first draft of synchronization tool

docker/sync.R

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+#!/usr/bin/Rscript
+
+options(stringsAsFactors=FALSE)
+
+#This requires the new changes that are in the rapimave devel branch!!
+library(rapimave)
+library(hgvsParseR)
+library(yogitools)
+
+baseURL <- "http://ec2-13-210-169-246.ap-southeast-2.compute.amazonaws.com/api/"
+
+#Caching directory
+cache.dir <- Sys.getenv("MAVEVIS_CACHE",unset="/var/www/mavevis/cache/")
+if (!file.exists(cache.dir)) {
+	stop("Cache directory does not exist!")
+}
+
+#a log file to record events
+logfile <- paste0(cache.dir,"daemon.log")
+
+#function to make log entries in the log file
+logger <- function(msg) {
+	con <- file(logfile,open="a")
+	writeLines(paste(Sys.time(),msg),con)
+	close(con)
+}
+
+logger("Starting new synchronization cyle.")
+
+#Open existing scorest index
+indexFile <- paste0(cache.dir,"searchIndex.csv")
+if (file.exists(indexFile)) {
+	index <- read.csv(indexFile)
+} else {
+	index <- NULL
+}
+
+#Open API connection
+rmave <- new.rapimave(baseURL)
+
+#Query list of scoresets
+scoresets <- rmave$getAllScoreSets()
+
+#Iterate overscoresets
+invisible(lapply(scoresets,function(scoreset) {
+
+	urn <- scoreset$getURN()
+	name <- scoreset$getTitle()
+
+	#No need to process if it's already known
+	if (!is.null(index) && urn %in% index$urn) {
+		return(NULL)
+	}
+
+	logger(paste("New scoreset found:",urn))
+
+	target <- scoreset$getTarget()
+	tname <- target$getName()
+	wtseq <- target$getSequence()
+	uniprot <- target$getXrefUniprot()
+
+	label <- paste0(urn,": ",tname," - ",name)
+
+	#Download scores and write to cache location
+	scoreTable <- rmave$getScores(urn)
+	scoreCacheFile <- paste0(cache.dir,urn,".csv")
+	write.table(scoreTable,scoreCacheFile,sep=",",row.names=FALSE)
+
+	#Parse score file to check for presence of syn/stop
+	if (grepl(" \\(",scoreTable$hgvs[[1]])) {
+		hgvsp <- sub("\\)$","",sapply(strsplit(scoreTable$hgvs," \\("),`[[`,2))
+	} else {
+		hgvsp <- scoreTable$hgvs
+	}
+	varInfo <- parseHGVS(hgvsp)
+	#TODO: pre-cache varInfo
+
+	hasStop <- any(varInfo$variant %in% c("Ter","*"))
+	hasSyn <- any(varInfo$type == "synonymous")
+
+	#add scoreset information to index
+	index <<- rbind(index,data.frame(
+		label=label,urn=urn,target=tname,wt=wtseq,
+		uniprot=uniprot$getID(),
+		syn=if (hasSyn) "auto" else "manual",
+		stop=if (hasStop) "auto" else "manual"
+	))
+
+	logger("...cached and indexed")
+})
+
+#TODO: pre-cache alignments PDB files and structure tracks.
+
+logger("Synchronization complete.")