diff NcbiGeneConn.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/NcbiGeneConn.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,56 @@
+if ( ! exists('NcbigeneConn')) { # Do not load again if already loaded
+
+	source('BiodbConn.R')
+	source('NcbigeneCompound.R')
+
+	#####################
+	# CLASS DECLARATION #
+	#####################
+
+	NcbigeneConn <- setRefClass("NcbigeneConn", contains = "BiodbConn")
+
+	###############
+	# CONSTRUCTOR #
+	###############
+
+	NcbigeneConn$methods( initialize = function(...) {
+		# From NCBI E-Utility manual: "In order not to overload the E-utility servers, NCBI recommends that users post no more than three URL requests per second and limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time during weekdays".
+		callSuper(scheduler = UrlRequestScheduler$new(n = 3), ...)
+	})
+
+	##########################
+	# GET ENTRY CONTENT TYPE #
+	##########################
+
+	NcbigeneConn$methods( getEntryContentType = function(type) {
+		return(RBIODB.XML)
+	})
+
+	#####################
+	# GET ENTRY CONTENT #
+	#####################
+	
+	NcbigeneConn$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.NCBIGENE, x)), FUN.VALUE = '')
+
+			return(content)
+		}
+
+		return(NULL)
+	})
+	
+	################
+	# CREATE ENTRY #
+	################
+	
+	NcbigeneConn$methods( createEntry = function(type, content, drop = TRUE) {
+		return(if (type == RBIODB.COMPOUND) createNcbigeneCompoundFromXml(content, drop = drop) else NULL)
+	})
+}