;
+    /**
+     * End time for the data source.
+     */
+    tend?: dayjs.Dayjs;
+    /**
+     * Forecast time period for the data source.
+     */
+    pforecast?: duration.Duration;
+    /**
+     * Archive time period for the data source.
+     */
+    parchive?: duration.Duration;
+    /**
+     * Tags associated with the data source.
+     */
+    tags?: string[];
+    /**
+     * Additional information about the data source.
+     */
+    info?: Record<string, unknown>;
+    /**
+     * Schema information for the data source.
+     */
+    schema: Schema;
+    /**
+     * Coordinate mappings for the data source.
+     */
+    coordinates: Coordinates;
+    /**
+     * Additional details about the data source.
+     */
+    details?: string;
+    /**
+     * Last modified date of the data source.
+     */
+    last_modified?: Date;
+    driver: string;
+};
+export {};
+//# sourceMappingURL=datasource.d.ts.map

package/dist/lib/datasource.d.ts.map

@@ -0,0 +1 @@
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package/dist/lib/query.d.ts

@@ -0,0 +1,161 @@
+import { Feature } from "geojson";
+import dayjs from "dayjs";
+import duration from "dayjs/plugin/duration";
+/**
+ * GeoFilterType enum representing types of geofilters.
+ */
+declare enum GeoFilterType {
+    Feature = "feature",
+    Bbox = "bbox"
+}
+/**
+ * GeoFilterInterp enum representing interpolation methods for geofilters.
+ */
+declare enum GeoFilterInterp {
+    Nearest = "nearest",
+    Linear = "linear"
+}
+/**
+ * LevelFilterInterp enum representing interpolation methods for level filters.
+ */
+declare enum LevelFilterInterp {
+    Nearest = "nearest",
+    Linear = "linear"
+}
+/**
+ * TimeFilterType enum representing types of time filters.
+ */
+declare enum TimeFilterType {
+    Range = "range",
+    Series = "series",
+    Trajectory = "trajectory"
+}
+/**
+ * LevelFilterType enum representing types of level filters.
+ */
+declare enum LevelFilterType {
+    Range = "range",
+    Series = "series"
+}
+/**
+ * ResampleType enum representing types of resampling.
+ */
+declare enum ResampleType {
+    Mean = "mean",
+    Nearest = "nearest",
+    Slinear = "linear"
+}
+/**
+ * AggregateOps enum representing aggregation operations.
+ */
+declare enum AggregateOps {
+    Mean = "mean",
+    Min = "min",
+    Max = "max",
+    Std = "std",
+    Sum = "sum"
+}
+/**
+ * Container enum representing data container types.
+ */
+declare enum Container {
+    GeoDataFrame = "geodataframe",
+    DataFrame = "dataframe",
+    Dataset = "dataset"
+}
+/**
+ * GeoFilter type representing a spatial subset or interpolation.
+ */
+export declare type GeoFilter = {
+    type: GeoFilterType;
+    geom: Array<number[]> | Feature;
+    interp?: GeoFilterInterp;
+    resolution?: number;
+    alltouched?: boolean;
+};
+/**
+ * LevelFilter type representing a vertical subset or interpolation.
+ */
+declare type LevelFilter = {
+    type: LevelFilterType;
+    levels: Array<number | null>;
+    interp?: LevelFilterInterp;
+};
+/**
+ * TimeFilter type representing a temporal subset or interpolation.
+ */
+export declare type TimeFilter = {
+    type?: TimeFilterType;
+    times: Array<Date | dayjs.Dayjs | duration.Duration | string>;
+    resolution?: string;
+    resample?: ResampleType;
+};
+/**
+ * Aggregate type representing aggregation operations.
+ */
+declare type Aggregate = {
+    operations: AggregateOps[];
+    spatial?: boolean;
+    temporal?: boolean;
+};
+/**
+ * CoordSelector type representing coordinate selection.
+ */
+declare type CoordSelector = {
+    coord: string;
+    values: Array<string | number>;
+};
+/**
+ * Query interface representing a Datamesh query.
+ */
+export interface IQuery {
+    datasource: string;
+    parameters?: Record<string, number | string | number[] | string[]>;
+    description?: string;
+    variables?: string[];
+    timefilter?: TimeFilter;
+    geofilter?: GeoFilter;
+    levelfilter?: LevelFilter;
+    coordfilter?: CoordSelector[];
+    crs?: string | number;
+    aggregate?: Aggregate;
+    limit?: number;
+    id?: string;
+}
+/**
+ * Stage interface representing the result of staging a query.
+ */
+export declare type Stage = {
+    query: Query;
+    qhash: string;
+    formats: string[];
+    size: number;
+    dlen: number;
+    coordmap: Record<string, string>;
+    container: Container;
+    sig: string;
+};
+/**
+ * Query class representing a Datamesh query.
+ */
+export declare class Query implements IQuery {
+    datasource: string;
+    parameters?: Record<string, number | string | number[] | string[]>;
+    description?: string;
+    variables?: string[];
+    timefilter?: TimeFilter;
+    geofilter?: GeoFilter;
+    levelfilter?: LevelFilter;
+    coordfilter?: CoordSelector[];
+    crs?: string | number;
+    aggregate?: Aggregate;
+    limit?: number;
+    id?: string;
+    constructor(query: IQuery);
+    /**
+     * Returns the query as a JSON object.
+     */
+    toJSON(): Record<string, unknown>;
+}
+export {};
+//# sourceMappingURL=query.d.ts.map

