diff --git a/documentation/prankweb.open-api.yaml b/documentation/prankweb.open-api.yaml index 10411608..8c666d8b 100644 --- a/documentation/prankweb.open-api.yaml +++ b/documentation/prankweb.open-api.yaml @@ -102,7 +102,7 @@ paths: schema: $ref: '#/components/schemas/TaskId' requestBody: - description: The request needs to contain the hash and the pocket number. + description: The request needs to contain the hash of the docking task. required: true content: application/json: @@ -228,8 +228,6 @@ components: properties: hash: type: string - pocket: - type: number DockingResponse: type: array items: diff --git a/executor-docking/Dockerfile b/executor-docking/Dockerfile index 9962b7a4..5ac8d341 100644 --- a/executor-docking/Dockerfile +++ b/executor-docking/Dockerfile @@ -84,7 +84,7 @@ RUN sed -i 's/^ parser = MMCIFParser(filename, modelsAs=modelsAs)$/ # Install dodo (docking in docker) # https://github.com/kiarka7/DODO -RUN wget -q https://raw.githubusercontent.com/kiarka7/DODO/28d8a35611a6086607f6abc1928a44961cb711ac/run_docking.py -O /opt/executor-docking/run_docking.py +RUN wget -q https://raw.githubusercontent.com/kiarka7/DODO/9d77b3b1f03a8b656eec5f5ae465ac9f2521965e/run_docking.py -O /opt/executor-docking/run_docking.py COPY --chown=user:user ./executor-docking/requirements.txt ./ RUN pip3 install -r requirements.txt diff --git a/executor-docking/run_task.py b/executor-docking/run_task.py index 76004e21..67297c17 100644 --- a/executor-docking/run_task.py +++ b/executor-docking/run_task.py @@ -78,7 +78,7 @@ def prepare_docking(input_file: str, structure_file_gzip: str, task_directory: s ligandFile = os.path.join(task_directory, "ligand.smi") with open(input_file) as inp, open(ligandFile, "w") as f: input_json = json.load(inp) - f.write(input_json["hash"]) + f.write(input_json["smiles"]) # prepare the input file new_input_file = os.path.join(task_directory, "docking_parameters.json") @@ -91,6 +91,7 @@ def prepare_docking(input_file: str, structure_file_gzip: str, task_directory: s out_json["output"] = os.path.join(task_directory, "public", "out_vina.pdbqt") out_json["center"] = input_json["bounding_box"]["center"] out_json["size"] = input_json["bounding_box"]["size"] + out_json["exhaustiveness"] = input_json["exhaustiveness"] json.dump(out_json, out) diff --git a/frontend/client/custom-types.ts b/frontend/client/custom-types.ts index 3c83407c..5272f0ef 100644 --- a/frontend/client/custom-types.ts +++ b/frontend/client/custom-types.ts @@ -245,9 +245,11 @@ export interface ServerTaskInfo { // info about the task returned from the serve lastChange: string; status: string; initialData: { - hash: string; //hash of the data - pocket: string; //pocket id - [key: string]: any; //other data + hash: string; //hash of the data + pocket: string; //pocket id + smiles: string; //SMILES representation of the ligand + exhaustiveness: string; //exhaustiveness value (for Autodock Vina) + [key: string]: any; //other data }; //initial data responseData: any; //response data } diff --git a/frontend/client/tasks/server-docking-task.tsx b/frontend/client/tasks/server-docking-task.tsx index ccd43ff7..3b801843 100644 --- a/frontend/client/tasks/server-docking-task.tsx +++ b/frontend/client/tasks/server-docking-task.tsx @@ -3,6 +3,7 @@ import { PocketData, Point3D, ServerTaskInfo, ServerTaskLocalStorageData } from import { getPocketAtomCoordinates } from "../viewer/molstar-visualise"; import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context"; +import { md5 } from 'hash-wasm'; /** * Computes distance of 2 points in 3D space. @@ -47,9 +48,9 @@ function computeBoundingBox(plugin: PluginUIContext, pocket: PocketData) { z: center.z }, size: { - x: Math.ceil(sideLength), - y: Math.ceil(sideLength), - z: Math.ceil(sideLength) + x: Math.ceil(sideLength) + 5, // the bounding box is a bit larger than the pocket for more accurate results + y: Math.ceil(sideLength) + 