From 2481333b00d786a3629decf7164fb318a1080d58 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Thu, 17 Nov 2022 20:20:25 +0100 Subject: [PATCH 001/154] changed pocket visuals --- .../viewer/components/draggable-dialog.tsx | 2 -- frontend/client/viewer/components/pocket.tsx | 20 +++++++++++-------- frontend/tsconfig.json | 3 ++- 3 files changed, 14 insertions(+), 11 deletions(-) diff --git a/frontend/client/viewer/components/draggable-dialog.tsx b/frontend/client/viewer/components/draggable-dialog.tsx index 96c83fb7..377be025 100644 --- a/frontend/client/viewer/components/draggable-dialog.tsx +++ b/frontend/client/viewer/components/draggable-dialog.tsx @@ -8,8 +8,6 @@ import DialogTitle from '@mui/material/DialogTitle'; import Paper, { PaperProps } from '@mui/material/Paper'; import Draggable from 'react-draggable'; import { PocketData } from "../../custom-types"; -import { MdOutlineInfo } from 'react-icons/md'; -import { IconContext } from "react-icons"; import PocketDetails from "./pocket-details"; function PaperComponent(props: PaperProps) { diff --git a/frontend/client/viewer/components/pocket.tsx b/frontend/client/viewer/components/pocket.tsx index 72284164..07419cd2 100644 --- a/frontend/client/viewer/components/pocket.tsx +++ b/frontend/client/viewer/components/pocket.tsx @@ -3,11 +3,6 @@ import { PocketData } from "../../custom-types"; import DraggableDialog from './draggable-dialog' import PocketDetails from "./pocket-details"; -import { AiOutlineEye } from 'react-icons/ai'; -import { IconContext } from "react-icons"; -import { FiCrosshair, FiArrowDownCircle, FiArrowUpCircle } from 'react-icons/fi'; -import { RiCloseFill, RiCheckFill } from 'react-icons/ri'; - import "bootstrap-icons/font/bootstrap-icons.css"; export default class Pocket extends React.Component @@ -101,9 +96,18 @@ export default class Pocket extends React.Component this.setState({ "pocketTextColor": this.computePocketTextColor() }); } + calculatePocketColorWithAlpha(alpha: number, bgColor: string) { + const color = (bgColor.charAt(0) === '#') ? bgColor.substring(1, 7) : bgColor; + const r = parseInt(color.substring(0, 2), 16); // hexToR + const g = parseInt(color.substring(2, 4), 16); // hexToG + const b = parseInt(color.substring(4, 6), 16); // hexToB + return `rgba(${r},${g},${b},${alpha})`; + } + render() { const pocket = this.props.pocket; - let pocketColor = "#" + this.props.pocket.color; + let pocketColor = this.calculatePocketColorWithAlpha(0.5, this.props.pocket.color!); + if (pocket.isVisible === undefined) { //for pockets that load for the first time pocket.isVisible = true; } @@ -127,9 +131,9 @@ export default class Pocket extends React.Component style={{"color": this.state.pocketTextColor}} > {this.state.visible ? - + : - + } diff --git a/frontend/tsconfig.json b/frontend/tsconfig.json index c944b9fe..02fd1cc5 100644 --- a/frontend/tsconfig.json +++ b/frontend/tsconfig.json @@ -15,7 +15,8 @@ "noEmit": false, // Do not emit output (meaning do not compile code, only perform type checking) "sourceMap": false, // Generate corresponding .map file "declaration": false, // Generate corresponding .d.ts file - "jsx": "react" + "jsx": "react", + "types": [] }, "exclude": [ "node_modules" From 1756b5493dca92ca7898e66f7f1cca5a02d84857 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Thu, 17 Nov 2022 22:10:03 +0100 Subject: [PATCH 002/154] changed alpha, aligned the buttons --- frontend/client/viewer/application.css | 2 +- frontend/client/viewer/components/pocket.tsx | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/frontend/client/viewer/application.css b/frontend/client/viewer/application.css index c7fb1280..1ab7b7d8 100644 --- a/frontend/client/viewer/application.css +++ b/frontend/client/viewer/application.css @@ -77,7 +77,7 @@ /* Bootstrap updates to make the view more compact. */ .card .card-header { - padding: 0.2rem 1rem 0 1rem; + padding: 0.2rem 0.5rem 0 0.5rem; } .card .card-body { diff --git a/frontend/client/viewer/components/pocket.tsx b/frontend/client/viewer/components/pocket.tsx index 07419cd2..1b524228 100644 --- a/frontend/client/viewer/components/pocket.tsx +++ b/frontend/client/viewer/components/pocket.tsx @@ -106,7 +106,7 @@ export default class Pocket extends React.Component render() { const pocket = this.props.pocket; - let pocketColor = this.calculatePocketColorWithAlpha(0.5, this.props.pocket.color!); + let pocketColor = this.calculatePocketColorWithAlpha(0.75, this.props.pocket.color!); if (pocket.isVisible === undefined) { //for pockets that load for the first time pocket.isVisible = true; @@ -119,10 +119,10 @@ export default class Pocket extends React.Component
-
+

Pocket {pocket.rank}

-
+
From 74ffceea09bc11fb2f704f4187ac698f4f450814 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 7 Jan 2023 13:19:02 +0100 Subject: [PATCH 004/154] Added an options for pocket visualisation. --- frontend/client/custom-types.ts | 9 +-- frontend/client/viewer/application.tsx | 2 +- .../client/viewer/components/tools-box.tsx | 8 ++- frontend/client/viewer/data-loader.ts | 7 ++- frontend/client/viewer/molstar-visualise.ts | 62 +++++++++++++++++-- 5 files changed, 72 insertions(+), 16 deletions(-) diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index a186e3b0..756be461 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -115,8 +115,10 @@ export enum PolymerViewType { } export enum PocketsViewType { - Atoms = 0, - Surface = 1 + Ball_Stick_Atoms_Color = 0, + Ball_Stick_Residues_Color = 1, + Surface_Atoms_Color = 2, + Surface_Residues_Color = 3 } export enum PolymerColorType { @@ -134,8 +136,7 @@ export interface PocketRepresentation { pocketId: string; type: PocketsViewType; representation: StateObjectSelector; //Mol* representation - coloredPocket: boolean; //there are two types of pocket representations, one for the whole residues and one for the atoms - //true represents the atoms, false the whole residues + coloredPocket: boolean; //for efficiency when overpainting } /** diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 8adf78d2..7f8bff5b 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -44,7 +44,7 @@ export async function renderProteinView(predictionInfo: PredictionInfo) { const container = (window.innerWidth >= 768) ? document.getElementById('pocket-list-aside') : document.getElementById('pocket-list-aside-mobile'); const root = createRoot(container!); root.render(); + pocketsView={PocketsViewType.Surface_Atoms_Color} polymerView={PolymerViewType.Gaussian_Surface} polymerColor={PolymerColorType.Clean}/>); } export class Application extends React.Component diff --git a/frontend/client/viewer/components/tools-box.tsx b/frontend/client/viewer/components/tools-box.tsx index d4da1379..bdb34e37 100644 --- a/frontend/client/viewer/components/tools-box.tsx +++ b/frontend/client/viewer/components/tools-box.tsx @@ -128,7 +128,7 @@ class ControlBoxContent extends React.Component<{
); } diff --git a/frontend/package-lock.json b/frontend/package-lock.json index 038f8416..692fad34 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -9,9 +9,10 @@ "dependencies": { "@babel/preset-env": "^7.18.6", "@babel/preset-react": "^7.18.6", - "@emotion/react": "^11.9.3", - "@emotion/styled": "^11.9.3", - "@mui/material": "^5.8.7", + "@emotion/react": "^11.10.5", + "@emotion/styled": "^11.10.5", + "@mui/lab": "^5.0.0-alpha.114", + "@mui/material": "^5.11.3", "@rcsb/rcsb-saguaro": "^2.1.2", "autoprefixer": "^10.4.7", "babel-loader": "^8.2.5", @@ -1611,11 +1612,11 @@ } }, "node_modules/@babel/runtime": { - "version": "7.18.6", - "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.18.6.tgz", - "integrity": "sha512-t9wi7/AW6XtKahAe20Yw0/mMljKq0B1r2fPdvaAdV/KPDZewFXdaaa6K7lxmZBZ8FBNpCiAT6iHPmd6QO9bKfQ==", + "version": "7.20.7", + "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.20.7.tgz", + "integrity": "sha512-UF0tvkUtxwAgZ5W/KrkHf0Rn0fdnLDU9ScxBrEVNUprE/MzirjK4MJUX1/BVDv00Sv8cljtukVK1aky++X1SjQ==", "dependencies": { - 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"@emotion/react": "^11.9.3", - "@emotion/styled": "^11.9.3", - "@mui/material": "^5.8.7", + "@emotion/react": "^11.10.5", + "@emotion/styled": "^11.10.5", + "@mui/lab": "^5.0.0-alpha.114", + "@mui/material": "^5.11.3", "@rcsb/rcsb-saguaro": "^2.1.2", "autoprefixer": "^10.4.7", "babel-loader": "^8.2.5", From 63ebf2ea8e37782432e701a08dc77fb3636019f2 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 7 Jan 2023 16:14:30 +0100 Subject: [PATCH 006/154] updated packages --- frontend/client/viewer/application.tsx | 7 +- frontend/package-lock.json | 9513 +++++++++++------------- frontend/package.json | 71 +- 3 files changed, 4392 insertions(+), 5199 deletions(-) diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 7f8bff5b..32dd18c5 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -150,12 +150,11 @@ export class Application extends React.Component e.trackId === "pocketsTrack"); + const track = this.state.pluginRcsb.getBoardData().find(e => e.trackId === "pocketsTrack"); if(track) { - track.trackData.filter((e : RcsbFvTrackDataElementInterface) => e.provenanceName === `pocket${index+1}`).forEach((foundPocket : RcsbFvTrackDataElementInterface) => (foundPocket.color = newColor)); + track.trackData!.filter((e : RcsbFvTrackDataElementInterface) => e.provenanceName === `pocket${index+1}`).forEach((foundPocket : RcsbFvTrackDataElementInterface) => (foundPocket.color = newColor)); const newData = track.trackData; - this.state.pluginRcsb.updateTrackData("pocketsTrack", newData); + this.state.pluginRcsb.updateTrackData("pocketsTrack", newData!); } //then resolve Mol* diff --git a/frontend/package-lock.json b/frontend/package-lock.json index 692fad34..80c02ae9 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -7,61 +7,74 @@ "name": "prankweb-frontend", "license": "MIT", "dependencies": { - "@babel/preset-env": "^7.18.6", + "@babel/preset-env": "^7.20.2", "@babel/preset-react": "^7.18.6", "@emotion/react": "^11.10.5", "@emotion/styled": "^11.10.5", "@mui/lab": "^5.0.0-alpha.114", "@mui/material": "^5.11.3", - "@rcsb/rcsb-saguaro": "^2.1.2", - "autoprefixer": "^10.4.7", - "babel-loader": "^8.2.5", - "bootstrap": "^5.1.3", - "bootstrap-icons": "^1.9.1", + "@rcsb/rcsb-saguaro": "^2.5.5", + "autoprefixer": "^10.4.13", + "babel-loader": "^9.1.2", + "bootstrap": "^5.2.3", + "bootstrap-icons": "^1.10.3", "clean-webpack-plugin": "^4.0.0", "copy-webpack-plugin": "^11.0.0", - "core-js": "^3.23.3", + "core-js": "^3.27.1", "cross-env": "^7.0.3", - "css-loader": "^6.7.1", + "css-loader": "^6.7.3", "express-http-proxy": "^1.6.3", "handlebars": "^4.7.7", - "handlebars-loader": "^1.7.2", - "html-loader": "^3.1.2", + "handlebars-loader": "^1.7.3", + "html-loader": "^4.2.0", "html-webpack-plugin": "^5.5.0", - "mini-css-extract-plugin": "^2.6.1", - "molstar": "^3.10.2", - "postcss-loader": "^7.0.0", + "mini-css-extract-plugin": "^2.7.2", + "molstar": "^3.28.0", + "postcss-loader": "^7.0.2", "react": "^18.2.0", "react-dom": "^18.2.0", "react-draggable": "^4.4.5", - "react-icons": "^4.4.0", - "sass": "^1.53.0", - "sass-loader": "^13.0.2", + "react-icons": "^4.7.1", + "sass": "^1.57.1", + "sass-loader": "^13.2.0", "style-loader": "^3.3.1", - "ts-loader": "^9.3.1", - "typescript": "^4.7.4", - "underscore-template-loader": "^1.1.0", - "webpack": "^5.73.0", - "webpack-cli": "^4.10.0", + "ts-loader": "^9.4.2", + "typescript": "^4.9.4", + "underscore-template-loader": "^1.2.0", + "webpack": "^5.75.0", + "webpack-cli": "^5.0.1", "webpack-merge": "^5.8.0", "webpackbar": "^5.0.2", - "winston": "^3.8.1", - "yaml": "^2.1.1" + "winston": "^3.8.2", + "yaml": "^2.2.1" }, "devDependencies": { - "@types/react": "^18.0.14", - "@types/react-dom": "^18.0.6", - "babel-eslint": "^10.1.0", - "babel-jest": "^28.1.2", - "eslint": "^8.18.0", - "eslint-loader": "^3.0.3", - "eslint-plugin-jest": "^26.5.3", - "eslint-plugin-react": "^7.30.1", + "@babel/core": "^7.20.12", + "@babel/eslint-parser": "^7.19.1", + "@types/react": "^18.0.26", + "@types/react-dom": "^18.0.10", + "babel-jest": "^29.3.1", + "eslint": "^8.31.0", + "eslint-plugin-jest": "^27.2.1", + "eslint-plugin-react": "^7.31.11", + "eslint-webpack-plugin": "^3.2.0", "exports-loader": "^4.0.0", - 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"@babel/preset-env": "^7.18.6", + "@babel/preset-env": "^7.20.2", "@babel/preset-react": "^7.18.6", "@emotion/react": "^11.10.5", "@emotion/styled": "^11.10.5", "@mui/lab": "^5.0.0-alpha.114", "@mui/material": "^5.11.3", - "@rcsb/rcsb-saguaro": "^2.1.2", - "autoprefixer": "^10.4.7", - "babel-loader": "^8.2.5", - "bootstrap": "^5.1.3", - "bootstrap-icons": "^1.9.1", + "@rcsb/rcsb-saguaro": "^2.5.5", + "autoprefixer": "^10.4.13", + "babel-loader": "^9.1.2", + "bootstrap": "^5.2.3", + "bootstrap-icons": "^1.10.3", "clean-webpack-plugin": "^4.0.0", "copy-webpack-plugin": "^11.0.0", - "core-js": "^3.23.3", + "core-js": "^3.27.1", "cross-env": "^7.0.3", - "css-loader": "^6.7.1", + "css-loader": "^6.7.3", "express-http-proxy": "^1.6.3", "handlebars": "^4.7.7", - "handlebars-loader": "^1.7.2", - "html-loader": "^3.1.2", + "handlebars-loader": "^1.7.3", + "html-loader": "^4.2.0", "html-webpack-plugin": "^5.5.0", - "mini-css-extract-plugin": "^2.6.1", - "molstar": "^3.10.2", - "postcss-loader": "^7.0.0", + "mini-css-extract-plugin": "^2.7.2", + "molstar": "^3.28.0", + "postcss-loader": "^7.0.2", "react": "^18.2.0", "react-dom": "^18.2.0", "react-draggable": "^4.4.5", - "react-icons": "^4.4.0", - "sass": "^1.53.0", - "sass-loader": "^13.0.2", + "react-icons": "^4.7.1", + "sass": "^1.57.1", + "sass-loader": "^13.2.0", "style-loader": "^3.3.1", - "ts-loader": "^9.3.1", - "typescript": "^4.7.4", - "underscore-template-loader": "^1.1.0", - "webpack": "^5.73.0", - "webpack-cli": "^4.10.0", + "ts-loader": "^9.4.2", + "typescript": "^4.9.4", + "underscore-template-loader": "^1.2.0", + "webpack": "^5.75.0", + "webpack-cli": "^5.0.1", "webpack-merge": "^5.8.0", "webpackbar": "^5.0.2", - "winston": "^3.8.1", - "yaml": "^2.1.1" + "winston": "^3.8.2", + "yaml": "^2.2.1" }, "devDependencies": { - "@types/react": "^18.0.14", - "@types/react-dom": "^18.0.6", - "babel-eslint": "^10.1.0", - "babel-jest": "^28.1.2", - "eslint": "^8.18.0", - "eslint-loader": "^3.0.3", - "eslint-plugin-jest": "^26.5.3", - "eslint-plugin-react": "^7.30.1", + "@babel/core": "^7.20.12", + "@babel/eslint-parser": "^7.19.1", + "@types/react": "^18.0.26", + "@types/react-dom": "^18.0.10", + "babel-jest": "^29.3.1", + "eslint": "^8.31.0", + "eslint-plugin-jest": "^27.2.1", + "eslint-plugin-react": "^7.31.11", + "eslint-webpack-plugin": "^3.2.0", "exports-loader": "^4.0.0", - "express": "^4.18.1", - "imports-loader": "^4.0.0", - "webpack-dev-middleware": "^5.3.3", - "webpack-hot-middleware": "^2.25.1" + "express": "^4.18.2", + "imports-loader": "^4.0.1", + "webpack-dev-middleware": "^6.0.1", + "webpack-hot-middleware": "^2.25.3" } } From 204e5e77d6d0bed8bf736732fb51cfb5aab98887 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 7 Jan 2023 16:24:00 +0100 Subject: [PATCH 007/154] custom scrollbars --- frontend/client/viewer/application.css | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/frontend/client/viewer/application.css b/frontend/client/viewer/application.css index 1ab7b7d8..1877f999 100644 --- a/frontend/client/viewer/application.css +++ b/frontend/client/viewer/application.css @@ -24,6 +24,24 @@ height: calc(30vh - 68px); } +#application-rcsb::-webkit-scrollbar { + height: 5px; /* horizontal scrollbar */ + width: 5px; /* vertical scrollbar */ +} + +#application-rcsb::-webkit-scrollbar-track { + background: #f1f1f1; +} + +#application-rcsb::-webkit-scrollbar-thumb { + background: #888; + border-radius: 10px; +} + +#application-rcsb::-webkit-scrollbar-thumb:hover { + background: #555; +} + #pocket-list-aside { height: 100%; } From b2fbf32ad68b1704747e68960330bcc5ffb7b06e Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 7 Jan 2023 16:50:51 +0100 Subject: [PATCH 008/154] first sample click --- .../viewer/components/pocket-client-task.tsx | 24 +++++++++++++++---- 1 file changed, 19 insertions(+), 5 deletions(-) diff --git a/frontend/client/viewer/components/pocket-client-task.tsx b/frontend/client/viewer/components/pocket-client-task.tsx index a9f914c1..a92bd507 100644 --- a/frontend/client/viewer/components/pocket-client-task.tsx +++ b/frontend/client/viewer/components/pocket-client-task.tsx @@ -6,17 +6,30 @@ export default class PocketClientTask extends React.Component title: string, inDialog: boolean // not needed now. but in other cases the implementation could be potentially different. }, { + computed: boolean, loading: boolean }> { constructor(props: any) { super(props); this.handleClick = this.handleClick.bind(this); - this.state = {loading: false}; + this.sampleClick = this.sampleClick.bind(this); + this.state = {loading: false, computed: false}; } - handleClick() { - this.state.loading ? this.setState({loading: false}) : this.setState({loading: true}); + async sampleClick() { + await new Promise(resolve => setTimeout(resolve, 3000)); + + this.setState({loading: false, computed: true}); + } + + async handleClick() { + //this.state.loading ? this.setState({loading: false}) : this.setState({loading: true}); + if(this.state.computed) { + return; + } + this.setState({loading: true}); + await this.sampleClick(); } render() { @@ -27,10 +40,11 @@ export default class PocketClientTask extends React.Component size="small" onClick={this.handleClick} loading={this.state.loading} - variant="outlined" + variant="contained" style={{float: "right", marginLeft: "1rem"}} > - Fetch data + {!this.state.computed && "Fetch data"} + {this.state.computed && "Computed"}
); From abd4ec793bc0fc8801e0fa996038ce4270a66506 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 7 Jan 2023 17:35:51 +0100 Subject: [PATCH 009/154] added example task --- frontend/client/custom-types.ts | 6 ++- frontend/client/viewer/client-example-task.ts | 12 ++++++ .../viewer/components/pocket-client-task.tsx | 41 ++++++++++++------- 3 files changed, 43 insertions(+), 16 deletions(-) create mode 100644 frontend/client/viewer/client-example-task.ts diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index 756be461..62ca4b42 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -204,4 +204,8 @@ export const DefaultPocketColors = [ "009E73", "0072B2", "DA74AD" -]; \ No newline at end of file +]; + +export interface SampleJSONData { + value: number; +} \ No newline at end of file diff --git a/frontend/client/viewer/client-example-task.ts b/frontend/client/viewer/client-example-task.ts new file mode 100644 index 00000000..9442eb02 --- /dev/null +++ b/frontend/client/viewer/client-example-task.ts @@ -0,0 +1,12 @@ +import { SampleJSONData } from "../custom-types"; + +let computed = false; + +export async function sendRandomJSONData() : Promise { + const data = { "value": 420 }; + if (computed) return data; + + computed = true; + await new Promise(resolve => setTimeout(resolve, 2000)); + return data; +} \ No newline at end of file diff --git a/frontend/client/viewer/components/pocket-client-task.tsx b/frontend/client/viewer/components/pocket-client-task.tsx index a92bd507..7e1d4739 100644 --- a/frontend/client/viewer/components/pocket-client-task.tsx +++ b/frontend/client/viewer/components/pocket-client-task.tsx @@ -1,11 +1,14 @@ import React from "react"; import { LoadingButton } from '@mui/lab'; +import { sendRandomJSONData } from '../client-example-task'; +import { SampleJSONData } from '../../custom-types'; export default class PocketClientTask extends React.Component <{ title: string, inDialog: boolean // not needed now. but in other cases the implementation could be potentially different. }, { + data: SampleJSONData | undefined, //this may be changed to any type (the best way is to define some interface) computed: boolean, loading: boolean }> { @@ -14,13 +17,13 @@ export default class PocketClientTask extends React.Component super(props); this.handleClick = this.handleClick.bind(this); this.sampleClick = this.sampleClick.bind(this); - this.state = {loading: false, computed: false}; + this.state = {loading: false, computed: false, data: undefined}; } async sampleClick() { - await new Promise(resolve => setTimeout(resolve, 3000)); + const json : SampleJSONData = await sendRandomJSONData(); - this.setState({loading: false, computed: true}); + this.setState({loading: false, computed: true, data: json}); } async handleClick() { @@ -35,18 +38,26 @@ export default class PocketClientTask extends React.Component render() { return (
- {this.props.title}: - - {!this.state.computed && "Fetch data"} - {this.state.computed && "Computed"} - + {this.props.title}: + { + !this.state.computed && + + {!this.state.computed && "Fetch data"} + {this.state.computed && "Computed"} + + } + { + this.state.computed && + {this.state.data!.value} + // here the data should be properly formatted and again, we may change this to a new component + }
); } -} \ No newline at end of file +} From a127f7ec4bdfa52c22f582298c51fb7ede154162 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 7 Jan 2023 18:35:18 +0100 Subject: [PATCH 010/154] changed task location --- frontend/client/{viewer => tasks}/client-example-task.ts | 2 +- frontend/client/viewer/components/pocket-client-task.tsx | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename frontend/client/{viewer => tasks}/client-example-task.ts (99%) diff --git a/frontend/client/viewer/client-example-task.ts b/frontend/client/tasks/client-example-task.ts similarity index 99% rename from frontend/client/viewer/client-example-task.ts rename to frontend/client/tasks/client-example-task.ts index 9442eb02..80efc7d9 100644 --- a/frontend/client/viewer/client-example-task.ts +++ b/frontend/client/tasks/client-example-task.ts @@ -9,4 +9,4 @@ export async function sendRandomJSONData() : Promise { computed = true; await new Promise(resolve => setTimeout(resolve, 2000)); return data; -} \ No newline at end of file +} diff --git a/frontend/client/viewer/components/pocket-client-task.tsx b/frontend/client/viewer/components/pocket-client-task.tsx index 7e1d4739..8d98b37f 100644 --- a/frontend/client/viewer/components/pocket-client-task.tsx +++ b/frontend/client/viewer/components/pocket-client-task.tsx @@ -1,6 +1,6 @@ import React from "react"; import { LoadingButton } from '@mui/lab'; -import { sendRandomJSONData } from '../client-example-task'; +import { sendRandomJSONData } from '../../tasks/client-example-task'; import { SampleJSONData } from '../../custom-types'; export default class PocketClientTask extends React.Component From 700a95e90c1eb3465d28fddf4be3f5ee370095c9 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 7 Jan 2023 18:37:49 +0100 Subject: [PATCH 011/154] changed URL params to fetch from info file --- frontend/client/analyze/analyze.ts | 3 +- frontend/client/viewer/viewer.ts | 50 ++++++++++-------------------- 2 files changed, 18 insertions(+), 35 deletions(-) diff --git a/frontend/client/analyze/analyze.ts b/frontend/client/analyze/analyze.ts index 08969649..e9dc149c 100644 --- a/frontend/client/analyze/analyze.ts +++ b/frontend/client/analyze/analyze.ts @@ -132,8 +132,7 @@ function renderQueued() { function renderTaskFinished(data: PredictionInfo) { //this method redirects to the viewer page with all the needed information - const result = `./viewer?id=${data.id}&database=${data.database}&created=${data.created}&lastChange=${data.lastChange} - &structureName=${data.metadata.structureName}&predictionName=${data.metadata.predictionName}&predictedStructure=${data.metadata.predictedStructure}`; + const result = `./viewer?id=${data.id}&database=${data.database}`; window.location.href = result; } diff --git a/frontend/client/viewer/viewer.ts b/frontend/client/viewer/viewer.ts index cd76425d..bb4c235c 100644 --- a/frontend/client/viewer/viewer.ts +++ b/frontend/client/viewer/viewer.ts @@ -1,50 +1,34 @@ import { renderProteinView } from "./application"; import "../bootstrap.scss"; +import { fetchPrediction } from "../prankweb-api"; -function getPredictionInfoFromUrl() { +function handleError() { + document.getElementById('message')!.style.display = 'block'; + document.getElementById('message-text')!.innerHTML = "
Incomplete or incorrect task specification.
Please go back to the home page."; + document.getElementById('analyze')!.style.display = 'none'; +} + +async function initialize() { const params = new URLSearchParams(window.location.search); let id = params.get("id"); let database = params.get("database"); - let created = params.get("created"); - let lastChange = params.get("lastChange"); - let structureName = params.get("structureName"); - let predictionName = params.get("predictionName"); - - if (id === null || database === null || created === null || lastChange === null || structureName === null || predictionName === null) { - return null; - } - let predictedStructure = params.get("predictedStructure"); - if (predictedStructure && predictedStructure === "undefined") { - predictedStructure = "false"; + if(id === null || database === null) { + handleError(); + return; } - return { - "id": id, - "database": database, - "created": created, - "lastChange": lastChange, - "status": "successful", //because we got here we know the task is finished - "metadata": { - "structureName": structureName, - "predictionName": predictionName, - "predictedStructure": (predictedStructure === 'true'), - } - } -} + let predictionInfo = await fetchPrediction(database, id); -function initialize() { - const data = getPredictionInfoFromUrl(); - if(data === null) { - document.getElementById('message')!.style.display = 'block'; - document.getElementById('message-text')!.innerHTML = "
Incomplete or incorrect task specification.
