diff --git a/babel.config.js b/babel.config.js index c596b5cb..2d4d4285 100644 --- a/babel.config.js +++ b/babel.config.js @@ -6,7 +6,6 @@ module.exports = { } } ], - '@babel/preset-react', - '@babel/preset-typescript' + '@babel/preset-react' ] }; diff --git a/opt/scopeserver/dataserver/modules/gserver/GServer.py b/opt/scopeserver/dataserver/modules/gserver/GServer.py index 025fb5b2..bee7a6f5 100644 --- a/opt/scopeserver/dataserver/modules/gserver/GServer.py +++ b/opt/scopeserver/dataserver/modules/gserver/GServer.py @@ -215,8 +215,8 @@ def getCellColorByFeatures(self, request, context): logger.debug("{0:.5f} seconds elapsed getting colours ---".format(time.time() - start_time)) return s_pb2.CellColorByFeaturesReply( color=None, - compressedColor=cell_color_by_features.get_hex_vec(), - hasAddCompressionLayer=False, + compressedColor=cell_color_by_features.get_compressed_hex_vec(), + hasAddCompressionLayer=True, vmax=cell_color_by_features.get_v_max(), maxVmax=cell_color_by_features.get_max_v_max(), cellIndices=cell_color_by_features.get_cell_indices(), diff --git a/package-lock.json b/package-lock.json index 7a66718d..867f3032 100644 --- a/package-lock.json +++ b/package-lock.json @@ -5,12 +5,12 @@ "requires": true, "dependencies": { "@babel/cli": { - "version": "7.12.1", - "resolved": "https://registry.npmjs.org/@babel/cli/-/cli-7.12.1.tgz", - "integrity": "sha512-eRJREyrfAJ2r42Iaxe8h3v6yyj1wu9OyosaUHW6UImjGf9ahGL9nsFNh7OCopvtcPL8WnEo7tp78wrZaZ6vG9g==", + "version": "7.12.8", + "resolved": "https://registry.npmjs.org/@babel/cli/-/cli-7.12.8.tgz", + "integrity": "sha512-/6nQj11oaGhLmZiuRUfxsujiPDc9BBReemiXgIbxc+M5W+MIiFKYwvNDJvBfnGKNsJTKbUfEheKc9cwoPHAVQA==", "dev": true, "requires": { - "@nicolo-ribaudo/chokidar-2": "^2.1.8", + "@nicolo-ribaudo/chokidar-2": "2.1.8-no-fsevents", "chokidar": "^3.4.0", "commander": "^4.0.1", "convert-source-map": "^1.1.0", @@ -117,22 +117,6 @@ "dev": true, "optional": true }, - "make-dir": { - 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"https://registry.npmjs.org/webpack-bundle-analyzer/-/webpack-bundle-analyzer-4.2.0.tgz", + "integrity": "sha512-gmjpdL/AJeGAftSzA+bjIPiChUffjBelcH2+3woCUiRpQfuwrTJuWRyZuqegiwBAroMJp7gIwcJaGeol039zbQ==", "dev": true, "requires": { "acorn": "^8.0.4", "acorn-walk": "^8.0.0", "chalk": "^4.1.0", "commander": "^6.2.0", - "ejs": "^3.1.5", "express": "^4.17.1", "filesize": "^6.1.0", - "gzip-size": "^5.1.1", + "gzip-size": "^6.0.0", "lodash": "^4.17.20", - "mkdirp": "^1.0.4", "opener": "^1.5.2", "ws": "^7.3.1" }, @@ -17627,12 +17559,6 @@ "integrity": "sha512-EykJT/Q1KjTWctppgIAgfSO0tKVuZUjhgMr17kqTumMl6Afv3EISleU7qZUzoXDFTAHTDC4NOoG/ZxU3EvlMPQ==", "dev": true }, - "mkdirp": { - "version": "1.0.4", - "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-1.0.4.tgz", - "integrity": "sha512-vVqVZQyf3WLx2Shd0qJ9xuvqgAyKPLAiqITEtqW0oIUjzo3PePDd6fW9iFz30ef7Ysp/oiWqbhszeGWW2T6Gzw==", - "dev": true - }, "supports-color": { "version": "7.2.0", "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz", @@ -17643,9 +17569,9 @@ } }, "ws": { - "version": "7.4.0", - "resolved": "https://registry.npmjs.org/ws/-/ws-7.4.0.tgz", - "integrity": "sha512-kyFwXuV/5ymf+IXhS6f0+eAFvydbaBW3zjpT6hUdAh/hbVjTIB5EHBGi0bPoCLSK2wcuz3BrEkB9LrYv1Nm4NQ==", + "version": "7.4.1", + "resolved": "https://registry.npmjs.org/ws/-/ws-7.4.1.tgz", + "integrity": "sha512-pTsP8UAfhy3sk1lSk/O/s4tjD0CRwvMnzvwr4OKGX7ZvqZtUyx4KIJB5JWbkykPoc55tixMGgTNoh3k4FkNGFQ==", "dev": true } } @@ -18137,15 +18063,6 @@ "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=" }, - "write": { - "version": "1.0.3", - "resolved": "https://registry.npmjs.org/write/-/write-1.0.3.tgz", - "integrity": "sha512-/lg70HAjtkUgWPVZhZcm+T4hkL8Zbtp1nFNOn3lRrxnlv50SRBv7cR7RqR+GMsd3hUXy9hWBo4CHTbFTcOYwig==", - "dev": true, - "requires": { - "mkdirp": "^0.5.1" - } - }, "write-file-atomic": { "version": "3.0.3", "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-3.0.3.tgz", @@ -18197,10 +18114,10 @@ "resolved": "https://registry.npmjs.org/y18n/-/y18n-4.0.0.tgz", "integrity": "sha512-r9S/ZyXu/Xu9q1tYlpsLIsa3EeLXXk0VwlxqTcFRfg9EhMW+17kbt9G0NrgCmhGb5vT2hyhJZLfDGx+7+5Uj/w==" }, - "yaml": { - "version": "1.10.0", - "resolved": "https://registry.npmjs.org/yaml/-/yaml-1.10.0.tgz", - "integrity": "sha512-yr2icI4glYaNG+KWONODapy2/jDdMSDnrONSjblABjD9B4Z5LgiircSt8m8sRZFNi08kG9Sm0uSHtEmP3zaEGg==", + "yallist": { + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz", + "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==", "dev": true }, "yargs": { @@ -18263,6 +18180,12 @@ "lodash": "^4.17.15", "yargs": "^13.3.0" } + }, + "yocto-queue": { + "version": "0.1.0", + "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", + "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", + "dev": true } } } diff --git a/package.json b/package.json index 46a2692d..9c5e3b72 100644 --- a/package.json +++ b/package.json @@ -41,21 +41,21 @@ "grpc-bus-websocket-client": "^0.3.1", "grpc-bus-websocket-server": "file:opt/scopeserver/bindserver", "grpc-caller": "^0.13.0", - "grpc-tools": "^1.9.0", - "immer": "^7.0.14", + "grpc-tools": "^1.10.0", + "immer": "^8.0.0", "js-file-download": "^0.4.12", "json-schema": "^0.2.3", "json2csv": "^4.0.1", - "pako": "^1.0.6", + "pako": "^2.0.2", "pixi.js": "^5.3.3", - "protobufjs": "^6.9.0", + "protobufjs": "^6.10.2", "public-ip": "^2.4.0", "ramda": "^0.27.0", "rc-slider": "^8.6.0", "react": "^16.14.0", "react-addons-css-transition-group": "^15.6.2", "react-cookie": "^4.0.3", - "react-cookie-consent": "^6.1.0", + "react-cookie-consent": "^6.2.0", "react-csv-reader": "^3.1.1", "react-dnd": "^2.5.4", "react-dnd-html5-backend": "^2.5.4", @@ -81,48 +81,46 @@ "url-loader": "^4.1.1" }, "devDependencies": { - "@babel/cli": "^7.12.1", - "@babel/core": "^7.12.3", + "@babel/cli": "^7.12.8", + "@babel/core": "^7.12.9", "@babel/plugin-proposal-class-properties": "^7.12.1", "@babel/plugin-proposal-object-rest-spread": "^7.12.1", "@babel/plugin-transform-runtime": "^7.12.1", - "@babel/preset-env": "^7.12.1", - "@babel/preset-react": "^7.12.5", - "@babel/preset-typescript": "^7.12.1", + "@babel/preset-env": "^7.12.7", + "@babel/preset-react": "^7.12.7", "@babel/runtime": "^7.12.5", "@redux-saga/testing-utils": "^1.1.3", "@testing-library/jest-dom": "^5.11.6", - "@testing-library/react": "^11.1.2", - "@types/jest": "^26.0.15", - "@types/react": "^16.9.56", - "@types/react-dom": "^16.9.9", + "@testing-library/react": "^11.2.2", + "@types/jest": "^26.0.16", + "@types/react": "^16.14.2", + "@types/react-dom": "^16.9.10", "@types/react-router-dom": "^5.1.6", - "@typescript-eslint/eslint-plugin": "^4.7.0", - "@typescript-eslint/parser": "^4.7.0", + "@typescript-eslint/eslint-plugin": "^4.9.0", + "@typescript-eslint/parser": "^4.9.0", "babel-jest": "^26.6.3", - "babel-loader": "^8.2.1", - "babel-plugin-redux-saga": "^1.1.2", - "cross-env": "^7.0.2", + "babel-loader": "^8.2.2", + "cross-env": "^7.0.3", "css-loader": "^5.0.1", - "eslint": "^7.13.0", - "eslint-config-prettier": "^6.15.0", - "eslint-plugin-prettier": "^3.1.3", + "eslint": "^7.15.0", + "eslint-config-prettier": "^7.0.0", + "eslint-plugin-prettier": "^3.2.0", "eslint-plugin-react": "^7.21.5", - "fork-ts-checker-webpack-plugin": "^6.0.1", - "google-protobuf": "^3.13.0", + "google-protobuf": "^3.14.0", "grpc": "^1.24.4", "grpc-loader": "^2.0.1", "jest": "^26.6.3", "jest-css-modules-transform": "4.0.1", - "prettier": "^2.1.2", + "prettier": "^2.2.1", "redux-devtools-extension": "^2.13.8", "script-loader": "^0.7.2", "style-loader": "^2.0.0", "terser-webpack-plugin": "^5.0.3", "ts-jest": "^26.4.4", - "typescript": "^4.0.5", - "webpack": "^5.4.0", - "webpack-bundle-analyzer": "^4.1.0", + "ts-loader": "^8.0.11", + "typescript": "^4.1.2", + "webpack": "^5.10.0", + "webpack-bundle-analyzer": "^4.2.0", "webpack-cli": "^4.2.0", "webpack-dev-server": "^3.11.0" }, diff --git a/src/components/App.jsx b/src/components/App.jsx index e5b3fbdc..29f3af32 100644 --- a/src/components/App.jsx +++ b/src/components/App.jsx @@ -4,7 +4,7 @@ import { connect } from 'react-redux'; import { withRouter, Route, Link } from 'react-router-dom'; import { withCookies, Cookies } from 'react-cookie'; import CookieConsent from 'react-cookie-consent'; - +import pako from 'pako'; import Favicon from 'react-favicon'; import { SCOPE_COOKIE, ONE_MINUTE } from './constants'; @@ -24,7 +24,6 @@ import { import { FullPageNotify } from './pages'; import { millisecondsToDays } from './utils'; -const pako = require('pako'); const publicIp = require('public-ip'); const timer = 60 * 1000; diff --git a/src/components/AppHeader.jsx b/src/components/AppHeader.jsx index 00f54dae..4a4084a2 100644 --- a/src/components/AppHeader.jsx +++ b/src/components/AppHeader.jsx @@ -15,8 +15,8 @@ import { BackendAPI } from './common/API'; import PropTypes from 'prop-types'; import { withCookies, Cookies } from 'react-cookie'; import Bitly from 'bitly4api'; +import pako from 'pako'; -const pako = require('pako'); let bitly = new Bitly(BITLY.token); import { toggleSidebar, consentToCookies } from '../redux/actions'; diff --git a/src/components/common/Viewer.jsx b/src/components/common/Viewer.jsx index 484f63df..e1036a67 100644 --- a/src/components/common/Viewer.jsx +++ b/src/components/common/Viewer.jsx @@ -5,9 +5,12 @@ import * as d3 from 'd3'; import * as R from 'ramda'; import { BackendAPI } from './API'; import { Dimmer, Loader } from 'semantic-ui-react'; +import pako from 'pako'; import Alert from 'react-popup'; import { debounce } from 'lodash'; +import { zipLists } from '../../util'; + const