diff --git a/ui/.env b/ui/.env index 1716243..7cd0520 100644 --- a/ui/.env +++ b/ui/.env @@ -9,5 +9,7 @@ VITE_TITLE="AlphaFind" VITE_DESCRIPTION="AlphaFind - protein search engine" VITE_KEYWORDS="alphafind, protein, search, similarity" VITE_ABSTRACT="AlphaFind" -VITE_COPYRIGHT="© 2023 MUNI FI" +VITE_COPYRIGHT="© 2024 MUNI FI" VITE_AUTHOR="Jakub Čillík" + +VITE_FOOTER_YEAR="%YEAR%" diff --git a/ui/README.md b/ui/README.md index a913033..e298138 100644 --- a/ui/README.md +++ b/ui/README.md @@ -3,7 +3,7 @@ AlphaFind ([https://alphafind.fi.muni.cz/](https://alphafind.fi.muni.cz/)) is a This repository contains the source code of the AlphaFind's front-end. -![public/alphafind.png](public/alphafind.png){width=40%} +![public/alphafind.png](public/alphafind.png) ## Running locally diff --git a/ui/package-lock.json b/ui/package-lock.json index c463576..22b327d 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -19,6 +19,7 @@ "bootstrap": "^5.3.2", "localforage": "^1.10.0", 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"funding": { + "type": "opencollective", + "url": "https://opencollective.com/unified" + } + }, + "node_modules/unist-util-visit-parents": { + "version": "6.0.1", + "resolved": "https://registry.npmjs.org/unist-util-visit-parents/-/unist-util-visit-parents-6.0.1.tgz", + "integrity": "sha512-L/PqWzfTP9lzzEa6CKs0k2nARxTdZduw3zyh8d2NVBnsyvHjSX4TWse388YrrQKbvI8w20fGjGlhgT96WwKykw==", + "dependencies": { + "@types/unist": "^3.0.0", + "unist-util-is": "^6.0.0" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/unified" + } }, "node_modules/universalify": { "version": "0.2.0", @@ -8380,6 +10756,14 @@ "node": ">= 4.0.0" } }, + "node_modules/unpipe": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/unpipe/-/unpipe-1.0.0.tgz", + "integrity": "sha512-pjy2bYhSsufwWlKwPc+l3cN7+wuJlK6uz0YdJEOlQDbl6jo/YlPi4mb8agUkVC8BF7V8NuzeyPNqRksA3hztKQ==", + "engines": { + "node": ">= 0.8" + } + }, "node_modules/update-browserslist-db": { "version": "1.0.13", 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"https://registry.npmjs.org/vfile-message/-/vfile-message-4.0.2.tgz", + "integrity": "sha512-jRDZ1IMLttGj41KcZvlrYAaI3CfqpLpfpf+Mfig13viT6NKvRzWZ+lXz0Y5D60w6uJIBAOGq9mSHf0gktF0duw==", + "dependencies": { + "@types/unist": "^3.0.0", + "unist-util-stringify-position": "^4.0.0" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/unified" + } + }, "node_modules/vite": { "version": "5.0.10", "resolved": "https://registry.npmjs.org/vite/-/vite-5.0.10.tgz", @@ -8683,7 +11127,6 @@ "version": "1.0.2", "resolved": "https://registry.npmjs.org/which-boxed-primitive/-/which-boxed-primitive-1.0.2.tgz", "integrity": "sha512-bwZdv0AKLpplFY2KZRX6TvyuN7ojjr7lwkg6ml0roIy9YeuSr7JS372qlNW18UQYzgYK9ziGcerWqZOmEn9VNg==", - "dev": true, "dependencies": { "is-bigint": "^1.0.1", "is-boolean-object": "^1.1.0", @@ -8711,16 +11154,15 @@ } }, "node_modules/which-typed-array": { - "version": "1.1.13", - "resolved": 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">= 6" + } + }, "node_modules/xml-name-validator": { "version": "5.0.0", "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-5.0.0.tgz", @@ -8888,6 +11338,15 @@ "funding": { "url": "https://github.com/sponsors/sindresorhus" } + }, + "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/ui/package.json b/ui/package.json index c790057..52f21dc 100644 --- a/ui/package.json +++ b/ui/package.json @@ -22,6 +22,7 @@ "bootstrap": "^5.3.2", "localforage": "^1.10.0", "match-sorter": "^6.3.1", + "molstar": "^4.0.1", "ngl": "^2.2.1", "react": "^18.2.0", "react-autocomplete-input": "^1.0.29", diff --git a/ui/public/alphafind.png b/ui/public/alphafind.png index ceb800d..34a4059 100644 Binary files a/ui/public/alphafind.png and b/ui/public/alphafind.png differ diff --git a/ui/src/components/ComparisonModal/ComparisonModal.tsx b/ui/src/components/ComparisonModal/ComparisonModal.tsx index 556d16a..cd496e8 100644 --- a/ui/src/components/ComparisonModal/ComparisonModal.tsx +++ b/ui/src/components/ComparisonModal/ComparisonModal.tsx @@ -6,13 +6,12 @@ import { QueryObjectContext } from "../../pages/ProteinSearch/ProteinSearch"; import "./comparison-modal.scss"; import ProteinVisualizer from "../ProteinVisualizer"; + const controlHintPopover = ( - {/* Controls */} @@ -100,6 +99,7 @@ export function ComparisonModal({ show, onHide, comparingUniProtId }: Props) {
+ {/* */}
diff --git a/ui/src/components/Description/Description.tsx b/ui/src/components/Description/Description.tsx index 4ac101a..0bcbf2f 100644 --- a/ui/src/components/Description/Description.tsx +++ b/ui/src/components/Description/Description.tsx @@ -15,6 +15,9 @@ export const Description = memo(() => { 3D visualizations of the structural superposition of the proteins are provided, and text filters can be used to find specific organisms or Uniprot IDs. For details about the methodology and usage, please see the manual. This website is free and open to all users and there is no login requirement. +
+ If you found AlphaFind helpful, please cite: Procházka, D., Slanináková, T., Oľha, J., Rošinec, A., Grešová, K., Jánošová, M., Čillík, J., Porubská, J., Svobodová, R., Dohnal, V., & Antol, M. (2024). AlphaFind: Discover structure similarity across the entire known proteome. Are you interested in a research collaboration? Feel free to contact us. +

); diff --git a/ui/src/components/ExampleVisualizations/ExampleVisualization.tsx b/ui/src/components/ExampleVisualizations/ExampleVisualization.tsx index db4cd36..3e5bf7a 100644 --- a/ui/src/components/ExampleVisualizations/ExampleVisualization.tsx +++ b/ui/src/components/ExampleVisualizations/ExampleVisualization.tsx @@ -1,19 +1,17 @@ +import { Link } from "react-router-dom"; import { Representation } from "../../common/enums"; import ProteinVisualizer from "../ProteinVisualizer"; import "./example-visualization.scss"; -const defaultStyle = { - height: 300 + "px", -}; - type Props = { i: number, exampleUniProtIds: string[] name: string; text: string; + limit?: number; }; -export function ExampleVisualization({i, exampleUniProtIds, name, text }: Props) { +export function ExampleVisualization({i, exampleUniProtIds, name, text, limit=50}: Props) { return (
-

{name}

+

{name}

); diff --git a/ui/src/components/ExampleVisualizations/ExampleVisualizations.tsx b/ui/src/components/ExampleVisualizations/ExampleVisualizations.tsx index 230b6dc..aea9038 100644 --- a/ui/src/components/ExampleVisualizations/ExampleVisualizations.tsx +++ b/ui/src/components/ExampleVisualizations/ExampleVisualizations.tsx @@ -3,19 +3,19 @@ import { ExampleVisualization } from "./ExampleVisualization"; import "./examples-visualizations.scss"; const examples = [ - ["I1VZV6","A0A3G2VQ77","C7S3C6", "A0A2K6R518","A0A0D9RKY6","H9EWV6","A0A3G2VT59",], + ["P69905", "P63108", "D1MGQ2", "A0A0K2BMD8","A0A341AFD2","Q5R9M5",], ["A0A1D6JW22","A0A3L6TI92","A0A317Y945","A0A835EH74",], ["Q9FFD0","A0A7J7D5F1","A0A067JHG6","B9IQ11",], ]; const names = [ - "Hemoglobin Alpha 1", + "Hemoglobin alpha 1", "Cytochrome P450", "PIN5 protein", ]; const texts = [ - "Hemoglobin is a protein that facilitates the transport of oxygen and other gases in red blood cells. Almost all vertebrates contain hemoglobin. It consists of four protein subunits (globins), and is one of the first proteins whose 3D structure has been experimentally determined. There are many types of hemoglobin, with hemoglobin Alpha 1 (encoded by the HBA1 gene) occurring in humans and being the main form of hemoglobin in adults. In this use case, AlphaFind shows us that highly similar hemoglobin structures can also be found in other species.", + "Hemoglobin is a protein that facilitates the transport of oxygen and other gases in red blood cells. Almost all vertebrates contain hemoglobin. It consists of four protein subunits (globins), and is one of the first proteins whose 3D structure has been experimentally determined. There are many types of hemoglobin, with hemoglobin alpha 1 (encoded by the HBA1 gene) occurring in humans and being the main form of hemoglobin in adults. In this use case, AlphaFind shows us that highly similar hemoglobin structures can also be found in other species.", "Cytochrome P450 are enzymes which are important for the metabolism of many endogenous compounds and xenobiotics. P450 enzymes have been identified across all biological kingdoms: animals, plants, fungi, bacteria and archaea, as well as in viruses. Cytochrome P450 proteins contain one chain which is composed of more than 20 sheets and helices. Their sequence similarity is very low. In this use case, we can see similarities among cytochrome P450 structures from various species. The search starts with a cytochrome from corn (Zea Mays), and within the first 50 hits, we find similar structures originating from various animals (mouse, cat, horse, etc.).", "The PIN proteins are transmembrane proteins which regulate plant growth by influencing auxin transport from the cytosol to the extracellular space. They only occur in plants and feature a configuration of 10 main helices that collectively form a pore. Eight types of PIN proteins are known (PIN1-PIN8), and recently, the structures of three PIN proteins were uncovered and published in Nature. The structure of the PIN5 protein differs from other PINs (Ung 2022) and has not yet been experimentally determined. This use case shows that the PIN5 protein structure is strongly conserved among many different plant species.", ]; @@ -24,7 +24,7 @@ export function ExampleVisualizations() { return ( - + diff --git a/ui/src/components/ExperimentalStructuresModal/ExperimentalStructuresModal.tsx b/ui/src/components/ExperimentalStructuresModal/ExperimentalStructuresModal.tsx new file mode 100644 index 0000000..9d6ea9a --- /dev/null +++ b/ui/src/components/ExperimentalStructuresModal/ExperimentalStructuresModal.tsx @@ -0,0 +1,48 @@ +import { faArrowUpRightFromSquare } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { Modal } from "react-bootstrap"; +import "./experimental-structures-modal.scss"; +import { ExperimentalStructuresModalAttributes } from "../ProteinTable/ProteinTable"; + +type Props = { + attrs: ExperimentalStructuresModalAttributes; + onHide: () => void; +}; + +export function ExperimentalStructuresModal({ attrs, onHide }: Props) { + if (attrs === null) + return (<>); + + const { experimentalStructures } = attrs; + + return ( + 0} + onHide={onHide} + aria-labelledby="contained-modal-title-vcenter" + centered + className="experimental-structures-modal" + > + + + Experimental Structures + + + +

+ Experimental structures (PDBe) corresponding to {attrs.entryUniProtId}: +

+ +
+
+ ); +} diff --git a/ui/src/components/ExperimentalStructuresModal/experimental-structures-modal.scss b/ui/src/components/ExperimentalStructuresModal/experimental-structures-modal.scss new file mode 100644 index 0000000..c54c850 --- /dev/null +++ b/ui/src/components/ExperimentalStructuresModal/experimental-structures-modal.scss @@ -0,0 +1,21 @@ +.experimental-structures-modal { + .modal-title { + font-size: 1.2rem; + } + + ul { + list-style: none; + // font-size: 1.1rem; + max-height: 450px; + overflow-y: scroll; + + li { + margin-bottom: 0.75rem; + // border-bottom: 1px solid #ccc; + } + } + + sup { + font-size: 0.7rem; + } +} diff --git a/ui/src/components/ExperimentalStructuresModal/index.tsx b/ui/src/components/ExperimentalStructuresModal/index.tsx new file mode 100644 index 0000000..d4dea2b --- /dev/null +++ b/ui/src/components/ExperimentalStructuresModal/index.tsx @@ -0,0 +1,3 @@ +import { ExperimentalStructuresModal } from "./ExperimentalStructuresModal"; + +export default ExperimentalStructuresModal; \ No newline at end of file diff --git a/ui/src/components/LoadInfoBox/LoadInfoBox.tsx b/ui/src/components/LoadInfoBox/LoadInfoBox.tsx deleted file mode 100644 index f2fdaeb..0000000 --- a/ui/src/components/LoadInfoBox/LoadInfoBox.tsx +++ /dev/null @@ -1,57 +0,0 @@ -import { Spinner } from "react-bootstrap"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { faLink } from "@fortawesome/free-solid-svg-icons"; -import { useContext } from "react"; -import "./load-info-box.scss"; -import { QueryObjectContext } from "../../pages/ProteinSearch/ProteinSearch"; - -type Props = { - loading: boolean; - originalInput: string; - searchTime: number; -}; - -export function LoadInfoBox({ loading, originalInput, searchTime }: Props) { - const queryObject = useContext(QueryObjectContext); - - let query = originalInput; - if (originalInput !== queryObject.uniProtId && queryObject.uniProtId !== "") - query = originalInput + " → " + queryObject.uniProtId; - - return ( -
    -
  • - Query:{query} -
  • - - {queryObject.name !== "" && ( -
  • - Name: {queryObject.name} -
  • - )} - - {queryObject.organism !== "" && ( -
  • - Organism: {queryObject.organism} -
  • - )} - - {queryObject.uniProtId !== "" && ( -
  • - {queryObject.uniProtId} in AlphaFold -
  • - )} - -
  • - Search Time: - {loading ? ( - - Loading... - - ) : ( - {searchTime.toFixed(3)} s - )} -
  • -
- ); -} diff --git a/ui/src/components/LoadInfoBox/index.tsx b/ui/src/components/LoadInfoBox/index.tsx deleted file mode 100644 index 68fd10c..0000000 --- a/ui/src/components/LoadInfoBox/index.tsx +++ /dev/null @@ -1,3 +0,0 @@ -import { LoadInfoBox } from "./LoadInfoBox"; - -export default LoadInfoBox; diff --git a/ui/src/components/LoadMoreButton/LoadMoreButton.tsx b/ui/src/components/LoadMoreButton/LoadMoreButton.tsx index f97674a..a3d54df 100644 --- a/ui/src/components/LoadMoreButton/LoadMoreButton.tsx +++ b/ui/src/components/LoadMoreButton/LoadMoreButton.tsx @@ -59,6 +59,7 @@ export function LoadMoreButton({ isLoading, loadMoreFn, queue, currentDataLength const availableCount = MAX_LIMIT - currentDataLength; + // Do not show button if the user reached upper limit if (availableCount <= 0) return (<>); diff --git a/ui/src/components/MainFooter/MainFooter.tsx b/ui/src/components/MainFooter/MainFooter.tsx index 74ae21d..6298f68 100644 --- a/ui/src/components/MainFooter/MainFooter.tsx +++ b/ui/src/components/MainFooter/MainFooter.tsx @@ -5,20 +5,23 @@ import "./main-footer.scss"; import { memo } from 'react'; export const MainFooter = memo(() => { + let footer_year: string = import.meta.env.VITE_FOOTER_YEAR; + footer_year = footer_year.replace("%YEAR%", new Date().getFullYear().toString()); + return ( <> diff --git a/ui/src/components/MainHeader/MainHeader.tsx b/ui/src/components/MainHeader/MainHeader.tsx index 341ea39..2a63884 100644 --- a/ui/src/components/MainHeader/MainHeader.tsx +++ b/ui/src/components/MainHeader/MainHeader.tsx @@ -3,6 +3,7 @@ import { Col, Container, Row } from "react-bootstrap"; import Description from "../Description"; import "./main-header.scss"; import { useUrlParams } from "../../common/utils"; +import { Link } from "react-router-dom"; export const MainHeader = memo(() => { const [urlParams] = useUrlParams(); @@ -12,7 +13,11 @@ export const MainHeader = memo(() => {
-

AlphaFind

+

+ + AlphaFind + +

Manual diff --git a/ui/src/components/MainNavbar/MainNavbar.tsx b/ui/src/components/MainNavbar/MainNavbar.tsx deleted file mode 100644 index d592a3c..0000000 --- a/ui/src/components/MainNavbar/MainNavbar.tsx +++ /dev/null @@ -1,32 +0,0 @@ -import { Container, Image, Nav, Navbar } from "react-bootstrap"; -import { NavLink } from "react-router-dom"; -import "./main-navbar.scss"; - -interface props { - setProgress: (value: number) => void; -} - -export function MainNavbar({ setProgress } : props) { - function handleClick() { - setProgress(1); - } - - return ( - <> - - - - - - - - - - - ); -} diff --git a/ui/src/components/MainNavbar/index.tsx b/ui/src/components/MainNavbar/index.tsx deleted file mode 100644 index f38ca45..0000000 --- a/ui/src/components/MainNavbar/index.tsx +++ /dev/null @@ -1,3 +0,0 @@ -import { MainNavbar } from "./MainNavbar"; - -export default MainNavbar; diff --git a/ui/src/components/MainNavbar/main-navbar.scss b/ui/src/components/MainNavbar/main-navbar.scss deleted file mode 100644 index 9f307f9..0000000 --- a/ui/src/components/MainNavbar/main-navbar.scss +++ /dev/null @@ -1,62 +0,0 @@ -.navbar.main { - background-color: rgba(22, 11, 22, 0.8); - backdrop-filter: blur(15px); - padding: 0; -} - -.navbar.main .navbar-nav { - margin: 0 auto; - padding: 0 0 1.5rem; -} - -.navbar.main .navbar-toggler:focus { - box-shadow: none; -} - -.navbar.main .nav-link { - display: flex; - justify-content: center; - align-items: center; - padding: 0.5rem; - border-radius: 8px; - color: #999; - font-weight: 600; -} - -.navbar.main .nav-link:hover { - color: white; -} - -.navbar.main .nav-link.active { - color: white; -} - -.navbar.main .navbar-brand { - padding: 0; - margin: 0; - display: flex; - justify-content: center; - align-items: center; -} - -.navbar.main .navbar-brand img { - max-height: 45px; -} - -@media (min-width: 992px) { - .navbar.main { - align-items: flex-start; - } - - .navbar.main .navbar-nav { - padding-bottom: 0; - } - - .navbar.main .navbar-brand { - height: 56px; - } - - .navbar.main .nav-link { - margin: 0 1rem; - } -} diff --git a/ui/src/components/ProteinTable/ProteinTable.tsx b/ui/src/components/ProteinTable/ProteinTable.tsx index 8e6a46c..ab15fc2 100644 --- a/ui/src/components/ProteinTable/ProteinTable.tsx +++ b/ui/src/components/ProteinTable/ProteinTable.tsx @@ -1,9 +1,8 @@ import { Button, Col, Row, Table } from "react-bootstrap"; -import { getCoreRowModel, getFilteredRowModel, getSortedRowModel, useReactTable, getGroupedRowModel, getExpandedRowModel, ColumnFiltersState, SortingState, CellContext } from "@tanstack/react-table"; -import { FormEvent, useState, useContext } from "react"; +import { getCoreRowModel, getFilteredRowModel, getSortedRowModel, useReactTable, getGroupedRowModel, getExpandedRowModel, ColumnFiltersState, SortingState } from "@tanstack/react-table"; +import { useState, useContext, createContext } from "react"; import { columns } from "../../pages/ProteinSearch/tableColumnsDefinition"; import ComparisonModal from "../ComparisonModal"; -import { onSearchHeader } from "../../pages/ProteinSearch/ProteinSearch"; import "./protein-table.scss"; import FilterInfo from "../FilterInfo"; import { ProteinTableRow } from "./ProteinTableRow"; @@ -18,25 +17,36 @@ export type Record = { rmsd: number; alignedLength: number; identicalAAs: number; - organism: string; - name: string; + organism: string | null; + name: string | null; + isReviewed: boolean; + taxId: number; + sequence: string; + gene: string; + experimentalStructures: string[] | null; }; -export interface CustomCellContext extends CellContext { - meta: { - isExpanded: boolean; - subRowsCount: number; - referenceUniProtId: string | null; - onSearch: onSearchHeader; - onClickModal: (event: FormEvent) => void; - }; -} +export type ExperimentalStructuresModalAttributes = { + entryUniProtId: string; + experimentalStructures: string[]; +} | null; + +export type ModalContextType = { + setExperimentalStructuresModalValue: (attrs: ExperimentalStructuresModalAttributes) => void; + setComparisonModalValue: (uniProtId: string) => void; +}; + +export const ModalContext = createContext({ + setComparisonModalValue: () => {}, + setExperimentalStructuresModalValue: () => {}, +}); type Props = { data: Record[]; + setExperimentalStructuresModalValue: React.Dispatch>; }; -export function ProteinTable({ data }: Props) { +export function ProteinTable({ data, setExperimentalStructuresModalValue }: Props) { const [proteinComparisonModalValue, setProteinComparisonModalValue] = useState(null); // React Table states const [sorting, setSorting] = useState([{ @@ -70,7 +80,6 @@ export function ProteinTable({ data }: Props) { return ( <> - {/*
*/} setProteinComparisonModalValue(null)} @@ -84,13 +93,17 @@ export function ProteinTable({ data }: Props) {
- {table.getRowModel().rows.map(row => - - )} + + {table.getRowModel().rows.map(row => + + )} +
@@ -109,7 +122,6 @@ export function ProteinTable({ data }: Props) { >Export all to CSV - {/* */} ); } diff --git a/ui/src/components/ProteinTable/ProteinTableCell.tsx b/ui/src/components/ProteinTable/ProteinTableCell.tsx new file mode 100644 index 0000000..5022552 --- /dev/null +++ b/ui/src/components/ProteinTable/ProteinTableCell.tsx @@ -0,0 +1,180 @@ +import { createSearchParams } from "react-router-dom"; +import { ModalContext, Record } from "./ProteinTable"; +import { Cell, Row, flexRender } from "@tanstack/react-table"; +import { Button, OverlayTrigger, Spinner, Tooltip } from "react-bootstrap"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { faAngleDown, faAngleRight, faFlask, faMagnifyingGlass, faObjectUngroup } from "@fortawesome/free-solid-svg-icons"; +import { FormEvent, ReactNode, useContext } from "react"; + +function getCellBackground(cell: Cell) { + if (cell.getIsGrouped()) + return '#ededed'; + + if (cell.getIsAggregated()) + return '#ededed'; + + if (cell.getIsPlaceholder()) + return '#fff'; + + return '#fff'; +} + +function makeSearchSimilarUrl(value: string) { + return `search?${ + createSearchParams({ + q: value as string, + }) + }`; +} + +function getGroupedCellContent(cell: Cell) { + function handleExpandRequest(event: FormEvent) { + event.preventDefault(); + cell.row.toggleExpanded(); + } + + const row = cell.row; + // Uncomment for grouping only rows with same organism if count > 1 + // if (row.subRows.length > 1) + return ( +
+ + + ({ row.subRows.length }) + + {flexRender(cell.column.columnDef.cell, cell.getContext())} +
+ ); + + // Uncomment for grouping only rows with same organism if count > 1 + // return flexRender(cell.column.columnDef.cell, cell.getContext()); +} + +function renderActionsCell(row: Row, openComparison: (event: FormEvent) => void) { + return ( +
+ { + row.original.uniProtId !== null && ( + <> + + + + ) + } +
+ ); +} + +function getGeneralCellContent(cell: Cell): JSX.Element | ReactNode { + if (cell.getIsGrouped()) + return getGroupedCellContent(cell); + + if (cell.getIsAggregated() || cell.getIsPlaceholder()) + return flexRender(cell.column.columnDef.aggregatedCell, cell.getContext()); + + return flexRender(cell.column.columnDef.cell, cell.getContext()); +} + +function renderUniProtIdCell( + cell: Cell, + isLoading: boolean, + openExperimentalStructures: (event: FormEvent) => void +) { + const link = `https://www.uniprot.org/uniprotkb/${cell.row.original.uniProtId}/entry`; + + const es = cell.row.original.experimentalStructures !== null && cell.row.original.experimentalStructures.length > 0; + + return ( + <> + + { + es + ? {flexRender(cell.column.columnDef.cell, cell.getContext())} + : flexRender(cell.column.columnDef.cell, cell.getContext()) + } + + { + isLoading + ? ( + + Looking for experimental structures... + + }> + + + ) + : ( + es && + + Experimental structures (PDBe) are present + + }> + + + ) + } + + ); +} + +function handleCellTypes( + cell: Cell, + isLoading: boolean, + openComparison: (event: FormEvent) => void, + openExperimentalStructures: (event: FormEvent) => void +) { + if (cell.column.id === "actions") + return renderActionsCell(cell.row, openComparison); + + if (cell.column.id === "uniProtId") + return renderUniProtIdCell(cell, isLoading, openExperimentalStructures); + + return getGeneralCellContent(cell); +} + +type Props = { + cell: Cell; +}; + +export function ProteinTableCell({ cell }: Props) { + const { setExperimentalStructuresModalValue, setComparisonModalValue } = useContext(ModalContext); + + const openComparison = (event: FormEvent) => { + event.preventDefault(); + setComparisonModalValue(cell.row.original.uniProtId); + }; + + const openExperimentalStructures = (event: FormEvent) => { + event.preventDefault(); + setExperimentalStructuresModalValue( + cell.row.original.experimentalStructures === null + ? null + : ({ + entryUniProtId: cell.row.original.uniProtId, + experimentalStructures: cell.row.original.experimentalStructures, + }) + ); + } + + const isLoading = cell.column.id === "uniProtId" && cell.row.original.experimentalStructures === null ? true : false; + + return ( + + {handleCellTypes(cell, isLoading, openComparison, openExperimentalStructures)} + + ); +} diff --git a/ui/src/components/ProteinTable/ProteinTableRow.tsx b/ui/src/components/ProteinTable/ProteinTableRow.tsx index 084ef35..dfabae8 100644 --- a/ui/src/components/ProteinTable/ProteinTableRow.tsx +++ b/ui/src/components/ProteinTable/ProteinTableRow.tsx @@ -1,88 +1,18 @@ -import { faAngleDown, faAngleRight } from "@fortawesome/free-solid-svg-icons"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { Cell, Row, flexRender } from "@tanstack/react-table"; -import { FormEvent } from "react"; -import { Button } from "react-bootstrap"; +import { Row } from "@tanstack/react-table"; import { Record } from "./ProteinTable"; - -function getCellBackground(cell: Cell) { - if (cell.getIsGrouped()) - return '#ededed'; - - if (cell.getIsAggregated()) - return '#ededed'; - - if (cell.getIsPlaceholder()) - return '#fff'; - - return '#fff'; -} - -function getGroupedCellContent(cell: Cell, row: Row, onClickExpand: (event: FormEvent) => void) { - // Uncomment for grouping only rows with same organism if count > 1 - // if (row.subRows.length > 1) - return ( -