5, + z: Math.ceil(sideLength) + 5 } }; } @@ -58,17 +59,20 @@ function computeBoundingBox(plugin: PluginUIContext, pocket: PocketData) { * Sends requests to the backend to compute the docking task and periodically checks if the task is finished. * @param prediction Prediction info * @param pocket Pocket data - * @param hash Task identifier (hash) + * @param smiles SMILES ligand identifier * @param plugin Mol* plugin + * @param exhaustiveness exhaustiveness value (for Autodock Vina) * @returns Completed task data */ -export async function computeDockingTaskOnBackend(prediction: PredictionInfo, pocket: PocketData, hash: string, plugin: PluginUIContext): Promise { - if (hash === "") { +export async function computeDockingTaskOnBackend(prediction: PredictionInfo, pocket: PocketData, smiles: string, plugin: PluginUIContext, exhaustiveness: string): Promise { + if (smiles === "") { return; } const box = computeBoundingBox(plugin, pocket); + const hash = await dockingHash(pocket.rank, smiles, exhaustiveness); + await fetch(`./api/v2/docking/${prediction.database}/${prediction.id}/post`, { method: 'POST', headers: { @@ -78,6 +82,8 @@ export async function computeDockingTaskOnBackend(prediction: PredictionInfo, po body: JSON.stringify({ "hash": hash, "pocket": pocket.rank, + "smiles": smiles, + "exhaustiveness": exhaustiveness, "bounding_box": box }), }).then((res) => { @@ -90,23 +96,27 @@ export async function computeDockingTaskOnBackend(prediction: PredictionInfo, po } /** - * 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 a hash that identifies this task. + * @param pocket Pocket identifier + * @param smiles SMILES identifier + * @param exhaustiveness exhaustiveness value (for Autodock Vina) * @returns Computed hash */ -export function dockingHash(prediction: PredictionInfo, pocket: PocketData, formData: string) { - return formData; +export async function dockingHash(pocket: string, smiles: string, exhaustiveness: string) { + return await md5(`${pocket}_${smiles}_${exhaustiveness}`); } /** * Downloads the result of the task. - * @param hash Task identifier (hash) + * @param smiles SMILES identifier * @param fileURL URL to download the result from + * @param pocket Pocket identifier + * @param exhaustiveness exhaustiveness value (for Autodock Vina) * @returns void */ -export function downloadDockingResult(hash: string, fileURL: string, pocket: string) { +export async function downloadDockingResult(smiles: string, fileURL: string, pocket: string, exhaustiveness: string) { + const hash = await dockingHash(pocket, smiles, exhaustiveness); + // https://stackoverflow.com/questions/50694881/how-to-download-file-in-react-js fetch(fileURL, { method: 'POST', @@ -115,8 +125,7 @@ export function downloadDockingResult(hash: string, fileURL: string, pocket: str 'Content-Type': 'application/json' }, body: JSON.stringify({ - "hash": hash, - "pocket": pocket + "hash": hash }) }) .then((response) => response.blob()) @@ -156,10 +165,14 @@ export async function pollForDockingTask(predictionInfo: PredictionInfo) { let savedTasks = localStorage.getItem(`${predictionInfo.id}_serverTasks`); if (!savedTasks) savedTasks = "[]"; const tasks: ServerTaskLocalStorageData[] = JSON.parse(savedTasks); + if (tasks.length === 0) return; + if (tasks.every((task: ServerTaskLocalStorageData) => task.status === "successful" || task.status === "failed")) return; tasks.forEach(async (task: ServerTaskLocalStorageData, i: number) => { if (task.status === "successful" || task.status === "failed") return; - const individualTask: ServerTaskInfo = taskStatusJSON["tasks"].find((t: ServerTaskInfo) => t.initialData.hash === task.params[0] && t.initialData.pocket === task.pocket.toString()); + const expectedHash = await dockingHash(task.pocket.toString(), task.params[0], task.params[1]); + + const individualTask: ServerTaskInfo = taskStatusJSON["tasks"].find((t: ServerTaskInfo) => t.initialData.hash === expectedHash); if (individualTask) { if (individualTask.status !