@sjcrh/proteinpaint-server 2.36.0 → 2.38.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.36.0",
+  "version": "2.38.0",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",
@@ -57,7 +57,7 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.35.0",
-    "@sjcrh/proteinpaint-rust": "2.34.0",
+    "@sjcrh/proteinpaint-rust": "2.38.0",
     "better-sqlite3": "^7.5.3",
     "body-parser": "^1.15.2",
     "canvas": "~2.9.3",

package/routes/termdb.getdescrstats.ts

@@ -0,0 +1,145 @@
+// import { getdescrstatsRequest, getdescrstatsResponse } from '#shared/types/routes/termdb.descrstats'
+import roundValue from '#shared/roundValue.js'
+import computePercentile from '#shared/compute.percentile.js'
+import * as termdbsql from '#src/termdb.sql.js'
+
+export const api: any = {
+	endpoint: 'termdb/descrstats',
+	methods: {
+		get: {
+			init,
+			request: {
+				typeId: 'getdescrstatsRequest'
+			},
+			response: {
+				typeId: 'getdescrstatsResponse'
+			},
+			examples: [
+				{
+					request: {
+						body: {
+							genome: 'hg38-test',
+							dslabel: 'TermdbTest',
+							embedder: 'localhost',
+							getdescrstats: 1,
+							tid: 'hrtavg',
+							filter: {
+								type: 'tvslst',
+								in: true,
+								join: '',
+								lst: [
+									{
+										tag: 'cohortFilter',
+										type: 'tvs',
+										tvs: {
+											term: {
+												name: 'Cohort',
+												type: 'categorical',
+												values: { ABC: { label: 'ABC' }, XYZ: { label: 'XYZ' } },
+												id: 'subcohort',
+												isleaf: false,
+												groupsetting: { disabled: true }
+											},
+											values: [{ key: 'ABC', label: 'ABC' }]
+										}
+									}
+								]
+							}
+						}
+					},
+					response: {
+						header: { status: 200 }
+					}
+				}
+			]
+		},
+		post: {
+			alternativeFor: 'get',
+			init
+		}
+	}
+}
+
+function init({ genomes }) {
+	return async (req: any, res: any): Promise<void> => {
+		const q = req.query // as getdescrstatsRequest
+		try {
+			const g = genomes[req.query.genome]
+			if (!g) throw 'invalid genome name'
+			const ds = g.datasets[req.query.dslabel]
+			if (!ds) throw 'invalid dataset name'
+			const tdb = ds.cohort.termdb
+			if (!tdb) throw 'invalid termdb object'
+
+			await trigger_getdescrstats(q, res, ds) // as getdescrstatsResponse
+		} 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)
+		}
+	}
+}
+
+async function trigger_getdescrstats(q: any, res: any, ds: any) {
+	const term = ds.cohort.termdb.q.termjsonByOneid(q.tid)
+	if (!term) throw 'invalid termid'
+	if (term.type != 'float' && term.type != 'integer') throw 'not numerical term'
+	const rows = await termdbsql.get_rows_by_one_key({
+		ds,
+		key: q.tid,
+		filter: q.filter ? (typeof q.filter == 'string' ? JSON.parse(q.filter) : q.filter) : null
+	})
+	const values: number[] = []
+	for (const { value } of rows) {
+		if (term.values && term.values[value] && term.values[value].uncomputable) {
+			// skip uncomputable values
+			continue
+		}
+		//skip computing for zeros if scale is log.
+		if (q.settings?.violin?.unit === 'log') {
+			if (value === 0) {
+				continue
+			}
+		}
+		values.push(value)
+	}
+
+	// compute statistics
+	// total
+	const total = values.length
+
+	// mean
+	const sum = values.reduce((a, b) => a + b, 0)
+	const mean = sum / total
+
+	// percentiles
+	const p25 = computePercentile(values, 25)
+	const median = computePercentile(values, 50)
+	const p75 = computePercentile(values, 75)
+
+	// standard deviation
+	// get sum of squared differences from mean
+	const sumSqDiff = values.map(v => (v - mean) ** 2).reduce((a, b) => a + b, 0)
+	// get variance
+	const variance = sumSqDiff / (values.length - 1)
+	// get standard deviation
+	const sd = Math.sqrt(variance)
+
+	// min/max
+	const min = Math.min(...values)
+	const max = Math.max(...values)
+
+	res.send({
+		values: [
+			{ id: 'total', label: 'n', value: total },
+			{ id: 'min', label: 'Minimum', value: roundValue(min, 2) },
+			{ id: 'p25', label: '1st quartile', value: roundValue(p25, 2) },
+			{ id: 'median', label: 'Median', value: roundValue(median, 2) },
+			{ id: 'mean', label: 'Mean', value: roundValue(mean, 2) },
+			{ id: 'p75', label: '3rd quartile', value: roundValue(p75, 2) },
+			{ id: 'max', label: 'Maximum', value: roundValue(max, 2) },
+			{ id: 'sd', label: 'Standard deviation', value: roundValue(sd, 2) }
+		]
+	})
+}

