Merge pull request #381 from ducku/issues/377-refactor-api-interface

Implement API Interface

src/APIInterface.mjs

@@ -0,0 +1,42 @@
+
+// Interface for handling function called from the tubemap frontend
+// Abstract class expecting different implmentations of the following functions
+// Substituting different subclasses should allow the functions to give the same result 
+export class APIInterface {
+    // Takes in and process a tube map view(viewTarget) from the tubemap container
+    // Expects a object to be returned with the necessary information to draw a tubemap from vg
+    // object should contain keys: graph, gam, region, coloredNodes
+    async getChunkedData(viewTarget) {
+        throw new Error("getChunkedData function not implemented");
+    }
+
+    // Returns files used to determine what options are available in the track picker
+    // Returns object with keys: files, bedFiles
+    async getFilenames() {
+        throw new Error("getFilenames function not implemented");
+    }
+
+    // Takes in a bedfile path or a url pointing to a raw bed file
+    // Returns object with key: bedRegions
+    // bedRegions contains information extrapolated from each line of the bedfile
+    async getBedRegions(bedFile) {
+        throw new Error("getBedRegions function not implemented");
+    }
+
+    // Takes in a graphFile path
+    // Returns object with key: pathNames
+    // Returns pathnames available in a graphfile
+    async getPathNames(graphFile) {
+        throw new Error("getPathNames function not implemented");
+    }
+
+    // Expects a bed file(or url) and a chunk name
+    // Attempts to download tracks associated with the chunk name from the bed file if it is a URL
+    // Returns object with key: tracks
+    // Returns tracks found from local directories as a tracks object
+    async getChunkTracks(bedFile, chunk) {
+        throw new Error("getChunkTracks function not implemented");
+    }
+}
+
+export default APIInterface;

src/App.js

@@ -14,6 +14,7 @@ import Footer from "./components/Footer";
 import { dataOriginTypes } from "./enums";
 import "./config-client.js";
 import { config } from "./config-global.mjs";
+import ServerAPI from "./ServerAPI.mjs";
 
 const EXAMPLE_TRACKS = [
   // Fake tracks for the generated examples.
@@ -46,6 +47,8 @@ class App extends Component {
   constructor(props) {
     super(props);
 
+    this.APIInterface = new ServerAPI(props.apiUrl);
+
     console.log('App component starting up with API URL: ' + props.apiUrl)
 
     // Set defaultViewTarget to either URL params (if present) or the first example
@@ -186,12 +189,14 @@ class App extends Component {
           apiUrl={this.props.apiUrl}
           defaultViewTarget={this.defaultViewTarget}
           getCurrentViewTarget={this.getCurrentViewTarget}
+          APIInterface={this.APIInterface}
         />
         <TubeMapContainer
           viewTarget={this.state.viewTarget}
           dataOrigin={this.state.dataOrigin}
           apiUrl={this.props.apiUrl}
           visOptions={this.state.visOptions}
+          APIInterface={this.APIInterface}
         />
         <CustomizationAccordion
           visOptions={this.state.visOptions}

src/App.test.js

@@ -1,16 +1,52 @@
+// Tests functionality without server
+
 import React from "react";
 import { render, screen, waitFor } from "@testing-library/react";
 import "@testing-library/jest-dom/extend-expect";
 import userEvent from "@testing-library/user-event";
 import App from "./App";
 
-import * as fetchAndParseModule from "./fetchAndParse";
-// Tests functionality without server
+import { fetchAndParse } from "./fetchAndParse";
+
 
-jest.mock("./fetchAndParse");
+// We want to be able to replace the `fetchAndParse` that *other* files see,
+// and we want to use *different* implementations for different tests in this
+// file. We can mock it with Jest, but Jest will move this call before the
+// imports when runnin the tests, so we can't access any file-level variables
+// in it. So we need to do some sneaky global trickery.
+
+// Register the given replacement function to be called instead of fetchAndParse.
+function setFetchAndParseMock(replacement) {
+  globalThis["__App.test.js_fetchAndParse_mock"] = replacement 
+}
+
+// Remove any replacement function and go back to the real fetchAndParse.
+function clearFetchAndParseMock() {
+  globalThis["__App.test.js_fetchAndParse_mock"] = undefined 
+}
+
+jest.mock("./fetchAndParse", () => {
+  // This dispatcher will replace fetchAndParse when we or anyone eles imports it.
+  function fetchAndParseDispatcher() {
+    // Ge tthe real fetchAndParse
+    const { fetchAndParse } = jest.requireActual("./fetchAndParse");
+    // Grab the replacement or the real one if no replacement is set
+    let functionToUse = globalThis["__App.test.js_fetchAndParse_mock"] ?? fetchAndParse;
+    // Give it any arguments we got and return its return value.
+    return functionToUse.apply(this, arguments);
+  };
+  // When someone asks for this module, hand them these contents instead.
+  return {
+    __esModule: true,
+    fetchAndParse: fetchAndParseDispatcher
+  };
+});
+
+// TODO: We won't need to do *any* of this if we actually get the ability to pass an API implementation into the app.
 
