Update dependencies (#363)

src/ensembl/package.json

@@ -48,19 +48,19 @@
     }
   },
   "dependencies": {
-    "@apollo/client": "3.1.5",
+    "@apollo/client": "3.2.3",
     "@reduxjs/toolkit": "1.4.0",
-    "@sentry/browser": "5.23.0",
+    "@sentry/browser": "5.25.0",
     "classnames": "2.2.6",
     "connected-react-router": "6.8.0",
     "core-js": "3.6.5",
-    "d3": "6.1.1",
+    "d3": "6.2.0",
     "dotenv": "8.2.0",
     "ensembl-genome-browser": "https://raw.githubusercontent.com/Ensembl/ensembl-genome-browser-assets/master/assets-80f51620ed443c640cdfd6b5aebd505b.tar.gz",
     "graphql": "15.3.0",
     "koa-proxy": "1.0.0-alpha.3",
     "lodash": "4.17.20",
-    "query-string": "6.13.1",
+    "query-string": "6.13.5",
     "react": "16.13.1",
     "react-cookie": "4.0.3",
     "react-dom": "16.13.1",
@@ -86,31 +86,31 @@
     "@babel/preset-env": "7.11.5",
     "@babel/preset-react": "7.10.4",
     "@babel/preset-typescript": "7.10.4",
-    "@storybook/addon-essentials": "6.0.21",
-    "@storybook/addons": "6.0.21",
-    "@storybook/react": "6.0.21",
-    "@storybook/theming": "6.0.21",
+    "@storybook/addon-essentials": "6.0.26",
+    "@storybook/addons": "6.0.26",
+    "@storybook/react": "6.0.26",
+    "@storybook/theming": "6.0.26",
     "@svgr/webpack": "5.4.0",
     "@types/classnames": "2.2.10",
-    "@types/d3": "5.7.2",
-    "@types/enzyme": "3.10.6",
+    "@types/d3": "5.16.3",
+    "@types/enzyme": "3.10.7",
     "@types/enzyme-adapter-react-16": "1.0.6",
-    "@types/faker": "5.1.0",
-    "@types/jest": "26.0.13",
-    "@types/lodash": "4.14.161",
-    "@types/node": "14.6.4",
-    "@types/prettier": "2.1.0",
-    "@types/react": "16.9.49",
+    "@types/faker": "5.1.2",
+    "@types/jest": "26.0.14",
+    "@types/lodash": "4.14.162",
+    "@types/node": "14.11.8",
+    "@types/prettier": "2.1.2",
+    "@types/react": "16.9.52",
     "@types/react-dom": "16.9.8",
     "@types/react-redux": "7.1.9",
-    "@types/react-router-dom": "5.1.5",
+    "@types/react-router-dom": "5.1.6",
     "@types/react-router-hash-link": "1.2.1",
     "@types/redux-mock-store": "1.0.2",
     "@types/webpack-env": "1.15.2",
-    "@typescript-eslint/eslint-plugin": "4.1.0",
-    "@typescript-eslint/parser": "4.1.0",
+    "@typescript-eslint/eslint-plugin": "4.4.0",
+    "@typescript-eslint/parser": "4.4.0",
     "babel-core": "7.0.0-bridge.0",
-    "babel-jest": "26.3.0",
+    "babel-jest": "26.5.2",
     "babel-loader": "8.1.0",
     "brotli-webpack-plugin": "1.1.0",
     "compression-webpack-plugin": "5.0.2",
@@ -118,13 +118,13 @@
     "copy-webpack-plugin": "6.1.0",
     "css-loader": "4.3.0",
     "enzyme": "3.11.0",
-    "enzyme-adapter-react-16": "1.15.4",
-    "enzyme-to-json": "3.5.0",
-    "eslint": "7.8.1",
-    "eslint-config-prettier": "6.11.0",
+    "enzyme-adapter-react-16": "1.15.5",
+    "enzyme-to-json": "3.6.1",
+    "eslint": "7.11.0",
+    "eslint-config-prettier": "6.12.0",
     "eslint-plugin-prettier": "3.1.4",
-    "eslint-plugin-react": "7.20.6",
-    "eslint-plugin-react-hooks": "4.1.0",
+    "eslint-plugin-react": "7.21.4",
+    "eslint-plugin-react-hooks": "4.1.2",
     "faker": "5.1.0",
     "file-loader": "6.1.0",
     "fork-ts-checker-webpack-plugin": "5.1.0",
@@ -133,33 +133,33 @@
     "husky": "4.3.0",
     "identity-obj-proxy": "3.0.0",
     "image-webpack-loader": "6.0.0",
-    "jest": "26.4.2",
+    "jest": "26.5.3",
     "jest-fetch-mock": "3.0.3",
     "jest-transform-stub": "2.0.0",
     "koa": "2.13.0",
     "koa-connect": "2.1.0",
     "koa-static": "5.0.0",
     "licence-manager": "git+https://github.com/Ensembl/ensembl-licence-manager.git#36b534d28ff26d345b4ba4da0cbc18e1e0f7a6b7",
-    "lint-staged": "10.3.0",
+    "lint-staged": "10.4.0",
     "mini-css-extract-plugin": "0.11.1",
     "node-sass": "4.14.1",
     "optimize-css-assets-webpack-plugin": "5.0.4",
     "postcss": "7.0.32",
     "postcss-loader": "4.0.1",
     "postcss-preset-env": "6.7.0",
-    "prettier": "2.1.1",
+    "prettier": "2.1.2",
     "redux-mock-store": "1.5.4",
     "rimraf": "3.0.2",
     "robotstxt-webpack-plugin": "7.0.0",
     "sass-loader": "10.0.2",
     "source-map-loader": "1.1.0",
     "style-loader": "1.2.1",
-    "stylelint": "13.7.0",
+    "stylelint": "13.7.2",
     "stylelint-config-recommended-scss": "4.2.0",
     "stylelint-scss": "3.18.0",
     "stylelint-webpack-plugin": "2.1.0",
     "terser-webpack-plugin": "4.1.0",
-    "typescript": "4.0.2",
+    "typescript": "4.0.3",
     "webpack": "4.44.1",
     "webpack-bundle-analyzer": "3.8.0",
     "webpack-cli": "3.3.12",

