diff PubchemConn.R @ 0:e66bb061af06 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 3529b25417f8e1a5836474c9adec4b696d35099d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PubchemConn.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,59 @@
+if ( ! exists('get.pubchem.compound.url')) { # Do not load again if already loaded
+
+	source('BiodbConn.R')
+	source('PubchemCompound.R')
+	
+	#####################
+	# CLASS DECLARATION #
+	#####################
+	
+	PubchemConn <- setRefClass("PubchemConn", contains = "BiodbConn")
+
+	##########################
+	# GET ENTRY CONTENT TYPE #
+	##########################
+
+	PubchemConn$methods( getEntryContentType = function(type) {
+		return(RBIODB.XML)
+	})
+
+	#####################
+	# GET ENTRY CONTENT #
+	#####################
+	
+	PubchemConn$methods( getEntryContent = function(type, id) {
+
+		if (type == RBIODB.COMPOUND) {
+
+			# Initialize return values
+			content <- rep(NA_character_, length(id))
+
+			# Request
+			content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(RBIODB.PUBCHEM, x, content.type = RBIODB.XML)), FUN.VALUE = '')
+
+			return(content)
+		}
+
+		return(NULL)
+	})
+	
+	################
+	# CREATE ENTRY #
+	################
+	
+	PubchemConn$methods( createEntry = function(type, content, drop = TRUE) {
+		return(if (type == RBIODB.COMPOUND) createPubchemCompoundFromXml(content, drop = drop) else NULL)
+	})
+
+	#########################
+	# GET PUBCHEM IMAGE URL #
+	#########################
+	
+	get.pubchem.image.url <- function(id) {
+	
+		url <- paste0('http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=', id, '&t=l')
+
+		return(url)
+	}
+	
+} # end of load safe guard