@sjcrh/proteinpaint-server 2.30.4 → 2.31.0

package/routes/termdb.getpercentile.ts

@@ -0,0 +1,117 @@
+// import { getpercentileRequest, getpercentileResponse } from '#shared/types/routes/termdb.getpercentile'
+import * as termdbsql from '#src/termdb.sql.js'
+import computePercentile from '#shared/compute.percentile.js'
+
+export const api: any = {
+	endpoint: 'termdb/getpercentile',
+	methods: {
+		get: {
+			init,
+			request: {
+				typeId: 'getpercentileRequest'
+			},
+			response: {
+				typeId: 'getpercentileResponse'
+			},
+			examples: [
+				{
+					request: {
+						body: {
+							genome: 'hg38-test',
+							dslabel: 'TermdbTest',
+							embedder: 'localhost',
+							getpercentile: [50],
+							tid: 'agedx',
+							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 getpercentileRequest
+		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'
+			await trigger_getpercentile(q, res, ds) // as getpercentileResponse
+		} 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_getpercentile(
+	q: { tid: string; getpercentile: number[]; filter: string },
+	res: { send: (arg0: { values: number[] }) => void },
+	ds: { cohort: { termdb: { q: { termjsonByOneid: (arg0: any) => 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 percentile_lst = q.getpercentile
+	const perc_values = [] as number[]
+	const values = [] as number[]
+	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
+	})
+	for (const { value } of rows) {
+		if (term.values && term.values[value] && term.values[value].uncomputable) {
+			// skip uncomputable values
+			continue
+		}
+
+		if (term.skip0forPercentile && value == 0) {
+			// quick fix: when the flag is true, will exclude 0 values from percentile computing
+			// to address an issue with computing knots
+			continue
+		}
+
+		values.push(Number(value))
+	}
+
+	// compute percentiles
+	for (const percentile of percentile_lst) {
+		const perc_value = computePercentile(values, percentile)
+		perc_values.push(perc_value)
+	}
+	res.send({ values: perc_values })
+}

package/routes/termdb.singlecellSamples.ts

@@ -0,0 +1,45 @@
+import {
+	TermdbSinglecellsamplesRequest,
+	TermdbSinglecellsamplesResponse
+} from '#shared/types/routes/termdb.singlecellSamples.ts'
+
+/* route returns list of samples with sc data
+this is due to the fact that sometimes not all samples in a dataset has sc data
+*/
+
+export const api: any = {
+	endpoint: 'termdb/singlecellSamples',
+	methods: {
+		get: {
+			init,
+			request: {
+				typeId: 'TermdbSinglecellsamplesRequest'
+			},
+			response: {
+				typeId: 'TermdbSinglecellsamplesResponse'
+			}
+		},
+		post: {
+			alternativeFor: 'get',
+			init
+		}
+	}
+}
+
+function init({ genomes }) {
+	return async (req: any, res: any): Promise<void> => {
+		const q = req.query as TermdbSinglecellsamplesRequest
+		try {
+			const g = genomes[q.genome]
+			if (!g) throw 'invalid genome name'
+			const ds = g.datasets[q.dslabel]
+			if (!ds) throw 'invalid dataset name'
+			if (!ds.queries?.singleCell) throw 'no singlecell data on this dataset'
+			const result = (await ds.queries.singleCell.samples.get(q)) as TermdbSinglecellsamplesResponse
+			res.send(result)
+		} catch (e: any) {
+			if (e instanceof Error && e.stack) console.log(e)
+			res.send({ error: e.message || e })
+		}
+	}
+}

package/routes/termdb.termbyid.ts

@@ -56,7 +56,11 @@ function init({ genomes }) {
 	}
 }
 
-async function trigger_gettermbyid(q, res, tdb) {
+async function trigger_gettermbyid(
+	q: { gettermbyid: any },
+	res: { send: (arg0: { term: any }) => void },
+	tdb: { q: { termjsonByOneid: (arg0: any) => any } }
+) {
 	const t = tdb.q.termjsonByOneid(q.gettermbyid)
 	res.send({
 		term: t ? copy_term(t) : undefined