src/ensembl/src/content/app/entity-viewer/gene-view/components/default-transcripts-list/DefaultTranscriptsList.tsx

@@ -101,7 +101,7 @@ const StripedBackground = (props: Props) => {
   const extendedTicks = [1, ...ticks, geneLength];
 
   const stripes = extendedTicks.map((tick) => {
-    const x = Math.floor(scale(tick));
+    const x = Math.floor(scale(tick) as number);
     const style = { left: `${x}px` };
     return <span key={x} className={styles.stripe} style={style} />;
   });

src/ensembl/src/content/app/entity-viewer/gene-view/components/default-transcripts-list/default-transcripts-list-item/DefaultTranscriptListItem.tsx

@@ -59,7 +59,7 @@ export const DefaultTranscriptListItem = (
     props.transcript
   );
   const transcriptStartX = scale(transcriptStart - geneStart); // FIXME In future, this should be done using relative position of transcript in gene
-  const transcriptWidth = scale(transcriptEnd - transcriptStart); // FIXME  this too should be based on relative coordinates of transcript
+  const transcriptWidth = scale(transcriptEnd - transcriptStart) as number; // FIXME  this too should be based on relative coordinates of transcript
 
   const defaultTranscriptLabelMap = {
     selected: {

src/ensembl/src/content/app/entity-viewer/gene-view/components/gene-overview-image/GeneOverviewImage.tsx

@@ -71,8 +71,8 @@ export const GeneImage = (props: GeneOverviewImageProps) => {
         start: transcriptStart,
         end: transcriptEnd
       } = getFeatureCoordinates(transcript);
-      const startX = scale(transcriptStart);
-      const endX = scale(transcriptEnd);
+      const startX = scale(transcriptStart) as number;
+      const endX = scale(transcriptEnd) as number;
       const y = 10;
       const width = Math.floor(endX - startX);
       return (

src/ensembl/src/content/app/entity-viewer/gene-view/components/unspliced-transcript/UnsplicedTranscript.tsx

@@ -163,8 +163,8 @@ const Backbone = (
           className={backboneClasses}
           y={0}
           height={1}
-          x={scale(start - transcriptStart) + 1}
-          width={Math.max(0, scale(end - start) - 2)}
+          x={(scale(start - transcriptStart) as number) + 1}
+          width={Math.max(0, (scale(end - start) as number) - 2)}
         />
       ))}
     </g>

src/ensembl/stories/entity-viewer/transcripts/UnsplicedTranscripts.stories.tsx

@@ -97,8 +97,8 @@ const MultipleTranscripts = (props: { gene: GeneType }) => {
       start: transcriptStart,
       end: transcriptEnd
     } = getFeatureCoordinates(transcript);
-    const startX = scale(transcriptStart);
-    const endX = scale(transcriptEnd);
+    const startX = scale(transcriptStart) as number;
+    const endX = scale(transcriptEnd) as number;
     const y = view === 'expanded' ? index * VERTICAL_SPACE : 10;
     const width = Math.floor(endX - startX);
     return (