MIN_SCALING_FACTOR = 1; const DEFAULT_POINT_COLOR = 'A6A6A6'; @@ -434,7 +437,7 @@ export default class Viewer extends Component { translatePointsInLasso(indices) { let ptsInLasso = []; - let idxInLasso = _.intersection(indices, this.state.coord.idx); + let idxInLasso = R.intersection(indices, this.state.coord.idx); ptsInLasso = idxInLasso.map((idx) => { return this.state.coord.idx.indexOf(idx); }); @@ -1067,9 +1070,29 @@ export default class Viewer extends Component { response ); } + // Convert object to ArrayBuffer + let responseBuffered = + response.compressedColor.toArrayBuffer(); + + // Uncompress if (response.hasAddCompressionLayer) { - // Uncompress - console.error('Zlib compression is not supported'); + pako.inflate( + responseBuffered, + (err, uncompressedMessage) => { + if (err) { + console.log(err); + } else { + this.endBenchmark( + 'getFeatureColors' + ); + let colors = this.chunkString( + uncompressedMessage.toString(), + 6 + ); + this.updateColors(response, colors); + } + } + ); } else { this.endBenchmark('getFeatureColors'); this.updateColors(response, response.color); @@ -1156,7 +1179,7 @@ export default class Viewer extends Component { }); let settings = BackendAPI.getSettings(); if (settings.sortCells) { - let pts = _.zip( + let pts = zipLists( this.state.coord.idx, this.state.coord.x, this.state.coord.y, @@ -1173,7 +1196,7 @@ export default class Viewer extends Component { }); this.endBenchmark('sort'); this.startBenchmark('map'); - pts.map((p, i) => { + pts.forEach((p, i) => { let point = this.getTexturedColorPoint(p[1], p[2], p[3]); point._originalData.idx = p[0]; this.mainLayer.addChildAt(point, i); diff --git a/src/components/common/ViewerSidebar.jsx b/src/components/common/ViewerSidebar.jsx index 4de26a48..99a81a7b 100644 --- a/src/components/common/ViewerSidebar.jsx +++ b/src/components/common/ViewerSidebar.jsx @@ -115,7 +115,7 @@ class ViewerSidebar extends Component { getButtonText = (text) => { switch (this.state.status) { case 'ready': - switch (button) { + switch (text) { case 'submit': return ( @@ -1374,7 +1374,7 @@ const viewerSidebar = withCookies(withRouter(ViewerSidebar)); const mapStateToProps = (rootState) => { return { - sessionIsRW: rootState.main.sessionMode === 'rw' + sessionIsRW: rootState.main.sessionMode === 'rw', }; }; diff --git a/src/components/pages/Compare.jsx b/src/components/pages/Compare.jsx index 1f1adf53..b9851529 100644 --- a/src/components/pages/Compare.jsx +++ b/src/components/pages/Compare.jsx @@ -573,7 +573,7 @@ class Compare extends Component { } this.setState({ crossAnnotations: cross }); } else { - console.log('Annotation cannot be found', viewer, name, remove); + console.log('Annotation cannot be found', viewer, name); } this.getCellMetadata(); } diff --git a/src/util.test.ts b/src/util.test.ts new file mode 100644 index 00000000..af734346 --- /dev/null +++ b/src/util.test.ts @@ -0,0 +1,42 @@ +import 'jest'; + +import { zipLists } from './util'; + +describe('zip arbitrary lists', () => { + it('zips the empty list', () => { + expect(zipLists([])).toEqual([]); + }); + + it('zips singleton lists', () => { + expect(zipLists([[1], [2], [3]])).toEqual([[1, 