package/routes/termdb.singlecellSamples.ts

@@ -51,6 +51,7 @@ function init({ genomes }) {
 			if (!ds) throw 'invalid dataset name'
 			if (!ds.queries?.singleCell) throw 'no singlecell data on this dataset'
 			result = (await ds.queries.singleCell.samples.get(q)) as TermdbSinglecellsamplesResponse
+			result.sameLegend = ds.queries.singleCell.samples.sameLegend
 		} catch (e: any) {
 			if (e.stack) console.log(e.stack)
 			result = {

package/routes/{termdb.termbyid.ts → termdb.termsbyids.ts}

@@ -1,32 +1,17 @@
-// import { gettermbyidRequest, gettermbyidResponse } from '#shared/types/routes/termdb.termbyid'
+import { gettermsbyidsRequest, gettermsbyidsResponse } from '#shared/types/routes/termdb.termsbyids.js'
 import { copy_term } from '#src/termdb.js'
 
 export const api: any = {
-	endpoint: 'termdb/termbyid',
+	endpoint: 'termdb/termsbyids',
 	methods: {
 		get: {
 			init,
 			request: {
-				typeId: 'gettermbyidRequest'
+				typeId: 'gettermsbyidsRequest'
 			},
 			response: {
-				typeId: 'gettermbyidResponse'
-			},
-			examples: [
-				{
-					request: {
-						body: {
-							genome: 'hg38-test',
-							dslabel: 'TermdbTest',
-							embedder: 'localhost',
-							gettermbyid: 'subcohort'
-						}
-					},
-					response: {
-						header: { status: 200 }
-					}
-				}
-			]
+				typeId: 'gettermsbyidsResponse'
+			}
 		},
 		post: {
 			alternativeFor: 'get',
@@ -46,7 +31,7 @@ function init({ genomes }) {
 			const tdb = ds.cohort.termdb
 			if (!tdb) throw 'invalid termdb object'
 
-			await trigger_gettermbyid(q, res, tdb) // as getcategoriesResponse
+			await trigger_gettermsbyid(q, res, tdb) // as getcategoriesResponse
 		} catch (e) {
 			// eslint-disable-next-line @typescript-eslint/ban-ts-comment
 			// @ts-ignore
@@ -56,13 +41,23 @@ function init({ genomes }) {
 	}
 }
 
-async function trigger_gettermbyid(
-	q: { gettermbyid: any },
-	res: { send: (arg0: { term: any }) => void },
+async function trigger_gettermsbyid(
+	q: { ids: any },
+	res: { send: (arg0: { terms: any }) => void },
 	tdb: { q: { termjsonByOneid: (arg0: any) => any } }
 ) {
-	const t = tdb.q.termjsonByOneid(q.gettermbyid)
+	const terms = {}
+	for (const id of q.ids) {
+		const term = tdb.q.termjsonByOneid(id)
+		if (term) {
+			if (term.type == 'categorical' && !term.values && !term.groupsetting?.inuse) {
+				term.values = {}
+				term.samplecount = {}
+			}
+		}
+		terms[id] = term ? copy_term(term) : undefined
+	}
 	res.send({
-		term: t ? copy_term(t) : undefined
+		terms
 	})
 }