-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'main' into dependabot/npm_and_yarn/screen2.0/types/node…
…-20.4.4
- Loading branch information
Showing
24 changed files
with
2,219 additions
and
317 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
177 changes: 177 additions & 0 deletions
177
screen2.0/src/app/applets/gene-expression/gene-autocomplete.tsx
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,177 @@ | ||
| "use client" | ||
| import React, { useState, useEffect, useCallback } from "react" | ||
| import { useRouter } from "next/navigation" | ||
|
|
||
| import { Autocomplete, TextField, Box, Button, debounce, Typography } from "@mui/material" | ||
|
|
||
| import Grid2 from "@mui/material/Unstable_Grid2/Grid2" | ||
| import { gene } from "./types" | ||
| import { QueryResponse } from "../../../../types/types" | ||
| import { Dispatch, SetStateAction } from "react" | ||
|
|
||
| const GENE_AUTOCOMPLETE_QUERY = ` | ||
| query ($assembly: String!, $name_prefix: [String!], $limit: Int) { | ||
| gene(assembly: $assembly, name_prefix: $name_prefix, limit: $limit) { | ||
| name | ||
| id | ||
| coordinates { | ||
| start | ||
| chromosome | ||
| end | ||
| } | ||
| } | ||
| } | ||
| ` | ||
|
|
||
| export default function GeneAutoComplete(props: { | ||
| assembly: string | ||
| gene: string | ||
| pathname: string | ||
| setGene: Dispatch<SetStateAction<string>> | ||
| }) { | ||
| const router = useRouter() | ||
|
|
||
| const [options, setOptions] = useState<string[]>([]) | ||
| const [geneDesc, setgeneDesc] = useState<{ name: string; desc: string }[]>() | ||
| const [geneList, setGeneList] = useState<gene[]>([]) | ||
| const [geneID, setGeneID] = useState<string>(props.gene ? props.gene : "OR51AB1P") | ||
| const [assembly, setAssembly] = useState<string>(props.assembly) | ||
| // const [current_gene, setGene] = useState<string>(props.gene ? props.gene : "OR51AB1P") | ||
|
|
||
| // gene descriptions | ||
| useEffect(() => { | ||
| const fetchData = async () => { | ||
| let f = await Promise.all( | ||
| options.map((gene) => | ||
| fetch("https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=" + gene.toUpperCase()) | ||
| .then((x) => x && x.json()) | ||
| .then((x) => { | ||
| const matches = (x as QueryResponse)[3] && (x as QueryResponse)[3].filter((x) => x[3] === gene.toUpperCase()) | ||
| return { | ||
| desc: matches && matches.length >= 1 ? matches[0][4] : "(no description available)", | ||
| name: gene, | ||
| } | ||
| }) | ||
| .catch(() => { | ||
| return { desc: "(no description available)", name: gene } | ||
| }) | ||
| ) | ||
| ) | ||
| setgeneDesc(f) | ||
| } | ||
|
|
||
| options && fetchData() | ||
| }, [options]) | ||
|
|
||
| // gene list | ||
| const onSearchChange = async (value: string) => { | ||
| setOptions([]) | ||
| const response = await fetch("https://ga.staging.wenglab.org/graphql", { | ||
| method: "POST", | ||
| body: JSON.stringify({ | ||
| query: GENE_AUTOCOMPLETE_QUERY, | ||
| variables: { | ||
| assembly: props.assembly, | ||
| name_prefix: value, | ||
| limit: 100, | ||
| }, | ||
| }), | ||
| headers: { "Content-Type": "application/json" }, | ||
| }) | ||
| const genesSuggestion = (await response.json()).data?.gene | ||
| if (genesSuggestion && genesSuggestion.length > 0) { | ||
| const r = genesSuggestion.map((g) => g.name) | ||
| const g = genesSuggestion.map((g) => { | ||
| return { | ||
| chrom: g.coordinates.chromosome, | ||
| start: g.coordinates.start, | ||
| end: g.coordinates.end, | ||
| id: g.id, | ||
| name: g.name, | ||
| } | ||
| }) | ||
| setOptions(r) | ||
| setGeneList(g) | ||
| } else if (genesSuggestion && genesSuggestion.length === 0) { | ||
| setOptions([]) | ||
| setGeneList([]) | ||
| } | ||
| } | ||
|
|
||
| // delay fetch | ||
| const debounceFn = useCallback(debounce(onSearchChange, 500), []) | ||
|
|
||
| return ( | ||
| <Box> | ||
| <Autocomplete | ||
| disablePortal | ||
| freeSolo={true} | ||
| id="gene-ids" | ||
| noOptionsText="e.g. Gm25142" | ||
| options={options} | ||
| size="small" | ||
| sx={{ width: 200 }} | ||
| ListboxProps={{ | ||
| style: { | ||
| maxHeight: "120px", | ||
| }, | ||
| }} | ||
| onChange={(event: React.ChangeEvent<HTMLInputElement>, value: string) => { | ||
| if (value != "") debounceFn(value) | ||
| setGeneID(value) | ||
| }} | ||
| onInputChange={(event: React.ChangeEvent<HTMLInputElement>, value: string) => { | ||
| if (value != "") debounceFn(value) | ||
| setGeneID(value) | ||
| }} | ||
| onKeyDown={(e) => { | ||
| if (e.key == "Enter") { | ||
| for (let g of geneList) { | ||
| if (g.name === geneID && g.end - g.start > 0) { | ||
| props.setGene(g.name) | ||
| // replace url if ge applet | ||
| if (props.pathname.split("/").includes("gene-expression")) router.replace(props.pathname + "?gene=" + g.name) | ||
| break | ||
| } | ||
| } | ||
| } | ||
| }} | ||
| renderInput={(props) => <TextField {...props} label={geneID} />} | ||
| renderOption={(props, opt) => { | ||
| return ( | ||
| <li {...props} key={props.id}> | ||
| <Grid2 container alignItems="center"> | ||
| <Grid2 sx={{ width: "calc(100% - 44px)" }}> | ||
| <Box component="span" sx={{ fontWeight: "regular" }}> | ||
| {opt} | ||
| </Box> | ||
| {geneDesc && geneDesc.find((g) => g.name === opt) && ( | ||
| <Typography variant="body2" color="text.secondary"> | ||
| {geneDesc.find((g) => g.name === opt)?.desc} | ||
| </Typography> | ||
| )} | ||
| </Grid2> | ||
| </Grid2> | ||
| </li> | ||
| ) | ||
| }} | ||
| /> | ||
| <Button | ||
| variant="text" | ||
| onClick={() => { | ||
| for (let g of geneList) { | ||
| if (g.name === geneID && g.end - g.start > 0) { | ||
| props.setGene(g.name) | ||
| // replace url if ge applet | ||
| if (props.pathname.split("/").includes("gene-expression")) router.replace(props.pathname + "?gene=" + g.name) | ||
| break | ||
| } | ||
| } | ||
| }} | ||
| color="primary" | ||
| > | ||
| Search | ||
| </Button> | ||
| </Box> | ||
| ) | ||
| } |
Oops, something went wrong.