@sjcrh/proteinpaint-server 2.19.1 → 2.25.0

package/src/routes/healthcheck.ts

@@ -0,0 +1,92 @@
+import serverconfig from '../serverconfig'
+import fs from 'fs'
+import child_process from 'child_process'
+import util from 'util'
+import pkg from '../../package.json'
+import { VersionInfo, GenomeBuildInfo, HealthCheckResponse } from '../../shared/types/healthcheck'
+
+const execPromise = util.promisify(child_process.exec)
+//const docs = require('../shared/doc')
+
+export function setRoute(app: any, genomes: any, basepath) {
+	app.get(basepath + '/healthcheck', async (req, res): Promise<void> => {
+		try {
+			const health = await getStat(genomes)
+			res.send(health)
+		} catch (e: any) {
+			res.send({ status: 'error', error: e.message || e })
+		}
+	})
+}
+
+async function getStat(genomes: any): Promise<HealthCheckResponse> {
+	const health = {
+		status: 'ok',
+		genomes: {},
+		versionInfo
+	} as HealthCheckResponse
+
+	const keys = serverconfig.features.healthcheck_keys || []
+
+	if (keys.includes('w')) {
+		const { stdout, stderr } = await execPromise('w | head -n1')
+		if (stderr) throw stderr
+		health.w = stdout
+			.toString()
+			.trim()
+			.split(' ')
+			.slice(-3)
+			.map(d => (d.endsWith(',') ? +d.slice(0, -1) : +d))
+	}
+
+	if (keys.includes('rs')) {
+		const { stdout, stderr } = await execPromise('ps aux | grep rsync -w')
+		if (stderr) throw stderr
+		health.rs = stdout.toString().trim().split('\n').length - 1
+	}
+
+	// report status of every genome
+	for (const gn in genomes) {
+		const genome = genomes[gn] //; console.log(genome.genedb)
+		const dbInfo = {} as GenomeBuildInfo // object to store status of this genome
+
+		if (genome.genedb) {
+			// genedb status
+			dbInfo.genedb = {
+				buildDate: genome.genedb.get_buildDate?.get().date || 'unknown',
+				tables: genome.genedb.tableSize
+			}
+		}
+
+		if (genome.termdbs) {
+			// genome-level termdb status e.g. msigdb
+			dbInfo.termdbs = {}
+			for (const key in genome.termdbs) {
+				const db = genome.termdbs[key]
+				dbInfo.termdbs[key] = {
+					buildDate: db.cohort.termdb.q.get_buildDate?.get().date || 'unknown'
+				}
+			}
+		}
+
+		if (Object.keys(dbInfo).length && health.genomes) health.genomes[gn] = dbInfo
+	}
+
+	return health
+}
+
+export const versionInfo: VersionInfo = {
+	pkgver: pkg.version,
+	codedate: get_codedate(),
+	launchdate: new Date(Date.now()).toString().split(' ').slice(0, 5).join(' ')
+}
+
+function get_codedate() {
+	const date1 =
+		(fs.existsSync('public/bin/proteinpaint.js') && fs.statSync(serverconfig.binpath + '/server.js').mtime) ||
+		new Date(0)
+	const date2 =
+		(fs.existsSync('public/bin/proteinpaint.js') && fs.statSync('public/bin/proteinpaint.js').mtime) || new Date(0)
+	const date = date1 > date2 ? date1 : date2
+	return date.toDateString()
+}

package/utils/cuminc.R

@@ -13,13 +13,15 @@
 
 # Input JSON:
 # {
-#   chartId: [
-#     {
-#       time: time to event
-#       event: event code (0 = censored, 1 = event, 2 = competing risk event)
-#       series: series ID
-#     }
-#   ]
+#   data:
+#     chartId: [
+#       {
+#         time: time to event
+#         event: event code (0 = censored, 1 = event, 2 = competing risk event)
+#         series: series ID
+#       }
+#     ],
+#   startTime: custom start time of cuminc curve
 # }
 #
 # Output JSON: