diff HmdbConn.R @ 1:45e985cd8e9e draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty

--- a/HmdbConn.R	Mon Jul 11 09:12:03 2016 -0400
+++ b/HmdbConn.R	Tue Jan 31 05:27:24 2017 -0500
@@ -1,48 +1,36 @@
-if ( ! exists('HmdbConn')) { # Do not load again if already loaded
+#####################
+# CLASS DECLARATION #
+#####################
+
+HmdbConn <- methods::setRefClass("HmdbConn", contains = "RemotedbConn")
 
-	source('BiodbConn.R')
-	source('HmdbCompound.R')
-	
-	#####################
-	# CLASS DECLARATION #
-	#####################
-	
-	HmdbConn <- setRefClass("HmdbConn", contains = "BiodbConn")
+##########################
+# GET ENTRY CONTENT TYPE #
+##########################
 
-	##########################
-	# GET ENTRY CONTENT TYPE #
-	##########################
+HmdbConn$methods( getEntryContentType = function() {
+	return(BIODB.XML)
+})
 
-	HmdbConn$methods( getEntryContentType = function(type) {
-		return(RBIODB.XML)
-	})
+#####################
+# GET ENTRY CONTENT #
+#####################
 
-	#####################
-	# GET ENTRY CONTENT #
-	#####################
-	
-	HmdbConn$methods( getEntryContent = function(type, id) {
+HmdbConn$methods( getEntryContent = function(id) {
 
-		if (type == RBIODB.COMPOUND) {
+	# Initialize return values
+	content <- rep(NA_character_, length(id))
 
-			# Initialize return values
-			content <- rep(NA_character_, length(id))
-
-			# Request
-			content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(RBIODB.HMDB, x, content.type = RBIODB.XML)), FUN.VALUE = '')
+	# Request
+	content <- vapply(id, function(x) .self$.get.url(get.entry.url(BIODB.HMDB, x, content.type = BIODB.XML)), FUN.VALUE = '')
 
-			return(content)
-		}
+	return(content)
+})
 
-		return(NULL)
-	})
-	
-	################
-	# CREATE ENTRY #
-	################
-	
-	HmdbConn$methods( createEntry = function(type, content, drop = TRUE) {
-		return(if (type == RBIODB.COMPOUND) createHmdbCompoundFromXml(content, drop = drop) else NULL)
-	})
-	
-} # end of load safe guard
+################
+# CREATE ENTRY #
+################
+
+HmdbConn$methods( createEntry = function(content, drop = TRUE) {
+	return(createHmdbEntryFromXml(content, drop = drop))
+})