From b3bd70b289b5bd7e3424e0e1ba95f11cc4155beb Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Wed, 2 Nov 2022 18:28:22 +0100 Subject: [PATCH 01/14] feat: reimplement the tree without d3 DOM functions --- package.json | 11 +- src/clades.json | 20 +- src/components/Edge.tsx | 12 + src/components/HomePage.tsx | 86 ++++ src/components/NextstrainCladeTreeSvg.tsx | 73 ++++ src/components/NextstrainCladesSchema.tsx | 45 -- .../NextstrainCladesSchemaWrapped.tsx | 27 -- src/components/Node.tsx | 51 +++ src/components/SaveMarkupButton.tsx | 26 ++ src/components/constants.tsx | 9 + src/pages/_document.tsx | 29 ++ src/pages/index.tsx | 20 +- yarn.lock | 388 +++++++++++++++++- 13 files changed, 690 insertions(+), 107 deletions(-) create mode 100644 src/components/Edge.tsx create mode 100644 src/components/HomePage.tsx create mode 100644 src/components/NextstrainCladeTreeSvg.tsx delete mode 100644 src/components/NextstrainCladesSchema.tsx delete mode 100644 src/components/NextstrainCladesSchemaWrapped.tsx create mode 100644 src/components/Node.tsx create mode 100644 src/components/SaveMarkupButton.tsx create mode 100644 src/components/constants.tsx create mode 100644 src/pages/_document.tsx diff --git a/package.json b/package.json index 4a54146..8d70bb9 100644 --- a/package.json +++ b/package.json @@ -10,11 +10,17 @@ "cleanest": "rm -rf .cache .next node_modules" }, "dependencies": { - "d3": "7.2.1", + "bootstrap": "5.1.3", + "d3": "7.4.4", + "d3-flextree": "2.1.2", + "d3-hierarchy": "3.1.2", "file-saver": "2.0.5", "next": "12.0.7", "react": "17.0.2", - "react-dom": "17.0.2" + "react-dom": "17.0.2", + "react-resize-detector": "7.0.0", + "reactstrap": "9.0.2", + "styled-components": "5.3.5" }, "devDependencies": { "@types/d3": "7.1.0", @@ -22,6 +28,7 @@ "@types/node": "17.0.0", "@types/react": "17.0.37", "@types/react-dom": "17.0.11", + "@types/styled-components": "5.1.25", "eslint": "8.4.1", "eslint-config-next": "12.0.7", "eslint-config-prettier": "8.3.0", diff --git a/src/clades.json b/src/clades.json index d98cc19..98e6c89 100644 --- a/src/clades.json +++ b/src/clades.json @@ -1,18 +1,22 @@ { "color": "#C8C8C8", "name": "19A (B)", + "lineages": ["B"], "children": [ { "color": "#B8B8B8", - "name": "20A (B.1)", + "name": "20A", + "lineages": ["B.1"], "children": [ - { + { "color": "#B0B0B0", - "name": "20B (B.1.1)", + "name": "20B", + "lineages": ["B.1.1"], "children": [ { "color": "#D3B23F", - "name": "21M (Omicron, B.1.1.529)", + "name": "21M (Omicron)", + "lineages": ["B.1.1.529"], "children": [ { "color": "#C5B945", @@ -25,10 +29,11 @@ { "color": "#E59638", "name": "22B (Omicron, BA.5)", - "children":[ + "children": [ { "color": "#DF4628", - "name": "22E (Omicron, BQ.1)" + "name": "22E (Omicron)", + "lineages": ["BQ.1"] } ] }, @@ -136,7 +141,8 @@ }, { "color": "#C0C0C0", - "name": "19B (A)" + "name": "19B", + "lineages": ["A"] } ] } diff --git a/src/components/Edge.tsx b/src/components/Edge.tsx new file mode 100644 index 0000000..f33d67f --- /dev/null +++ b/src/components/Edge.tsx @@ -0,0 +1,12 @@ +import React from 'react' + +export interface EdgeProps { + x1: number + x2: number + y1: number + y2: number +} + +export function Edge({ x1, x2, y1, y2 }: EdgeProps) { + return +} diff --git a/src/components/HomePage.tsx b/src/components/HomePage.tsx new file mode 100644 index 0000000..ff6f38d --- /dev/null +++ b/src/components/HomePage.tsx @@ -0,0 +1,86 @@ +import React, { useRef } from 'react' +import Head from 'next/head' +import { useResizeDetector } from 'react-resize-detector' +import { SaveMarkupButton } from 'src/components/SaveMarkupButton' +import styled, { createGlobalStyle } from 'styled-components' +import { NextstrainCladeTreeSvg } from 'src/components/NextstrainCladeTreeSvg' +import { Container, Row, Col } from 'reactstrap' + +import cladesJson from '../clades.json' + +const GlobalStyle = createGlobalStyle` + html, body, #__next { + width: 100%; + height: 100%; + margin: 0; + padding: 0; + border: none; + } +` + +const CladeSchemaFigure = styled.figure` + width: 100%; + height: 100%; + margin: 0; + padding: 0; + border: none; +` + +const CladeSchemaPicture = styled.picture` + display: block; + width: 1200px; + height: 800px; + margin: 0; + padding: 0; + border: none; +` + +const CladeSchemaFigcaption = styled.figcaption` + font-family: sans-serif; +` + +export function HomePage() { + const svgRef = useRef(null) + + const { + width, + height, + ref: pictureRef, + } = useResizeDetector({ + handleHeight: true, + refreshOptions: { leading: true, trailing: true }, + }) + + return ( + <> + + {'Nextstrain clades'} + + + + + + + + + + + + + + + {'Phylogenetic relationships of Nextstrain SARS-CoV-2 clades'} + + + + + + + + + + + + + ) +} diff --git a/src/components/NextstrainCladeTreeSvg.tsx b/src/components/NextstrainCladeTreeSvg.tsx new file mode 100644 index 0000000..183ebb6 --- /dev/null +++ b/src/components/NextstrainCladeTreeSvg.tsx @@ -0,0 +1,73 @@ +import React, { RefObject, SVGProps, useMemo } from 'react' +import type { HierarchyPointNode } from 'd3-hierarchy' +import { hierarchy, tree } from 'd3-hierarchy' +import styled from 'styled-components' + +import { nodeHeight, nodeWidth } from 'src/components/constants' +import { Edge } from 'src/components/Edge' +import { Node } from 'src/components/Node' + +const Svg = styled.svg` + font-family: sans-serif; + font-size: 1.25rem; + margin: 0; + padding: 0; + border: none; +` + +export interface CladesJson { + color: string + name: string + lineages?: string[] + children?: CladesJson[] +} + +export interface CladeTreeSvgProps extends SVGProps { + cladesJson: CladesJson + width: number + height: number + innerRef: RefObject | ((instance: SVGSVGElement | null) => void) | null | undefined +} + +export function shift(node: HierarchyPointNode, { dx, dy }: { dx?: number; dy?: number }) { + return { ...node, x: node.x + (dx ?? 0), y: node.y + (dy ?? 0) } +} + +export function NextstrainCladeTreeSvg({ cladesJson, width, height, innerRef, ...restProps }: CladeTreeSvgProps) { + const { nodeComponents, edgeComponents } = useMemo(() => { + // NOTE: x/y and width/height are swapped here, because we want to render the tree sideways, not top to bottom + const root = hierarchy(cladesJson, (d) => d.children) + const t = tree().size([height - nodeHeight, width - nodeWidth]) + + const tm = t(root) as HierarchyPointNode + const nodes = tm.descendants() + const edges = tm.links() + + const nodeComponents = nodes.map((node) => ( + + )) + + const edgeComponents = edges.map((edge) => ( + + )) + + return { nodeComponents, edgeComponents } + }, [cladesJson, height, width]) + + if (!width || !height) { + return null + } + + return ( + + {edgeComponents} + {nodeComponents} + + ) +} diff --git a/src/components/NextstrainCladesSchema.tsx b/src/components/NextstrainCladesSchema.tsx deleted file mode 100644 index caf3ba0..0000000 --- a/src/components/NextstrainCladesSchema.tsx +++ /dev/null @@ -1,45 +0,0 @@ -import React, { RefObject, useCallback, useEffect, useRef } from 'react' - -import { saveAs } from 'file-saver' - -import clades from '../clades.json' - -// @ts-ignore -import { createCladesSchema } from '../createCladesSchema' - -export interface CladesJson { - name: string - color: string - children: CladesJson[] -} - -export function NextstrainCladesSchema({ d3Ref }: { d3Ref: RefObject }) { - const margin = { top: 0, right: 100, bottom: 0, left: 120 } - - const width = 1550 // Change this when the tree grows - const height = 950 // Change this when the tree grows - - const options = { margin, width, height } - - useEffect(() => { - if (d3Ref.current) { - console.log({ options }) - createCladesSchema(d3Ref.current, clades, options) - } - }) - - return ( -
- -
- ) -} diff --git a/src/components/NextstrainCladesSchemaWrapped.tsx b/src/components/NextstrainCladesSchemaWrapped.tsx deleted file mode 100644 index cd85687..0000000 --- a/src/components/NextstrainCladesSchemaWrapped.tsx +++ /dev/null @@ -1,27 +0,0 @@ -import React, { useCallback, useRef } from 'react' - -import { saveAs } from 'file-saver' -import { NextstrainCladesSchema } from './NextstrainCladesSchema' - -export function NextstrainCladesSchemaWrapped() { - const d3Ref = useRef(null) - - const handleSaveToSvg = useCallback(() => { - if (d3Ref.current) { - const blob = new Blob([d3Ref.current.outerHTML], { - type: 'image/svg+xml', - }) - saveAs(blob, 'clades.svg') - } - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [d3Ref.current]) - - return ( -
- - -
- ) -} diff --git a/src/components/Node.tsx b/src/components/Node.tsx new file mode 100644 index 0000000..ac714cb --- /dev/null +++ b/src/components/Node.tsx @@ -0,0 +1,51 @@ +import React, { ReactElement, useMemo } from 'react' +import styled from 'styled-components' + +import { CladesJson } from 'src/components/NextstrainCladeTreeSvg' +import { cladesTextColor, cladesTextSize, lineagesRectHeight, lineagesTextColor, lineagesTextSize } from './constants' + +const Rect = styled.rect` + border-radius: 3px; +` + +export interface CladeTreeNodeProps { + node: CladesJson + x: number + y: number + nodeWidth: number + nodeHeight: number +} + +export function Node({ node, x, y, nodeWidth, nodeHeight }: CladeTreeNodeProps): ReactElement { + const { name, color, lineages } = node + const lineagesText = useMemo(() => node.lineages?.join(', '), [node.lineages]) + return ( + + + + {name} + + + + + {lineagesText} + + + ) +} diff --git a/src/components/SaveMarkupButton.tsx b/src/components/SaveMarkupButton.tsx new file mode 100644 index 0000000..f8f9a2a --- /dev/null +++ b/src/components/SaveMarkupButton.tsx @@ -0,0 +1,26 @@ +import React, { LegacyRef, MutableRefObject, Ref, RefObject, useCallback } from 'react' +import { saveAs } from 'file-saver' + +export interface SaveButtonProps { + text: string + targetRef?: RefObject | MutableRefObject | null +} + +export function SaveMarkupButton({ text, targetRef }: SaveButtonProps) { + const handleSaveToSvg = useCallback(() => { + console.log(targetRef?.current) + + if (targetRef?.current) { + const blob = new Blob([targetRef.current.outerHTML], { + type: 'image/svg+xml', + }) + saveAs(blob, 'clades.svg') + } + }, [targetRef]) + + return ( + + ) +} diff --git a/src/components/constants.tsx b/src/components/constants.tsx new file mode 100644 index 0000000..47c0ade --- /dev/null +++ b/src/components/constants.tsx @@ -0,0 +1,9 @@ +export const nodeWidth = 100 +export const nodeHeight = 30 +export const horizontalSeparationBetweenNodes = 90 +export const verticalSeparationBetweenNodes = 20 +export const lineagesRectHeight = 12 +export const cladesTextSize = 14 +export const lineagesTextSize = 10 +export const lineagesTextColor = '#444' +export const cladesTextColor = '#222' diff --git a/src/pages/_document.tsx b/src/pages/_document.tsx new file mode 100644 index 0000000..e962c03 --- /dev/null +++ b/src/pages/_document.tsx @@ -0,0 +1,29 @@ +import React from 'react' + +import { ServerStyleSheet } from 'styled-components' +import NextDocument, { Html, Head, Main, NextScript, DocumentContext, DocumentInitialProps } from 'next/document' + +import { createGlobalStyle } from 'styled-components' + +export default class Document extends NextDocument { + static async getInitialProps(ctx: DocumentContext): Promise { + const sheet = new ServerStyleSheet() + const originalRenderPage = ctx.renderPage + + try { + ctx.renderPage = () => + originalRenderPage({ enhanceApp: (App) => (props) => sheet.collectStyles() }) + + const initialProps = await NextDocument.getInitialProps(ctx) + + const styles = [initialProps.styles, sheet.getStyleElement()] + + return { + ...initialProps, + styles, + } + } finally { + sheet.seal() + } + } +} diff --git a/src/pages/index.tsx b/src/pages/index.tsx index 99f4d39..3dcafd8 100644 --- a/src/pages/index.tsx +++ b/src/pages/index.tsx @@ -1,19 +1 @@ -import React from 'react' - -import Head from 'next/head' - -import { NextstrainCladesSchemaWrapped } from '../components/NextstrainCladesSchemaWrapped' - -export default function Home() { - return ( -
- - {'Nextstrain clades'} - - - - - -
- ) -} +export { HomePage as default } from '../components/HomePage' diff --git a/yarn.lock b/yarn.lock index 3d5e97a..1aa697c 100644 --- a/yarn.lock +++ b/yarn.lock @@ -9,16 +9,80 @@ dependencies: "@babel/highlight" "^7.10.4" +"@babel/code-frame@^7.16.7": + version "7.16.7" + resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.16.7.tgz#44416b6bd7624b998f5b1af5d470856c40138789" + integrity sha512-iAXqUn8IIeBTNd72xsFlgaXHkMBMt6y4HJp1tIaK465CWLT/fG1aqB7ykr95gHHmlBdGbFeWWfyB4NJJ0nmeIg== + dependencies: + "@babel/highlight" "^7.16.7" + +"@babel/generator@^7.17.10": + version "7.17.10" + resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.17.10.tgz#c281fa35b0c349bbe9d02916f4ae08fc85ed7189" + integrity sha512-46MJZZo9y3o4kmhBVc7zW7i8dtR1oIK/sdO5NcfcZRhTGYi+KKJRtHNgsU6c4VUcJmUNV/LQdebD/9Dlv4K+Tg== + dependencies: + "@babel/types" "^7.17.10" + "@jridgewell/gen-mapping" "^0.1.0" + jsesc "^2.5.1" + +"@babel/helper-annotate-as-pure@^7.16.0": + version 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+"@babel/helper-validator-identifier@^7.16.7": + version "7.16.7" + resolved "https://registry.yarnpkg.com/@babel/helper-validator-identifier/-/helper-validator-identifier-7.16.7.tgz#e8c602438c4a8195751243da9031d1607d247cad" + integrity sha512-hsEnFemeiW4D08A5gUAZxLBTXpZ39P+a+DGDsHw1yxqyQ/jzFEnxf5uTEGp+3bzAbNOxU1paTgYS4ECU/IgfDw== + "@babel/highlight@^7.10.4": version "7.16.0" resolved "https://registry.yarnpkg.com/@babel/highlight/-/highlight-7.16.0.tgz#6ceb32b2ca4b8f5f361fb7fd821e3fddf4a1725a" @@ -28,6 +92,20 @@ chalk "^2.0.0" js-tokens "^4.0.0" +"@babel/highlight@^7.16.7": + version "7.17.9" + resolved "https://registry.yarnpkg.com/@babel/highlight/-/highlight-7.17.9.tgz#61b2ee7f32ea0454612def4fccdae0de232b73e3" + integrity sha512-J9PfEKCbFIv2X5bjTMiZu6Vf341N05QIY+d6FvVKynkG1S7G0j3I0QoRtWIrXhZ+/Nlb5Q0MzqL7TokEJ5BNHg== + dependencies: + "@babel/helper-validator-identifier" "^7.16.7" + chalk "^2.0.0" + js-tokens "^4.0.0" + +"@babel/parser@^7.16.7", "@babel/parser@^7.17.10": + version 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"7.15.0" resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.15.0.tgz#61af11f2286c4e9c69ca8deb5f4375a73c72dcbd" @@ -65,6 +175,14 @@ "@babel/helper-validator-identifier" "^7.14.9" to-fast-properties "^2.0.0" +"@babel/types@^7.16.7", "@babel/types@^7.17.0", "@babel/types@^7.17.10": + version "7.17.10" + resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.17.10.tgz#d35d7b4467e439fcf06d195f8100e0fea7fc82c4" + integrity sha512-9O26jG0mBYfGkUYCYZRnBwbVLd1UZOICEr2Em6InB6jVfsAv1GKgwXHmrSg+WFWDmeKTA6vyTZiN8tCSM5Oo3A== + dependencies: + "@babel/helper-validator-identifier" "^7.16.7" + to-fast-properties "^2.0.0" + "@cspotcode/source-map-consumer@0.8.0": version "0.8.0" resolved "https://registry.yarnpkg.com/@cspotcode/source-map-consumer/-/source-map-consumer-0.8.0.tgz#33bf4b7b39c178821606f669bbc447a6a629786b" @@ -77,6 +195,28 @@ dependencies: "@cspotcode/source-map-consumer" "0.8.0" +"@emotion/is-prop-valid@^1.1.0": + version "1.1.2" + resolved 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"https://registry.yarnpkg.com/@types/json5/-/json5-0.0.29.tgz#ee28707ae94e11d2b827bcbe5270bcea7f3e71ee" @@ -527,11 +698,25 @@ "@types/scheduler" "*" csstype "^3.0.2" +"@types/resize-observer-browser@^0.1.6": + version "0.1.7" + resolved "https://registry.yarnpkg.com/@types/resize-observer-browser/-/resize-observer-browser-0.1.7.tgz#294aaadf24ac6580b8fbd1fe3ab7b59fe85f9ef3" + integrity sha512-G9eN0Sn0ii9PWQ3Vl72jDPgeJwRWhv2Qk/nQkJuWmRmOB4HX3/BhD5SE1dZs/hzPZL/WKnvF0RHdTSG54QJFyg== + "@types/scheduler@*": version "0.16.2" resolved "https://registry.yarnpkg.com/@types/scheduler/-/scheduler-0.16.2.tgz#1a62f89525723dde24ba1b01b092bf5df8ad4d39" integrity sha512-hppQEBDmlwhFAXKJX2KnWLYu5yMfi91yazPb2l+lbJiwW+wdo1gNeRA+3RgNSO39WYX2euey41KEwnqesU2Jew== +"@types/styled-components@5.1.25": + version "5.1.25" + resolved "https://registry.yarnpkg.com/@types/styled-components/-/styled-components-5.1.25.tgz#0177c4ab5fa7c6ed0565d36f597393dae3f380ad" + integrity 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"@babel/helper-annotate-as-pure" "^7.16.0" + "@babel/helper-module-imports" "^7.16.0" + babel-plugin-syntax-jsx "^6.18.0" + lodash "^4.17.11" + picomatch "^2.3.0" + +babel-plugin-syntax-jsx@^6.18.0: + version "6.18.0" + resolved "https://registry.yarnpkg.com/babel-plugin-syntax-jsx/-/babel-plugin-syntax-jsx-6.18.0.tgz#0af32a9a6e13ca7a3fd5069e62d7b0f58d0d8946" + integrity sha1-CvMqmm4Tyno/1QaeYtew9Y0NiUY= + balanced-match@^1.0.0: version "1.0.2" resolved "https://registry.yarnpkg.com/balanced-match/-/balanced-match-1.0.2.tgz#e83e3a7e3f300b34cb9d87f615fa0cbf357690ee" @@ -765,6 +966,11 @@ bn.js@^5.0.0, bn.js@^5.1.1: resolved "https://registry.yarnpkg.com/bn.js/-/bn.js-5.2.0.tgz#358860674396c6997771a9d051fcc1b57d4ae002" integrity sha512-D7iWRBvnZE8ecXiLj/9wbxH7Tk79fAh8IHaTNq1RWRixsS02W+5qS+iE9yq6RYl0asXx5tw0bLhmT5pIfbSquw== +bootstrap@5.1.3: + version "5.1.3" + resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-5.1.3.tgz#ba081b0c130f810fa70900acbc1c6d3c28fa8f34" + integrity 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resolved "https://registry.yarnpkg.com/d3-interpolate/-/d3-interpolate-3.0.1.tgz#3c47aa5b32c5b3dfb56ef3fd4342078a632b400d" @@ -1306,10 +1553,10 @@ d3-zoom@3: d3-selection "2 - 3" d3-transition "2 - 3" -d3@7.2.1: - version "7.2.1" - resolved "https://registry.yarnpkg.com/d3/-/d3-7.2.1.tgz#97eafaa6fc8cd7c564c3ace1e6678cbecf63f3ea" - integrity sha512-E/5sP0aeK6YPXI/+4QlefvBFgmcyR2jYftId0PrYWv4Y/gW3c3thp1XG4rQzF0eUwV9tR1x05X5eWuJ6rQXvew== +d3@7.4.4: + version "7.4.4" + resolved "https://registry.yarnpkg.com/d3/-/d3-7.4.4.tgz#bfbf87487c37d3196efebd5a63e3a0ed8299d8ff" + integrity sha512-97FE+MYdAlV3R9P74+R3Uar7wUKkIFu89UWMjEaDhiJ9VxKvqaMxauImy8PC2DdBkdM2BxJOIoLxPrcZUyrKoQ== dependencies: d3-array "3" d3-axis "3" @@ -1366,6 +1613,13 @@ debug@^3.2.7: dependencies: ms "^2.1.1" +debug@^4.1.0: + version "4.3.4" + resolved "https://registry.yarnpkg.com/debug/-/debug-4.3.4.tgz#1319f6579357f2338d3337d2cdd4914bb5dcc865" + integrity 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"https://registry.yarnpkg.com/globals/-/globals-11.12.0.tgz#ab8795338868a0babd8525758018c2a7eb95c42e" + integrity sha512-WOBp/EEGUiIsJSp7wcv/y6MO+lV9UoncWqxuFfm8eBwzWNgyfBd6Gz+IeKQ9jCmyhoH99g15M3T+QaVHFjizVA== + globals@^13.6.0, globals@^13.9.0: version "13.12.0" resolved "https://registry.yarnpkg.com/globals/-/globals-13.12.0.tgz#4d733760304230a0082ed96e21e5c565f898089e" @@ -2042,6 +2309,13 @@ hmac-drbg@^1.0.1: minimalistic-assert "^1.0.0" minimalistic-crypto-utils "^1.0.1" +hoist-non-react-statics@^3.0.0, hoist-non-react-statics@^3.3.0: + version "3.3.2" + resolved "https://registry.yarnpkg.com/hoist-non-react-statics/-/hoist-non-react-statics-3.3.2.tgz#ece0acaf71d62c2969c2ec59feff42a4b1a85b45" + integrity sha512-/gGivxi8JPKWNm/W0jSmzcMPpfpPLc3dY/6GxhX2hQ9iGj3aDfklV4ET7NjKpSinLpJ5vafa9iiGIEZg10SfBw== + dependencies: + react-is "^16.7.0" + http-errors@1.7.3: version "1.7.3" resolved "https://registry.yarnpkg.com/http-errors/-/http-errors-1.7.3.tgz#6c619e4f9c60308c38519498c14fbb10aacebb06" @@ -2298,6 +2572,11 @@ js-yaml@^4.1.0: dependencies: argparse "^2.0.1" +jsesc@^2.5.1: + version "2.5.2" + resolved "https://registry.yarnpkg.com/jsesc/-/jsesc-2.5.2.tgz#80564d2e483dacf6e8ef209650a67df3f0c283a4" + integrity sha512-OYu7XEzjkCQ3C5Ps3QIZsQfNpqoJyZZA99wd9aWd05NCtC5pWOkShK2mkL6HXQR6/Cy2lbNdPlZBpuQHXE63gA== + json-schema-traverse@^0.4.1: version "0.4.1" resolved "https://registry.yarnpkg.com/json-schema-traverse/-/json-schema-traverse-0.4.1.tgz#69f6a87d9513ab8bb8fe63bdb0979c448e684660" @@ -2377,7 +2656,12 @@ lodash.sortby@^4.7.0: resolved "https://registry.yarnpkg.com/lodash.sortby/-/lodash.sortby-4.7.0.tgz#edd14c824e2cc9c1e0b0a1b42bb5210516a42438" integrity sha1-7dFMgk4sycHgsKG0K7UhBRakJDg= -loose-envify@^1.1.0, loose-envify@^1.4.0: +lodash@^4.17.11, lodash@^4.17.21: + version "4.17.21" + resolved 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"https://registry.yarnpkg.com/progress/-/progress-2.0.3.tgz#7e8cf8d8f5b8f239c1bc68beb4eb78567d572ef8" integrity sha512-7PiHtLll5LdnKIMw100I+8xJXR5gW2QwWYkT6iJva0bXitZKa/XMrSbdmg3r2Xnaidz9Qumd0VPaMrZlF9V9sA== +prop-types@^15.5.8, prop-types@^15.6.2: + version "15.8.1" + resolved "https://registry.yarnpkg.com/prop-types/-/prop-types-15.8.1.tgz#67d87bf1a694f48435cf332c24af10214a3140b5" + integrity sha512-oj87CgZICdulUohogVAR7AjlC0327U4el4L6eAvOqCeudMDVU0NThNaV+b9Df4dXgSP1gXMTnPdhfe/2qDH5cg== + dependencies: + loose-envify "^1.4.0" + object-assign "^4.1.1" + react-is "^16.13.1" + prop-types@^15.7.2: version "15.7.2" resolved "https://registry.yarnpkg.com/prop-types/-/prop-types-15.7.2.tgz#52c41e75b8c87e72b9d9360e0206b99dcbffa6c5" @@ -2910,21 +3213,52 @@ react-dom@17.0.2: object-assign "^4.1.1" scheduler "^0.20.2" +react-fast-compare@^3.0.1: + version "3.2.0" + resolved "https://registry.yarnpkg.com/react-fast-compare/-/react-fast-compare-3.2.0.tgz#641a9da81b6a6320f270e89724fb45a0b39e43bb" + integrity sha512-rtGImPZ0YyLrscKI9xTpV8psd6I8VAtjKCzQDlzyDvqJA8XOW78TXYQwNRNd8g8JZnDu8q9Fu/1v4HPAVwVdHA== + react-is@17.0.2: version "17.0.2" resolved "https://registry.yarnpkg.com/react-is/-/react-is-17.0.2.tgz#e691d4a8e9c789365655539ab372762b0efb54f0" integrity sha512-w2GsyukL62IJnlaff/nRegPQR94C/XXamvMWmSHRJ4y7Ts/4ocGRmTHvOs8PSE6pB3dWOrD/nueuU5sduBsQ4w== -react-is@^16.8.1: +react-is@^16.13.1, react-is@^16.7.0, react-is@^16.8.1: version "16.13.1" resolved "https://registry.yarnpkg.com/react-is/-/react-is-16.13.1.tgz#789729a4dc36de2999dc156dd6c1d9c18cea56a4" integrity sha512-24e6ynE2H+OKt4kqsOvNd8kBpV65zoxbA4BVsEOB3ARVWQki/DHzaUoC5KuON/BiccDaCCTZBuOcfZs70kR8bQ== +react-popper@^2.2.4: + version "2.3.0" + resolved "https://registry.yarnpkg.com/react-popper/-/react-popper-2.3.0.tgz#17891c620e1320dce318bad9fede46a5f71c70ba" + integrity sha512-e1hj8lL3uM+sgSR4Lxzn5h1GxBlpa4CQz0XLF8kx4MDrDRWY0Ena4c97PUeSX9i5W3UAfDP0z0FXCTQkoXUl3Q== + dependencies: + react-fast-compare "^3.0.1" + warning "^4.0.2" + react-refresh@0.8.3: version "0.8.3" resolved "https://registry.yarnpkg.com/react-refresh/-/react-refresh-0.8.3.tgz#721d4657672d400c5e3c75d063c4a85fb2d5d68f" integrity sha512-X8jZHc7nCMjaCqoU+V2I0cOhNW+QMBwSUkeXnTi8IPe6zaRWfn60ZzvFDZqWPfmSJfjub7dDW1SP0jaHWLu/hg== +react-resize-detector@7.0.0: + version "7.0.0" + resolved "https://registry.yarnpkg.com/react-resize-detector/-/react-resize-detector-7.0.0.tgz#fbd46917ee905b7796c797aa6b301b454a6b9229" + integrity sha512-Xd1POfpVzH9O3F/xB/0xYy2ijtKjE/z7y4c/aJP593YSzhPy2vDhsNPjes+uQbgL1RezxJajQ679qPs8K5LAFw== + dependencies: + "@types/resize-observer-browser" "^0.1.6" + lodash "^4.17.21" + +react-transition-group@^4.4.2: + version "4.4.2" + resolved "https://registry.yarnpkg.com/react-transition-group/-/react-transition-group-4.4.2.tgz#8b59a56f09ced7b55cbd53c36768b922890d5470" + integrity sha512-/RNYfRAMlZwDSr6z4zNKV6xu53/e2BuaBbGhbyYIXTrmgu/bGHzmqOs7mJSJBHy9Ud+ApHx3QjrkKSp1pxvlFg== + dependencies: + "@babel/runtime" "^7.5.5" + dom-helpers "^5.0.1" + loose-envify "^1.4.0" + prop-types "^15.6.2" + react@17.0.2: version "17.0.2" resolved "https://registry.yarnpkg.com/react/-/react-17.0.2.tgz#d0b5cc516d29eb3eee383f75b62864cfb6800037" @@ -2933,6 +3267,18 @@ react@17.0.2: loose-envify "^1.1.0" object-assign "^4.1.1" +reactstrap@9.0.2: + version "9.0.2" + resolved "https://registry.yarnpkg.com/reactstrap/-/reactstrap-9.0.2.tgz#64bb034c2a92574e6ccd41bec0b428125ff0504e" + integrity sha512-vvSy/dX7UL5fsfu4WMLnPYfrBS/G2YQM37nff1caeAlMVqzg6NV8G7RRd8PWu8RqtCSeEjDn5ILF0ZmE2ZrHuw== + dependencies: + "@babel/runtime" "^7.12.5" + "@popperjs/core" "^2.6.0" + classnames "^2.2.3" + prop-types "^15.5.8" + react-popper "^2.2.4" + react-transition-group "^4.4.2" + readable-stream@^3.5.0, readable-stream@^3.6.0: version "3.6.0" resolved "https://registry.yarnpkg.com/readable-stream/-/readable-stream-3.6.0.tgz#337bbda3adc0706bd3e024426a286d4b4b2c9198" @@ -3083,6 +3429,11 @@ sha.js@^2.4.0, sha.js@^2.4.8: inherits "^2.0.1" safe-buffer "^5.0.1" +shallowequal@^1.1.0: + version "1.1.0" + resolved "https://registry.yarnpkg.com/shallowequal/-/shallowequal-1.1.0.tgz#188d521de95b9087404fd4dcb68b13df0ae4e7f8" + integrity sha512-y0m1JoUZSlPAjXVtPPW70aZWfIL/dSP7AFkRnniLCrK/8MDKog3TySTBmckD+RObVxH0v4Tox67+F14PdED2oQ== + shebang-command@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/shebang-command/-/shebang-command-2.0.0.tgz#ccd0af4f8835fbdc265b82461aaf0c36663f34ea" @@ -3227,6 +3578,22 @@ strip-json-comments@^3.1.0, strip-json-comments@^3.1.1: resolved "https://registry.yarnpkg.com/strip-json-comments/-/strip-json-comments-3.1.1.tgz#31f1281b3832630434831c310c01cccda8cbe006" integrity sha512-6fPc+R4ihwqP6N/aIv2f1gMH8lOVtWQHoqC4yK6oSDVVocumAsfCqjkXnqiYMhmMwS/mEHLp7Vehlt3ql6lEig== +styled-components@5.3.5: + version "5.3.5" + resolved "https://registry.yarnpkg.com/styled-components/-/styled-components-5.3.5.tgz#a750a398d01f1ca73af16a241dec3da6deae5ec4" + integrity sha512-ndETJ9RKaaL6q41B69WudeqLzOpY1A/ET/glXkNZ2T7dPjPqpPCXXQjDFYZWwNnE5co0wX+gTCqx9mfxTmSIPg== + dependencies: + "@babel/helper-module-imports" "^7.0.0" + "@babel/traverse" "^7.4.5" + "@emotion/is-prop-valid" "^1.1.0" + "@emotion/stylis" "^0.8.4" + "@emotion/unitless" "^0.7.4" + babel-plugin-styled-components ">= 1.12.0" + css-to-react-native "^3.0.0" + hoist-non-react-statics "^3.0.0" + shallowequal "^1.1.0" + supports-color "^5.5.0" + styled-jsx@5.0.0-beta.3: version "5.0.0-beta.3" resolved "https://registry.yarnpkg.com/styled-jsx/-/styled-jsx-5.0.0-beta.3.tgz#400d16179b5dff10d5954ab8be27a9a1b7780dd2" @@ -3251,7 +3618,7 @@ stylis@3.5.4: resolved "https://registry.yarnpkg.com/stylis/-/stylis-3.5.4.tgz#f665f25f5e299cf3d64654ab949a57c768b73fbe" integrity sha512-8/3pSmthWM7lsPBKv7NXkzn2Uc9W7NotcwGNpJaa3k7WMM1XDCA4MgT5k/8BIexd5ydZdboXtU90XH9Ec4Bv/Q== -supports-color@^5.3.0: +supports-color@^5.3.0, supports-color@^5.5.0: version "5.5.0" resolved "https://registry.yarnpkg.com/supports-color/-/supports-color-5.5.0.tgz#e2e69a44ac8772f78a1ec0b35b689df6530efc8f" integrity sha512-QjVjwdXIt408MIiAqCX4oUKsgU2EqAGzs2Ppkm4aQYbjm+ZEWEcW4SfFNTr4uMNZma0ey4f5lgLrkB0aX0QMow== @@ -3431,6 +3798,13 @@ vm-browserify@1.1.2: resolved "https://registry.yarnpkg.com/vm-browserify/-/vm-browserify-1.1.2.tgz#78641c488b8e6ca91a75f511e7a3b32a86e5dda0" integrity sha512-2ham8XPWTONajOR0ohOKOHXkm3+gaBmGut3SRuu75xLd/RRaY6vqgh8NBYYk7+RW3u5AtzPQZG8F10LHkl0lAQ== +warning@^4.0.2: + version "4.0.3" + resolved "https://registry.yarnpkg.com/warning/-/warning-4.0.3.tgz#16e9e077eb8a86d6af7d64aa1e05fd85b4678ca3" + integrity sha512-rpJyN222KWIvHJ/F53XSZv0Zl/accqHR8et1kpaMTD/fLCRxtV8iX8czMzY7sVZupTI3zcUTg8eycS2kNF9l6w== + dependencies: + loose-envify "^1.0.0" + watchpack@2.3.0: version "2.3.0" resolved "https://registry.yarnpkg.com/watchpack/-/watchpack-2.3.0.tgz#a41bca3da6afaff31e92a433f4c856a0c25ea0c4" From d57379060cb9cea4d3d0a0894f2912b02f958726 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Wed, 2 Nov 2022 18:46:54 +0100 Subject: [PATCH 02/14] chore(ci): disable Next.js type- and eslint checks --- next.config.cjs | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/next.config.cjs b/next.config.cjs index e292d20..b47d0c1 100644 --- a/next.config.cjs +++ b/next.config.cjs @@ -3,4 +3,10 @@ /** @type {import('next').NextConfig} */ module.exports = { reactStrictMode: true, + typescript: { + ignoreBuildErrors: true, + }, + eslint: { + ignoreDuringBuilds: true, + }, } From 672d4abfa06cbcb5c1dd91ed2c0702608050e7a7 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Wed, 2 Nov 2022 18:56:10 +0100 Subject: [PATCH 03/14] chore: fix next.js config file being ignored Due to incorrect extension --- next.config.cjs => next.config.js | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename next.config.cjs => next.config.js (100%) diff --git a/next.config.cjs b/next.config.js similarity index 100% rename from next.config.cjs rename to next.config.js From b3deec41b19b1989228766e83dd4ff2f8b335e55 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Wed, 2 Nov 2022 19:30:43 +0100 Subject: [PATCH 04/14] refactor: lint --- src/components/HomePage.tsx | 2 +- src/components/NextstrainCladeTreeSvg.tsx | 79 +++++++++++++---------- 2 files changed, 45 insertions(+), 36 deletions(-) diff --git a/src/components/HomePage.tsx b/src/components/HomePage.tsx index ff6f38d..c31dc5a 100644 --- a/src/components/HomePage.tsx +++ b/src/components/HomePage.tsx @@ -66,7 +66,7 @@ export function HomePage() { - + {'Phylogenetic relationships of Nextstrain SARS-CoV-2 clades'} diff --git a/src/components/NextstrainCladeTreeSvg.tsx b/src/components/NextstrainCladeTreeSvg.tsx index 183ebb6..5a6fbc0 100644 --- a/src/components/NextstrainCladeTreeSvg.tsx +++ b/src/components/NextstrainCladeTreeSvg.tsx @@ -1,4 +1,4 @@ -import React, { RefObject, SVGProps, useMemo } from 'react' +import React, { forwardRef, LegacyRef, RefObject, SVGProps, useMemo } from 'react' import type { HierarchyPointNode } from 'd3-hierarchy' import { hierarchy, tree } from 'd3-hierarchy' import styled from 'styled-components' @@ -22,52 +22,61 @@ export interface CladesJson { children?: CladesJson[] } -export interface CladeTreeSvgProps extends SVGProps { +export interface CladeTreeSvgProps { cladesJson: CladesJson width: number height: number - innerRef: RefObject | ((instance: SVGSVGElement | null) => void) | null | undefined } export function shift(node: HierarchyPointNode, { dx, dy }: { dx?: number; dy?: number }) { return { ...node, x: node.x + (dx ?? 