Implement load() to handle JSON fetching and object creation.

README.md

@@ -48,13 +48,11 @@ const fetch_range = async (path, start, end) => {
 };
 ```
 
-Once that's done, we use the **wobbegong.js** library to set up our interface to the SummarizedExperiment:
+Once that's done, we use the **wobbegong.js** library to load the interface to the SummarizedExperiment:
 
 ```js
 import * as wob from "wobbegong";
-const se_summary = await fetch_json("my_dataset/summary.json");
-const se = new wob.SummarizedExperiment(se_summary, "my_dataset", fetch_json, fetch_range)
-
+const se = await wob.load("my_dataset", fetch_json, fetch_range);
 se.numberOfRows();
 se.numberOfColumns();
 se.isSingleCellExperiment();

package.json

@@ -4,7 +4,7 @@
     "name": "wobbegong",
     "description": "Retrieving parts of a SummarizedExperiment via HTTP range requests.",
     "license": "MIT",
-    "version": "0.1.1",
+    "version": "0.1.2",
     "keywords": [
         "single-cell",
         "scRNA-seq",

src/index.js

@@ -3,3 +3,4 @@ export * from "./DataFrame.js";
 export * from "./Matrix.js";
 export * from "./ReducedDimensionResult.js";
 export * from "./SummarizedExperiment.js";
+export * from "./load.js";

src/load.js

@@ -0,0 +1,27 @@
+import { SummarizedExperiment } from "./SummarizedExperiment.js";
+import { DataFrame } from "./DataFrame.js";
+
+/**
+ * Load an interface to a SummarizedExperiment or a DataFrame.
+ *
+ * @param {string} path - Path to a directory containing a SummarizedExperiment or DataFrame.
+ * This may be a relative or absolute path, depending on how the files are hosted.
+ * @param {function} fetch_json - A function that accepts `path`, a path to a file inside `path`.
+ * It should retrieve the contents of `path` and load them as a JSON object.
+ * It may also return a promise that resolves to such an object.
+ * @param {function} fetch_range - A function that accepts `file` (a path to a file inside `path`), `start` and `end`.
+ * It should retrieve bytes from `path` in the interval `[start, end)` and return a Uint8Array containing those bytes.
+ * It may also return a promise that resolves to such a Uint8Array.
+ *
+ * @return {DataFrame|SummarizedExperiment} Interface to a {@link DataFrame} or {@link SummarizedExperiment},
+ * depending on the object at `path`.
+ */
+export async function load(path, load_json, load_range) {
+    const summary = await load_json(path + "/summary.json");
+    if (summary.object == "data_frame") {
+        return new DataFrame(summary, path, load_range);
+    } else if ([ "summarized_experiment", "single_cell_experiment"].indexOf(summary.object) >= 0) {
+        return new SummarizedExperiment(summary, path, load_json, load_range)
+    }
+    throw new Error("unknown object type '" + summary.object + "' at path '" + path + "'");
+}

tests/load.test.js

@@ -0,0 +1,21 @@
+import * as wob from "../src/index.js";
+import { localFetchRange, localFetchJson } from "./utils.js";
+import * as fs from "fs";
+import * as p from "path";
+import * as u from "url";
+
+test("load works for SummarizedExperiments", async () => {
+    const path = p.join(p.dirname(u.fileURLToPath(import.meta.url)), "mock-files", "full");
+    const my_se = await wob.load(path, localFetchJson, localFetchRange);
+    expect(my_se instanceof wob.SummarizedExperiment).toBe(true);
+    expect(my_se.numberOfRows()).toEqual(50);
+    expect(my_se.numberOfColumns()).toEqual(20);
+})
+
+test("load works for DataFrames", async () => {
+    const path = p.join(p.dirname(u.fileURLToPath(import.meta.url)), "mock-files", "full", "column_data");
+    const my_df = await wob.load(path, localFetchJson, localFetchRange);
+    expect(my_df instanceof wob.DataFrame).toBe(true);
+    expect(my_df.numberOfRows()).toEqual(20);
+    expect(my_df.numberOfColumns()).toEqual(4);
+})