 beforeEach(() => {
   jest.resetAllMocks();
+  clearFetchAndParseMock();
 });
 
 const getRegionInput = () => {
@@ -23,15 +59,17 @@ it("renders without crashing", () => {
 });
 
 it("renders with error when api call to server throws", async () => {
-  fetchAndParseModule.fetchAndParse = () => {
+  setFetchAndParseMock(() => {
     throw new Error("Mock Server Error");
-  };
+  });
   render(<App />);
-  expect(screen.getAllByText(/Mock Server Error/i)[0]).toBeInTheDocument();
+  await waitFor(() => {
+    expect(screen.getAllByText(/Mock Server Error/i)[0]).toBeInTheDocument();
+  });
 });
 
 it("renders without crashing when sent bad fetch data from server", async () => {
-  fetchAndParseModule.fetchAndParse = () => ({});
+  setFetchAndParseMock(() => ({}));
   render(<App />);
 
   await waitFor(() => {

src/ServerAPI.mjs

@@ -0,0 +1,72 @@
+import { fetchAndParse } from "./fetchAndParse.js";
+import { APIInterface } from "./APIInterface.mjs";
+
+export class ServerAPI extends APIInterface {
+    constructor(apiUrl) {
+        super();
+        this.apiUrl = apiUrl;
+    }
+
+    // Each function takes a cancelSignal to cancel the fetch request if we will unmount component
+
+    async getChunkedData(viewTarget, cancelSignal) {
+        const json = await fetchAndParse(`${this.apiUrl}/getChunkedData`, {
+            signal: cancelSignal,
+            method: "POST",
+            headers: {
+            "Content-Type": "application/json",
+            },
+            body: JSON.stringify(viewTarget),
+        });
+        return json;
+    }
+
+    async getFilenames(cancelSignal) {
+        const json = await fetchAndParse(`${this.apiUrl}/getFilenames`, {
+            signal: cancelSignal,
+            method: "GET",
+            headers: {
+            "Content-Type": "application/json",
+            },
+        });
+        return json;
+    }
+
+    async getBedRegions(bedFile, cancelSignal) {
+        const json = await fetchAndParse(`${this.apiUrl}/getBedRegions`, {
+            signal: cancelSignal,
+            method: "POST",
+            headers: {
+            "Content-Type": "application/json",
+            },
+            body: JSON.stringify({ bedFile }),
+        });
+        return json;
+    }
+
+    async getPathNames(graphFile, cancelSignal) {
+        const json = await fetchAndParse(`${this.apiUrl}/getPathNames`, {
+            signal: cancelSignal,
+            method: "POST",
+            headers: {
+            "Content-Type": "application/json",
+            },
+            body: JSON.stringify({ graphFile }),
+        });
+        return json
+    }
+
+    async getChunkTracks(bedFile, chunk, cancelSignal) {
+        const json = await fetchAndParse(`${this.apiUrl}/getChunkTracks`, {
+            signal: cancelSignal,
+            method: "POST",
+            headers: {
+            "Content-Type": "application/json",
+            },
+            body: JSON.stringify({ bedFile: bedFile, chunk: chunk }),
+        });
+        return json;
+    }
+}
+
+export default ServerAPI;