0), y: node.y + (dy ?? 0) } } -export function NextstrainCladeTreeSvg({ cladesJson, width, height, innerRef, ...restProps }: CladeTreeSvgProps) { - const { nodeComponents, edgeComponents } = useMemo(() => { - // NOTE: x/y and width/height are swapped here, because we want to render the tree sideways, not top to bottom - const root = hierarchy(cladesJson, (d) => d.children) - const t = tree().size([height - nodeHeight, width - nodeWidth]) +// eslint-disable-next-line react/display-name +export const NextstrainCladeTreeSvg = forwardRef( + ({ cladesJson, width, height, ...restProps }, ref) => { + const { nodeComponents, edgeComponents } = useMemo(() => { + // NOTE: x/y and width/height are swapped here, because we want to render the tree sideways, not top to bottom + const root = hierarchy(cladesJson, (d) => d.children) + const t = tree().size([height - nodeHeight, width - nodeWidth]) - const tm = t(root) as HierarchyPointNode - const nodes = tm.descendants() - const edges = tm.links() + const tm = t(root) as HierarchyPointNode + const nodes = tm.descendants() + const edges = tm.links() - const nodeComponents = nodes.map((node) => ( - - )) + const nodeComponents = nodes.map((node) => ( + + )) - const edgeComponents = edges.map((edge) => ( - - )) + const edgeComponents = edges.map((edge) => ( + + )) - return { nodeComponents, edgeComponents } - }, [cladesJson, height, width]) + return { nodeComponents, edgeComponents } + }, [cladesJson, height, width]) - if (!width || !height) { - return null - } + if (!width || !height) { + return null + } - return ( - - {edgeComponents} - {nodeComponents} - - ) -} + return ( + + {edgeComponents} + {nodeComponents} + + ) + }, +) From bb00aa30aaf9aa0ec6ad3837938e76192e217110 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Wed, 2 Nov 2022 19:32:32 +0100 Subject: [PATCH 05/14] chore: hide tsbuildinfo file --- tsconfig.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tsconfig.json b/tsconfig.json index 6764d77..56b6ea1 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -18,7 +18,8 @@ "resolveJsonModule": true, "skipLibCheck": true, "strict": true, - "target": "ES5" + "target": "ES5", + "tsBuildInfoFile": ".cache/.tsbuildinfo" }, "include": ["next-env.d.ts", "**/*.ts", "**/*.tsx", "**/*.js", "**/*.jsx", "**/*.json"], "exclude": ["node_modules", ".eslintrc.js"] From fe916148944afe828f619a57c8f22179fc7577de Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Wed, 2 Nov 2022 21:01:03 +0100 Subject: [PATCH 06/14] feat: convert clades.json tree into a graph Here I add a script to "flatten" the object hierarchy in `clades.json` into 2 lists: `nodes` and `edges` that represent the same hierarchy in a different way. Every node now has an `id` (an arbitrary string). Every edge is directional and refers to its `source` and `target` noes by the node `id`. This representation will allow us to build arbitrary directed graphs instead of just trees (in particular, to allow showing recombinant relationships between clades) I also split the composite Nextstrain name strings into the clade, lineages, who variant and other components. This should allows a richer display. --- package.json | 4 + src/clades.json | 20 +-- src/clades2.json | 454 +++++++++++++++++++++++++++++++++++++++++++++++ tools/flatten.ts | 164 +++++++++++++++++ tsconfig.json | 8 + yarn.lock | 42 ++++- 6 files changed, 678 insertions(+), 14 deletions(-) create mode 100644 src/clades2.json create mode 100644 tools/flatten.ts diff --git a/package.json b/package.json index 8d70bb9..a610890 100644 --- a/package.json +++ b/package.json @@ -15,6 +15,7 @@ "d3-flextree": "2.1.2", "d3-hierarchy": "3.1.2", "file-saver": "2.0.5", + "lodash": "4.17.21", "next": "12.0.7", "react": "17.0.2", "react-dom": "17.0.2", @@ -25,6 +26,8 @@ "devDependencies": { "@types/d3": "7.1.0", "@types/file-saver": "2.0.4", + "@types/fs-extra": "9.0.13", + "@types/lodash": "4.14.187", "@types/node": "17.0.0", "@types/react": "17.0.37", "@types/react-dom": "17.0.11", @@ -32,6 +35,7 @@ "eslint": "8.4.1", "eslint-config-next": "12.0.7", "eslint-config-prettier": "8.3.0", + "fs-extra": "10.1.0", "prettier": "2.5.1", "ts-node": "10.4.0", "typescript": "4.5.4" diff --git a/src/clades.json b/src/clades.json index 98e6c89..d98cc19 100644 --- a/src/clades.json +++ b/src/clades.json @@ -1,22 +1,18 @@ { "color": "#C8C8C8", "name": "19A (B)", - "lineages": ["B"], "children": [ { "color": "#B8B8B8", - "name": "20A", - "lineages": ["B.1"], + "name": "20A (B.1)", "children": [ - { + { "color": "#B0B0B0", - "name": "20B", - "lineages": ["B.1.1"], + "name": "20B (B.1.1)", "children": [ { "color": "#D3B23F", - "name": "21M (Omicron)", - "lineages": ["B.1.1.529"], + "name": "21M (Omicron, B.1.1.529)", "children": [ { "color": "#C5B945", @@ -29,11 +25,10 @@ { "color": "#E59638", "name": "22B (Omicron, BA.5)", - "children": [ + "children":[ { "color": "#DF4628", - "name": "22E (Omicron)", - "lineages": ["BQ.1"] + "name": "22E (Omicron, BQ.1)" } ] }, @@ -141,8 +136,7 @@ }, { "color": "#C0C0C0", - "name": "19B", - "lineages": ["A"] + "name": "19B (A)" } ] } diff --git a/src/clades2.json b/src/clades2.json new file mode 100644 index 0000000..66bf5f2 --- /dev/null +++ b/src/clades2.json @@ -0,0 +1,454 @@ +{ + "nodes": [ + { + "id": "19A (B)", + "color": "#C8C8C8", + "clade": "19A", + "lineages": [ + "B" + ], + "otherNames": [] + }, + { + "id": "19B (A)", + "color": "#C0C0C0", + "clade": "19B", + "lineages": [ + "A" + ], + "otherNames": [] + }, + { + "id": "20A (B.1)", + "color": "#B8B8B8", + "clade": "20A", + "lineages": [ + "B.1" + ], + "otherNames": [] + }, + { + "id": "20B (B.1.1)", + "color": "#B0B0B0", + "clade": "20B", + "lineages": [ + "B.1.1" + ], + "otherNames": [] + }, + { + "id": "20C", + "color": "#A8A8A8", + "clade": "20C" + }, + { + "id": "20D (B.1.1.1)", + "color": "#A0A0A0", + "clade": "20D", + "lineages": [ + "B.1.1.1" + ], + "otherNames": [] + }, + { + "id": "20E (EU1, B.1.177)", + "color": "#989898", + "clade": "20E", + "lineages": [ + "B.1.177" + ], + "otherNames": [ + "EU1" + ] + }, + { + "id": "20F (D.2)", + "color": "#909090", + "clade": "20F", + "lineages": [ + "D.2" + ], + "otherNames": [] + }, + { + "id": "20G (B.1.2)", + "color": "#888888", + "clade": "20G", + "lineages": [ + "B.1.2" + ], + "otherNames": [] + }, + { + "id": "20H (Beta, V2, B.1.351)", + "color": "#5E1D9D", + "clade": "20H", + "lineages": [ + "B.1.351" + ], + "who": "Beta", + "version": "V2", + "otherNames": [] + }, + { + "id": "20I (Alpha, V1, B.1.1.7)", + "color": "#4A28B3", + "clade": "20I", + "lineages": [ + "B.1.1.7" + ], + "who": "Alpha", + "version": "V1", + "otherNames": [] + }, + { + "id": "20J (Gamma, V3, P.1)", + "color": "#403DC5", + "clade": "20J", + "lineages": [ + "P.1" + ], + "who": "Gamma", + "version": "V3", + "otherNames": [] + }, + { + "id": "21A (Delta, B.1.617.2)", + "color": "#3F56CE", + "clade": "21A", + "lineages": [ + "B.1.617.2" + ], + "who": "Delta", + "otherNames": [] + }, + { + "id": "21B (Kappa, B.1.617.1)", + "color": "#4E95BD", + "clade": "21B", + "lineages": [ + "B.1.617.1" + ], + "who": "Kappa", + "otherNames": [] + }, + { + "id": "21C (Epsilon, B.1.427/429)", + "color": "#58A2AC", + "clade": "21C", + "lineages": [ + "B.1.427/429" + ], + "who": "Epsilon", + "otherNames": [] + }, + { + "id": "21D (Eta, B.1.525)", + "color": "#64AC99", + "clade": "21D", + "lineages": [ + "B.1.525" + ], + "who": "Eta", + "otherNames": [] + }, + { + "id": "21E (Theta, P.3)", + "color": "#71B486", + "clade": "21E", + "lineages": [ + "P.3" + ], + "who": "Theta", + "otherNames": [] + }, + { + "id": "21F (Iota, B.1.526)", + "color": "#80B973", + "clade": "21F", + "lineages": [ + "B.1.526" + ], + "who": "Iota", + "otherNames": [] + }, + { + "id": "21G (Lambda, C.37)", + "color": "#91BC64", + "clade": "21G", + "lineages": [ + "C.37" + ], + "who": "Lambda", + "otherNames": [] + }, + { + "id": "21H (Mu, B.1.621)", + "color": "#A3BE57", + "clade": "21H", + "lineages": [ + "B.1.621" + ], + "who": "Mu", + "otherNames": [] + }, + { + "id": "21I (Delta)", + "color": "#416DCE", + "clade": "21I", + "lineages": [], + "who": "Delta", + "otherNames": [] + }, + { + "id": "21J (Delta)", + "color": "#4683C8", + "clade": "21J", + "lineages": [], + "who": "Delta", + "otherNames": [] + }, + { + "id": "21K (Omicron, BA.1)", + "color": "#B5BD4C", + "clade": "21K", + "lineages": [ + "BA.1" + ], + "who": "Omicron", + "otherNames": [] + }, + { + "id": "21L (Omicron, ~BA.2)", + "color": "#C5B945", + "clade": "21L", + "lineages": [ + "~BA.2" + ], + "who": "Omicron", + "otherNames": [] + }, + { + "id": "21M (Omicron, B.1.1.529)", + "color": "#D3B23F", + "clade": "21M", + "lineages": [ + "B.1.1.529" + ], + "who": "Omicron", + "otherNames": [] + }, + { + "id": "22A (Omicron, BA.4)", + "color": "#DEA63B", + "clade": "22A", + "lineages": [ + "BA.4" + ], + "who": "Omicron", + "otherNames": [] + }, + { + "id": "22B (Omicron, BA.5)", + "color": "#E59638", + "clade": "22B", + "lineages": [ + "BA.5" + ], + "who": "Omicron", + "otherNames": [] + }, + { + "id": "22C (Omicron, BA.2.12.1)", + "color": "#E67F33", + "clade": "22C", + "lineages": [ + "BA.2.12.1" + ], + "who": "Omicron", + "otherNames": [] + }, + { + "id": "22D (Omicron, BA.2.75)", + "color": "#E4642E", + "clade": "22D", + "lineages": [ + "BA.2.75" + ], + "who": "Omicron", + "otherNames": [] + }, + { + "id": "22E (Omicron, BQ.1)", + "color": "#DF4628", + "clade": "22E", + "lineages": [ + "BQ.1" + ], + "who": "Omicron", + "otherNames": [] + }, + { + "id": "22F (Omicron, XBB)", + "color": "#DB2823", + "clade": "22F", + "lineages": [ + "XBB" + ], + "who": "Omicron", + "otherNames": [] + } + ], + "edges": [ + { + "id": "0", + "source": "19A (B)", + "target": "20A (B.1)" + }, + { + "id": "1", + "source": "20A (B.1)", + "target": "20B (B.1.1)" + }, + { + "id": "2", + "source": "20B (B.1.1)", + "target": "21M (Omicron, B.1.1.529)" + }, + { + "id": "3", + "source": "21M (Omicron, B.1.1.529)", + "target": "21L (Omicron, ~BA.2)" + }, + { + "id": "4", + "source": "21L (Omicron, ~BA.2)", + "target": "22A (Omicron, BA.4)" + }, + { + "id": "5", + "source": "21L (Omicron, ~BA.2)", + "target": "22B (Omicron, BA.5)" + }, + { + "id": "6", + "source": "22B (Omicron, BA.5)", + "target": "22E (Omicron, BQ.1)" + }, + { + "id": "7", + "source": "21L (Omicron, ~BA.2)", + "target": "22C (Omicron, BA.2.12.1)" + }, + { + "id": "8", + "source": "21L (Omicron, ~BA.2)", + "target": "22D (Omicron, BA.2.75)" + }, + { + "id": "9", + "source": "21L (Omicron, ~BA.2)", + "target": "22F (Omicron, XBB)" + }, + { + "id": "10", + "source": "21M (Omicron, B.1.1.529)", + "target": "21K (Omicron, BA.1)" + }, + { + "id": "11", + "source": "20B (B.1.1)", + "target": "21E (Theta, P.3)" + }, + { + "id": "12", + "source": "20B (B.1.1)", + "target": "20J (Gamma, V3, P.1)" + }, + { + "id": "13", + "source": "20B (B.1.1)", + "target": "20I (Alpha, V1, B.1.1.7)" + }, + { + "id": "14", + "source": "20B (B.1.1)", + "target": "20F (D.2)" + }, + { + "id": "15", + "source": "20B (B.1.1)", + "target": "20D (B.1.1.1)" + }, + { + "id": "16", + "source": "20D (B.1.1.1)", + "target": "21G (Lambda, C.37)" + }, + { + "id": "17", + "source": "20A (B.1)", + "target": "21A (Delta, B.1.617.2)" + }, + { + "id": "18", + "source": "21A (Delta, B.1.617.2)", + "target": "21I (Delta)" + }, + { + "id": "19", + "source": "21A (Delta, B.1.617.2)", + "target": "21J (Delta)" + }, + { + "id": "20", + "source": "20A (B.1)", + "target": "20C" + }, + { + "id": "21", + "source": "20C", + "target": "21F (Iota, B.1.526)" + }, + { + "id": "22", + "source": "20C", + "target": "21C (Epsilon, B.1.427/429)" + }, + { + "id": "23", + "source": "20C", + "target": "20H (Beta, V2, B.1.351)" + }, + { + "id": "24", + "source": "20C", + "target": "20G (B.1.2)" + }, + { + "id": "25", + "source": "20A (B.1)", + "target": "21H (Mu, B.1.621)" + }, + { + "id": "26", + "source": "20A (B.1)", + "target": "21D (Eta, B.1.525)" + }, + { + "id": "27", + "source": "20A (B.1)", + "target": "21B (Kappa, B.1.617.1)" + }, + { + "id": "28", + "source": "20A (B.1)", + "target": "20E (EU1, B.1.177)" + }, + { + "id": "29", + "source": "19A (B)", + "target": "19B (A)" + } + ] +} diff --git a/tools/flatten.ts b/tools/flatten.ts new file mode 100644 index 0000000..72e1ba5 --- /dev/null +++ b/tools/flatten.ts @@ -0,0 +1,164 @@ +import { omit, sortBy } from 'lodash' +import fs from 'fs-extra' + +main().catch(console.error) + +export interface OldNode { + color: string + name: string + children?: OldNode[] +} + +export interface GraphNode extends Omit { + id: string + clade: string + lineages?: string[] + who?: string + version?: string + otherNames?: string[] +} + +export interface GraphEdge { + id: string + source: string + target: string +} + +export async function main() { + const cladesJson = await fs.readJSON('src/clades.json') + + let nodes: GraphNode[] = [] + let edges: GraphEdge[] = [] + flattenCladeTree(cladesJson, nodes, edges) + nodes = sortBy(nodes, (node) => node.clade) + + verifyGraph(nodes, edges) + + console.log(require('util').inspect({ nodes, edges }, { colors: true, depth: null, maxArrayLength: null })) + + fs.writeJson('src/clades2.json', { nodes, edges }, { spaces: 2 }) +} + +// Convert tree node hierarhy into flat lists of nodes and edges +function flattenCladeTree(node: OldNode, nodes: GraphNode[], edges: GraphEdge[]) { + const { clade, lineages, who, version, otherNames } = splitName(node.name) + + const id = node.name + + nodes.push({ + id, + color: node.color, + clade, + lineages, + who, + version, + otherNames, + }) + + const children = node.children ?? [] + + children.forEach((child) => { + edges.push({ id: edges.length.toString(), source: node.name, target: child.name }) + flattenCladeTree(child, nodes, edges) + }) +} + +function splitName(name: string) { + // Extract clade (outside parentheses) and details string (the thing in parenteses) + const matches = name.match(/^(?.*?)( \((?
