@sjcrh/proteinpaint-server 2.26.1 → 2.27.1

package/routes/gdc.topVariablyExpressedGenes.ts

@@ -0,0 +1,97 @@
+import { GdcTopVariablyExpressedGenesResponse } from '#shared/types/routes/gdc.topVariablyExpressedGenes.ts'
+import { getCasesWithExressionDataFromCohort } from '../src/mds3.gdc.js'
+//import path from 'path'
+import got from 'got'
+import serverconfig from '../src/serverconfig.js'
+
+// TODO change when api is released to prod
+//const apihost = process.env.PP_GDC_HOST || 'https://api.gdc.cancer.gov'
+const apihost = 'https://uat-portal.gdc.cancer.gov/auth/api/v0/gene_expression/gene_selection'
+
+const gdcGenome = 'hg38'
+const gdcDslabel = 'GDC'
+
+export const api = {
+	endpoint: 'gdc/topVariablyExpressedGenes',
+	methods: {
+		get: {
+			init({ genomes }) {
+				return async (req: any, res: any): Promise<void> => {
+					try {
+						// following logic requires hg38 gdc dataset
+						const genome = genomes[gdcGenome]
+						if (!genome) throw 'hg38 genome missing'
+						const ds = genome.datasets?.[gdcDslabel]
+						if (!ds) throw 'gdc dataset missing'
+						const genes = await getGenes(req.query, ds)
+						const payload = { genes } as GdcTopVariablyExpressedGenesResponse
+						res.send(payload)
+					} catch (e: any) {
+						res.send({ status: 'error', error: e.message || e })
+					}
+				}
+			},
+			request: {
+				typeId: null
+				//valid: default to type checker
+			},
+			response: {
+				typeId: 'GdcTopVariablyExpressedGenesResponse'
+				// will combine this with type checker
+				//valid: (t) => {}
+			}
+		}
+	}
+}
+
+/*
+req.query {
+	filter0 // optional gdc GFF cohort filter, invisible and read only
+		FIXME should there be pp filter too?
+	maxGenes: int
+}
+
+ds { } // server-side ds object
+
+*/
+async function getGenes(q: any, ds: any) {
+	if (serverconfig.features.gdcGenes) {
+		// for testing only; delete when api issue is resolved
+		return serverconfig.features.gdcGenes as string[]
+	}
+
+	// based on current cohort, get list of cases with exp data, as input of next api query
+	const caseLst = await getCasesWithExressionDataFromCohort(q, ds)
+	if (caseLst.length == 0) {
+		// there are no cases with gene exp data
+		return [] as string[]
+	}
+
+	// change to this when api is available on prod
+	// const url = path.join(apihost, '/gene_expression/gene_selection')
+
+	const response = await got.post(apihost, {
+		headers: { 'Content-Type': 'application/json', Accept: 'application/json' },
+		body: JSON.stringify({
+			case_ids: caseLst,
+			//gene_ids: [] // this should not be a required parameter
+			size: q.maxGenes || 100
+		})
+	})
+
+	const re = JSON.parse(response.body)
+	// {"gene_selection":[{"gene_id":"ENSG00000141510","log2_uqfpkm_median":3.103430497010492,"log2_uqfpkm_stddev":0.8692021350485105,"symbol":"TP53"}, ... ]}
+
+	const genes = [] as string[]
+	if (!Array.isArray(re.gene_selection)) throw 're.gene_selection[] is not array'
+	for (const i of re.gene_selection) {
+		if (i.gene_id && typeof i.gene_id == 'string') {
+			genes.push(i.gene_id) // ensg
+		} else if (i.symbol && typeof i.symbol == 'string') {
+			genes.push(i.symbol)
+		} else {
+			throw 'one of re.gene_selection[] is missing both gene_id and symbol'
+		}
+	}
+	return genes
+}

package/routes/genelookup.ts

@@ -1,11 +1,14 @@
 import { getResult } from '#src/gene.js'
+import { GeneLookupRequest, GeneLookupResponse } from '#shared/types/routes/genelookup.ts'
 