Please go back to the home page."; - document.getElementById('analyze')!.style.display = 'none'; + if(predictionInfo.content === null) { + handleError(); return; } + document.getElementById('footer')!.style.display = 'none'; - renderProteinView(data!); //we have already checked that data is not null + renderProteinView(predictionInfo.content); }; -initialize(); +initialize(); \ No newline at end of file From b003bb7d45955723ee532cd459d485f39969c0a7 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 7 Jan 2023 22:09:36 +0100 Subject: [PATCH 012/154] first attempt with debouncing --- frontend/client/viewer/rcsb-visualise.ts | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/frontend/client/viewer/rcsb-visualise.ts b/frontend/client/viewer/rcsb-visualise.ts index 599027d9..23e785cb 100644 --- a/frontend/client/viewer/rcsb-visualise.ts +++ b/frontend/client/viewer/rcsb-visualise.ts @@ -3,6 +3,8 @@ import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionData, AlphaFoldColorsRcsb, AlphaFoldThresholdsRcsb, DefaultPocketColors } from '../custom-types'; import { highlightInViewerLabelIdWithoutFocus, highlightInViewerAuthId } from "./molstar-visualise"; +let lastElement: number = -1; + /** * Method which initializes the Rcsb viewer and adds the tracks to it. * @param data Prediction data @@ -82,15 +84,21 @@ function elementClicked(predictionData: PredictionData, molstarPlugin: PluginUIC * @param trackData Data of the clicked track */ function onHighlight(data: PredictionData, molstarPlugin: PluginUIContext, trackData: Array) { - if(trackData && trackData.length > 0) { - if(data) { - let element = data.structure.indices[trackData[0].begin - 1]; - if(element) { - let id = Number(element.substring(element.indexOf('_') + 1)); - highlightInViewerLabelIdWithoutFocus(molstarPlugin, element[0], [id]); + if(trackData.length === 0) return; + lastElement = trackData[0].begin; + + //first attempt to debounce the function + setTimeout(() => { + if(trackData && trackData.length > 0 && lastElement === trackData[0].begin) { + if(data) { + let element = data.structure.indices[trackData[0].begin - 1]; + if(element) { + let id = Number(element.substring(element.indexOf('_') + 1)); + highlightInViewerLabelIdWithoutFocus(molstarPlugin, element[0], [id]); + } } } - } + }, 100); } /** From 02e599d17b263cf624f4e4380c7a5b80a0eb5018 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sun, 15 Jan 2023 21:11:17 +0100 Subject: [PATCH 013/154] Added a method returning surface atoms coords. --- frontend/client/viewer/molstar-visualise.ts | 26 ++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/frontend/client/viewer/molstar-visualise.ts b/frontend/client/viewer/molstar-visualise.ts index 897ebbaa..dc81ed4f 100644 --- a/frontend/client/viewer/molstar-visualise.ts +++ b/frontend/client/viewer/molstar-visualise.ts @@ -1,7 +1,7 @@ import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context'; import { Color } from "molstar/lib/mol-util/color"; import { Asset } from "molstar/lib/mol-util/assets"; -import { AlphaFoldColorsMolStar, AlphaFoldThresholdsMolStar, PredictionData, PocketData, MolstarResidue, ChainData, PolymerRepresentation, PolymerColorType, PolymerViewType, PocketRepresentation, PocketsViewType } from '../custom-types'; +import { AlphaFoldColorsMolStar, AlphaFoldThresholdsMolStar, PredictionData, PocketData, MolstarResidue, ChainData, PolymerRepresentation, PolymerColorType, PolymerViewType, PocketRepresentation, PocketsViewType, Point3D } from '../custom-types'; import { StateTransforms } from "molstar/lib/mol-plugin-state/transforms"; import { MolScriptBuilder as MS } from "molstar/lib/mol-script/language/builder"; import { createStructureRepresentationParams } from "molstar/lib/mol-plugin-state/helpers/structure-representation-params"; @@ -886,6 +886,30 @@ export function highlightInViewerAuthId(plugin: PluginUIContext, chain: string, plugin.managers.camera.focusLoci(loci); } +/** + * Method which returns coordinates of the surface atoms + * @param plugin Mol* plugin + * @param ids Surface atom ids + * @returns An array of coordinates + */ +export function getPocketAtomCoordinates(plugin: PluginUIContext, ids: string[]) { + const coordinates: Point3D[] = []; + + //could this be potentially improved? not sure whether we can do it just with one selection + for(let i of ids) { + const sel = getSurfaceAtomSelection(plugin, [i]); + const loci = getStructureElementLoci(StructureSelection.toLociWithSourceUnits(sel)); + + if(loci) { + const structureElement = StructureElement.Stats.ofLoci(loci); + const location = structureElement.firstElementLoc; + coordinates.push({x: StructureProperties.atom.x(location), y: StructureProperties.atom.y(location), z: StructureProperties.atom.z(location)}); + } + } + + return coordinates; +} + //cc: https://github.com/scheuerv/molart/ function getStructureElementLoci(loci: Loci): StructureElement.Loci | undefined { if (loci.kind == "bond-loci") { From 59a79f6c4f69beca53b819c5ea79ce28ed667228 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sun, 15 Jan 2023 21:12:18 +0100 Subject: [PATCH 014/154] Added a new type for points in 3D space. --- frontend/client/custom-types.ts | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index 62ca4b42..4f924ec9 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -206,6 +206,12 @@ export const DefaultPocketColors = [ "DA74AD" ]; -export interface SampleJSONData { - value: number; +export interface ClientTaskData { + numericValue?: number; +} + +export interface Point3D { + x: number; + y: number; + z: number; } \ No newline at end of file From c19a49003f6fe2723bf2e4f4494d4a241e8a7b55 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sun, 15 Jan 2023 21:12:45 +0100 Subject: [PATCH 015/154] Preparations for the client volume calculation. --- frontend/client/tasks/client-atoms-volume.ts | 25 +++++++++++++++++++ frontend/client/tasks/client-example-task.ts | 12 --------- frontend/client/viewer/application.tsx | 1 + .../viewer/components/draggable-dialog.tsx | 8 +++--- .../viewer/components/pocket-client-task.tsx | 25 +++++++++++-------- .../viewer/components/pocket-details.tsx | 4 ++- .../client/viewer/components/pocket-list.tsx | 5 +++- frontend/client/viewer/components/pocket.tsx | 8 +++--- 8 files changed, 57 insertions(+), 31 deletions(-) create mode 100644 frontend/client/tasks/client-atoms-volume.ts delete mode 100644 frontend/client/tasks/client-example-task.ts diff --git a/frontend/client/tasks/client-atoms-volume.ts b/frontend/client/tasks/client-atoms-volume.ts new file mode 100644 index 00000000..d55a19d4 --- /dev/null +++ b/frontend/client/tasks/client-atoms-volume.ts @@ -0,0 +1,25 @@ +import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; +import { PocketData, ClientTaskData } from "../custom-types"; +import { getPocketAtomCoordinates } from "../viewer/molstar-visualise"; + +//const pocketVolumes = new Map>(); + +export async function computePocketVolume(plugin: PluginUIContext, pocket: PocketData) { + + /*if(pocketVolumes.has(pocket.name)) { + return pocketVolumes.get(pocket.name)!; + }*/ + + const coords = getPocketAtomCoordinates(plugin, pocket.surface); + + for(const coord of coords) { + console.log(`${coord.x} ${coord.y} ${coord.z}`); + } + + const data = { "numericValue": 420 }; + + //pocketVolumes.set(pocket.name, Promise.resolve(data)); + + await new Promise(resolve => setTimeout(resolve, 2000)); + return data; +} diff --git a/frontend/client/tasks/client-example-task.ts b/frontend/client/tasks/client-example-task.ts deleted file mode 100644 index 80efc7d9..00000000 --- a/frontend/client/tasks/client-example-task.ts +++ /dev/null @@ -1,12 +0,0 @@ -import { SampleJSONData } from "../custom-types"; - -let computed = false; - -export async function sendRandomJSONData() : Promise { - const data = { "value": 420 }; - if (computed) return data; - - computed = true; - await new Promise(resolve => setTimeout(resolve, 2000)); - return data; -} diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 32dd18c5..1e40b3f6 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -227,6 +227,7 @@ export class Application extends React.Component
); diff --git a/frontend/client/viewer/components/draggable-dialog.tsx b/frontend/client/viewer/components/draggable-dialog.tsx index 377be025..288d8ac9 100644 --- a/frontend/client/viewer/components/draggable-dialog.tsx +++ b/frontend/client/viewer/components/draggable-dialog.tsx @@ -9,6 +9,7 @@ import Paper, { PaperProps } from '@mui/material/Paper'; import Draggable from 'react-draggable'; import { PocketData } from "../../custom-types"; import PocketDetails from "./pocket-details"; +import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context'; function PaperComponent(props: PaperProps) { return ( @@ -16,7 +17,8 @@ function PaperComponent(props: PaperProps) { } export default class DraggableDialog extends React.Component<{ - pocket: PocketData + pocket: PocketData, + plugin: PluginUIContext }, { visible: boolean }> { @@ -25,7 +27,7 @@ export default class DraggableDialog extends React.Component<{ visible: false, }; - constructor(props: {pocket: PocketData}) { + constructor(props: {pocket: PocketData, plugin: PluginUIContext}) { super(props); this.toggleDetailsVisibility = this.toggleDetailsVisibility.bind(this); } @@ -70,7 +72,7 @@ export default class DraggableDialog extends React.Component<{ - + diff --git a/frontend/client/viewer/components/pocket-client-task.tsx b/frontend/client/viewer/components/pocket-client-task.tsx index 8d98b37f..f67a44ea 100644 --- a/frontend/client/viewer/components/pocket-client-task.tsx +++ b/frontend/client/viewer/components/pocket-client-task.tsx @@ -1,14 +1,17 @@ import React from "react"; import { LoadingButton } from '@mui/lab'; -import { sendRandomJSONData } from '../../tasks/client-example-task'; -import { SampleJSONData } from '../../custom-types'; +import { computePocketVolume } from '../../tasks/client-atoms-volume'; +import { ClientTaskData, PocketData } from '../../custom-types'; +import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; export default class PocketClientTask extends React.Component <{ title: string, - inDialog: boolean // not needed now. but in other cases the implementation could be potentially different. + inDialog: boolean, // not needed now. but in other cases the implementation could be potentially different. + pocket: PocketData, + plugin: PluginUIContext }, { - data: SampleJSONData | undefined, //this may be changed to any type (the best way is to define some interface) + data: ClientTaskData | undefined, //this may be changed to any type (the best way is to define some interface) computed: boolean, loading: boolean }> { @@ -16,23 +19,22 @@ export default class PocketClientTask extends React.Component constructor(props: any) { super(props); this.handleClick = this.handleClick.bind(this); - this.sampleClick = this.sampleClick.bind(this); + this.clickCompute = this.clickCompute.bind(this); this.state = {loading: false, computed: false, data: undefined}; } - async sampleClick() { - const json : SampleJSONData = await sendRandomJSONData(); + async clickCompute() { + const json : ClientTaskData = await computePocketVolume(this.props.plugin, this.props.pocket); this.setState({loading: false, computed: true, data: json}); } async handleClick() { - //this.state.loading ? this.setState({loading: false}) : this.setState({loading: true}); if(this.state.computed) { return; } this.setState({loading: true}); - await this.sampleClick(); + await this.clickCompute(); } render() { @@ -54,8 +56,9 @@ export default class PocketClientTask extends React.Component } { this.state.computed && - {this.state.data!.value} - // here the data should be properly formatted and again, we may change this to a new component + {this.state.data!.numericValue} + // here the data should be properly formatted based on the returned type + // i.e for number arrays we could potentially add a diagram instead of just showing a number }
); diff --git a/frontend/client/viewer/components/pocket-details.tsx b/frontend/client/viewer/components/pocket-details.tsx index e9654981..337286ae 100644 --- a/frontend/client/viewer/components/pocket-details.tsx +++ b/frontend/client/viewer/components/pocket-details.tsx @@ -2,11 +2,13 @@ import React from "react"; import { PocketData } from "../../custom-types"; import PocketProperty from "./pocket-property"; import PocketClientTask from "./pocket-client-task"; +import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; export default class PocketDetails extends React.Component <{ pocket: PocketData, inDialog: boolean, + plugin: PluginUIContext }, {}> { constructor(props: any) { @@ -31,7 +33,7 @@ export default class PocketDetails extends React.Component {this.checkValidValue(pocket.avgConservation) && } {this.checkValidValue(pocket.avgAlphaFold) && } {this.props.inDialog && } - {this.props.inDialog && } + {this.props.inDialog && }
); } diff --git a/frontend/client/viewer/components/pocket-list.tsx b/frontend/client/viewer/components/pocket-list.tsx index 546f8ff1..5268b119 100644 --- a/frontend/client/viewer/components/pocket-list.tsx +++ b/frontend/client/viewer/components/pocket-list.tsx @@ -3,6 +3,7 @@ import { PredictionData } from "../../custom-types"; import Pocket from "./pocket"; import "./pocket-list.css"; +import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; export default class PocketList extends React.Component <{ @@ -11,7 +12,8 @@ export default class PocketList extends React.Component setPocketVisibility: (index: number, isVisible: boolean) => void, showOnlyPocket: (index: number) => void, focusPocket: (index: number) => void, - highlightPocket: (index: number, isHighlighted: boolean) => void + highlightPocket: (index: number, isHighlighted: boolean) => void, + plugin: PluginUIContext }, {}> { render() { @@ -44,6 +46,7 @@ export default class PocketList extends React.Component showOnlyPocket={this.props.showOnlyPocket} focusPocket={this.props.focusPocket} highlightPocket={this.props.highlightPocket} + plugin={this.props.plugin} /> ))}
); diff --git a/frontend/client/viewer/components/pocket.tsx b/frontend/client/viewer/components/pocket.tsx index 1b524228..475251fe 100644 --- a/frontend/client/viewer/components/pocket.tsx +++ b/frontend/client/viewer/components/pocket.tsx @@ -4,6 +4,7 @@ import DraggableDialog from './draggable-dialog' import PocketDetails from "./pocket-details"; import "bootstrap-icons/font/bootstrap-icons.css"; +import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; export default class Pocket extends React.Component <{ @@ -12,7 +13,8 @@ export default class Pocket extends React.Component setPocketVisibility: (index: number, isVisible: boolean) => void, showOnlyPocket: (index: number) => void, focusPocket: (index: number) => void, - highlightPocket: (index: number, isHighlighted: boolean) => void + highlightPocket: (index: number, isHighlighted: boolean) => void, + plugin: PluginUIContext }, { visible: boolean, details: boolean, @@ -139,12 +141,12 @@ export default class Pocket extends React.Component - {this.state.visible && } + {this.state.visible && } {this.state.visible &&
- +
); } diff --git a/frontend/package-lock.json b/frontend/package-lock.json index 80c02ae9..cef869a8 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -31,6 +31,7 @@ "mini-css-extract-plugin": "^2.7.2", "molstar": "^3.28.0", "postcss-loader": "^7.0.2", + "quickhull3d": "^2.1.0", "react": "^18.2.0", "react-dom": "^18.2.0", "react-draggable": "^4.4.5", @@ -6255,6 +6256,14 @@ "node": ">=8.0.0" } }, + "node_modules/get-plane-normal": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/get-plane-normal/-/get-plane-normal-1.0.0.tgz", + "integrity": "sha512-MUtCvFQCerkHvH97PyZ6IzUzxrJbkie7CA8oB/065l6Ui7UUq3JwiEMzXRasY0AotKmlj8/RieDDwvs9jLr+Sw==", + "dependencies": { + "gl-vec3": "^1.0.3" + } + }, "node_modules/get-symbol-description": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/get-symbol-description/-/get-symbol-description-1.0.0.tgz", @@ -6270,6 +6279,11 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/gl-vec3": { + "version": "1.1.3", + "resolved": "https://registry.npmjs.org/gl-vec3/-/gl-vec3-1.1.3.tgz", + "integrity": "sha512-jduKUqT0SGH02l8Yl+mV1yVsDfYgQAJyXGxkJQGyxPLHRiW25DwVIRPt6uvhrEMHftJfqhqKthRcyZqNEl9Xdw==" + }, "node_modules/glob": { "version": "7.2.3", "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", @@ -8284,6 +8298,14 @@ "node": ">=8" } }, + "node_modules/point-line-distance": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/point-line-distance/-/point-line-distance-1.0.0.tgz", + "integrity": "sha512-v8ikKuyqcs6nv776u6ygBzQoYg+FylS+JZDNmG/IsHpQ9ifUpshd20clVr0jI9J8WFKSOHIz/FlT3CnYVQg38A==", + "dependencies": { + "gl-vec3": "^1.0.3" + } + }, "node_modules/postcss": { "version": "8.4.21", "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.21.tgz", @@ -8524,6 +8546,17 @@ } ] }, + "node_modules/quickhull3d": { + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/quickhull3d/-/quickhull3d-2.1.0.tgz", + "integrity": "sha512-R5X1cTScwn0Eo3MVD7On6WGmEc28xttkaU2dwY7vdTjn7sixvc3rhl4G8uQNCZ6w4zE9LMlY8gHO7zC6/UoSDA==", + "dependencies": { + "debug": "^4.3.4", + "get-plane-normal": "^1.0.0", + "gl-vec3": "^1.1.3", + "point-line-distance": "^1.0.0" + } + }, "node_modules/randombytes": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/randombytes/-/randombytes-2.1.0.tgz", @@ -14863,6 +14896,14 @@ "integrity": "sha512-pjzuKtY64GYfWizNAJ0fr9VqttZkNiK2iS430LtIHzjBEr6bX8Am2zm4sW4Ro5wjWW5cAlRL1qAMTcXbjNAO2Q==", "dev": true }, + "get-plane-normal": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/get-plane-normal/-/get-plane-normal-1.0.0.tgz", + "integrity": "sha512-MUtCvFQCerkHvH97PyZ6IzUzxrJbkie7CA8oB/065l6Ui7UUq3JwiEMzXRasY0AotKmlj8/RieDDwvs9jLr+Sw==", + "requires": { + "gl-vec3": "^1.0.3" + } + }, "get-symbol-description": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/get-symbol-description/-/get-symbol-description-1.0.0.tgz", @@ -14872,6 +14913,11 @@ "get-intrinsic": "^1.1.1" } }, + "gl-vec3": { + "version": "1.1.3", + "resolved": "https://registry.npmjs.org/gl-vec3/-/gl-vec3-1.1.3.tgz", + "integrity": "sha512-jduKUqT0SGH02l8Yl+mV1yVsDfYgQAJyXGxkJQGyxPLHRiW25DwVIRPt6uvhrEMHftJfqhqKthRcyZqNEl9Xdw==" + }, "glob": { "version": "7.2.3", "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", @@ -16300,6 +16346,14 @@ "find-up": "^4.0.0" } }, + "point-line-distance": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/point-line-distance/-/point-line-distance-1.0.0.tgz", + "integrity": "sha512-v8ikKuyqcs6nv776u6ygBzQoYg+FylS+JZDNmG/IsHpQ9ifUpshd20clVr0jI9J8WFKSOHIz/FlT3CnYVQg38A==", + "requires": { + "gl-vec3": "^1.0.3" + } + }, "postcss": { "version": "8.4.21", "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.21.tgz", @@ -16453,6 +16507,17 @@ "resolved": "https://registry.npmjs.org/queue-microtask/-/queue-microtask-1.2.3.tgz", "integrity": "sha512-NuaNSa6flKT5JaSYQzJok04JzTL1CA6aGhv5rfLW3PgqA+M2ChpZQnAC8h8i4ZFkBS8X5RqkDBHA7r4hej3K9A==" }, + "quickhull3d": { + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/quickhull3d/-/quickhull3d-2.1.0.tgz", + "integrity": "sha512-R5X1cTScwn0Eo3MVD7On6WGmEc28xttkaU2dwY7vdTjn7sixvc3rhl4G8uQNCZ6w4zE9LMlY8gHO7zC6/UoSDA==", + "requires": { + "debug": "^4.3.4", + "get-plane-normal": "^1.0.0", + "gl-vec3": "^1.1.3", + "point-line-distance": "^1.0.0" + } + }, "randombytes": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/randombytes/-/randombytes-2.1.0.tgz", diff --git a/frontend/package.json b/frontend/package.json index 57088528..249434e5 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -32,6 +32,7 @@ "mini-css-extract-plugin": "^2.7.2", "molstar": "^3.28.0", "postcss-loader": "^7.0.2", + "quickhull3d": "^2.1.0", "react": "^18.2.0", "react-dom": "^18.2.0", "react-draggable": "^4.4.5", From 82aad29eecf5272da516bd0eeda440773c0c578a Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 16 Jan 2023 11:12:48 +0100 Subject: [PATCH 017/154] Added method annotations. --- frontend/client/tasks/client-atoms-volume.ts | 31 ++++++++++++++------ 1 file changed, 22 insertions(+), 9 deletions(-) diff --git a/frontend/client/tasks/client-atoms-volume.ts b/frontend/client/tasks/client-atoms-volume.ts index fb3b6623..1b7dc965 100644 --- a/frontend/client/tasks/client-atoms-volume.ts +++ b/frontend/client/tasks/client-atoms-volume.ts @@ -5,18 +5,31 @@ import qh from 'quickhull3d'; const pocketVolumes = new Map(); -// https://stackoverflow.com/questions/1406029/how-to-calculate-the-volume-of-a-3d-mesh-object-the-surface-of-which-is-made-up-t -function SignedVolumeOfTriangle(p1: Point3D, p2: Point3D, p3: Point3D) { - const v321 = p3.x*p2.y*p1.z; - const v231 = p2.x*p3.y*p1.z; - const v312 = p3.x*p1.y*p2.z; - const v132 = p1.x*p3.y*p2.z; - const v213 = p2.x*p1.y*p3.z; - const v123 = p1.x*p2.y*p3.z; +/** + * This method computes the volume of a triangle in 3D space. + * https://stackoverflow.com/questions/1406029/ + * @param p1 First point of the triangle + * @param p2 Second point of the triangle + * @param p3 Third point of the triangle + * @returns Volume of the triangle + */ +function computeTriangleVolume(p1: Point3D, p2: Point3D, p3: Point3D) { + const v321 = p3.x * p2.y * p1.z; + const v231 = p2.x * p3.y * p1.z; + const v312 = p3.x * p1.y * p2.z; + const v132 = p1.x * p3.y * p2.z; + const v213 = p2.x * p1.y * p3.z; + const v123 = p1.x * p2.y * p3.z; return (1.0/6.0)*(-v321 + v231 + v312 - v132 - v213 + v123); } +/** + * This method computes the volume of a pocket. + * @param plugin Mol* plugin + * @param pocket Pocket data + * @returns Computed pocket volume + */ export async function computePocketVolume(plugin: PluginUIContext, pocket: PocketData): Promise { if(pocketVolumes.has(pocket.name)) { @@ -40,7 +53,7 @@ export async function computePocketVolume(plugin: PluginUIContext, pocket: Pocke const volumes = []; for(const face of hull) { - volumes.push(SignedVolumeOfTriangle(coords[face[0]], coords[face[1]], coords[face[2]])); + volumes.push(computeTriangleVolume(coords[face[0]], coords[face[1]], coords[face[2]])); } const finalVolume = Math.abs(volumes.reduce((a, b) => a + b, 0)); From f3f16c2302e1084c2e20d5150a69a23d6bd49c17 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Fri, 24 Feb 2023 10:28:04 +0100 Subject: [PATCH 018/154] Changed pocket details header visual --- frontend/client/viewer/components/draggable-dialog.tsx | 8 +++++--- frontend/client/viewer/components/pocket.tsx | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/frontend/client/viewer/components/draggable-dialog.tsx b/frontend/client/viewer/components/draggable-dialog.tsx index 288d8ac9..4912af99 100644 --- a/frontend/client/viewer/components/draggable-dialog.tsx +++ b/frontend/client/viewer/components/draggable-dialog.tsx @@ -18,7 +18,9 @@ function PaperComponent(props: PaperProps) { export default class DraggableDialog extends React.Component<{ pocket: PocketData, - plugin: PluginUIContext + plugin: PluginUIContext, + pocketTextColor: string, + pocketHeaderColor: string }, { visible: boolean }> { @@ -27,7 +29,7 @@ export default class DraggableDialog extends React.Component<{ visible: false, }; - constructor(props: {pocket: PocketData, plugin: PluginUIContext}) { + constructor(props: {pocket: PocketData, plugin: PluginUIContext, pocketTextColor: string, pocketHeaderColor: string}) { super(props); this.toggleDetailsVisibility = this.toggleDetailsVisibility.bind(this); } @@ -67,7 +69,7 @@ export default class DraggableDialog extends React.Component<{ width: 'fit-content', // exactly the same size as its contents }} > - + Pocket {this.props.pocket.rank} diff --git a/frontend/client/viewer/components/pocket.tsx b/frontend/client/viewer/components/pocket.tsx index 475251fe..c07c61bc 100644 --- a/frontend/client/viewer/components/pocket.tsx +++ b/frontend/client/viewer/components/pocket.tsx @@ -146,7 +146,7 @@ export default class Pocket extends React.Component
- +
); diff --git a/frontend/client/viewer/components/draggable-dialog.tsx b/frontend/client/viewer/components/draggable-dialog.tsx index 4912af99..401c05ce 100644 --- a/frontend/client/viewer/components/draggable-dialog.tsx +++ b/frontend/client/viewer/components/draggable-dialog.tsx @@ -10,6 +10,7 @@ import Draggable from 'react-draggable'; import { PocketData } from "../../custom-types"; import PocketDetails from "./pocket-details"; import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context'; +import { PredictionInfo } from '../../prankweb-api'; function PaperComponent(props: PaperProps) { return ( @@ -19,6 +20,7 @@ function PaperComponent(props: PaperProps) { export default class DraggableDialog extends React.Component<{ pocket: PocketData, plugin: PluginUIContext, + prediction: PredictionInfo, pocketTextColor: string, pocketHeaderColor: string }, { @@ -29,7 +31,7 @@ export default class DraggableDialog extends React.Component<{ visible: false, }; - constructor(props: {pocket: PocketData, plugin: PluginUIContext, pocketTextColor: string, pocketHeaderColor: string}) { + constructor(props: any) { super(props); this.toggleDetailsVisibility = this.toggleDetailsVisibility.bind(this); } @@ -74,7 +76,7 @@ export default class DraggableDialog extends React.Component<{ - + diff --git a/frontend/client/viewer/components/pocket-details.tsx b/frontend/client/viewer/components/pocket-details.tsx index 7caad94a..87d4dc19 100644 --- a/frontend/client/viewer/components/pocket-details.tsx +++ b/frontend/client/viewer/components/pocket-details.tsx @@ -1,14 +1,17 @@ import React from "react"; -import { ClientTaskType, PocketData } from "../../custom-types"; +import { ClientTaskType, PocketData, ServerTaskType } from "../../custom-types"; import PocketProperty from "./pocket-property"; import PocketClientTask from "./pocket-client-task"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; +import PocketServerTask from "./pocket-server-task"; +import { PredictionInfo } from "../../prankweb-api"; export default class PocketDetails extends React.Component <{ pocket: PocketData, inDialog: boolean, - plugin: PluginUIContext + plugin: PluginUIContext, + prediction: PredictionInfo }, {}> { constructor(props: any) { @@ -34,7 +37,8 @@ export default class PocketDetails extends React.Component {this.checkValidValue(pocket.avgAlphaFold) && } {this.props.inDialog && } {this.props.inDialog && } -
+ {this.props.inDialog && } +
); } } \ No newline at end of file diff --git a/frontend/client/viewer/components/pocket-list.tsx b/frontend/client/viewer/components/pocket-list.tsx index 5268b119..dbb7882d 100644 --- a/frontend/client/viewer/components/pocket-list.tsx +++ b/frontend/client/viewer/components/pocket-list.tsx @@ -4,6 +4,7 @@ import Pocket from "./pocket"; import "./pocket-list.css"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; +import { PredictionInfo } from "../../prankweb-api"; export default class PocketList extends React.Component <{ @@ -13,7 +14,8 @@ export default class PocketList extends React.Component showOnlyPocket: (index: number) => void, focusPocket: (index: number) => void, highlightPocket: (index: number, isHighlighted: boolean) => void, - plugin: PluginUIContext + plugin: PluginUIContext, + prediction: PredictionInfo }, {}> { render() { @@ -47,6 +49,7 @@ export default class PocketList extends React.Component focusPocket={this.props.focusPocket} highlightPocket={this.props.highlightPocket} plugin={this.props.plugin} + prediction={this.props.prediction} /> ))}
); diff --git a/frontend/client/viewer/components/pocket-server-task.tsx b/frontend/client/viewer/components/pocket-server-task.tsx new file mode 100644 index 00000000..9ea74571 --- /dev/null +++ b/frontend/client/viewer/components/pocket-server-task.tsx @@ -0,0 +1,121 @@ +import React from "react"; +import { LoadingButton } from '@mui/lab'; +import { ClientTaskType, PocketData, ServerTaskType } from '../../custom-types'; +import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; +import { PredictionInfo } from "../../prankweb-api"; + +export default class PocketServerTask extends React.Component + <{ + title: string, + inDialog: boolean, // not needed now. but in other cases the implementation could be potentially different. + pocket: PocketData, + plugin: PluginUIContext, + taskType: ServerTaskType, + prediction: PredictionInfo + }, { + data: any, //this may be changed to any type (the best way is to define some interface) + computed: boolean, + loading: boolean + }> { + + constructor(props: any) { + super(props); + this.handleClick = this.handleClick.bind(this); + this.clickCompute = this.clickCompute.bind(this); + this.state = {loading: false, computed: false, data: undefined}; + } + + async clickCompute() { + switch(this.props.taskType) { + case ServerTaskType.Sample: + const json = await fetch(`./api/v2/sample/v3/${this.props.prediction.id}/post`).then(res => res.json()).catch(err => console.log(err)); + //TODO: handle error in a better way + if(json["status"] !== "successful") { + setTimeout(() => this.clickCompute(), 1000); + } + const data = await fetch(`./api/v2/sample/v3/${this.props.prediction.id}/public/result.json`).then(res => res.json()).catch(err => console.log(err)); + /* + let data = { + "type": ServerTaskType.Sample, + "pockets": [ + { + "rank": "1", + "count": 37 + }, + { + "rank": "2", + "count": 14 + }, + { + "rank": "3", + "count": 12 + }, + { + "rank": "4", + "count": 11 + }, + { + "rank": "5", + "count": 11 + }, + { + "rank": "6", + "count": 13 + }, + { + "rank": "7", + "count": 8 + } + ] + } + */ + const dataWrapper = { + "type": ServerTaskType.Sample, + "pockets": data + } + this.setState({loading: false, computed: true, data: dataWrapper}); + break; + default: + //will not happen + break; + } + } + + async handleClick() { + if(this.state.computed) { + return; + } + this.setState({loading: true}); + await this.clickCompute(); + } + + render() { + return ( +
+ {this.props.title}: + { + !this.state.computed && + + {!this.state.computed && "Compute"} + {this.state.computed && "Computed"} + + } + { + this.state.computed && + this.state.data!["type"] === ServerTaskType.Sample && + + {this.state.data!["pockets"].filter((e: any) => e["rank"] == this.props.pocket.rank)[0]["count"]} + + // here the data should be properly formatted based on the returned type + // i.e for number arrays we could potentially add a diagram instead of just showing a number + } +
+ ); + } +} diff --git a/frontend/client/viewer/components/pocket.tsx b/frontend/client/viewer/components/pocket.tsx index c07c61bc..db3a5666 100644 --- a/frontend/client/viewer/components/pocket.tsx +++ b/frontend/client/viewer/components/pocket.tsx @@ -5,6 +5,7 @@ import PocketDetails from "./pocket-details"; import "bootstrap-icons/font/bootstrap-icons.css"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; +import { PredictionInfo } from "../../prankweb-api"; export default class Pocket extends React.Component <{ @@ -14,7 +15,8 @@ export default class Pocket extends React.Component showOnlyPocket: (index: number) => void, focusPocket: (index: number) => void, highlightPocket: (index: number, isHighlighted: boolean) => void, - plugin: PluginUIContext + plugin: PluginUIContext, + prediction: PredictionInfo }, { visible: boolean, details: boolean, @@ -141,12 +143,12 @@ export default class Pocket extends React.Component
- {this.state.visible && } + {this.state.visible && } {this.state.visible &&
- +
); } diff --git a/frontend/client/viewer/components/pocket-details.tsx b/frontend/client/viewer/components/pocket-details.tsx index 87d4dc19..88c8c696 100644 --- a/frontend/client/viewer/components/pocket-details.tsx +++ b/frontend/client/viewer/components/pocket-details.tsx @@ -36,8 +36,9 @@ export default class PocketDetails extends React.Component {this.checkValidValue(pocket.avgConservation) && } {this.checkValidValue(pocket.avgAlphaFold) && } {this.props.inDialog && } - {this.props.inDialog && } + {this.props.inDialog && } {this.props.inDialog && } + {this.props.inDialog && }
); } From 90022994b2907add7c7060793902c29c314ac1c9 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Fri, 10 Mar 2023 19:05:06 +0100 Subject: [PATCH 029/154] Changed frontend sample task request to POST --- .../viewer/components/pocket-server-task.tsx | 68 ++++++++----------- 1 file changed, 30 insertions(+), 38 deletions(-) diff --git a/frontend/client/viewer/components/pocket-server-task.tsx b/frontend/client/viewer/components/pocket-server-task.tsx index 558c2942..ce781c0c 100644 --- a/frontend/client/viewer/components/pocket-server-task.tsx +++ b/frontend/client/viewer/components/pocket-server-task.tsx @@ -25,51 +25,43 @@ export default class PocketServerTask extends React.Component this.state = {loading: false, computed: false, data: undefined}; } - async clickCompute() { + async clickCompute(firstFetch: boolean = true) { switch(this.props.taskType) { case ServerTaskType.Sample: - const json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/post`).then(res => res.json()).catch(err => console.log(err)); + if(firstFetch) { + let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/post`, { + method: 'POST', + headers: { + 'Accept': 'application/json', + 'Content-Type': 'application/json' + }, + body: JSON.stringify({ + "hash": "SOME_HASH", + "pocket": this.props.pocket.rank, + }), + }).then(res => res.json()).catch(err => console.log(err)); + } + + let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/tasks`, {cache: "no-store"}).then(res => res.json()).catch(err => console.log(err)); //TODO: handle error in a better way - if(json["status"] !== "successful") { - setTimeout(() => this.clickCompute(), 1000); + + console.log(json); + if((json["tasks"].filter((e: any) => e["data"]["hash"] === "SOME_HASH")[0]["status"]) !== "successful") { + setTimeout(() => this.clickCompute(false), 1000); return; } - const data = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/public/result.json`).then(res => res.json()).catch(err => console.log(err)); - /* - let data = { - "type": ServerTaskType.Sample, - "pockets": [ - { - "rank": "1", - "count": 37 - }, - { - "rank": "2", - "count": 14 - }, - { - "rank": "3", - "count": 12 - }, - { - "rank": "4", - "count": 11 - }, - { - "rank": "5", - "count": 11 - }, - { - "rank": "6", - "count": 13 + + const data = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/public/result.json`, { + method: 'POST', + headers: { + 'Accept': 'application/json', + 'Content-Type': 'application/json' }, - { - "rank": "7", - "count": 8 + body: JSON.stringify({ + "hash": "SOME_HASH", } - ] - } - */ + )}).then(res => res.json()).catch(err => console.log(err)); + //TODO: handle error in a better way const dataWrapper = { "type": ServerTaskType.Sample, "pockets": data From 4023b118aab767aa7a3ef7f7ddcddd44833a1ba5 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 11 Mar 2023 14:57:54 +0100 Subject: [PATCH 030/154] Added a dialog to send a server task with params --- .../viewer/components/pocket-server-task.tsx | 91 ++++++++++++++++--- 1 file changed, 78 insertions(+), 13 deletions(-) diff --git a/frontend/client/viewer/components/pocket-server-task.tsx b/frontend/client/viewer/components/pocket-server-task.tsx index ce781c0c..ce3e559c 100644 --- a/frontend/client/viewer/components/pocket-server-task.tsx +++ b/frontend/client/viewer/components/pocket-server-task.tsx @@ -1,6 +1,7 @@ import React from "react"; import { LoadingButton } from '@mui/lab'; -import { ClientTaskType, PocketData, ServerTaskType } from '../../custom-types'; +import { Modal, Box, Typography, TextField } from "@mui/material"; +import { PocketData, ServerTaskType } from '../../custom-types'; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; @@ -13,30 +14,48 @@ export default class PocketServerTask extends React.Component taskType: ServerTaskType, prediction: PredictionInfo }, { - data: any, //this may be changed to any type (the best way is to define some interface) + responseData: any, //this may be changed to any type (the best way is to define some interface) computed: boolean, - loading: boolean + loading: boolean, + modalOpen: boolean, + formData: string, + hash: string }> { constructor(props: any) { super(props); - this.handleClick = this.handleClick.bind(this); + this.handleFormClick = this.handleFormClick.bind(this); this.clickCompute = this.clickCompute.bind(this); - this.state = {loading: false, computed: false, data: undefined}; + this.handleModalClick = this.handleModalClick.bind(this); + this.state = {loading: false, computed: false, responseData: undefined, modalOpen: false, formData: "", hash: ""}; } async clickCompute(firstFetch: boolean = true) { switch(this.props.taskType) { case ServerTaskType.Sample: if(firstFetch) { - let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/post`, { + // compute a hash + const hash = this.state.formData; + console.log(hash); + this.setState({hash: hash}); + + //then look if the task already exists + //TODO: should we check this here or in the backend? + let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/tasks`, {cache: "no-store"}).then(res => res.json()).catch(err => console.log(err)); + if((json["tasks"].filter((e: any) => e["data"]["hash"] === this.state.hash)).length > 0) { + this.clickCompute(false); + return; + } + + //if not, create a new task + await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/post`, { method: 'POST', headers: { 'Accept': 'application/json', 'Content-Type': 'application/json' }, body: JSON.stringify({ - "hash": "SOME_HASH", + "hash": hash, "pocket": this.props.pocket.rank, }), }).then(res => res.json()).catch(err => console.log(err)); @@ -46,7 +65,7 @@ export default class PocketServerTask extends React.Component //TODO: handle error in a better way console.log(json); - if((json["tasks"].filter((e: any) => e["data"]["hash"] === "SOME_HASH")[0]["status"]) !== "successful") { + if((json["tasks"].filter((e: any) => e["data"]["hash"] === this.state.hash)[0]["status"]) !== "successful") { setTimeout(() => this.clickCompute(false), 1000); return; } @@ -58,7 +77,7 @@ export default class PocketServerTask extends React.Component 'Content-Type': 'application/json' }, body: JSON.stringify({ - "hash": "SOME_HASH", + "hash": this.state.hash, } )}).then(res => res.json()).catch(err => console.log(err)); //TODO: handle error in a better way @@ -66,7 +85,7 @@ export default class PocketServerTask extends React.Component "type": ServerTaskType.Sample, "pockets": data } - this.setState({loading: false, computed: true, data: dataWrapper}); + this.setState({loading: false, computed: true, responseData: dataWrapper}); break; default: //will not happen @@ -74,7 +93,7 @@ export default class PocketServerTask extends React.Component } } - async handleClick() { + async handleFormClick() { if(this.state.computed) { return; } @@ -82,12 +101,57 @@ export default class PocketServerTask extends React.Component await this.clickCompute(); } + handleModalClick() { + this.setState({modalOpen: !this.state.modalOpen}); + } + render() { return (
{this.props.title}: { !this.state.computed && +
+ + {!this.state.computed && "Compute"} + {this.state.computed && "Computed"} + + + + + Enter the molecule for docking in pocket {this.props.pocket.rank} (SMILES or PDB) + + {this.setState({formData: e.target.value})}} + /> + + {!this.state.computed && "Compute"} + {this.state.computed && "Computed"} + + + +
