@oceanum/datamesh 0.1.0 → 0.2.0

package/dist/lib/connector.d.ts

@@ -1,12 +1,14 @@
-import { Datasource } from "./datasource";
-import { IQuery } from "./query";
-import { Dataset, DatameshStore } from "./datamodel";
+import { Datasource } from './datasource';
+import { IQuery } from './query';
+import { Dataset, DatameshStore, TempStore } from './datamodel';
 /**
  * Datamesh connector class.
  *
  * All datamesh operations are methods of this class.
+ *
  */
-declare class Connector {
+export declare class Connector {
+    static LAZY_LOAD_SIZE: number;
     private _token;
     private _proto;
     private _host;
@@ -15,14 +17,13 @@ declare class Connector {
     /**
      * Datamesh connector constructor
      *
-     * @param token - Your datamesh access token. Defaults to environment variable DATAMESH_TOKEN if defined else $DATAMESH_TOKEN
+     * @param token - Your datamesh access token. Defaults to environment variable DATAMESH_TOKEN is defined else as literal string "DATAMESH_TOKEN". DO NOT put your Datamesh token directly into public facing browser code.
      * @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.
+     * @param _gateway - URL of gateway service. Defaults to "https://gateway.datamesh.oceanum.io".
      *
      * @throws {Error} - If a valid token is not provided.
      */
-    constructor(token?: string, service?: string, gateway?: string);
+    constructor(token?: string, service?: string, _gateway?: string);
     /**
      * Get datamesh host.
      *
@@ -55,10 +56,9 @@ declare class Connector {
      *
      * @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>;
+    private dataRequest;
     /**
      * Stage a query to the datamesh.
      *
@@ -70,11 +70,9 @@ declare class Connector {
      * 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>;
+    query(query: IQuery): Promise<Dataset</** @ignore */ /** @ignore */ DatameshStore | TempStore> | null>;
     /**
      * Get a datasource instance from the datamesh.
      *
@@ -88,10 +86,8 @@ declare class Connector {
      *
      * @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.
+     * @returns The dataset.
      */
-    loadDatasource(datasourceId: string, parameters?: Record<string, string | number>): Promise<Dataset<DatameshStore> | null>;
+    loadDatasource(datasourceId: string, parameters?: Record<string, string | number>): Promise<Dataset</** @ignore */ DatameshStore> | null>;
 }
-export default Connector;
 //# sourceMappingURL=connector.d.ts.map

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

@@ -1 +1 @@
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package/dist/lib/datamodel.d.ts