package/dist/lib/query.d.ts.map

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package/dist/lib/zarr.d.ts

@@ -0,0 +1,20 @@
+import { UseStore } from "idb-keyval";
+import { AsyncReadable, AsyncMutable, AbsolutePath } from "@zarrita/storage";
+export declare class CachedHTTPStore implements AsyncReadable {
+    cache: UseStore | undefined;
+    url: string;
+    cache_prefix: string;
+    fetchOptions: RequestInit;
+    constructor(root: string, authHeaders: Record<string, string>, parameters?: Record<string, string | number>, chunks?: string, downsample?: Record<string, number>, nocache?: boolean);
+    get(item: string, options?: RequestInit, retry?: number): Promise<Uint8Array | undefined>;
+}
+export declare class IDBStore implements AsyncMutable {
+    root: string;
+    cache: UseStore;
+    constructor(root: string);
+    get(key: AbsolutePath): Promise<Uint8Array | undefined>;
+    has(key: AbsolutePath): Promise<boolean>;
+    set(key: AbsolutePath, value: Uint8Array): Promise<void>;
+    delete(key: AbsolutePath): Promise<void>;
+}
+//# sourceMappingURL=zarr.d.ts.map

package/dist/lib/zarr.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"zarr.d.ts","sourceRoot":"","sources":["../../src/lib/zarr.ts"],"names":[],"mappings":"AAAA,OAAO,EAKL,QAAQ,EACT,MAAM,YAAY,CAAC;AAEpB,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAM7E,qBAAa,eAAgB,YAAW,aAAa;IACnD,KAAK,EAAE,QAAQ,GAAG,SAAS,CAAC;IAC5B,GAAG,EAAE,MAAM,CAAC;IACZ,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,WAAW,CAAC;gBAExB,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACnC,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC,EAC5C,MAAM,CAAC,EAAE,MAAM,EACf,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACnC,OAAO,CAAC,EAAE,OAAO;IAiBb,GAAG,CACP,IAAI,EAAE,MAAM,EACZ,OAAO,CAAC,EAAE,WAAW,EACrB,KAAK,SAAI,GACR,OAAO,CAAC,UAAU,GAAG,SAAS,CAAC;CAsCnC;AAED,qBAAa,QAAS,YAAW,YAAY;IAExB,IAAI,EAAE,MAAM;IAD/B,KAAK,EAAE,QAAQ,CAAC;gBACG,IAAI,EAAE,MAAM;IAIzB,GAAG,CAAC,GAAG,EAAE,YAAY,GAAG,OAAO,CAAC,UAAU,GAAG,SAAS,CAAC;IAQvD,GAAG,CAAC,GAAG,EAAE,YAAY,GAAG,OAAO,CAAC,OAAO,CAAC;IAIxC,GAAG,CAAC,GAAG,EAAE,YAAY,EAAE,KAAK,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC;IAIxD,MAAM,CAAC,GAAG,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC;CAG/C"}

package/dist/test/fixtures.d.ts

@@ -0,0 +1,8 @@
+/// <reference lib="dom" />
+import { Schema } from "../lib/datasource";
+export declare const dataset: Schema;
+export declare const datameshTest: import("@vitest/runner/dist/tasks-K5XERDtv").e<{
+    metadata: ({}: {}, use: Function) => Promise<void>;
+    dataset: ({}: {}, use: Function) => Promise<void>;
+}>;
+//# sourceMappingURL=fixtures.d.ts.map

package/dist/test/fixtures.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"fixtures.d.ts","sourceRoot":"","sources":["../../src/test/fixtures.ts"],"names":[],"mappings":";AAGA,OAAO,EAAc,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAkDvD,eAAO,MAAM,OAAO,EAAE,MAerB,CAAC;AAEF,eAAO,MAAM,YAAY;4BACG,QAAQ;2BAsBT,QAAQ;EAqBjC,CAAC"}