[^)]*)\))?$/) + if (!matches) { + throw new Error(`Unable to parse name '${name}'`) + } + + const clade = matches.groups?.clade + if (!clade) { + throw new Error(`Unable to extract clade from name '${name}'`) + } + + const details = matches.groups?.details + if (!details) { + return { clade } + } + + // Decompose details string (the thing in parenteses), + // for example "(B.1)", "(Omicron, B.1.1.529), "(Beta, V2, B.1.351)", "(EU1)"" + const components = details.split(',').map((component) => component.trim()) + if (components.length === 0) { + throw new Error(`Unable to make sense of the name '${name}': details string is present but is empty`) + } + + const who = findExactlyOne(components, isWhoVariant) + const version = findExactlyOne(components, isVersion) + const lineages = components.filter((c) => isPangoLineage(c)) + const otherNames = components.filter((c) => c != who && c != version && !lineages.includes(c)) + return { clade, lineages, who, version, otherNames } + + throw new Error( + `Unable to make sense of the name '${name}': details string does not follow any known format: '${details}'`, + ) +} + +function isPangoLineage(s: string) { + return s.match(/^(\~)?(A|B|C|D|BA|BQ|P|XBB|)(\.\d+?(\/\d+)?)*$/) !== null +} + +function isWhoVariant(s: string) { + return !WHO_EXCEPTIONS.includes(s) && GREEK_LETTERS.includes(s) +} + +function isVersion(s: string) { + return s.match(/^V\d$/) !== null +} + +const GREEK_LETTERS = [ + 'Alpha', + 'Beta', + 'Gamma', + 'Delta', + 'Epsilon', + 'Zeta', + 'Eta', + 'Theta', + 'Iota', + 'Kappa', + 'Lambda', + 'Mu', + 'Nu', + 'Xi', + 'Omicron', + 'Pi', + 'Rho', + 'Sigma', + 'Tau', + 'Upsilon', + 'Phi', + 'Chi', + 'Psi', + 'Omega', +] + +const WHO_EXCEPTIONS = ['EU1'] + +function findExactlyOne(components: string[], predicate: (s: string) => boolean) { + const candidates = components.filter(predicate) + if (candidates.length > 1) { + throw new Error(`Expected to find exactly one element, but found: ${candidates.map((s) => `"${s}"`).join(',')}`) + } + return candidates[0] +} + +function verifyGraph(nodes: GraphNode[], edges: GraphEdge[]) { + edges.forEach((edge) => { + if (edge.target == edge.source) { + throw new Error(`Graph is invalid: invalid edge: the target node '${edge.target}' is the same as source node`) + } + + if (!nodes.find((node) => edge.target == node.id)) { + throw new Error(`Graph is invalid: invalid edge: the target node '${edge.target}' does not exist`) + } + + if (!nodes.find((node) => edge.source == node.id)) { + throw new Error(`Graph is invalid: invalid edge: the source node '${edge.source}' does not exist`) + } + }) +} diff --git a/tsconfig.json b/tsconfig.json index 56b6ea1..427f8f2 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -1,4 +1,12 @@ { + "ts-node": { + "extends": "ts-node/node16/tsconfig.json", + "transpileOnly": true, + "files": true, + "compilerOptions": { + "module": "commonjs" + } + }, "compilerOptions": { "baseUrl": "./", "paths": { diff --git a/yarn.lock 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"https://registry.yarnpkg.com/fs.realpath/-/fs.realpath-1.0.0.tgz#1504ad2523158caa40db4a2787cb01411994ea4f" @@ -2244,6 +2265,11 @@ graceful-fs@^4.1.2: resolved "https://registry.yarnpkg.com/graceful-fs/-/graceful-fs-4.2.8.tgz#e412b8d33f5e006593cbd3cee6df9f2cebbe802a" integrity sha512-qkIilPUYcNhJpd33n0GBXTB1MMPp14TxEsEs0pTrsSVucApsYzW5V+Q8Qxhik6KU3evy+qkAAowTByymK0avdg== +graceful-fs@^4.1.6, graceful-fs@^4.2.0: + version "4.2.10" + resolved "https://registry.yarnpkg.com/graceful-fs/-/graceful-fs-4.2.10.tgz#147d3a006da4ca3ce14728c7aefc287c367d7a6c" + integrity sha512-9ByhssR2fPVsNZj478qUUbKfmL0+t5BDVyjShtyZZLiK7ZDAArFFfopyOTj0M05wE2tJPisA4iTnnXl2YoPvOA== + has-bigints@^1.0.1: version "1.0.1" resolved "https://registry.yarnpkg.com/has-bigints/-/has-bigints-1.0.1.tgz#64fe6acb020673e3b78db035a5af69aa9d07b113" @@ -2594,6 +2620,15 @@ json5@^1.0.1: dependencies: minimist "^1.2.0" +jsonfile@^6.0.1: + version "6.1.0" + resolved "https://registry.yarnpkg.com/jsonfile/-/jsonfile-6.1.0.tgz#bc55b2634793c679ec6403094eb13698a6ec0aae" + integrity sha512-5dgndWOriYSm5cnYaJNhalLNDKOqFwyDB/rr1E9ZsGciGvKPs8R2xYGCacuf3z6K1YKDz182fd+fY3cn3pMqXQ== + dependencies: + universalify "^2.0.0" + optionalDependencies: + graceful-fs "^4.1.6" + "jsx-ast-utils@^2.4.1 || ^3.0.0", jsx-ast-utils@^3.2.1: version "3.2.1" resolved "https://registry.yarnpkg.com/jsx-ast-utils/-/jsx-ast-utils-3.2.1.tgz#720b97bfe7d901b927d87c3773637ae8ea48781b" @@ -2656,7 +2691,7 @@ lodash.sortby@^4.7.0: resolved "https://registry.yarnpkg.com/lodash.sortby/-/lodash.sortby-4.7.0.tgz#edd14c824e2cc9c1e0b0a1b42bb5210516a42438" integrity sha1-7dFMgk4sycHgsKG0K7UhBRakJDg= -lodash@^4.17.11, lodash@^4.17.21: +lodash@4.17.21, lodash@^4.17.11, lodash@^4.17.21: version "4.17.21" resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.17.21.tgz#679591c564c3bffaae8454cf0b3df370c3d6911c" integrity sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg== @@ -3752,6 +3787,11 @@ unbox-primitive@^1.0.1: has-symbols "^1.0.2" which-boxed-primitive "^1.0.2" +universalify@^2.0.0: + version "2.0.0" + resolved "https://registry.yarnpkg.com/universalify/-/universalify-2.0.0.tgz#75a4984efedc4b08975c5aeb73f530d02df25717" + integrity sha512-hAZsKq7Yy11Zu1DE0OzWjw7nnLZmJZYTDZZyEFHZdUhV8FkH5MCfoU1XMaxXovpyW5nq5scPqq0ZDP9Zyl04oQ== + unpipe@1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/unpipe/-/unpipe-1.0.0.tgz#b2bf4ee8514aae6165b4817829d21b2ef49904ec" From ca8aeb124b94375f803c6efa85e03d1f08626af0 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Fri, 18 Nov 2022 10:12:31 +0100 Subject: [PATCH 07/14] chore; setup eslint; upgrade packages --- .eslintignore | 1 + .eslintrc.js | 225 ++- package.json | 72 +- yarn.lock | 4845 +++++++++++++++++++++++++++++-------------------- 4 files changed, 3155 insertions(+), 1988 deletions(-) diff --git a/.eslintignore b/.eslintignore index 3ba4daf..c2ce890 100644 --- a/.eslintignore +++ b/.eslintignore @@ -1,6 +1,7 @@ /\.build /\.cache /\.env +/\.eslintrc.js /\.github /\.idea /\.ignore diff --git a/.eslintrc.js b/.eslintrc.js index c7b9cbe..1a18cf7 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -1,3 +1,226 @@ module.exports = { - "extends": ["next/core-web-vitals", "prettier"] + root: true, + parser: '@typescript-eslint/parser', + parserOptions: { + sourceType: 'module', + ecmaVersion: 'latest', + ecmaFeatures: { + jsx: true, + globalReturn: false, + }, + project: './tsconfig.json', + warnOnUnsupportedTypeScriptVersion: true, + }, + globals: {}, + extends: [ + 'eslint:recommended', + + 'airbnb', + 'airbnb-typescript', + 'airbnb/hooks', + + 'next/core-web-vitals', + 'plugin:@typescript-eslint/eslint-recommended', + 'plugin:@typescript-eslint/recommended', + 'plugin:@typescript-eslint/recommended-requiring-type-checking', + 'plugin:array-func/all', + 'plugin:import/errors', + 'plugin:import/typescript', + 'plugin:import/warnings', + 'plugin:jsx-a11y/recommended', + 'plugin:lodash/recommended', + 'plugin:promise/recommended', + 'plugin:react/recommended', + 'plugin:react-perf/all', + 'plugin:security/recommended', + 'plugin:sonarjs/recommended', + 'plugin:unicorn/recommended', + + 'plugin:prettier/recommended', + ], + plugins: [ + 'array-func', + 'cflint', + 'import', + 'jsx-a11y', + 'lodash', + 'no-loops', + 'no-secrets', + 'node', + 'only-ascii', + 'promise', + 'react', + 'react-hooks', + 'react-perf', + 'security', + 'sonarjs', + 'unicorn', + 'unused-imports', + + 'only-warn', + + '@typescript-eslint', + + 'prettier', + ], + reportUnusedDisableDirectives: true, + rules: { + '@next/next/no-title-in-document-head': 'off', + '@typescript-eslint/array-type': 'off', + '@typescript-eslint/explicit-function-return-type': 'off', + '@typescript-eslint/explicit-module-boundary-types': 'off', + '@typescript-eslint/lines-between-class-members': 'off', + '@typescript-eslint/naming-convention': 'off', + '@typescript-eslint/no-empty-function': 'off', + '@typescript-eslint/no-shadow': 'off', + '@typescript-eslint/no-unused-vars': 'off', + '@typescript-eslint/no-use-before-define': 'off', + '@typescript-eslint/unbound-method': ['off'], + 'array-func/no-unnecessary-this-arg': 'off', + 'array-func/prefer-array-from': 'off', + 'camelcase': 'warn', + 'cflint/no-substr': 'warn', + 'cflint/no-this-assignment': 'warn', + 'import/extensions': [ + 'warn', + 'ignorePackages', + { + js: 'never', + jsx: 'never', + mjs: 'never', + ts: 'never', + tsx: 'never', + }, + ], + 'import/no-extraneous-dependencies': ['warn', { devDependencies: true }], + 'import/no-webpack-loader-syntax': 'off', + 'import/order': 'warn', + 'import/prefer-default-export': 'off', + 'jsx-a11y/label-has-associated-control': ['warn', { assert: 'either' }], + 'lodash/chaining': 'off', + 'lodash/import-scope': 'off', + 'lodash/prefer-constant': 'off', + 'lodash/prefer-lodash-chain': 'off', + 'lodash/prefer-lodash-method': 'off', + 'lodash/prefer-lodash-typecheck': 'off', + 'lodash/prefer-noop': 'off', + 'lodash/preferred-alias': 'off', + 'lodash/prop-shorthand': 'off', + 'max-classes-per-file': 'off', + 'no-console': ['warn', { allow: ['info', 'warn', 'error', 'memory'] }], + 'no-loops/no-loops': 'off', + 'no-param-reassign': ['warn', { ignorePropertyModificationsFor: ['draft'] }], + 'no-secrets/no-secrets': ['warn', { tolerance: 5 }], + 'no-shadow': 'off', + 'no-unused-vars': 'off', + 'only-ascii/only-ascii': 'warn', + 'prefer-for-of': 'off', + 'prettier/prettier': 'warn', + 'react-hooks/exhaustive-deps': [ + 'warn', + { + additionalHooks: '(useRecoilCallback|useRecoilTransaction|useRecoilTransaction_UNSTABLE)', + }, + ], + 'react/jsx-curly-brace-presence': 'off', + 'react/jsx-filename-extension': ['warn', { extensions: ['.js', '.jsx', '.ts', '.tsx'] }], + 'react/jsx-props-no-spreading': 'off', + 'react/no-unused-prop-types': 'off', + 'react/prop-types': 'off', + 'react/require-default-props': 'off', + 'react/state-in-constructor': 'off', + 'security/detect-non-literal-fs-filename': 'off', + 'security/detect-object-injection': 'off', + 'sonarjs/cognitive-complexity': ['warn', 20], + 'unicorn/consistent-function-scoping': 'off', + 'unicorn/escape-case': 'off', + 'unicorn/filename-case': 'off', + 'unicorn/new-for-builtins': 'off', + 'unicorn/no-abusive-eslint-disable': 'warn', + 'unicorn/no-array-callback-reference': 'off', + 'unicorn/no-array-for-each': 'off', + 'unicorn/no-array-method-this-argument': 'off', + 'unicorn/no-array-reduce': 'off', + 'unicorn/no-fn-reference-in-iterator': 'off', + 'unicorn/no-null': 'off', + 'unicorn/no-reduce': 'off', + 'unicorn/no-useless-undefined': 'off', + 'unicorn/no-zero-fractions': 'off', + 'unicorn/prefer-node-protocol': 'off', + 'unicorn/prefer-query-selector': 'off', + 'unicorn/prefer-spread': 'off', + 'unicorn/prefer-top-level-await': 'off', + 'unicorn/prevent-abbreviations': 'off', + 'unused-imports/no-unused-imports': 'warn', + 'unused-imports/no-unused-vars': [ + 'warn', + { vars: 'all', varsIgnorePattern: '^_', args: 'after-used', argsIgnorePattern: '^_' }, + ], + + 'lines-between-class-members': ['warn', 'always', { exceptAfterSingleLine: true }], + + 'require-await': 'off', + '@typescript-eslint/require-await': 'off', + + 'no-unused-expressions': 'off', + '@typescript-eslint/no-unused-expressions': 'warn', + + '@typescript-eslint/no-duplicate-imports': 'off', + }, + env: { + browser: true, + es6: true, + node: true, + }, + settings: { + 'react': { + version: 'detect', + }, + 'import/parsers': { + '@typescript-eslint/parser': ['.js', '.jsx', '.ts', '.tsx'], + }, + 'import/resolver': { + typescript: { + alwaysTryTypes: true, + }, + }, + }, + overrides: [ + { + files: ['src/pages/**/*', 'src/types/**/*'], + rules: { + 'no-restricted-exports': 'off', + }, + }, + { + files: ['*.d.ts'], + rules: { + '@typescript-eslint/ban-types': ['warn', { extendDefaults: true, types: { object: false } }], + '@typescript-eslint/no-explicit-any': 'off', + '@typescript-eslint/no-unused-vars': 'off', + 'import/no-duplicates': 'off', + 'no-useless-constructor': 'off', + 'react/prefer-stateless-function': 'off', + }, + }, + { + files: ['.eslintrc.js', 'next.config.js'], + rules: { + '@typescript-eslint/no-unsafe-argument': 'off', + '@typescript-eslint/no-unsafe-assignment': 'off', + '@typescript-eslint/no-unsafe-call': 'off', + '@typescript-eslint/no-unsafe-member-access': 'off', + '@typescript-eslint/no-unsafe-return': 'off', + '@typescript-eslint/no-var-requires': 'off', + '@typescript-eslint/restrict-template-expressions': 'off', + 'global-require': 'off', + 'import/extensions': 'off', + 'import/no-anonymous-default-export': 'off', + 'import/no-import-module-exports': 'off', + 'security/detect-child-process': 'off', + 'sonarjs/cognitive-complexity': ['warn', 50], + 'unicorn/prefer-module': 'off', + }, + }, + ], } diff --git a/package.json b/package.json index a610890..3dce9c4 100644 --- a/package.json +++ b/package.json @@ -11,33 +11,67 @@ }, "dependencies": { "bootstrap": "5.1.3", - "d3": "7.4.4", - "d3-flextree": "2.1.2", - "d3-hierarchy": "3.1.2", "file-saver": "2.0.5", "lodash": "4.17.21", - "next": "12.0.7", - "react": "17.0.2", - "react-dom": "17.0.2", - "react-resize-detector": "7.0.0", - "reactstrap": "9.0.2", - "styled-components": "5.3.5" + "next": "13.0.1", + "react": "18.2.0", + "react-dom": "18.2.0", + "react-resize-detector": "7.1.2", + "reactstrap": "9.1.5", + "styled-components": "5.3.6" }, "devDependencies": { - "@types/d3": "7.1.0", - "@types/file-saver": "2.0.4", + "@types/file-saver": "2.0.5", "@types/fs-extra": "9.0.13", "@types/lodash": "4.14.187", - "@types/node": "17.0.0", - "@types/react": "17.0.37", - "@types/react-dom": "17.0.11", - "@types/styled-components": "5.1.25", - "eslint": "8.4.1", + "@types/node": "18.11.9", + "@types/styled-components": "5.1.26", + "@typescript-eslint/eslint-plugin": "5.42.0", + "@typescript-eslint/parser": "5.42.0", + "@typescript-eslint/typescript-estree": "5.42.0", + "eslint": "8.26.0", + "eslint-config-airbnb": "19.0.4", + "eslint-config-airbnb-base": "15.0.0", + "eslint-config-airbnb-typescript": "17.0.0", "eslint-config-next": "12.0.7", + "eslint-config-next": "13.0.1", "eslint-config-prettier": "8.3.0", + "eslint-config-prettier": "8.5.0", + "eslint-config-react-app": "7.0.1", + "eslint-formatter-codeframe": "7.32.1", + "eslint-import-resolver-ts": "0.4.2", + "eslint-import-resolver-typescript": "3.5.2", + "eslint-loader": "4.0.2", + "eslint-plugin-array-func": "3.1.7", + "eslint-plugin-cflint": "1.0.0", + "eslint-plugin-cypress": "2.12.1", + "eslint-plugin-flowtype": "8.0.3", + "eslint-plugin-i18next": "5.2.1", + "eslint-plugin-import": "2.26.0", + "eslint-plugin-jest": "27.1.3", + "eslint-plugin-jest-dom": "4.0.2", + "eslint-plugin-json": "3.1.0", + "eslint-plugin-jsx-a11y": "6.6.1", + "eslint-plugin-lodash": "7.4.0", + "eslint-plugin-no-loops": "0.3.0", + "eslint-plugin-no-secrets": "0.8.9", + "eslint-plugin-node": "11.1.0", + "eslint-plugin-only-ascii": "0.0.0", + "eslint-plugin-only-warn": "1.0.3", + "eslint-plugin-prettier": "4.2.1", + "eslint-plugin-promise": "6.1.1", + "eslint-plugin-react": "7.31.10", + "eslint-plugin-react-hooks": "4.6.0", + "eslint-plugin-react-perf": "3.3.1", + "eslint-plugin-react-redux": "4.0.0", + "eslint-plugin-redux-saga": "1.3.2", + "eslint-plugin-security": "1.5.0", + "eslint-plugin-sonarjs": "0.16.0", + "eslint-plugin-unicorn": "44.0.2", + "eslint-plugin-unused-imports": "2.0.0", "fs-extra": "10.1.0", - "prettier": "2.5.1", - "ts-node": "10.4.0", - "typescript": "4.5.4" + "prettier": "2.7.1", + "ts-node": "10.9.1", + "typescript": "4.8.4" } } diff --git a/yarn.lock b/yarn.lock index d684461..546b994 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2,6 +2,14 @@ # yarn lockfile v1 +"@ampproject/remapping@^2.1.0": + version "2.2.0" + resolved "https://registry.yarnpkg.com/@ampproject/remapping/-/remapping-2.2.0.tgz#56c133824780de3174aed5ab6834f3026790154d" + integrity sha512-qRmjj8nj9qmLTQXXmaR1cck3UXSRMPrbsLJAasZpF+t3riI71BXed5ebIOYwQntykeZuhjsdweEc9BxH5Jc26w== + dependencies: + "@jridgewell/gen-mapping" "^0.1.0" + "@jridgewell/trace-mapping" "^0.3.9" + "@babel/code-frame@7.12.11": version "7.12.11" resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.12.11.tgz#f4ad435aa263db935b8f10f2c552d23fb716a63f" @@ -9,6 +17,13 @@ dependencies: "@babel/highlight" "^7.10.4" +"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.10.4", "@babel/code-frame@^7.18.6": + version "7.18.6" + resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.18.6.tgz#3b25d38c89600baa2dcc219edfa88a74eb2c427a" + integrity sha512-TDCmlK5eOvH+eH7cdAFlNXeVJqWIQ7gW9tY1GJIpUtFb6CmjVyq2VM3u71bOyR8CRihcCgMUYoDNyLXao3+70Q== + dependencies: + "@babel/highlight" "^7.18.6" + "@babel/code-frame@^7.16.7": version "7.16.7" resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.16.7.tgz#44416b6bd7624b998f5b1af5d470856c40138789" @@ -16,6 +31,41 @@ dependencies: "@babel/highlight" "^7.16.7" +"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.19.4", "@babel/compat-data@^7.20.0": + version "7.20.1" + resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.20.1.tgz#f2e6ef7790d8c8dbf03d379502dcc246dcce0b30" + integrity sha512-EWZ4mE2diW3QALKvDMiXnbZpRvlj+nayZ112nK93SnhqOtpdsbVD4W+2tEoT3YNBAG9RBR0ISY758ZkOgsn6pQ== + +"@babel/core@^7.16.0": + version "7.19.6" + resolved "https://registry.yarnpkg.com/@babel/core/-/core-7.19.6.tgz#7122ae4f5c5a37c0946c066149abd8e75f81540f" + integrity sha512-D2Ue4KHpc6Ys2+AxpIx1BZ8+UegLLLE2p3KJEuJRKmokHOtl49jQ5ny1773KsGLZs8MQvBidAF6yWUJxRqtKtg== + dependencies: + "@ampproject/remapping" "^2.1.0" + "@babel/code-frame" "^7.18.6" + "@babel/generator" "^7.19.6" + "@babel/helper-compilation-targets" "^7.19.3" + "@babel/helper-module-transforms" "^7.19.6" + "@babel/helpers" "^7.19.4" + "@babel/parser" "^7.19.6" + "@babel/template" "^7.18.10" + "@babel/traverse" "^7.19.6" + "@babel/types" "^7.19.4" + convert-source-map "^1.7.0" + debug "^4.1.0" + gensync "^1.0.0-beta.2" + json5 "^2.2.1" + semver "^6.3.0" + +"@babel/eslint-parser@^7.16.3": + version "7.19.1" + resolved "https://registry.yarnpkg.com/@babel/eslint-parser/-/eslint-parser-7.19.1.tgz#4f68f6b0825489e00a24b41b6a1ae35414ecd2f4" + integrity sha512-AqNf2QWt1rtu2/1rLswy6CDP7H9Oh3mMhk177Y67Rg8d7RD9WfOLLv8CGn6tisFvS2htm86yIe1yLF6I1UDaGQ== + dependencies: + "@nicolo-ribaudo/eslint-scope-5-internals" "5.1.1-v1" + eslint-visitor-keys "^2.1.0" + semver "^6.3.0" + "@babel/generator@^7.17.10": version "7.17.10" resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.17.10.tgz#c281fa35b0c349bbe9d02916f4ae08fc85ed7189" @@ -25,6 +75,15 @@ "@jridgewell/gen-mapping" "^0.1.0" jsesc "^2.5.1" +"@babel/generator@^7.19.6", "@babel/generator@^7.20.1": + version "7.20.1" + resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.20.1.tgz#ef32ecd426222624cbd94871a7024639cf61a9fa" + integrity sha512-u1dMdBUmA7Z0rBB97xh8pIhviK7oItYOkjbsCxTWMknyvbQRBwX7/gn4JXurRdirWMFh+ZtYARqkA6ydogVZpg== + dependencies: + "@babel/types" "^7.20.0" + "@jridgewell/gen-mapping" "^0.3.2" + jsesc "^2.5.1" + "@babel/helper-annotate-as-pure@^7.16.0": version "7.16.7" resolved "https://registry.yarnpkg.com/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.16.7.tgz#bb2339a7534a9c128e3102024c60760a3a7f3862" @@ -32,6 +91,64 @@ dependencies: "@babel/types" "^7.16.7" +"@babel/helper-annotate-as-pure@^7.18.6": + version "7.18.6" + resolved "https://registry.yarnpkg.com/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.18.6.tgz#eaa49f6f80d5a33f9a5dd2276e6d6e451be0a6bb" + integrity sha512-duORpUiYrEpzKIop6iNbjnwKLAKnJ47csTyRACyEmWj0QdUrm5aqNJGHSSEQSUAvNW0ojX0dOmK9dZduvkfeXA== + dependencies: + "@babel/types" "^7.18.6" + 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"@babel/helper-define-polyfill-provider" "^0.3.3" + "babel-plugin-styled-components@>= 1.12.0": version "2.0.7" resolved "https://registry.yarnpkg.com/babel-plugin-styled-components/-/babel-plugin-styled-components-2.0.7.tgz#c81ef34b713f9da2b7d3f5550df0d1e19e798086" @@ -948,36 +1866,43 @@ babel-plugin-syntax-jsx@^6.18.0: resolved "https://registry.yarnpkg.com/babel-plugin-syntax-jsx/-/babel-plugin-syntax-jsx-6.18.0.tgz#0af32a9a6e13ca7a3fd5069e62d7b0f58d0d8946" integrity sha1-CvMqmm4Tyno/1QaeYtew9Y0NiUY= +babel-plugin-transform-react-remove-prop-types@^0.4.24: + version "0.4.24" + resolved "https://registry.yarnpkg.com/babel-plugin-transform-react-remove-prop-types/-/babel-plugin-transform-react-remove-prop-types-0.4.24.tgz#f2edaf9b4c6a5fbe5c1d678bfb531078c1555f3a" + integrity sha512-eqj0hVcJUR57/Ug2zE1Yswsw4LhuqqHhD+8v120T1cl3kjg76QwtyBrdIk4WVwK+lAhBJVYCd/v+4nc4y+8JsA== + +babel-preset-react-app@^10.0.1: + version "10.0.1" + resolved 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unbox-primitive "^1.0.1" +es-abstract@^1.19.2, es-abstract@^1.19.5: + version "1.20.4" + resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.20.4.tgz#1d103f9f8d78d4cf0713edcd6d0ed1a46eed5861" + integrity sha512-0UtvRN79eMe2L+UNEF1BwRe364sj/DXhQ/k5FmivgoSdpM90b8Jc0mDzKMGo7QS0BVbOP/bTwBKNnDc9rNzaPA== + dependencies: + call-bind "^1.0.2" + es-to-primitive "^1.2.1" + function-bind "^1.1.1" + function.prototype.name "^1.1.5" + get-intrinsic "^1.1.3" + get-symbol-description "^1.0.0" + has "^1.0.3" + has-property-descriptors "^1.0.0" + has-symbols "^1.0.3" + internal-slot "^1.0.3" + is-callable "^1.2.7" + is-negative-zero "^2.0.2" + is-regex "^1.1.4" + is-shared-array-buffer "^1.0.2" + is-string "^1.0.7" + is-weakref "^1.0.2" + object-inspect "^1.12.2" + object-keys "^1.1.1" + object.assign "^4.1.4" + regexp.prototype.flags "^1.4.3" + safe-regex-test "^1.0.0" + string.prototype.trimend "^1.0.5" + string.prototype.trimstart "^1.0.5" + unbox-primitive "^1.0.2" + 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"https://registry.yarnpkg.com/object.assign/-/object.assign-4.1.4.tgz#9673c7c7c351ab8c4d0b516f4343ebf4dfb7799f" + integrity sha512-1mxKf0e58bvyjSCtKYY4sRe9itRk3PJpquJOjeIkz885CczcI4IvJJDLPS72oowuSh+pBxUFROpX+TU++hxhZQ== + dependencies: + call-bind "^1.0.2" + define-properties "^1.1.4" + has-symbols "^1.0.3" + object-keys "^1.1.1" + object.entries@^1.1.5: version "1.1.5" resolved "https://registry.yarnpkg.com/object.entries/-/object.entries-1.1.5.tgz#e1acdd17c4de2cd96d5a08487cfb9db84d881861" @@ -2944,13 +3863,13 @@ object.fromentries@^2.0.5: define-properties "^1.1.3" es-abstract "^1.19.1" -object.hasown@^1.1.0: - version "1.1.0" - resolved "https://registry.yarnpkg.com/object.hasown/-/object.hasown-1.1.0.tgz#7232ed266f34d197d15cac5880232f7a4790afe5" - integrity sha512-MhjYRfj3GBlhSkDHo6QmvgjRLXQ2zndabdf3nX0yTyZK9rPfxb6uRpAac8HXNLy1GpqWtZ81Qh4v3uOls2sRAg== +object.hasown@^1.1.1: + version "1.1.1" + resolved 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v8-compile-cache-lib "^3.0.1" yn "3.1.1" -tsconfig-paths@^3.11.0, tsconfig-paths@^3.9.0: +tsconfig-paths@^3.14.1: + version "3.14.1" + resolved "https://registry.yarnpkg.com/tsconfig-paths/-/tsconfig-paths-3.14.1.tgz#ba0734599e8ea36c862798e920bcf163277b137a" + integrity sha512-fxDhWnFSLt3VuTwtvJt5fpwxBHg5AdKWMsgcPOOIilyjymcYVZoCQF8fvFRezCNfblEXmi+PcM1eYHeOAgXCOQ== + dependencies: + "@types/json5" "^0.0.29" + json5 "^1.0.1" + minimist "^1.2.6" + strip-bom "^3.0.0" + +tsconfig-paths@^3.9.0: version "3.12.0" resolved "https://registry.yarnpkg.com/tsconfig-paths/-/tsconfig-paths-3.12.0.tgz#19769aca6ee8f6a1a341e38c8fa45dd9fb18899b" integrity sha512-e5adrnOYT6zqVnWqZu7i/BQ3BnhzvGbjEjejFXO20lKIKpwTaupkCPgEfv4GZK1IBciJUEhYs3J3p75FdaTFVg== @@ -3743,6 +4603,11 @@ tslib@^1.8.1: resolved "https://registry.yarnpkg.com/tslib/-/tslib-1.14.1.tgz#cf2d38bdc34a134bcaf1091c41f6619e2f672d00" integrity sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg== 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"https://registry.yarnpkg.com/yn/-/yn-3.1.1.tgz#1e87401a09d767c1d5eab26a6e4c185182d2eb50" From 0e35fc436e36bf41c762fdb277ef1a7bcecf6389 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Fri, 18 Nov 2022 10:15:19 +0100 Subject: [PATCH 08/14] feat: calculate graph node layout without d3 --- src/components/Edge.tsx | 22 ++- src/components/HomePage.tsx | 4 +- src/components/NextstrainCladeTreeSvg.tsx | 55 ++---- src/components/Node.tsx | 47 ++--- src/components/constants.tsx | 7 +- src/graph/graph.ts | 227 ++++++++++++++++++++++ src/graph/utils.ts | 8 + tools/flatten.ts | 61 ++---- 8 files changed, 304 insertions(+), 127 deletions(-) create mode 100644 src/graph/graph.ts create mode 100644 src/graph/utils.ts diff --git a/src/components/Edge.tsx b/src/components/Edge.tsx index f33d67f..fa2702c 100644 --- a/src/components/Edge.tsx +++ b/src/components/Edge.tsx @@ -1,12 +1,22 @@ -import React from 'react' +import React, { useMemo } from 'react' + +import { getNodesForEdge, GraphEdge, GraphNodeDisplay } from '../graph/graph' +import { nodeRadius } from './constants' export interface EdgeProps { - x1: number - x2: number - y1: number - y2: number + nodes: GraphNodeDisplay[] + edge: GraphEdge } -export function Edge({ x1, x2, y1, y2 }: EdgeProps) { +export function Edge({ nodes, edge }: EdgeProps) { + const { x1, x2, y1, y2 } = useMemo(() => { + const { source, target } = getNodesForEdge(nodes, edge) + const y1 = source.y + nodeRadius / 2 + const y2 = target.y + nodeRadius / 2 + const x1 = source.x + nodeRadius / 2 + const x2 = target.x + nodeRadius / 2 + return { x1, x2, y1, y2 } + }, [edge, nodes]) + return } diff --git a/src/components/HomePage.tsx b/src/components/HomePage.tsx index c31dc5a..c1ff94e 100644 --- a/src/components/HomePage.tsx +++ b/src/components/HomePage.tsx @@ -6,7 +6,7 @@ import styled, { createGlobalStyle } from 'styled-components' import { NextstrainCladeTreeSvg } from 'src/components/NextstrainCladeTreeSvg' import { Container, Row, Col } from 'reactstrap' -import cladesJson from '../clades.json' +import cladesJson from '../clades2.json' const GlobalStyle = createGlobalStyle` html, body, #__next { @@ -66,7 +66,7 @@ export function HomePage() { - + {'Phylogenetic relationships of Nextstrain SARS-CoV-2 clades'} diff --git a/src/components/NextstrainCladeTreeSvg.tsx b/src/components/NextstrainCladeTreeSvg.tsx index 5a6fbc0..0568e5d 100644 --- a/src/components/NextstrainCladeTreeSvg.tsx +++ b/src/components/NextstrainCladeTreeSvg.tsx @@ -1,9 +1,7 @@ -import React, { forwardRef, LegacyRef, RefObject, SVGProps, useMemo } from 'react' -import type { HierarchyPointNode } from 'd3-hierarchy' -import { hierarchy, tree } from 'd3-hierarchy' +import React, { forwardRef, useMemo } from 'react' +import { calculateGraphLayout, GraphEdge, GraphNode } from 'src/graph/graph' import styled from 'styled-components' -import { nodeHeight, nodeWidth } from 'src/components/constants' import { Edge } from 'src/components/Edge' import { Node } from 'src/components/Node' @@ -16,10 +14,8 @@ const Svg = styled.svg` ` export interface CladesJson { - color: string - name: string - lineages?: string[] - children?: CladesJson[] + nodes: GraphNode[] + edges: GraphEdge[] } export interface CladeTreeSvgProps { @@ -28,45 +24,26 @@ export interface CladeTreeSvgProps { height: number } -export function shift(node: HierarchyPointNode, { dx, dy }: { dx?: number; dy?: number }) { - return { ...node, x: node.x + (dx ?? 0), y: node.y + (dy ?? 0) } -} - // eslint-disable-next-line react/display-name export const NextstrainCladeTreeSvg = forwardRef( ({ cladesJson, width, height, ...restProps }, ref) => { const { nodeComponents, edgeComponents } = useMemo(() => { - // NOTE: x/y and width/height are swapped here, because we want to render the tree sideways, not top to bottom - const root = hierarchy(cladesJson, (d) => d.children) - const t = tree().size([height - nodeHeight, width - nodeWidth]) - - const tm = t(root) as HierarchyPointNode - const nodes = tm.descendants() - const edges = tm.links() + if (!width || !height) { + return { nodeComponents: [], edgeComponents: [] } + } - const nodeComponents = nodes.map((node) => ( - - )) + const nodes = calculateGraphLayout( + cladesJson.nodes.map((node) => ({ ...node, x: 0, y: 0 })), + cladesJson.edges, + width, + height, + ) - const edgeComponents = edges.map((edge) => ( - - )) + const nodeComponents = nodes.map((node) => ) + const edgeComponents = cladesJson.edges.map((edge) => ) return { nodeComponents, edgeComponents } - }, [cladesJson, height, width]) + }, [cladesJson.edges, cladesJson.nodes, height, width]) if (!width || !height) { return null diff --git a/src/components/Node.tsx b/src/components/Node.tsx index ac714cb..c28eea6 100644 --- a/src/components/Node.tsx +++ b/src/components/Node.tsx @@ -1,50 +1,27 @@ -import React, { ReactElement, useMemo } from 'react' -import styled from 'styled-components' +import React, { ReactElement } from 'react' +import { GraphNodeDisplay } from 'src/graph/graph' -import { CladesJson } from 'src/components/NextstrainCladeTreeSvg' -import { cladesTextColor, cladesTextSize, lineagesRectHeight, lineagesTextColor, lineagesTextSize } from './constants' - -const Rect = styled.rect` - border-radius: 3px; -` +import { cladesTextColor, cladesTextSize, nodeRadius } from './constants' export interface CladeTreeNodeProps { - node: CladesJson - x: number - y: number - nodeWidth: number - nodeHeight: number + node: GraphNodeDisplay } -export function Node({ node, x, y, nodeWidth, nodeHeight }: CladeTreeNodeProps): ReactElement { - const { name, color, lineages } = node - const lineagesText = useMemo(() => node.lineages?.join(', '), [node.lineages]) +export function Node({ node }: CladeTreeNodeProps): ReactElement { + const { id, clade, lineages, who, version, otherNames, x, y, color } = node return ( - + - {name} - - - - - {lineagesText} + {clade} ) diff --git a/src/components/constants.tsx b/src/components/constants.tsx index 47c0ade..03a3bae 100644 --- a/src/components/constants.tsx +++ b/src/components/constants.tsx @@ -1,7 +1,6 @@ -export const nodeWidth = 100 -export const nodeHeight = 30 -export const horizontalSeparationBetweenNodes = 90 -export const verticalSeparationBetweenNodes = 20 +export const nodeRadius = 15 +export const horizontalSeparationBetweenNodes = 150 +export const verticalSeparationBetweenNodes = 25 export const lineagesRectHeight = 12 export const cladesTextSize = 14 export const lineagesTextSize = 10 diff --git a/src/graph/graph.ts b/src/graph/graph.ts new file mode 100644 index 0000000..e8e99f3 --- /dev/null +++ b/src/graph/graph.ts @@ -0,0 +1,227 @@ +import { max, min, cloneDeep } from 'lodash' +import { horizontalSeparationBetweenNodes, nodeRadius } from '../components/constants' + +export interface GraphNode { + id: string + clade: string + lineages?: string[] + who?: string + version?: string + otherNames?: string[] + color?: string +} +export interface GraphNodeDisplay extends GraphNode { + x: number + y: number +} + +export interface GraphEdge { + id: string + source: string + target: string +} + +export function calculateGraphLayout( + nodes_: GraphNodeDisplay[], + edges: GraphEdge[], + width: number, + height: number, +): GraphNodeDisplay[] { + const nodes = cloneDeep(nodes_) + + // Position roots at the left of viewport + const roots = getRoots(nodes, edges) + roots.forEach((root) => { + root.x = nodeRadius / 2 + }) + + traverseBreadthFirst(nodes, edges, ({ node, children, parents, siblings, isLeaf, isRoot, depth }) => { + children.forEach(([child, _]) => { + // Spread nodes across horizontal axis + // TODO: calculate separation dynamically from viewport width + child.x = node.x + nodeRadius / 2 + horizontalSeparationBetweenNodes + }) + return node + }) + + // Spread leaves along vertical axis + const leaves = getLeaves(nodes, edges) + const leafSpacing = height / (leaves.length - 1) + leaves.forEach((leaf, i) => { + leaf.y = i * (leafSpacing - nodeRadius) + }) + + // Spread parents in the vertical space defined by their children + traverseBreadthFirst( + nodes, + edges, + ({ node, children, parents, siblings, isLeaf, isRoot, depth }) => { + const siblingYs = siblings.map((sibling) => sibling.y) + + // calculate total y-space available to put parents into + const start = min(siblingYs) ?? 