- - - ({ row.subRows.length }) - - {flexRender(cell.column.columnDef.cell, cell.getContext())} -
- ); - - // Uncomment for grouping only rows with same organism if count > 1 - // return flexRender(cell.column.columnDef.cell, cell.getContext()); -} - -function getCellContent(cell: Cell, row: Row, onClickExpand: (event: FormEvent) => void) { - if (cell.getIsGrouped()) - return getGroupedCellContent(cell, row, onClickExpand); - - if (cell.getIsAggregated() || cell.getIsPlaceholder()) - return flexRender(cell.column.columnDef.aggregatedCell, cell.getContext()); - - return flexRender(cell.column.columnDef.cell, cell.getContext()); -} +import { ProteinTableCell } from "./ProteinTableCell"; type Props = { row: Row; - setProteinComparisonModalValue: (value: string | null) => void; }; -export const ProteinTableRow = ({ row, setProteinComparisonModalValue }: Props) => { - const onClickModal = (event: FormEvent) => { - event.preventDefault(); - setProteinComparisonModalValue(row.original.uniProtId); - }; - - const onClickExpand = (event: FormEvent) => { - event.preventDefault(); - row.toggleExpanded(); - }; - +export const ProteinTableRow = ({ row }: Props) => { return ( - {row.getVisibleCells().map(cell => - - {cell.column.id === 'actions' ? - flexRender(cell.column.columnDef.cell, { - ...cell.getContext(), - meta: { - isExpanded: row.getIsExpanded(), - subRowsCount: row.subRows.length, - onClickModal: onClickModal, - } - }) : - getCellContent(cell, row, onClickExpand) - } - - )} + {row.getVisibleCells().map(cell => )} ); }; diff --git a/ui/src/components/ProteinTable/exportToCsv.ts b/ui/src/components/ProteinTable/exportToCsv.ts index af1e0d7..9a97f3f 100644 --- a/ui/src/components/ProteinTable/exportToCsv.ts +++ b/ui/src/components/ProteinTable/exportToCsv.ts @@ -4,7 +4,7 @@ import { Record } from "./ProteinTable"; import { displayPercentage } from "../../common/utils"; function makeHeader() { - return `UniProtID;Name;Organism;TM-Score;RMSD;Aligned Residues\n`; + return `UniProtID;Name;Organism;TM-Score;RMSD;Aligned Residues;Taxonomy ID;Experimental PDB IDs;Sequence;Gene;Is Reviewed (SwissProt)\n`; } function prepareDataForExport(data: Row[]) { @@ -16,10 +16,11 @@ function prepareDataForExport(data: Row[]) { const tmScore: string = (row.getValue("tmScore") as number).toFixed(4); const rmsd: string = (row.getValue("rmsd") as number).toFixed(3); const aligned_residues: string = displayPercentage(row.getValue("alignedLength")); - + const experimentalStructures = row.original.experimentalStructures === null ? "[]" : JSON.stringify(row.original.experimentalStructures); - output += `${row.getValue("uniProtId")};${row.original.name};${row.getValue("organism")};${tmScore};${rmsd};${aligned_residues}`; + output += `${row.original.uniProtId};"${row.original.name}";"${row.original.organism}";${tmScore};${rmsd};${aligned_residues};`; + output += `${row.original.taxId};${experimentalStructures};${row.original.sequence};${row.original.gene};${row.original.isReviewed}`; if (i < data.length - 1) output += "\n"; diff --git a/ui/src/components/ProteinTable/protein-table.scss b/ui/src/components/ProteinTable/protein-table.scss index 4df3df5..6b151bd 100644 --- a/ui/src/components/ProteinTable/protein-table.scss +++ b/ui/src/components/ProteinTable/protein-table.scss @@ -15,7 +15,7 @@ } .protein-table thead th.uniProtId > div { - min-width: 130px; + min-width: 145px; } .protein-table thead th.tmScore > div { @@ -23,7 +23,7 @@ } .protein-table thead th.rmsd > div { - min-width: 130px; + min-width: 110px; } .protein-table thead th.alignedLength > div { diff --git a/ui/src/components/ProteinVisualizer/ProteinVisualizer.tsx b/ui/src/components/ProteinVisualizer/ProteinVisualizer.tsx index f448199..3de297c 100644 --- a/ui/src/components/ProteinVisualizer/ProteinVisualizer.tsx +++ b/ui/src/components/ProteinVisualizer/ProteinVisualizer.tsx @@ -1,6 +1,6 @@ import { faAngleLeft, faAngleRight, faExpand } from "@fortawesome/free-solid-svg-icons"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { Component, Stage } from "ngl"; +import { Component, Stage, StructureComponent, superpose } from "ngl"; import { CSSProperties, ChangeEvent, Dispatch, MutableRefObject, useEffect, useRef, useState } from "react" import { Button, Form, OverlayTrigger, Spinner, Tooltip } from "react-bootstrap"; import { ColorHEX, makeColorTransitions, makeTransparencyTransitions } from "../../common/utils"; @@ -115,6 +115,43 @@ function setupComponent(component: Component, name: string, color: ColorHEX, tra return component; } +function downloadStructures(uniProtIds: string[], stage: MutableRefObject, colors: ColorHEX[], transparencies: number[], defaultRepresentation: Representation) { + const promises = []; + + for (let i = 0; i < uniProtIds.length; i++) { + const promise = stage.current?.loadFile(`https://alphafold.ebi.ac.uk/files/AF-${uniProtIds[i]}-F1-model_v3.pdb`) + .then(o => { + if (o instanceof Component) + return setupComponent(o, uniProtIds[i], colors[i], transparencies[i], defaultRepresentation); + + throw new Error("Invalid object type"); + }); + + if (promise === undefined) + continue; + + promises.push(promise); + } + + return promises; +} + +function performSuperposition(components: Component[]) { + const native = components[0]; + // There preconditions are necessary to ensure component posesses structure property + if (!(native instanceof StructureComponent)) + return; + + for (let i = 1; i < components.length; i++) { + const target = components[i]; + if (!(target instanceof StructureComponent)) + continue; + + // last param 'true' - whether to use sequence alignment + superpose(native.structure, target.structure, true); + } +} + function setupVisualizer(stage: MutableRefObject, uniProtIds: string[], setPreviewState: Dispatch>, @@ -122,38 +159,22 @@ function setupVisualizer(stage: MutableRefObject, const colors = uniProtIds.length === 2 ? defaultColors : [defaultColors[0], ...makeColorTransitions(uniProtIds.length)]; const transparencies = uniProtIds.length === 2 ? [1, 1] : [1, ...makeTransparencyTransitions(uniProtIds.length - 1).reverse()]; - const promises = []; - for (let i = 0; i < uniProtIds.length; i++) { - promises.push( - stage.current?.loadFile(`https://alphafold.ebi.ac.uk/files/AF-${uniProtIds[i]}-F1-model_v3.pdb`) - .then(o => { - if (o instanceof Component) - return setupComponent(o, uniProtIds[i], colors[i], transparencies[i], defaultRepresentation); - }) - ); - } + const promisedComponents = downloadStructures(uniProtIds, stage, colors, transparencies, defaultRepresentation); - Promise.all(promises) - .then(responses => { - for (let i = 1; i < responses.length; i++) { - // @ts-expect-error - private property - (responses[0])?.superpose(responses[i]); - } - // Unused - // When identical 3D models, shift one sliiightly - // if ((responses[0])?.name === (responses[1])?.name) - // (responses[0])?.setPosition([0.1,0,0]); - - (responses[0])?.updateRepresentations({ + Promise.all(promisedComponents) + .then(components => { + if (components.length > 1) + performSuperposition(components); + + components[0].updateRepresentations({ position: true, }); // Focus and center on object or the whole scene - // responses[0].autoView(); stage.current?.autoView(); - // setTimeout(() => { + setTimeout(() => { setPreviewState(PreviewState.Success); - // }, 500); + }, 500); }) .catch(error => { setPreviewState(PreviewState.Error); @@ -262,7 +283,8 @@ function changeRepresentation(stage: Stage | null, setControls: Dispatch stage.handleResize(); window.addEventListener("resize", handler, false); @@ -539,6 +564,7 @@ export function ProteinVisualizer({ }; }, [JSON.stringify(uniProtIds)]); + // Function to shows loader for 3D canvas and after particular time automatically hides it function requestLoader() { setPreviewState(PreviewState.Initial); diff --git a/ui/src/components/SearchMetaBox/SearchMetaBox.tsx b/ui/src/components/SearchMetaBox/SearchMetaBox.tsx new file mode 100644 index 0000000..240b4ad --- /dev/null +++ b/ui/src/components/SearchMetaBox/SearchMetaBox.tsx @@ -0,0 +1,113 @@ +import { Button, OverlayTrigger, Spinner, Tooltip } from "react-bootstrap"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { faFlask } from "@fortawesome/free-solid-svg-icons"; +import { useContext, useEffect, useState } from "react"; +import "./search-meta-box.scss"; +import { QueryObjectContext } from "../../pages/ProteinSearch/ProteinSearch"; +import { ExperimentalStructuresModalAttributes } from "../ProteinTable/ProteinTable"; +import { getPdbIds } from "../../data/uniProtApiWrapper"; + +type Props = { + loading: boolean; + originalInput: string; + searchTime: number; + setExperimentalStructuresModalValue: React.Dispatch>; +}; + +export function SearchMetaBox({ loading, originalInput, searchTime, setExperimentalStructuresModalValue }: Props) { + const [experimentalStructures, setExperimentalStructures] = useState(null); + const queryObject = useContext(QueryObjectContext); + + useEffect(() => { + // Reset on new UniProt ID + setExperimentalStructures(null); + + // Do not perform on an empty query + if (queryObject.uniProtId === "") + return; + + async function fetch() { + const promisedStructures = await getPdbIds(queryObject.uniProtId); + const structures = promisedStructures.results.map(structure => structure.to); + + setExperimentalStructures(structures); + } + + fetch(); + }, [queryObject.uniProtId]); + + let queryString = originalInput; + if (originalInput !