 function init({ genomes }) {
 	return (req: any, res: any): void => {
 		try {
+			const q = req.query as GeneLookupRequest
 			const g = genomes[req.query.genome]
 			if (!g) throw 'invalid genome name'
-			res.send(getResult(g, req.query))
+			const result = getResult(g, req.query) as GeneLookupResponse
+			res.send(result)
 		} catch (e: any) {
 			res.send({ error: e.message || e })
 			if (e.stack) console.log(e.stack)
@@ -45,14 +48,3 @@ export const api: any = {
 		}
 	}
 }
-
-export type GeneLookupRequest = {
-	input: string
-	genome: string
-	deep: boolean
-}
-
-export type GeneLookupResponse = {
-	error?: string
-	hits: string[]
-}

package/routes/healthcheck.ts

@@ -1,13 +1,14 @@
 import { getStat } from '#src/health.ts'
+import { HealthCheckResponse } from '#shared/types/routes/healthcheck.ts'
 
 export const api = {
 	endpoint: 'healthcheck',
 	methods: {
 		get: {
 			init({ genomes }) {
-				return async (req: any, res: any): Promise<void> => {
+				return async (req: undefined, res: any): Promise<void> => {
 					try {
-						const health = await getStat(genomes)
+						const health = (await getStat(genomes)) as HealthCheckResponse
 						res.send(health)
 					} catch (e: any) {
 						res.send({ status: 'error', error: e.message || e })
@@ -26,47 +27,3 @@ export const api = {
 		}
 	}
 }
-
-/**
- * for documentation only, to signify integer: not type-checked statically
- */
-type int = number
-
-/**
- * Information aboute the server build version and dates,
- * including the date when the server was last launched
- */
-export type VersionInfo = {
-	pkgver: string
-	codedate: string
-	launchdate: string
-}
-
-type BuildByGenome = {
-	[index: string]: GenomeBuildInfo
-}
-
-export type GenomeBuildInfo = {
-	genedb: DbInfo
-	termdbs?: {
-		[index: string]: DbInfo
-	}
-}
-
-type DbInfo = {
-	buildDate: string // "unknown" or a Date-convertible string
-	tables?: {
-		[index: string]: int
-	}
-}
-
-/**
- * Server sttus and data related to it's health
- */
-export type HealthCheckResponse = {
-	status: 'ok' | 'error'
-	genomes: BuildByGenome
-	versionInfo: VersionInfo
-	w?: number[]
-	rs?: number
-}

package/routes/termdb.violin.ts

@@ -0,0 +1,78 @@
+import { trigger_getViolinPlotData } from '#src/termdb.violin.js'
+// import { getViolinRequest, getViolinResponse } from '#shared/types/routes/termdb.violin'
+
+export const api: any = {
+	endpoint: 'termdb/violin',
+	methods: {
+		get: {
+			init,
+			request: {
+				typeId: 'getViolinRequest'
+			},
+			response: {
+				typeId: 'getViolinResponse'
+			},
+			examples: [
+				{
+					request: {
+						body: {
+							genome: 'hg38-test',
+							dslabel: 'TermdbTest',
+							embedder: 'localhost',
+							devicePixelRatio: 2.200000047683716,
+							maxThickness: 150,
+							screenThickness: 1218,
+							filter: {
+								type: 'tvslst',
+								in: true,
+								join: '',
+								lst: [
+									{
+										tag: 'cohortFilter',
+										type: 'tvs',
+										tvs: { term: { id: 'subcohort', type: 'categorical' }, values: [{ key: 'ABC', label: 'ABC' }] }
+									}
+								]
+							},
+							svgw: 227.27272234672367,
+							orientation: 'horizontal',
+							datasymbol: 'bean',
+							radius: 5,
+							strokeWidth: 0.2,
+							axisHeight: 60,
+							rightMargin: 50,
+							unit: 'abs',
+							plotThickness: 150,
+							termid: 'agedx'
+						}
+					},
+					response: {
+						header: { status: 200 }
+					}
+				}
+			]
+		},
+		post: {
+			alternativeFor: 'get',
+			init
+		}
+	}
+}
+
+function init({ genomes }) {
+	return async (req: any, res: any): Promise<void> => {
+		const q = req.query // as getViolinRequest
+		try {
+			const g = genomes[req.query.genome]
+			const ds = g.datasets[req.query.dslabel]
+			if (!g) throw 'invalid genome name'
+			const data = await trigger_getViolinPlotData(req.query, null, ds, g) // as getViolinResponse
+			res.send(data)
+		} catch (e) {
+			// eslint-disable-next-line @typescript-eslint/ban-ts-comment
+			// @ts-ignore
+			res.send({ error: e?.message || e })
+			if (e instanceof Error && e.stack) console.log(e)
+		}
+	}
+}