+ + /* + */ } { this.state.computed && - this.state.data!["type"] === ServerTaskType.Sample && + this.state.responseData!["type"] === ServerTaskType.Sample && - {this.state.data!["pockets"].filter((e: any) => e["rank"] == this.props.pocket.rank)[0]["count"]} + {this.state.responseData!["pockets"].filter((e: any) => e["rank"] == this.props.pocket.rank)[0]["count"]} // here the data should be properly formatted based on the returned type // i.e for number arrays we could potentially add a diagram instead of just showing a number From 07dae92403f78fc8e69dee9c1c309c4b94a35348 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 11 Mar 2023 17:49:55 +0100 Subject: [PATCH 031/154] Added a sample tasks list --- .../client/tasks/client-get-sample-tasks.ts | 3 +- frontend/client/viewer/application.tsx | 4 ++ .../viewer/components/pocket-server-task.tsx | 4 +- .../client/viewer/components/task-list.tsx | 51 +++++++++++++++++++ 4 files changed, 58 insertions(+), 4 deletions(-) create mode 100644 frontend/client/viewer/components/task-list.tsx diff --git a/frontend/client/tasks/client-get-sample-tasks.ts b/frontend/client/tasks/client-get-sample-tasks.ts index af295856..ab7a923e 100644 --- a/frontend/client/tasks/client-get-sample-tasks.ts +++ b/frontend/client/tasks/client-get-sample-tasks.ts @@ -3,8 +3,7 @@ import { PredictionInfo } from "../prankweb-api"; export async function getSampleTaskCount(prediction: PredictionInfo): Promise { - const json = await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/tasks`).then(res => res.json()).catch(err => console.log(err)); - //TODO: handle error in a better way + const json = await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/tasks`).then(res => res.json()).catch(err => { console.log(err); setTimeout(() => getSampleTaskCount(prediction))} ); const numOfTasks = json["tasks"].length; return { "numericValue": numOfTasks, diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index a2fff1f7..361b266d 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -7,6 +7,7 @@ import { PredictionInfo, getApiDownloadUrl } from "../prankweb-api"; import { StructureInformation } from "./components/structure-information"; import ToolsBox from "./components/tools-box"; import PocketList from "./components/pocket-list"; +import TaskList from "./components/task-list"; import { sendDataToPlugins } from './data-loader'; import { PocketsViewType, PolymerColorType, PolymerViewType, PredictionData, ReactApplicationProps, ReactApplicationState } from "../custom-types"; @@ -220,6 +221,9 @@ export class Application extends React.Component + res.json()).catch(err => console.log(err)); + let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/tasks`, {cache: "no-store"}).then(res => res.json()) + .catch(err => { console.log(err); return this.clickCompute(true)}); if((json["tasks"].filter((e: any) => e["data"]["hash"] === this.state.hash)).length > 0) { this.clickCompute(false); return; diff --git a/frontend/client/viewer/components/task-list.tsx b/frontend/client/viewer/components/task-list.tsx new file mode 100644 index 00000000..30f56c20 --- /dev/null +++ b/frontend/client/viewer/components/task-list.tsx @@ -0,0 +1,51 @@ +import React from "react"; +import { PredictionInfo } from "../../prankweb-api"; + +import "bootstrap-icons/font/bootstrap-icons.css"; + +export default class TaskList extends React.Component< + { + prediction: PredictionInfo + }, + { + tasks: any + }> { + + constructor(props: any) { + super(props); + this.getTaskList = this.getTaskList.bind(this); + this.state = {tasks: []}; + } + + componentDidMount() { + this.getTaskList(); + } + + async getTaskList() { + let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/tasks`, {cache: "no-store"}).then(res => res.json()).catch(err => console.log(err)); + //let json = {"tasks": [{"id": 0, "created": "2023-03-10T18:04:23", "lastChange": "2023-03-10T18:04:23", "status": "successful", "data": {"hash": "SOME_HASH", "pocket": "1"}}], "identifier": "2SRC"}; + //TODO: handle error in a better way + this.setState({tasks: json["tasks"]}); + setTimeout(() => this.getTaskList(), 7000); + } + + render() { + return ( +
+
+

Tasks

+
+
    + {this.state.tasks.map((task: any, index: any) => { + if(task["status"] === "successful") { + return
  • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]}`}
  • + } + else if(task["status"] === "running") { + return
  • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]} running`}
  • + } + })} +
+
+ ) + } +} \ No newline at end of file From 7ac11facea514d74077ebe4929bfc7c773ec9b3b Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 11 Mar 2023 18:51:21 +0100 Subject: [PATCH 032/154] Some error fixes --- executor-docking/run_task.py | 3 +++ frontend/client/tasks/client-get-sample-tasks.ts | 2 +- frontend/client/viewer/components/pocket-server-task.tsx | 5 ++--- frontend/client/viewer/components/task-list.tsx | 2 +- web-server/src/sample_task.py | 8 ++++++++ 5 files changed, 15 insertions(+), 5 deletions(-) diff --git a/executor-docking/run_task.py b/executor-docking/run_task.py index 95965de9..5165449f 100644 --- a/executor-docking/run_task.py +++ b/executor-docking/run_task.py @@ -7,6 +7,7 @@ import datetime import enum import json +import time class Status(enum.Enum): QUEUED = "queued" @@ -26,6 +27,8 @@ def _save_status_file(path: str, status: any, taskId: int): def _save_json(path: str, content: any): path_swp = path + ".swp" + if(os.path.exists(path_swp)): + time.sleep(1) with open(path_swp, "w", encoding="utf-8") as stream: json.dump(content, stream, ensure_ascii=True) os.replace(path_swp, path) diff --git a/frontend/client/tasks/client-get-sample-tasks.ts b/frontend/client/tasks/client-get-sample-tasks.ts index ab7a923e..e22db8fa 100644 --- a/frontend/client/tasks/client-get-sample-tasks.ts +++ b/frontend/client/tasks/client-get-sample-tasks.ts @@ -3,7 +3,7 @@ import { PredictionInfo } from "../prankweb-api"; export async function getSampleTaskCount(prediction: PredictionInfo): Promise { - const json = await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/tasks`).then(res => res.json()).catch(err => { console.log(err); setTimeout(() => getSampleTaskCount(prediction))} ); + const json = await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/tasks`).then(res => res.json()).catch(err => { console.log(err); setTimeout(() => getSampleTaskCount(prediction), 1000)} ); const numOfTasks = json["tasks"].length; return { "numericValue": numOfTasks, diff --git a/frontend/client/viewer/components/pocket-server-task.tsx b/frontend/client/viewer/components/pocket-server-task.tsx index 007f83cd..ec6efb8f 100644 --- a/frontend/client/viewer/components/pocket-server-task.tsx +++ b/frontend/client/viewer/components/pocket-server-task.tsx @@ -41,8 +41,8 @@ export default class PocketServerTask extends React.Component //then look if the task already exists //TODO: should we check this here or in the backend? let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/tasks`, {cache: "no-store"}).then(res => res.json()) - .catch(err => { console.log(err); return this.clickCompute(true)}); - if((json["tasks"].filter((e: any) => e["data"]["hash"] === this.state.hash)).length > 0) { + .catch(err => { console.log(err); }); + if(json && (json["tasks"].filter((e: any) => e["data"]["hash"] === this.state.hash)).length > 0) { this.clickCompute(false); return; } @@ -64,7 +64,6 @@ export default class PocketServerTask extends React.Component let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/tasks`, {cache: "no-store"}).then(res => res.json()).catch(err => console.log(err)); //TODO: handle error in a better way - console.log(json); if((json["tasks"].filter((e: any) => e["data"]["hash"] === this.state.hash)[0]["status"]) !== "successful") { setTimeout(() => this.clickCompute(false), 1000); return; diff --git a/frontend/client/viewer/components/task-list.tsx b/frontend/client/viewer/components/task-list.tsx index 30f56c20..5dceb946 100644 --- a/frontend/client/viewer/components/task-list.tsx +++ b/frontend/client/viewer/components/task-list.tsx @@ -25,7 +25,7 @@ export default class TaskList extends React.Component< let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/tasks`, {cache: "no-store"}).then(res => res.json()).catch(err => console.log(err)); //let json = {"tasks": [{"id": 0, "created": "2023-03-10T18:04:23", "lastChange": "2023-03-10T18:04:23", "status": "successful", "data": {"hash": "SOME_HASH", "pocket": "1"}}], "identifier": "2SRC"}; //TODO: handle error in a better way - this.setState({tasks: json["tasks"]}); + if(json) this.setState({tasks: json["tasks"]}); setTimeout(() => this.getTaskList(), 7000); } diff --git a/web-server/src/sample_task.py b/web-server/src/sample_task.py index 60038011..f86d6c8a 100644 --- a/web-server/src/sample_task.py +++ b/web-server/src/sample_task.py @@ -81,12 +81,20 @@ def post_task(self, identifier: str, data: dict): f.seek(0) f.write(json.dumps(fileData)) + os.makedirs(os.path.join(directory, str(taskinfo.taskId)), exist_ok=True) + with open(os.path.join(directory, str(taskinfo.taskId), "input.json"), "w+") as f: + f.write(json.dumps(data)) + submit_directory_for_sample_task(taskinfo.directory, taskinfo.taskId) return self._response_file(directory, "info.json") #else we create a new info file taskinfo = TaskInfo(directory=directory, identifier=identifier, data=data) + os.makedirs(os.path.join(directory, "0"), exist_ok=True) + with open(os.path.join(directory, "0", "input.json"), "w+") as f: + f.write(json.dumps(data)) + return _create_sample_task_file(taskinfo) def get_all_tasks(self, identifier: str): From de8fd0b16ec18e01e9e6c240885fad3ca1e0e518 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 11 Mar 2023 19:05:01 +0100 Subject: [PATCH 033/154] Moved saving input to a function --- web-server/src/sample_task.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/web-server/src/sample_task.py b/web-server/src/sample_task.py index f86d6c8a..ddb07193 100644 --- a/web-server/src/sample_task.py +++ b/web-server/src/sample_task.py @@ -81,20 +81,14 @@ def post_task(self, identifier: str, data: dict): f.seek(0) f.write(json.dumps(fileData)) - os.makedirs(os.path.join(directory, str(taskinfo.taskId)), exist_ok=True) - with open(os.path.join(directory, str(taskinfo.taskId), "input.json"), "w+") as f: - f.write(json.dumps(data)) - + _save_input(taskinfo, data) submit_directory_for_sample_task(taskinfo.directory, taskinfo.taskId) return self._response_file(directory, "info.json") #else we create a new info file taskinfo = TaskInfo(directory=directory, identifier=identifier, data=data) - os.makedirs(os.path.join(directory, "0"), exist_ok=True) - with open(os.path.join(directory, "0", "input.json"), "w+") as f: - f.write(json.dumps(data)) - + _save_input(taskinfo, data) return _create_sample_task_file(taskinfo) def get_all_tasks(self, identifier: str): @@ -132,6 +126,12 @@ def _mime_type(file_name: str) -> str: ext = file_name[file_name.rindex("."):] return extensions.get(ext, "text/plain") +def _save_input(taskinfo: TaskInfo, data: dict): + """Save input data for given task.""" + os.makedirs(os.path.join(taskinfo.directory, str(taskinfo.taskId)), exist_ok=True) + with open(os.path.join(taskinfo.directory, str(taskinfo.taskId), "input.json"), "w+") as f: + f.write(json.dumps(data)) + def _info_file(taskinfo: TaskInfo) -> str: return os.path.join(taskinfo.directory, "info.json") From e1ad156bfb850d388810cc74ee4e3ee38434e713 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 13 Mar 2023 11:37:18 +0100 Subject: [PATCH 034/154] A few React changes --- frontend/client/custom-types.ts | 14 +++++++-- .../client/tasks/client-get-sample-tasks.ts | 12 +++++-- frontend/client/viewer/application.tsx | 12 +++++++ .../viewer/components/draggable-dialog.tsx | 7 +++-- .../viewer/components/pocket-details.tsx | 5 +-- .../client/viewer/components/pocket-list.tsx | 6 ++-- .../viewer/components/pocket-server-task.tsx | 31 +++++++------------ frontend/client/viewer/components/pocket.tsx | 9 +++--- .../client/viewer/components/task-list.tsx | 23 +++----------- 9 files changed, 65 insertions(+), 54 deletions(-) diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index 4cee21f2..abddfb25 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -159,6 +159,7 @@ export interface ReactApplicationState { polymerColor: PolymerColorType, isShowOnlyPredicted: boolean, pluginRcsb: RcsbFv | undefined, + serverTasks: ServerTaskData[] } /** @@ -212,7 +213,7 @@ export enum ClientTaskType { } export interface ClientTaskData { - type: ClientTaskType; + type?: ClientTaskType; numericValue?: number; } @@ -224,4 +225,13 @@ export interface Point3D { export enum ServerTaskType { Sample = 0 -} \ No newline at end of file +} + +export interface ServerTaskData { + type?: ServerTaskType; + id: string; + created: string; + lastChange: string; + status: string; + data: any; +} \ No newline at end of file diff --git a/frontend/client/tasks/client-get-sample-tasks.ts b/frontend/client/tasks/client-get-sample-tasks.ts index e22db8fa..725be90a 100644 --- a/frontend/client/tasks/client-get-sample-tasks.ts +++ b/frontend/client/tasks/client-get-sample-tasks.ts @@ -4,9 +4,15 @@ import { PredictionInfo } from "../prankweb-api"; export async function getSampleTaskCount(prediction: PredictionInfo): Promise { const json = await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/tasks`).then(res => res.json()).catch(err => { console.log(err); setTimeout(() => getSampleTaskCount(prediction), 1000)} ); - const numOfTasks = json["tasks"].length; + if(json) { + const numOfTasks = json["tasks"].length; + return { + "numericValue": numOfTasks, + "type": ClientTaskType.SampleTaskCount + }; + } return { - "numericValue": numOfTasks, + "numericValue": 0, "type": ClientTaskType.SampleTaskCount - }; + } } \ No newline at end of file diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 361b266d..d83c37dd 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -59,6 +59,7 @@ export class Application extends React.Component res.json()).catch(err => console.log(err)); + //let json = {"tasks": [{"id": 0, "created": "2023-03-10T18:04:23", "lastChange": "2023-03-10T18:04:23", "status": "successful", "data": {"hash": "SOME_HASH", "pocket": "1"}}], "identifier": "2SRC"}; + //TODO: handle error in a better way + if(json) this.setState({serverTasks: json["tasks"]}); + setTimeout(() => this.getTaskList(), 7000); + } + render() { console.log("Application::render"); if (this.state.isLoading) { @@ -223,6 +233,7 @@ export class Application extends React.Component
); diff --git a/frontend/client/viewer/components/draggable-dialog.tsx b/frontend/client/viewer/components/draggable-dialog.tsx index 401c05ce..a6d531f6 100644 --- a/frontend/client/viewer/components/draggable-dialog.tsx +++ b/frontend/client/viewer/components/draggable-dialog.tsx @@ -7,7 +7,7 @@ import DialogContentText from '@mui/material/DialogContentText'; import DialogTitle from '@mui/material/DialogTitle'; import Paper, { PaperProps } from '@mui/material/Paper'; import Draggable from 'react-draggable'; -import { PocketData } from "../../custom-types"; +import { PocketData, ServerTaskData } from "../../custom-types"; import PocketDetails from "./pocket-details"; import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context'; import { PredictionInfo } from '../../prankweb-api'; @@ -22,7 +22,8 @@ export default class DraggableDialog extends React.Component<{ plugin: PluginUIContext, prediction: PredictionInfo, pocketTextColor: string, - pocketHeaderColor: string + pocketHeaderColor: string, + serverTasks: ServerTaskData[] }, { visible: boolean }> { @@ -76,7 +77,7 @@ export default class DraggableDialog extends React.Component<{ - + diff --git a/frontend/client/viewer/components/pocket-details.tsx b/frontend/client/viewer/components/pocket-details.tsx index 88c8c696..374dd298 100644 --- a/frontend/client/viewer/components/pocket-details.tsx +++ b/frontend/client/viewer/components/pocket-details.tsx @@ -1,5 +1,5 @@ import React from "react"; -import { ClientTaskType, PocketData, ServerTaskType } from "../../custom-types"; +import { ClientTaskType, PocketData, ServerTaskData, ServerTaskType } from "../../custom-types"; import PocketProperty from "./pocket-property"; import PocketClientTask from "./pocket-client-task"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; @@ -12,6 +12,7 @@ export default class PocketDetails extends React.Component inDialog: boolean, plugin: PluginUIContext, prediction: PredictionInfo + serverTasks: ServerTaskData[] }, {}> { constructor(props: any) { @@ -37,7 +38,7 @@ export default class PocketDetails extends React.Component {this.checkValidValue(pocket.avgAlphaFold) && } {this.props.inDialog && } {this.props.inDialog && } - {this.props.inDialog && } + {this.props.inDialog && } {this.props.inDialog && }
); diff --git a/frontend/client/viewer/components/pocket-list.tsx b/frontend/client/viewer/components/pocket-list.tsx index dbb7882d..1c2aad5a 100644 --- a/frontend/client/viewer/components/pocket-list.tsx +++ b/frontend/client/viewer/components/pocket-list.tsx @@ -1,5 +1,5 @@ import React from "react"; -import { PredictionData } from "../../custom-types"; +import { PredictionData, ServerTaskData } from "../../custom-types"; import Pocket from "./pocket"; import "./pocket-list.css"; @@ -15,7 +15,8 @@ export default class PocketList extends React.Component focusPocket: (index: number) => void, highlightPocket: (index: number, isHighlighted: boolean) => void, plugin: PluginUIContext, - prediction: PredictionInfo + prediction: PredictionInfo, + serverTasks: ServerTaskData[] }, {}> { render() { @@ -50,6 +51,7 @@ export default class PocketList extends React.Component highlightPocket={this.props.highlightPocket} plugin={this.props.plugin} prediction={this.props.prediction} + serverTasks={this.props.serverTasks} /> ))}
); diff --git a/frontend/client/viewer/components/pocket-server-task.tsx b/frontend/client/viewer/components/pocket-server-task.tsx index ec6efb8f..4b996a03 100644 --- a/frontend/client/viewer/components/pocket-server-task.tsx +++ b/frontend/client/viewer/components/pocket-server-task.tsx @@ -1,7 +1,7 @@ import React from "react"; import { LoadingButton } from '@mui/lab'; import { Modal, Box, Typography, TextField } from "@mui/material"; -import { PocketData, ServerTaskType } from '../../custom-types'; +import { PocketData, ServerTaskData, ServerTaskType } from '../../custom-types'; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; @@ -12,7 +12,8 @@ export default class PocketServerTask extends React.Component pocket: PocketData, plugin: PluginUIContext, taskType: ServerTaskType, - prediction: PredictionInfo + prediction: PredictionInfo, + serverTasks: ServerTaskData[] }, { responseData: any, //this may be changed to any type (the best way is to define some interface) computed: boolean, @@ -61,11 +62,16 @@ export default class PocketServerTask extends React.Component }).then(res => res.json()).catch(err => console.log(err)); } - let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/tasks`, {cache: "no-store"}).then(res => res.json()).catch(err => console.log(err)); - //TODO: handle error in a better way + //check if the task is finished + let matchingTasks = (this.props.serverTasks.filter((e: any) => e["data"]["hash"] === this.state.hash)); - if((json["tasks"].filter((e: any) => e["data"]["hash"] === this.state.hash)[0]["status"]) !== "successful") { - setTimeout(() => this.clickCompute(false), 1000); + if(matchingTasks.length === 0) { + setTimeout(() => this.clickCompute(false), 2000); + return; + } + + if(matchingTasks[0]["status"] !== "successful") { + setTimeout(() => this.clickCompute(false), 2000); return; } @@ -149,19 +155,6 @@ export default class PocketServerTask extends React.Component - - /* - - {!this.state.computed && "Compute"} - {this.state.computed && "Computed"} - - */ } { this.state.computed && diff --git a/frontend/client/viewer/components/pocket.tsx b/frontend/client/viewer/components/pocket.tsx index db3a5666..7fd33cd2 100644 --- a/frontend/client/viewer/components/pocket.tsx +++ b/frontend/client/viewer/components/pocket.tsx @@ -1,5 +1,5 @@ import React from "react"; -import { PocketData } from "../../custom-types"; +import { PocketData, ServerTaskData } from "../../custom-types"; import DraggableDialog from './draggable-dialog' import PocketDetails from "./pocket-details"; @@ -16,7 +16,8 @@ export default class Pocket extends React.Component focusPocket: (index: number) => void, highlightPocket: (index: number, isHighlighted: boolean) => void, plugin: PluginUIContext, - prediction: PredictionInfo + prediction: PredictionInfo, + serverTasks: ServerTaskData[] }, { visible: boolean, details: boolean, @@ -143,12 +144,12 @@ export default class Pocket extends React.Component - {this.state.visible && } + {this.state.visible && } {this.state.visible &&
- +
    - {this.state.tasks.map((task: any, index: any) => { + {this.props.tasks.map((task: any, index: any) => { if(task["status"] === "successful") { return
  • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]}`}
  • } From bbcdd80b6d993108e38e093c2a6c159be711927f Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 13 Mar 2023 13:41:45 +0100 Subject: [PATCH 035/154] Dockerfile node update --- gateway/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gateway/Dockerfile b/gateway/Dockerfile index 0955cfc0..767b8469 100644 --- a/gateway/Dockerfile +++ b/gateway/Dockerfile @@ -1,7 +1,7 @@ # # Build web-application. # -FROM node:17.2-bullseye AS frontend +FROM node:19.7-bullseye AS frontend ARG GOOGLE_ANALYTICS From 82c5a32489ff1d798d91e36f58cbf29bf998ecac Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 13 Mar 2023 14:18:15 +0100 Subject: [PATCH 036/154] Some server task changes --- frontend/client/custom-types.ts | 3 +- frontend/client/viewer/application.tsx | 15 +++++++-- .../viewer/components/pocket-details.tsx | 16 +++++++++- .../components/pocket-running-tasks.tsx | 32 +++++++++++++++++++ .../viewer/components/pocket-server-task.tsx | 20 ++++++++---- 5 files changed, 74 insertions(+), 12 deletions(-) create mode 100644 frontend/client/viewer/components/pocket-running-tasks.tsx diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index abddfb25..dfcfcb5f 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -233,5 +233,6 @@ export interface ServerTaskData { created: string; lastChange: string; status: string; - data: any; + data: any; //initial data + responseData: any; } \ No newline at end of file diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index d83c37dd..8fc77559 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -10,7 +10,7 @@ import PocketList from "./components/pocket-list"; import TaskList from "./components/task-list"; import { sendDataToPlugins } from './data-loader'; -import { PocketsViewType, PolymerColorType, PolymerViewType, PredictionData, ReactApplicationProps, ReactApplicationState } from "../custom-types"; +import { PocketsViewType, PolymerColorType, PolymerViewType, PredictionData, ReactApplicationProps, ReactApplicationState, ServerTaskData } from "../custom-types"; import { DefaultPluginUISpec } from 'molstar/lib/mol-plugin-ui/spec'; import { createPluginUI } from 'molstar/lib/mol-plugin-ui'; @@ -193,8 +193,17 @@ export class Application extends React.Component res.json()).catch(err => console.log(err)); //let json = {"tasks": [{"id": 0, "created": "2023-03-10T18:04:23", "lastChange": "2023-03-10T18:04:23", "status": "successful", "data": {"hash": "SOME_HASH", "pocket": "1"}}], "identifier": "2SRC"}; - //TODO: handle error in a better way - if(json) this.setState({serverTasks: json["tasks"]}); + //TODO: handle error in a better way, but we do not really care if the poll fails sometimes + if(json) { + //append the new tasks to the existing ones + let newTasks: ServerTaskData[] = this.state.serverTasks; + json["tasks"].forEach((task: any) => { + if(!newTasks.find((t: any) => t.id === task.id)) { + newTasks.push(task); + } + }); + this.setState({serverTasks: newTasks}); + } setTimeout(() => this.getTaskList(), 7000); } diff --git a/frontend/client/viewer/components/pocket-details.tsx b/frontend/client/viewer/components/pocket-details.tsx index 374dd298..61869620 100644 --- a/frontend/client/viewer/components/pocket-details.tsx +++ b/frontend/client/viewer/components/pocket-details.tsx @@ -5,6 +5,7 @@ import PocketClientTask from "./pocket-client-task"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import PocketServerTask from "./pocket-server-task"; import { PredictionInfo } from "../../prankweb-api"; +import RunningTasks from "./pocket-running-tasks"; export default class PocketDetails extends React.Component <{ @@ -13,13 +14,25 @@ export default class PocketDetails extends React.Component plugin: PluginUIContext, prediction: PredictionInfo serverTasks: ServerTaskData[] - }, {}> { + }, { + serverTasks: ServerTaskData[] + //updated: boolean + }> { constructor(props: any) { super(props); + this.state = {serverTasks: this.props.serverTasks}; this.checkValidValue = this.checkValidValue.bind(this); } + componentDidUpdate(prevProps: any){ + if(prevProps.serverTasks !== this.props.serverTasks){ + this.setState({ + serverTasks: this.props.serverTasks + }); + } + } + checkValidValue(data: number | undefined) { //here double equal sign is used intentionally if(data == undefined || data == 0) return false; @@ -40,6 +53,7 @@ export default class PocketDetails extends React.Component {this.props.inDialog && } {this.props.inDialog && } {this.props.inDialog && } + {this.props.inDialog && }
); } diff --git a/frontend/client/viewer/components/pocket-running-tasks.tsx b/frontend/client/viewer/components/pocket-running-tasks.tsx new file mode 100644 index 00000000..177e33c3 --- /dev/null +++ b/frontend/client/viewer/components/pocket-running-tasks.tsx @@ -0,0 +1,32 @@ +import React from "react"; +import { PocketData, ServerTaskData } from "../../custom-types"; +import PocketProperty from "./pocket-property"; + +export default class RunningTasks extends React.Component + <{ + pocket: PocketData, + inDialog: boolean, + serverTasks: ServerTaskData[] + }, {}> { + + constructor(props: any) { + super(props); + } + + render() { + return ( +
+ {this.props.inDialog && this.props.serverTasks.map((e: ServerTaskData, index) => { + if(e.responseData && e.data.pocket === this.props.pocket.rank) { + return p.rank === this.props.pocket.rank)?.count + }/> + } + else if(e.status === "running" || e.status === "queued") { + return + } + })} +
+ ); + } +} \ No newline at end of file diff --git a/frontend/client/viewer/components/pocket-server-task.tsx b/frontend/client/viewer/components/pocket-server-task.tsx index 4b996a03..220c0645 100644 --- a/frontend/client/viewer/components/pocket-server-task.tsx +++ b/frontend/client/viewer/components/pocket-server-task.tsx @@ -41,9 +41,7 @@ export default class PocketServerTask extends React.Component //then look if the task already exists //TODO: should we check this here or in the backend? - let json = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/tasks`, {cache: "no-store"}).then(res => res.json()) - .catch(err => { console.log(err); }); - if(json && (json["tasks"].filter((e: any) => e["data"]["hash"] === this.state.hash)).length > 0) { + if(this.props.serverTasks && (this.props.serverTasks.filter((e: any) => e["data"]["hash"] === this.state.hash && e["data"]["pocket"] === this.props.pocket.rank)).length > 0) { this.clickCompute(false); return; } @@ -59,19 +57,22 @@ export default class PocketServerTask extends React.Component "hash": hash, "pocket": this.props.pocket.rank, }), - }).then(res => res.json()).catch(err => console.log(err)); + }).then(res => res.json()).catch(err => { + console.log(err); + this.clickCompute(true); //repeat the request + }); } //check if the task is finished - let matchingTasks = (this.props.serverTasks.filter((e: any) => e["data"]["hash"] === this.state.hash)); + let matchingTasks = (this.props.serverTasks.filter((e: any) => e["data"]["hash"] === this.state.hash && e["data"]["pocket"] === this.props.pocket.rank)); if(matchingTasks.length === 0) { - setTimeout(() => this.clickCompute(false), 2000); + setTimeout(() => this.clickCompute(false), 1000); return; } if(matchingTasks[0]["status"] !== "successful") { - setTimeout(() => this.clickCompute(false), 2000); + setTimeout(() => this.clickCompute(false), 1000); return; } @@ -85,11 +86,16 @@ export default class PocketServerTask extends React.Component "hash": this.state.hash, } )}).then(res => res.json()).catch(err => console.log(err)); + if(!data) { + setTimeout(() => this.clickCompute(false), 3000); + return; + } //TODO: handle error in a better way const dataWrapper = { "type": ServerTaskType.Sample, "pockets": data } + matchingTasks[0]["responseData"] = dataWrapper; this.setState({loading: false, computed: true, responseData: dataWrapper}); break; default: From 46d02effaa3ee3195fe18206713a86294799e4ba Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 13 Mar 2023 14:51:09 +0100 Subject: [PATCH 037/154] Added toggling for task list --- .../client/viewer/components/task-list.tsx | 74 +++++++++++++++---- 1 file changed, 59 insertions(+), 15 deletions(-) diff --git a/frontend/client/viewer/components/task-list.tsx b/frontend/client/viewer/components/task-list.tsx index e6413a56..6227bd1f 100644 --- a/frontend/client/viewer/components/task-list.tsx +++ b/frontend/client/viewer/components/task-list.tsx @@ -8,29 +8,73 @@ export default class TaskList extends React.Component< { prediction: PredictionInfo tasks: ServerTaskData[] - },{}> { + },{ + expanded: boolean + }> { constructor(props: any) { super(props); + this.toggleExpanded = this.toggleExpanded.bind(this); + this.state = {expanded: false}; + } + + toggleExpanded() { + this.setState({expanded: !this.state.expanded}); } render() { return ( -
-
-

Tasks

-
-
    - {this.props.tasks.map((task: any, index: any) => { - if(task["status"] === "successful") { - return
  • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]}`}
  • - } - else if(task["status"] === "running") { - return
  • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]} running`}
  • - } - })} -
+
+
+

+ Tasks + +

+
+ {this.state.expanded &&
+
+ } +
+ ); + } +} + +class TaskListContent extends React.Component<{ + prediction: PredictionInfo + tasks: ServerTaskData[] + }, {}> { + + constructor(props: any) { + super(props); + } + + render() { + return ( +
    + {this.props.tasks.map((task: any, index: any) => { + if(task["status"] === "successful") { + return
  • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]}`}
  • + } + else if(task["status"] === "running") { + return
  • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]} running`}
  • + } + })} +
) } } \ No newline at end of file From 5eb7f68a6067657227497250fed6406f7074682e Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 20 Mar 2023 15:53:10 +0100 Subject: [PATCH 038/154] Changed tasks --- frontend/client/viewer/components/pocket-running-tasks.tsx | 2 +- frontend/client/viewer/components/task-list.tsx | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/frontend/client/viewer/components/pocket-running-tasks.tsx b/frontend/client/viewer/components/pocket-running-tasks.tsx index 177e33c3..87c23d96 100644 --- a/frontend/client/viewer/components/pocket-running-tasks.tsx +++ b/frontend/client/viewer/components/pocket-running-tasks.tsx @@ -22,7 +22,7 @@ export default class RunningTasks extends React.Component e.responseData.pockets.find((p: any) => p.rank === this.props.pocket.rank)?.count }/> } - else if(e.status === "running" || e.status === "queued") { + else if(e.data.pocket === this.props.pocket.rank && (e.status === "running" || e.status === "queued")) { return } })} diff --git a/frontend/client/viewer/components/task-list.tsx b/frontend/client/viewer/components/task-list.tsx index 6227bd1f..4058440d 100644 --- a/frontend/client/viewer/components/task-list.tsx +++ b/frontend/client/viewer/components/task-list.tsx @@ -73,6 +73,9 @@ class TaskListContent extends React.Component<{ else if(task["status"] === "running") { return
  • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]} running`}
  • } + else if(task["status"] === "queued") { + return
  • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]} queued`}
  • + } })} ) From 93f4f3b71d2625d0e0c8c8772514ae9edfd2bf48 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 20 Mar 2023 16:03:22 +0100 Subject: [PATCH 039/154] Docker-compose changes --- docker-compose-prankweb.yml | 2 +- docker-compose.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docker-compose-prankweb.yml b/docker-compose-prankweb.yml index fb550e28..f97145b0 100644 --- a/docker-compose-prankweb.yml +++ b/docker-compose-prankweb.yml @@ -59,7 +59,7 @@ services: args: UID: ${UID} GID: ${GID} - command: ["celery", "--app=celery_p2rank", "worker", "--concurrency=4", "--hostname=executor-p2rank"] + command: ["celery", "--app=celery_p2rank", "--queues=p2rank", "worker", "--concurrency=4", "--hostname=executor-p2rank"] environment: CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672" LOCK_DIRECTORY: "/data/prankweb/lock" diff --git a/docker-compose.yml b/docker-compose.yml index 4ed2d02e..542450f8 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -59,7 +59,7 @@ services: args: UID: ${UID:-5988} GID: ${GID:-5988} - command: ["celery", "--app=celery_p2rank", "worker", "--concurrency=4", "--hostname=executor-p2rank"] + command: ["celery", "--app=celery_p2rank", "--queues=p2rank", "worker", "--concurrency=4", "--hostname=executor-p2rank"] depends_on: rabbitmq: condition: service_healthy From 203a2b100a05790b7e30134325109a77f292ec45 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 20 Mar 2023 16:59:23 +0100 Subject: [PATCH 040/154] Fixed Docker-compose files --- docker-compose-prankweb.yml | 2 +- docker-compose.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docker-compose-prankweb.yml b/docker-compose-prankweb.yml index f97145b0..bea7949c 100644 --- a/docker-compose-prankweb.yml +++ b/docker-compose-prankweb.yml @@ -59,7 +59,7 @@ services: args: UID: ${UID} GID: ${GID} - command: ["celery", "--app=celery_p2rank", "--queues=p2rank", "worker", "--concurrency=4", "--hostname=executor-p2rank"] + command: ["celery", "--app=celery_p2rank", "worker", "--queues=p2rank", "--concurrency=4", "--hostname=executor-p2rank"] environment: CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672" LOCK_DIRECTORY: "/data/prankweb/lock" diff --git a/docker-compose.yml b/docker-compose.yml index 542450f8..dfe31646 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -59,7 +59,7 @@ services: args: UID: ${UID:-5988} GID: ${GID:-5988} - command: ["celery", "--app=celery_p2rank", "--queues=p2rank", "worker", "--concurrency=4", "--hostname=executor-p2rank"] + command: ["celery", "--app=celery_p2rank", "worker", "--queues=p2rank", "--concurrency=4", "--hostname=executor-p2rank"] depends_on: rabbitmq: condition: service_healthy From 391dfbc60cf7a09d6bcf07a517b9dc66b4b44db0 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 20 Mar 2023 23:34:42 +0100 Subject: [PATCH 041/154] Moved checking of task existence to backend --- executor-docking/run_task.py | 6 +++++- frontend/client/viewer/application.tsx | 1 - frontend/client/viewer/components/pocket-server-task.tsx | 7 ------- web-server/src/sample_task.py | 5 +++++ 4 files changed, 10 insertions(+), 9 deletions(-) diff --git a/executor-docking/run_task.py b/executor-docking/run_task.py index 5165449f..ebc4ec98 100644 --- a/executor-docking/run_task.py +++ b/executor-docking/run_task.py @@ -39,8 +39,12 @@ def get_prediction_path(docking_directory: str): def execute_directory_task(directory: str, taskId: int): #print(os.listdir(os.path.join(directory, "..", "..", "..", ".."))) - if not os.path.exists(directory) or not os.path.isdir(directory): + + final_file = os.path.join(directory, str(taskId), "public", "result.json") + + if not os.path.exists(directory) or not os.path.isdir(directory) or os.path.exists(final_file): return + #first update the status file status_file = os.path.join(directory, "info.json") status = _load_json(status_file) diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 8fc77559..d3e7af8f 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -192,7 +192,6 @@ export class Application extends React.Component res.json()).catch(err => console.log(err)); - //let json = {"tasks": [{"id": 0, "created": "2023-03-10T18:04:23", "lastChange": "2023-03-10T18:04:23", "status": "successful", "data": {"hash": "SOME_HASH", "pocket": "1"}}], "identifier": "2SRC"}; //TODO: handle error in a better way, but we do not really care if the poll fails sometimes if(json) { //append the new tasks to the existing ones diff --git a/frontend/client/viewer/components/pocket-server-task.tsx b/frontend/client/viewer/components/pocket-server-task.tsx index 220c0645..2a558c67 100644 --- a/frontend/client/viewer/components/pocket-server-task.tsx +++ b/frontend/client/viewer/components/pocket-server-task.tsx @@ -39,13 +39,6 @@ export default class PocketServerTask extends React.Component const hash = this.state.formData; this.setState({hash: hash}); - //then look if the task already exists - //TODO: should we check this here or in the backend? - if(this.props.serverTasks && (this.props.serverTasks.filter((e: any) => e["data"]["hash"] === this.state.hash && e["data"]["pocket"] === this.props.pocket.rank)).length > 0) { - this.clickCompute(false); - return; - } - //if not, create a new task await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/post`, { method: 'POST', diff --git a/web-server/src/sample_task.py b/web-server/src/sample_task.py index ddb07193..b7bb6c83 100644 --- a/web-server/src/sample_task.py +++ b/web-server/src/sample_task.py @@ -76,6 +76,11 @@ def post_task(self, identifier: str, data: dict): with open(os.path.join(directory, "info.json"), "r+") as f: fileData = json.load(f) + #we check if the task already exists + for task in fileData["tasks"]: + if task["data"] == data: + return self._response_file(directory, "info.json") + taskinfo.taskId = len(fileData["tasks"]) fileData["tasks"].append(_create_info(taskinfo)) f.seek(0) From a827e6d88009dfa58a1ce80ddc4de952831a6e53 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 25 Mar 2023 14:28:10 +0100 Subject: [PATCH 042/154] Docking executor code cleanup --- docker-compose.yml | 1 + executor-docking/Dockerfile | 4 +-- executor-docking/celery_docking.py | 13 +++---- executor-docking/run_task.py | 54 ++++++++++++++++++------------ 4 files changed, 40 insertions(+), 32 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index dfe31646..31fac70e 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -77,6 +77,7 @@ services: args: UID: ${UID} GID: ${GID} + command: ["celery", "--app=celery_docking", "worker", "--queues=docking", "--concurrency=4", "--hostname=executor-docking"] environment: CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672" restart: unless-stopped diff --git a/executor-docking/Dockerfile b/executor-docking/Dockerfile index be69c747..b5f3f887 100644 --- a/executor-docking/Dockerfile +++ b/executor-docking/Dockerfile @@ -1,5 +1,5 @@ # -# executor +# executor-docking # FROM debian:bookworm-20230208 @@ -44,5 +44,3 @@ RUN chmod a+x ./run_task.py WORKDIR /opt/executor-docking USER ${UID}:${GID} - -CMD ["celery", "--app=celery_docking", "worker", "--queues=docking", "--concurrency=4", "--hostname=executor-docking-p2rank"] diff --git a/executor-docking/celery_docking.py b/executor-docking/celery_docking.py index 4b36ce08..ab233202 100644 --- a/executor-docking/celery_docking.py +++ b/executor-docking/celery_docking.py @@ -7,19 +7,16 @@ if "CELERY_BROKER_URL" in os.environ: prankweb.conf.update({ - "broker_url": - os.environ["CELERY_BROKER_URL"] + "broker_url": os.environ["CELERY_BROKER_URL"] }) elif "CELERY_BROKER_PATH" in os.environ: + folder = os.environ["CELERY_BROKER_PATH"] prankweb.conf.update({ "broker_url": "filesystem://", "broker_transport_options": { - "data_folder_in": - os.environ["CELERY_BROKER_PATH"] + "/queue/", - "data_folder_out": - os.environ["CELERY_BROKER_PATH"] + "/queue/", - "data_folder_processed": - os.environ["CELERY_BROKER_PATH"] + "/processed/" + "data_folder_in": folder + "/queue/", + "data_folder_out": folder + "/queue/", + "data_folder_processed": folder + "/processed/" }, }) diff --git a/executor-docking/run_task.py b/executor-docking/run_task.py index 5165449f..39633884 100644 --- a/executor-docking/run_task.py +++ b/executor-docking/run_task.py @@ -9,22 +9,35 @@ import json import time +""" +A class to represent a task status. +Notice that those values are written to the info.json file that is used by the frontend, +so any changes here should be reflected in the frontend as well. +""" class Status(enum.Enum): QUEUED = "queued" RUNNING = "running" FAILED = "failed" SUCCESSFUL = "successful" +""" +Method to load a json file from a given path. +""" def _load_json(path: str): with open(path, encoding="utf-8") as stream: return json.load(stream) +""" +Method to save the status file. It will update the lastChange field with the current time. +""" def _save_status_file(path: str, status: any, taskId: int): now = datetime.datetime.today() status["tasks"][taskId]["lastChange"] = now.strftime('%Y-%m-%dT%H:%M:%S') _save_json(path, status) - +""" +Method to save a json file to a given path. +""" def _save_json(path: str, content: any): path_swp = path + ".swp" if(os.path.exists(path_swp)): @@ -33,14 +46,20 @@ def _save_json(path: str, content: any): json.dump(content, stream, ensure_ascii=True) os.replace(path_swp, path) +""" +Method to get the path to the prediction file from the docking directory. +""" def get_prediction_path(docking_directory: str): #currently assuming that the docking and predictions paths are different just by the name return os.path.join(str.replace(docking_directory, "docking", "predictions"), "public", "prediction.json") +""" +Method to execute a task for a given directory and a given taskId. +""" def execute_directory_task(directory: str, taskId: int): - #print(os.listdir(os.path.join(directory, "..", "..", "..", ".."))) if not os.path.exists(directory) or not os.path.isdir(directory): return + #first update the status file status_file = os.path.join(directory, "info.json") status = _load_json(status_file) @@ -49,18 +68,17 @@ def execute_directory_task(directory: str, taskId: int): _save_status_file(status_file, status, taskId) #then load the prediction file - pred_path = get_prediction_path(directory) - prediction = _load_json(pred_path) + prediction = _load_json(get_prediction_path(directory)) - #parse the prediction file and do some calculations - obj = [] + #parse the prediction file and do some calculations - in this case just counting the number of residues per pocket + result = [] for pocket in prediction["pockets"]: - obj.append({ + result.append({ "rank": pocket["rank"], "count": len(pocket["residues"]) }) - final_obj = json.dumps(obj) + result_json = json.dumps(result) #save the result file os.makedirs(os.path.join(directory, str(taskId), "public"), exist_ok=True) @@ -68,25 +86,19 @@ def execute_directory_task(directory: str, taskId: int): with open(result_file, "w", encoding="utf-8") as stream: try: - stream.write(final_obj) + stream.write(result_json) finally: stream.flush() - #update the status file + #update the status file, reload it first to make sure we don't overwrite any changes + status = _load_json(status_file) + status["tasks"][taskId]["status"] = Status.SUCCESSFUL.value _save_status_file(status_file, status, taskId) - """ - log_file = os.path.join(directory, "logTest") - with open(log_file, "w", encoding="utf-8") as stream: - try: - stream.write(f"Starting task at {datetime.datetime.now()}") - stream.write(f"Directory: {directory}") - stream.write(f"Prediction: {prediction}") - finally: - stream.flush() - """ - +""" +Default main method. +""" def main(arguments): pass From ae0a432e9a87491a0ded6d43efb5a28976b9dd07 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 25 Mar 2023 15:20:56 +0100 Subject: [PATCH 043/154] Code cleanup for Python files --- executor-docking/run_task.py | 43 ++++++------ web-server/src/celery_client.py | 13 ++-- web-server/src/commons.py | 10 +++ web-server/src/database.py | 7 +- web-server/src/example_post.py | 13 ---- web-server/src/example_post2.py | 13 ---- web-server/src/sample_task.py | 121 +++++++++++++++++++++++--------- 7 files changed, 124 insertions(+), 96 deletions(-) create mode 100644 web-server/src/commons.py delete mode 100644 web-server/src/example_post.py delete mode 100644 web-server/src/example_post2.py diff --git a/executor-docking/run_task.py b/executor-docking/run_task.py index 39633884..4961fb58 100644 --- a/executor-docking/run_task.py +++ b/executor-docking/run_task.py @@ -9,36 +9,36 @@ import json import time -""" -A class to represent a task status. -Notice that those values are written to the info.json file that is used by the frontend, -so any changes here should be reflected in the frontend as well. -""" class Status(enum.Enum): + """ + A class to represent a task status. + Notice that those values are written to the info.json file that is used by the frontend, + so any changes here should be reflected in the frontend as well. + """ QUEUED = "queued" RUNNING = "running" FAILED = "failed" SUCCESSFUL = "successful" -""" -Method to load a json file from a given path. -""" def _load_json(path: str): + """ + Method to load a json file from a given path. + """ with open(path, encoding="utf-8") as stream: return json.load(stream) -""" -Method to save the status file. It will update the lastChange field with the current time. -""" def _save_status_file(path: str, status: any, taskId: int): + """ + Method to save the status file. It will update the lastChange field with the current time. + """ now = datetime.datetime.today() status["tasks"][taskId]["lastChange"] = now.strftime('%Y-%m-%dT%H:%M:%S') _save_json(path, status) -""" -Method to save a json file to a given path. -""" def _save_json(path: str, content: any): + """ + Method to save a json file to a given path. + """ path_swp = path + ".swp" if(os.path.exists(path_swp)): time.sleep(1) @@ -46,17 +46,17 @@ def _save_json(path: str, content: any): json.dump(content, stream, ensure_ascii=True) os.replace(path_swp, path) -""" -Method to get the path to the prediction file from the docking directory. -""" def get_prediction_path(docking_directory: str): + """ + Method to get the path to the prediction file from the docking directory. + """ #currently assuming that the docking and predictions paths are different just by the name return os.path.join(str.replace(docking_directory, "docking", "predictions"), "public", "prediction.json") -""" -Method to execute a task for a given directory and a given taskId. -""" def execute_directory_task(directory: str, taskId: int): + """ + Method to execute a task for a given directory and a given taskId. + """ if not os.path.exists(directory) or not os.path.isdir(directory): return @@ -96,9 +96,6 @@ def execute_directory_task(directory: str, taskId: int): status["tasks"][taskId]["status"] = Status.SUCCESSFUL.value _save_status_file(status_file, status, taskId) -""" -Default main method. -""" def main(arguments): pass diff --git a/web-server/src/celery_client.py b/web-server/src/celery_client.py index fc4dca51..5088b670 100644 --- a/web-server/src/celery_client.py +++ b/web-server/src/celery_client.py @@ -12,19 +12,16 @@ if "CELERY_BROKER_URL" in os.environ: prankweb.conf.update({ - "broker_url": - os.environ["CELERY_BROKER_URL"] + "broker_url": os.environ["CELERY_BROKER_URL"] }) elif "CELERY_BROKER_PATH" in os.environ: + folder = os.environ["CELERY_BROKER_PATH"] prankweb.conf.update({ "broker_url": "filesystem://", "broker_transport_options": { - "data_folder_in": - os.environ["CELERY_BROKER_PATH"] + "/queue/", - "data_folder_out": - os.environ["CELERY_BROKER_PATH"] + "/queue/", - "data_folder_processed": - os.environ["CELERY_BROKER_PATH"] + "/processed/" + "data_folder_in": folder + "/queue/", + "data_folder_out": folder + "/queue/", + "data_folder_processed": folder + "/processed/" }, }) diff --git a/web-server/src/commons.py b/web-server/src/commons.py new file mode 100644 index 00000000..f828ec46 --- /dev/null +++ b/web-server/src/commons.py @@ -0,0 +1,10 @@ +#This file contains common structures and methods used by the web-server. + +extensions = { + ".json": "application/json", + ".csv": "text/csv", + ".zip": "application/zip" +} + +if __name__ == "__main__": + pass \ No newline at end of file diff --git a/web-server/src/database.py b/web-server/src/database.py index 63d31939..33d4eaba 100644 --- a/web-server/src/database.py +++ b/web-server/src/database.py @@ -4,12 +4,7 @@ import flask import werkzeug.utils import abc - -extensions = { - ".json": "application/json", - ".csv": "text/csv", - ".zip": "application/zip", -} +from .commons import extensions class Database(metaclass=abc.ABCMeta): diff --git a/web-server/src/example_post.py b/web-server/src/example_post.py deleted file mode 100644 index 818e55d9..00000000 --- a/web-server/src/example_post.py +++ /dev/null @@ -1,13 +0,0 @@ -import requests - -# POST request -url = 'http://localhost:8020/api/v2/sample/v3/2SRC/public/result.json' - -# send some data -headers = {'Content-Type': 'multipart/form-data'} - -# send the request -r = requests.post(url, headers=headers, json={"hash": "dobryden2"}) - -# print the response -print(r.text) \ No newline at end of file diff --git a/web-server/src/example_post2.py b/web-server/src/example_post2.py deleted file mode 100644 index dd054031..00000000 --- a/web-server/src/example_post2.py +++ /dev/null @@ -1,13 +0,0 @@ -import requests - -# POST request -url = 'http://localhost:8020/api/v2/sample/v3/2SRC/post' - -# send some data -headers = {'Content-Type': 'multipart/form-data'} - -# send the request -r = requests.post(url, headers=headers, json={"hash": "dobryden", "dataD": "12345"}) - -# print the response -print(r.text) \ No newline at end of file diff --git a/web-server/src/sample_task.py b/web-server/src/sample_task.py index ddb07193..2a2c6071 100644 --- a/web-server/src/sample_task.py +++ b/web-server/src/sample_task.py @@ -8,14 +8,9 @@ import re import werkzeug.utils +from .commons import extensions from .celery_client import submit_directory_for_sample_task -extensions = { - ".json": "application/json", - ".csv": "text/csv", - ".zip": "application/zip", -} - @dataclasses.dataclass class TaskInfo: # Directory with given task. @@ -24,27 +19,40 @@ class TaskInfo: identifier: str # Data for given task. data: typing.Optional[dict] = None - # Task numeric identifier. + # Task numeric identifier - decided by the server. taskId: typing.Optional[int] = None class SampleTask: - - def __init__(self, database_name: str): - self.name = database_name - self.root = os.path.join(self._get_sample_task_directory(), self.name) + """ + Class for handling sample tasks. Prepares directories and files for given task to get executed by Celery. + """ + # Database name. + database_name: str + # Root directory for all tasks. + root_path: str - def get_file_with_post_param(self, identifier: str, file_name: str, param: str): - directory = self._get_directory(identifier) + def __init__(self, database_name: str): + """ + Constructor for SampleTask class, initializes the root path. + """ + self.database_name = database_name + self.root_path = os.path.join(self._get_sample_task_directory(), self.database_name) + + def get_file_with_post_param(self, prediction_id: str, file_name: str, data_hash: str): + """ + Gets a file from a task with a given identifier and a given file name. + """ + directory = self._get_directory(prediction_id) if directory is None or not os.path.isdir(directory): return "", 404 try: #we have to find the task id in the info file - with open(os.path.join(directory, "info.json"), "r") as f: + with open(_info_file_str(directory), "r") as f: found = False fileData = json.load(f) for task in fileData["tasks"]: - if task["data"]["hash"] == param: + if task["data"]["hash"] == data_hash: directory = os.path.join(directory, str(task["id"])) found = True break @@ -53,6 +61,8 @@ def get_file_with_post_param(self, identifier: str, file_name: str, param: str): except OSError: return "", 404 + + #if we successfully found the task directory, we can return the file, if it exists public_directory = os.path.join(directory, "public") file_name = self._secure_filename(file_name) @@ -63,18 +73,24 @@ def get_file_with_post_param(self, identifier: str, file_name: str, param: str): @staticmethod def _secure_filename(file_name: str) -> str: - """Sanitize given file name.""" + """ + Sanitizes the given file name. + """ return werkzeug.utils.secure_filename(file_name) - def post_task(self, identifier: str, data: dict): - directory = self._get_directory(identifier) + def post_task(self, prediction_id: str, data: dict): + """ + Posts a task with a given identifier and given data. + Updates/creates the info file, saves the input data and submits the task to Celery. + """ + directory = self._get_directory(prediction_id) if directory is None: return "", 404 if os.path.exists(directory): #if the info file exists, we have to append the new info to the existing file - taskinfo = TaskInfo(directory=directory, identifier=identifier, data=data) + taskinfo = TaskInfo(directory=directory, identifier=prediction_id, data=data) - with open(os.path.join(directory, "info.json"), "r+") as f: + with open(_info_file(taskinfo), "r+") as f: fileData = json.load(f) taskinfo.taskId = len(fileData["tasks"]) fileData["tasks"].append(_create_info(taskinfo)) @@ -83,16 +99,19 @@ def post_task(self, identifier: str, data: dict): _save_input(taskinfo, data) submit_directory_for_sample_task(taskinfo.directory, taskinfo.taskId) - return self._response_file(directory, "info.json") + return self._response_file(taskinfo.directory, "info.json") #else we create a new info file - taskinfo = TaskInfo(directory=directory, identifier=identifier, data=data) + taskinfo = TaskInfo(directory=directory, identifier=prediction_id, data=data) _save_input(taskinfo, data) return _create_sample_task_file(taskinfo) - def get_all_tasks(self, identifier: str): - directory = self._get_directory(identifier) + def get_all_tasks(self, prediction_id: str): + """ + Returns the info file for a given prediction. + """ + directory = self._get_directory(prediction_id) if directory is None: return "", 404 if os.path.exists(directory): @@ -100,19 +119,27 @@ def get_all_tasks(self, identifier: str): return "", 404 - def _get_directory(self, identifier: str) -> typing.Optional[str]: - """Return directory for task with given identifier.""" - if not re.match("[_,\w]+", identifier): + def _get_directory(self, prediction_id: str) -> typing.Optional[str]: + """ + Returns a directory for a task with given prediction ID. + """ + if not re.match("[_,\w]+", prediction_id): return None - directory = identifier[1:3] - return os.path.join(self.root, directory, identifier) + directory = prediction_id[1:3] + return os.path.join(self.root_path, directory, prediction_id) def _response_file(self, directory: str, file_name: str, mimetype=None): + """ + Returns a file from a given directory. + """ if mimetype is None: mimetype = self._mime_type(file_name) return flask.send_from_directory(directory, file_name, mimetype=mimetype) def _get_sample_task_directory(self) -> str: + """ + Returns the root directory for all tasks. + """ dc = os.environ.get( "PRANKWEB_DATA_DOCKING", # For local development. @@ -122,32 +149,54 @@ def _get_sample_task_directory(self) -> str: @staticmethod def _mime_type(file_name: str) -> str: - """Detect file mime type.""" + """ + Detect file mime type. + """ ext = file_name[file_name.rindex("."):] return extensions.get(ext, "text/plain") def _save_input(taskinfo: TaskInfo, data: dict): - """Save input data for given task.""" + """ + Save input data for given task. + """ os.makedirs(os.path.join(taskinfo.directory, str(taskinfo.taskId)), exist_ok=True) with open(os.path.join(taskinfo.directory, str(taskinfo.taskId), "input.json"), "w+") as f: f.write(json.dumps(data)) def _info_file(taskinfo: TaskInfo) -> str: + """ + Returns a path to info file for given task. + """ return os.path.join(taskinfo.directory, "info.json") +def _info_file_str(directory: str) -> str: + """ + Returns a path to info file for given task. + """ + return os.path.join(directory, "info.json") + def _prepare_prediction_directory(taskinfo: TaskInfo): - """Initialize content of a directory for given task.""" + """ + Initialize contents of a directory for given task. + This only happens once per prediction for one type of a task. + """ taskinfo.taskId = 0 info = _create_info(taskinfo) json_info_skeleton = {"tasks": [info], "identifier": taskinfo.identifier} _save_json(_info_file(taskinfo), json_info_skeleton) return info -def _save_json(path: str, content): +def _save_json(path: str, content: any): + """ + Saves content as a JSON file. + """ with open(path, "w", encoding="utf-8") as stream: json.dump(content, stream, ensure_ascii=True) def _create_info(taskinfo: TaskInfo): + """ + Returns a JSON object with info about one task. + """ now = datetime.datetime.today().strftime("%Y-%m-%dT%H:%M:%S") return { "id": taskinfo.taskId, @@ -158,6 +207,9 @@ def _create_info(taskinfo: TaskInfo): } def _create_sample_task_file(taskinfo: TaskInfo, force=False): + """ + Creates a directory for a task and initializes it. + """ try: os.makedirs(taskinfo.directory, exist_ok=True) except OSError: @@ -168,6 +220,9 @@ def _create_sample_task_file(taskinfo: TaskInfo, force=False): return flask.make_response(flask.jsonify(info), 201) def _prediction_can_not_be_created(taskinfo: TaskInfo): + """ + Handles a situation when a prediction can not be created. + """ # Not the best, but it is possible that someone else created # the task before us, so we wait some time, so they can finish the # initialization. From 3c3c4a881b01ca90fbbedbc6354d173d1f501658 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 25 Mar 2023 17:28:17 +0100 Subject: [PATCH 044/154] Updated documentation for .ts files --- frontend/client/tasks/client-atoms-volume.ts | 7 ++----- frontend/client/tasks/client-get-sample-tasks.ts | 14 +++++++++++++- 2 files changed, 15 insertions(+), 6 deletions(-) diff --git a/frontend/client/tasks/client-atoms-volume.ts b/frontend/client/tasks/client-atoms-volume.ts index 1b7dc965..5073a219 100644 --- a/frontend/client/tasks/client-atoms-volume.ts +++ b/frontend/client/tasks/client-atoms-volume.ts @@ -3,6 +3,7 @@ import { PocketData, ClientTaskData, ClientTaskType, Point3D } from "../custom-t import { getPocketAtomCoordinates } from "../viewer/molstar-visualise"; import qh from 'quickhull3d'; +// Cache for pocket volumes const pocketVolumes = new Map(); /** @@ -41,16 +42,12 @@ export async function computePocketVolume(plugin: PluginUIContext, pocket: Pocke const coords = getPocketAtomCoordinates(plugin, pocket.surface); - /*for(const coord of coords) { - console.log(`${coord.x} ${coord.y} ${coord.z}`); - }*/ - const points: Array> = []; coords.forEach(coord => points.push([coord.x, coord.y, coord.z])); const hull = qh(points); //compute the convex hull - const volumes = []; + const volumes: number[] = []; for(const face of hull) { volumes.push(computeTriangleVolume(coords[face[0]], coords[face[1]], coords[face[2]])); diff --git a/frontend/client/tasks/client-get-sample-tasks.ts b/frontend/client/tasks/client-get-sample-tasks.ts index 725be90a..00071840 100644 --- a/frontend/client/tasks/client-get-sample-tasks.ts +++ b/frontend/client/tasks/client-get-sample-tasks.ts @@ -1,9 +1,20 @@ import { ClientTaskData, ClientTaskType } from "../custom-types"; import { PredictionInfo } from "../prankweb-api"; +/** + * This method fetches the number of tasks associated with this prediction. + * @param prediction Prediction info + * @returns Data with a number of tasks +*/ export async function getSampleTaskCount(prediction: PredictionInfo): Promise { - const json = await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/tasks`).then(res => res.json()).catch(err => { console.log(err); setTimeout(() => getSampleTaskCount(prediction), 1000)} ); + const json = await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/tasks`) + .then(res => res.json()) + .catch(err => { + console.log(err); + setTimeout(() => getSampleTaskCount(prediction), 1000); + }); + if(json) { const numOfTasks = json["tasks"].length; return { @@ -11,6 +22,7 @@ export async function getSampleTaskCount(prediction: PredictionInfo): Promise Date: Sat, 25 Mar 2023 17:35:37 +0100 Subject: [PATCH 045/154] Dependencies update --- frontend/package-lock.json | 11234 ++++++++--------------------------- frontend/package.json | 50 +- 2 files changed, 2650 insertions(+), 8634 deletions(-) diff --git a/frontend/package-lock.json b/frontend/package-lock.json index cef869a8..b81496bb 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -1,6 +1,6 @@ { "name": "prankweb-frontend", - "lockfileVersion": 2, + "lockfileVersion": 3, "requires": true, "packages": { "": { @@ -9,18 +9,18 @@ "dependencies": { "@babel/preset-env": "^7.20.2", "@babel/preset-react": "^7.18.6", - "@emotion/react": "^11.10.5", - "@emotion/styled": "^11.10.5", - "@mui/lab": "^5.0.0-alpha.114", - "@mui/material": "^5.11.3", - "@rcsb/rcsb-saguaro": "^2.5.5", - "autoprefixer": "^10.4.13", + "@emotion/react": "^11.10.6", + "@emotion/styled": "^11.10.6", + "@mui/lab": "^5.0.0-alpha.124", + "@mui/material": "^5.11.14", + "@rcsb/rcsb-saguaro": "^2.5.9", + "autoprefixer": "^10.4.14", "babel-loader": "^9.1.2", "bootstrap": "^5.2.3", "bootstrap-icons": "^1.10.3", "clean-webpack-plugin": "^4.0.0", "copy-webpack-plugin": "^11.0.0", - "core-js": "^3.27.1", + "core-js": "^3.29.1", "cross-env": "^7.0.3", "css-loader": "^6.7.3", "express-http-proxy": "^1.6.3", @@ -28,21 +28,21 @@ "handlebars-loader": "^1.7.3", "html-loader": "^4.2.0", "html-webpack-plugin": "^5.5.0", - "mini-css-extract-plugin": "^2.7.2", - "molstar": "^3.28.0", - "postcss-loader": "^7.0.2", + "mini-css-extract-plugin": "^2.7.5", + "molstar": "^3.32.0", + "postcss-loader": "^7.1.0", "quickhull3d": "^2.1.0", "react": "^18.2.0", "react-dom": "^18.2.0", "react-draggable": "^4.4.5", - "react-icons": "^4.7.1", - "sass": "^1.57.1", - "sass-loader": "^13.2.0", - "style-loader": "^3.3.1", + "react-icons": "^4.8.0", + "sass": "^1.60.0", + "sass-loader": "^13.2.1", + "style-loader": "^3.3.2", "ts-loader": "^9.4.2", - "typescript": "^4.9.4", + "typescript": "^5.0.2", "underscore-template-loader": "^1.2.0", - "webpack": "^5.75.0", + "webpack": "^5.76.3", "webpack-cli": "^5.0.1", "webpack-merge": "^5.8.0", "webpackbar": "^5.0.2", @@ -50,19 +50,19 @@ "yaml": "^2.2.1" }, "devDependencies": { - "@babel/core": "^7.20.12", - "@babel/eslint-parser": "^7.19.1", - "@types/react": "^18.0.26", - "@types/react-dom": "^18.0.10", - "babel-jest": "^29.3.1", - "eslint": "^8.31.0", + "@babel/core": "^7.21.3", + "@babel/eslint-parser": "^7.21.3", + "@types/react": "^18.0.29", + "@types/react-dom": "^18.0.11", + "babel-jest": "^29.5.0", + "eslint": "^8.36.0", "eslint-plugin-jest": "^27.2.1", - "eslint-plugin-react": "^7.31.11", - "eslint-webpack-plugin": "^3.2.0", + "eslint-plugin-react": "^7.32.2", + "eslint-webpack-plugin": "^4.0.0", "exports-loader": "^4.0.0", "express": "^4.18.2", "imports-loader": "^4.0.1", - "webpack-dev-middleware": "^6.0.1", + "webpack-dev-middleware": "^6.0.2", "webpack-hot-middleware": "^2.25.3" } }, @@ -90,28 +90,28 @@ } }, "node_modules/@babel/compat-data": { - "version": "7.20.10", - "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.20.10.tgz", - "integrity": "sha512-sEnuDPpOJR/fcafHMjpcpGN5M2jbUGUHwmuWKM/YdPzeEDJg8bgmbcWQFUfE32MQjti1koACvoPVsDe8Uq+idg==", + "version": "7.21.0", + "resolved": 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"https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", - "dev": true + "dev": true, + "engines": { + "node": ">=10" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } } } } diff --git a/frontend/package.json b/frontend/package.json index 249434e5..f07d8c41 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -10,18 +10,18 @@ "dependencies": { "@babel/preset-env": "^7.20.2", "@babel/preset-react": "^7.18.6", - "@emotion/react": "^11.10.5", - "@emotion/styled": "^11.10.5", - "@mui/lab": "^5.0.0-alpha.114", - "@mui/material": "^5.11.3", - "@rcsb/rcsb-saguaro": "^2.5.5", - "autoprefixer": "^10.4.13", + "@emotion/react": "^11.10.6", + "@emotion/styled": "^11.10.6", + "@mui/lab": "^5.0.0-alpha.124", + "@mui/material": "^5.11.14", + "@rcsb/rcsb-saguaro": "^2.5.9", + "autoprefixer": "^10.4.14", "babel-loader": "^9.1.2", "bootstrap": "^5.2.3", "bootstrap-icons": "^1.10.3", "clean-webpack-plugin": "^4.0.0", "copy-webpack-plugin": "^11.0.0", - "core-js": "^3.27.1", + "core-js": "^3.29.1", "cross-env": "^7.0.3", "css-loader": "^6.7.3", "express-http-proxy": "^1.6.3", @@ -29,21 +29,21 @@ "handlebars-loader": "^1.7.3", "html-loader": "^4.2.0", "html-webpack-plugin": "^5.5.0", - "mini-css-extract-plugin": "^2.7.2", - "molstar": "^3.28.0", - "postcss-loader": "^7.0.2", + "mini-css-extract-plugin": "^2.7.5", + "molstar": "^3.32.0", + "postcss-loader": "^7.1.0", "quickhull3d": "^2.1.0", "react": "^18.2.0", "react-dom": "^18.2.0", "react-draggable": "^4.4.5", - "react-icons": "^4.7.1", - "sass": "^1.57.1", - "sass-loader": "^13.2.0", - "style-loader": "^3.3.1", + "react-icons": "^4.8.0", + "sass": "^1.60.0", + "sass-loader": "^13.2.1", + "style-loader": "^3.3.2", "ts-loader": "^9.4.2", - "typescript": "^4.9.4", + "typescript": "^5.0.2", "underscore-template-loader": "^1.2.0", - "webpack": "^5.75.0", + "webpack": "^5.76.3", "webpack-cli": "^5.0.1", "webpack-merge": "^5.8.0", "webpackbar": "^5.0.2", @@ -51,19 +51,19 @@ "yaml": "^2.2.1" }, "devDependencies": { - "@babel/core": "^7.20.12", - "@babel/eslint-parser": "^7.19.1", - "@types/react": "^18.0.26", - "@types/react-dom": "^18.0.10", - "babel-jest": "^29.3.1", - "eslint": "^8.31.0", + "@babel/core": "^7.21.3", + "@babel/eslint-parser": "^7.21.3", + "@types/react": "^18.0.29", + "@types/react-dom": "^18.0.11", + "babel-jest": "^29.5.0", + "eslint": "^8.36.0", "eslint-plugin-jest": "^27.2.1", - "eslint-plugin-react": "^7.31.11", - "eslint-webpack-plugin": "^3.2.0", + "eslint-plugin-react": "^7.32.2", + "eslint-webpack-plugin": "^4.0.0", "exports-loader": "^4.0.0", "express": "^4.18.2", "imports-loader": "^4.0.1", - "webpack-dev-middleware": "^6.0.1", + "webpack-dev-middleware": "^6.0.2", "webpack-hot-middleware": "^2.25.3" } } From 3dc280eaba3ea8c301ab95fa332d8ecd3255f4c4 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 25 Mar 2023 17:55:58 +0100 Subject: [PATCH 046/154] Documentation of some .ts files --- frontend/client/custom-types.ts | 8 ++++--- frontend/client/prankweb-api.ts | 40 ++++++++++++++++++++++++++++++--- 2 files changed, 42 insertions(+), 6 deletions(-) diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index dfcfcb5f..933685b9 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -207,6 +207,9 @@ export const DefaultPocketColors = [ "DA74AD" ]; +/** + * These enums/interfaces are used to represent various client/server tasks and their data. + */ export enum ClientTaskType { Volume = 0, SampleTaskCount = 1 @@ -226,13 +229,12 @@ export interface Point3D { export enum ServerTaskType { Sample = 0 } - export interface ServerTaskData { type?: ServerTaskType; id: string; created: string; lastChange: string; status: string; - data: any; //initial data - responseData: any; + data: any; //initial data + responseData: any; //response data } \ No newline at end of file diff --git a/frontend/client/prankweb-api.ts b/frontend/client/prankweb-api.ts index 0795c4ff..8683d424 100644 --- a/frontend/client/prankweb-api.ts +++ b/frontend/client/prankweb-api.ts @@ -1,9 +1,16 @@ +/** + * An enum containing the possible task statuses. + * Corresponds to values in the JSON files from the backend. + */ export enum TaskStatus { queued = "queued", successful = "successful", failed = "failed", } +/** + * Information about a prediction, as returned by the API. + */ export interface PredictionInfo { id: string; database: string; @@ -17,18 +24,27 @@ export interface PredictionInfo { } } +/** + * A wrapper around the response from the API containing the status code and the content. + */ export interface HttpWrap { statusCode: number; content: T | null; } +/** + * A method to fetch the prediction info from the API. + * @param database The database to fetch the prediction from. + * @param id The ID of the prediction. + * @returns A promise that resolves to the prediction info. + */ export async function fetchPrediction( database: string, id: string ): Promise> { // We need to navigate to the root, and then we can request the data. const url = getApiEndpoint(database, id); const response = await fetch(url); - let result; + var result; try { result = await response.json(); } catch { @@ -43,10 +59,22 @@ export async function fetchPrediction( }; } -export function getApiEndpoint(database: string, code: string) { - return `./api/v2/prediction/${database}/${code.toUpperCase()}`; +/** + * A method to get the API endpoint for a prediction. + * @param database The database to fetch the prediction from. + * @param id The ID of the prediction. + * @returns An URL to the API endpoint for the prediction. + */ +export function getApiEndpoint(database: string, id: string) { + return `./api/v2/prediction/${database}/${id.toUpperCase()}`; } +/** + * A method to fetch the prediction log from the API. + * @param database The database to fetch the prediction from. + * @param id The ID of the prediction. + * @returns A promise that resolves to the prediction log. + */ export async function fetchPredictionLog( database: string, id: string ): Promise { @@ -58,6 +86,12 @@ export async function fetchPredictionLog( return response.text(); } +/** + * A method to fetch the whole prediction ZIP file from the API. + * @param database The database to fetch the prediction from. + * @param id The ID of the prediction. + * @returns An URL to the ZIP file. + */ export function getApiDownloadUrl({database, id}: PredictionInfo) { return `./api/v2/prediction/${database}/${id}/public/prankweb.zip`; } From 6c56639fbdb39c9710f923d9e8816d09d3c119a0 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 25 Mar 2023 19:13:42 +0100 Subject: [PATCH 047/154] Documentation update --- frontend/client/viewer/application.tsx | 26 +++++++++++++---- frontend/client/viewer/data-loader.ts | 11 +++++++ frontend/client/viewer/molstar-visualise.ts | 10 +++++++ frontend/client/viewer/rcsb-visualise.ts | 32 ++++++++++----------- frontend/client/viewer/viewer.ts | 15 +++++++--- 5 files changed, 68 insertions(+), 26 deletions(-) diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index d3e7af8f..02b91d92 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -18,6 +18,10 @@ import 'molstar/lib/mol-plugin-ui/skin/light.scss'; import { RcsbFv, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro"; import { highlightSurfaceAtomsInViewerLabelId, overPaintPolymer, updatePolymerView, showPocketInCurrentRepresentation } from './molstar-visualise'; +/** + * A function to render the actual PrankWeb viewer. + * @param predictionInfo Information about the prediction to be visualised. + */ export async function renderProteinView(predictionInfo: PredictionInfo) { const wrapper = document.getElementById('application-molstar')!; const MolstarPlugin = await createPluginUI(wrapper, { @@ -48,6 +52,9 @@ export async function renderProteinView(predictionInfo: PredictionInfo) { pocketsView={PocketsViewType.Surface_Atoms_Color} polymerView={PolymerViewType.Gaussian_Surface} polymerColor={PolymerColorType.Clean}/>); } +/** + * A React component containing all of the components other than the Mol* and RCSB plugins. + */ export class Application extends React.Component { state = { @@ -59,7 +66,7 @@ export class Application extends React.Component res.json()).catch(err => console.log(err)); - //TODO: handle error in a better way, but we do not really care if the poll fails sometimes + let json = await fetch(`./api/v2/sample/${this.props.predictionInfo.database}/${this.props.predictionInfo.id}/tasks`, {cache: "no-store"}) + .then(res => res.json()) + .catch(); //we could handle the error in a better way, but we do not care if the poll fails sometimes if(json) { //append the new tasks to the existing ones let newTasks: ServerTaskData[] = this.state.serverTasks; @@ -203,11 +218,12 @@ export class Application extends React.Component this.getTaskList(), 7000); } render() { - console.log("Application::render"); + //console.log("Application::render"); if (this.state.isLoading) { return (
    diff --git a/frontend/client/viewer/data-loader.ts b/frontend/client/viewer/data-loader.ts index 2deb32aa..39abb92f 100644 --- a/frontend/client/viewer/data-loader.ts +++ b/frontend/client/viewer/data-loader.ts @@ -46,6 +46,12 @@ export async function sendDataToPlugins(molstarPlugin: PluginUIContext, database return [prediction, rcsbPlugin]; } +/** + * Finds the indices of the residues in the structure. + * @param toBeFound Residues to be found + * @param allResidues All residues in the structure + * @returns Indices of the residues in the structure + */ function getResidueIndices(toBeFound: string[], allResidues: string[]) { let final : number[] = []; toBeFound.forEach(residue => { @@ -91,6 +97,11 @@ function computePocketConservationAndAFAverage(data: PredictionData) { return data; } +/** + * Attempts to download a JSON file from a given URL. + * @param url URL + * @returns JSON file, if successful + */ async function downloadJsonFromUrl(url: string) { try { const response = await fetch(url, { diff --git a/frontend/client/viewer/molstar-visualise.ts b/frontend/client/viewer/molstar-visualise.ts index dc81ed4f..dd470949 100644 --- a/frontend/client/viewer/molstar-visualise.ts +++ b/frontend/client/viewer/molstar-visualise.ts @@ -141,6 +141,7 @@ export function updatePolymerView(value: PolymerViewType, plugin: PluginUIContex } } + //lastly, show only the selected representation for(const element of polymerRepresentations) { if(element.type === value) { setSubtreeVisibility(plugin.state.data, element.representation.ref, false); @@ -384,6 +385,11 @@ async function overPaintPocketsWithAlphaFold(plugin: PluginUIContext, prediction } } +/** + * Computes the normalized conservation scores and saves them in the global conservationNormalized variable. + * @param prediction Prediction data + * @returns void + */ function computeNormalizedConservation(prediction: PredictionData) { if(!prediction.structure.scores.conservation) return; //by the definition of conservation scoring the maximum is log_2(20) @@ -581,6 +587,10 @@ async function createPocketFromJsonByAtoms(plugin: PluginUIContext, structure: S const atomsSelection = group2.apply(StateTransforms.Model.StructureSelectionFromExpression, {expression: atomsExpression}); const color = Number("0x" + pocket.color); + //NOTE: the following piece of code could be transformed into a function, + //for better readability & clarity it is not done here + //moreover, the function would potentially depend on internal Mol* implementation + //the first one selects the whole residues and does not color them -> for overpaints const repr_surface : StateObjectSelector = wholeResiduesSelection.apply(StateTransforms.Representation.StructureRepresentation3D, createStructureRepresentationParams(plugin, structure.data, { type: 'gaussian-surface', diff --git a/frontend/client/viewer/rcsb-visualise.ts b/frontend/client/viewer/rcsb-visualise.ts index 23e785cb..ae0135b0 100644 --- a/frontend/client/viewer/rcsb-visualise.ts +++ b/frontend/client/viewer/rcsb-visualise.ts @@ -3,6 +3,7 @@ import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionData, AlphaFoldColorsRcsb, AlphaFoldThresholdsRcsb, DefaultPocketColors } from '../custom-types'; import { highlightInViewerLabelIdWithoutFocus, highlightInViewerAuthId } from "./molstar-visualise"; +//contains the last highlighted element let lastElement: number = -1; /** @@ -66,13 +67,11 @@ function calculateViewerWidth() { * @param event Mouse event */ function elementClicked(predictionData: PredictionData, molstarPlugin: PluginUIContext, trackData?: RcsbFvTrackDataElementInterface, event?: MouseEvent) { - if(trackData) { - if(predictionData) { - let element = predictionData.structure.indices[trackData.begin - 1]; - if(element) { - let id = Number(element.substring(element.indexOf('_') + 1)); - highlightInViewerAuthId(molstarPlugin, element[0], [id]); - } + if(trackData && predictionData) { + let element = predictionData.structure.indices[trackData.begin - 1]; + if(element) { + let id = Number(element.substring(element.indexOf('_') + 1)); + highlightInViewerAuthId(molstarPlugin, element[0], [id]); } } } @@ -87,15 +86,13 @@ function onHighlight(data: PredictionData, molstarPlugin: PluginUIContext, track if(trackData.length === 0) return; lastElement = trackData[0].begin; - //first attempt to debounce the function + //100ms debounce setTimeout(() => { - if(trackData && trackData.length > 0 && lastElement === trackData[0].begin) { - if(data) { - let element = data.structure.indices[trackData[0].begin - 1]; - if(element) { - let id = Number(element.substring(element.indexOf('_') + 1)); - highlightInViewerLabelIdWithoutFocus(molstarPlugin, element[0], [id]); - } + if(data && trackData && trackData.length > 0 && lastElement === trackData[0].begin) { + let element = data.structure.indices[trackData[0].begin - 1]; + if(element) { + let id = Number(element.substring(element.indexOf('_') + 1)); + highlightInViewerLabelIdWithoutFocus(molstarPlugin, element[0], [id]); } } }, 100); @@ -113,7 +110,7 @@ function createRowConfigDataRcsb(data: PredictionData) { trackHeight: 20, trackColor: "#F9F9F9", displayType: RcsbFvDisplayTypes.SEQUENCE, - nonEmptyDisplay: true, //??? + nonEmptyDisplay: true, rowTitle: "SEQUENCE", trackData: [{ begin: 1, @@ -126,7 +123,7 @@ function createRowConfigDataRcsb(data: PredictionData) { const bindingData : RcsbFvTrackData = []; //create the blocks - //seems complicated but we need to create the "holes" as well + //we need to create the "holes" as well for(let i = 0; i < data.structure.binding.length; i++) { let firstElement = data.structure.binding[i]; if(i < data.structure.binding.length - 1) { @@ -159,6 +156,7 @@ function createRowConfigDataRcsb(data: PredictionData) { for(let y = 0; y < data.pockets.length; y++) { //first we need to assign a color to a pocket data.pockets[y].color = pickColor(y); + //create the blocks with the same principle... for(let i = 0; i < data.pockets[y].residues.length; i++) { let firstElement = data.pockets[y].residues[i]; diff --git a/frontend/client/viewer/viewer.ts b/frontend/client/viewer/viewer.ts index bb4c235c..3219891d 100644 --- a/frontend/client/viewer/viewer.ts +++ b/frontend/client/viewer/viewer.ts @@ -1,26 +1,33 @@ import { renderProteinView } from "./application"; -import "../bootstrap.scss"; +//import "../bootstrap.scss"; import { fetchPrediction } from "../prankweb-api"; +/** + * A function that handles wrong input. + */ function handleError() { document.getElementById('message')!.style.display = 'block'; document.getElementById('message-text')!.innerHTML = "
    Incomplete or incorrect task specification.