== queryObject.uniProtId && queryObject.uniProtId !== "") + queryString = originalInput + " → " + queryObject.uniProtId; + + function openExperimentalStructuresModal(event: React.MouseEvent) { + event.preventDefault(); + setExperimentalStructuresModalValue({ + entryUniProtId: queryObject.uniProtId, + experimentalStructures: experimentalStructures as string[], + }); + } + + return ( +
    +
  • + Query:{queryString} +
  • + + {queryObject.name !== "" && ( +
  • + Name: {queryObject.name} +
  • + )} + + {queryObject.organism !== "" && ( +
  • + Organism: {queryObject.organism} +
  • + )} + + {queryObject.uniProtId !== "" && ( +
  • + {queryObject.uniProtId} in UniProt + + { + experimentalStructures === null ? ( + + Looking for experimental structures... + + }> + + + ) : (experimentalStructures.length > 0 && + + Experimental structures (PDBe) are present + + }> + + + ) + } +
  • + )} + +
  • + Search Time: + {loading ? ( + + Loading... + + ) : ( + {searchTime.toFixed(3)} s + )} +
  • +
+ ); +} diff --git a/ui/src/components/SearchMetaBox/index.tsx b/ui/src/components/SearchMetaBox/index.tsx new file mode 100644 index 0000000..7591011 --- /dev/null +++ b/ui/src/components/SearchMetaBox/index.tsx @@ -0,0 +1,3 @@ +import { SearchMetaBox } from "./SearchMetaBox"; + +export default SearchMetaBox; diff --git a/ui/src/components/LoadInfoBox/load-info-box.scss b/ui/src/components/SearchMetaBox/search-meta-box.scss similarity index 100% rename from ui/src/components/LoadInfoBox/load-info-box.scss rename to ui/src/components/SearchMetaBox/search-meta-box.scss diff --git a/ui/src/pages/ProteinSearch/data-loading.ts b/ui/src/data/dataLoading.ts similarity index 56% rename from ui/src/pages/ProteinSearch/data-loading.ts rename to ui/src/data/dataLoading.ts index 23e87b8..ad927ed 100644 --- a/ui/src/pages/ProteinSearch/data-loading.ts +++ b/ui/src/data/dataLoading.ts @@ -1,7 +1,8 @@ -import { Record } from "../../components/ProteinTable/ProteinTable"; -import { calcOffsetLimit } from "../../common/utils"; +import { Record } from "../components/ProteinTable/ProteinTable"; +import { calcOffsetLimit } from "../common/utils"; import { callUniProtMapping, canBePdbID } from "./pdbToUniProtMapping"; -import getGeneMapping from "./geneToUniProtMapping"; +import { SearchResult } from "../pages/ProteinSearch/ProteinSearch"; +import { ResponseMapping, getPdbIds, mapGeneToUniProt } from "./uniProtApiWrapper"; type ParsedAPIResponse = { @@ -76,7 +77,8 @@ async function tryMapping(queryValue: string, mutableResult: CallBackendResponse // if that failed, the input can be a gene symbol if (uniProtId === "") - uniProtId = await getGeneMapping(queryValue) + // uniProtId = await getGeneMapping(queryValue) + uniProtId = await mapGeneToUniProt(queryValue); // if that failed, the input may still be valid UniProt ID but it is not in our database if (uniProtId === "") { @@ -95,30 +97,41 @@ async function tryMapping(queryValue: string, mutableResult: CallBackendResponse return uniProtId; } -async function rec(queryValue: string, fn: (v: string) => Promise, mutableResult: CallBackendResponse) { - const response = await fn(queryValue); +async function searchAndMap( + queryValue: string, + fn: (v: string) => Promise, + mutable: CallBackendResponse +) { + const response = await fn(queryValue); - // No matter what there is waiting queue + if (response.search_time !== undefined) + mutable.apiResponse.search_time = response.search_time; + + // No matter what, there is waiting queue if (response.queue_position !== undefined) { - mutableResult.apiResponse.queue_position = response.queue_position; - return response; + mutable.originalSearchValue = queryValue; + mutable.apiResponse.queue_position = response.queue_position; + + return; } // We got results if (response.results.length > 0) { - mutableResult.originalSearchValue = queryValue; - return response; + mutable.originalSearchValue = queryValue; + mutable.apiResponse.results = response.results; + + return; } // We got no results, try mapping - const newQueryValue = await tryMapping(queryValue, mutableResult); + const newQueryValue = await tryMapping(queryValue, mutable); // Mapping was not successful -> there are indeed no results if (newQueryValue === "") - return response; + return; // Mapping was successful -> try again the same function with new value to handle possible waiting queue - return rec(newQueryValue, fn, mutableResult); + await searchAndMap(newQueryValue, fn, mutable); } /** @@ -130,7 +143,7 @@ async function rec(queryValue: string, fn: (v: string) => Promise { +export async function fetchBackend(queryValue: string, limit: number, currentRowCount: number): Promise { const fn = (v: string) => fetchLMI(v, currentRowCount, limit); const result: CallBackendResponse = { @@ -142,10 +155,7 @@ export async function fetchBackend(queryValue: string, currentRowCount: number, isInAlphaFoldDB: false, }; - const response = await rec(queryValue, fn, result); - result.apiResponse.results = response.results; - if (response.search_time !== undefined) - result.apiResponse.search_time = response.search_time; + await searchAndMap(queryValue, fn, result); return result; } @@ -158,8 +168,25 @@ export async function fetchBackend(queryValue: string, currentRowCount: number, async function fetchSingleMetadata(object: APIRawResponseRecord): Promise { const res = await fetch(`https://www.alphafold.ebi.ac.uk/api/prediction/${object.object_id}?key=AIzaSyCeurAJz7ZGjPQUtEaerUkBZ3TaBkXrY94`); - if (!res.ok) - throw new Error(`${res.status} ${res.statusText}`); + if (!res.ok) { + console.error(`${res.status} ${res.statusText}`); + + return { + rmsd: object.rmsd, + tmScore: object.tm_score, + alignedLength: object.aligned_percentage, + identicalAAs: object.sequence_aligned_percentage, + experimentalStructuresExists: false, + uniProtId: object.object_id, + name: null, + organism: null, + isReviewed: false, + taxId: 0, + sequence: "", + gene: "", + experimentalStructures: null, + }; + } const json = await res.json(); @@ -172,6 +199,11 @@ async function fetchSingleMetadata(object: APIRawResponseRecord): Promise { +export async function fetchData( + searchParams: [string, number], + currentData: Record[], + mappedUnitProtId: string | null +): Promise { + // To prevent calling mapping again + let searchValue = searchParams[0]; + if (mappedUnitProtId !== null) + searchValue = mappedUnitProtId; + + const backendResponse = await fetchBackend(searchValue, searchParams[1], currentData?.length); + const response: ParsedAPIResponse = { data: [], - searchTime: 0, - originalSearchValue: queryValue, - isValueValidUniProtID: false, - isInAlphaFoldDB: false, + searchTime: backendResponse.apiResponse.search_time ?? 0, + originalSearchValue: backendResponse.originalSearchValue, + isValueValidUniProtID: backendResponse.isValueValidUniProtID, + isInAlphaFoldDB: backendResponse.isInAlphaFoldDB, }; - const backendResponse = await fetchBackend(queryValue, currentData?.length, limit); - - response.originalSearchValue = backendResponse.originalSearchValue; - response.isInAlphaFoldDB = backendResponse.isInAlphaFoldDB; - response.isValueValidUniProtID = backendResponse.isValueValidUniProtID; - response.searchTime = backendResponse.apiResponse.search_time ?? 