From 2e3e282aa822841b99b2b608b9988719f7eae9ba Mon Sep 17 00:00:00 2001 From: Oliver Dudgeon <22367286+OliverDudgeon@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:44:58 +0100 Subject: [PATCH] feat(viewers): add SDF file viewer --- components/MolCard/CalculationsTable.tsx | 61 ++ components/MolCard/DepictMolecule.tsx | 65 +++ components/MolCard/MolCard.tsx | 60 ++ components/MolCard/index.ts | 1 + components/ScatterPlot/ScatterPlot.tsx | 197 +++++++ .../ViewFilePopover/FileViewersList.tsx | 4 + .../ViewFilePopover/SDFViewerListItem.tsx | 49 ++ features/SDFViewer.tsx | 170 ++++++ next.config.mjs | 2 +- package.json | 1 + pages/project/file.tsx | 4 +- pages/viewer/sdf.tsx | 64 +++ pnpm-lock.yaml | 536 ++++++++++++------ types/nextjs-routes.d.ts | 3 +- utils/api/fetchHelpers.ts | 4 + utils/api/plaintextViewerSSR.ts | 3 +- utils/app/routes.ts | 3 + 17 files changed, 1038 insertions(+), 189 deletions(-) create mode 100644 components/MolCard/CalculationsTable.tsx create mode 100644 components/MolCard/DepictMolecule.tsx create mode 100644 components/MolCard/MolCard.tsx create mode 100644 components/MolCard/index.ts create mode 100644 components/ScatterPlot/ScatterPlot.tsx create mode 100644 components/ViewFilePopover/SDFViewerListItem.tsx create mode 100644 features/SDFViewer.tsx create mode 100644 pages/viewer/sdf.tsx create mode 100644 utils/api/fetchHelpers.ts diff --git a/components/MolCard/CalculationsTable.tsx b/components/MolCard/CalculationsTable.tsx new file mode 100644 index 000000000..c129edbff --- /dev/null +++ b/components/MolCard/CalculationsTable.tsx @@ -0,0 +1,61 @@ +import { Table, TableBody, TableCell, TableRow, Tooltip, Typography } from "@mui/material"; + +export interface CalculationsTableProps { + properties: { name: string; value: string | undefined }[]; + tableWidth?: number; + calcs?: { [key: string]: string }; + blacklist?: string[]; + fontSize?: number | string; +} + +const CalculationsTable = ({ + calcs, + blacklist = [], + properties, + fontSize, + tableWidth, +}: CalculationsTableProps) => { + return ( + + + {properties + .filter((property) => !blacklist.includes(property.name)) + .map(({ name, value = "" }, index) => { + // TODO: round number-like value to 2 sf + const displayName = calcs?.[name] ?? name; + return ( + + + + {displayName} + + + + + + {value} + + + + + ); + })} + +
+ ); +}; + +export default CalculationsTable; diff --git a/components/MolCard/DepictMolecule.tsx b/components/MolCard/DepictMolecule.tsx new file mode 100644 index 000000000..ab83e68b6 --- /dev/null +++ b/components/MolCard/DepictMolecule.tsx @@ -0,0 +1,65 @@ +import { styled } from "@mui/styles"; + +export interface DepictMoleculeProps { + smiles: string; + width?: number; + height?: number; + margin?: number; + expand?: boolean; + background?: string; + colorScheme?: string; + explicitHOnly?: boolean; + highlightAtoms?: number[]; + highlightColor?: string; + outerGlow?: boolean; + mcs?: string; + mcsColor?: string; + noStereo?: boolean; + alt?: string; + fragnet_server?: string; + depict_route?: string; +} + +export const DepictMolecule = (props: DepictMoleculeProps) => { + const { + smiles, + width, + height, + margin = 0, + expand = true, + noStereo = false, + mcs = "", + mcsColor = "0xFFAAAAAA", + fragnet_server = "https://squonk.informaticsmatters.org", + depict_route = "/fragnet-depict-api/fragnet-depict/moldepict", + } = props; + + const params = { + mol: smiles, + m: String(margin), + expand: String(expand), + mcs: String(mcs), + noStereo: String(noStereo), + mcsColor, + }; + const searchParams = Object.keys(params).map( + (key) => `${key}=${encodeURIComponent(params[key as keyof typeof params])}`, + ); + + return ( + {smiles + ); +}; + +const Image = styled("img")({ + overflow: "hidden", + display: "inline-block", + maxWidth: "100%", + height: "auto", +}); diff --git a/components/MolCard/MolCard.tsx b/components/MolCard/MolCard.tsx new file mode 100644 index 000000000..e68bdfe14 --- /dev/null +++ b/components/MolCard/MolCard.tsx @@ -0,0 +1,60 @@ +import { Children, useState } from "react"; + +import type { CardActionsProps, CardProps } from "@mui/material"; +import { Card, CardActions, CardContent } from "@mui/material"; + +import { DepictMolecule } from "./DepictMolecule"; + +export interface MolCardProps extends CardProps { + smiles: string; + children?: React.ReactNode; + depictNoStereo?: boolean; + depictWidth?: number; + depictHeight?: number; + depictmcs?: string; + bgColor?: string; + actions?: (hover?: boolean) => React.ReactNode; + actionsProps?: CardActionsProps; + onClick?: () => void; +} + +/* Generic card rendering molecule depiction with optional content and actions. */ +export const MolCard = ({ + children, + smiles, + depictNoStereo = false, + depictWidth, + depictHeight, + depictmcs, + bgColor, + actions = () => undefined, + actionsProps, + onClick, + ...cardProps +}: MolCardProps) => { + const [hover, setHover] = useState(false); + + return ( + setHover(true)} + onMouseLeave={() => setHover(false)} + > + + + {Children.only(children)} + + + {actions(hover)} + + + ); +}; diff --git a/components/MolCard/index.ts b/components/MolCard/index.ts new file mode 100644 index 000000000..9cb38f3ee --- /dev/null +++ b/components/MolCard/index.ts @@ -0,0 +1 @@ +export * from "./MolCard"; diff --git a/components/ScatterPlot/ScatterPlot.tsx b/components/ScatterPlot/ScatterPlot.tsx new file mode 100644 index 000000000..75572ec1e --- /dev/null +++ b/components/ScatterPlot/ScatterPlot.tsx @@ -0,0 +1,197 @@ +import type { Dispatch, SetStateAction } from "react"; +import { useState } from "react"; +import type { PlotParams } from "react-plotly.js"; + +import { + Box, + CircularProgress, + MenuItem, + Switch, + TextField, + Tooltip, + Typography, +} from "@mui/material"; +import dynamic from "next/dynamic"; +import type { PlotDatum } from "plotly.js-basic-dist"; + +import type { Molecule } from "../../features/SDFViewer"; + +const Plot = dynamic( + () => import("../../components/viz/Plot").then((mod) => mod.Plot), + { + ssr: false, // Plotly only works when browser APIs are in scope + loading: () => , + }, +); + +// Utils + +export const isNumber = (x: unknown): x is number => typeof x === "number"; + +const getPropArrayFromMolecules = (molecules: Molecule[], prop: string | null) => { + if (prop === "id") { + return molecules.map((molecule) => molecule.id); + } + return molecules.map((molecule) => (prop ? molecule.properties[prop] ?? null : null)); +}; + +type AxisSeries = ReturnType; + +const scaleToSize = (sizeaxis: AxisSeries) => { + const sx = sizeaxis + .filter((value): value is string => value !== null) + .map((value) => Number.parseFloat(value)); + const min = Math.min(...sx); + const max = Math.max(...sx); + + const scaledSizes = sx.map((v) => (45 * (v - min)) / max + 5); + + if (min >= max) { + return { sizes: 10 }; + } + + return { sizes: scaledSizes, min, max }; +}; + +const validateColours = (colouraxis: AxisSeries) => { + const cx = colouraxis + .filter((value): value is string => value !