R/runQuery.R

In BaderLab/netDx: Network-based patient classifier

#' Run a query
#'
#' @param dbPath (char) path to directory with GeneMANIA generic database
#' @param queryFiles (list(char)) paths to query files
#' @param resDir (char) path to output directory
#' @param verbose (logical) print messages
#' @param JavaMemory (integer) Memory for GeneMANIA (in Gb) - a total of 
#' numCores*GMmemory will be used and distributed for all GM threads
#' @param numCores (integer) number of CPU cores for parallel processing
#' @param debugMode (logical) when TRUE runs jobs in serial instead of parallel and 
#' prints verbose messages. Also prints system Java calls.
#' @return (char) path to GeneMANIA query result files with patient similarity
#' rankings (*PRANK) and feature weights (*NRANK)
#' of results file
#' @examples
#' dbPath <- system.file("extdata","dbPath",package="netDx")
#' queryFile <- system.file("extdata","GM_query.txt",package="netDx")
#' runQuery(dbPath, queryFile,tempdir())
#' @export
runQuery <- function(dbPath, queryFiles, resDir, verbose = TRUE, 
		JavaMemory = 6L, numCores = 1L,debugMode=FALSE) {
    
    GM_jar <- getGMjar_path()
    qBase <- basename(queryFiles[[1]][1])
    logFile <- paste(resDir,sprintf("%s.log",qBase))
    queryStrings <- paste(queryFiles, collapse = " ")

	args <- c()
	java_ver <- suppressWarnings(system2("java", 
		args="--version",stdout=TRUE,stderr=NULL))
	if (any(grep(" 11",java_ver)) || any(grep(" 12",java_ver)) || any(grep(" 13",java_ver)) || any(grep(" 14",java_ver)) || any(grep(" 16",java_ver))) {
		if (verbose) message("Java 11 or later detected")
	} else {
		if (verbose) message("Java 8 detected")
		args <- c(args,"-d64")
	}

    args <- c(args, sprintf("-Xmx%iG", JavaMemory * numCores), "-cp", GM_jar)
    args <- c(args, "org.genemania.plugin.apps.QueryRunner")
    args <- c(args, "--data", dbPath, "--in", "flat", "--out", "flat")
    args <- c(args, "--threads", numCores, "--results", resDir, 
			unlist(queryFiles))
    args <- c(args, "--netdx-flag", "true")  #,'2>1','/dev/null')
    
    # file is not actually created - is already split in PRANK and 
		# NRANK segments on
    # GeneMANIA side
    resFile <- paste(resDir,sprintf("%s-results.report.txt",qBase),
		sep=getFileSep())
    t0 <- Sys.time()
	if (debugMode) {
		message(sprintf("java %s",paste(args,collapse=" ")))
    	system2("java", args, wait = TRUE)
	} else {
    	system2("java", args, wait = TRUE, stdout = NULL, stderr = NULL)
	}
    if (verbose) 
        message(sprintf("QueryRunner time taken: %1.1f s", Sys.time() - t0))
    Sys.sleep(3)
    return(resFile)
}