0; - if (backendResponse.apiResponse.queue_position !== undefined) response.queuePosition = backendResponse.apiResponse.queue_position; @@ -235,3 +271,69 @@ export async function fetchData(queryValue: string, currentData: Record[], limit return response; } + +export async function fetchExperimentalStructures( + data: Record[], + setSearchResults: React.Dispatch>, + searchParams: React.MutableRefObject<[string, number]> +) { + const spCopy = [searchParams.current[0], searchParams.current[1]]; + const BATCH_SIZE = 5; + + const dataCopy = [...data]; + + /** + * Performs the fetch in batches to prevent crashing the browser from too many requests + * + * Works this way: + * Loops current results + * If the current result has no experimental structures, add it to the batch + * If the batch is full, make the fetch and update the results + * + * Handles also the case if "load more" actions was performed + */ + let i = 0; + let batch: [number, Promise][] = []; + while (i < dataCopy.length) { + // Prevent race conditions + // e.g., case if exp. structures are still loading but user requests to load more + // or performs new search + + if (spCopy[0] !== searchParams.current[0] || spCopy[1] !== searchParams.current[1]) + break; + + // Adds to batch if there are no experimental structures + if (dataCopy[i].experimentalStructures === null) + batch.push([i, getPdbIds(dataCopy[i].uniProtId)]); + + if (batch.length === BATCH_SIZE) { + // Prepare the requests + const promises = batch.map(item => item[1]); + // Run the requests + const results = await Promise.all(promises); + + results.forEach((result, index) => { + const pdbIds = result.results.map(item => item.to); + dataCopy[batch[index][0]].experimentalStructures = pdbIds; + }); + + // Prevent race conditions + // e.g., case if exp. structures are still loading but user requests to load more + // or performs new search + if (spCopy[0] !== searchParams.current[0] || spCopy[1] !== searchParams.current[1]) + break; + + // Update the table + setSearchResults(prev => ({ + meta: prev.meta, + data: dataCopy, + })); + + + batch = []; + await new Promise(resolve => setTimeout(resolve, 3000)); + } + + i++; + } +} diff --git a/ui/src/pages/ProteinSearch/pdbToUniProtMapping.tsx b/ui/src/data/pdbToUniProtMapping.tsx similarity index 100% rename from ui/src/pages/ProteinSearch/pdbToUniProtMapping.tsx rename to ui/src/data/pdbToUniProtMapping.tsx diff --git a/ui/src/data/uniProtApiWrapper.ts b/ui/src/data/uniProtApiWrapper.ts new file mode 100644 index 0000000..1562501 --- /dev/null +++ b/ui/src/data/uniProtApiWrapper.ts @@ -0,0 +1,135 @@ +const baseUrl = 'https://rest.uniprot.org/idmapping'; +const jobSubmitUrl = '/run'; +const jobStatusUrl = '/status'; +const jobResultsUrl = '/stream'; +const POLLING_INTERVAL = 2000; + +type SubmitMapping = { + jobId: string; +}; + +type StatusMapping = { + jobStatus: string; + results?: unknown[]; +}; + +type Mapping = { + from: string; + to: string; +}; + +export type ResponseMapping = { + results: Mapping[]; +}; + +async function submitJob(payload: FormData) { + const url = baseUrl + jobSubmitUrl; + + const response = await fetch(url, { + method: 'POST', + body: payload, + }); + + if (!response.ok) + throw new Error(`Failed to submit mapping job: ${response.statusText}`); + + const data: SubmitMapping = await response.json(); + + return data.jobId; +} + +async function isJobFinished(jobId: string) { + const url = `${baseUrl}${jobStatusUrl}/${jobId}`; + + const response = await fetch(url); + + if (!response.ok) + throw new Error(`Failed to check job status: ${response.statusText}`); + + const data: StatusMapping = await response.json(); + + if ("jobStatus" in data) { + if (data.jobStatus === "RUNNING") { + console.log(`UniProt ID to PDB ID mapping: Retrying in ${POLLING_INTERVAL / 1000}s`); + + return false; + } + + if (data.jobStatus === "FINISHED") + return true; + } + + if ("results" in data) + return true; + + throw new Error(`Unexpected response from server: ${data}`); +} + +async function getResults(jobId: string) { + const url = `${baseUrl}${jobResultsUrl}/${jobId}`; + + const response = await fetch(url); + + if (!response.ok) + throw new Error(`Failed to get mapping results: ${response.statusText}`); + + const data: T = await response.json(); + + return data; +} + +async function performAction(payload: FormData) { + const jobId = await submitJob(payload); + + if (!jobId) + throw new Error('Failed to perform action'); + + await new Promise(resolve => setTimeout(resolve, 1000)); + + while (!await isJobFinished(jobId)) + await new Promise(resolve => setTimeout(resolve, POLLING_INTERVAL)); + + await new Promise(resolve => setTimeout(resolve, 1000)); + const result = await getResults(jobId); + + return result; +} + +export async function getPdbIds(uniProtId: string) { + const formData = new FormData(); + formData.append('from', 'UniProtKB_AC-ID'); + formData.append('to', 'PDB'); + formData.append('ids', uniProtId); + + let results; + try { + results = await performAction(formData); + } catch (error) { + const resp: ResponseMapping = { + results: [] + }; + + return resp; + } + + return results; +} + +export async function mapGeneToUniProt(geneSymbol: string) { + const formData = new FormData(); + formData.append('from', 'Gene_Name'); + formData.append('to', 'UniProtKB'); + formData.append('ids', geneSymbol); + + let results; + try { + results = await performAction(formData); + } catch (error) { + return ""; + } + + if (results.results.length === 0) + return ""; + + return results.results[0].to; +} \ No newline at end of file diff --git a/ui/src/pages/ProteinSearch/ProteinSearch.tsx b/ui/src/pages/ProteinSearch/ProteinSearch.tsx index 7a83163..fb773ef 100644 --- a/ui/src/pages/ProteinSearch/ProteinSearch.tsx +++ b/ui/src/pages/ProteinSearch/ProteinSearch.tsx @@ -1,4 +1,4 @@ -import { FormEvent, createContext, useCallback, useEffect, useRef, useState } from "react"; +import { FormEvent, createContext, useCallback, useEffect, useLayoutEffect, useRef, useState } from "react"; import { Col, Container, Row } from "react-bootstrap"; import 'react-autocomplete-input/dist/bundle.css'; import { useQuery } from "@tanstack/react-query"; @@ -7,18 +7,19 @@ import "./protein-search.scss"; import { calcEstimatedSearchTime, calcOffsetLimit, useUrlParams } from "../../common/utils"; import SearchInput from "../../components/SearchInput"; import ProteinVisualizer from "../../components/ProteinVisualizer"; -import LoadInfoBox from "../../components/LoadInfoBox"; import CustomSpinner from "../../components/CustomSpinner"; import ProteinTable from "../../components/ProteinTable"; import LoadMoreButton from "../../components/LoadMoreButton"; import { LoadingState, Representation } from "../../common/enums"; -import { fetchData, fetchQueryObjectMetadata } from "./data-loading"; -import { Record } from "../../components/ProteinTable/ProteinTable"; +import { fetchData, fetchExperimentalStructures, fetchQueryObjectMetadata } from "../../data/dataLoading"; +import { ExperimentalStructuresModalAttributes, Record } from "../../components/ProteinTable/ProteinTable"; +import SearchMetaBox from "../../components/SearchMetaBox"; +import ExperimentalStructuresModal from "../../components/ExperimentalStructuresModal"; export const DEFAULT_LIMIT = 50; export const MAX_LIMIT = 1_000; -type SearchResult = { +export type SearchResult = { data: Record[]; meta: { searchTime: number; @@ -31,7 +32,6 @@ export type QueryObject = { organism: string; }; -export type onSearchHeader = (event: FormEvent, value: string | undefined) => void; export type onLoadMoreHeader = (count: number) => void; export const QueryObjectContext = createContext({ @@ -58,6 +58,10 @@ function renderNoResults(isQueryValidUniProtID: boolean, isInAlphaFoldDB: boolea export function ProteinSearch() { const [inputValue, setInputValue] = useState(""); const searchParams = useRef<[string, number]>(["", DEFAULT_LIMIT]); + // Helper value that holds the mapped UniProt ID + // Used to check whether mapping has been performed successfully and to prevent + // repetitive mapping calls + const mappedUniProtId = useRef(null); const [loadingState, setLoadingState] = useState(LoadingState.Overview); const [isLoadingMore, setIsLoadingMore] = useState(false); @@ -71,10 +75,12 @@ export function ProteinSearch() { }); const [urlParams, setUrlParams] = useUrlParams(); + + const [experimentalStructuresModalValue, setExperimentalStructuresModalValue] = useState(null); const dataQ = useQuery({ queryKey: ["data", searchParams.current[0], searchParams.current[1]], - queryFn: () => fetchData(searchParams.current[0], searchResult.data, searchParams.current[1]), + queryFn: () => fetchData(searchParams.current, searchResult.data, mappedUniProtId.current), refetchOnWindowFocus: false, refetchOnMount: false, refetchOnReconnect: false, @@ -83,18 +89,15 @@ export function ProteinSearch() { staleTime: 1e15, }); - const originalSearchValue = dataQ.data?.originalSearchValue ?? searchParams.current[0]; - const queryMetadataQ = useQuery({ - queryKey: ["queryObjectMetadata", originalSearchValue], - queryFn: () => fetchQueryObjectMetadata(originalSearchValue), + queryKey: ["queryObjectMetadata", mappedUniProtId.current], + queryFn: () => fetchQueryObjectMetadata(mappedUniProtId.current!), refetchOnWindowFocus: false, refetchOnMount: false, - enabled: dataQ.data !