== null) + .map((value) => Number.parseFloat(value)); + + const min = Math.min(...cx); + const max = Math.max(...cx); + + if (min >= max) { + return { colours: 1 }; + } + + return { colours: colouraxis, min, max }; +}; + +export interface ScatterPlotProps { + molecules: Molecule[]; + properties: string[]; + selectPoints: (ids: string[]) => void; + width: number; +} + +export const ScatterPlot = ({ molecules, properties, selectPoints, width }: ScatterPlotProps) => { + // const selectedPoints = selection.map((id) => molecules.findIndex((m) => m.id === id)); + + const [showColourBar, setShowColourBar] = useState(true); + + const [xprop, setXprop] = useState(properties[0]); + const [yprop, setYprop] = useState(properties[1]); + const [cprop, setCprop] = useState(properties[2]); + const [sprop, setSprop] = useState(properties[3]); + + const xaxis = getPropArrayFromMolecules(molecules, xprop); + const yaxis = getPropArrayFromMolecules(molecules, yprop); + + const colouraxis = getPropArrayFromMolecules(molecules, cprop); + const sizeaxis = getPropArrayFromMolecules(molecules, sprop); + + const { sizes, ...sizeExtent } = scaleToSize(sizeaxis); + const { colours } = validateColours(colouraxis); + + return ( + <> + m.id), // Add custom data for use in selection + // selectedpoints: selectedPoints.length ? selectedPoints : undefined, // null or undefined? + type: "scatter", + mode: "markers", + marker: { + color: colours, + size: sizes, + colorscale: "Bluered", + colorbar: showColourBar ? {} : undefined, + }, + }, + ]} + layout={{ + width, + height: width, + margin: { t: 10, r: 10, b: 50, l: 50 }, + dragmode: "select", + selectionrevision: 1, + hovermode: "closest", + xaxis: { title: xprop }, + yaxis: { title: yprop }, + }} + onDeselect={() => selectPoints([])} + onSelected={(event) => { + // @types is wrong here, we need `?.` as points can be undefined (double click event) + const points = event.points as PlotDatum[] | undefined; + points?.length && selectPoints(points.map((p) => p.customdata) as string[]); + }} + /> + +
+ + x-axis + + +
+
+ + y-axis + + +
+
+ + colour-axis + + + + setShowColourBar(!showColourBar)} /> + + {/*
+ ({colourExtent.min !== undefined && `${colourExtent.min}–${colourExtent.max}`}) +
*/} +
+
+ + size-axis + + +
+ ({sizeExtent.min !== undefined && `${sizeExtent.min}–${sizeExtent.max}`}) +
+
+ + + ); +}; + +interface AxisSelectorProps { + properties: string[]; + prop: string; + onPropChange: Dispatch>; +} + +const AxisSelector = ({ properties, prop = "", onPropChange }: AxisSelectorProps) => { + return ( + onPropChange(event.target.value)}> + {properties.map((property) => ( + + {property} + + ))} + + ); +}; diff --git a/components/ViewFilePopover/FileViewersList.tsx b/components/ViewFilePopover/FileViewersList.tsx index dde1ea6d4..1fa8ff400 100644 --- a/components/ViewFilePopover/FileViewersList.tsx +++ b/components/ViewFilePopover/FileViewersList.tsx @@ -3,6 +3,7 @@ import { List } from "@mui/material"; import { useCurrentProjectId } from "../../hooks/projectHooks"; import { BrowserViewerListItem } from "./BrowserViewerListItem"; import { FilePlainTextViewerListItem } from "./FilePlainTextViewerListItem"; +import { SDFViewerListItem } from "./SDFViewerListItem"; export interface FileViewersListProps { fileName: string; @@ -24,6 +25,9 @@ export const FileViewersList = ({ fileName, path, onClick }: FileViewersListProp onClick={onClick} /> )} + {(fileName.endsWith(".sdf") || fileName.endsWith(".sdf.gz")) && ( + + )} ); }; diff --git a/components/ViewFilePopover/SDFViewerListItem.tsx b/components/ViewFilePopover/SDFViewerListItem.tsx new file mode 100644 index 000000000..80f8c0439 --- /dev/null +++ b/components/ViewFilePopover/SDFViewerListItem.tsx @@ -0,0 +1,49 @@ +import { Description as DescriptionIcon } from "@mui/icons-material"; +import { ListItemButton, ListItemIcon, ListItemText } from "@mui/material"; +import A from "next/link"; +import { useRouter } from "next/router"; + +import { useProjectBreadcrumbs } from "../../hooks/projectPathHooks"; + +export interface SDFViewerListItemProps { + fileName: string; + path?: string; + onClick: () => void; +} + +export const