@sjcrh/proteinpaint-server 2.34.1 → 2.35.1

package/utils/edge.R

@@ -4,20 +4,20 @@
 
 # Checking if all R packages are installed or not, if not installing each one of them
 
-jsonlite_path <- system.file(package='jsonlite')
-if (nchar(jsonlite_path) == 0) {
-  install.packages("jsonlite", repos='https://cran.case.edu/')
-}
-
-edgeR_path <- system.file(package='edgeR')
-if (nchar(edgeR_path) == 0) {
-  BiocManager::install("edgeR")
-}
-
-readr_path <- system.file(package='readr')
-if (nchar(readr_path) == 0) {
-  install.packages("readr", repos='https://cran.case.edu/')
-}
+#jsonlite_path <- system.file(package='jsonlite')
+#if (nchar(jsonlite_path) == 0) {
+#  install.packages("jsonlite", repos='https://cran.case.edu/')
+#}
+#
+#edgeR_path <- system.file(package='edgeR')
+#if (nchar(edgeR_path) == 0) {
+#  BiocManager::install("edgeR")
+#}
+#
+#readr_path <- system.file(package='readr')
+#if (nchar(readr_path) == 0) {
+#  install.packages("readr", repos='https://cran.case.edu/')
+#}
 
 
 library(jsonlite)

package/utils/fastclust.R

@@ -3,27 +3,34 @@
 
 # Image is in Rplots.pdf
 
-# Checking if all R packages are installed or not, if not installing each one of them
-
-ggplot2_path <- system.file(package='ggplot2')
-if (nchar(ggplot2_path) == 0) {
-  install.packages("ggplot2", repos='https://cran.case.edu/')
-}
-
-jsonlite_path <- system.file(package='jsonlite')
-if (nchar(jsonlite_path) == 0) {
-  install.packages("jsonlite", repos='https://cran.case.edu/')
-}
-
-dendextend_path <- system.file(package='dendextend')
-if (nchar(dendextend_path) == 0) {
-  install.packages("dendextend", repos='https://cran.case.edu/')
-}
-
-reshape_path <- system.file(package='reshape')
-if (nchar(reshape_path) == 0) {
-  install.packages("reshape", repos='https://cran.case.edu/')
-}
+############################
+#      !!! NOTE !!!        #
+############################
+# must not auto-install missing package in any R script!
+# declare required packages in dockerfile
+# at 2023/12, a problem emerged for pp container running in gdc qa-pink
+# since the docker images lacks the packages, but the auto-install was prevented due to container safety (no internet query)
+# this script will not run, leading to hard to decipher crashing
+
+#ggplot2_path <- system.file(package='ggplot2')
+#if (nchar(ggplot2_path) == 0) {
+#  install.packages("ggplot2", repos='https://cran.case.edu/')
+#}
+#
+#jsonlite_path <- system.file(package='jsonlite')
+#if (nchar(jsonlite_path) == 0) {
+#  install.packages("jsonlite", repos='https://cran.case.edu/')
+#}
+#
+#dendextend_path <- system.file(package='dendextend')
+#if (nchar(dendextend_path) == 0) {
+#  install.packages("dendextend", repos='https://cran.case.edu/')
+#}
+#
+#reshape_path <- system.file(package='reshape')
+#if (nchar(reshape_path) == 0) {
+#  install.packages("reshape", repos='https://cran.case.edu/')
+#}
 
 #flashClust_path <- system.file(package='flashClust')
 #if (nchar(flashClust_path) == 0) {

package/routes/gdc.topVariablyExpressedGenes.ts

@@ -1,124 +0,0 @@
-import {
-	GdcTopVariablyExpressedGenesRequest,
-	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 make it general purpose based on ds.queries.geneExpression.topVariablyExpressedGenes{}; wait till case/gene link changes are done
-// https://github.com/NCI-GDC/gdcapi/blob/develop/openapi/gene-expression.yaml
-const apihost = process.env.PP_GDC_HOST || 'https://api.gdc.cancer.gov'
-// may override the geneExpHost for developers without access to qa/portal environments
-const geneExpHost = serverconfig.features?.geneExpHost || apihost
-
-const gdcGenome = 'hg38'
-const gdcDslabel = 'GDC'
-
-export const api = {
-	endpoint: 'gdc/topVariablyExpressedGenes',
-	methods: {
-		get: {
-			init,
-			request: {
-				typeId: 'GdcTopVariablyExpressedGenesRequest'
-			},
-			response: {
-				typeId: 'GdcTopVariablyExpressedGenesResponse'
-			}
-		}
-	}
-}
-
-function 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 as GdcTopVariablyExpressedGenesRequest, ds, genome)
-			const payload = { genes } as GdcTopVariablyExpressedGenesResponse
-			res.send(payload)
-		} catch (e: any) {
-			res.send({ status: 'error', error: e.message || e })
-		}
-	}
-}
-
-/*
- */
-async function getGenes(q: GdcTopVariablyExpressedGenesRequest, ds: any, genome: any) {
-	if (serverconfig.features.gdcGenes) {
-		// for testing only; delete when api issue is resolved
-		return serverconfig.features.gdcGenes as string[]
-	}
-	if (!ds.__gdc.doneCaching) {
-		throw `The server has not finished caching the case IDs: try again in ~2 minutes`
-	}
-
-	// 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(geneExpHost, '/gene_expression/gene_selection')
-
-	try {
-		const response = await got.post(url, {
-			headers: { 'Content-Type': 'application/json', Accept: 'application/json' },
-			body: JSON.stringify({
-				// !!! temporarily limit the case_ids length, otherwise the request times out !!!
-				case_ids: caseLst.slice(0, 20),
-
-				// temporary!! restrict pool to cgc due to slow api. delete when new api is online
-				gene_ids: tempGetCGCgenes(genome),
-
-				// when gene_ids is deleted, enable this
-				//gene_type: 'protein_coding',
-
-				selection_size: Number(q.maxGenes) // FIXME it's defined as number but why it's string??
-			})
-		})
-
-		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') {
-				// is ensg, convert to symbol
-				const t = genome.genedb.getNameByAlias.get(i.gene_id)
-				if (t) genes.push(t.name) // 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
-	} catch (e: any) {
-		console.log(e.stack || e)
-		throw e
-	}
-}
-
-function tempGetCGCgenes(genome: any) {
-	const lst = [] as string[] // list of ENSG ids from cgc genes
-	// don't think there's need to preparse genome.geneset, as this function is only temporary
-	for (const s of genome.geneset[0].lst) {
-		const a = genome.genedb.getAliasByName.all(s)
-		if (a) {
-			for (const b of a) {
-				if (b.alias.startsWith('ENSG')) lst.push(b.alias)
-			}
-		}
-	}
-	return lst
-}