== undefined && dataQ.data.data.length > 0, + enabled: mappedUniProtId.current !== null, retry: false, }); - /** * Responsible for handling the data from the main query. */ @@ -112,6 +115,9 @@ export function ProteinSearch() { return; } + // Saved (possibly mapped) UniProt ID + mappedUniProtId.current = dataQ.data?.originalSearchValue; + // QUEUE if (dataQ.data?.queuePosition !== undefined) { let refetchTimer: NodeJS.Timeout; @@ -119,10 +125,6 @@ export function ProteinSearch() { if (!isLoadingMore) setLoadingState(LoadingState.WaitingInQueue); - if (searchParams.current[0] !== dataQ.data?.originalSearchValue) - searchParams.current[0] = dataQ.data?.originalSearchValue; - - const queuePosition = dataQ.data.queuePosition; if (queuePosition <= 5) refetchTimer = setTimeout(() => dataQ.refetch(), 3000); @@ -132,6 +134,7 @@ export function ProteinSearch() { return () => clearTimeout(refetchTimer); } else if (dataQ.data.data.length === 0) { // NO RESULTS - wrong input + mappedUniProtId.current = null; setLoadingState(LoadingState.ShowingResults); setSearchResult({ data: [], @@ -143,11 +146,17 @@ export function ProteinSearch() { return; } + // Prevent recalculation of search time when not needed + const searchTime = ( + searchResult.meta.searchTime === 0 || + isLoadingMore + ) ? (performance.now() - timerStart.current) / 1000 : searchResult.meta.searchTime; + // RESULTS setSearchResult({ data: dataQ.data.data, meta: { - searchTime: (performance.now() - timerStart.current) / 1000, + searchTime: searchTime, } }); @@ -157,21 +166,17 @@ export function ProteinSearch() { } setLoadingState(LoadingState.ShowingResults); - + return () => {}; - }, [JSON.stringify(dataQ.data), dataQ.status, dataQ.fetchStatus]); + }, [JSON.stringify(dataQ.data), dataQ.status, dataQ.fetchStatus]); - const queryObject: QueryObject = { - uniProtId: originalSearchValue, - name: queryMetadataQ.data?.name ?? "-", - organism: queryMetadataQ.data?.organism ?? "-", - }; - // Reset query object if the search value is not valid - if (searchResult.data.length === 0) { - queryObject.name = ""; - queryObject.uniProtId = ""; - queryObject.organism = ""; - } + useEffect(() => { + if (searchResult.data.length === 0) + return; + + fetchExperimentalStructures(searchResult.data, setSearchResult, searchParams); + }, [searchParams.current[0], searchResult.data.length]); + /** * This is a fix for a bug where the window is unfocused and the user is in the queue. @@ -196,30 +201,70 @@ export function ProteinSearch() { * First use case is when the user uses URl with defined params -> automatic search * is performed. * - * Second use case is when the URL params change (e.g. user changes the URL manually). + * Second use case is when the URL params change (e.g. user changes the URL manually) + * e.g., browser back/forward buttons */ useEffect(() => { - if (loadingState !== LoadingState.Overview) - return; + if (urlParams.searchQuery === null) { + // Reset everything + setInputValue(""); + setLoadingState(LoadingState.Overview); + setSearchResult({ + data: [], + meta: { + searchTime: 0, + } + }); + mappedUniProtId.current = null; + searchParams.current = ["", DEFAULT_LIMIT]; - if (urlParams.searchQuery === null) return; - + } + // Match typeable input with URL - if (urlParams.searchQuery !== inputValue) + if (urlParams.searchQuery.toLowerCase() !== inputValue) setInputValue(urlParams.searchQuery); - const searchQuery = urlParams.searchQuery; - const timeoutPointer = setTimeout(() => { + let timeoutPointer: NodeJS.Timeout; + if (loadingState === LoadingState.Overview) { + timeoutPointer = setTimeout(() => { + timerStart.current = performance.now(); + setLoadingState(LoadingState.Fetching); + + // searchQuery is indeed defined, not null string + searchParams.current = [urlParams.searchQuery!, urlParams.limit !== null ? urlParams.limit : DEFAULT_LIMIT]; + mappedUniProtId.current = null; + }, 800); + } + + // Following code is preparation for full handling of browser back/forward actions + /* if (loadingState === LoadingState.Fetching || loadingState === LoadingState.WaitingInQueue) { timerStart.current = performance.now(); setLoadingState(LoadingState.Fetching); - searchParams.current = [searchQuery, urlParams.limit !== null ? urlParams.limit : DEFAULT_LIMIT]; - }, 800); + // searchQuery is indeed defined, not null string + searchParams.current = [urlParams.searchQuery!, urlParams.limit !== null ? urlParams.limit : DEFAULT_LIMIT]; + mappedUniProtId.current = null; + } else { + // loadingState === LoadingState.ShowingResults + console.log(urlParams); + + if (isLoadingMore) + searchParams.current[1] = urlParams.limit !== null ? urlParams.limit : DEFAULT_LIMIT; + } */ return () => clearTimeout(timeoutPointer); }, [urlParams.searchQuery, urlParams.limit]); + // Added support for changing the title of the page + useLayoutEffect(() => { + let title = `${import.meta.env.VITE_TITLE}`; + if (searchParams.current[0].length > 0) + title += ` | ${searchParams.current[0]}`; + + document.title = title; + }, [searchParams.current[0]]); + /** * Main entrypoint for the search. */ @@ -246,7 +291,8 @@ export function ProteinSearch() { timerStart.current = performance.now(); // Trigger search searchParams.current = [parsedInputValue, DEFAULT_LIMIT]; - }, [inputValue, searchParams.current[0]]); + mappedUniProtId.current = null; + }, [inputValue]); /** * Entrypoint for loading more results (pressing the button) @@ -256,11 +302,18 @@ export function ProteinSearch() { const newLimit = searchParams.current[1] + count; - setUrlParams(queryObject.uniProtId, newLimit); + setUrlParams(searchParams.current[0], newLimit); timerStart.current = performance.now(); searchParams.current[1] = newLimit; - }, [queryObject.uniProtId, searchParams.current[1]]); + }, [searchParams.current[0], searchParams.current[1]]); + + // QUERY OBJECT + const queryObject: QueryObject = { + uniProtId: mappedUniProtId.current ?? "", + name: queryMetadataQ.data?.name ?? "", + organism: queryMetadataQ.data?.organism ?? "", + }; // SHORTCUTS for RENDERING const isQueryValidUniProtID = dataQ.data?.isValueValidUniProtID ?? true; @@ -287,9 +340,13 @@ export function ProteinSearch() { const emptyResults = searchResult.data.length === 0; const isLoading = dataQ.isFetching || isLoadingMore || isFetchingState || isWaitingInQueueState; - + return ( + setExperimentalStructuresModalValue(null)} + />