SDFViewerListItem = ({ fileName, path, onClick }: SDFViewerListItemProps) => { + const router = useRouter(); + + const breadcrumbs = useProjectBreadcrumbs(); + path === undefined && (path = breadcrumbs.join("/")); + + return ( + + onClick()} + > + + + + + + + ); +}; diff --git a/features/SDFViewer.tsx b/features/SDFViewer.tsx new file mode 100644 index 000000000..62e305d82 --- /dev/null +++ b/features/SDFViewer.tsx @@ -0,0 +1,170 @@ +import { useEffect, useMemo, useState, useTransition } from "react"; + +import type { SDFRecord } from "@squonk/sdf-parser"; +import { createSDFTransformer } from "@squonk/sdf-parser"; + +import { Box, LinearProgress, Typography } from "@mui/material"; +import { nanoid } from "nanoid"; + +import { MolCard } from "../components/MolCard"; +import CalculationsTable from "../components/MolCard/CalculationsTable"; +import { ScatterPlot } from "../components/ScatterPlot/ScatterPlot"; +import { isResponseJson } from "../utils/api/fetchHelpers"; +import { API_ROUTES } from "../utils/app/routes"; + +const getCards = (molecules: Must[]) => { + return molecules.slice(0, 50).map((molecule) => { + const smiles = molecule.molFile.split(/\r?\n/)[0]; + const properties = Object.entries(molecule.properties).map((property) => ({ + name: property[0], + value: property[1], + })); + return ( + + { + acc[key] = key; + return acc; + }, {} as Record)} + fontSize="0.7rem" + properties={properties} + /> + + ); + }); +}; + +const getPropArrayFromRecords = (molecules: Molecule[] | SDFRecord[]): string[] => { + return molecules.reduce((properties, molecule) => { + Object.keys(molecule.properties).forEach((key) => { + if (!properties.includes(key)) { + properties.push(key); + } + }); + return properties; + }, []); +}; + +const useSDFRecords = (projectId: string, path: string, fileName: string) => { + const [records, setRecords] = useState([]); + const [isFetching, setIsFetching] = useState(false); + const [isPending, startTransition] = useTransition(); + const [error, setError] = useState(); + + useEffect(() => { + const compressed = fileName.endsWith(".gz"); + const fetchFile = async () => { + setIsFetching(true); + + let response: Response; + + try { + response = await fetch(API_ROUTES.projectFile(projectId, path, fileName, "/api/dm-api")); + } catch { + throw new Error("Unable to fetch file due to a network error. Try again."); + } + + if (response.ok) { + if (response.body !== null) { + let stream: ReadableStream = response.body; + if (compressed) { + stream = response.body.pipeThrough(new DecompressionStream("gzip")); + } + await stream + .pipeThrough(new TextDecoderStream()) + .pipeThrough(createSDFTransformer()) + .pipeTo( + new WritableStream({ + write(chunk) { + startTransition(() => { + setRecords((prev) => [...prev, chunk]); + }); + }, + }), + ); + } else { + throw new Error("No stream from response"); + } + + setIsFetching(false); + } else { + const isJson = isResponseJson(response); + const data = isJson ? await response.json() : null; + const error = (data && data.message) || response.status; + throw new Error(error); + } + }; + + fetchFile().catch((err) => { + setError(err.message); + }); + }, [fileName, path, projectId]); + + return { records, isFetching, isPending, error }; +}; + +export interface Molecule extends SDFRecord { + id: string; +} + +export type Must = { + [P in keyof T]-?: NonNullable; +}; + +export const recordsToMolecules = (records: SDFRecord[]): Must[] => { + return records + .filter((record): record is Must => !!record.molFile) + .map((record) => ({ + id: nanoid(), + ...record, + })); +}; + +export interface SDFViewerProps { + project: string; + path: string; + file: string; +} + +export const SDFViewer = ({ project, path, file }: SDFViewerProps) => { + const { records, isPending, isFetching } = useSDFRecords(project, path, file); + + const molecules = useMemo(() => recordsToMolecules(records), [records]); + const properties = useMemo(() => getPropArrayFromRecords(records), [records]); + + const [selection, setSelection] = useState([]); + + if (isPending || isFetching) { + return ( + <> + Loading and parsing data + + + ); + } + + return ( + theme.spacing(2), + alignItems: "start", + }} + > + + setSelection(points)} + width={600} + /> + + {getCards( + selection + .map((id) => molecules.find((molecule) => molecule.id === id)) + .filter((molecule): molecule is Must => !!molecule), + )} + + ); +}; diff --git a/next.config.mjs b/next.config.mjs index 52fc6d873..7fb84ae2f 100644 --- a/next.config.mjs +++ b/next.config.mjs @@ -31,7 +31,7 @@ let nextConfig = { // reactStrictMode: true, // TODO: Blocked by @rjsf Form using UNSAFE_componentWillReceiveProps pageExtensions: ["js", "ts", "jsx", "tsx", "mdx"], basePath: process.env.NEXT_PUBLIC_BASE_PATH || undefined, - transpilePackages: process.env.MONOREPO ? ["@squonk/mui-theme"] : [], + transpilePackages: process.env.MONOREPO ? ["@squonk/mui-theme", "@squonk/sdf-parser"] : [], modularizeImports: { "@mui/icons-material": { transform: "@mui/icons-material/{{member}}" }, }, diff --git a/package.json b/package.json index 563f5f8b3..1c109dbb1 100644 --- a/package.json +++ b/package.json @@ -56,6 +56,7 @@ "@squonk/account-server-client": "2.0.6", "@squonk/data-manager-client": "1.1.10", "@squonk/mui-theme": "3.0.2", + "@squonk/sdf-parser": "1.0.4", "@tanstack/match-sorter-utils": "8.8.4", "@tanstack/react-query": "4.32.0", "@tanstack/react-query-devtools": "4.32.0", diff --git a/pages/project/file.tsx b/pages/project/file.tsx index 6c9d1b895..8a6e9aeeb 100644 --- a/pages/project/file.tsx +++ b/pages/project/file.tsx @@ -11,7 +11,7 @@ import type { NotSuccessful, Successful } from "../../utils/api/plaintextViewerS import { plaintextViewerSSR } from "../../utils/api/plaintextViewerSSR"; import { createErrorProps } from "../../utils/api/serverSidePropsError"; import { pathFromQuery } from "../../utils/app/paths"; -import { API_ROUTES } from "../../utils/app/routes"; +import { projectFileURL } from "../../utils/app/routes"; import { getFullReturnTo } from "../../utils/next/ssr"; export type FileProps = Successful | NotSuccessful; @@ -38,7 +38,7 @@ export const getServerSideProps: GetServerSideProps = async (ctx) => compressed = true; } - const url = process.env.DATA_MANAGER_API_SERVER + API_ROUTES.projectFile(project, path, file); + const url = projectFileURL(project, path, file); return await plaintextViewerSSR(req, res, { url, compressed }); }, diff --git a/pages/viewer/sdf.tsx b/pages/viewer/sdf.tsx new file mode 100644 index 000000000..468ad8bf6 --- /dev/null +++ b/pages/viewer/sdf.tsx @@ -0,0 +1,64 @@ +import { withPageAuthRequired as withPageAuthRequiredCSR } from "@auth0/nextjs-auth0/client"; +import { Container, Typography } from "@mui/material"; +import Head from "next/head"; +import { useRouter } from "next/router"; + +import { RoleRequired } from "../../components/auth/RoleRequired"; +import { CenterLoader } from "../../components/CenterLoader"; +import { AS_ROLES, DM_ROLES } from "../../constants/auth"; +import type { SDFViewerProps } from "../../features/SDFViewer"; +import { SDFViewer } from "../../features/SDFViewer"; +import Layout from "../../layouts/Layout"; + +const SDF = () => { + const { query } = useRouter(); + + const { project, path, file } = query; + + return ( + <> + + Squonk | SDF Viewer + + + + + + {typeof project !== "string" || + typeof path !== "string" || + typeof file !