    Please go back to the home page."; document.getElementById('analyze')!.style.display = 'none'; } +/** + * A function that initializes the viewer. + * @returns void + */ async function initialize() { const params = new URLSearchParams(window.location.search); - let id = params.get("id"); - let database = params.get("database"); + const id = params.get("id"); + const database = params.get("database"); if(id === null || database === null) { handleError(); return; } - let predictionInfo = await fetchPrediction(database, id); + const predictionInfo = await fetchPrediction(database, id); if(predictionInfo.content === null) { handleError(); From 0fa693d00c1e274777a07ee24c87ad5c22c92c14 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 25 Mar 2023 19:35:32 +0100 Subject: [PATCH 048/154] Revert Bootstrap change --- frontend/client/viewer/viewer.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/client/viewer/viewer.ts b/frontend/client/viewer/viewer.ts index 3219891d..7f40b2d4 100644 --- a/frontend/client/viewer/viewer.ts +++ b/frontend/client/viewer/viewer.ts @@ -1,6 +1,6 @@ import { renderProteinView } from "./application"; -//import "../bootstrap.scss"; +import "../bootstrap.scss"; import { fetchPrediction } from "../prankweb-api"; /** From a2fde087b02f83d13b059b3b59c3d878e2f65f84 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 25 Mar 2023 23:06:53 +0100 Subject: [PATCH 049/154] Frontend code refactor --- frontend/client/custom-types.ts | 13 ++- ...toms-volume.ts => client-atoms-volume.tsx} | 12 ++- ...e-tasks.ts => client-get-sample-tasks.tsx} | 12 ++- frontend/client/tasks/server-sample-task.tsx | 68 +++++++++++++++ frontend/client/viewer/application.tsx | 15 +++- .../viewer/components/pocket-client-task.tsx | 35 ++------ .../viewer/components/pocket-details.tsx | 26 +----- .../components/pocket-dialog-details.tsx | 53 ++++++++++++ .../components/pocket-running-tasks.tsx | 10 +-- ...sx => pocket-server-parametrized-task.tsx} | 82 +++---------------- .../client/viewer/components/task-list.tsx | 14 ++-- web-server/src/sample_task.py | 6 +- 12 files changed, 200 insertions(+), 146 deletions(-) rename frontend/client/tasks/{client-atoms-volume.ts => client-atoms-volume.tsx} (87%) rename frontend/client/tasks/{client-get-sample-tasks.ts => client-get-sample-tasks.tsx} (76%) create mode 100644 frontend/client/tasks/server-sample-task.tsx create mode 100644 frontend/client/viewer/components/pocket-dialog-details.tsx rename frontend/client/viewer/components/{pocket-server-task.tsx => pocket-server-parametrized-task.tsx} (54%) diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index 933685b9..0e3ddc24 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -217,7 +217,7 @@ export enum ClientTaskType { export interface ClientTaskData { type?: ClientTaskType; - numericValue?: number; + data: any; } export interface Point3D { @@ -229,12 +229,17 @@ export interface Point3D { export enum ServerTaskType { Sample = 0 } + export interface ServerTaskData { - type?: ServerTaskType; + type: ServerTaskType; + data: ServerTaskDataContents; +} + +export interface ServerTaskDataContents { id: string; created: string; lastChange: string; status: string; - data: any; //initial data + initialData: any; //initial data responseData: any; //response data -} \ No newline at end of file +} \ No newline at end of file diff --git a/frontend/client/tasks/client-atoms-volume.ts b/frontend/client/tasks/client-atoms-volume.tsx similarity index 87% rename from frontend/client/tasks/client-atoms-volume.ts rename to frontend/client/tasks/client-atoms-volume.tsx index 5073a219..a662280e 100644 --- a/frontend/client/tasks/client-atoms-volume.ts +++ b/frontend/client/tasks/client-atoms-volume.tsx @@ -1,3 +1,5 @@ +import React from "react"; + import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PocketData, ClientTaskData, ClientTaskType, Point3D } from "../custom-types"; import { getPocketAtomCoordinates } from "../viewer/molstar-visualise"; @@ -35,7 +37,7 @@ export async function computePocketVolume(plugin: PluginUIContext, pocket: Pocke if(pocketVolumes.has(pocket.name)) { return { - "numericValue": pocketVolumes.get(pocket.name), + "data": pocketVolumes.get(pocket.name), "type": ClientTaskType.Volume }; } @@ -58,9 +60,15 @@ export async function computePocketVolume(plugin: PluginUIContext, pocket: Pocke pocketVolumes.set(pocket.name, finalVolume); const data: ClientTaskData = { - "numericValue": finalVolume, + "data": finalVolume, "type": ClientTaskType.Volume }; return data; } + +export function renderOnTaskVolumeCompleted(data: ClientTaskData) { + return ( + {data.data} + ); +} \ No newline at end of file diff --git a/frontend/client/tasks/client-get-sample-tasks.ts b/frontend/client/tasks/client-get-sample-tasks.tsx similarity index 76% rename from frontend/client/tasks/client-get-sample-tasks.ts rename to frontend/client/tasks/client-get-sample-tasks.tsx index 00071840..1f8cb1ba 100644 --- a/frontend/client/tasks/client-get-sample-tasks.ts +++ b/frontend/client/tasks/client-get-sample-tasks.tsx @@ -1,3 +1,5 @@ +import React from "react"; + import { ClientTaskData, ClientTaskType } from "../custom-types"; import { PredictionInfo } from "../prankweb-api"; @@ -18,13 +20,19 @@ export async function getSampleTaskCount(prediction: PredictionInfo): Promise{data.data} + ); } \ No newline at end of file diff --git a/frontend/client/tasks/server-sample-task.tsx b/frontend/client/tasks/server-sample-task.tsx new file mode 100644 index 00000000..a14d222b --- /dev/null +++ b/frontend/client/tasks/server-sample-task.tsx @@ -0,0 +1,68 @@ +import React from "react"; + +import { PredictionInfo } from "../prankweb-api"; +import { PocketData } from "../custom-types"; +import { ServerTaskData } from "../custom-types"; + +export async function computeSampleTaskOnBackend(firstFetch: boolean, prediction: PredictionInfo, pocket: PocketData, hash: string, serverTasks: ServerTaskData[]) { + if(firstFetch) { + await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/post`, { + method: 'POST', + headers: { + 'Accept': 'application/json', + 'Content-Type': 'application/json' + }, + body: JSON.stringify({ + "hash": hash, + "pocket": pocket.rank, + }), + }).then((res) => { + //wait 3 seconds before checking if the task is finished + setTimeout(() => {}, 3000); + return res.json(); + } + ).catch(err => { + console.log(err); + setTimeout(() => computeSampleTaskOnBackend(true, prediction, pocket, hash, serverTasks), 1000); //repeat the request + }); + } + + //check if the task is finished + let matchingTasks = (serverTasks.filter((e: ServerTaskData) => e.data.initialData.hash === hash && e.data.initialData.pocket === pocket.rank)); + + if(matchingTasks.length === 0) { + setTimeout(() => computeSampleTaskOnBackend(false, prediction, pocket, hash, serverTasks), 1000); //repeat the request + return; + } + + if(matchingTasks[0].data.status !== "successful") { + setTimeout(() => computeSampleTaskOnBackend(false, prediction, pocket, hash, serverTasks), 1000); //repeat the request + return; + } + + const data = await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/public/result.json`, { + method: 'POST', + headers: { + 'Accept': 'application/json', + 'Content-Type': 'application/json' + }, + body: JSON.stringify({ + "hash": hash, + } + )}).then(res => res.json()).catch(err => console.log(err)); + if(!data) { + setTimeout(() => computeSampleTaskOnBackend(false, prediction, pocket, hash, serverTasks), 3000); //repeat the request + return; + } + + matchingTasks[0].data.responseData = data; + return data; +} + +export function renderOnServerSampleTaskCompleted(responseData: any, pocket: PocketData) { + return ( + + {responseData.filter((e: any) => e["rank"] == pocket.rank)[0]["count"]} + + ); +} \ No newline at end of file diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 02b91d92..076fbf26 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -10,7 +10,7 @@ import PocketList from "./components/pocket-list"; import TaskList from "./components/task-list"; import { sendDataToPlugins } from './data-loader'; -import { PocketsViewType, PolymerColorType, PolymerViewType, PredictionData, ReactApplicationProps, ReactApplicationState, ServerTaskData } from "../custom-types"; +import { PocketsViewType, PolymerColorType, PolymerViewType, PredictionData, ReactApplicationProps, ReactApplicationState, ServerTaskData, ServerTaskType } from "../custom-types"; import { DefaultPluginUISpec } from 'molstar/lib/mol-plugin-ui/spec'; import { createPluginUI } from 'molstar/lib/mol-plugin-ui'; @@ -205,15 +205,22 @@ export class Application extends React.Component res.json()) - .catch(); //we could handle the error in a better way, but we do not care if the poll fails sometimes + .catch(err => { + setTimeout(() => this.getTaskList(), 7000); + return; + }); //we could handle the error in a better way, but we do not care if the poll fails sometimes if(json) { //append the new tasks to the existing ones let newTasks: ServerTaskData[] = this.state.serverTasks; json["tasks"].forEach((task: any) => { - if(!newTasks.find((t: any) => t.id === task.id)) { - newTasks.push(task); + if(!newTasks.find((t: ServerTaskData) => t.data.id === task.id)) { + newTasks.push({ + "type": ServerTaskType.Sample, + "data": task + }); } }); this.setState({serverTasks: newTasks}); diff --git a/frontend/client/viewer/components/pocket-client-task.tsx b/frontend/client/viewer/components/pocket-client-task.tsx index 4d7cebb1..9af0c146 100644 --- a/frontend/client/viewer/components/pocket-client-task.tsx +++ b/frontend/client/viewer/components/pocket-client-task.tsx @@ -1,7 +1,6 @@ import React from "react"; import { LoadingButton } from '@mui/lab'; -import { computePocketVolume } from '../../tasks/client-atoms-volume'; -import { getSampleTaskCount } from "../../tasks/client-get-sample-tasks"; + import { ClientTaskData, ClientTaskType, PocketData } from '../../custom-types'; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; @@ -13,7 +12,9 @@ export default class PocketClientTask extends React.Component pocket: PocketData, plugin: PluginUIContext, taskType: ClientTaskType, - prediction: PredictionInfo + prediction: PredictionInfo, + compute: () => Promise, + renderOnComplete: (data: ClientTaskData) => JSX.Element }, { data: ClientTaskData | undefined, //this may be changed to any type (the best way is to define some interface) computed: boolean, @@ -27,21 +28,10 @@ export default class PocketClientTask extends React.Component this.state = {loading: false, computed: false, data: undefined}; } + async clickCompute() { - let json: ClientTaskData | null = null; - switch(this.props.taskType) { - case ClientTaskType.Volume: - json = await computePocketVolume(this.props.plugin, this.props.pocket); - this.setState({loading: false, computed: true, data: json}); - break; - case ClientTaskType.SampleTaskCount: - json = await getSampleTaskCount(this.props.prediction); - this.setState({loading: false, computed: true, data: json}); - break; - default: - //will not happen - break; - } + const json = await this.props.compute(); + this.setState({loading: false, computed: true, data: json}); } async handleClick() { @@ -70,16 +60,7 @@ export default class PocketClientTask extends React.Component } { - this.state.computed && - this.state.data!.type === ClientTaskType.Volume && - {this.state.data!.numericValue} - // here the data should be properly formatted based on the returned type - // i.e for number arrays we could potentially add a diagram instead of just showing a number - } - { - this.state.computed && - this.state.data!.type === ClientTaskType.SampleTaskCount && - {this.state.data!.numericValue} + this.state.computed && this.props.renderOnComplete(this.state.data!) }
    ); diff --git a/frontend/client/viewer/components/pocket-details.tsx b/frontend/client/viewer/components/pocket-details.tsx index 61869620..428cb007 100644 --- a/frontend/client/viewer/components/pocket-details.tsx +++ b/frontend/client/viewer/components/pocket-details.tsx @@ -1,11 +1,9 @@ import React from "react"; -import { ClientTaskType, PocketData, ServerTaskData, ServerTaskType } from "../../custom-types"; +import { PocketData, ServerTaskData } from "../../custom-types"; import PocketProperty from "./pocket-property"; -import PocketClientTask from "./pocket-client-task"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; -import PocketServerTask from "./pocket-server-task"; import { PredictionInfo } from "../../prankweb-api"; -import RunningTasks from "./pocket-running-tasks"; +import PocketDialogDetails from "./pocket-dialog-details"; export default class PocketDetails extends React.Component <{ @@ -14,25 +12,13 @@ export default class PocketDetails extends React.Component plugin: PluginUIContext, prediction: PredictionInfo serverTasks: ServerTaskData[] - }, { - serverTasks: ServerTaskData[] - //updated: boolean - }> { + }, {}> { constructor(props: any) { super(props); - this.state = {serverTasks: this.props.serverTasks}; this.checkValidValue = this.checkValidValue.bind(this); } - componentDidUpdate(prevProps: any){ - if(prevProps.serverTasks !== this.props.serverTasks){ - this.setState({ - serverTasks: this.props.serverTasks - }); - } - } - checkValidValue(data: number | undefined) { //here double equal sign is used intentionally if(data == undefined || data == 0) return false; @@ -49,11 +35,7 @@ export default class PocketDetails extends React.Component {this.checkValidValue(pocket.avgConservation) && } {this.checkValidValue(pocket.avgAlphaFold) && } - {this.props.inDialog && } - {this.props.inDialog && } - {this.props.inDialog && } - {this.props.inDialog && } - {this.props.inDialog && } + {this.props.inDialog && }
    ); } diff --git a/frontend/client/viewer/components/pocket-dialog-details.tsx b/frontend/client/viewer/components/pocket-dialog-details.tsx new file mode 100644 index 00000000..9cde49f4 --- /dev/null +++ b/frontend/client/viewer/components/pocket-dialog-details.tsx @@ -0,0 +1,53 @@ +import React from "react"; + +import PocketProperty from "./pocket-property"; +import PocketClientTask from "./pocket-client-task"; +import PocketServerParametrizedTask from "./pocket-server-parametrized-task"; +import RunningTasks from "./pocket-running-tasks"; + +import { computePocketVolume, renderOnTaskVolumeCompleted } from "../../tasks/client-atoms-volume"; +import { getSampleTaskCount, renderOnTaskSampleTasksCountCompleted } from "../../tasks/client-get-sample-tasks"; + +import { PocketData, ServerTaskData, ClientTaskType, ServerTaskType } from "../../custom-types"; +import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; +import { PredictionInfo } from "../../prankweb-api"; +import { computeSampleTaskOnBackend, renderOnServerSampleTaskCompleted } from "../../tasks/server-sample-task"; + +export default class PocketDialogDetails extends React.Component + <{ + pocket: PocketData, + inDialog: boolean, + plugin: PluginUIContext, + prediction: PredictionInfo + serverTasks: ServerTaskData[] + }, { + serverTasks: ServerTaskData[] + }> { + + constructor(props: any) { + super(props); + this.state = {serverTasks: this.props.serverTasks}; + } + + componentDidUpdate(prevProps: any) { + if(prevProps.serverTasks !== this.props.serverTasks){ + this.setState({ + serverTasks: this.props.serverTasks + }); + } + } + + render() { + return ( +
    + + computePocketVolume(this.props.plugin, this.props.pocket)} renderOnComplete={renderOnTaskVolumeCompleted} /> + getSampleTaskCount(this.props.prediction)} renderOnComplete={renderOnTaskSampleTasksCountCompleted}/> + computeSampleTaskOnBackend(true, this.props.prediction, this.props.pocket, hash, this.props.serverTasks)} + renderOnComplete={(data, pocket) => renderOnServerSampleTaskCompleted(data, pocket)} /> + +
    + ); + } +} \ No newline at end of file diff --git a/frontend/client/viewer/components/pocket-running-tasks.tsx b/frontend/client/viewer/components/pocket-running-tasks.tsx index 87c23d96..bfa00d86 100644 --- a/frontend/client/viewer/components/pocket-running-tasks.tsx +++ b/frontend/client/viewer/components/pocket-running-tasks.tsx @@ -17,13 +17,13 @@ export default class RunningTasks extends React.Component return (
    {this.props.inDialog && this.props.serverTasks.map((e: ServerTaskData, index) => { - if(e.responseData && e.data.pocket === this.props.pocket.rank) { - return p.rank === this.props.pocket.rank)?.count + if(e.data.responseData && e.data.initialData.pocket === this.props.pocket.rank) { + return p.rank === this.props.pocket.rank)?.count }/> } - else if(e.data.pocket === this.props.pocket.rank && (e.status === "running" || e.status === "queued")) { - return + else if(e.data.responseData && e.data.initialData.pocket === this.props.pocket.rank && (e.data.status === "running" || e.data.status === "queued")) { + return } })}
    diff --git a/frontend/client/viewer/components/pocket-server-task.tsx b/frontend/client/viewer/components/pocket-server-parametrized-task.tsx similarity index 54% rename from frontend/client/viewer/components/pocket-server-task.tsx rename to frontend/client/viewer/components/pocket-server-parametrized-task.tsx index 2a558c67..f5fcd881 100644 --- a/frontend/client/viewer/components/pocket-server-task.tsx +++ b/frontend/client/viewer/components/pocket-server-parametrized-task.tsx @@ -5,7 +5,7 @@ import { PocketData, ServerTaskData, ServerTaskType } from '../../custom-types'; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; -export default class PocketServerTask extends React.Component +export default class PocketServerParametrizedTask extends React.Component <{ title: string, inDialog: boolean, // not needed now. but in other cases the implementation could be potentially different. @@ -13,7 +13,10 @@ export default class PocketServerTask extends React.Component plugin: PluginUIContext, taskType: ServerTaskType, prediction: PredictionInfo, - serverTasks: ServerTaskData[] + serverTasks: ServerTaskData[], + modalDescription: string, + compute: (hash: string) => Promise + renderOnComplete: (responseData: any, pocket: PocketData) => JSX.Element }, { responseData: any, //this may be changed to any type (the best way is to define some interface) computed: boolean, @@ -32,68 +35,12 @@ export default class PocketServerTask extends React.Component } async clickCompute(firstFetch: boolean = true) { - switch(this.props.taskType) { - case ServerTaskType.Sample: - if(firstFetch) { - // compute a hash - const hash = this.state.formData; - this.setState({hash: hash}); + const hash = this.state.formData; + this.setState({hash: hash}); - //if not, create a new task - await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/post`, { - method: 'POST', - headers: { - 'Accept': 'application/json', - 'Content-Type': 'application/json' - }, - body: JSON.stringify({ - "hash": hash, - "pocket": this.props.pocket.rank, - }), - }).then(res => res.json()).catch(err => { - console.log(err); - this.clickCompute(true); //repeat the request - }); - } - - //check if the task is finished - let matchingTasks = (this.props.serverTasks.filter((e: any) => e["data"]["hash"] === this.state.hash && e["data"]["pocket"] === this.props.pocket.rank)); - - if(matchingTasks.length === 0) { - setTimeout(() => this.clickCompute(false), 1000); - return; - } - - if(matchingTasks[0]["status"] !== "successful") { - setTimeout(() => this.clickCompute(false), 1000); - return; - } - - const data = await fetch(`./api/v2/sample/${this.props.prediction.database}/${this.props.prediction.id}/public/result.json`, { - method: 'POST', - headers: { - 'Accept': 'application/json', - 'Content-Type': 'application/json' - }, - body: JSON.stringify({ - "hash": this.state.hash, - } - )}).then(res => res.json()).catch(err => console.log(err)); - if(!data) { - setTimeout(() => this.clickCompute(false), 3000); - return; - } - //TODO: handle error in a better way - const dataWrapper = { - "type": ServerTaskType.Sample, - "pockets": data - } - matchingTasks[0]["responseData"] = dataWrapper; - this.setState({loading: false, computed: true, responseData: dataWrapper}); - break; - default: - //will not happen - break; + const data = await this.props.compute(hash); + if(data) { + this.setState({loading: false, computed: true, responseData: data}); } } @@ -135,7 +82,7 @@ export default class PocketServerTask extends React.Component - Enter the molecule for docking in pocket {this.props.pocket.rank} (SMILES or PDB) + {this.props.modalDescription} - {this.state.responseData!["pockets"].filter((e: any) => e["rank"] == this.props.pocket.rank)[0]["count"]} - - // here the data should be properly formatted based on the returned type - // i.e for number arrays we could potentially add a diagram instead of just showing a number + this.props.renderOnComplete(this.state.responseData!, this.props.pocket) }
    ); diff --git a/frontend/client/viewer/components/task-list.tsx b/frontend/client/viewer/components/task-list.tsx index 4058440d..65e0fd70 100644 --- a/frontend/client/viewer/components/task-list.tsx +++ b/frontend/client/viewer/components/task-list.tsx @@ -66,15 +66,15 @@ class TaskListContent extends React.Component<{ render() { return (
      - {this.props.tasks.map((task: any, index: any) => { - if(task["status"] === "successful") { - return
    • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]}`}
    • + {this.props.tasks.map((task: ServerTaskData, index: number) => { + if(task.data["status"] === "successful") { + return
    • {`${task.data["id"]} ${task.data.initialData["hash"]} ${task.data.lastChange}`}
    • } - else if(task["status"] === "running") { - return
    • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]} running`}
    • + else if(task.data["status"] === "running") { + return
    • {`${task.data["id"]} ${task.data.initialData["hash"]} ${task.data.lastChange} running`}
    • } - else if(task["status"] === "queued") { - return
    • {`${task["id"]} ${task["data"]["hash"]} ${task["lastChange"]} queued`}
    • + else if(task.data["status"] === "queued") { + return
    • {`${task.data["id"]} ${task.data.initialData["hash"]} ${task.data.lastChange} queued`}
    • } })}
    diff --git a/web-server/src/sample_task.py b/web-server/src/sample_task.py index 065a7485..40981b35 100644 --- a/web-server/src/sample_task.py +++ b/web-server/src/sample_task.py @@ -52,7 +52,7 @@ def get_file_with_post_param(self, prediction_id: str, file_name: str, data_hash found = False fileData = json.load(f) for task in fileData["tasks"]: - if task["data"]["hash"] == data_hash: + if task["initialData"]["hash"] == data_hash: directory = os.path.join(directory, str(task["id"])) found = True break @@ -94,7 +94,7 @@ def post_task(self, prediction_id: str, data: dict): fileData = json.load(f) #we check if the task already exists for task in fileData["tasks"]: - if task["data"] == data: + if task["initialData"] == data: return self._response_file(directory, "info.json") taskinfo.taskId = len(fileData["tasks"]) @@ -208,7 +208,7 @@ def _create_info(taskinfo: TaskInfo): "created": now, "lastChange": now, "status": "queued", - "data": taskinfo.data + "initialData": taskinfo.data } def _create_sample_task_file(taskinfo: TaskInfo, force=False): From fad6e41f4036ac1ae7221b7d0fc319df789f34c2 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sun, 26 Mar 2023 14:28:30 +0200 Subject: [PATCH 050/154] Documentation changes --- frontend/client/custom-types.ts | 2 +- frontend/client/tasks/client-atoms-volume.tsx | 9 +++++++-- frontend/client/tasks/client-get-sample-tasks.tsx | 7 ++++++- .../client/viewer/components/draggable-dialog.tsx | 10 ++++++++-- .../client/viewer/components/pocket-client-task.tsx | 12 +++++++++--- .../client/viewer/components/pocket-details.tsx | 13 +++++++++---- frontend/client/viewer/components/pocket-list.tsx | 4 ++++ .../client/viewer/components/pocket-property.tsx | 3 +++ 8 files changed, 47 insertions(+), 13 deletions(-) diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index 0e3ddc24..1bd6c518 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -216,7 +216,7 @@ export enum ClientTaskType { } export interface ClientTaskData { - type?: ClientTaskType; + type: ClientTaskType; data: any; } diff --git a/frontend/client/tasks/client-atoms-volume.tsx b/frontend/client/tasks/client-atoms-volume.tsx index a662280e..e2c3a2be 100644 --- a/frontend/client/tasks/client-atoms-volume.tsx +++ b/frontend/client/tasks/client-atoms-volume.tsx @@ -9,7 +9,7 @@ import qh from 'quickhull3d'; const pocketVolumes = new Map(); /** - * This method computes the volume of a triangle in 3D space. + * Computes the volume of a triangle in 3D space. * https://stackoverflow.com/questions/1406029/ * @param p1 First point of the triangle * @param p2 Second point of the triangle @@ -28,7 +28,7 @@ function computeTriangleVolume(p1: Point3D, p2: Point3D, p3: Point3D) { } /** - * This method computes the volume of a pocket. + * Computes the volume of a pocket. * @param plugin Mol* plugin * @param pocket Pocket data * @returns Computed pocket volume @@ -67,6 +67,11 @@ export async function computePocketVolume(plugin: PluginUIContext, pocket: Pocke return data; } +/** + * Renders the final data of this task as a JSX element. + * @param data Data to render + * @returns JSX element + */ export function renderOnTaskVolumeCompleted(data: ClientTaskData) { return ( {data.data} diff --git a/frontend/client/tasks/client-get-sample-tasks.tsx b/frontend/client/tasks/client-get-sample-tasks.tsx index 1f8cb1ba..84f6c7ba 100644 --- a/frontend/client/tasks/client-get-sample-tasks.tsx +++ b/frontend/client/tasks/client-get-sample-tasks.tsx @@ -4,7 +4,7 @@ import { ClientTaskData, ClientTaskType } from "../custom-types"; import { PredictionInfo } from "../prankweb-api"; /** - * This method fetches the number of tasks associated with this prediction. + * Fetches the number of tasks associated with this prediction. * @param prediction Prediction info * @returns Data with a number of tasks */ @@ -31,6 +31,11 @@ export async function getSampleTaskCount(prediction: PredictionInfo): Promise{data.data} diff --git a/frontend/client/viewer/components/draggable-dialog.tsx b/frontend/client/viewer/components/draggable-dialog.tsx index a6d531f6..b53a32df 100644 --- a/frontend/client/viewer/components/draggable-dialog.tsx +++ b/frontend/client/viewer/components/draggable-dialog.tsx @@ -17,6 +17,11 @@ function PaperComponent(props: PaperProps) { ); } +/** + * This component is a draggable dialog that shows the details of a pocket. + * Is intended to work on desktops. + * User may interact with the elements around the dialog. + */ export default class DraggableDialog extends React.Component<{ pocket: PocketData, plugin: PluginUIContext, @@ -42,6 +47,7 @@ export default class DraggableDialog extends React.Component<{ this.setState({ "visible": !this.state.visible }); } + //code inspired by //https://stackoverflow.com/questions/61335587/how-can-material-uis-dialog-allow-interaction-behind-the-dialog/65925039#65925039 render() { @@ -61,12 +67,12 @@ export default class DraggableDialog extends React.Component<{ Promise, - renderOnComplete: (data: ClientTaskData) => JSX.Element + compute: () => Promise, //the computation that returns a promise with the data to be rendered + renderOnComplete: (data: ClientTaskData) => JSX.Element //called when the computation is complete }, { - data: ClientTaskData | undefined, //this may be changed to any type (the best way is to define some interface) + data: ClientTaskData | undefined, computed: boolean, loading: boolean }> { diff --git a/frontend/client/viewer/components/pocket-details.tsx b/frontend/client/viewer/components/pocket-details.tsx index 428cb007..7adeb105 100644 --- a/frontend/client/viewer/components/pocket-details.tsx +++ b/frontend/client/viewer/components/pocket-details.tsx @@ -5,6 +5,11 @@ import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; import PocketDialogDetails from "./pocket-dialog-details"; +/** + * This component displays the details of a pocket. + * The interface is common for both the dialog and the card + * with the dialog having more details including tasks. + */ export default class PocketDetails extends React.Component <{ pocket: PocketData, @@ -16,10 +21,10 @@ export default class PocketDetails extends React.Component constructor(props: any) { super(props); - this.checkValidValue = this.checkValidValue.bind(this); + this.checkNumberIsZeroOrUndefined = this.checkNumberIsZeroOrUndefined.bind(this); } - checkValidValue(data: number | undefined) { + checkNumberIsZeroOrUndefined(data: number | undefined) { //here double equal sign is used intentionally if(data == undefined || data == 0) return false; return true; @@ -33,8 +38,8 @@ export default class PocketDetails extends React.Component - {this.checkValidValue(pocket.avgConservation) && } - {this.checkValidValue(pocket.avgAlphaFold) && } + {this.checkNumberIsZeroOrUndefined(pocket.avgConservation) && } + {this.checkNumberIsZeroOrUndefined(pocket.avgAlphaFold) && } {this.props.inDialog && }
    ); diff --git a/frontend/client/viewer/components/pocket-list.tsx b/frontend/client/viewer/components/pocket-list.tsx index 1c2aad5a..abc88a79 100644 --- a/frontend/client/viewer/components/pocket-list.tsx +++ b/frontend/client/viewer/components/pocket-list.tsx @@ -6,6 +6,10 @@ import "./pocket-list.css"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; +/** + * This component displays the list of pockets. + * For each pocket, it displays a card with the pocket details. + */ export default class PocketList extends React.Component <{ data: PredictionData, diff --git a/frontend/client/viewer/components/pocket-property.tsx b/frontend/client/viewer/components/pocket-property.tsx index 24f35fe8..a7478964 100644 --- a/frontend/client/viewer/components/pocket-property.tsx +++ b/frontend/client/viewer/components/pocket-property.tsx @@ -1,5 +1,8 @@ import React from "react"; +/** + * This component displays a single property of a pocket. + */ export default class PocketProperty extends React.Component <{ title: string, From 92e3aec2ebd8577a1a91c19535708dfc2dcd5f1e Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sun, 26 Mar 2023 16:07:18 +0200 Subject: [PATCH 051/154] Frontend tweaks --- frontend/client/tasks/server-sample-task.tsx | 78 +++++++++------ .../components/pocket-dialog-details.tsx | 15 ++- .../components/pocket-running-tasks.tsx | 30 ++++-- .../pocket-server-parametrized-task.tsx | 97 +++++++++++-------- frontend/client/viewer/components/pocket.tsx | 15 +++ .../components/structure-information.tsx | 6 ++ .../client/viewer/components/task-list.tsx | 13 ++- .../client/viewer/components/tools-box.tsx | 22 +++-- 8 files changed, 186 insertions(+), 90 deletions(-) diff --git a/frontend/client/tasks/server-sample-task.tsx b/frontend/client/tasks/server-sample-task.tsx index a14d222b..3dc07d6f 100644 --- a/frontend/client/tasks/server-sample-task.tsx +++ b/frontend/client/tasks/server-sample-task.tsx @@ -1,42 +1,49 @@ import React from "react"; import { PredictionInfo } from "../prankweb-api"; -import { PocketData } from "../custom-types"; +import { PocketData, ServerTaskType } from "../custom-types"; import { ServerTaskData } from "../custom-types"; -export async function computeSampleTaskOnBackend(firstFetch: boolean, prediction: PredictionInfo, pocket: PocketData, hash: string, serverTasks: ServerTaskData[]) { - if(firstFetch) { - await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/post`, { - method: 'POST', - headers: { - 'Accept': 'application/json', - 'Content-Type': 'application/json' - }, - body: JSON.stringify({ - "hash": hash, - "pocket": pocket.rank, - }), - }).then((res) => { - //wait 3 seconds before checking if the task is finished - setTimeout(() => {}, 3000); - return res.json(); - } - ).catch(err => { - console.log(err); - setTimeout(() => computeSampleTaskOnBackend(true, prediction, pocket, hash, serverTasks), 1000); //repeat the request - }); +import PocketProperty from "../viewer/components/pocket-property"; + +/** + * Sends requests to the backend to compute the sample task and periodically checks if the task is finished. + * @param firstFetch True if this is the first request (including fails), false otherwise + * @param prediction Prediction info + * @param pocket Pocket data + * @param hash Task identifier (hash) + * @param serverTasks A list of all server tasks + * @returns Completed task data + */ +export async function computeSampleTaskOnBackend(firstFetch: boolean, prediction: PredictionInfo, pocket: PocketData, hash: string, serverTasks: ServerTaskData[]): Promise{ + if(hash === "") { + return; } + await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/post`, { + method: 'POST', + headers: { + 'Accept': 'application/json', + 'Content-Type': 'application/json' + }, + body: JSON.stringify({ + "hash": hash, + "pocket": pocket.rank, + }), + }).then((res) => { + setTimeout(() => {}, 500); //wait for the backend to process the request + } + ).catch(err => { + console.log(err); + }); //check if the task is finished - let matchingTasks = (serverTasks.filter((e: ServerTaskData) => e.data.initialData.hash === hash && e.data.initialData.pocket === pocket.rank)); + let matchingTasks = (serverTasks.filter((e: ServerTaskData) => e.type === ServerTaskType.Sample && e.data.initialData.hash === hash && e.data.initialData.pocket === pocket.rank)); if(matchingTasks.length === 0) { - setTimeout(() => computeSampleTaskOnBackend(false, prediction, pocket, hash, serverTasks), 1000); //repeat the request return; } if(matchingTasks[0].data.status !== "successful") { - setTimeout(() => computeSampleTaskOnBackend(false, prediction, pocket, hash, serverTasks), 1000); //repeat the request return; } @@ -51,7 +58,6 @@ export async function computeSampleTaskOnBackend(firstFetch: boolean, prediction } )}).then(res => res.json()).catch(err => console.log(err)); if(!data) { - setTimeout(() => computeSampleTaskOnBackend(false, prediction, pocket, hash, serverTasks), 3000); //repeat the request return; } @@ -59,10 +65,22 @@ export async function computeSampleTaskOnBackend(firstFetch: boolean, prediction return data; } -export function renderOnServerSampleTaskCompleted(responseData: any, pocket: PocketData) { +/** + * Returns a JSX element that renders the final data of this task. + * @param responseData Response data received from the backend (i.e. the result of the task) + * @param pocket Pocket data + * @returns JSX element + */ +export function renderOnServerSampleTaskCompleted(responseData: any, pocket: PocketData, hash: string) { + return ( + p.rank === pocket.rank)?.count + }/> + ); +} + +export function renderOnServerSampleTaskRunning(pocket: PocketData, hash: string) { return ( - - {responseData.filter((e: any) => e["rank"] == pocket.rank)[0]["count"]} - + ); } \ No newline at end of file diff --git a/frontend/client/viewer/components/pocket-dialog-details.tsx b/frontend/client/viewer/components/pocket-dialog-details.tsx index 9cde49f4..d594e79c 100644 --- a/frontend/client/viewer/components/pocket-dialog-details.tsx +++ b/frontend/client/viewer/components/pocket-dialog-details.tsx @@ -13,6 +13,11 @@ import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; import { computeSampleTaskOnBackend, renderOnServerSampleTaskCompleted } from "../../tasks/server-sample-task"; +/** + * This component displays further details of a pocket + * when the pocket is displayed in a dialog. + * It includes tasks that can be run on the pocket. + */ export default class PocketDialogDetails extends React.Component <{ pocket: PocketData, @@ -29,6 +34,12 @@ export default class PocketDialogDetails extends React.Component this.state = {serverTasks: this.props.serverTasks}; } + /** + * Forces the component to update when the serverTasks prop changes. + * This is needed because the serverTasks prop is updated by a parent component + * (Application component). + * @param prevProps Previous props + */ componentDidUpdate(prevProps: any) { if(prevProps.serverTasks !== this.props.serverTasks){ this.setState({ @@ -43,9 +54,9 @@ export default class PocketDialogDetails extends React.Component computePocketVolume(this.props.plugin, this.props.pocket)} renderOnComplete={renderOnTaskVolumeCompleted} /> getSampleTaskCount(this.props.prediction)} renderOnComplete={renderOnTaskSampleTasksCountCompleted}/> - computeSampleTaskOnBackend(true, this.props.prediction, this.props.pocket, hash, this.props.serverTasks)} - renderOnComplete={(data, pocket) => renderOnServerSampleTaskCompleted(data, pocket)} /> + renderOnComplete={(data, pocket, hash) => renderOnServerSampleTaskCompleted(data, pocket, hash)} /> ); diff --git a/frontend/client/viewer/components/pocket-running-tasks.tsx b/frontend/client/viewer/components/pocket-running-tasks.tsx index bfa00d86..36f3cf3d 100644 --- a/frontend/client/viewer/components/pocket-running-tasks.tsx +++ b/frontend/client/viewer/components/pocket-running-tasks.tsx @@ -1,7 +1,11 @@ import React from "react"; -import { PocketData, ServerTaskData } from "../../custom-types"; +import { PocketData, ServerTaskData, ServerTaskType } from "../../custom-types"; import PocketProperty from "./pocket-property"; +import { renderOnServerSampleTaskCompleted, renderOnServerSampleTaskRunning } from "../../tasks/server-sample-task"; +/** + * This component displays the list of finished or incomplete tasks for a pocket. + */ export default class RunningTasks extends React.Component <{ pocket: PocketData, @@ -17,14 +21,26 @@ export default class RunningTasks extends React.Component return (