src/components/HeaderForm.js

@@ -2,7 +2,6 @@ import React, { Component } from "react";
 import PropTypes from "prop-types";
 import { Container, Row, Col, Label, Alert, Button } from "reactstrap";
 import { dataOriginTypes } from "../enums";
-import { fetchAndParse } from "../fetchAndParse";
 import "../config-client.js";
 import { config } from "../config-global.mjs";
 import DataPositionFormRow from "./DataPositionFormRow";
@@ -172,6 +171,7 @@ class HeaderForm extends Component {
   componentDidMount() {
     this.fetchCanceler = new AbortController();
     this.cancelSignal = this.fetchCanceler.signal;
+    this.api = this.props.APIInterface;
     this.initState();
     this.getMountedFilenames();
     this.setUpWebsocket();
@@ -298,13 +298,7 @@ class HeaderForm extends Component {
   getMountedFilenames = async () => {
     this.setState({ error: null });
     try {
-      const json = await fetchAndParse(`${this.props.apiUrl}/getFilenames`, {
-        signal: this.cancelSignal, // (so we can cancel the fetch request if we will unmount component)
-        method: "GET",
-        headers: {
-          "Content-Type": "application/json",
-        },
-      });
+      const json = await this.api.getFilenames(this.cancelSignal);
       if (!json.files || json.files.length === 0) {
         // We did not get back a graph, only (possibly) an error.
         const error =
@@ -355,14 +349,7 @@ class HeaderForm extends Component {
   getBedRegions = async (bedFile) => {
     this.setState({ error: null });
     try {
-      const json = await fetchAndParse(`${this.props.apiUrl}/getBedRegions`, {
-        signal: this.cancelSignal, // (so we can cancel the fetch request if we will unmount component)
-        method: "POST",
-        headers: {
-          "Content-Type": "application/json",
-        },
-        body: JSON.stringify({ bedFile }),
-      });
+      const json = await this.api.getBedRegions(bedFile, this.cancelSignal);
       // We need to do all our parsing here, if we expect the catch to catch errors.
       if (!json.bedRegions || !(json.bedRegions["desc"] instanceof Array)) {
         throw new Error(
@@ -392,14 +379,7 @@ class HeaderForm extends Component {
   getPathNames = async (graphFile) => {
     this.setState({ error: null });
     try {
-      const json = await fetchAndParse(`${this.props.apiUrl}/getPathNames`, {
-        signal: this.cancelSignal, // (so we can cancel the fetch request if we will unmount component)
-        method: "POST",
-        headers: {
-          "Content-Type": "application/json",
-        },
-        body: JSON.stringify({ graphFile }),
-      });
+      const json = await this.api.getPathNames(graphFile, this.cancelSignal);
       // We need to do all our parsing here, if we expect the catch to catch errors.
       let pathNames = json.pathNames;
       if (!(pathNames instanceof Array)) {
@@ -565,13 +545,7 @@ class HeaderForm extends Component {
       console.log("New tracks have been applied");
     } else if (this.state.bedFile && chunk) {
       // Try to retrieve tracks from the server
-      const json = await fetchAndParse(`${this.props.apiUrl}/getChunkTracks`, {
-        method: "POST",
-        headers: {
-          "Content-Type": "application/json",
-        },
-        body: JSON.stringify({ bedFile: this.state.bedFile, chunk: chunk }),
-      });
+      const json = await this.api.getChunkTracks(this.state.bedFile, chunk, this.cancelSignal);
 
       // Replace tracks if request returns non-falsey value
       if (json.tracks) {
@@ -912,6 +886,7 @@ HeaderForm.propTypes = {
   setDataOrigin: PropTypes.func.isRequired,
   setCurrentViewTarget: PropTypes.func.isRequired,
   defaultViewTarget: PropTypes.any, // Header Form State, may be null if no params in URL. see Types.ts
+  APIInterface: PropTypes.object.isRequired,
 };
 
 export default HeaderForm;

src/components/TubeMapContainer.js

@@ -6,7 +6,6 @@ import isEqual from "react-fast-compare";
 import TubeMap from "./TubeMap";
 import * as tubeMap from "../util/tubemap";
 import { dataOriginTypes } from "../enums";
-import { fetchAndParse } from "../fetchAndParse";
 import PopUpInfoDialog from "./PopUpInfoDialog";
 
 
@@ -20,6 +19,7 @@ class TubeMapContainer extends Component {
   componentDidMount() {
     this.fetchCanceler = new AbortController();
     this.cancelSignal = this.fetchCanceler.signal;
+    this.api = this.props.APIInterface;
     this.getRemoteTubeMapData();
   }
 
@@ -129,14 +129,7 @@ class TubeMapContainer extends Component {
   getRemoteTubeMapData = async () => {
     this.setState({ isLoading: true, error: null });
     try {
-      const json = await fetchAndParse(`${this.props.apiUrl}/getChunkedData`, {
-        signal: this.cancelSignal, // (so we can cancel the fetch request if we will unmount component)
-        method: "POST",
-        headers: {
-          "Content-Type": "application/json",
-        },
-        body: JSON.stringify(this.props.viewTarget),
-      });
+      const json = await this.api.getChunkedData(this.props.viewTarget, this.cancelSignal);
       if (json.graph === undefined) {
         // We did not get back a graph, even if we didn't get an error either.
         const error = "Fetching remote data returned error";
@@ -284,6 +277,7 @@ TubeMapContainer.propTypes = {
   dataOrigin: PropTypes.oneOf(Object.values(dataOriginTypes)).isRequired,
   viewTarget: PropTypes.object.isRequired,
   visOptions: PropTypes.object.isRequired,
+  APIInterface: PropTypes.object.isRequired,
 };
 
 export default TubeMapContainer;