== "string" ? ( + + ) : ( + + )} + + + + + + ); +}; + +const SDFView = ({ project, path, file }: SDFViewerProps) => { + // path and file to display + const filePath = path === "" ? file : path + "/" + file; + + // normalise path for request + if (!path.startsWith("/")) { + path = "/" + path; + } + + return ( + <> + + Squonk | {filePath} + + + {filePath} + + + + ); +}; + +export default withPageAuthRequiredCSR(SDF); diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index e806231aa..02b76fea8 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -25,6 +25,7 @@ specifiers: '@squonk/data-manager-client': 1.1.10 '@squonk/eslint-config': 0.5.0 '@squonk/mui-theme': 3.0.2 + '@squonk/sdf-parser': 1.0.4 '@tanstack/match-sorter-utils': 8.8.4 '@tanstack/react-query': 4.32.0 '@tanstack/react-query-devtools': 4.32.0 @@ -97,6 +98,7 @@ dependencies: '@squonk/account-server-client': 2.0.6_2ayegm275zmfehdiuggn4nwj24 '@squonk/data-manager-client': 1.1.10_2ayegm275zmfehdiuggn4nwj24 '@squonk/mui-theme': 3.0.2_@mui+material@5.14.2 + '@squonk/sdf-parser': 1.0.4 '@tanstack/match-sorter-utils': 8.8.4 '@tanstack/react-query': 4.32.0_biqbaboplfbrettd7655fr4n2y '@tanstack/react-query-devtools': 4.32.0_xzqwv52z3lkencxda3hsqynkyy @@ -1035,8 +1037,8 @@ packages: rollup: 2.78.0 dev: false - 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is-typed-array: 1.1.10 - dev: false /which/2.0.2: resolution: {integrity: sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==} diff --git a/types/nextjs-routes.d.ts b/types/nextjs-routes.d.ts index da315d3fb..087b6c232 100644 --- a/types/nextjs-routes.d.ts +++ b/types/nextjs-routes.d.ts @@ -42,7 +42,8 @@ declare module "nextjs-routes" { | DynamicRoute<"/results/instance/[instanceId]", { "instanceId": string }> | DynamicRoute<"/results/task/[taskId]", { "taskId": string }> | StaticRoute<"/results"> - | DynamicRoute<"/unit/[unitId]/charges", { "unitId": string }>; + | DynamicRoute<"/unit/[unitId]/charges", { "unitId": string }> + | StaticRoute<"/viewer/sdf">; interface StaticRoute { pathname: Pathname; diff --git a/utils/api/fetchHelpers.ts b/utils/api/fetchHelpers.ts new file mode 100644 index 000000000..889e726b1 --- /dev/null +++ b/utils/api/fetchHelpers.ts @@ -0,0 +1,4 @@ +import type { Response as NFResponse } from "node-fetch"; + +export const isResponseJson = (response: Response | NFResponse) => + !!response.headers.get("content-type")?.includes("application/json"); diff --git a/utils/api/plaintextViewerSSR.ts b/utils/api/plaintextViewerSSR.ts index b3f169920..8d7931662 100644 --- a/utils/api/plaintextViewerSSR.ts +++ b/utils/api/plaintextViewerSSR.ts @@ -4,6 +4,7 @@ import type { IncomingMessage, ServerResponse } from "node:http"; import { createGunzip } from "node:zlib"; import fetch from "node-fetch"; +import { isResponseJson } from "./fetchHelpers"; import { createErrorProps } from "./serverSidePropsError"; const MAX_BYTES = 100_000; @@ -74,7 +75,7 @@ export const plaintextViewerSSR = async ( } if (!response.ok) { - const isJson = response.headers.get("content-type")?.includes("application/json"); + const isJson = isResponseJson(response); const data = isJson ? await response.json() : null; const error = (data && (data as any).message) || response.status; captureException(error); diff --git a/utils/app/routes.ts b/utils/app/routes.ts index e434f89b5..0637e2c59 100644 --- a/utils/app/routes.ts +++ b/utils/app/routes.ts @@ -13,6 +13,9 @@ export const API_ROUTES = { `${proxy}/dataset/${datasetId}/${version}`, }; +export const projectFileURL: (typeof API_ROUTES)["projectFile"] = (project, path, file) => + process.env.DATA_MANAGER_API_SERVER + API_ROUTES.projectFile(project, path, file); + export const projectURL = (projectId: string) => window.location.origin + (process.env.NEXT_PUBLIC_BASE_PATH ?? "") +