    {this.props.inDialog && this.props.serverTasks.map((e: ServerTaskData, index) => { - if(e.data.responseData && e.data.initialData.pocket === this.props.pocket.rank) { - return p.rank === this.props.pocket.rank)?.count - }/> + //finished task in this session + if(e.data.responseData && e.data.initialData.pocket === this.props.pocket.rank && e.data.status === "successful") { + switch(e.type) { + case ServerTaskType.Sample: + return renderOnServerSampleTaskCompleted(e.data.responseData, this.props.pocket, e.data.initialData.hash); + default: + return + } } - else if(e.data.responseData && e.data.initialData.pocket === this.props.pocket.rank && (e.data.status === "running" || e.data.status === "queued")) { - return + //queued, running, incomplete task + else if (e.data.initialData.pocket === this.props.pocket.rank && e.data.status !== "successful") { + switch(e.type) { + case ServerTaskType.Sample: + return renderOnServerSampleTaskRunning(this.props.pocket, e.data.initialData.hash); + default: + return + } } + //NOT rendering tasks that are not related to this pocket + //and tasks not completed in this session })}
    ); diff --git a/frontend/client/viewer/components/pocket-server-parametrized-task.tsx b/frontend/client/viewer/components/pocket-server-parametrized-task.tsx index f5fcd881..aa110ad6 100644 --- a/frontend/client/viewer/components/pocket-server-parametrized-task.tsx +++ b/frontend/client/viewer/components/pocket-server-parametrized-task.tsx @@ -5,10 +5,17 @@ import { PocketData, ServerTaskData, ServerTaskType } from '../../custom-types'; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; +/** + * This component displays and handles a task that is meant to be run on the server-side. + * It is parametrized by a hash (string) that is used to identify the task which is computed + * after an user input. + * It is expected that the compute and renderOnComplete functions are provided by an additional + * file that contains the logic for the specific task. + */ export default class PocketServerParametrizedTask extends React.Component <{ title: string, - inDialog: boolean, // not needed now. but in other cases the implementation could be potentially different. + inDialog: boolean, pocket: PocketData, plugin: PluginUIContext, taskType: ServerTaskType, @@ -16,9 +23,9 @@ export default class PocketServerParametrizedTask extends React.Component serverTasks: ServerTaskData[], modalDescription: string, compute: (hash: string) => Promise - renderOnComplete: (responseData: any, pocket: PocketData) => JSX.Element + renderOnComplete: (responseData: any, pocket: PocketData, hash: string) => JSX.Element }, { - responseData: any, //this may be changed to any type (the best way is to define some interface) + responseData: any, computed: boolean, loading: boolean, modalOpen: boolean, @@ -34,11 +41,16 @@ export default class PocketServerParametrizedTask extends React.Component this.state = {loading: false, computed: false, responseData: undefined, modalOpen: false, formData: "", hash: ""}; } - async clickCompute(firstFetch: boolean = true) { - const hash = this.state.formData; - this.setState({hash: hash}); + async clickCompute() { + if(this.state.hash === "") { + const hash = this.state.formData; + this.setState({hash: hash}); + } - const data = await this.props.compute(hash); + const data = await this.props.compute(this.state.hash); + if(!data) { + setTimeout(() => this.clickCompute(), 1000); + } if(data) { this.setState({loading: false, computed: true, responseData: data}); } @@ -56,55 +68,60 @@ export default class PocketServerParametrizedTask extends React.Component this.setState({modalOpen: !this.state.modalOpen}); } + // currently after clicking the compute button, a modal is shown for the user to input the task parameters render() { return ( -
    - {this.props.title}: +
    { !this.state.computed && -
    - - {!this.state.computed && "Compute"} - {this.state.computed && "Computed"} - - - - - {this.props.modalDescription} - - {this.setState({formData: e.target.value})}} - /> +
    + { + this.props.title + ((this.state.hash === "") ? "" : " (" + this.state.hash + ")") + }: +
    {!this.state.computed && "Compute"} {this.state.computed && "Computed"} - - + + + + {this.props.modalDescription} + + {this.setState({formData: e.target.value})}} + /> + + {!this.state.computed && "Compute"} + {this.state.computed && "Computed"} + + + +
    } { this.state.computed && - this.props.renderOnComplete(this.state.responseData!, this.props.pocket) + this.props.renderOnComplete(this.state.responseData!, this.props.pocket, this.state.hash) }
    ); diff --git a/frontend/client/viewer/components/pocket.tsx b/frontend/client/viewer/components/pocket.tsx index 7fd33cd2..b0be6bb1 100644 --- a/frontend/client/viewer/components/pocket.tsx +++ b/frontend/client/viewer/components/pocket.tsx @@ -7,6 +7,11 @@ import "bootstrap-icons/font/bootstrap-icons.css"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; +/** + * This component displays information about a pocket. + * Currently represented as a Bootstrap card. + * Includes interactions with the Mol* and RCSB plugins. + */ export default class Pocket extends React.Component <{ pocket: PocketData, @@ -81,6 +86,10 @@ export default class Pocket extends React.Component this.setState({ "details": true }); } + /** + * Computes the color of the text in the pocket card header (for better readability). + * @returns Color of the text in the pocket card header. + */ computePocketTextColor() { if (!this.props.pocket.isVisible) { return "white"; @@ -101,6 +110,12 @@ export default class Pocket extends React.Component this.setState({ "pocketTextColor": this.computePocketTextColor() }); } + /** + * Calculates the color of the pocket with the given alpha value. + * @param alpha Alpha value of the color + * @param bgColor Color in the format #RRGGBB + * @returns Calculated color in the format rgba(R,G,B,alpha) + */ calculatePocketColorWithAlpha(alpha: number, bgColor: string) { const color = (bgColor.charAt(0) === '#') ? bgColor.substring(1, 7) : bgColor; const r = parseInt(color.substring(0, 2), 16); // hexToR diff --git a/frontend/client/viewer/components/structure-information.tsx b/frontend/client/viewer/components/structure-information.tsx index c20fed65..9efdd5d6 100644 --- a/frontend/client/viewer/components/structure-information.tsx +++ b/frontend/client/viewer/components/structure-information.tsx @@ -6,6 +6,12 @@ type Metadata = { predictedStructure?: boolean; }; +/** + * This component displays very simple information about the structure + * such as the structure identifier. + * @param props + * @returns + */ export function StructureInformation( props: { metadata: Metadata, database: string } ) { diff --git a/frontend/client/viewer/components/task-list.tsx b/frontend/client/viewer/components/task-list.tsx index 65e0fd70..90b97f1c 100644 --- a/frontend/client/viewer/components/task-list.tsx +++ b/frontend/client/viewer/components/task-list.tsx @@ -4,6 +4,10 @@ import { PredictionInfo } from "../../prankweb-api"; import "bootstrap-icons/font/bootstrap-icons.css"; import { ServerTaskData } from "../../custom-types"; +/** + * This component lists the tasks associated with a prediction. + * Currently represented in the Bootstrap style. + */ export default class TaskList extends React.Component< { prediction: PredictionInfo @@ -54,6 +58,9 @@ export default class TaskList extends React.Component< } } +/** + * This component provides the content of the task list. + */ class TaskListContent extends React.Component<{ prediction: PredictionInfo tasks: ServerTaskData[] @@ -68,13 +75,13 @@ class TaskListContent extends React.Component<{
      {this.props.tasks.map((task: ServerTaskData, index: number) => { if(task.data["status"] === "successful") { - return
    • {`${task.data["id"]} ${task.data.initialData["hash"]} ${task.data.lastChange}`}
    • + return
    • {`${task.type} ${task.data.id} ${task.data.initialData["hash"]} ${task.data.lastChange}`}
    • } else if(task.data["status"] === "running") { - return
    • {`${task.data["id"]} ${task.data.initialData["hash"]} ${task.data.lastChange} running`}
    • + return
    • {`${task.type} ${task.data.id} ${task.data.initialData["hash"]} ${task.data.lastChange} running`}
    • } else if(task.data["status"] === "queued") { - return
    • {`${task.data["id"]} ${task.data.initialData["hash"]} ${task.data.lastChange} queued`}
    • + return
    • {`${task.type} ${task.data.id} ${task.data.initialData["hash"]} ${task.data.lastChange} queued`}
    • } })}
    diff --git a/frontend/client/viewer/components/tools-box.tsx b/frontend/client/viewer/components/tools-box.tsx index bdb34e37..362a911f 100644 --- a/frontend/client/viewer/components/tools-box.tsx +++ b/frontend/client/viewer/components/tools-box.tsx @@ -3,6 +3,12 @@ import React from "react"; import "./tools-box.css"; import { PocketsViewType, PolymerViewType, PolymerColorType, PredictionData } from "../../custom-types"; +/** + * This component displays the tools for the viewer. + * The tools allow the user to change the view of the polymer and pockets. + * Also allows the user to download the prediction and change the visualization colors. + * Currently represented in the Bootstrap style. + */ export default class ToolsBox extends React.Component<{ predictionData: PredictionData, downloadUrl: string, @@ -17,14 +23,11 @@ export default class ToolsBox extends React.Component<{ isShowOnlyPredicted: boolean, onShowConfidentChange: () => void, }, { - /** - * True for expanded component, false for minimized component. - */ - visible: boolean + expanded: boolean }> { state = { - "visible": true, + "expanded": true, "showConfident": false, }; @@ -34,7 +37,7 @@ export default class ToolsBox extends React.Component<{ } toggleVisible() { - this.setState({"visible": !this.state.visible}); + this.setState({"expanded": !this.state.expanded}); } render() { @@ -49,7 +52,7 @@ export default class ToolsBox extends React.Component<{ title="Show/Hide tools." onClick={this.toggleVisible} > - {this.state.visible ? + {this.state.expanded ? : @@ -57,7 +60,7 @@ export default class ToolsBox extends React.Component<{
    - {this.state.visible &&
    + {this.state.expanded &&
    Date: Sat, 1 Apr 2023 14:45:12 +0200 Subject: [PATCH 052/154] Froentend tweaks --- frontend/client/viewer/application.tsx | 3 +-- frontend/client/viewer/molstar-visualise.ts | 8 ++++---- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 076fbf26..c517055a 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -209,9 +209,8 @@ export class Application extends React.Component res.json()) .catch(err => { - setTimeout(() => this.getTaskList(), 7000); return; - }); //we could handle the error in a better way, but we do not care if the poll fails sometimes + }); //we could handle the error, but we do not care if the poll fails sometimes if(json) { //append the new tasks to the existing ones let newTasks: ServerTaskData[] = this.state.serverTasks; diff --git a/frontend/client/viewer/molstar-visualise.ts b/frontend/client/viewer/molstar-visualise.ts index dd470949..26882441 100644 --- a/frontend/client/viewer/molstar-visualise.ts +++ b/frontend/client/viewer/molstar-visualise.ts @@ -555,9 +555,9 @@ async function overPaintPocketsWithConservation(plugin: PluginUIContext, predict export async function createPocketsGroupFromJson(plugin: PluginUIContext, structure: StateObjectSelector, groupName: string, prediction: PredictionData) { const builder = plugin.state.data.build(); const group = builder.to(structure).apply(StateTransforms.Misc.CreateGroup, {label: groupName}, {ref: groupName}); - for(let i = 0; i < prediction.pockets.length; i++) { - createPocketFromJsonByAtoms(plugin, structure, prediction.pockets[i], `Pocket ${i+1}`, group); - } + prediction.pockets.map((pocket, i) => { + createPocketFromJson(plugin, structure, pocket, `Pocket ${i+1}`, group); + }); await builder.commit(); } @@ -571,7 +571,7 @@ export async function createPocketsGroupFromJson(plugin: PluginUIContext, struct * @param group Group to which the pocket will be assigned (from createPocketsGroupFromJson()) * @returns void */ -async function createPocketFromJsonByAtoms(plugin: PluginUIContext, structure: StateObjectSelector, pocket: PocketData, groupName: string, group: any) { //group should not be any but i cannot figure out the right type +async function createPocketFromJson(plugin: PluginUIContext, structure: StateObjectSelector, pocket: PocketData, groupName: string, group: any) { //group should not be any but i cannot figure out the right type const group2 = group.apply(StateTransforms.Misc.CreateGroup, {label: groupName}, {ref: groupName}, {selectionTags: groupName}); const atomsExpression = MS.struct.generator.atomGroups({ From 92f5382eab3b2e1a814e6637d9bc82bc019cbf92 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 1 Apr 2023 15:54:03 +0200 Subject: [PATCH 053/154] Documentation --- frontend/client/viewer/molstar-visualise.ts | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/frontend/client/viewer/molstar-visualise.ts b/frontend/client/viewer/molstar-visualise.ts index 26882441..78463317 100644 --- a/frontend/client/viewer/molstar-visualise.ts +++ b/frontend/client/viewer/molstar-visualise.ts @@ -13,6 +13,7 @@ import { Loci } from "molstar/lib/mol-model/loci"; import { Bundle } from "molstar/lib/mol-model/structure/structure/element/bundle"; import { setSubtreeVisibility } from 'molstar/lib/mol-plugin/behavior/static/state'; import { StateObjectSelector } from 'molstar/lib/mol-state'; +import { Expression } from 'molstar/lib/mol-script/language/expression'; //the representations are updated by the React component states let polymerRepresentations: PolymerRepresentation[] = []; @@ -183,7 +184,7 @@ export async function overPaintPolymer(value: PolymerColorType, plugin: PluginUI */ async function overPaintStructureClear(plugin: PluginUIContext, prediction: PredictionData) { const chains : ChainData[] = []; - const params = []; + const params : any = []; for (let i = 0; i < prediction.structure.indices.length; i++) { let splitIndice = prediction.structure.indices[i].split("_"); @@ -227,7 +228,7 @@ async function overPaintPocketsClear(plugin: PluginUIContext, prediction: Predic for(const pocket of prediction.pockets) { const builder = plugin.state.data.build(); const chains : ChainData[] = []; - const params = []; + const params : any = []; for(const residue of pocket.residues) { let splitResidue = residue.split("_"); @@ -269,7 +270,7 @@ async function overPaintPocketsClear(plugin: PluginUIContext, prediction: Predic async function overPaintStructureWithAlphaFold(plugin: PluginUIContext, prediction: PredictionData) { //paints the structure with the alpha fold prediction if(!prediction.structure.scores.plddt) return; - const params = []; + const params : any = []; const selections : ChainData[] = []; //create the selections for the pockets @@ -337,7 +338,7 @@ async function overPaintPocketsWithAlphaFold(plugin: PluginUIContext, prediction for(const pocket of prediction.pockets) { const builder = plugin.state.data.build(); - const params = []; + const params : any = []; const selections : ChainData[] = []; for(const residue of pocket.residues) { @@ -412,7 +413,7 @@ async function overPaintStructureWithConservation(plugin: PluginUIContext, predi //if the normalized conservation is not computed yet if(conservationNormalized === undefined) computeNormalizedConservation(prediction); - const params = []; + const params : any = []; const thresholds = [0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0]; const colors : Color[] = []; @@ -495,7 +496,7 @@ async function overPaintPocketsWithConservation(plugin: PluginUIContext, predict for(const pocket of prediction.pockets) { const builder = plugin.state.data.build(); - const params = []; + const params : any = []; const selections : ChainData[] = []; for(const residue of pocket.residues) { @@ -749,7 +750,7 @@ export function highlightInViewerLabelIdWithoutFocus(plugin: PluginUIContext, ch * @param plugin Mol* plugin * @param ids Surface atoms ids * @param focus Focus on the surface atoms (if false, it will only highlight them) - * @returns + * @returns void */ export function highlightSurfaceAtomsInViewerLabelId(plugin: PluginUIContext, ids: string[], focus: boolean) { const data = plugin.managers.structure.hierarchy.current.structures[0]?.cell.obj?.data; @@ -796,6 +797,7 @@ function getSelectionFromChainAuthId(plugin: PluginUIContext, chainId: string, p * @param plugin Mol* plugin * @param prediction Prediction data * @param structure Mol* structure (returned from the first call of loadStructureIntoMolstar()) + * @returns void */ export async function addPredictedPolymerRepresentation(plugin: PluginUIContext, prediction: PredictionData, structure: StateObjectSelector) { const builder = plugin.state.data.build(); @@ -849,14 +851,14 @@ export async function addPredictedPolymerRepresentation(plugin: PluginUIContext, * @returns Expression with the selection of the confident residues */ export function getConfidentResiduesFromPrediction(prediction: PredictionData) { - const queries = []; + const queries : Expression[] = []; //for each chain create a query for the residues let totalIndex = 0; for(let i = 0; i < prediction.structure.regions.length; i++) { const chain = prediction.structure.regions[i].name; const positions = prediction.structure.indices.slice(totalIndex, prediction.structure.regions[i].end + 1); - const newPositions = []; + const newPositions : number[] = []; for(let y = 0; y < positions.length; y++) { if(prediction.structure.scores.plddt![totalIndex + y] > 70) { From 61c6b7d7e9976fcc83f378e711bb1c091a159e0e Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 1 Apr 2023 21:43:40 +0200 Subject: [PATCH 054/154] Documentation changes --- frontend/client/viewer/molstar-visualise.ts | 1 + frontend/client/viewer/rcsb-visualise.ts | 15 +++++++++++---- frontend/tsconfig.json | 2 +- 3 files changed, 13 insertions(+), 5 deletions(-) diff --git a/frontend/client/viewer/molstar-visualise.ts b/frontend/client/viewer/molstar-visualise.ts index 78463317..dd747c08 100644 --- a/frontend/client/viewer/molstar-visualise.ts +++ b/frontend/client/viewer/molstar-visualise.ts @@ -937,6 +937,7 @@ function getStructureElementLoci(loci: Loci): StructureElement.Loci | undefined * @param plugin Mol* plugin * @param predictionData Prediction data * @param rcsbPlugin Rcsb plugin + * @returns void */ export function linkMolstarToRcsb(plugin: PluginUIContext, predictionData: PredictionData, rcsbPlugin: RcsbFv) { //cc: https://github.com/scheuerv/molart/ diff --git a/frontend/client/viewer/rcsb-visualise.ts b/frontend/client/viewer/rcsb-visualise.ts index ae0135b0..463783e3 100644 --- a/frontend/client/viewer/rcsb-visualise.ts +++ b/frontend/client/viewer/rcsb-visualise.ts @@ -38,7 +38,7 @@ export function initRcsb(data: PredictionData, molstarPlugin: PluginUIContext) { } /** - * Method to calculate the width of the viewer + * Method to calculate the width of the viewer. * @returns The width */ function calculateViewerWidth() { @@ -65,6 +65,7 @@ function calculateViewerWidth() { * @param molstarPlugin Mol* plugin * @param trackData Data of the clicked track * @param event Mouse event + * @returns void */ function elementClicked(predictionData: PredictionData, molstarPlugin: PluginUIContext, trackData?: RcsbFvTrackDataElementInterface, event?: MouseEvent) { if(trackData && predictionData) { @@ -81,6 +82,8 @@ function elementClicked(predictionData: PredictionData, molstarPlugin: PluginUIC * @param data Prediction data * @param molstarPlugin Mol* plugin * @param trackData Data of the clicked track + * @param event Mouse event + * @returns void */ function onHighlight(data: PredictionData, molstarPlugin: PluginUIContext, trackData: Array) { if(trackData.length === 0) return; @@ -196,7 +199,7 @@ function createRowConfigDataRcsb(data: PredictionData) { //then resolve the conservation, if available if(data.structure.scores.conservation && !data.structure.scores.conservation.every((value) => value === 0)) { - const conservationData = []; + const conservationData: RcsbFvTrackData = []; //we need to normalize the scores to fit in properly //by the definition of conservation scoring the maximum is log_2(20) @@ -224,7 +227,7 @@ function createRowConfigDataRcsb(data: PredictionData) { //then resolve alphafold scores, if available if(data.structure.scores.plddt && !data.structure.scores.plddt.every((value) => value === 0)) { - const alphafoldData = []; + const alphafoldData: RcsbFvTrackData = []; //we need to normalize the scores to fit in properly //by the definition of alphafold scores the maximum should be possibly 100 @@ -255,7 +258,11 @@ function createRowConfigDataRcsb(data: PredictionData) { return rowConfigData; } -/** Method that returns log_x(y) */ +/** Method that returns log_x(y). + * @param x Base + * @param y Number + * @returns log_x(y) +*/ function getLogBaseX(x : number, y : number) { return Math.log(y) / Math.log(x); } diff --git a/frontend/tsconfig.json b/frontend/tsconfig.json index 02fd1cc5..779b05bb 100644 --- a/frontend/tsconfig.json +++ b/frontend/tsconfig.json @@ -11,7 +11,7 @@ "strict": true, "module": "esnext", "moduleResolution": "node", // Resolve modules using Node.js style - //"allowJs": true, + "allowJs": false, "noEmit": false, // Do not emit output (meaning do not compile code, only perform type checking) "sourceMap": false, // Generate corresponding .map file "declaration": false, // Generate corresponding .d.ts file From d756bb839d3ac9e4a4d66f2454ceb476caffe0e2 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Wed, 5 Apr 2023 20:29:10 +0200 Subject: [PATCH 055/154] Task interface changes --- frontend/client/custom-types.ts | 5 ++++- frontend/client/tasks/server-sample-task.tsx | 9 ++++++--- .../client/viewer/components/pocket-client-task.tsx | 8 ++++---- .../client/viewer/components/pocket-running-tasks.tsx | 11 ++++++++--- .../components/pocket-server-parametrized-task.tsx | 10 +++++----- 5 files changed, 27 insertions(+), 16 deletions(-) diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index 1bd6c518..86e7317f 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -240,6 +240,9 @@ export interface ServerTaskDataContents { created: string; lastChange: string; status: string; - initialData: any; //initial data + initialData: { + pocket: string; //pocket id + [key: string]: any; //other data + }; //initial data responseData: any; //response data } \ No newline at end of file diff --git a/frontend/client/tasks/server-sample-task.tsx b/frontend/client/tasks/server-sample-task.tsx index 3dc07d6f..0bf9e405 100644 --- a/frontend/client/tasks/server-sample-task.tsx +++ b/frontend/client/tasks/server-sample-task.tsx @@ -62,7 +62,10 @@ export async function computeSampleTaskOnBackend(firstFetch: boolean, prediction } matchingTasks[0].data.responseData = data; - return data; + return { + "data": matchingTasks[0].data, + "type": ServerTaskType.Sample + }; } /** @@ -71,10 +74,10 @@ export async function computeSampleTaskOnBackend(firstFetch: boolean, prediction * @param pocket Pocket data * @returns JSX element */ -export function renderOnServerSampleTaskCompleted(responseData: any, pocket: PocketData, hash: string) { +export function renderOnServerSampleTaskCompleted(taskData: ServerTaskData, pocket: PocketData, hash: string) { return ( p.rank === pocket.rank)?.count + taskData.data.responseData.find((p: any) => p.rank === pocket.rank)?.count }/> ); } diff --git a/frontend/client/viewer/components/pocket-client-task.tsx b/frontend/client/viewer/components/pocket-client-task.tsx index 99411683..5dd237a3 100644 --- a/frontend/client/viewer/components/pocket-client-task.tsx +++ b/frontend/client/viewer/components/pocket-client-task.tsx @@ -22,7 +22,7 @@ export default class PocketClientTask extends React.Component compute: () => Promise, //the computation that returns a promise with the data to be rendered renderOnComplete: (data: ClientTaskData) => JSX.Element //called when the computation is complete }, { - data: ClientTaskData | undefined, + taskData: ClientTaskData | undefined, computed: boolean, loading: boolean }> { @@ -31,13 +31,13 @@ export default class PocketClientTask extends React.Component super(props); this.handleClick = this.handleClick.bind(this); this.clickCompute = this.clickCompute.bind(this); - this.state = {loading: false, computed: false, data: undefined}; + this.state = {loading: false, computed: false, taskData: undefined}; } async clickCompute() { const json = await this.props.compute(); - this.setState({loading: false, computed: true, data: json}); + this.setState({loading: false, computed: true, taskData: json}); } async handleClick() { @@ -66,7 +66,7 @@ export default class PocketClientTask extends React.Component } { - this.state.computed && this.props.renderOnComplete(this.state.data!) + this.state.computed && this.props.renderOnComplete(this.state.taskData!) }
    ); diff --git a/frontend/client/viewer/components/pocket-running-tasks.tsx b/frontend/client/viewer/components/pocket-running-tasks.tsx index 36f3cf3d..4dd7fa35 100644 --- a/frontend/client/viewer/components/pocket-running-tasks.tsx +++ b/frontend/client/viewer/components/pocket-running-tasks.tsx @@ -15,6 +15,11 @@ export default class RunningTasks extends React.Component constructor(props: any) { super(props); + this.defaultImplementation = this.defaultImplementation.bind(this); + } + + defaultImplementation(serverTask: ServerTaskData, index: number) { + return } render() { @@ -25,9 +30,9 @@ export default class RunningTasks extends React.Component if(e.data.responseData && e.data.initialData.pocket === this.props.pocket.rank && e.data.status === "successful") { switch(e.type) { case ServerTaskType.Sample: - return renderOnServerSampleTaskCompleted(e.data.responseData, this.props.pocket, e.data.initialData.hash); + return renderOnServerSampleTaskCompleted(e, this.props.pocket, e.data.initialData.hash); default: - return + return this.defaultImplementation(e, index); } } //queued, running, incomplete task @@ -36,7 +41,7 @@ export default class RunningTasks extends React.Component case ServerTaskType.Sample: return renderOnServerSampleTaskRunning(this.props.pocket, e.data.initialData.hash); default: - return + return this.defaultImplementation(e, index); } } //NOT rendering tasks that are not related to this pocket diff --git a/frontend/client/viewer/components/pocket-server-parametrized-task.tsx b/frontend/client/viewer/components/pocket-server-parametrized-task.tsx index aa110ad6..ef6763a0 100644 --- a/frontend/client/viewer/components/pocket-server-parametrized-task.tsx +++ b/frontend/client/viewer/components/pocket-server-parametrized-task.tsx @@ -23,9 +23,9 @@ export default class PocketServerParametrizedTask extends React.Component serverTasks: ServerTaskData[], modalDescription: string, compute: (hash: string) => Promise - renderOnComplete: (responseData: any, pocket: PocketData, hash: string) => JSX.Element + renderOnComplete: (responseData: ServerTaskData, pocket: PocketData, hash: string) => JSX.Element }, { - responseData: any, + taskData: ServerTaskData | undefined, computed: boolean, loading: boolean, modalOpen: boolean, @@ -38,7 +38,7 @@ export default class PocketServerParametrizedTask extends React.Component this.handleFormClick = this.handleFormClick.bind(this); this.clickCompute = this.clickCompute.bind(this); this.handleModalClick = this.handleModalClick.bind(this); - this.state = {loading: false, computed: false, responseData: undefined, modalOpen: false, formData: "", hash: ""}; + this.state = {loading: false, computed: false, taskData: undefined, modalOpen: false, formData: "", hash: ""}; } async clickCompute() { @@ -52,7 +52,7 @@ export default class PocketServerParametrizedTask extends React.Component setTimeout(() => this.clickCompute(), 1000); } if(data) { - this.setState({loading: false, computed: true, responseData: data}); + this.setState({loading: false, computed: true, taskData: data}); } } @@ -121,7 +121,7 @@ export default class PocketServerParametrizedTask extends React.Component } { this.state.computed && - this.props.renderOnComplete(this.state.responseData!, this.props.pocket, this.state.hash) + this.props.renderOnComplete(this.state.taskData!, this.props.pocket, this.state.hash) }
    ); From bb16ad9bae25702b7baa59a723b60e96b84e2683 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 8 Apr 2023 12:16:31 +0200 Subject: [PATCH 056/154] Pocket server task change --- frontend/client/viewer/components/pocket-dialog-details.tsx | 2 +- .../viewer/components/pocket-server-parametrized-task.tsx | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/frontend/client/viewer/components/pocket-dialog-details.tsx b/frontend/client/viewer/components/pocket-dialog-details.tsx index d594e79c..806d5d07 100644 --- a/frontend/client/viewer/components/pocket-dialog-details.tsx +++ b/frontend/client/viewer/components/pocket-dialog-details.tsx @@ -56,7 +56,7 @@ export default class PocketDialogDetails extends React.Component getSampleTaskCount(this.props.prediction)} renderOnComplete={renderOnTaskSampleTasksCountCompleted}/> computeSampleTaskOnBackend(true, this.props.prediction, this.props.pocket, hash, this.props.serverTasks)} - renderOnComplete={(data, pocket, hash) => renderOnServerSampleTaskCompleted(data, pocket, hash)} /> + renderOnComplete={(data, hash) => renderOnServerSampleTaskCompleted(data, this.props.pocket, hash)} />