@@ -1,17 +1,18 @@
-import { CachedHTTPStore } from "./zarr";
+import { DataType, Listable, Location } from '@zarrita/core';
+import { Mutable, AsyncReadable } from '@zarrita/storage';
+import { Slice } from '@zarrita/indexing';
+import { Table } from 'apache-arrow';
+import { Geometry, FeatureCollection } from 'geojson';
+import { Schema, Coordinates } from './datasource';
 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;
+export type ATypedArray = Int8Array | Int16Array | Int32Array | BigInt64Array | Uint8Array | Uint16Array | Uint32Array | BigUint64Array | Float32Array | Float64Array;
+export type Scalar = string | number | boolean;
+export type NDArray = Scalar[] | Scalar[][] | Scalar[][][] | Scalar[][][][] | ATypedArray[] | ATypedArray[][] | ATypedArray[][][] | ATypedArray[][][][];
+export type Data = NDArray | ATypedArray | Scalar;
 /**
  * Represents a data variable.
  */
-export declare type DataVariable = {
+export type DataVariable = {
     /**
      * Attributes of the variable.
      */
@@ -29,12 +30,16 @@ export declare type DataVariable = {
      */
     data?: Data;
 };
-export declare type DatameshStore = Location<Listable<AsyncReadable>>;
-export declare type TempStore = Location<Mutable>;
+/** @ignore */
+export type DatameshStore = Location<Listable<AsyncReadable>>;
+/** @ignore */
+export type TempStore = Location<Mutable>;
 /**
  * Represents a data variable within a dataset.
  */
-export declare class DataVar<DType extends DataType, S extends TempStore | DatameshStore> {
+export declare class DataVar<
+/** @ignore */
+DType extends DataType, S extends TempStore | DatameshStore> {
     /**
      * Creates an instance of DataVar.
      * @param id - The identifier for the data variable.
@@ -58,36 +63,39 @@ export declare class DataVar<DType extends DataType, S extends TempStore | Datam
  * Represents a dataset with dimensions, data variables, and attributes.
  * Implements the DatasetApi interface.
  */
-export declare class Dataset<S extends DatameshStore | TempStore> {
+export declare class Dataset</** @ignore */ 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.
+     * @param coordinates - The coordinates map 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>;
+    coordinates: Coordinates;
     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);
+    constructor(dims: Record<string, number>, data_vars: S extends TempStore ? Record<string, DataVar<DataType, TempStore>> : Record<string, DataVar<DataType, DatameshStore>>, attrs: Record<string, unknown>, coordinates: Coordinates, root: S);
     /**
      * Creates a Dataset instance from a Zarr store.
-     * @param gateway - The URL of the datamesh gateway.
+     * @param url - 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>>>>;
+    static zarr(url: string, authHeaders: Record<string, string>, parameters?: Record<string, string | number>, chunks?: string, downsample?: Record<string, number>): Promise<Dataset<DatameshStore>>;
+    static fromArrow(data: Table, coordmap: Coordinates): Promise<Dataset<TempStore>>;
     /**
      * 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>;
+    static init(datasource: Schema, coordinates?: Coordinates): Promise<Dataset<TempStore>>;
     /**
-     * Converts the data variables into a dataframe format.
+     * Converts the dataset 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.
@@ -95,14 +103,36 @@ export declare class Dataset<S extends DatameshStore | TempStore> {
      * @remarks
      * This method iterates over the data variables, retrieves their dimensions and data,
      * and then flattens the data into a dataframe structure.
+     * Time coordinates are converted to IDO8601 format.
+     * BigInt datatypes are coerced to number.
      *
      * @example
      * ```typescript
-     * const dataframe = await instance.to_dataframe();
+     * const dataframe = await instance.asDataframe();
      * console.log(dataframe);
      * ```
      */
-    to_dataframe(): Promise<Record<string, unknown>[]>;
+    asDataframe(): Promise<Record<string, unknown>[]>;
+    /**
+     * Converts the dataset into a GeoJSON Feature.
+     * @param geometry - Optional GeoJSON geometry to apply to all records, otherwise geometry column is required. Will override geometry column if present.
+     *
+     * @returns {Promise<FeatureCollection>} A promise that resolves to an array of records,
+     * where each record represents a row in the dataframe.
+     *
+     * @throws Will throw an error if no geometry is found in data or as a parameter
+     *
+     * @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.asDataframe();
+     * console.log(dataframe);
+     * ```
+     */
+    asGeojson(geom?: Geometry): Promise<FeatureCollection>;
     /**
      * Asynchronously assigns data to a variable in the dataset.
      *
@@ -110,14 +140,13 @@ export declare class Dataset<S extends DatameshStore | TempStore> {
      * @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 coordinates - Optional. A record of coordinates to be associated with 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>;
+    assign(varid: string, dims: string[], data: Data, attrs?: Record<string, unknown>, coordinates?: Coordinates, chunks?: number[]): Promise<void>;
 }
-export {};
 //# sourceMappingURL=datamodel.d.ts.map

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package/dist/lib/datasource.d.ts

@@ -1,36 +1,15 @@
-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 = {
+import { Geometry } from 'geojson';
+import { default as dayjs } from 'dayjs';
+import { default as duration } from 'dayjs/plugin/duration';
+import { DataVariable } from './datamodel';
+export type Coordinate = "s" | "e" | "b" | "c" | "q" | "n" | "m" | "t" | "z" | "y" | "x" | "g" | "f" | "d" | "i" | "j" | "k";
+export type Coordinates = {
     [key in Coordinate]?: string;
 };
 /**
  * Represents the schema of a data source.
  */
-export declare type Schema = {
+export type Schema = {
     /**
      * Attributes of the schema.
      */
@@ -51,7 +30,7 @@ export declare type Schema = {
 /**
  * Represents a data source.
  */
-export declare type Datasource = {
+export type Datasource = {
     /**
      * Unique identifier for the data source.
      */
@@ -114,5 +93,4 @@ export declare type Datasource = {
     last_modified?: Date;
     driver: string;
 };
-export {};
 //# sourceMappingURL=datasource.d.ts.map

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

@@ -1 +1 @@
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package/dist/lib/observe.d.ts

@@ -0,0 +1,3 @@
+/** @ignore */
+export declare function measureTime(target: any, propertyKey: string, descriptor: PropertyDescriptor): PropertyDescriptor;
+//# sourceMappingURL=observe.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"observe.d.ts","sourceRoot":"","sources":["../../src/lib/observe.ts"],"names":[],"mappings":"AAAA,cAAc;AACd,wBAAgB,WAAW,CACzB,MAAM,EAAE,GAAG,EACX,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,kBAAkB,sBAgB/B"}

