diff MassbankConn.R @ 1:253d531a0193 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b

--- a/MassbankConn.R	Tue Jul 12 12:02:37 2016 -0400
+++ b/MassbankConn.R	Sat Sep 03 17:02:01 2016 -0400
@@ -1,43 +1,69 @@
 if ( ! exists('MassbankConn')) { # Do not load again if already loaded
 
-	source('BiodbConn.R')
+	source('RemotedbConn.R')
+	source('MassdbConn.R')
 	source('MassbankSpectrum.R')
 
 	#####################
 	# CLASS DECLARATION #
 	#####################
 	
-	MassbankConn <- setRefClass("MassbankConn", contains = "BiodbConn")
+	MassbankConn <- setRefClass("MassbankConn", contains = c("RemotedbConn", "MassdbConn"))
 
 	##########################
 	# GET ENTRY CONTENT TYPE #
 	##########################
 
 	MassbankConn$methods( getEntryContentType = function(type) {
-		return(if (type == RBIODB.SPECTRUM) RBIODB.TXT else NULL) 
+		return(if (type == BIODB.SPECTRUM) BIODB.TXT else NULL) 
 	})
 
 	#####################
 	# GET ENTRY CONTENT #
 	#####################
 	
-	MassbankConn$methods( getEntryContent = function(type, id) {
+	MassbankConn$methods( getEntryContent = function(type, ids) {
 
-		if (type == RBIODB.SPECTRUM) {
+		# Debug
+		.self$.print.debug.msg(paste0("Get entry content(s) for ", length(ids)," id(s)..."))
+
+		if (type == BIODB.SPECTRUM) {
+
+			URL.MAX.LENGTH <- 2083
 
 			# Initialize return values
-			content <- rep(NA_character_, length(id))
+			content <- rep(NA_character_, length(ids))
+
+			# Loop on all
+			n <- 0
+			while (n < length(ids)) {
 
-			# Request
-			xmlstr <- .self$.scheduler$getUrl(get.entry.url(RBIODB.MASSBANK, id, RBIODB.TXT))
+				# Get list of accession ids to retrieve
+				accessions <- ids[(n + 1):length(ids)]
+
+				# Create URL request
+				x <- get.entry.url(class = BIODB.MASSBANK, accession = accessions, content.type = BIODB.TXT, max.length = URL.MAX.LENGTH)
+
+				# Debug
+				.self$.print.debug.msg(paste0("Send URL request for ", x$n," id(s)..."))
 
-			# Parse XML and get text
-			if ( ! is.na(xmlstr)) {
-				library(XML)
-				xml <-  xmlInternalTreeParse(xmlstr, asText = TRUE)
-				ns <- c(ax21 = "http://api.massbank/xsd")
-				returned.ids <- xpathSApply(xml, "//ax21:id", xmlValue, namespaces = ns)
-				content[match(returned.ids, id)] <- xpathSApply(xml, "//ax21:info", xmlValue, namespaces = ns)
+				# Send request
+				xmlstr <- .self$.scheduler$getUrl(x$url)
+
+				# Increase number of entries retrieved
+				n <- n + x$n
+
+				# Parse XML and get text
+				if ( ! is.na(xmlstr)) {
+					library(XML)
+					xml <-  xmlInternalTreeParse(xmlstr, asText = TRUE)
+					ns <- c(ax21 = "http://api.massbank/xsd")
+					returned.ids <- xpathSApply(xml, "//ax21:id", xmlValue, namespaces = ns)
+					content[match(returned.ids, ids)] <- xpathSApply(xml, "//ax21:info", xmlValue, namespaces = ns)
+				}
+
+				# Debug
+				.self$.print.debug.msg(paste0("Now ", length(ids) - n," id(s) left to be retrieved..."))
 			}
 
 			return(content)
@@ -54,6 +80,13 @@
 	# content       A file content, downloaded from the public database.
 	# RETURN        A spectrum instance.
 	MassbankConn$methods( createEntry = function(type, content, drop = TRUE) {
-		return(if (type == RBIODB.SPECTRUM) createMassbankSpectrumFromTxt(content, drop = drop) else NULL)
+		return(if (type == BIODB.SPECTRUM) createMassbankSpectrumFromTxt(content, drop = drop) else NULL)
+	})
+
+	#################
+	# GET MZ VALUES #
+	#################
+	
+	MassbankConn$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
 	})
 }