== task.status) { //update the status @@ -167,6 +180,7 @@ export async function pollForDockingTask(predictionInfo: PredictionInfo) { //download the computed data if (individualTask.status === "successful") { + const hash = await dockingHash(task.pocket.toString(), individualTask.initialData.smiles, individualTask.initialData.exhaustiveness); const data = await fetch(`./api/v2/docking/${predictionInfo.database}/${predictionInfo.id}/public/result.json`, { method: 'POST', headers: { @@ -174,8 +188,7 @@ export async function pollForDockingTask(predictionInfo: PredictionInfo) { 'Content-Type': 'application/json' }, body: JSON.stringify({ - "hash": task.params[0], - "pocket": task.pocket, + "hash": hash }) }).then(res => res.json()).catch(err => console.log(err)); tasks[i].responseData = data; diff --git a/frontend/client/viewer/application.tsx b/frontend/client/viewer/application.tsx index 070ceeed..2bd1d101 100644 --- a/frontend/client/viewer/application.tsx +++ b/frontend/client/viewer/application.tsx @@ -13,8 +13,9 @@ import { PocketsViewType, PolymerColorType, PolymerViewType, PredictionData, Rea import { DefaultPluginUISpec } from 'molstar/lib/mol-plugin-ui/spec'; 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 { RcsbFv, RcsbFvTrackDataElementInterface, RcsbFvTrackData } from "@rcsb/rcsb-saguaro"; import { highlightSurfaceAtomsInViewerLabelId, overPaintPolymer, updatePolymerView, showPocketInCurrentRepresentation } from './molstar-visualise'; +import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18'; /** * A function to render the actual PrankWeb viewer. @@ -22,26 +23,31 @@ import { highlightSurfaceAtomsInViewerLabelId, overPaintPolymer, updatePolymerVi */ export async function renderProteinView(predictionInfo: PredictionInfo) { const wrapper = document.getElementById('application-molstar')!; - const MolstarPlugin = await createPluginUI(wrapper, { - ...DefaultPluginUISpec(), - layout: { - initial: { - isExpanded: false, - showControls: true, - controlsDisplay: "reactive", - regionState: { - top: "hidden", //sequence - left: (window.innerWidth > 1200) ? "collapsed" : "hidden", - //tree with some components, hide for small and medium screens - bottom: "hidden", //shows log information - right: "hidden" //structure tools + const MolstarPlugin = await createPluginUI( + { + target: wrapper, + render: renderReact18, + spec: { + ...DefaultPluginUISpec(), + layout: { + initial: { + isExpanded: false, + showControls: true, + controlsDisplay: "reactive", + regionState: { + top: "hidden", //sequence + left: (window.innerWidth > 1200) ? "collapsed" : "hidden", + //tree with some components, hide for small and medium screens + bottom: "hidden", //shows log information + right: "hidden" //structure tools + } + } + }, + components: { + remoteState: 'none' } } - }, - components: { - remoteState: 'none' - } - }); + }); // If the Mol* plugin is maximized, hide the React components. MolstarPlugin.layout.events.updated.subscribe(() => { @@ -199,9 +205,10 @@ export class Application extends React.Component e.trackId === "pocketsTrack"); + const track = this.state.pluginRcsb.getBoardData().find(e => e.trackId.indexOf("pocketsTrack") !== -1); if (track) { - track.trackData!.filter((e: RcsbFvTrackDataElementInterface) => e.provenanceName === `pocket${index + 1}`).forEach((foundPocket: RcsbFvTrackDataElementInterface) => (foundPocket.color = newColor)); + // this shouldn't be any but I couldn't find a way to avoid it + track.trackData!.filter((e: any) => e.provenanceName === `pocket${index + 1}`).forEach((foundPocket: RcsbFvTrackDataElementInterface) => (foundPocket.color = newColor)); const newData = track.trackData; this.state.pluginRcsb.updateTrackData("pocketsTrack", newData!); } diff --git a/frontend/client/viewer/components/prediction-info-tab.tsx