@sjcrh/proteinpaint-server 2.25.0 → 2.26.0

package/utils/fastclust.R

@@ -42,9 +42,9 @@ args <- commandArgs(trailingOnly = T)
 if (length(args) != 1) stop("Usage: Rscript test.R in.json > results")
 infile <- args[1]
 input <- fromJSON(infile)
-
+normalized_matrix <- t(scale(t(input$matrix))) # Applying z-score normalization
 # For columns (i.e samples)
-RowDist <- dist(input$matrix, method = "euclidean") # Transposing the matrix
+RowDist <- dist(normalized_matrix, method = "euclidean") # Transposing the matrix
 
 # Hierarchical clustering
 print (input$cluster_method)
@@ -76,7 +76,7 @@ print ("RowCoordinates")
 print (row_node_coordinates)
 
 # For columns (i.e samples)
-ColumnDist <- dist(t(input$matrix), method = "euclidean") # Transposing the matrix
+ColumnDist <- dist(t(normalized_matrix), method = "euclidean") # Transposing the matrix
 
 # Hierarchical clustering
 
@@ -95,7 +95,7 @@ print (col_node_coordinates)
 print ("Done")
 # Sorting the matrix
 
-SortedMatrix  <- input$matrix[RowDend$order, ColumnDend$order]
+SortedMatrix  <- normalized_matrix[RowDend$order, ColumnDend$order]
 SortedRowNames <- input$row_names[RowDend$order]
 SortedColumnNames <- input$col_names[ColumnDend$order]
 
@@ -104,9 +104,11 @@ colnames(m) <- SortedColumnNames
 rownames(m) <- SortedRowNames
 cat("rownames",RowDend$order,"\n",sep="\t")
 cat("colnames",ColumnDend$order,"\n",sep="\t")
+cat ("OutputMatrix",normalized_matrix,"\n",sep="\t") # This outputs the 2D array in 1D column-wise. This is later converted to 2D array in nodejs.
+
 
-df  <- melt(m)
-colnames(df) <- c("Genes", "Samples", "value")
+#df  <- melt(m)
+#colnames(df) <- c("Genes", "Samples", "value")
 
 #ggplot(df, aes(x = Genes, y = Samples, fill = value)) + geom_tile() + scale_fill_gradient(low="blue", high="red") + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
 

package/src/routes/healthcheck.ts

@@ -1,92 +0,0 @@
-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()
-}