    ); diff --git a/frontend/client/viewer/components/pocket-server-parametrized-task.tsx b/frontend/client/viewer/components/pocket-server-parametrized-task.tsx index ef6763a0..18f72d5d 100644 --- a/frontend/client/viewer/components/pocket-server-parametrized-task.tsx +++ b/frontend/client/viewer/components/pocket-server-parametrized-task.tsx @@ -23,7 +23,7 @@ export default class PocketServerParametrizedTask extends React.Component serverTasks: ServerTaskData[], modalDescription: string, compute: (hash: string) => Promise - renderOnComplete: (responseData: ServerTaskData, pocket: PocketData, hash: string) => JSX.Element + renderOnComplete: (responseData: ServerTaskData, hash: string) => JSX.Element }, { taskData: ServerTaskData | undefined, computed: boolean, @@ -121,7 +121,7 @@ export default class PocketServerParametrizedTask extends React.Component } { this.state.computed && - this.props.renderOnComplete(this.state.taskData!, this.props.pocket, this.state.hash) + this.props.renderOnComplete(this.state.taskData!, this.state.hash) } ); From 15190ee72963c3c96728063f0eb6a007409fcecc Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 8 Apr 2023 12:35:34 +0200 Subject: [PATCH 057/154] Pocket files naming --- frontend/client/viewer/components/pocket-dialog-details.tsx | 4 ++-- frontend/client/viewer/components/pocket-running-tasks.tsx | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/frontend/client/viewer/components/pocket-dialog-details.tsx b/frontend/client/viewer/components/pocket-dialog-details.tsx index 806d5d07..c557be5a 100644 --- a/frontend/client/viewer/components/pocket-dialog-details.tsx +++ b/frontend/client/viewer/components/pocket-dialog-details.tsx @@ -3,7 +3,7 @@ import React from "react"; import PocketProperty from "./pocket-property"; import PocketClientTask from "./pocket-client-task"; import PocketServerParametrizedTask from "./pocket-server-parametrized-task"; -import RunningTasks from "./pocket-running-tasks"; +import PocketRunningTasks from "./pocket-running-tasks"; import { computePocketVolume, renderOnTaskVolumeCompleted } from "../../tasks/client-atoms-volume"; import { getSampleTaskCount, renderOnTaskSampleTasksCountCompleted } from "../../tasks/client-get-sample-tasks"; @@ -57,7 +57,7 @@ export default class PocketDialogDetails extends React.Component computeSampleTaskOnBackend(true, this.props.prediction, this.props.pocket, hash, this.props.serverTasks)} renderOnComplete={(data, hash) => renderOnServerSampleTaskCompleted(data, this.props.pocket, hash)} /> - + ); } diff --git a/frontend/client/viewer/components/pocket-running-tasks.tsx b/frontend/client/viewer/components/pocket-running-tasks.tsx index 4dd7fa35..2d2ab49a 100644 --- a/frontend/client/viewer/components/pocket-running-tasks.tsx +++ b/frontend/client/viewer/components/pocket-running-tasks.tsx @@ -6,7 +6,7 @@ import { renderOnServerSampleTaskCompleted, renderOnServerSampleTaskRunning } fr /** * This component displays the list of finished or incomplete tasks for a pocket. */ -export default class RunningTasks extends React.Component +export default class PocketRunningTasks extends React.Component <{ pocket: PocketData, inDialog: boolean, From 05dcb66fdbabf856c5b93d730047c2eb5a0122a5 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sun, 16 Apr 2023 20:37:49 +0200 Subject: [PATCH 058/154] Toolbox update naming --- frontend/client/viewer/application.tsx | 4 ++-- .../client/viewer/components/{tools-box.css => tool-box.css} | 0 .../client/viewer/components/{tools-box.tsx => tool-box.tsx} | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) rename frontend/client/viewer/components/{tools-box.css => tool-box.css} (100%) rename frontend/client/viewer/components/{tools-box.tsx => tool-box.tsx} (98%) diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index c517055a..94d82488 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -5,7 +5,7 @@ import "./application.css"; import { PredictionInfo, getApiDownloadUrl } from "../prankweb-api"; import { StructureInformation } from "./components/structure-information"; -import ToolsBox from "./components/tools-box"; +import ToolBox from "./components/tool-box"; import PocketList from "./components/pocket-list"; import TaskList from "./components/task-list"; @@ -243,7 +243,7 @@ export class Application extends React.Component - Date: Wed, 26 Apr 2023 11:56:03 +0200 Subject: [PATCH 059/154] Updated sample task info.json creation --- web-server/src/sample_task.py | 37 ++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 16 deletions(-) diff --git a/web-server/src/sample_task.py b/web-server/src/sample_task.py index 40981b35..66acdc9f 100644 --- a/web-server/src/sample_task.py +++ b/web-server/src/sample_task.py @@ -89,22 +89,27 @@ def post_task(self, prediction_id: str, data: dict): if os.path.exists(directory): #if the info file exists, we have to append the new info to the existing file taskinfo = TaskInfo(directory=directory, identifier=prediction_id, data=data) - - with open(_info_file(taskinfo), "r+") as f: - fileData = json.load(f) - #we check if the task already exists - for task in fileData["tasks"]: - if task["initialData"] == data: - return self._response_file(directory, "info.json") - - taskinfo.taskId = len(fileData["tasks"]) - fileData["tasks"].append(_create_info(taskinfo)) - f.seek(0) - f.write(json.dumps(fileData)) - - _save_input(taskinfo, data) - submit_directory_for_sample_task(taskinfo.directory, taskinfo.taskId) - return self._response_file(taskinfo.directory, "info.json") + try: + with open(_info_file(taskinfo), "r+") as f: + fileData = json.load(f) + #we check if the task already exists + for task in fileData["tasks"]: + if task["initialData"] == data: + return self._response_file(directory, "info.json") + + taskinfo.taskId = len(fileData["tasks"]) + fileData["tasks"].append(_create_info(taskinfo)) + f.seek(0) + f.write(json.dumps(fileData)) + + _save_input(taskinfo, data) + submit_directory_for_sample_task(taskinfo.directory, taskinfo.taskId) + return self._response_file(taskinfo.directory, "info.json") + + except: + #else we create a new info file + _save_input(taskinfo, data) + return _create_sample_task_file(taskinfo) #else we create a new info file taskinfo = TaskInfo(directory=directory, identifier=prediction_id, data=data) From b9126c0be93fe413ad3c64754f7b1fa90a9dc86e Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Wed, 26 Apr 2023 11:58:17 +0200 Subject: [PATCH 060/154] Fixed sample task --- web-server/src/sample_task.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/web-server/src/sample_task.py b/web-server/src/sample_task.py index 66acdc9f..d597932a 100644 --- a/web-server/src/sample_task.py +++ b/web-server/src/sample_task.py @@ -108,12 +108,14 @@ def post_task(self, prediction_id: str, data: dict): except: #else we create a new info file + taskinfo.taskId = 0 _save_input(taskinfo, data) return _create_sample_task_file(taskinfo) #else we create a new info file taskinfo = TaskInfo(directory=directory, identifier=prediction_id, data=data) - + taskinfo.taskId = 0 + _save_input(taskinfo, data) return _create_sample_task_file(taskinfo) From 283cd876a27d9e151c6329f09a24dd8ad179ef0c Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sat, 29 Apr 2023 14:50:36 +0200 Subject: [PATCH 061/154] Docking initials, added bounding box, renames --- executor-docking/celery_docking.py | 7 +- executor-docking/run_task.py | 7 +- frontend/client/custom-types.ts | 5 +- ...tasks.tsx => client-get-docking-tasks.tsx} | 12 +- frontend/client/tasks/server-docking-task.tsx | 140 ++++++++++++++++++ frontend/client/tasks/server-sample-task.tsx | 89 ----------- frontend/client/viewer/application.tsx | 6 +- .../components/pocket-dialog-details.tsx | 12 +- .../components/pocket-running-tasks.tsx | 10 +- web-server/src/api_v2.py | 26 ++-- web-server/src/celery_client.py | 7 +- .../src/{sample_task.py => docking_task.py} | 69 +++++---- 12 files changed, 230 insertions(+), 160 deletions(-) rename frontend/client/tasks/{client-get-sample-tasks.tsx => client-get-docking-tasks.tsx} (64%) create mode 100644 frontend/client/tasks/server-docking-task.tsx delete mode 100644 frontend/client/tasks/server-sample-task.tsx rename web-server/src/{sample_task.py => docking_task.py} (78%) diff --git a/executor-docking/celery_docking.py b/executor-docking/celery_docking.py index ab233202..29970867 100644 --- a/executor-docking/celery_docking.py +++ b/executor-docking/celery_docking.py @@ -20,7 +20,7 @@ }, }) - +""" @celery.signals.setup_logging.connect def setup_celery_logging(**kwargs): # We do nothing here to disable logging. @@ -29,9 +29,10 @@ def setup_celery_logging(**kwargs): # https://github.com/celery/celery/issues/2509 prankweb.log.setup() +""" -@prankweb.task(name="sample_task") -def celery_run_sample_task(directory: str, taskId): +@prankweb.task(name="docking") +def celery_run_docking(directory: str, taskId): if os.path.isdir(directory): run_task.execute_directory_task(directory, taskId) else: diff --git a/executor-docking/run_task.py b/executor-docking/run_task.py index b8dc3300..7f452d79 100644 --- a/executor-docking/run_task.py +++ b/executor-docking/run_task.py @@ -57,7 +57,7 @@ def execute_directory_task(directory: str, taskId: int): """ Method to execute a task for a given directory and a given taskId. """ - + result_file = os.path.join(directory, str(taskId), "public", "result.json") #check if the directory exists - if not, we did not ask for this task @@ -72,6 +72,11 @@ def execute_directory_task(directory: str, taskId: int): status["tasks"][taskId]["status"] = Status.RUNNING.value _save_status_file(status_file, status, taskId) + #load the input file + with open(os.path.join(directory, str(taskId), "input.json"), encoding="utf-8") as f: + cfg = json.load(f) + print(cfg["bounding_box"]) + #then load the prediction file prediction = _load_json(get_prediction_path(directory)) diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index 86e7317f..0280bc5c 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -212,7 +212,7 @@ export const DefaultPocketColors = [ */ export enum ClientTaskType { Volume = 0, - SampleTaskCount = 1 + DockingTaskCount = 1 } export interface ClientTaskData { @@ -227,7 +227,7 @@ export interface Point3D { } export enum ServerTaskType { - Sample = 0 + Docking = 0 } export interface ServerTaskData { @@ -241,6 +241,7 @@ export interface ServerTaskDataContents { lastChange: string; status: string; initialData: { + hash: string; //hash of the data pocket: string; //pocket id [key: string]: any; //other data }; //initial data diff --git a/frontend/client/tasks/client-get-sample-tasks.tsx b/frontend/client/tasks/client-get-docking-tasks.tsx similarity index 64% rename from frontend/client/tasks/client-get-sample-tasks.tsx rename to frontend/client/tasks/client-get-docking-tasks.tsx index 84f6c7ba..f518a79c 100644 --- a/frontend/client/tasks/client-get-sample-tasks.tsx +++ b/frontend/client/tasks/client-get-docking-tasks.tsx @@ -8,26 +8,26 @@ import { PredictionInfo } from "../prankweb-api"; * @param prediction Prediction info * @returns Data with a number of tasks */ -export async function getSampleTaskCount(prediction: PredictionInfo): Promise { +export async function getDockingTaskCount(prediction: PredictionInfo): Promise { - const json = await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/tasks`) + const json = await fetch(`./api/v2/docking/${prediction.database}/${prediction.id}/tasks`) .then(res => res.json()) .catch(err => { console.log(err); - setTimeout(() => getSampleTaskCount(prediction), 1000); + setTimeout(() => getDockingTaskCount(prediction), 1000); }); if(json) { const numOfTasks = json["tasks"].length; return { "data": numOfTasks, - "type": ClientTaskType.SampleTaskCount + "type": ClientTaskType.DockingTaskCount }; } return { "data": 0, - "type": ClientTaskType.SampleTaskCount + "type": ClientTaskType.DockingTaskCount } } @@ -36,7 +36,7 @@ export async function getSampleTaskCount(prediction: PredictionInfo): Promise{data.data} ); diff --git a/frontend/client/tasks/server-docking-task.tsx b/frontend/client/tasks/server-docking-task.tsx new file mode 100644 index 00000000..6df31856 --- /dev/null +++ b/frontend/client/tasks/server-docking-task.tsx @@ -0,0 +1,140 @@ +import React from "react"; + +import { PredictionInfo } from "../prankweb-api"; +import { PocketData, ServerTaskType, Point3D } from "../custom-types"; +import { ServerTaskData } from "../custom-types"; + +import PocketProperty from "../viewer/components/pocket-property"; +import { getPocketAtomCoordinates } from "../viewer/molstar-visualise"; +import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; + +function twoPointsDistance(point1: Point3D, point2: Point3D) { + return Math.sqrt(Math.pow(point1.x - point2.x, 2) + Math.pow(point1.y - point2.y, 2) + Math.pow(point1.z - point2.z, 2)); +} + +function computeBoundingBox(plugin: PluginUIContext, pocket: PocketData) { + const coords = getPocketAtomCoordinates(plugin, pocket.surface); + + /*const points: Array> = []; + coords.forEach(coord => { + console.log(coord); + points.push([coord.x, coord.y, coord.z]); + });*/ + + const center: Point3D = { + x: Number(pocket.center[0]), + y: Number(pocket.center[1]), + z: Number(pocket.center[2]) + }; + //compute max distance from the center + let maxDistance = 0; + coords.forEach(coord => { + console.log(coord); + const distance = twoPointsDistance(coord, center); + if(distance > maxDistance) { + maxDistance = distance; + } + }); + + let diagonal = maxDistance * 2; + let sideLength = diagonal / Math.sqrt(3); + + return { + center: { + x: center.x, + y: center.y, + z: center.z + }, + size: { + x: Math.ceil(sideLength), + y: Math.ceil(sideLength), + z: Math.ceil(sideLength) + } + }; +} + +/** + * Sends requests to the backend to compute the docking task and periodically checks if the task is finished. + * @param firstFetch True if this is the first request (including fails), false otherwise + * @param prediction Prediction info + * @param pocket Pocket data + * @param hash Task identifier (hash) + * @param serverTasks A list of all server tasks + * @returns Completed task data + */ +export async function computeDockingTaskOnBackend(firstFetch: boolean, prediction: PredictionInfo, pocket: PocketData, hash: string, serverTasks: ServerTaskData[], plugin: PluginUIContext): Promise{ + if(hash === "") { + return; + } + + const box = computeBoundingBox(plugin, pocket); + + await fetch(`./api/v2/docking/${prediction.database}/${prediction.id}/post`, { + method: 'POST', + headers: { + 'Accept': 'application/json', + 'Content-Type': 'application/json' + }, + body: JSON.stringify({ + "hash": hash, + "pocket": pocket.rank, + "bounding_box": box + }), + }).then((res) => { + setTimeout(() => {}, 500); //wait for the backend to process the request + } + ).catch(err => { + console.log(err); + }); + + //check if the task is finished + let matchingTasks = (serverTasks.filter((e: ServerTaskData) => e.type === ServerTaskType.Docking && e.data.initialData.hash === hash && e.data.initialData.pocket === pocket.rank)); + + if(matchingTasks.length === 0) { + return; + } + + if(matchingTasks[0].data.status !== "successful") { + return; + } + + const data = await fetch(`./api/v2/docking/${prediction.database}/${prediction.id}/public/result.json`, { + method: 'POST', + headers: { + 'Accept': 'application/json', + 'Content-Type': 'application/json' + }, + body: JSON.stringify({ + "hash": hash, + } + )}).then(res => res.json()).catch(err => console.log(err)); + if(!data) { + return; + } + + matchingTasks[0].data.responseData = data; + return { + "data": matchingTasks[0].data, + "type": ServerTaskType.Docking + }; +} + +/** + * Returns a JSX element that renders the final data of this task. + * @param responseData Response data received from the backend (i.e. the result of the task) + * @param pocket Pocket data + * @returns JSX element + */ +export function renderOnServerDockingTaskCompleted(taskData: ServerTaskData, pocket: PocketData, hash: string) { + return ( + p.rank === pocket.rank)?.count + }/> + ); +} + +export function renderOnServerDockingTaskRunning(pocket: PocketData, hash: string) { + return ( + + ); +} \ No newline at end of file diff --git a/frontend/client/tasks/server-sample-task.tsx b/frontend/client/tasks/server-sample-task.tsx deleted file mode 100644 index 0bf9e405..00000000 --- a/frontend/client/tasks/server-sample-task.tsx +++ /dev/null @@ -1,89 +0,0 @@ -import React from "react"; - -import { PredictionInfo } from "../prankweb-api"; -import { PocketData, ServerTaskType } from "../custom-types"; -import { ServerTaskData } from "../custom-types"; - -import PocketProperty from "../viewer/components/pocket-property"; - -/** - * Sends requests to the backend to compute the sample task and periodically checks if the task is finished. - * @param firstFetch True if this is the first request (including fails), false otherwise - * @param prediction Prediction info - * @param pocket Pocket data - * @param hash Task identifier (hash) - * @param serverTasks A list of all server tasks - * @returns Completed task data - */ -export async function computeSampleTaskOnBackend(firstFetch: boolean, prediction: PredictionInfo, pocket: PocketData, hash: string, serverTasks: ServerTaskData[]): Promise{ - if(hash === "") { - return; - } - await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/post`, { - method: 'POST', - headers: { - 'Accept': 'application/json', - 'Content-Type': 'application/json' - }, - body: JSON.stringify({ - "hash": hash, - "pocket": pocket.rank, - }), - }).then((res) => { - setTimeout(() => {}, 500); //wait for the backend to process the request - } - ).catch(err => { - console.log(err); - }); - - //check if the task is finished - let matchingTasks = (serverTasks.filter((e: ServerTaskData) => e.type === ServerTaskType.Sample && e.data.initialData.hash === hash && e.data.initialData.pocket === pocket.rank)); - - if(matchingTasks.length === 0) { - return; - } - - if(matchingTasks[0].data.status !== "successful") { - return; - } - - const data = await fetch(`./api/v2/sample/${prediction.database}/${prediction.id}/public/result.json`, { - method: 'POST', - headers: { - 'Accept': 'application/json', - 'Content-Type': 'application/json' - }, - body: JSON.stringify({ - "hash": hash, - } - )}).then(res => res.json()).catch(err => console.log(err)); - if(!data) { - return; - } - - matchingTasks[0].data.responseData = data; - return { - "data": matchingTasks[0].data, - "type": ServerTaskType.Sample - }; -} - -/** - * Returns a JSX element that renders the final data of this task. - * @param responseData Response data received from the backend (i.e. the result of the task) - * @param pocket Pocket data - * @returns JSX element - */ -export function renderOnServerSampleTaskCompleted(taskData: ServerTaskData, pocket: PocketData, hash: string) { - return ( - p.rank === pocket.rank)?.count - }/> - ); -} - -export function renderOnServerSampleTaskRunning(pocket: PocketData, hash: string) { - return ( - - ); -} \ No newline at end of file diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 94d82488..676d9262 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -205,8 +205,8 @@ export class Application extends React.Component res.json()) .catch(err => { return; @@ -217,7 +217,7 @@ export class Application extends React.Component { if(!newTasks.find((t: ServerTaskData) => t.data.id === task.id)) { newTasks.push({ - "type": ServerTaskType.Sample, + "type": ServerTaskType.Docking, "data": task }); } diff --git a/frontend/client/viewer/components/pocket-dialog-details.tsx b/frontend/client/viewer/components/pocket-dialog-details.tsx index c557be5a..2c270267 100644 --- a/frontend/client/viewer/components/pocket-dialog-details.tsx +++ b/frontend/client/viewer/components/pocket-dialog-details.tsx @@ -6,12 +6,12 @@ import PocketServerParametrizedTask from "./pocket-server-parametrized-task"; import PocketRunningTasks from "./pocket-running-tasks"; import { computePocketVolume, renderOnTaskVolumeCompleted } from "../../tasks/client-atoms-volume"; -import { getSampleTaskCount, renderOnTaskSampleTasksCountCompleted } from "../../tasks/client-get-sample-tasks"; +import { getDockingTaskCount, renderOnTaskDockingTasksCountCompleted } from "../../tasks/client-get-docking-tasks"; import { PocketData, ServerTaskData, ClientTaskType, ServerTaskType } from "../../custom-types"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; -import { computeSampleTaskOnBackend, renderOnServerSampleTaskCompleted } from "../../tasks/server-sample-task"; +import { computeDockingTaskOnBackend, renderOnServerDockingTaskCompleted } from "../../tasks/server-docking-task"; /** * This component displays further details of a pocket @@ -53,10 +53,10 @@ export default class PocketDialogDetails extends React.Component
    computePocketVolume(this.props.plugin, this.props.pocket)} renderOnComplete={renderOnTaskVolumeCompleted} /> - getSampleTaskCount(this.props.prediction)} renderOnComplete={renderOnTaskSampleTasksCountCompleted}/> - computeSampleTaskOnBackend(true, this.props.prediction, this.props.pocket, hash, this.props.serverTasks)} - renderOnComplete={(data, hash) => renderOnServerSampleTaskCompleted(data, this.props.pocket, hash)} /> + getDockingTaskCount(this.props.prediction)} renderOnComplete={renderOnTaskDockingTasksCountCompleted}/> + computeDockingTaskOnBackend(true, this.props.prediction, this.props.pocket, hash, this.props.serverTasks, this.props.plugin)} + renderOnComplete={(data, hash) => renderOnServerDockingTaskCompleted(data, this.props.pocket, hash)} />
    ); diff --git a/frontend/client/viewer/components/pocket-running-tasks.tsx b/frontend/client/viewer/components/pocket-running-tasks.tsx index 2d2ab49a..efaf8ecc 100644 --- a/frontend/client/viewer/components/pocket-running-tasks.tsx +++ b/frontend/client/viewer/components/pocket-running-tasks.tsx @@ -1,7 +1,7 @@ import React from "react"; import { PocketData, ServerTaskData, ServerTaskType } from "../../custom-types"; import PocketProperty from "./pocket-property"; -import { renderOnServerSampleTaskCompleted, renderOnServerSampleTaskRunning } from "../../tasks/server-sample-task"; +import { renderOnServerDockingTaskCompleted, renderOnServerDockingTaskRunning } from "../../tasks/server-docking-task"; /** * This component displays the list of finished or incomplete tasks for a pocket. @@ -29,8 +29,8 @@ export default class PocketRunningTasks extends React.Component //finished task in this session if(e.data.responseData && e.data.initialData.pocket === this.props.pocket.rank && e.data.status === "successful") { switch(e.type) { - case ServerTaskType.Sample: - return renderOnServerSampleTaskCompleted(e, this.props.pocket, e.data.initialData.hash); + case ServerTaskType.Docking: + return renderOnServerDockingTaskCompleted(e, this.props.pocket, e.data.initialData.hash); default: return this.defaultImplementation(e, index); } @@ -38,8 +38,8 @@ export default class PocketRunningTasks extends React.Component //queued, running, incomplete task else if (e.data.initialData.pocket === this.props.pocket.rank && e.data.status !== "successful") { switch(e.type) { - case ServerTaskType.Sample: - return renderOnServerSampleTaskRunning(this.props.pocket, e.data.initialData.hash); + case ServerTaskType.Docking: + return renderOnServerDockingTaskRunning(this.props.pocket, e.data.initialData.hash); default: return this.defaultImplementation(e, index); } diff --git a/web-server/src/api_v2.py b/web-server/src/api_v2.py index cd35bf79..8db31305 100644 --- a/web-server/src/api_v2.py +++ b/web-server/src/api_v2.py @@ -4,7 +4,7 @@ from .database_v2 import register_database_v2 from .database_v3 import register_database_v3 -from .sample_task import SampleTask +from .docking_task import DockingTask api_v2 = Blueprint("api_v2", __name__) @@ -63,30 +63,30 @@ def route_get_file(database_name: str, prediction_name: str, file_name: str): @api_v2.route( - "/sample///post", + "/docking///post", methods=["POST"] ) -def route_post_sample_file(database_name: str, prediction_name: str): +def route_post_docking_file(database_name: str, prediction_name: str): data = request.get_json(force=True) or {} - st = SampleTask(database_name=database_name) - return st.post_task(prediction_name.upper(), data) + dt = DockingTask(database_name=database_name) + return dt.post_task(prediction_name.upper(), data) @api_v2.route( - "/sample///public/", + "/docking///public/", methods=["POST"] ) -def route_get_sample_file(database_name: str, prediction_name: str, file_name: str): +def route_get_docking_file_with_param(database_name: str, prediction_name: str, file_name: str): data = request.get_json(force=True) param = data.get("hash", None) if data is None or param is None: return "", 404 - st = SampleTask(database_name=database_name) - return st.get_file_with_post_param(prediction_name.upper(), file_name, param) + dt = DockingTask(database_name=database_name) + return dt.get_file_with_post_param(prediction_name.upper(), file_name, param) @api_v2.route( - "/sample///tasks", + "/docking///tasks", methods=["GET"] ) -def route_get_all_sample_tasks(database_name: str, prediction_name: str): - st = SampleTask(database_name=database_name) - return st.get_all_tasks(prediction_name.upper()) \ No newline at end of file +def route_get_all_docking_tasks(database_name: str, prediction_name: str): + dt = DockingTask(database_name=database_name) + return dt.get_all_tasks(prediction_name.upper()) \ No newline at end of file diff --git a/web-server/src/celery_client.py b/web-server/src/celery_client.py index 5088b670..5020aeff 100644 --- a/web-server/src/celery_client.py +++ b/web-server/src/celery_client.py @@ -5,8 +5,9 @@ prankweb.conf.update({ "task_routes": { + # the key is the name of the task, the value is the name of the queue 'prediction': 'p2rank', - 'sample_task': 'docking', + 'docking': 'docking', } }) @@ -29,5 +30,5 @@ def submit_directory_for_execution(directory): prankweb.send_task("prediction", args=[directory]) -def submit_directory_for_sample_task(directory, taskId): - prankweb.send_task("sample_task", args=[directory, taskId]) +def submit_directory_for_docking(directory, taskId): + prankweb.send_task("docking", args=[directory, taskId]) diff --git a/web-server/src/sample_task.py b/web-server/src/docking_task.py similarity index 78% rename from web-server/src/sample_task.py rename to web-server/src/docking_task.py index d597932a..460ae8e7 100644 --- a/web-server/src/sample_task.py +++ b/web-server/src/docking_task.py @@ -9,7 +9,7 @@ import werkzeug.utils from .commons import extensions -from .celery_client import submit_directory_for_sample_task +from .celery_client import submit_directory_for_docking @dataclasses.dataclass class TaskInfo: @@ -22,9 +22,9 @@ class TaskInfo: # Task numeric identifier - decided by the server. taskId: typing.Optional[int] = None -class SampleTask: +class DockingTask: """ - Class for handling sample tasks. Prepares directories and files for given task to get executed by Celery. + Class for handling docking tasks. Prepares directories and files for given task to get executed by Celery. """ # Database name. database_name: str @@ -33,10 +33,10 @@ class SampleTask: def __init__(self, database_name: str): """ - Constructor for SampleTask class, initializes the root path. + Constructor for DockingTask class, initializes the root path. """ self.database_name = database_name - self.root_path = os.path.join(self._get_sample_task_directory(), self.database_name) + self.root_path = os.path.join(self._get_docking_task_directory(), self.database_name) def get_file_with_post_param(self, prediction_id: str, file_name: str, data_hash: str): """ @@ -60,7 +60,7 @@ def get_file_with_post_param(self, prediction_id: str, file_name: str, data_hash return "", 404 except OSError: - return "", 404 + return "", 500 #if we successfully found the task directory, we can return the file, if it exists @@ -86,38 +86,46 @@ def post_task(self, prediction_id: str, data: dict): directory = self._get_directory(prediction_id) if directory is None: return "", 404 + if data is None: #user did not provide any data with the post request + return "", 400 if os.path.exists(directory): #if the info file exists, we have to append the new info to the existing file taskinfo = TaskInfo(directory=directory, identifier=prediction_id, data=data) - try: - with open(_info_file(taskinfo), "r+") as f: - fileData = json.load(f) - #we check if the task already exists - for task in fileData["tasks"]: - if task["initialData"] == data: - return self._response_file(directory, "info.json") - - taskinfo.taskId = len(fileData["tasks"]) - fileData["tasks"].append(_create_info(taskinfo)) - f.seek(0) - f.write(json.dumps(fileData)) - - _save_input(taskinfo, data) - submit_directory_for_sample_task(taskinfo.directory, taskinfo.taskId) - return self._response_file(taskinfo.directory, "info.json") + if(os.path.exists(_info_file(taskinfo))): + try: + with open(_info_file(taskinfo), "r+") as f: + fileData = json.load(f) + #we check if the task already exists + for task in fileData["tasks"]: + if task["initialData"] == { + "hash": data["hash"], + "pocket": data["pocket"], + }: + return self._response_file(directory, "info.json") - except: + taskinfo.taskId = len(fileData["tasks"]) + fileData["tasks"].append(_create_info(taskinfo)) + f.seek(0) + f.write(json.dumps(fileData)) + + _save_input(taskinfo, data) + submit_directory_for_docking(taskinfo.directory, taskinfo.taskId) + return self._response_file(taskinfo.directory, "info.json") + except: + #something went wrong on our side + return "", 500 + else: #else we create a new info file taskinfo.taskId = 0 _save_input(taskinfo, data) - return _create_sample_task_file(taskinfo) + return _create_docking_task_file(taskinfo) #else we create a new info file taskinfo = TaskInfo(directory=directory, identifier=prediction_id, data=data) taskinfo.taskId = 0 _save_input(taskinfo, data) - return _create_sample_task_file(taskinfo) + return _create_docking_task_file(taskinfo) def get_all_tasks(self, prediction_id: str): """ @@ -148,7 +156,7 @@ def _response_file(self, directory: str, file_name: str, mimetype=None): mimetype = self._mime_type(file_name) return flask.send_from_directory(directory, file_name, mimetype=mimetype) - def _get_sample_task_directory(self) -> str: + def _get_docking_task_directory(self) -> str: """ Returns the root directory for all tasks. """ @@ -215,10 +223,13 @@ def _create_info(taskinfo: TaskInfo): "created": now, "lastChange": now, "status": "queued", - "initialData": taskinfo.data + "initialData": { + "hash": taskinfo.data["hash"], + "pocket": taskinfo.data["pocket"] + } } -def _create_sample_task_file(taskinfo: TaskInfo, force=False): +def _create_docking_task_file(taskinfo: TaskInfo, force=False): """ Creates a directory for a task and initializes it. """ @@ -228,7 +239,7 @@ def _create_sample_task_file(taskinfo: TaskInfo, force=False): if not force: return _prediction_can_not_be_created(taskinfo) info = _prepare_prediction_directory(taskinfo) - submit_directory_for_sample_task(taskinfo.directory, taskinfo.taskId) + submit_directory_for_docking(taskinfo.directory, taskinfo.taskId) return flask.make_response(flask.jsonify(info), 201) def _prediction_can_not_be_created(taskinfo: TaskInfo): From 17798beee2b21fd86606752ca3d3babd46427c0f Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sun, 30 Apr 2023 15:59:38 +0200 Subject: [PATCH 062/154] Frontend fixes --- frontend/client/tasks/server-docking-task.tsx | 63 +++++++++---------- frontend/client/viewer/application.tsx | 10 ++- 2 files changed, 38 insertions(+), 35 deletions(-) diff --git a/frontend/client/tasks/server-docking-task.tsx b/frontend/client/tasks/server-docking-task.tsx index 6df31856..65e00d50 100644 --- a/frontend/client/tasks/server-docking-task.tsx +++ b/frontend/client/tasks/server-docking-task.tsx @@ -29,7 +29,6 @@ function computeBoundingBox(plugin: PluginUIContext, pocket: PocketData) { //compute max distance from the center let maxDistance = 0; coords.forEach(coord => { - console.log(coord); const distance = twoPointsDistance(coord, center); if(distance > maxDistance) { maxDistance = distance; @@ -67,6 +66,34 @@ export async function computeDockingTaskOnBackend(firstFetch: boolean, predictio return; } + let matchingTasks = (serverTasks.filter((e: ServerTaskData) => e.type === ServerTaskType.Docking && e.data.initialData.hash === hash && e.data.initialData.pocket === pocket.rank)); + + //check if the task is finished + if(matchingTasks.length !== 0) { + if(matchingTasks[0].data.status === "successful") { + const data = await fetch(`./api/v2/docking/${prediction.database}/${prediction.id}/public/result.json`, { + method: 'POST', + headers: { + 'Accept': 'application/json', + 'Content-Type': 'application/json' + }, + body: JSON.stringify({ + "hash": hash, + } + )}).then(res => res.json()).catch(err => console.log(err)); + if(!data) { + return; + } + + matchingTasks[0].data.responseData = data; + return { + "data": matchingTasks[0].data, + "type": ServerTaskType.Docking + }; + } + return; + } + const box = computeBoundingBox(plugin, pocket); await fetch(`./api/v2/docking/${prediction.database}/${prediction.id}/post`, { @@ -81,42 +108,12 @@ export async function computeDockingTaskOnBackend(firstFetch: boolean, predictio "bounding_box": box }), }).then((res) => { - setTimeout(() => {}, 500); //wait for the backend to process the request + //let the next call handle the response } ).catch(err => { console.log(err); }); - - //check if the task is finished - let matchingTasks = (serverTasks.filter((e: ServerTaskData) => e.type === ServerTaskType.Docking && e.data.initialData.hash === hash && e.data.initialData.pocket === pocket.rank)); - - if(matchingTasks.length === 0) { - return; - } - - if(matchingTasks[0].data.status !== "successful") { - return; - } - - const data = await fetch(`./api/v2/docking/${prediction.database}/${prediction.id}/public/result.json`, { - method: 'POST', - headers: { - 'Accept': 'application/json', - 'Content-Type': 'application/json' - }, - body: JSON.stringify({ - "hash": hash, - } - )}).then(res => res.json()).catch(err => console.log(err)); - if(!data) { - return; - } - - matchingTasks[0].data.responseData = data; - return { - "data": matchingTasks[0].data, - "type": ServerTaskType.Docking - }; + return; } /** diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 676d9262..2f3e51a5 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -10,7 +10,7 @@ import PocketList from "./components/pocket-list"; import TaskList from "./components/task-list"; import { sendDataToPlugins } from './data-loader'; -import { PocketsViewType, PolymerColorType, PolymerViewType, PredictionData, ReactApplicationProps, ReactApplicationState, ServerTaskData, ServerTaskType } from "../custom-types"; +import { PocketsViewType, PolymerColorType, PolymerViewType, PredictionData, ReactApplicationProps, ReactApplicationState, ServerTaskData, ServerTaskDataContents, ServerTaskType } from "../custom-types"; import { DefaultPluginUISpec } from 'molstar/lib/mol-plugin-ui/spec'; import { createPluginUI } from 'molstar/lib/mol-plugin-ui'; @@ -213,14 +213,20 @@ export class Application extends React.Component { + json["tasks"].forEach((task: ServerTaskDataContents) => { if(!newTasks.find((t: ServerTaskData) => t.data.id === task.id)) { newTasks.push({ "type": ServerTaskType.Docking, "data": task }); } + else if (newTasks.find((t: ServerTaskData) => t.data.status !== task.status)) { + //update the status + const index = newTasks.findIndex((t: ServerTaskData) => t.data.id === task.id); + newTasks[index].data = task; + } }); this.setState({serverTasks: newTasks}); } From 97372f30493989ac6c1ea3e6a623ceecd8e93aef Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sun, 30 Apr 2023 16:15:20 +0200 Subject: [PATCH 063/154] Frontend more changes --- frontend/client/tasks/server-docking-task.tsx | 6 +++ .../components/pocket-running-tasks.tsx | 39 ++++++++++++------- .../client/viewer/components/task-list.tsx | 3 ++ 3 files changed, 34 insertions(+), 14 deletions(-) diff --git a/frontend/client/tasks/server-docking-task.tsx b/frontend/client/tasks/server-docking-task.tsx index 65e00d50..ebe22af5 100644 --- a/frontend/client/tasks/server-docking-task.tsx +++ b/frontend/client/tasks/server-docking-task.tsx @@ -134,4 +134,10 @@ export function renderOnServerDockingTaskRunning(pocket: PocketData, hash: strin return ( ); +} + +export function renderOnServerDockingTaskFailed(pocket: PocketData, hash: string) { + return ( + + ); } \ No newline at end of file diff --git a/frontend/client/viewer/components/pocket-running-tasks.tsx b/frontend/client/viewer/components/pocket-running-tasks.tsx index efaf8ecc..4d32b029 100644 --- a/frontend/client/viewer/components/pocket-running-tasks.tsx +++ b/frontend/client/viewer/components/pocket-running-tasks.tsx @@ -1,7 +1,7 @@ import React from "react"; import { PocketData, ServerTaskData, ServerTaskType } from "../../custom-types"; import PocketProperty from "./pocket-property"; -import { renderOnServerDockingTaskCompleted, renderOnServerDockingTaskRunning } from "../../tasks/server-docking-task"; +import { renderOnServerDockingTaskCompleted, renderOnServerDockingTaskFailed, renderOnServerDockingTaskRunning } from "../../tasks/server-docking-task"; /** * This component displays the list of finished or incomplete tasks for a pocket. @@ -23,29 +23,40 @@ export default class PocketRunningTasks extends React.Component } render() { + type MethodMap = { + [key in ServerTaskType]: (e: ServerTaskData) => JSX.Element; + } + + const completedMethods: MethodMap = { + [ServerTaskType.Docking]: (e: ServerTaskData) => renderOnServerDockingTaskCompleted(e, this.props.pocket, e.data.initialData.hash) + } + + const runningMethods: MethodMap = { + [ServerTaskType.Docking]: (e: ServerTaskData) => renderOnServerDockingTaskRunning(this.props.pocket, e.data.initialData.hash) + } + + const failedMethods: MethodMap = { + [ServerTaskType.Docking]: (e: ServerTaskData) => renderOnServerDockingTaskFailed(this.props.pocket, e.data.initialData.hash) + } + return (
