diff LipidmapsConn.R @ 1:45e985cd8e9e draft

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

--- a/LipidmapsConn.R	Mon Jul 11 09:12:03 2016 -0400
+++ b/LipidmapsConn.R	Tue Jan 31 05:27:24 2017 -0500
@@ -1,57 +1,46 @@
-if ( ! exists('LipdmapsConn')) { # Do not load again if already loaded
-
-	source('BiodbConn.R')
-	source('LipidmapsCompound.R')
+#####################
+# CLASS DECLARATION #
+#####################
 
-	#####################
-	# CLASS DECLARATION #
-	#####################
+LipidmapsConn <- methods::setRefClass("LipidmapsConn", contains = "RemotedbConn")
 
-	LipidmapsConn <- setRefClass("LipidmapsConn", contains = "BiodbConn")
+###############
+# CONSTRUCTOR #
+###############
 
-	###############
-	# CONSTRUCTOR #
-	###############
+LipidmapsConn$methods( initialize = function(...) {
+	# From http://www.lipidmaps.org/data/structure/programmaticaccess.html:
+	# If you write a script to automate calls to LMSD, please be kind and do not hit our server more often than once per 20 seconds. We may have to kill scripts that hit our server more frequently.
+	callSuper(scheduler = UrlRequestScheduler$new(t = 20), ...)
+})
 
-	LipidmapsConn$methods( initialize = function(...) {
-		# From http://www.lipidmaps.org/data/structure/programmaticaccess.html:
-		# If you write a script to automate calls to LMSD, please be kind and do not hit our server more often than once per 20 seconds. We may have to kill scripts that hit our server more frequently.
-		callSuper(scheduler = UrlRequestScheduler$new(t = 20), ...)
-	})
-
-	##########################
-	# GET ENTRY CONTENT TYPE #
-	##########################
-
-	LipidmapsConn$methods( getEntryContentType = function(type) {
-		return(RBIODB.CSV)
-	})
+##########################
+# GET ENTRY CONTENT TYPE #
+##########################
 
-	#####################
-	# GET ENTRY CONTENT #
-	#####################
-
-	LipidmapsConn$methods( getEntryContent = function(type, id) {
+LipidmapsConn$methods( getEntryContentType = function() {
+	return(BIODB.CSV)
+})
 
-		if (type == RBIODB.COMPOUND) {
+#####################
+# GET ENTRY CONTENT #
+#####################
 
-			# Initialize return values
-			content <- rep(NA_character_, length(id))
+LipidmapsConn$methods( getEntryContent = function(id) {
 
-			# Request
-			content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(RBIODB.LIPIDMAPS, x, content.type = RBIODB.CSV)), FUN.VALUE = '')
+	# Initialize return values
+	content <- rep(NA_character_, length(id))
 
-			return(content)
-		}
+	# Request
+	content <- vapply(id, function(x) .self$.get.url(get.entry.url(BIODB.LIPIDMAPS, x, content.type = BIODB.CSV)), FUN.VALUE = '')
 
-		return(NULL)
-	})
+	return(content)
+})
 
-	################
-	# CREATE ENTRY #
-	################
+################
+# CREATE ENTRY #
+################
 
-	LipidmapsConn$methods( createEntry = function(type, content, drop = TRUE) {
-		return(if (type == RBIODB.COMPOUND) createLipidmapsCompoundFromCsv(content, drop = drop) else NULL)
-	})
-}
+LipidmapsConn$methods( createEntry = function(content, drop = TRUE) {
+	return(createLipidmapsEntryFromCsv(content, drop = drop))
+})