package/dist/lib/query.d.ts

@@ -1,74 +1,47 @@
-import { Feature } from "geojson";
-import dayjs from "dayjs";
-import duration from "dayjs/plugin/duration";
+import { Feature } from 'geojson';
+import { default as dayjs } from 'dayjs';
+import { default as duration } from 'dayjs/plugin/duration';
 /**
- * GeoFilterType enum representing types of geofilters.
+ * GeoFilterType type representing types of geofilters.
  */
-declare enum GeoFilterType {
-    Feature = "feature",
-    Bbox = "bbox"
-}
+export type GeoFilterType = "feature" | "bbox";
 /**
- * GeoFilterInterp enum representing interpolation methods for geofilters.
+ * GeoFilterInterp type representing interpolation methods for geofilters.
  */
-declare enum GeoFilterInterp {
-    Nearest = "nearest",
-    Linear = "linear"
-}
+export type GeoFilterInterp = "nearest" | "linear";
 /**
- * LevelFilterInterp enum representing interpolation methods for level filters.
+ * LevelFilterInterp type representing interpolation methods for level filters.
  */
-declare enum LevelFilterInterp {
-    Nearest = "nearest",
-    Linear = "linear"
-}
+export type LevelFilterInterp = "nearest" | "linear";
 /**
- * TimeFilterType enum representing types of time filters.
+ * TimeFilterType type representing types of time filters.
  */
-declare enum TimeFilterType {
-    Range = "range",
-    Series = "series",
-    Trajectory = "trajectory"
-}
+export type TimeFilterType = "range" | "series" | "trajectory";
 /**
- * LevelFilterType enum representing types of level filters.
+ * LevelFilterType type representing types of level filters.
  */
-declare enum LevelFilterType {
-    Range = "range",
-    Series = "series"
-}
+export type LevelFilterType = "range" | "series";
 /**
- * ResampleType enum representing types of resampling.
+ * ResampleType type representing types of resampling.
  */
-declare enum ResampleType {
-    Mean = "mean",
-    Nearest = "nearest",
-    Slinear = "linear"
-}
+export type ResampleType = "mean" | "nearest" | "linear";
 /**
- * AggregateOps enum representing aggregation operations.
+ * AggregateOps type representing aggregation operations.
  */
-declare enum AggregateOps {
-    Mean = "mean",
-    Min = "min",
-    Max = "max",
-    Std = "std",
-    Sum = "sum"
-}
+export type AggregateOps = "mean" | "min" | "max" | "std" | "sum";
 /**
- * Container enum representing data container types.
+ * Container type representing data container types.
  */
-declare enum Container {
-    GeoDataFrame = "geodataframe",
-    DataFrame = "dataframe",
-    Dataset = "dataset"
+export type Container = "geodataframe" | "dataframe" | "dataset";
+export interface GeoFilterFeature extends Omit<Feature, "properties"> {
+    properties?: Record<string, unknown> | undefined;
 }
 /**
  * GeoFilter type representing a spatial subset or interpolation.
  */
-export declare type GeoFilter = {
+export type GeoFilter = {
     type: GeoFilterType;
-    geom: Array<number[]> | Feature;
+    geom: Array<number[]> | GeoFilterFeature;
     interp?: GeoFilterInterp;
     resolution?: number;
     alltouched?: boolean;
@@ -76,7 +49,7 @@ export declare type GeoFilter = {
 /**
  * LevelFilter type representing a vertical subset or interpolation.
  */
-declare type LevelFilter = {
+export type LevelFilter = {
     type: LevelFilterType;
     levels: Array<number | null>;
     interp?: LevelFilterInterp;
@@ -84,7 +57,7 @@ declare type LevelFilter = {
 /**
  * TimeFilter type representing a temporal subset or interpolation.
  */
-export declare type TimeFilter = {
+export type TimeFilter = {
     type?: TimeFilterType;
     times: Array<Date | dayjs.Dayjs | duration.Duration | string>;
     resolution?: string;
@@ -93,7 +66,7 @@ export declare type TimeFilter = {
 /**
  * Aggregate type representing aggregation operations.
  */
-declare type Aggregate = {
+export type Aggregate = {
     operations: AggregateOps[];
     spatial?: boolean;
     temporal?: boolean;
@@ -101,7 +74,7 @@ declare type Aggregate = {
 /**
  * CoordSelector type representing coordinate selection.
  */
-declare type CoordSelector = {
+export type CoordSelector = {
     coord: string;
     values: Array<string | number>;
 };
@@ -125,13 +98,15 @@ export interface IQuery {
 /**
  * Stage interface representing the result of staging a query.
  */
-export declare type Stage = {
+/** @ignore */
+export type Stage = {
     query: Query;
     qhash: string;
     formats: string[];
     size: number;
     dlen: number;
     coordmap: Record<string, string>;
+    coordkeys: Record<string, string>;
     container: Container;
     sig: string;
 };
@@ -157,5 +132,4 @@ export declare class Query implements IQuery {
      */
     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

@@ -1,5 +1,5 @@
-import { UseStore } from "idb-keyval";
-import { AsyncReadable, AsyncMutable, AbsolutePath } from "@zarrita/storage";
+import { UseStore } from 'idb-keyval';
+import { AsyncReadable, AsyncMutable, AbsolutePath } from '@zarrita/storage';
 export declare class CachedHTTPStore implements AsyncReadable {
     cache: UseStore | undefined;
     url: string;