Upgrade dependencies, refactor tests (#38)

higlass · Jan 11, 2023 · f26b9df · f26b9df
1 parent 06c9b87
commit f26b9df
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Showing 13 changed files with 8,001 additions and 21,221 deletions.
diff --git a/karma.conf.js b/karma.conf.js
@@ -4,7 +4,7 @@ require('babel-polyfill');
 module.exports = function(config) {
   config.set({
     basePath: '',
-    frameworks: ['jasmine', 'server-side'],
+    frameworks: ['jasmine'],
 
     files: [
       'node_modules/babel-polyfill/dist/polyfill.js',
@@ -38,7 +38,6 @@ module.exports = function(config) {
       'karma-sourcemap-loader',
       'karma-chrome-launcher',
       'karma-phantomjs-launcher',
-      'karma-server-side',
       'karma-verbose-reporter'
     ],
 

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "higlass-transcripts",
-  "version": "0.3.7",
+  "version": "0.3.8",
   "description": "Gene transcripts track for HiGlass",
   "private": false,
   "author": "Alexander Veit",
@@ -20,11 +20,9 @@
   ],
   "repository": "github:higlass/higlass-transcripts",
   "devDependencies": {
-    "autoprefixer": "^8.6.5",
     "babel-core": "^6.26.3",
     "babel-loader": "^7.1.5",
     "babel-preset-env": "^1.7.0",
-    "box-intersect": "^1.0.1",
     "file-loader": "^1.1.11",
     "html-loader": "^0.5.5",
     "html-webpack-plugin": "^3.1.0",
@@ -36,10 +34,6 @@
     "unminified-webpack-plugin": "^2.0.0",
     "webpack-cli": "^3.3.11",
     "webpack-dev-server": "^3.10.3",
-    "fetch-mock": "^8.3.2",
-    "karma-server-side": "^1.8.0",
-    "fs-extra": "^8.1.0",
-    "fs": "0.0.2",
     "jasmine": "^2.99.0",
     "karma": "^4.4.1",
     "karma-chrome-launcher": "^3.1.0",
@@ -53,10 +47,10 @@
     "babel-preset-react": "^6.24.1",
     "enzyme": "^3.11.0",
     "enzyme-adapter-react-16": "^1.6.0",
-    "i": "^0.3.6",
     "sourcemap": "^0.1.0",
     "webpack": "^4.43.0",
-    "higlass": "^1.11.11"
+    "higlass": "^1.11.11",
+    "cheerio": "=1.0.0-rc.3"
   },
   "scripts": {
     "build-es": "rm -rf ./es/* && npx babel ./src/scripts/ --out-dir ./es/ --env-name esm",
@@ -70,7 +64,7 @@
     "d3-scale": "^4.0.2",
     "d3-color": "^3.1.0",
     "higlass-register": "^0.3.0",
-    "@gmod/indexedfasta": "1.1.0",
-    "generic-filehandle": "2.2.3"
+    "@gmod/indexedfasta": "^2.0.0",
+    "generic-filehandle": "^3.0.0"
   }
 }
diff --git a/src/index.html b/src/index.html
@@ -9,12 +9,12 @@
     }
   </style>
   <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css">
-  <link rel="stylesheet" href="https://unpkg.com/[email protected].8/dist/hglib.css">
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected].11/dist/hglib.css">
   <link rel="stylesheet" href="hglib.css">
   <script src="https://cdnjs.cloudflare.com/ajax/libs/pixi.js/5.2.3/pixi.min.js"></script>
-  <script crossorigin src="https://unpkg.com/react@16/umd/react.development.js"></script>
-  <script crossorigin src="https://unpkg.com/react-dom@16/umd/react-dom.development.js"></script>
-  <script crossorigin src="https://unpkg.com/[email protected].8/dist/hglib.min.js"></script>
+  <script crossorigin src="https://cdn.jsdelivr.net/npm/react@16/umd/react.development.js"></script>
+  <script crossorigin src="https://cdn.jsdelivr.net/npm/react-dom@16/umd/react-dom.development.js"></script>
+  <script crossorigin src="https://cdn.jsdelivr.net/npm/[email protected].11/dist/hglib.min.js"></script>
   <script src="https://cdnjs.cloudflare.com/ajax/libs/react-bootstrap/0.32.1/react-bootstrap.min.js"></script>
 </head>
 <body>
@@ -29,7 +29,7 @@
 <div style="height: 1500px"></div>
 </body>
 <script src="hglib.js"></script>
-<script crossorigin src="https://unpkg.com/higlass-sequence/dist/higlass-sequence.js"></script>
+<script crossorigin src="https://cdn.jsdelivr.net/npm/higlass-sequence/dist/higlass-sequence.js"></script>
 <script>
   var viewConfig =
   {

diff --git a/test/AminoAcidTests.js b/test/AminoAcidTests.js
@@ -1,12 +1,11 @@
 import { expect } from "chai";
 import register from "higlass-register";
 