    {this.props.inDialog && this.props.serverTasks.map((e: ServerTaskData, index) => { //finished task in this session if(e.data.responseData && e.data.initialData.pocket === this.props.pocket.rank && e.data.status === "successful") { - switch(e.type) { - case ServerTaskType.Docking: - return renderOnServerDockingTaskCompleted(e, this.props.pocket, e.data.initialData.hash); - default: - return this.defaultImplementation(e, index); - } + return completedMethods[e.type](e); } //queued, running, incomplete task - else if (e.data.initialData.pocket === this.props.pocket.rank && e.data.status !== "successful") { - switch(e.type) { - case ServerTaskType.Docking: - return renderOnServerDockingTaskRunning(this.props.pocket, e.data.initialData.hash); - default: - return this.defaultImplementation(e, index); - } + else if (e.data.initialData.pocket === this.props.pocket.rank && e.data.status === "queued" || e.data.status === "running") { + return runningMethods[e.type](e); + } + //failed task + else if (e.data.initialData.pocket === this.props.pocket.rank && e.data.status === "failed") { + return failedMethods[e.type](e); } //NOT rendering tasks that are not related to this pocket //and tasks not completed in this session + return this.defaultImplementation(e, index); })}
    ); diff --git a/frontend/client/viewer/components/task-list.tsx b/frontend/client/viewer/components/task-list.tsx index 90b97f1c..7cdae247 100644 --- a/frontend/client/viewer/components/task-list.tsx +++ b/frontend/client/viewer/components/task-list.tsx @@ -80,6 +80,9 @@ class TaskListContent extends React.Component<{ else if(task.data["status"] === "running") { return
  • {`${task.type} ${task.data.id} ${task.data.initialData["hash"]} ${task.data.lastChange} running`}
  • } + else if(task.data["status"] === "failed") { + return
  • {`${task.type} ${task.data.id} ${task.data.initialData["hash"]} ${task.data.lastChange} failed`}
  • + } else if(task.data["status"] === "queued") { return
  • {`${task.type} ${task.data.id} ${task.data.initialData["hash"]} ${task.data.lastChange} queued`}
  • } From 8e4f395bad05da3132fa180d0eb17c304748f6da Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 1 May 2023 01:17:07 +0200 Subject: [PATCH 064/154] Implemented basic docking --- executor-docking/Dockerfile | 42 ++++++++- executor-docking/bin/lepro_linux_x86 | Bin 0 -> 393682 bytes executor-docking/celery_docking.py | 2 + executor-docking/run_docking.py | 84 ++++++++++++++++++ executor-docking/run_task.py | 74 ++++++++++----- frontend/client/tasks/server-docking-task.tsx | 63 +++++++++++-- .../components/pocket-dialog-details.tsx | 6 +- .../components/pocket-running-tasks.tsx | 10 ++- .../pocket-server-parametrized-task.tsx | 9 +- web-server/src/docking_task.py | 4 +- 10 files changed, 256 insertions(+), 38 deletions(-) create mode 100644 executor-docking/bin/lepro_linux_x86 create mode 100644 executor-docking/run_docking.py diff --git a/executor-docking/Dockerfile b/executor-docking/Dockerfile index b5f3f887..cd983c61 100644 --- a/executor-docking/Dockerfile +++ b/executor-docking/Dockerfile @@ -9,10 +9,9 @@ ARG CELERY_BROKER_URL="amqp://user-develop:develop@localhost:5672" RUN apt-get update \ && apt-get -y --no-install-recommends install \ wget curl \ - python3 python3-pip \ - openjdk-17-jre-headless \ - libgomp1 vim \ - python3-venv + python3 python3-pip vim \ + python3-venv \ + openbabel libopenbabel-dev nano ARG UID=5988 ARG GID=5988 @@ -39,6 +38,41 @@ RUN pip3 install -r requirements.txt COPY --chown=user:user ./executor-docking/ ./ RUN chmod a+x ./run_task.py +# docking tools +# lepro as a binary +RUN chmod a+x ./bin/lepro_linux_x86 + +ENV PATH="${PATH}:/opt/executor-docking/bin" + +# install meeko and other python packages +RUN pip3 install -U meeko numpy scipy rdkit pandas + +# install adfr +# inspired by https://github.com/coleygroup/pyscreener + +RUN wget -O ADFRsuite.tar.gz https://ccsb.scripps.edu/adfr/download/1038/ -q \ + && mv ADFRsuite.tar.gz ../ && cd .. \ + && tar -xzvf ADFRsuite.tar.gz \ + && cd ADFRsuite_* \ + && echo "Y" | ./install.sh -d . -c 0 \ + && cd .. \ + && rm -rf ADFRsuite.tar.gz + +# a trick to work around a bug in MolKit MMCIF parser (MolKit/__init__.py calls MMCIFParser with an argument modelsAs=True, which is not supported by the parser) +RUN sed -i 's/^ parser = MMCIFParser(filename, modelsAs=modelsAs)$/ parser = MMCIFParser(filename)/' /opt/ADFRsuite_x86_64Linux_1.0/CCSBpckgs/MolKit/__init__.py + +ENV PATH="${PATH}:/opt/ADFRsuite_x86_64Linux_1.0/bin" + +# install vina + +RUN mkdir /opt/vina && cd /opt/vina \ + && wget https://vina.scripps.edu/wp-content/uploads/sites/55/2020/12/autodock_vina_1_1_2_linux_x86.tgz -q \ + && tar -xzvf autodock_vina_1_1_2_linux_x86.tgz \ + && mkdir /opt/vina/bin \ + && mv autodock_vina_1_1_2_linux_x86/bin/* /opt/vina/bin/ + +ENV PATH="${PATH}:/opt/vina/bin" + # # environment WORKDIR /opt/executor-docking diff --git a/executor-docking/bin/lepro_linux_x86 b/executor-docking/bin/lepro_linux_x86 new file mode 100644 index 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zY8`_8%c}62?PwM2o;Eyg&~cW$RH!0vx`ja^gEPlBzEs*&Mv0z zM(==A)=`2|8d-Tje5s2$7T;PONg53AFD+pAtCgu=mCduqfLi4Gh_>+%HUve>>$Cz+ zPHhg=y}lzXc=D^e*tuI-5p8_aIB4O|1Q^HVfrLd+Xlq1%Q+t(O#BH5QMH00PAh(>_ zM17=n3Q0D$`ogXhH93iG@qx@nCe~akenlg)8D82z!Y4a=S//public/ + #split docking_directory to get database_name and prediction_name result = [] - for pocket in prediction["pockets"]: - result.append({ - "rank": pocket["rank"], - "count": len(pocket["residues"]) - }) - + database_name = docking_directory.split("/")[4] + if "user-upload" in database_name: + prediction_name = docking_directory.split("/")[5] + else: + prediction_name = docking_directory.split("/")[6] + + result_url = "./api/v2/docking/" + database_name + "/" + prediction_name + "/public/out_vina.pdbqt" + result.append({ + "url": result_url + }) result_json = json.dumps(result) - #save the result file - os.makedirs(os.path.join(directory, str(taskId), "public"), exist_ok=True) + #save the result file (this directory should already exist, though...) + os.makedirs(os.path.join(docking_directory, str(taskId), "public"), exist_ok=True) with open(result_file, "w", encoding="utf-8") as stream: try: diff --git a/frontend/client/tasks/server-docking-task.tsx b/frontend/client/tasks/server-docking-task.tsx index ebe22af5..d56184ef 100644 --- a/frontend/client/tasks/server-docking-task.tsx +++ b/frontend/client/tasks/server-docking-task.tsx @@ -1,4 +1,5 @@ import React from "react"; +import { Button } from '@mui/material'; import { PredictionInfo } from "../prankweb-api"; import { PocketData, ServerTaskType, Point3D } from "../custom-types"; @@ -123,21 +124,73 @@ export async function computeDockingTaskOnBackend(firstFetch: boolean, predictio * @returns JSX element */ export function renderOnServerDockingTaskCompleted(taskData: ServerTaskData, pocket: PocketData, hash: string) { + let shorterHash = hash; + if(hash.length > 15) { + shorterHash = hash.substring(0, 15) + "..."; + } return ( - p.rank === pocket.rank)?.count + + + ) }/> ); } export function renderOnServerDockingTaskRunning(pocket: PocketData, hash: string) { + let shorterHash = hash; + if(hash.length > 15) { + shorterHash = hash.substring(0, 15) + "..."; + } return ( - + ); } export function renderOnServerDockingTaskFailed(pocket: PocketData, hash: string) { + let shorterHash = hash; + if(hash.length > 15) { + shorterHash = hash.substring(0, 15) + "..."; + } return ( - + ); -} \ No newline at end of file +} + +export function dockingHash(prediction: PredictionInfo, pocket: PocketData, formData: string) { + return formData; +} + +function downloadResult(hash: string, fileURL: string) { + // https://stackoverflow.com/questions/50694881/how-to-download-file-in-react-js + fetch(fileURL, { + method: 'POST', + headers: { + 'Accept': 'application/json', + 'Content-Type': 'application/json' + }, + body: JSON.stringify({ + "hash": hash, + }) + }) + .then((response) => response.blob()) + .then((blob) => { + // Create blob link to download + const url = window.URL.createObjectURL( + new Blob([blob]), + ); + const link = document.createElement('a'); + link.href = url; + link.setAttribute( + 'download', + `result.pdbqt`, + ); + + document.body.appendChild(link); + link.click(); + link.parentNode!.removeChild(link); + }); +} diff --git a/frontend/client/viewer/components/pocket-dialog-details.tsx b/frontend/client/viewer/components/pocket-dialog-details.tsx index 2c270267..143b7fbb 100644 --- a/frontend/client/viewer/components/pocket-dialog-details.tsx +++ b/frontend/client/viewer/components/pocket-dialog-details.tsx @@ -11,7 +11,7 @@ import { getDockingTaskCount, renderOnTaskDockingTasksCountCompleted } from "../ import { PocketData, ServerTaskData, ClientTaskType, ServerTaskType } from "../../custom-types"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; import { PredictionInfo } from "../../prankweb-api"; -import { computeDockingTaskOnBackend, renderOnServerDockingTaskCompleted } from "../../tasks/server-docking-task"; +import { computeDockingTaskOnBackend, dockingHash, renderOnServerDockingTaskCompleted } from "../../tasks/server-docking-task"; /** * This component displays further details of a pocket @@ -55,8 +55,8 @@ export default class PocketDialogDetails extends React.Component computePocketVolume(this.props.plugin, this.props.pocket)} renderOnComplete={renderOnTaskVolumeCompleted} /> getDockingTaskCount(this.props.prediction)} renderOnComplete={renderOnTaskDockingTasksCountCompleted}/> computeDockingTaskOnBackend(true, this.props.prediction, this.props.pocket, hash, this.props.serverTasks, this.props.plugin)} - renderOnComplete={(data, hash) => renderOnServerDockingTaskCompleted(data, this.props.pocket, hash)} /> + modalDescription={"Enter the molecule for docking in pocket " + this.props.pocket.rank + " (in SMILES format)"} compute={(hash) => computeDockingTaskOnBackend(true, this.props.prediction, this.props.pocket, hash, this.props.serverTasks, this.props.plugin)} + renderOnComplete={(data, hash) => renderOnServerDockingTaskCompleted(data, this.props.pocket, hash)} hashMethod={(prediction, pocket, formData) => dockingHash(prediction, pocket, formData)}/> ); diff --git a/frontend/client/viewer/components/pocket-running-tasks.tsx b/frontend/client/viewer/components/pocket-running-tasks.tsx index 4d32b029..6afbf072 100644 --- a/frontend/client/viewer/components/pocket-running-tasks.tsx +++ b/frontend/client/viewer/components/pocket-running-tasks.tsx @@ -52,11 +52,15 @@ export default class PocketRunningTasks extends React.Component } //failed task else if (e.data.initialData.pocket === this.props.pocket.rank && e.data.status === "failed") { - return failedMethods[e.type](e); + const date = Date.parse(e.data.lastChange); + const now = Date.now(); + //if the task failed in the last 60 minutes, we display it, otherwise we ignore it + if(now - date < 60 * 60 * 1000) { + return failedMethods[e.type](e); + } } //NOT rendering tasks that are not related to this pocket - //and tasks not completed in this session - return this.defaultImplementation(e, index); + //and tasks not completed in this session (apart from failed/running tasks) })} ); diff --git a/frontend/client/viewer/components/pocket-server-parametrized-task.tsx b/frontend/client/viewer/components/pocket-server-parametrized-task.tsx index 18f72d5d..402bb3f7 100644 --- a/frontend/client/viewer/components/pocket-server-parametrized-task.tsx +++ b/frontend/client/viewer/components/pocket-server-parametrized-task.tsx @@ -24,6 +24,7 @@ export default class PocketServerParametrizedTask extends React.Component modalDescription: string, compute: (hash: string) => Promise renderOnComplete: (responseData: ServerTaskData, hash: string) => JSX.Element + hashMethod: (prediction: PredictionInfo, pocket: PocketData, formData: string) => string }, { taskData: ServerTaskData | undefined, computed: boolean, @@ -43,7 +44,7 @@ export default class PocketServerParametrizedTask extends React.Component async clickCompute() { if(this.state.hash === "") { - const hash = this.state.formData; + const hash = this.props.hashMethod(this.props.prediction, this.props.pocket, this.state.formData); this.setState({hash: hash}); } @@ -70,13 +71,17 @@ export default class PocketServerParametrizedTask extends React.Component // currently after clicking the compute button, a modal is shown for the user to input the task parameters render() { + let shortHash = this.state.hash; + if(this.state.hash.length > 15) { + shortHash = this.state.hash.substring(0, 15) + "..."; + } return (

    { !this.state.computed &&
    { - this.props.title + ((this.state.hash === "") ? "" : " (" + this.state.hash + ")") + this.props.title + ((this.state.hash === "") ? "" : " (" + shortHash + ")") }:
    typing.Optional[str]: """ if not re.match("[_,\w]+", prediction_id): return None + if "user-upload" in self.database_name: + return os.path.join(self.root_path, prediction_id) directory = prediction_id[1:3] - return os.path.join(self.root_path, directory, prediction_id) + return os.path.join(self.root_path, directory, prediction_id) def _response_file(self, directory: str, file_name: str, mimetype=None): """ From 69a8610523243d8ce857171a4e59e2c7413cf065 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Tue, 2 May 2023 14:34:12 +0200 Subject: [PATCH 065/154] Documentation, code cleanup --- frontend/client/prankweb-api.ts | 2 +- frontend/client/tasks/server-docking-task.tsx | 45 ++++++++++++++++--- web-server/src/docking_task.py | 2 +- 3 files changed, 40 insertions(+), 9 deletions(-) diff --git a/frontend/client/prankweb-api.ts b/frontend/client/prankweb-api.ts index 8683d424..bd8155a8 100644 --- a/frontend/client/prankweb-api.ts +++ b/frontend/client/prankweb-api.ts @@ -44,7 +44,7 @@ export async function fetchPrediction( // We need to navigate to the root, and then we can request the data. const url = getApiEndpoint(database, id); const response = await fetch(url); - var result; + let result; try { result = await response.json(); } catch { diff --git a/frontend/client/tasks/server-docking-task.tsx b/frontend/client/tasks/server-docking-task.tsx index d56184ef..1c25095a 100644 --- a/frontend/client/tasks/server-docking-task.tsx +++ b/frontend/client/tasks/server-docking-task.tsx @@ -9,18 +9,24 @@ import PocketProperty from "../viewer/components/pocket-property"; import { getPocketAtomCoordinates } from "../viewer/molstar-visualise"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; +/** + * Computes distance of 2 points in 3D space. + * @param point1 First point + * @param point2 Second point + * @returns Distance between the points +*/ function twoPointsDistance(point1: Point3D, point2: Point3D) { return Math.sqrt(Math.pow(point1.x - point2.x, 2) + Math.pow(point1.y - point2.y, 2) + Math.pow(point1.z - point2.z, 2)); } +/** + * Computes a bounding box for the given pocket. + * @param plugin Mol* plugin + * @param pocket Pocket data + * @returns Bounding box +*/ function computeBoundingBox(plugin: PluginUIContext, pocket: PocketData) { - const coords = getPocketAtomCoordinates(plugin, pocket.surface); - - /*const points: Array> = []; - coords.forEach(coord => { - console.log(coord); - points.push([coord.x, coord.y, coord.z]); - });*/ + const coords: Point3D[] = getPocketAtomCoordinates(plugin, pocket.surface); const center: Point3D = { x: Number(pocket.center[0]), @@ -140,6 +146,12 @@ export function renderOnServerDockingTaskCompleted(taskData: ServerTaskData, poc ); } +/** + * Returns a JSX element that renders the visuals when the task is running. + * @param pocket Pocket data + * @param hash Task identifier (hash) + * @returns JSX element + */ export function renderOnServerDockingTaskRunning(pocket: PocketData, hash: string) { let shorterHash = hash; if(hash.length > 15) { @@ -150,6 +162,12 @@ export function renderOnServerDockingTaskRunning(pocket: PocketData, hash: strin ); } +/** + * Returns a JSX element that renders the visuals when the task failed. + * @param pocket Pocket data + * @param hash Task identifier (hash) + * @returns JSX element +*/ export function renderOnServerDockingTaskFailed(pocket: PocketData, hash: string) { let shorterHash = hash; if(hash.length > 15) { @@ -160,10 +178,23 @@ export function renderOnServerDockingTaskFailed(pocket: PocketData, hash: string ); } +/** + * Returns a hash that identifies this task, in this case directly the user input. + * @param prediction Prediction info + * @param pocket Pocket data + * @param formData Form data (user input) + * @returns Computed hash +*/ export function dockingHash(prediction: PredictionInfo, pocket: PocketData, formData: string) { return formData; } +/** + * Downloads the result of the task. + * @param hash Task identifier (hash) + * @param fileURL URL to download the result from + * @returns void +*/ function downloadResult(hash: string, fileURL: string) { // https://stackoverflow.com/questions/50694881/how-to-download-file-in-react-js fetch(fileURL, { diff --git a/web-server/src/docking_task.py b/web-server/src/docking_task.py index c9cc31d9..adf3aa06 100644 --- a/web-server/src/docking_task.py +++ b/web-server/src/docking_task.py @@ -262,4 +262,4 @@ def _prediction_can_not_be_created(taskinfo: TaskInfo): return "", 500 if __name__ == "__main__": - pass \ No newline at end of file + pass From dfd8a83265604899fcd01a706e3bf0c6eeb22818 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Wed, 3 May 2023 10:43:12 +0200 Subject: [PATCH 066/154] Fixed showing previously computed tasks --- frontend/client/viewer/application.tsx | 2 ++ 1 file changed, 2 insertions(+) diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 2f3e51a5..e572a140 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -225,6 +225,8 @@ export class Application extends React.Component t.data.status !== task.status)) { //update the status const index = newTasks.findIndex((t: ServerTaskData) => t.data.id === task.id); + let formerResponseData = newTasks[index].data.responseData; + task.responseData = formerResponseData; newTasks[index].data = task; } }); From e8d8dd86dbec8657462734208119174a86bccf36 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Thu, 4 May 2023 19:51:33 +0200 Subject: [PATCH 067/154] Frontend design changes --- frontend/client/tasks/server-docking-task.tsx | 2 +- frontend/client/viewer/components/task-list.tsx | 13 +------------ 2 files changed, 2 insertions(+), 13 deletions(-) diff --git a/frontend/client/tasks/server-docking-task.tsx b/frontend/client/tasks/server-docking-task.tsx index 1c25095a..dc62eb7b 100644 --- a/frontend/client/tasks/server-docking-task.tsx +++ b/frontend/client/tasks/server-docking-task.tsx @@ -138,7 +138,7 @@ export function renderOnServerDockingTaskCompleted(taskData: ServerTaskData, poc - ) diff --git a/frontend/client/viewer/components/task-list.tsx b/frontend/client/viewer/components/task-list.tsx index 7cdae247..0e6b1e71 100644 --- a/frontend/client/viewer/components/task-list.tsx +++ b/frontend/client/viewer/components/task-list.tsx @@ -74,18 +74,7 @@ class TaskListContent extends React.Component<{ return (
      {this.props.tasks.map((task: ServerTaskData, index: number) => { - if(task.data["status"] === "successful") { - return
    • {`${task.type} ${task.data.id} ${task.data.initialData["hash"]} ${task.data.lastChange}`}
    • - } - else if(task.data["status"] === "running") { - return
    • {`${task.type} ${task.data.id} ${task.data.initialData["hash"]} ${task.data.lastChange} running`}
    • - } - else if(task.data["status"] === "failed") { - return
    • {`${task.type} ${task.data.id} ${task.data.initialData["hash"]} ${task.data.lastChange} failed`}
    • - } - else if(task.data["status"] === "queued") { - return
    • {`${task.type} ${task.data.id} ${task.data.initialData["hash"]} ${task.data.lastChange} queued`}
    • - } + return
    • {`Task ${task.data.id} (hash ${task.data.initialData["hash"]}, pocket ${task.data.initialData.pocket}, last updated ${task.data.lastChange})`}
    • })}
    ) From 41fbf280bee1c984b63f7cf2c71a2391d178fb13 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Sun, 7 May 2023 17:09:58 +0200 Subject: [PATCH 068/154] Added default docker-compose env variables --- docker-compose.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 31fac70e..045624fe 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -31,7 +31,7 @@ services: build: https://github.com/mher/flower.git command: "celery flower --url_prefix=service/flower" environment: - CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672" + CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER:-user}:${RABBITMQ_DEFAULT_PASS:-1234}@rabbitmq:5672" depends_on: rabbitmq: condition: service_healthy @@ -46,7 +46,7 @@ services: rabbitmq: condition: service_healthy environment: - CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672" + CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER:-user}:${RABBITMQ_DEFAULT_PASS:-1234}@rabbitmq:5672" PRANKWEB_DATA_PREDICTIONS: "/data/prankweb/predictions/" PRANKWEB_DATA_DOCKING: "/data/prankweb/docking/" volumes: @@ -64,7 +64,7 @@ services: rabbitmq: condition: service_healthy environment: - CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672" + CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER:-user}:${RABBITMQ_DEFAULT_PASS:-1234}@rabbitmq:5672" LOCK_DIRECTORY: "/data/prankweb/lock" volumes: - conservation:/data/conservation @@ -75,11 +75,11 @@ services: context: ./ dockerfile: ./executor-docking/Dockerfile args: - UID: ${UID} - GID: ${GID} + UID: ${UID:-5988} + GID: ${GID:-5988} command: ["celery", "--app=celery_docking", "worker", "--queues=docking", "--concurrency=4", "--hostname=executor-docking"] environment: - CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672" + CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER:-user}:${RABBITMQ_DEFAULT_PASS:-1234}@rabbitmq:5672" restart: unless-stopped volumes: - docking:/data/prankweb/docking From dfe4373b78a15e4a2857c26b046f919c18058f80 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Mon, 10 Jul 2023 21:19:11 +0200 Subject: [PATCH 069/154] temp-fix p2rank Dockerfile --- executor-p2rank/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/executor-p2rank/Dockerfile b/executor-p2rank/Dockerfile index 60f12f9d..a67a9a7d 100644 --- a/executor-p2rank/Dockerfile +++ b/executor-p2rank/Dockerfile @@ -107,7 +107,7 @@ RUN apt-get update \ && apt-get -y --no-install-recommends install \ wget curl \ python3 python3-pip python3-venv \ - openjdk-17-jre-headless \ + default-jre \ libgomp1 vim # https://github.com/python/cpython/issues/102134 From 22aff9b9134caa42378639f011bf6e65ee050ecb Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Tue, 11 Jul 2023 13:12:48 +0200 Subject: [PATCH 070/154] Added docking to docker-compose-prankweb --- docker-compose-prankweb.yml | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) diff --git a/docker-compose-prankweb.yml b/docker-compose-prankweb.yml index cc4e6f10..6dd0d6a8 100644 --- a/docker-compose-prankweb.yml +++ b/docker-compose-prankweb.yml @@ -61,16 +61,34 @@ services: UID: ${UID} GID: ${GID} command: ["celery", "--app=celery_p2rank", "worker", "--queues=p2rank", "--concurrency=4", "--hostname=executor-p2rank"] + depends_on: + rabbitmq: + condition: service_healthy environment: CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672" LOCK_DIRECTORY: "/data/prankweb/lock" restart: unless-stopped volumes: - conservation:/data/conservation - - predictions:/data/prankweb + - predictions:/data/prankweb/predictions + - docking:/data/prankweb/docking + executor-docking: + build: + context: ./ + dockerfile: ./executor-docking/Dockerfile + args: + UID: ${UID} + GID: ${GID} + command: ["celery", "--app=celery_docking", "worker", "--queues=docking", "--concurrency=4", "--hostname=executor-docking"] + environment: + CELERY_BROKER_URL: "amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672" + restart: unless-stopped + volumes: + - docking:/data/prankweb/docking + - predictions:/data/prankweb/predictions depends_on: rabbitmq: - condition: service_healthy + condition: service_healthy monitor: build: context: ./ @@ -101,3 +119,6 @@ volumes: services: external: True name: prankweb_services + docking: + external: True + name: prankweb_docking \ No newline at end of file From f00ac9ef9614e9f31bdf2890045c2a39dde6c3e0 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Wed, 12 Jul 2023 13:00:09 +0200 Subject: [PATCH 071/154] Show number of tasks only related to the pocket --- frontend/client/tasks/client-get-docking-tasks.tsx | 8 ++++---- .../client/viewer/components/pocket-dialog-details.tsx | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/frontend/client/tasks/client-get-docking-tasks.tsx b/frontend/client/tasks/client-get-docking-tasks.tsx index f518a79c..8eb3d1b9 100644 --- a/frontend/client/tasks/client-get-docking-tasks.tsx +++ b/frontend/client/tasks/client-get-docking-tasks.tsx @@ -1,6 +1,6 @@ import React from "react"; -import { ClientTaskData, ClientTaskType } from "../custom-types"; +import { ClientTaskData, ClientTaskType, PocketData, ServerTaskDataContents } from "../custom-types"; import { PredictionInfo } from "../prankweb-api"; /** @@ -8,17 +8,17 @@ import { PredictionInfo } from "../prankweb-api"; * @param prediction Prediction info * @returns Data with a number of tasks */ -export async function getDockingTaskCount(prediction: PredictionInfo): Promise { +export async function getDockingTaskCount(prediction: PredictionInfo, pocket: PocketData): Promise { const json = await fetch(`./api/v2/docking/${prediction.database}/${prediction.id}/tasks`) .then(res => res.json()) .catch(err => { console.log(err); - setTimeout(() => getDockingTaskCount(prediction), 1000); + setTimeout(() => getDockingTaskCount(prediction, pocket), 1000); }); if(json) { - const numOfTasks = json["tasks"].length; + const numOfTasks = json["tasks"].filter((task: ServerTaskDataContents) => task.initialData.pocket == pocket.rank).length; return { "data": numOfTasks, "type": ClientTaskType.DockingTaskCount diff --git a/frontend/client/viewer/components/pocket-dialog-details.tsx b/frontend/client/viewer/components/pocket-dialog-details.tsx index 143b7fbb..92ae8ed1 100644 --- a/frontend/client/viewer/components/pocket-dialog-details.tsx +++ b/frontend/client/viewer/components/pocket-dialog-details.tsx @@ -53,7 +53,7 @@ export default class PocketDialogDetails extends React.Component
    computePocketVolume(this.props.plugin, this.props.pocket)} renderOnComplete={renderOnTaskVolumeCompleted} /> - getDockingTaskCount(this.props.prediction)} renderOnComplete={renderOnTaskDockingTasksCountCompleted}/> + getDockingTaskCount(this.props.prediction, this.props.pocket)} renderOnComplete={renderOnTaskDockingTasksCountCompleted}/> computeDockingTaskOnBackend(true, this.props.prediction, this.props.pocket, hash, this.props.serverTasks, this.props.plugin)} renderOnComplete={(data, hash) => renderOnServerDockingTaskCompleted(data, this.props.pocket, hash)} hashMethod={(prediction, pocket, formData) => dockingHash(prediction, pocket, formData)}/> From 8b560226071a9181a39d170b10fe423776a704a9 Mon Sep 17 00:00:00 2001 From: Lukas Polak Date: Thu, 10 Aug 2023 14:55:18 +0200 Subject: [PATCH 072/154] Initial layout changes --- frontend/client/viewer/application.css | 24 +++++++------ frontend/client/viewer/application.tsx | 12 +++++-- .../components/visualization-tool-box.css | 12 +++++++ .../components/visualization-tool-box.tsx | 35 +++++++++++++++++++ frontend/client/viewer/rcsb-visualise.ts | 4 +++ frontend/client/viewer/viewer.html | 11 ++++-- 6 files changed, 81 insertions(+), 17 deletions(-) create mode 100644 frontend/client/viewer/components/visualization-tool-box.css create mode 100644 frontend/client/viewer/components/visualization-tool-box.tsx diff --git a/frontend/client/viewer/application.css b/frontend/client/viewer/application.css index 1877f999..ff58129e 100644 --- a/frontend/client/viewer/application.css +++ b/frontend/client/viewer/application.css @@ -12,9 +12,16 @@ } #application-molstar { - position: absolute; - bottom: 0; - height: 70vh; + position: relative; + height: 55vh; + width: 100%; +} + +#visualization-toolbox { + position: relative; + height: 15vh; + width: 100%; + background-color: lightgray; } #application-rcsb { @@ -22,6 +29,7 @@ overflow-x: auto; overflow-y: auto; height: calc(30vh - 68px); + margin-bottom: 10px; } #application-rcsb::-webkit-scrollbar { @@ -42,8 +50,9 @@ background: #555; } -#pocket-list-aside { +#information { height: 100%; + overflow-y: auto; } @media (max-width: 767px) { @@ -63,13 +72,6 @@ } } -/* Set for Bootstrap md breakpoint. */ -@media (min-width: 768px) { - #pocket-list-aside { - overflow-y: scroll; - } -} - #sequence-view { user-select: none; } diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index e572a140..1425f9d4 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -17,6 +17,7 @@ import { createPluginUI } from 'molstar/lib/mol-plugin-ui'; import 'molstar/lib/mol-plugin-ui/skin/light.scss'; import { RcsbFv, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro"; import { highlightSurfaceAtomsInViewerLabelId, overPaintPolymer, updatePolymerView, showPocketInCurrentRepresentation } from './molstar-visualise'; +import { VisualizationToolBox } from "./components/visualization-tool-box"; /** * A function to render the actual PrankWeb viewer. @@ -46,10 +47,15 @@ export async function renderProteinView(predictionInfo: PredictionInfo) { }); // Render pocket list on the right side (or bottom for smartphones) using React. - const container = (window.innerWidth >= 768) ? document.getElementById('pocket-list-aside') : document.getElementById('pocket-list-aside-mobile'); - const root = createRoot(container!); - root.render(= 768) ? document.getElementById('pocket-list-aside') : document.getElementById('pocket-list-aside-mobile'); + const pocketListRoot = createRoot(pocketListContainer!); + pocketListRoot.render(); + + // Render the tool box on the bottom of the visualization using React. + const toolBoxContainer = document.getElementById('visualization-toolbox'); + const toolBoxRoot = createRoot(toolBoxContainer!); + toolBoxRoot.render(); } /** diff --git a/frontend/client/viewer/components/visualization-tool-box.css b/frontend/client/viewer/components/visualization-tool-box.css new file mode 100644 index 00000000..4b61caaa --- /dev/null +++ b/frontend/client/viewer/components/visualization-tool-box.css @@ -0,0 +1,12 @@ +.visualization-toolbox-container { + display: flex; + justify-content: space-evenly; + align-items: center; + padding-top: 10px; +} + +.visualization-toolbox-option-title { + font-size: 1.2em; + font-weight: bold; + text-align: center; +} \ No newline at end of file diff --git a/frontend/client/viewer/components/visualization-tool-box.tsx b/frontend/client/viewer/components/visualization-tool-box.tsx new file mode 100644 index 00000000..44a63720 --- /dev/null +++ b/frontend/client/viewer/components/visualization-tool-box.tsx @@ -0,0 +1,35 @@ +import { Button } from "@mui/material"; +import React from "react"; + +import "./visualization-tool-box.css" + +export class VisualizationToolBox extends React.Component<{}, {}> { + + render() { + return ( +
    +
    +
    + Option 1 +
    +
    + +
    +
    + +
    +
    + Option 2 +
    +
    + +
    +
    +
    + ); + } +} \ No newline at end of file diff --git a/frontend/client/viewer/rcsb-visualise.ts b/frontend/client/viewer/rcsb-visualise.ts index 463783e3..fcea94c3 100644 --- a/frontend/client/viewer/rcsb-visualise.ts +++ b/frontend/client/viewer/rcsb-visualise.ts @@ -44,6 +44,7 @@ export function initRcsb(data: PredictionData, molstarPlugin: PluginUIContext) { function calculateViewerWidth() { const width = window.innerWidth; + const xs = 768; const lg = 1200; @@ -52,6 +53,9 @@ function calculateViewerWidth() { if(width <= xs) return width; + //TODO: temp solution, needs to be changed + return Math.floor(width * (5/12)) - 250; + if(width <= lg) { return Math.floor(width * (8/12)) - 230; } diff --git a/frontend/client/viewer/viewer.html b/frontend/client/viewer/viewer.html index eca0b5e3..e671a84e 100644 --- a/frontend/client/viewer/viewer.html +++ b/frontend/client/viewer/viewer.html @@ -16,9 +16,14 @@