2, 3]]); + + expect(zipLists([[1]])).toEqual([[1]]); + + expect(zipLists([[1, 2, 3]])).toEqual([[1, 2, 3]]); + }); + + it('zips a pair of lists', () => { + expect( + zipLists([ + [1, 2], + [3, 4], + ]) + ).toEqual([ + [1, 3], + [2, 4], + ]); + }); + + it('zips 3 lists', () => { + expect( + zipLists([ + [1, 2], + [3, 4], + [5, 6], + ]) + ).toEqual([ + [1, 3, 5], + [2, 4, 6], + ]); + }); +}); diff --git a/src/util.ts b/src/util.ts new file mode 100644 index 00000000..2f99ce96 --- /dev/null +++ b/src/util.ts @@ -0,0 +1,26 @@ +/* Utility functions */ + +import * as R from 'ramda'; + +/** + * zip() but for an arbitrary number of lists. + * Normally you should use R.zip, but sometimes you may want to "zip" + * more than 2 arrays. + * + * Examples: + * zipLists([]) => [] + * zipLists([[1], [2], [3]]) => [[1, 2, 3]] + * zipLists([[1, 2], ['a', 'b']]) => [[1, 'a'], [2, 'b']] + */ +export const zipLists = (l: Array>): Array> => { + const acc: Array | undefined = R.head(l); + const data: Array> | undefined = R.tail(l); + + if (acc !== undefined && data !== undefined) { + const zipped: Readonly = R.isEmpty(data) + ? l + : R.reduce(R.zip, acc, data); + return R.map(R.flatten, zipped); + } + return []; +}; diff --git a/webpack.config.js b/webpack.config.js index 61d86993..d909fa52 100644 --- a/webpack.config.js +++ b/webpack.config.js @@ -3,7 +3,6 @@ const webpack = require('webpack'); const fs = require('fs'); const pkg = require('./package.json'); const TerserPlugin = require('terser-webpack-plugin'); -const ForkTsCheckerWebpackPlugin = require('fork-ts-checker-webpack-plugin'); const BundleAnalyzerPlugin = require('webpack-bundle-analyzer') .BundleAnalyzerPlugin; @@ -22,8 +21,8 @@ let config = { devServer: { host: '0.0.0.0', port: _config.mPort, - disableHostCheck: true, - publicPath: '/dist', + disableHostCheck: true, + publicPath: '/dist', }, output: { filename: pkg.name + '.js', @@ -35,7 +34,7 @@ let config = { module: { rules: [ { - test: /\.(t|j)s(x?)$/, + test: /\.js(x?)$/, exclude: /node_modules/, use: [ { @@ -45,7 +44,6 @@ let config = { babelrc: false, presets: [ '@babel/preset-env', - '@babel/preset-typescript', '@babel/preset-react', ], plugins: [ @@ -55,26 +53,30 @@ let config = { ], ['@babel/plugin-proposal-object-rest-spread'], ['@babel/transform-runtime'], - ['babel-plugin-redux-saga'], ], }, }, ], }, + { + test: /\.tsx?$/, + use: 'ts-loader', + exclude: /node_modules/, + }, { test: /\.css$/, - use: ['style-loader', 'css-loader'] + use: ['style-loader', 'css-loader'], }, { - test: /\.(png|woff|woff2|eot|ttf|svg)$/, - use: [ - { - loader: 'url-loader', - options: { - limit: 100000, - } - }, - ] + test: /\.(png|woff|woff2|eot|ttf|svg)$/, + use: [ + { + loader: 'url-loader', + options: { + limit: 100000, + }, + }, + ], }, ], }, @@ -113,7 +115,6 @@ let config = { }), __TEST_ONLY__: false, }), - new ForkTsCheckerWebpackPlugin(), new BundleAnalyzerPlugin({ openAnalyzer: false }), ], }; @@ -124,9 +125,9 @@ if (process.env.NODE_ENV === 'production') { minimizer: [new TerserPlugin()], }; } else { - config.optimization = { - moduleIds: 'named' - } + config.optimization = { + moduleIds: 'named', + }; } module.exports = config;