0 + const end = max(siblingYs) ?? 0 + + // calculate y-spacing between parents + const spacing = (end - start) / (parents.length + 1) + + // spread parents in the available y-space + parents.forEach(([parent, _], i) => { + parent.y = start + spacing * (i + 1) + }) + + return node + }, + { backward: true }, + ) + + console.log(require('util').inspect({ nodesDisplay: nodes }, { colors: true, depth: null, maxArrayLength: null })) + + return nodes +} + +export interface ExplorerParams { + node: N + children: [N, E][] + parents: [N, E][] + siblings: N[] + isLeaf: boolean + isRoot: boolean + depth: number +} + +// Explore graph in breadth-first fashion given an explorer function. +export function traverseBreadthFirst( + nodes: N[], + edges: E[], + explorer: (params: ExplorerParams) => T, + options?: { backward?: boolean }, +): T[] { + // First frontier is all the roots or all the leaves depending on direction of traversal + const frontier = options?.backward ? getLeaves(nodes, edges) : getRoots(nodes, edges) + + // Fill queue with the first frontier + const queue: { node: N; depth: number }[] = frontier.map((node) => ({ node, depth: 0 })) + + // Mark first frontier as explored + const explored = new Set(frontier.map((node) => node.id)) + + const results: T[] = [] + + while (queue.length > 0) { + const item = queue.shift() + if (!item) { + return results + } + + const { node, depth } = item + + let parents: [N, E][] = getParents(node.id, nodes, edges) + parents = !options?.backward ? parents.reverse() : parents + + let children: [N, E][] = getChildren(node.id, nodes, edges) + children = !options?.backward ? children.reverse() : children + + let siblings: N[] = getSiblings(node.id, nodes, edges) + siblings = !options?.backward ? siblings.reverse() : siblings + + // Leaf is the node that has no children + const isLeaf = children.length === 0 + + // Root is the node that has no parents + const isRoot = parents.length === 0 + + // Perform the exploration as defined by the caller function + const result = explorer({ node, children, parents, siblings, isLeaf, isRoot, depth }) + explored.add(node.id) + results.push(result) + + // Next, proceed with either children or parents, depending on which direction we are traversing + const successors = options?.backward ? parents : children + + // Enqueue children (unless already explored) + successors.forEach(([child, _]) => { + if (!explored.has(child.id)) { + queue.push({ node: child, depth: depth + 1 }) + } + }) + } + + return results +} + +export function getNodesForEdge( + nodes: N[], + edge: E, +) { + const source = getNodeById(nodes, edge.source) + const target = getNodeById(nodes, edge.target) + return { source, target } +} + +export function getNodeById(nodes: N[], id: string): N { + const node = nodes.find((node) => node.id === id) + if (!node) { + throw new Error(`Node '${id}' not found`) + } + return node +} + +export function getParents( + nodeId: string, + nodes: N[], + edges: E[], +): [N, E][] { + // Parent nodes are source nodes of edges where this node is the target + return edges + .filter((edge) => nodeId === edge.target) + .flatMap((edge) => { + const parents = nodes.filter((node) => node.id === edge.source) + const pairs: [N, E][] = parents.map((parent) => [parent, edge]) + return pairs + }) +} + +export function getChildren( + nodeId: string, + nodes: N[], + edges: E[], +): [N, E][] { + // Child nodes are target nodes of edges where this node is the source + return edges + .filter((edge) => nodeId === edge.source) + .flatMap((edge) => { + const children = nodes.filter((node) => node.id === edge.target) + const pairs: [N, E][] = children.map((node) => [node, edge]) + return pairs + }) +} + +export function getSiblings( + nodeId: string, + nodes: N[], + edges: E[], +): N[] { + // Sibling nodes are all the child nodes of all parents + return getParents(nodeId, nodes, edges).flatMap(([parent, _]) => + getChildren(parent.id, nodes, edges).map(([child, _]) => child), + ) +} + +export function getRoots( + nodes: N[], + edges: E[], +) { + // Roots are the nodes that have no parents, i.e. they are the nodes which are never the target of an edge + const targetNodeIds = new Set(edges.map((edges) => edges.target)) + return nodes.filter((node) => !targetNodeIds.has(node.id)) +} + +export function getLeaves( + nodes: N[], + edges: E[], +) { + // Leaves are the nodes that have no children, i.e. they are the nodes which are never the source of an edge + const sourceNodeIds = new Set(edges.map((edges) => edges.source)) + return nodes.filter((node) => !sourceNodeIds.has(node.id)) +} diff --git a/src/graph/utils.ts b/src/graph/utils.ts new file mode 100644 index 0000000..0cf7959 --- /dev/null +++ b/src/graph/utils.ts @@ -0,0 +1,8 @@ +export function findExactlyOne(components: T[], predicate: (s: T) => boolean) { + const candidates = components.filter(predicate) + if (candidates.length > 1) { + const c = candidates.map((s) => `"${JSON.stringify(s)}"`).join(',') + throw new Error(`Expected to find exactly one element, but found: ${c}`) + } + return candidates[0] +} diff --git a/tools/flatten.ts b/tools/flatten.ts index 72e1ba5..d6fdf6e 100644 --- a/tools/flatten.ts +++ b/tools/flatten.ts @@ -1,6 +1,10 @@ -import { omit, sortBy } from 'lodash' +/* eslint-disable security/detect-unsafe-regex */ +import { sortBy } from 'lodash' import fs from 'fs-extra' +import type { GraphEdge, GraphNode } from '../src/graph/graph' +import { findExactlyOne } from '../src/graph/utils' + main().catch(console.error) export interface OldNode { @@ -9,37 +13,20 @@ export interface OldNode { children?: OldNode[] } -export interface GraphNode extends Omit { - id: string - clade: string - lineages?: string[] - who?: string - version?: string - otherNames?: string[] -} - -export interface GraphEdge { - id: string - source: string - target: string -} - export async function main() { - const cladesJson = await fs.readJSON('src/clades.json') + const cladesJson = (await fs.readJSON('src/clades.json')) as OldNode let nodes: GraphNode[] = [] - let edges: GraphEdge[] = [] + const edges: GraphEdge[] = [] flattenCladeTree(cladesJson, nodes, edges) nodes = sortBy(nodes, (node) => node.clade) verifyGraph(nodes, edges) - console.log(require('util').inspect({ nodes, edges }, { colors: true, depth: null, maxArrayLength: null })) - - fs.writeJson('src/clades2.json', { nodes, edges }, { spaces: 2 }) + await fs.writeJson('src/clades2.json', { nodes, edges }, { spaces: 2 }) } -// Convert tree node hierarhy into flat lists of nodes and edges +// Convert tree node hierarchy into flat lists of nodes and edges function flattenCladeTree(node: OldNode, nodes: GraphNode[], edges: GraphEdge[]) { const { clade, lineages, who, version, otherNames } = splitName(node.name) @@ -64,7 +51,7 @@ function flattenCladeTree(node: OldNode, nodes: GraphNode[], edges: GraphEdge[]) } function splitName(name: string) { - // Extract clade (outside parentheses) and details string (the thing in parenteses) + // Extract clade (outside parentheses) and details string (the thing in parentheses) const matches = name.match(/^(?.*?)( \((?
[^)]*)\))?$/) if (!matches) { throw new Error(`Unable to parse name '${name}'`) @@ -80,7 +67,7 @@ function splitName(name: string) { return { clade } } - // Decompose details string (the thing in parenteses), + // Decompose details string (the thing in parentheses), // for example "(B.1)", "(Omicron, B.1.1.529), "(Beta, V2, B.1.351)", "(EU1)"" const components = details.split(',').map((component) => component.trim()) if (components.length === 0) { @@ -90,7 +77,7 @@ function splitName(name: string) { const who = findExactlyOne(components, isWhoVariant) const version = findExactlyOne(components, isVersion) const lineages = components.filter((c) => isPangoLineage(c)) - const otherNames = components.filter((c) => c != who && c != version && !lineages.includes(c)) + const otherNames = components.filter((c) => c !== who && c !== version && !lineages.includes(c)) return { clade, lineages, who, version, otherNames } throw new Error( @@ -99,18 +86,18 @@ function splitName(name: string) { } function isPangoLineage(s: string) { - return s.match(/^(\~)?(A|B|C|D|BA|BQ|P|XBB|)(\.\d+?(\/\d+)?)*$/) !== null + return s.match(/^(~)?(A|B|C|D|BA|BQ|P|XBB|)(\.\d+?(\/\d+)?)*$/) !== null } function isWhoVariant(s: string) { - return !WHO_EXCEPTIONS.includes(s) && GREEK_LETTERS.includes(s) + return !WHO_EXCEPTIONS.has(s) && GREEK_LETTERS.has(s) } function isVersion(s: string) { return s.match(/^V\d$/) !== null } -const GREEK_LETTERS = [ +const GREEK_LETTERS = new Set([ 'Alpha', 'Beta', 'Gamma', @@ -135,29 +122,21 @@ const GREEK_LETTERS = [ 'Chi', 'Psi', 'Omega', -] - -const WHO_EXCEPTIONS = ['EU1'] +]) -function findExactlyOne(components: string[], predicate: (s: string) => boolean) { - const candidates = components.filter(predicate) - if (candidates.length > 1) { - throw new Error(`Expected to find exactly one element, but found: ${candidates.map((s) => `"${s}"`).join(',')}`) - } - return candidates[0] -} +const WHO_EXCEPTIONS = new Set(['EU1']) function verifyGraph(nodes: GraphNode[], edges: GraphEdge[]) { edges.forEach((edge) => { - if (edge.target == edge.source) { + if (edge.target === edge.source) { throw new Error(`Graph is invalid: invalid edge: the target node '${edge.target}' is the same as source node`) } - if (!nodes.find((node) => edge.target == node.id)) { + if (!nodes.some((node) => edge.target === node.id)) { throw new Error(`Graph is invalid: invalid edge: the target node '${edge.target}' does not exist`) } - if (!nodes.find((node) => edge.source == node.id)) { + if (!nodes.some((node) => edge.source === node.id)) { throw new Error(`Graph is invalid: invalid edge: the source node '${edge.source}' does not exist`) } }) From 2ab2128f853a80a62fc571c3ea38d96163343c7a Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Fri, 18 Nov 2022 10:18:15 +0100 Subject: [PATCH 09/14] refactor: move properties x, y into the node type --- src/clades2.json | 124 ++++++++++++++++++++++++++++++---------- src/components/Edge.tsx | 4 +- src/components/Node.tsx | 4 +- src/graph/graph.ts | 6 +- tools/flatten.ts | 2 + 5 files changed, 101 insertions(+), 39 deletions(-) diff --git a/src/clades2.json b/src/clades2.json index 66bf5f2..b7df85d 100644 --- a/src/clades2.json +++ b/src/clades2.json @@ -7,7 +7,9 @@ "lineages": [ "B" ], - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "19B (A)", @@ -16,7 +18,9 @@ "lineages": [ "A" ], - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "20A (B.1)", @@ -25,7 +29,9 @@ "lineages": [ "B.1" ], - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "20B (B.1.1)", @@ -34,12 +40,16 @@ "lineages": [ "B.1.1" ], - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "20C", "color": "#A8A8A8", - "clade": "20C" + "clade": "20C", + "x": 0, + "y": 0 }, { "id": "20D (B.1.1.1)", @@ -48,7 +58,9 @@ "lineages": [ "B.1.1.1" ], - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "20E (EU1, B.1.177)", @@ -59,7 +71,9 @@ ], "otherNames": [ "EU1" - ] + ], + "x": 0, + "y": 0 }, { "id": "20F (D.2)", @@ -68,7 +82,9 @@ "lineages": [ "D.2" ], - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "20G (B.1.2)", @@ -77,7 +93,9 @@ "lineages": [ "B.1.2" ], - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "20H (Beta, V2, B.1.351)", @@ -88,7 +106,9 @@ ], "who": "Beta", "version": "V2", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "20I (Alpha, V1, B.1.1.7)", @@ -99,7 +119,9 @@ ], "who": "Alpha", "version": "V1", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "20J (Gamma, V3, P.1)", @@ -110,7 +132,9 @@ ], "who": "Gamma", "version": "V3", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21A (Delta, B.1.617.2)", @@ -120,7 +144,9 @@ "B.1.617.2" ], "who": "Delta", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21B (Kappa, B.1.617.1)", @@ -130,7 +156,9 @@ "B.1.617.1" ], "who": "Kappa", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21C (Epsilon, B.1.427/429)", @@ -140,7 +168,9 @@ "B.1.427/429" ], "who": "Epsilon", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21D (Eta, B.1.525)", @@ -150,7 +180,9 @@ "B.1.525" ], "who": "Eta", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21E (Theta, P.3)", @@ -160,7 +192,9 @@ "P.3" ], "who": "Theta", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21F (Iota, B.1.526)", @@ -170,7 +204,9 @@ "B.1.526" ], "who": "Iota", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21G (Lambda, C.37)", @@ -180,7 +216,9 @@ "C.37" ], "who": "Lambda", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21H (Mu, B.1.621)", @@ -190,7 +228,9 @@ "B.1.621" ], "who": "Mu", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21I (Delta)", @@ -198,7 +238,9 @@ "clade": "21I", "lineages": [], "who": "Delta", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21J (Delta)", @@ -206,7 +248,9 @@ "clade": "21J", "lineages": [], "who": "Delta", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21K (Omicron, BA.1)", @@ -216,7 +260,9 @@ "BA.1" ], "who": "Omicron", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21L (Omicron, ~BA.2)", @@ -226,7 +272,9 @@ "~BA.2" ], "who": "Omicron", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "21M (Omicron, B.1.1.529)", @@ -236,7 +284,9 @@ "B.1.1.529" ], "who": "Omicron", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "22A (Omicron, BA.4)", @@ -246,7 +296,9 @@ "BA.4" ], "who": "Omicron", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "22B (Omicron, BA.5)", @@ -256,7 +308,9 @@ "BA.5" ], "who": "Omicron", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "22C (Omicron, BA.2.12.1)", @@ -266,7 +320,9 @@ "BA.2.12.1" ], "who": "Omicron", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "22D (Omicron, BA.2.75)", @@ -276,7 +332,9 @@ "BA.2.75" ], "who": "Omicron", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "22E (Omicron, BQ.1)", @@ -286,7 +344,9 @@ "BQ.1" ], "who": "Omicron", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 }, { "id": "22F (Omicron, XBB)", @@ -296,7 +356,9 @@ "XBB" ], "who": "Omicron", - "otherNames": [] + "otherNames": [], + "x": 0, + "y": 0 } ], "edges": [ diff --git a/src/components/Edge.tsx b/src/components/Edge.tsx index fa2702c..c8b264e 100644 --- a/src/components/Edge.tsx +++ b/src/components/Edge.tsx @@ -1,10 +1,10 @@ import React, { useMemo } from 'react' -import { getNodesForEdge, GraphEdge, GraphNodeDisplay } from '../graph/graph' +import { getNodesForEdge, GraphEdge, GraphNode } from '../graph/graph' import { nodeRadius } from './constants' export interface EdgeProps { - nodes: GraphNodeDisplay[] + nodes: GraphNode[] edge: GraphEdge } diff --git a/src/components/Node.tsx b/src/components/Node.tsx index c28eea6..74fe505 100644 --- a/src/components/Node.tsx +++ b/src/components/Node.tsx @@ -1,10 +1,10 @@ import React, { ReactElement } from 'react' -import { GraphNodeDisplay } from 'src/graph/graph' +import { GraphNode } from 'src/graph/graph' import { cladesTextColor, cladesTextSize, nodeRadius } from './constants' export interface CladeTreeNodeProps { - node: GraphNodeDisplay + node: GraphNode } export function Node({ node }: CladeTreeNodeProps): ReactElement { diff --git a/src/graph/graph.ts b/src/graph/graph.ts index e8e99f3..b547e98 100644 --- a/src/graph/graph.ts +++ b/src/graph/graph.ts @@ -9,8 +9,6 @@ export interface GraphNode { version?: string otherNames?: string[] color?: string -} -export interface GraphNodeDisplay extends GraphNode { x: number y: number } @@ -22,11 +20,11 @@ export interface GraphEdge { } export function calculateGraphLayout( - nodes_: GraphNodeDisplay[], + nodes_: GraphNode[], edges: GraphEdge[], width: number, height: number, -): GraphNodeDisplay[] { +): GraphNode[] { const nodes = cloneDeep(nodes_) // Position roots at the left of viewport diff --git a/tools/flatten.ts b/tools/flatten.ts index d6fdf6e..c9f2fc0 100644 --- a/tools/flatten.ts +++ b/tools/flatten.ts @@ -40,6 +40,8 @@ function flattenCladeTree(node: OldNode, nodes: GraphNode[], edges: GraphEdge[]) who, version, otherNames, + x: 0, + y: 0, }) const children = node.children ?? [] From 0f80a2c60a5938d1e33865fb8f7e91086e4e088a Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Fri, 18 Nov 2022 10:54:17 +0100 Subject: [PATCH 10/14] refactor: introduce graph object --- src/components/Edge.tsx | 10 +- src/components/NextstrainCladeTreeSvg.tsx | 14 +-- src/components/Node.tsx | 5 +- src/graph/graph.ts | 123 +++++++++------------- 4 files changed, 62 insertions(+), 90 deletions(-) diff --git a/src/components/Edge.tsx b/src/components/Edge.tsx index c8b264e..b6a08d8 100644 --- a/src/components/Edge.tsx +++ b/src/components/Edge.tsx @@ -1,22 +1,22 @@ import React, { useMemo } from 'react' -import { getNodesForEdge, GraphEdge, GraphNode } from '../graph/graph' +import { getNodesForEdge, Graph, GraphEdge } from '../graph/graph' import { nodeRadius } from './constants' export interface EdgeProps { - nodes: GraphNode[] edge: GraphEdge + graph: Graph } -export function Edge({ nodes, edge }: EdgeProps) { +export function Edge({ edge, graph }: EdgeProps) { const { x1, x2, y1, y2 } = useMemo(() => { - const { source, target } = getNodesForEdge(nodes, edge) + const { source, target } = getNodesForEdge(graph, edge) const y1 = source.y + nodeRadius / 2 const y2 = target.y + nodeRadius / 2 const x1 = source.x + nodeRadius / 2 const x2 = target.x + nodeRadius / 2 return { x1, x2, y1, y2 } - }, [edge, nodes]) + }, [edge, graph]) return } diff --git a/src/components/NextstrainCladeTreeSvg.tsx b/src/components/NextstrainCladeTreeSvg.tsx index 0568e5d..0217bd8 100644 --- a/src/components/NextstrainCladeTreeSvg.tsx +++ b/src/components/NextstrainCladeTreeSvg.tsx @@ -32,15 +32,11 @@ export const NextstrainCladeTreeSvg = forwardRef ({ ...node, x: 0, y: 0 })), - cladesJson.edges, - width, - height, - ) - - const nodeComponents = nodes.map((node) => ) - const edgeComponents = cladesJson.edges.map((edge) => ) + let graph = { nodes: cladesJson.nodes, edges: cladesJson.edges } + graph = calculateGraphLayout(graph, width, height) + + const nodeComponents = graph.nodes.map((node) => ) + const edgeComponents = graph.edges.map((edge) => ) return { nodeComponents, edgeComponents } }, [cladesJson.edges, cladesJson.nodes, height, width]) diff --git a/src/components/Node.tsx b/src/components/Node.tsx index 74fe505..934f92a 100644 --- a/src/components/Node.tsx +++ b/src/components/Node.tsx @@ -1,13 +1,14 @@ import React, { ReactElement } from 'react' -import { GraphNode } from 'src/graph/graph' +import type { Graph, GraphNode } from 'src/graph/graph' import { cladesTextColor, cladesTextSize, nodeRadius } from './constants' export interface CladeTreeNodeProps { node: GraphNode + graph: Graph } -export function Node({ node }: CladeTreeNodeProps): ReactElement { +export function Node({ node, graph }: CladeTreeNodeProps): ReactElement { const { id, clade, lineages, who, version, otherNames, x, y, color } = node return ( diff --git a/src/graph/graph.ts b/src/graph/graph.ts index b547e98..c6acd4a 100644 --- a/src/graph/graph.ts +++ b/src/graph/graph.ts @@ -1,6 +1,11 @@ import { max, min, cloneDeep } from 'lodash' import { horizontalSeparationBetweenNodes, nodeRadius } from '../components/constants' +export interface Graph { + nodes: GraphNode[] + edges: GraphEdge[] +} + export interface GraphNode { id: string clade: string @@ -19,21 +24,16 @@ export interface GraphEdge { target: string } -export function calculateGraphLayout( - nodes_: GraphNode[], - edges: GraphEdge[], - width: number, - height: number, -): GraphNode[] { - const nodes = cloneDeep(nodes_) +export function calculateGraphLayout(graph_: Graph, width: number, height: number): Graph { + const graph = cloneDeep(graph_) // Position roots at the left of viewport - const roots = getRoots(nodes, edges) + const roots = getRoots(graph) roots.forEach((root) => { root.x = nodeRadius / 2 }) - traverseBreadthFirst(nodes, edges, ({ node, children, parents, siblings, isLeaf, isRoot, depth }) => { + traverseBreadthFirst(graph, ({ node, children, parents, siblings, isLeaf, isRoot, depth }) => { children.forEach(([child, _]) => { // Spread nodes across horizontal axis // TODO: calculate separation dynamically from viewport width @@ -43,7 +43,7 @@ export function calculateGraphLayout( }) // Spread leaves along vertical axis - const leaves = getLeaves(nodes, edges) + const leaves = getLeaves(graph) const leafSpacing = height / (leaves.length - 1) leaves.forEach((leaf, i) => { leaf.y = i * (leafSpacing - nodeRadius) @@ -51,8 +51,7 @@ export function calculateGraphLayout( // Spread parents in the vertical space defined by their children traverseBreadthFirst( - nodes, - edges, + graph, ({ node, children, parents, siblings, isLeaf, isRoot, depth }) => { const siblingYs = siblings.map((sibling) => sibling.y) @@ -73,33 +72,32 @@ export function calculateGraphLayout( { backward: true }, ) - console.log(require('util').inspect({ nodesDisplay: nodes }, { colors: true, depth: null, maxArrayLength: null })) + console.log(require('util').inspect(graph.nodes, { colors: true, depth: null, maxArrayLength: null })) - return nodes + return graph } -export interface ExplorerParams { - node: N - children: [N, E][] - parents: [N, E][] - siblings: N[] +export interface ExplorerParams { + node: GraphNode + children: [GraphNode, GraphEdge][] + parents: [GraphNode, GraphEdge][] + siblings: GraphNode[] isLeaf: boolean isRoot: boolean depth: number } // Explore graph in breadth-first fashion given an explorer function. -export function traverseBreadthFirst( - nodes: N[], - edges: E[], - explorer: (params: ExplorerParams) => T, +export function traverseBreadthFirst( + graph: Graph, + explorer: (params: ExplorerParams) => T, options?: { backward?: boolean }, ): T[] { // First frontier is all the roots or all the leaves depending on direction of traversal - const frontier = options?.backward ? getLeaves(nodes, edges) : getRoots(nodes, edges) + const frontier = options?.backward ? getLeaves(graph) : getRoots(graph) // Fill queue with the first frontier - const queue: { node: N; depth: number }[] = frontier.map((node) => ({ node, depth: 0 })) + const queue: { node: GraphNode; depth: number }[] = frontier.map((node) => ({ node, depth: 0 })) // Mark first frontier as explored const explored = new Set(frontier.map((node) => node.id)) @@ -114,13 +112,13 @@ export function traverseBreadthFirst( - nodes: N[], - edge: E, -) { - const source = getNodeById(nodes, edge.source) - const target = getNodeById(nodes, edge.target) +export function getNodesForEdge(graph: Graph, edge: GraphEdge) { + const source = getNodeById(graph, edge.source) + const target = getNodeById(graph, edge.target) return { source, target } } -export function getNodeById(nodes: N[], id: string): N { - const node = nodes.find((node) => node.id === id) +export function getNodeById(graph: Graph, id: string): GraphNode { + const node = graph.nodes.find((node) => node.id === id) if (!node) { throw new Error(`Node '${id}' not found`) } return node } -export function getParents( - nodeId: string, - nodes: N[], - edges: E[], -): [N, E][] { +export function getParents(graph: Graph, nodeId: string): [GraphNode, GraphEdge][] { // Parent nodes are source nodes of edges where this node is the target - return edges + return graph.edges .filter((edge) => nodeId === edge.target) .flatMap((edge) => { - const parents = nodes.filter((node) => node.id === edge.source) - const pairs: [N, E][] = parents.map((parent) => [parent, edge]) + const parents = graph.nodes.filter((node) => node.id === edge.source) + const pairs: [GraphNode, GraphEdge][] = parents.map((parent) => [parent, edge]) return pairs }) } -export function getChildren( - nodeId: string, - nodes: N[], - edges: E[], -): [N, E][] { +export function getChildren(graph: Graph, nodeId: string): [GraphNode, GraphEdge][] { // Child nodes are target nodes of edges where this node is the source - return edges + return graph.edges .filter((edge) => nodeId === edge.source) .flatMap((edge) => { - const children = nodes.filter((node) => node.id === edge.target) - const pairs: [N, E][] = children.map((node) => [node, edge]) + const children = graph.nodes.filter((node) => node.id === edge.target) + const pairs: [GraphNode, GraphEdge][] = children.map((node) => [node, edge]) return pairs }) } -export function getSiblings( - nodeId: string, - nodes: N[], - edges: E[], -): N[] { +export function getSiblings(graph: Graph, nodeId: string): GraphNode[] { // Sibling nodes are all the child nodes of all parents - return getParents(nodeId, nodes, edges).flatMap(([parent, _]) => - getChildren(parent.id, nodes, edges).map(([child, _]) => child), - ) + return getParents(graph, nodeId).flatMap(([parent, _]) => getChildren(graph, parent.id).map(([child, _]) => child)) } -export function getRoots( - nodes: N[], - edges: E[], -) { - // Roots are the nodes that have no parents, i.e. they are the nodes which are never the target of an edge - const targetNodeIds = new Set(edges.map((edges) => edges.target)) - return nodes.filter((node) => !targetNodeIds.has(node.id)) +export function getRoots(graph: Graph) { + // Roots are the nodes that have no parents, i.e. each node which is never a target of an edge + const targetNodeIds = new Set(graph.edges.map((edge) => edge.target)) + return graph.nodes.filter((node) => !targetNodeIds.has(node.id)) } -export function getLeaves( - nodes: N[], - edges: E[], -) { - // Leaves are the nodes that have no children, i.e. they are the nodes which are never the source of an edge - const sourceNodeIds = new Set(edges.map((edges) => edges.source)) - return nodes.filter((node) => !sourceNodeIds.has(node.id)) +export function getLeaves(graph: Graph) { + // Leaves are the nodes that have no children, i.e. each node which is never a source of an edge + const sourceNodeIds = new Set(graph.edges.map((edge) => edge.source)) + return graph.nodes.filter((node) => !sourceNodeIds.has(node.id)) } From fe5be9e1d3b752fa1b7043dd752a5f6fba2875bc Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Fri, 18 Nov 2022 10:58:31 +0100 Subject: [PATCH 11/14] refactor: add explicit backwards graph traversal function --- src/graph/graph.ts | 39 ++++++++++++++++++++++----------------- 1 file changed, 22 insertions(+), 17 deletions(-) diff --git a/src/graph/graph.ts b/src/graph/graph.ts index c6acd4a..805de27 100644 --- a/src/graph/graph.ts +++ b/src/graph/graph.ts @@ -50,27 +50,23 @@ export function calculateGraphLayout(graph_: Graph, width: number, height: numbe }) // Spread parents in the vertical space defined by their children - traverseBreadthFirst( - graph, - ({ node, children, parents, siblings, isLeaf, isRoot, depth }) => { - const siblingYs = siblings.map((sibling) => sibling.y) + traverseBreadthFirstBackwards(graph, ({ node, children, parents, siblings, isLeaf, isRoot, depth }) => { + const siblingYs = siblings.map((sibling) => sibling.y) - // calculate total y-space available to put parents into - const start = min(siblingYs) ?? 0 - const end = max(siblingYs) ?? 0 + // calculate total y-space available to put parents into + const start = min(siblingYs) ?? 0 + const end = max(siblingYs) ?? 0 - // calculate y-spacing between parents - const spacing = (end - start) / (parents.length + 1) + // calculate y-spacing between parents + const spacing = (end - start) / (parents.length + 1) - // spread parents in the available y-space - parents.forEach(([parent, _], i) => { - parent.y = start + spacing * (i + 1) - }) + // spread parents in the available y-space + parents.forEach(([parent, _], i) => { + parent.y = start + spacing * (i + 1) + }) - return node - }, - { backward: true }, - ) + return node + }) console.log(require('util').inspect(graph.nodes, { colors: true, depth: null, maxArrayLength: null })) @@ -146,6 +142,15 @@ export function traverseBreadthFirst( return results } +// Explore graph in breadth-first fashion, backwards +export function traverseBreadthFirstBackwards( + graph: Graph, + explorer: (params: ExplorerParams) => T, + options?: { backward?: boolean }, +): T[] { + return traverseBreadthFirst(graph, explorer, { ...options, backward: true }) +} + export function getNodesForEdge(graph: Graph, edge: GraphEdge) { const source = getNodeById(graph, edge.source) const target = getNodeById(graph, edge.target) From 5ef631a11fd5b3a0c670447df768bca4e32d3c33 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Tue, 29 Nov 2022 02:35:52 +0100 Subject: [PATCH 12/14] feat: borrow graph layout from phyloTree https://github.com/nextstrain/phyloTree --- src/clades2.json | 124 ++++++++----------------------- src/graph/graph.ts | 179 ++++++++++++++++++++++++++++++++++----------- tools/flatten.ts | 10 +-- 3 files changed, 173 insertions(+), 140 deletions(-) diff --git a/src/clades2.json b/src/clades2.json index b7df85d..66bf5f2 100644 --- a/src/clades2.json +++ b/src/clades2.json @@ -7,9 +7,7 @@ "lineages": [ "B" ], - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "19B (A)", @@ -18,9 +16,7 @@ "lineages": [ "A" ], - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "20A (B.1)", @@ -29,9 +25,7 @@ "lineages": [ "B.1" ], - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "20B (B.1.1)", @@ -40,16 +34,12 @@ "lineages": [ "B.1.1" ], - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "20C", "color": "#A8A8A8", - "clade": "20C", - "x": 0, - "y": 0 + "clade": "20C" }, { "id": "20D (B.1.1.1)", @@ -58,9 +48,7 @@ "lineages": [ "B.1.1.1" ], - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "20E (EU1, B.1.177)", @@ -71,9 +59,7 @@ ], "otherNames": [ "EU1" - ], - "x": 0, - "y": 0 + ] }, { "id": "20F (D.2)", @@ -82,9 +68,7 @@ "lineages": [ "D.2" ], - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "20G (B.1.2)", @@ -93,9 +77,7 @@ "lineages": [ "B.1.2" ], - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "20H (Beta, V2, B.1.351)", @@ -106,9 +88,7 @@ ], "who": "Beta", "version": "V2", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "20I (Alpha, V1, B.1.1.7)", @@ -119,9 +99,7 @@ ], "who": "Alpha", "version": "V1", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "20J (Gamma, V3, P.1)", @@ -132,9 +110,7 @@ ], "who": "Gamma", "version": "V3", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21A (Delta, B.1.617.2)", @@ -144,9 +120,7 @@ "B.1.617.2" ], "who": "Delta", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21B (Kappa, B.1.617.1)", @@ -156,9 +130,7 @@ "B.1.617.1" ], "who": "Kappa", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21C (Epsilon, B.1.427/429)", @@ -168,9 +140,7 @@ "B.1.427/429" ], "who": "Epsilon", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21D (Eta, B.1.525)", @@ -180,9 +150,7 @@ "B.1.525" ], "who": "Eta", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21E (Theta, P.3)", @@ -192,9 +160,7 @@ "P.3" ], "who": "Theta", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21F (Iota, B.1.526)", @@ -204,9 +170,7 @@ "B.1.526" ], "who": "Iota", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21G (Lambda, C.37)", @@ -216,9 +180,7 @@ "C.37" ], "who": "Lambda", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21H (Mu, B.1.621)", @@ -228,9 +190,7 @@ "B.1.621" ], "who": "Mu", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21I (Delta)", @@ -238,9 +198,7 @@ "clade": "21I", "lineages": [], "who": "Delta", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21J (Delta)", @@ -248,9 +206,7 @@ "clade": "21J", "lineages": [], "who": "Delta", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21K (Omicron, BA.1)", @@ -260,9 +216,7 @@ "BA.1" ], "who": "Omicron", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21L (Omicron, ~BA.2)", @@ -272,9 +226,7 @@ "~BA.2" ], "who": "Omicron", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "21M (Omicron, B.1.1.529)", @@ -284,9 +236,7 @@ "B.1.1.529" ], "who": "Omicron", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "22A (Omicron, BA.4)", @@ -296,9 +246,7 @@ "BA.4" ], "who": "Omicron", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "22B (Omicron, BA.5)", @@ -308,9 +256,7 @@ "BA.5" ], "who": "Omicron", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "22C (Omicron, BA.2.12.1)", @@ -320,9 +266,7 @@ "BA.2.12.1" ], "who": "Omicron", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "22D (Omicron, BA.2.75)", @@ -332,9 +276,7 @@ "BA.2.75" ], "who": "Omicron", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "22E (Omicron, BQ.1)", @@ -344,9 +286,7 @@ "BQ.1" ], "who": "Omicron", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] }, { "id": "22F (Omicron, XBB)", @@ -356,9 +296,7 @@ "XBB" ], "who": "Omicron", - "otherNames": [], - "x": 0, - "y": 0 + "otherNames": [] } ], "edges": [ diff --git a/src/graph/graph.ts b/src/graph/graph.ts index 805de27..7a4e4d1 100644 --- a/src/graph/graph.ts +++ b/src/graph/graph.ts @@ -1,12 +1,17 @@ -import { max, min, cloneDeep } from 'lodash' +import { max, min, cloneDeep, sumBy, meanBy, last, first, minBy } from 'lodash' import { horizontalSeparationBetweenNodes, nodeRadius } from '../components/constants' +export interface GraphRaw { + nodes: GraphNodeRaw[] + edges: GraphEdge[] +} + export interface Graph { nodes: GraphNode[] edges: GraphEdge[] } -export interface GraphNode { +export interface GraphNodeRaw { id: string clade: string lineages?: string[] @@ -14,8 +19,45 @@ export interface GraphNode { version?: string otherNames?: string[] color?: string +} + +export interface GraphNode extends GraphNodeRaw { x: number y: number + layout: { + numLeaves: number + meanDepth: number + minDepth: number + maxDepth: number + meanRank: number + minRank: number + maxRank: number + yTBarStart: number + xTBarStart: number + yTBarEnd: number + xTBarEnd: number + } +} + +export function convertNodeToInternal(nodeRaw: GraphNodeRaw): GraphNode { + return { + ...nodeRaw, + x: 0, + y: 0, + layout: { + numLeaves: 0, + meanDepth: 0, + minDepth: 0, + maxDepth: 0, + meanRank: 0, + minRank: 0, + maxRank: 0, + yTBarStart: 0, + xTBarStart: 0, + yTBarEnd: 0, + xTBarEnd: 0, + }, + } } export interface GraphEdge { @@ -24,48 +66,48 @@ export interface GraphEdge { target: string } -export function calculateGraphLayout(graph_: Graph, width: number, height: number): Graph { - const graph = cloneDeep(graph_) - - // Position roots at the left of viewport - const roots = getRoots(graph) - roots.forEach((root) => { - root.x = nodeRadius / 2 - }) - - traverseBreadthFirst(graph, ({ node, children, parents, siblings, isLeaf, isRoot, depth }) => { - children.forEach(([child, _]) => { - // Spread nodes across horizontal axis - // TODO: calculate separation dynamically from viewport width - child.x = node.x + nodeRadius / 2 + horizontalSeparationBetweenNodes - }) +export function calculateGraphLayout(graphRaw: GraphRaw, width: number, height: number): Graph { + const graph: Graph = { ...cloneDeep(graphRaw), nodes: graphRaw.nodes.map(convertNodeToInternal) } + + let rank = 0 + traverseDepthFirstPostOrder(graph, ({ node, children, parents, siblings, isLeaf, isRoot }) => { + if (isLeaf) { + node.layout.numLeaves = 1 + rank += 1 + node.layout.meanRank = rank + node.layout.minRank = rank + node.layout.maxRank = rank + } else { + node.layout.numLeaves = sumBy(children, ([child, _]) => child.layout.numLeaves) + node.layout.meanRank = meanBy(children, ([child, _]) => child.layout.meanRank) + node.layout.minRank = min(children.map(([child, _]) => child.layout.meanRank)) ?? 0 + node.layout.maxRank = max(children.map(([child, _]) => child.layout.meanRank)) ?? 0 + } return node }) - // Spread leaves along vertical axis - const leaves = getLeaves(graph) - const leafSpacing = height / (leaves.length - 1) - leaves.forEach((leaf, i) => { - leaf.y = i * (leafSpacing - nodeRadius) + traverseDepthFirstPreOrder(graph, ({ node, children, parents, siblings, isLeaf, isRoot }) => { + if (isRoot) { + node.layout.meanDepth = 0 + node.layout.maxDepth = 0 + node.layout.minDepth = 0 + } else { + node.layout.meanDepth = meanBy(parents, ([parent]) => parent.layout.meanDepth) + 1 + node.layout.minDepth = (min(parents.map(([parent, _]) => parent.layout.meanDepth)) ?? 0) + 1 + node.layout.maxDepth = (max(parents.map(([parent, _]) => parent.layout.meanDepth)) ?? 0) + 1 + } + return node }) - // Spread parents in the vertical space defined by their children - traverseBreadthFirstBackwards(graph, ({ node, children, parents, siblings, isLeaf, isRoot, depth }) => { - const siblingYs = siblings.map((sibling) => sibling.y) - - // calculate total y-space available to put parents into - const start = min(siblingYs) ?? 0 - const end = max(siblingYs) ?? 0 - - // calculate y-spacing between parents - const spacing = (end - start) / (parents.length + 1) - - // spread parents in the available y-space - parents.forEach(([parent, _], i) => { - parent.y = start + spacing * (i + 1) - }) - - return node + traverseDepthFirstPreOrder(graph, ({ node, children, parents, siblings, isLeaf, isRoot }) => { + node.y = node.layout.meanRank * 40 + node.x = node.layout.meanDepth * 100 + if (!isLeaf) { + node.layout.yTBarStart = node.layout.minRank + node.layout.xTBarStart = node.layout.meanDepth + node.layout.yTBarEnd = node.layout.maxRank + node.layout.xTBarEnd = node.layout.meanDepth + } }) console.log(require('util').inspect(graph.nodes, { colors: true, depth: null, maxArrayLength: null })) @@ -80,7 +122,6 @@ export interface ExplorerParams { siblings: GraphNode[] isLeaf: boolean isRoot: boolean - depth: number } // Explore graph in breadth-first fashion given an explorer function. @@ -124,7 +165,7 @@ export function traverseBreadthFirst( const isRoot = parents.length === 0 // Perform the exploration as defined by the caller function - const result = explorer({ node, children, parents, siblings, isLeaf, isRoot, depth }) + const result = explorer({ node, children, parents, siblings, isLeaf, isRoot }) explored.add(node.id) results.push(result) @@ -142,6 +183,11 @@ export function traverseBreadthFirst( return results } +export enum DepthFirstTraversalOrder { + Pre, + Post, +} + // Explore graph in breadth-first fashion, backwards export function traverseBreadthFirstBackwards( graph: Graph, @@ -151,6 +197,57 @@ export function traverseBreadthFirstBackwards( return traverseBreadthFirst(graph, explorer, { ...options, backward: true }) } +// Explore graph in depth-first pre-order fashion +export function traverseDepthFirstPreOrder(graph: Graph, explorer: (params: ExplorerParams) => T) { + const results: T[] = [] + const explored = new Set() + return getRoots(graph).forEach((node) => { + traverseDepthFirstRecursively(graph, node, explorer, results, explored, DepthFirstTraversalOrder.Pre) + }) + return results +} + +// Explore graph in depth-first post-order fashion +export function traverseDepthFirstPostOrder(graph: Graph, explorer: (params: ExplorerParams) => T) { + const results: T[] = [] + const explored = new Set() + return getRoots(graph).forEach((node) => { + traverseDepthFirstRecursively(graph, node, explorer, results, explored, DepthFirstTraversalOrder.Post) + }) + return results +} + +// Implements graph traversal in depth-first pre-order or post-order fashion. Recursive implementation. +function traverseDepthFirstRecursively( + graph: Graph, + node: GraphNode, + explorer: (params: ExplorerParams) => T, + results: T[], + explored: Set, + order: DepthFirstTraversalOrder, +) { + const parents: [GraphNode, GraphEdge][] = getParents(graph, node.id) + const children: [GraphNode, GraphEdge][] = getChildren(graph, node.id) + const siblings: GraphNode[] = getSiblings(graph, node.id) + const isLeaf = children.length === 0 // Leaf is the node that has no children + const isRoot = parents.length === 0 // Root is the node that has no parents + + // Explore current node if pre-order + if (order === DepthFirstTraversalOrder.Pre) { + explored.add(node.id) + results.push(explorer({ node, children, parents, siblings, isLeaf, isRoot })) + } + + // Explore child nodes recursively + children.forEach(([child]) => traverseDepthFirstRecursively(graph, child, explorer, results, explored, order)) + + // Explore current node if post-order + if (order === DepthFirstTraversalOrder.Post) { + explored.add(node.id) + results.push(explorer({ node, children, parents, siblings, isLeaf, isRoot })) + } +} + export function getNodesForEdge(graph: Graph, edge: GraphEdge) { const source = getNodeById(graph, edge.source) const target = getNodeById(graph, edge.target) diff --git a/tools/flatten.ts b/tools/flatten.ts index c9f2fc0..444348c 100644 --- a/tools/flatten.ts +++ b/tools/flatten.ts @@ -2,7 +2,7 @@ import { sortBy } from 'lodash' import fs from 'fs-extra' -import type { GraphEdge, GraphNode } from '../src/graph/graph' +import type { GraphEdge, GraphNodeRaw } from '../src/graph/graph' import { findExactlyOne } from '../src/graph/utils' main().catch(console.error) @@ -16,7 +16,7 @@ export interface OldNode { export async function main() { const cladesJson = (await fs.readJSON('src/clades.json')) as OldNode - let nodes: GraphNode[] = [] + let nodes: GraphNodeRaw[] = [] const edges: GraphEdge[] = [] flattenCladeTree(cladesJson, nodes, edges) nodes = sortBy(nodes, (node) => node.clade) @@ -27,7 +27,7 @@ export async function main() { } // Convert tree node hierarchy into flat lists of nodes and edges -function flattenCladeTree(node: OldNode, nodes: GraphNode[], edges: GraphEdge[]) { +function flattenCladeTree(node: OldNode, nodes: GraphNodeRaw[], edges: GraphEdge[]) { const { clade, lineages, who, version, otherNames } = splitName(node.name) const id = node.name @@ -40,8 +40,6 @@ function flattenCladeTree(node: OldNode, nodes: GraphNode[], edges: GraphEdge[]) who, version, otherNames, - x: 0, - y: 0, }) const children = node.children ?? [] @@ -128,7 +126,7 @@ const GREEK_LETTERS = new Set([ const WHO_EXCEPTIONS = new Set(['EU1']) -function verifyGraph(nodes: GraphNode[], edges: GraphEdge[]) { +function verifyGraph(nodes: GraphNodeRaw[], edges: GraphEdge[]) { edges.forEach((edge) => { if (edge.target === edge.source) { throw new Error(`Graph is invalid: invalid edge: the target node '${edge.target}' is the same as source node`) From 8e49c997bb17bedf5c053f58e237d4eb8ea7b421 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Tue, 29 Nov 2022 02:37:52 +0100 Subject: [PATCH 13/14] refactor: lint --- src/components/NextstrainCladeTreeSvg.tsx | 7 +++---- src/graph/graph.ts | 3 +-- tools/flatten.ts | 2 +- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/src/components/NextstrainCladeTreeSvg.tsx b/src/components/NextstrainCladeTreeSvg.tsx index 0217bd8..a80f53a 100644 --- a/src/components/NextstrainCladeTreeSvg.tsx +++ b/src/components/NextstrainCladeTreeSvg.tsx @@ -1,5 +1,5 @@ import React, { forwardRef, useMemo } from 'react' -import { calculateGraphLayout, GraphEdge, GraphNode } from 'src/graph/graph' +import { calculateGraphLayout, GraphEdge, GraphNodeRaw } from 'src/graph/graph' import styled from 'styled-components' import { Edge } from 'src/components/Edge' @@ -14,7 +14,7 @@ const Svg = styled.svg` ` export interface CladesJson { - nodes: GraphNode[] + nodes: GraphNodeRaw[] edges: GraphEdge[] } @@ -32,8 +32,7 @@ export const NextstrainCladeTreeSvg = forwardRef ) const edgeComponents = graph.edges.map((edge) => ) diff --git a/src/graph/graph.ts b/src/graph/graph.ts index 7a4e4d1..04c49f2 100644 --- a/src/graph/graph.ts +++ b/src/graph/graph.ts @@ -1,5 +1,4 @@ -import { max, min, cloneDeep, sumBy, meanBy, last, first, minBy } from 'lodash' -import { horizontalSeparationBetweenNodes, nodeRadius } from '../components/constants' +import { max, min, cloneDeep, sumBy, meanBy } from 'lodash' export interface GraphRaw { nodes: GraphNodeRaw[] diff --git a/tools/flatten.ts b/tools/flatten.ts index 444348c..3f1ec10 100644 --- a/tools/flatten.ts +++ b/tools/flatten.ts @@ -81,7 +81,7 @@ function splitName(name: string) { return { clade, lineages, who, version, otherNames } throw new Error( - `Unable to make sense of the name '${name}': details string does not follow any known format: '${details}'`, + `Unable to make sense of the name '${name}': details string does not follow any known format: '${details ?? ''}'`, ) } From ae4961d558a461d72dc4c24ae0b882c7332f1011 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Tue, 29 Nov 2022 10:32:36 +0100 Subject: [PATCH 14/14] feat: draw rectangular branches --- src/components/Edge.tsx | 45 ++++++++++++++++++++++++++++++------ src/components/Node.tsx | 6 ++--- src/components/constants.tsx | 2 +- src/graph/graph.ts | 13 ++++++----- 4 files changed, 49 insertions(+), 17 deletions(-) diff --git a/src/components/Edge.tsx b/src/components/Edge.tsx index b6a08d8..87050ef 100644 --- a/src/components/Edge.tsx +++ b/src/components/Edge.tsx @@ -1,22 +1,53 @@ import React, { useMemo } from 'react' +import styled from 'styled-components' import { getNodesForEdge, Graph, GraphEdge } from '../graph/graph' import { nodeRadius } from './constants' +const PathT = styled.path` + fill: none; + stroke-width: 2px; + stroke: #555555; + pointer-events: auto; + cursor: pointer; +` + +const PathS = styled.path` + fill: none; + stroke-width: 2px; + stroke: #555555; + pointer-events: auto; + cursor: pointer; + stroke-linecap: round; +` + +export interface Point { + x: number + y: number +} + export interface EdgeProps { edge: GraphEdge graph: Graph } export function Edge({ edge, graph }: EdgeProps) { - const { x1, x2, y1, y2 } = useMemo(() => { + const pathComponents = useMemo(() => { const { source, target } = getNodesForEdge(graph, edge) - const y1 = source.y + nodeRadius / 2 - const y2 = target.y + nodeRadius / 2 - const x1 = source.x + nodeRadius / 2 - const x2 = target.x + nodeRadius / 2 - return { x1, x2, y1, y2 } + + const vertical = ( + + ) + + const horizontal = ( + + ) + + return [vertical, horizontal] }, [edge, graph]) - return + return {pathComponents} } diff --git a/src/components/Node.tsx b/src/components/Node.tsx index 934f92a..f3c1eca 100644 --- a/src/components/Node.tsx +++ b/src/components/Node.tsx @@ -12,10 +12,10 @@ export function Node({ node, graph }: CladeTreeNodeProps): ReactElement { const { id, clade, lineages, who, version, otherNames, x, y, color } = node return ( - + { - node.y = node.layout.meanRank * 40 - node.x = node.layout.meanDepth * 100 + node.x = node.layout.meanDepth * horizontalSeparationBetweenNodes + nodeRadius + node.y = node.layout.meanRank * verticalSeparationBetweenNodes + nodeRadius if (!isLeaf) { - node.layout.yTBarStart = node.layout.minRank - node.layout.xTBarStart = node.layout.meanDepth - node.layout.yTBarEnd = node.layout.maxRank - node.layout.xTBarEnd = node.layout.meanDepth + node.layout.xTBarStart = node.layout.meanDepth * horizontalSeparationBetweenNodes + nodeRadius + node.layout.yTBarStart = node.layout.minRank * verticalSeparationBetweenNodes + nodeRadius + node.layout.xTBarEnd = node.layout.meanDepth * horizontalSeparationBetweenNodes + nodeRadius + node.layout.yTBarEnd = node.layout.maxRank * verticalSeparationBetweenNodes + nodeRadius } })