@@ -313,10 +370,11 @@ export function ProteinSearch() { />} - {!isOverviewState && } @@ -325,7 +383,7 @@ export function ProteinSearch() { {isShowingResultsState && ( !emptyResults ? (<> - + ) : renderNoResults(isQueryValidUniProtID, isInAlphaFoldDB) )} diff --git a/ui/src/pages/ProteinSearch/geneToUniProtMapping.tsx b/ui/src/pages/ProteinSearch/geneToUniProtMapping.tsx deleted file mode 100644 index 28cc45f..0000000 --- a/ui/src/pages/ProteinSearch/geneToUniProtMapping.tsx +++ /dev/null @@ -1,100 +0,0 @@ -type SubmitMapping = { - jobId: string; -}; - -type StatusMapping = { - jobStatus: string; -}; - -type Mapping = { - from: string; - to: string; -}; - -type ResponseMapping = { - results: Mapping[]; -}; - -async function waitForMappingReady(jobStatusUrl: string) { - const POLLING_INTERVAL = 2000; - - try { - const response = await fetch(jobStatusUrl); - const data: StatusMapping = await response.json(); - - if ('jobStatus' in data) { - if (data.jobStatus === 'RUNNING') { - console.log(`Gene symbol to UniProtID mapping: Retrying in ${POLLING_INTERVAL / 1000}s`); - - await new Promise(resolve => setTimeout(resolve, POLLING_INTERVAL)); - - return waitForMappingReady(jobStatusUrl); - } - - if (data.jobStatus === 'FINISHED') - return true; - } - - // the 'status' call gets translated into 'results' call once the job is finished - if ('results' in data) - return true; - - throw new Error(`Unexpected response from server: ${data}`); - } catch (error) { - console.error('Error:', error); - - return false; - } -} - -const getGeneMapping = async (geneSymbol: string): Promise => { - const baseUrl = 'https://rest.uniprot.org/idmapping' - const jobSubmitUrl = baseUrl + '/run'; - const jobStatusUrl = baseUrl + '/status'; - const jobResultsUrl = baseUrl + '/stream'; - const formData = new FormData(); - formData.append('from', 'Gene_Name'); - formData.append('to', 'UniProtKB'); - formData.append('ids', geneSymbol); - - try { - // Making the API call using the fetch function - const response = await fetch(jobSubmitUrl, { - method: 'POST', - body: formData - }); - - // Check if the response status is OK (status code 200) - if (!response.ok) - return ''; - - // Submit the job - const jobSubmitData: SubmitMapping = await response.json(); - - // Check if the job is finished - const isJobFinished: boolean = await waitForMappingReady(jobStatusUrl + '/' + jobSubmitData.jobId); - - if (isJobFinished) { - // Get the results - const response = await fetch(jobResultsUrl + '/' + jobSubmitData.jobId); - const data: ResponseMapping = await response.json(); - - if (data.results.length === 0) - return ''; - - // even if there are multiple results (e.g. for `NLGN1`), we only return the first one - return data.results[0].to; - } - - console.error('"Job finished" check returned false'); - return ''; - - } catch (error) { - // Handle errors during the API call - console.error('Error during API call:', error); - - return ''; - } -}; - -export default getGeneMapping; diff --git a/ui/src/pages/ProteinSearch/tableColumnsDefinition.tsx b/ui/src/pages/ProteinSearch/tableColumnsDefinition.tsx index e789066..5962edf 100644 --- a/ui/src/pages/ProteinSearch/tableColumnsDefinition.tsx +++ b/ui/src/pages/ProteinSearch/tableColumnsDefinition.tsx @@ -1,9 +1,6 @@ -import { Button, OverlayTrigger, Tooltip } from "react-bootstrap"; -import { CustomCellContext, Record } from "../../components/ProteinTable/ProteinTable"; +import { OverlayTrigger, Tooltip } from "react-bootstrap"; +import { Record } from "../../components/ProteinTable/ProteinTable"; import { createColumnHelper, Row as TableRow } from "@tanstack/react-table"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { faMagnifyingGlass, faObjectUngroup } from "@fortawesome/free-solid-svg-icons"; -import { createSearchParams } from "react-router-dom"; import { displayPercentage } from "../../common/utils"; function getBestRow(rows: TableRow[]): TableRow { @@ -22,14 +19,6 @@ function getBestRow(rows: TableRow[]): TableRow { return rows[minIndex]; } -function makeSearchSimilarUrl(value: string) { - return `search?${ - createSearchParams({ - q: value as string, - }) - }`; -} - const columnHelper = createColumnHelper(); const organismCol = columnHelper.accessor('organism', { @@ -67,16 +56,8 @@ export const columns = [ organismCol, columnHelper.accessor('uniProtId', { header: () => <>UniProt ID, - cell: context => ( - context.row.original.uniProtId === null - ? (Unknown) - : ({context.row.original.uniProtId}) - ), - aggregatedCell: context => ( - context.row.original.uniProtId === null - ? (Unknown) - : ({context.getValue()}) - ), + cell: context => context.getValue(), + aggregatedCell: context => context.getValue(), enableColumnFilter: true, aggregationFn: (_, childRows) => getBestRow(childRows).getValue('uniProtId'), sortingFn: (rowA, rowB) => { @@ -191,19 +172,6 @@ export const columns = [ columnHelper.display({ header: () => <>Superposition, - id: "actions", - cell: context => { - const contextCasted = context as CustomCellContext; - - return ( -
- {contextCasted.row.original.uniProtId !== null ? - (<> - - - ): undefined} -
- ); - }, + id: "actions", }), ]; diff --git a/ui/tests/custom-spinner.test.tsx b/ui/tests/custom-spinner.test.tsx index f9aa476..c053ee4 100644 --- a/ui/tests/custom-spinner.test.tsx +++ b/ui/tests/custom-spinner.test.tsx @@ -6,7 +6,7 @@ describe('CustomSpinner', () => { it('0', () => { const queue = { position: 10, - readyUrl: 'http://localhost:5173/search?q=I1VZV6', + readyUrl: 'http://localhost:5173/search?q=P69905', estimatedTime: 1 }; diff --git a/ui/tests/load-info-box.test.tsx b/ui/tests/load-info-box.test.tsx index 6473713..bee64c5 100644 --- a/ui/tests/load-info-box.test.tsx +++ b/ui/tests/load-info-box.test.tsx @@ -1,15 +1,15 @@ import { render } from "@testing-library/react"; import { describe, expect, it } from "vitest"; -import LoadInfoBox from "../src/components/LoadInfoBox"; import { QueryObject, QueryObjectContext } from "../src/pages/ProteinSearch/ProteinSearch"; +import SearchMetaBox from "../src/components/SearchMetaBox"; describe('LoadInfoBox', () => { it('0', () => { const loading = false; - const originalInput = "I1VZV6"; + const originalInput = "P69905"; const searchTime = 1; - const { container } = render(); + const { container } = render( {}} />); const el = container.querySelector('.load-info'); expect(el).exist; @@ -20,7 +20,7 @@ describe('LoadInfoBox', () => { it('1', () => { const loading = false; - const originalInput = "I1VZV6"; + const originalInput = "P69905"; const searchTime = 1; const queryObject: QueryObject = { @@ -31,7 +31,7 @@ describe('LoadInfoBox', () => { const { container } = render( - + {}} /> ); @@ -47,7 +47,7 @@ describe('LoadInfoBox', () => { it('1', () => { const loading = true; - const originalInput = "I1VZV6"; + const originalInput = "P69905"; const searchTime = 1; const queryObject: QueryObject = { @@ -58,7 +58,7 @@ describe('LoadInfoBox', () => { const { container } = render( - + {}} /> ); diff --git a/ui/tests/protein-table.test.tsx b/ui/tests/protein-table.test.tsx index 3a6961c..978e00e 100644 --- a/ui/tests/protein-table.test.tsx +++ b/ui/tests/protein-table.test.tsx @@ -15,6 +15,11 @@ const data: Record[] = [{ identicalAAs: 4, organism: "Organism 1", name: "Name A", + isReviewed: true, + gene: "Gene A", + sequence: "ASJDHAJKLSHDKJLASHD", + taxId: 1, + experimentalStructures: [], }, { uniProtId: "B", experimentalStructuresExists: true, @@ -24,6 +29,11 @@ const data: Record[] = [{ identicalAAs: 4, organism: "Organism 2", name: "Name B", + isReviewed: false, + gene: "Gene A", + sequence: "ASJDHAJKLSHDKJLASHD", + taxId: 1, + experimentalStructures: [], }, { uniProtId: "C", experimentalStructuresExists: true, @@ -33,6 +43,11 @@ const data: Record[] = [{ identicalAAs: 4, organism: "Organism 2", name: "Name C", + isReviewed: false, + gene: "Gene A", + sequence: "ASJDHAJKLSHDKJLASHD", + taxId: 1, + experimentalStructures: [], }, { uniProtId: "D", experimentalStructuresExists: true, @@ -42,6 +57,11 @@ const data: Record[] = [{ identicalAAs: 4, organism: "Organism 3", name: "Name D", + isReviewed: false, + gene: "Gene A", + sequence: "ASJDHAJKLSHDKJLASHD", + taxId: 1, + experimentalStructures: [], }, { uniProtId: "E", experimentalStructuresExists: true, @@ -51,6 +71,11 @@ const data: Record[] = [{ identicalAAs: 4, organism: "Organism 3", name: "Name E", + isReviewed: false, + gene: "Gene A", + sequence: "ASJDHAJKLSHDKJLASHD", + taxId: 1, + experimentalStructures: [], }, { uniProtId: "F", experimentalStructuresExists: true, @@ -60,6 +85,11 @@ const data: Record[] = [{ identicalAAs: 4, organism: "Organism 2", name: "Name F", + isReviewed: false, + gene: "Gene A", + sequence: "ASJDHAJKLSHDKJLASHD", + taxId: 1, + experimentalStructures: [], }]; describe("ProteinTable", () => { @@ -73,7 +103,7 @@ describe("ProteinTable", () => { act(() => { render( - + {}} /> ); }); @@ -136,7 +166,7 @@ describe("ProteinTable", () => { act(() => { render( - + {}} /> ); }); @@ -177,7 +207,7 @@ describe("ProteinTable", () => { act(() => { render( - + {}} /> ); }); @@ -218,7 +248,7 @@ describe("ProteinTable", () => { act(() => { render( - + {}} /> ); });