-import FetchMockHelper from "./utils/FetchMockHelper";
 
-import { HiGlassComponent, getTrackObjectFromHGC } from "higlass";
+
+import { getTrackObjectFromHGC } from "higlass";
 
 import {
-  waitForDataLoaded,
   mountHGComponent,
   removeHGComponent,
 } from "./utils/test-helpers";
@@ -21,55 +20,34 @@ register({
   config: TranscriptsTrack.config,
 });
 
-describe("Amino acid", () => {
-  const fetchMockHelper = new FetchMockHelper("", "AminoAcidTests");
+describe("Amino acid tests", () => {
+  let hgc = null;
+  let div = null;
 
-  beforeAll(async () => {
-    await fetchMockHelper.activateFetchMock();
+  beforeAll((done) => {
+    [div, hgc] = mountHGComponent(div, hgc, viewConf, done);
   });
 
-  describe("Amino acid tests", () => {
-    let hgc = null;
-    let div = null;
-
-    beforeAll((done) => {
-      [div, hgc] = mountHGComponent(div, hgc, viewConf, done);
-    });
-
-    it("tests that the export works and contains the correct data", (done) => {
-
-      const trackObj = getTrackObjectFromHGC(
-        hgc.instance(),
-        viewConf.views[0].uid,
-        viewConf.views[0].tracks.top[0].uid
-      );
-      const tile = trackObj.visibleAndFetchedTiles()[0];
-
-      setTimeout(() => {  
-
-
-        console.log(tile.aaInfo.exonOffsets["ENST00000378404.3_chr1_3021483_3022903"]);
-        console.log(tile.aaInfo.aminoAcids);
-
-        done();
-       }, 2000);
-
-
-
-
-
-
+  it("tests that the export works and contains the correct data", (done) => {
 
+    const trackObj = getTrackObjectFromHGC(
+      hgc.instance(),
+      viewConf.views[0].uid,
+      viewConf.views[0].tracks.top[0].uid
+    );
+    const tile = trackObj.visibleAndFetchedTiles()[0];
 
+    setTimeout(() => {  
 
-    });
+      console.log(tile.aaInfo.exonOffsets["ENST00000378404.3_chr1_3021483_3022903"]);
+      console.log(tile.aaInfo.aminoAcids);
+
+      done();
+     }, 2000);
 
-    afterAll(() => {
-      removeHGComponent(div);
-    });
   });
 
-  afterAll(async () => {
-    await fetchMockHelper.storeDataAndResetFetchMock();
+  afterAll(() => {
+    removeHGComponent(div);
   });
 });
diff --git a/test/SVGExportTests.js b/test/SVGExportTests.js
@@ -1,12 +1,9 @@
 import { expect } from "chai";
 import register from "higlass-register";
 
-import FetchMockHelper from "./utils/FetchMockHelper";
-
-import { HiGlassComponent, getTrackObjectFromHGC } from "higlass";
+import { getTrackObjectFromHGC } from "higlass";
 
 import {
-  waitForDataLoaded,
   mountHGComponent,
   removeHGComponent,
 } from "./utils/test-helpers";
@@ -21,53 +18,43 @@ register({
   config: TranscriptsTrack.config,
 });
 
+
 describe("SVG export", () => {
-  const fetchMockHelper = new FetchMockHelper("", "SVGExport");
+  let hgc = null;
+  let div = null;
 
-  beforeAll(async () => {
-    await fetchMockHelper.activateFetchMock();
+  beforeAll((done) => {
+    [div, hgc] = mountHGComponent(div, hgc, viewConf, done);
   });
 
-  describe("SVG export", () => {
-    let hgc = null;
-    let div = null;
-
-    beforeAll((done) => {
-      [div, hgc] = mountHGComponent(div, hgc, viewConf, done);
-    });
+  it("tests that the export works and contains the correct data", (done) => {
+    hgc.instance().handleExportSVG();
 
-    it("tests that the export works and contains the correct data", (done) => {
-      hgc.instance().handleExportSVG();
+    const trackObj = getTrackObjectFromHGC(
+      hgc.instance(),
+      viewConf.views[0].uid,
+      viewConf.views[0].tracks.top[1].uid
+    );
 
-      const trackObj = getTrackObjectFromHGC(
-        hgc.instance(),
-        viewConf.views[0].uid,
-        viewConf.views[0].tracks.top[1].uid
-      );
+    const tile = trackObj.visibleAndFetchedTiles()[1];
+    const exon = tile.allExonsForSVG[1];
 
-      const tile = trackObj.visibleAndFetchedTiles()[1];
-      const exon = tile.allExonsForSVG[1];
+    expect(exon.rect[0]).to.equal(282.39750000000004);
+    expect(exon.rect[5]).to.equal(33);
+    expect(exon.color).to.equal("#C0EAAF");
 