b/frontend/client/viewer/components/prediction-info-tab.tsx index c31d62c8..cc25a110 100644 --- a/frontend/client/viewer/components/prediction-info-tab.tsx +++ b/frontend/client/viewer/components/prediction-info-tab.tsx @@ -53,7 +53,7 @@ export default function PredictionInfoTab(props: { predictionInfo: PredictionInf }, { name: "P2Rank version", - value: props.predictionData.metadata.p2rank_version || "unknown, possibly 2.4" + value: props.predictionData.metadata.p2rank_version || "< 2.4" }, { name: "", diff --git a/frontend/client/viewer/components/tasks-tab.tsx b/frontend/client/viewer/components/tasks-tab.tsx index 1ba9a05e..3c5ab2bd 100644 --- a/frontend/client/viewer/components/tasks-tab.tsx +++ b/frontend/client/viewer/components/tasks-tab.tsx @@ -27,6 +27,7 @@ type TaskTypeMenuItem = { name: string, compute: (params: string[], customName: string, pocketIndex: number) => void; parameterDescriptions: string[]; + parameterDefaults?: string[]; }; export default function TasksTab(props: { pockets: PocketData[], predictionInfo: PredictionInfo, plugin: PluginUIContext, initialPocket: number; }) { @@ -72,6 +73,22 @@ export default function TasksTab(props: { pockets: PocketData[], predictionInfo: type: TaskType.Server, name: "Docking", compute: (params, customName, pocketIndex) => { + // check if exhaustiveness is a number + const exhaustiveness = params[1].replaceAll(",", ".").replaceAll(" ", ""); + if (isNaN(parseFloat(exhaustiveness))) { + setInvalidInput(true); + return; + } + + // 1-64 is the allowed range + if (Number(exhaustiveness) < 1 || Number(exhaustiveness) > 64) { + setInvalidInput(true); + return; + } + + setInvalidInput(false); + const smiles = params[0].replaceAll(" ", ""); + let savedTasks = localStorage.getItem(`${props.predictionInfo.id}_serverTasks`); if (!savedTasks) savedTasks = "[]"; const tasks: ServerTaskLocalStorageData[] = JSON.parse(savedTasks); @@ -86,11 +103,13 @@ export default function TasksTab(props: { pockets: PocketData[], predictionInfo: "discriminator": "server", }); localStorage.setItem(`${props.predictionInfo.id}_serverTasks`, JSON.stringify(tasks)); - computeDockingTaskOnBackend(props.predictionInfo, props.pockets[pocketIndex], params[0], props.plugin); + computeDockingTaskOnBackend(props.predictionInfo, props.pockets[pocketIndex], smiles, props.plugin, exhaustiveness); }, parameterDescriptions: [ "Enter the molecule in SMILES format (e.g. c1ccccc1)", - ] + "Enter the exhaustiveness for Autodock Vina (recommended: 32, allowed range: 1-64)" + ], + parameterDefaults: ["", "32"] } ]; @@ -99,11 +118,13 @@ export default function TasksTab(props: { pockets: PocketData[], predictionInfo: const [name, setName] = React.useState(""); const [parameters, setParameters] = React.useState([]); const [forceUpdate, setForceUpdate] = React.useState(0); + const [invalidInput, setInvalidInput] = React.useState(false); const handleTaskTypeChange = (event: SelectChangeEvent) => { const newTask = tasks.find(task => task.id == Number(event.target.value))!; setTask(newTask); - setParameters(Array(newTask.parameterDescriptions.length).fill("")); + if (newTask.parameterDefaults) setParameters(newTask.parameterDefaults); + else setParameters(Array(newTask.parameterDescriptions.length).fill("")); }; const handlePocketRankChange = (event: SelectChangeEvent) => { @@ -197,6 +218,14 @@ export default function TasksTab(props: { pockets: PocketData[], predictionInfo: ) } + { + invalidInput && + + + Error: The task could not be created. Check the formatting. + + + } diff --git a/frontend/client/viewer/components/tasks-table.tsx b/frontend/client/viewer/components/tasks-table.tsx index 3c9aac1f..95aa3bb2 100644 --- a/frontend/client/viewer/components/tasks-table.tsx +++ b/frontend/client/viewer/components/tasks-table.tsx @@ -10,6 +10,7 @@ import Tooltip from '@mui/material/Tooltip'; import { visuallyHidden } from '@mui/utils'; import { useInterval } from "./tools"; +import "bootstrap-icons/font/bootstrap-icons.css"; import { PocketData } from "../../custom-types"; import { ClientTaskLocalStorageData, ServerTaskLocalStorageData, ServerTaskTypeDescriptors, ClientTaskTypeDescriptors, ClientTaskType, ServerTaskType } from "../../custom-types"; import { downloadDockingResult, pollForDockingTask } from "../../tasks/server-docking-task"; @@ -43,6 +44,11 @@ const headCells: HeadCell[] = [ label: 'Status/result', tooltip: 'Task status or result' }, + { + id: null, + label: '', + tooltip: 'Delete task from the list' + } //more are added dynamically, if needed ]; @@ -110,7 +116,7 @@ export function TasksTable(props: { pocket: PocketData | null, predictionInfo: P const handleResultClick = (serverTask: ServerTaskLocalStorageData) => { switch (serverTask.type) { case ServerTaskType.Docking: - downloadDockingResult(serverTask.params[0], serverTask.responseData[0].url, serverTask.pocket.toString()); + downloadDockingResult(serverTask.params[0], serverTask.responseData[0].url, serverTask.pocket.toString(), serverTask.params[1]); break; default: break; @@ -160,6 +166,27 @@ export function TasksTable(props: { pocket: PocketData | null, predictionInfo: P }; useInterval(pollDocking, 1000 * 7); + const removeClientTaskFromLocalStorage = (task: ClientTaskLocalStorageData) => () => { + const clientTasksParsed: ClientTaskLocalStorageData[] = JSON.parse(localStorage.getItem(`${props.predictionInfo.id}_clientTasks`) || "[]"); + const newClientTasks = clientTasksParsed.filter((t: ClientTaskLocalStorageData) => t.created !== task.created); + localStorage.setItem(`${props.predictionInfo.id}_clientTasks`, JSON.stringify(newClientTasks)); + setRender(numRenders + 1); + }; + + const removeServerTaskFromLocalStorage = (task: ServerTaskLocalStorageData) => () => { + const serverTasksParsed: ServerTaskLocalStorageData[] = JSON.parse(localStorage.getItem(`${props.predictionInfo.id}_serverTasks`) || "[]"); + const newServerTasks = serverTasksParsed.filter((t: ServerTaskLocalStorageData) => t.created !== task.created); + localStorage.setItem(`${props.predictionInfo.id}_serverTasks`, JSON.stringify(newServerTasks)); + setRender(numRenders + 1); + }; + + const makeDateMoreReadable = (date: string) => { + // expected format: "2023-10-07T14:00:00.000Z" + date = date.replace("T", " "); + // remove .000Z + return date.slice(0, -5); + }; + return ( {task.pocket}} {ClientTaskTypeDescriptors[task.type]} {"-"} - {task.created} + {makeDateMoreReadable(task.created)} {(!isNaN(task.data)) ? task.data.toFixed(1) : task.data} {task.type === ClientTaskType.Volume && " ų"} + + + ); } @@ -190,8 +222,13 @@ export function TasksTable(props: { pocket: PocketData | null, predictionInfo: P {props.pocket === null && {task.pocket}} {ServerTaskTypeDescriptors[task.type]} {task.name} - {task.created} + {makeDateMoreReadable(task.created)} {task.status === "successful" ? handleResultClick(task)} style={{ color: "blue", textDecoration: "underline", cursor: "pointer" }}>successful : task.status} + + + ); } diff --git a/frontend/client/viewer/molstar-visualise.ts b/frontend/client/viewer/molstar-visualise.ts index 9265c430..2a8a7a38 100644 --- a/frontend/client/viewer/molstar-visualise.ts +++ b/frontend/client/viewer/molstar-visualise.ts @@ -82,25 +82,24 @@ export async function loadStructureIntoMolstar(plugin: PluginUIContext, structur }); } - //adds water molecules - const water = await plugin.builders.structure.tryCreateComponentStatic(structure, 'water'); - if (water) { - await plugin.builders.structure.representation.addRepresentation(water, { - type: 'ball-and-stick', - }); - } - - //adds ligands - const ligands = await plugin.builders.structure.tryCreateComponentStatic(structure, 'ligand'); - if (ligands) { - await plugin.builders.structure.representation.addRepresentation(ligands, { - type: 'ball-and-stick', - }); - } + await createLigandRepresentations(plugin, structure); return [model, structure]; } +async function createLigandRepresentations(plugin: PluginUIContext, structure: StateObjectSelector) { + const shownGroups = ["water", "ion", "ligand", "nucleic", "lipid", "branched", "non-standard", "coarse"] as const; + + for (const group of shownGroups) { + const component = await plugin.builders.structure.tryCreateComponentStatic(structure, group); + if (component) { + plugin.builders.structure.representation.addRepresentation(component, { + type: 'ball-and-stick', + }); + } + } +} + /** Method returning log_x(y) */ function getLogBaseX(x: number, y: number) { return Math.log(y) / Math.log(x); diff --git a/frontend/client/viewer/rcsb-visualise.ts b/frontend/client/viewer/rcsb-visualise.ts index 6499e585..598a9a9b 100644 --- a/frontend/client/viewer/rcsb-visualise.ts +++ b/frontend/client/viewer/rcsb-visualise.ts @@ -1,10 +1,12 @@ -import { RcsbFv, RcsbFvDisplayTypes, RcsbFvTrackDataElementInterface, RcsbFvRowConfigInterface, RcsbFvBoardConfigInterface, RcsbFvTrackData } from "@rcsb/rcsb-saguaro"; +import { RcsbFv, RcsbFvDisplayTypes, RcsbFvTrackDataElementInterface, RcsbFvBoardConfigInterface, RcsbFvRowExtendedConfigInterface, RcsbFvTrackData } from "@rcsb/rcsb-saguaro"; 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 +// contains the last highlighted element let lastElement: number = -1; +// ID of the DOM element where the plugin is placed +const domElementId = "application-rcsb"; /* This is a workaround for the RcsbFvDisplayTypes being const enum with string values. @@ -44,12 +46,12 @@ export function initRcsb(data: PredictionData, molstarPlugin: PluginUIContext) { includeAxis: true, highlightHoverPosition: true, highlightHoverCallback: (trackData: Array) => onHighlight(data, molstarPlugin, trackData), - elementClickCallBack: (trackData?: RcsbFvTrackDataElementInterface, event?: MouseEvent) => elementClicked(data, molstarPlugin, trackData, event) + elementClickCallback: (trackData?: RcsbFvTrackDataElementInterface, event?: MouseEvent) => elementClicked(data, molstarPlugin, trackData, event) }; const rowConfigData = createRowConfigDataRcsb(data); - const elementId = "application-rcsb"; //div where the plugin is placed + const elementId = domElementId; // div where the plugin is placed let rcsbPlugin = new RcsbFv({ rowConfigData, @@ -67,7 +69,6 @@ export function initRcsb(data: PredictionData, molstarPlugin: PluginUIContext) { function calculateViewerWidth() { const width = window.innerWidth; - const xs = 768; const lg = 1200; @@ -76,14 +77,8 @@ function calculateViewerWidth() { if (width <= xs) return width; - //TODO: temp solution, needs to be changed + // not the best solution, but it works for this layout return Math.floor(width * (7 / 12)) - 250; - - if (width <= lg) { - return Math.floor(width * (8 / 12)) - 230; - } - - return Math.floor(width * (10 / 12)) - 230; } /** @@ -134,8 +129,9 @@ function onHighlight(data: PredictionData, molstarPlugin: PluginUIContext, track * @returns Configuration for the viewer */ function createRowConfigDataRcsb(data: PredictionData) { - const rowConfigData: Array = []; + const rowConfigData: Array = []; rowConfigData.push({ + boardId: domElementId, trackId: "sequenceTrack", trackHeight: 20, trackColor: "#F9F9F9", @@ -144,7 +140,7 @@ function createRowConfigDataRcsb(data: PredictionData) { rowTitle: "SEQUENCE", trackData: [{ begin: 1, - value: data.structure.sequence.join('') + label: data.structure.sequence.join('') }] }); @@ -169,6 +165,7 @@ function createRowConfigDataRcsb(data: PredictionData) { } rowConfigData.push({ + boardId: domElementId, trackId: "bindingsTrack", trackHeight: 20, trackColor: "#F9F9F9", @@ -214,6 +211,7 @@ function createRowConfigDataRcsb(data: PredictionData) { } rowConfigData.push({ + boardId: domElementId, trackId: "pocketsTrack", trackHeight: 20, trackColor: "#F9F9F9", @@ -241,6 +239,7 @@ function createRowConfigDataRcsb(data: PredictionData) { } rowConfigData.push({ + boardId: domElementId, trackId: "conservationTrack", trackHeight: 40, trackColor: "#F9F9F9", @@ -268,6 +267,7 @@ function createRowConfigDataRcsb(data: PredictionData) { } rowConfigData.push({ + boardId: domElementId, trackId: "alphafoldTrack", trackHeight: 40, trackColor: "#F9F9F9", diff --git a/frontend/package-lock.json b/frontend/package-lock.json index 4314aa80..f7e1ef8f 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -7,52 +7,53 @@ "name": "prankweb-frontend", "license": "MIT", "dependencies": { - "@mui/icons-material": "^5.14.12", - "@mui/lab": "^5.0.0-alpha.147", - "@mui/material": "^5.14.12", - "@rcsb/rcsb-saguaro": "^2.5.13", - "autoprefixer": "^10.4.16", - "bootstrap": "^5.3.2", - "bootstrap-icons": "^1.11.1", + "@mui/icons-material": "^5.15.11", + "@mui/lab": "^5.0.0-alpha.166", + "@mui/material": "^5.15.11", + "@rcsb/rcsb-saguaro": "^3.0.7", + "autoprefixer": "^10.4.18", + "bootstrap": "^5.3.3", + "bootstrap-icons": "^1.11.3", "clean-webpack-plugin": "^4.0.0", - "copy-webpack-plugin": "^11.0.0", - "core-js": "^3.33.0", + "copy-webpack-plugin": "^12.0.2", + "core-js": "^3.36.0", "cross-env": "^7.0.3", - "css-loader": "^6.8.1", + "css-loader": "^6.10.0", "express-http-proxy": "^2.0.0", "handlebars": "^4.7.8", "handlebars-loader": "^1.7.3", - "html-loader": "^4.2.0", - "html-webpack-plugin": "^5.5.3", 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"sha512-j9iR8g+/t0lArF4V6NE/QCfT+CO7iLqrXAHZbJdo+LfjqP1vR8Fg5bSiaq6Q2lOD1AUEVrEVIgABvBFYojJVYQ==", + "bin": { + "yaml": "bin.mjs" + }, "engines": { "node": ">= 14" } + }, + "node_modules/zwitch": { + "version": "2.0.4", + "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz", + "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==", + "funding": { + "type": "github", + "url": "https://github.com/sponsors/wooorm" + } } } } diff --git a/frontend/package.json b/frontend/package.json index 72e7d795..5707d846 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -7,51 +7,52 @@ "build": "cross-env NODE_ENV=production webpack --config build/webpack.production.js" }, "dependencies": { - "@mui/icons-material": "^5.14.12", - "@mui/lab": "^5.0.0-alpha.147", - "@mui/material": "^5.14.12", - "@rcsb/rcsb-saguaro": "^2.5.13", - "autoprefixer": "^10.4.16", - "bootstrap": "^5.3.2", - "bootstrap-icons": "^1.11.1", + "@mui/icons-material": "^5.15.11", + "@mui/lab": "^5.0.0-alpha.166", + "@mui/material": "^5.15.11", + "@rcsb/rcsb-saguaro": "^3.0.7", + "autoprefixer": "^10.4.18", + "bootstrap": "^5.3.3", + "bootstrap-icons": "^1.11.3", "clean-webpack-plugin": "^4.0.0", - "copy-webpack-plugin": "^11.0.0", - "core-js": "^3.33.0", + "copy-webpack-plugin": "^12.0.2", + "core-js": "^3.36.0", "cross-env": "^7.0.3", - "css-loader": "^6.8.1", + "css-loader": "^6.10.0", "express-http-proxy": "^2.0.0", "handlebars": "^4.7.8", "handlebars-loader": "^1.7.3", - "html-loader": "^4.2.0", - "html-webpack-plugin": "^5.5.3", - "mini-css-extract-plugin": "^2.7.6", - "molstar": "^3.40.1", - "postcss-loader": "^7.3.3", + "hash-wasm": "^4.11.0", + "html-loader": "^5.0.0", + "html-webpack-plugin": "^5.6.0", + "mini-css-extract-plugin": "^2.8.1", + "molstar": "^4.0.1", + "postcss-loader": "^8.1.1", "quickhull3d": "^2.1.0", "react": "^18.2.0", "react-dom": "^18.2.0", "react-draggable": "^4.4.6", - "react-icons": "^4.11.0", - "sass": "^1.69.0", - "sass-loader": "^13.3.2", - "style-loader": "^3.3.3", - "typescript": "^5.2.2", + "react-icons": "^5.0.1", + "sass": "^1.71.1", + "sass-loader": "^14.1.1", + "style-loader": "^3.3.4", + "typescript": "^5.3.3", "underscore-template-loader": "^1.2.0", - "webpack": "^5.88.2", + "webpack": "^5.90.3", "webpack-cli": "^5.1.4", - "webpack-merge": "^5.9.0", - "webpackbar": "^5.0.2", + "webpack-merge": "^5.10.0", + "webpackbar": "^6.0.1", "winston": "^3.11.0", - "yaml": "^2.3.2" + "yaml": "^2.4.0" }, "devDependencies": { - "@types/react": "^18.2.25", - "@types/react-dom": "^18.2.11", - "esbuild-loader": "^4.0.2", - "exports-loader": "^4.0.0", - "express": "^4.18.2", - "imports-loader": "^4.0.1", - "webpack-dev-middleware": "^6.1.1", - "webpack-hot-middleware": "^2.25.4" + "@types/react": "^18.2.61", + "@types/react-dom": "^18.2.19", + "esbuild-loader": "^4.0.3", + "exports-loader": "^5.0.0", + "express": "^4.18.3", + "imports-loader": "^5.0.0", + "webpack-dev-middleware": "^7.0.0", + "webpack-hot-middleware": "^2.26.1" } } diff --git a/frontend/server/configuration.js b/frontend/server/configuration.js index 835ed770..c02ed6f7 100644 --- a/frontend/server/configuration.js +++ b/frontend/server/configuration.js @@ -8,4 +8,4 @@ module.exports = { // Use the option bellow to proxy commands to task runner instance. // This allows you to run tasks or connect to existing instance (https://prankweb.cz). "proxy-service": "https://prankweb.cz", -} +}; diff --git a/web-server/src/api_v2.py b/web-server/src/api_v2.py index 1334d77a..b47103fb 100644 --- a/web-server/src/api_v2.py +++ b/web-server/src/api_v2.py @@ -71,8 +71,11 @@ def route_get_file(database_name: str, prediction_name: str, file_name: str): def route_post_docking_file(database_name: str, prediction_name: str): """Post a docking task to the server. Request body should be a JSON object with the following fields: - - hash: str (SMILES for the ligand) - - pocket: int (pocket number)""" + - hash: str (a hash of the ligand with parameters) + - pocket: int (pocket number) + - smiles: str (SMILES for the ligand) + - exhaustiveness: float (exhaustiveness value) + - bounding_box: dict (bounding box for the docking)""" data = request.get_json(force=True) or {} dt = DockingTask(database_name=database_name) return dt.post_task(prediction_name.upper(), data) @@ -84,15 +87,13 @@ def route_post_docking_file(database_name: str, prediction_name: str): def route_get_docking_file_with_param(database_name: str, prediction_name: str, file_name: str): """Get a docking file from the server. Request body should be a JSON object with the following fields: - - hash: str (SMILES for the ligand) - - pocket: int (pocket number)""" + - hash: str (a hash of the ligand with parameters)""" data = request.get_json(force=True) param = data.get("hash", None) - pocket = data.get("pocket", None) - if data is None or param is None or pocket is None: + if data is None or param is None: return "", 404 dt = DockingTask(database_name=database_name) - return dt.get_file_with_post_param(prediction_name.upper(), file_name, param, str(pocket)) + return dt.get_file_with_post_param(prediction_name.upper(), file_name, param) @api_v2.route( "/docking///tasks", diff --git a/web-server/src/docking_task.py b/web-server/src/docking_task.py index c2f59730..b7330cc9 100644 --- a/web-server/src/docking_task.py +++ b/web-server/src/docking_task.py @@ -38,7 +38,7 @@ def __init__(self, database_name: str): self.database_name = 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, pocket: str): + 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. """ @@ -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["initialData"]["hash"] == data_hash and task["initialData"]["pocket"] == pocket: + if task["initialData"]["hash"] == data_hash: directory = os.path.join(directory, str(task["id"])) found = True break @@ -99,10 +99,7 @@ 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["initialData"] == { - "hash": data["hash"], - "pocket": data["pocket"], - }: + if task["initialData"]["hash"] == data["hash"]: return self._response_file(directory, "info.json") taskinfo.taskId = len(fileData["tasks"]) @@ -223,7 +220,9 @@ def _create_info(taskinfo: TaskInfo): "status": "queued", "initialData": { "hash": taskinfo.data["hash"], - "pocket": taskinfo.data["pocket"] + "pocket": taskinfo.data["pocket"], + "smiles": taskinfo.data["smiles"], + "exhaustiveness": taskinfo.data["exhaustiveness"], } }