-      expect(exon.rect[0]).to.equal(285.4775);
-      expect(exon.rect[5]).to.equal(33);
-      expect(exon.color).to.equal("#C0EAAF");
+    const exon2 = tile.allExonsForSVG[2];
 
-      const exon2 = tile.allExonsForSVG[2];
+    expect(exon2.rect[0]).to.equal(324.7475);
+    expect(exon2.rect[5]).to.equal(33);
+    expect(exon2.color).to.equal("#bdbfff");
 
-      expect(exon2.rect[0]).to.equal(324.7475);
-      expect(exon2.rect[5]).to.equal(33);
-      expect(exon2.color).to.equal("#bdbfff");
 
-
-      done();
-    });
-
-    afterAll(() => {
-      removeHGComponent(div);
-    });
+    done();
   });
 
-  afterAll(async () => {
-    await fetchMockHelper.storeDataAndResetFetchMock();
+  afterAll(() => {
+    removeHGComponent(div);
   });
 });
+
diff --git a/test/TranscriptsTests.js b/test/TranscriptsTests.js
@@ -1,12 +1,9 @@
 import { expect } from "chai";
 import register from "higlass-register";
 
-import FetchMockHelper from "./utils/FetchMockHelper";
-
-import { HiGlassComponent, getTrackObjectFromHGC } from "higlass";
+import { getTrackObjectFromHGC } from "higlass";
 
 import {
-  waitForDataLoaded,
   mountHGComponent,
   removeHGComponent,
 } from "./utils/test-helpers";
@@ -21,70 +18,45 @@ register({
   config: TranscriptsTrack.config,
 });
 
-describe("Transcripts", () => {
-  const fetchMockHelper = new FetchMockHelper("", "TranscriptTests");
-
-  beforeAll(async () => {
-    await fetchMockHelper.activateFetchMock();
-  });
-
-  describe("Transcripts tests", () => {
-    let hgc = null;
-    let div = null;
-
-    beforeAll((done) => {
-      [div, hgc] = mountHGComponent(div, hgc, viewConf, done);
-    });
-
-    it("tests that basic infos are correct", (done) => {
-
-
 
-      const trackObj = getTrackObjectFromHGC(
-        hgc.instance(),
-        viewConf.views[0].uid,
-        viewConf.views[0].tracks.top[0].uid
-      );
 
-      //const tile = trackObj.visibleAndFetchedTiles()[2];
+describe("Transcripts tests", () => {
+  let hgc = null;
+  let div = null;
 
-      expect(trackObj.trackHeight).to.equal(106);
-      expect(Object.keys(trackObj.transcriptInfo).length).to.equal(5);
-
-      const transcriptInfo = trackObj.transcriptInfo["ENST00000270722.9_chr1_3069211_3438621"];
-      expect(transcriptInfo.transcriptName).to.equal("PRDM16-201");
-      expect(transcriptInfo.txStart).to.equal(3069210);
-      expect(transcriptInfo.displayOrder).to.equal(4);
-
-      // Check position info
-      const posInfo = trackObj.transcriptPositionInfo[3][0]
-      expect(posInfo[1]).to.equal(3434342);
-
-      expect(trackObj.areTranscriptsHidden).to.equal(false);
+  beforeAll((done) => {
+    [div, hgc] = mountHGComponent(div, hgc, viewConf, done);
+  });
 
-      // Check vertical positioning of exon
-
-      // const exonPos1 = tile.allExonsForSVG[4].rect[1];
-      // const exonPos2 = tile.allExonsForSVG[4].rect[5];
-      // expect(exonPos1).to.equal(41);
-      // expect(exonPos2).to.equal(47);
+  it("tests that basic infos are correct", (done) => {
 
-      done();
+    const trackObj = getTrackObjectFromHGC(
+      hgc.instance(),
+      viewConf.views[0].uid,
+      viewConf.views[0].tracks.top[0].uid
+    );
 
-      // setTimeout(() => {
+    //const tile = trackObj.visibleAndFetchedTiles()[2];
 
-      // }, 1000);
+    expect(trackObj.trackHeight).to.equal(106);
+    expect(Object.keys(trackObj.transcriptInfo).length).to.equal(5);
 
+    const transcriptInfo = trackObj.transcriptInfo["ENST00000270722.10_chr1_3069203_3438621"];
+    expect(transcriptInfo.transcriptName).to.equal("PRDM16-201");
+    expect(transcriptInfo.txStart).to.equal(3069202);
+    expect(transcriptInfo.displayOrder).to.equal(3);
 
-
-    });
+    // Check position info
+    const posInfo = trackObj.transcriptPositionInfo[3][0]
+    expect(posInfo[1]).to.equal(3438621);
+    expect(trackObj.areTranscriptsHidden).to.equal(false);
+    done();
 
-    afterAll(() => {
-      removeHGComponent(div);
-    });
   });
 
-  afterAll(async () => {
-    await fetchMockHelper.storeDataAndResetFetchMock();
+  afterAll(() => {
+    removeHGComponent(div);
   });
 });
+
+