diff NcbigeneConn.R @ 2:20d69a062da3 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NcbigeneConn.R	Thu Mar 02 08:55:00 2017 -0500
@@ -0,0 +1,45 @@
+#####################
+# CLASS DECLARATION #
+#####################
+
+NcbigeneConn <- methods::setRefClass("NcbigeneConn", contains = "RemotedbConn")
+
+###############
+# 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$methods( getEntryContentType = function() {
+	return(BIODB.XML)
+})
+
+#####################
+# GET ENTRY CONTENT #
+#####################
+
+NcbigeneConn$methods( getEntryContent = function(id) {
+
+	# Initialize return values
+	content <- rep(NA_character_, length(id))
+
+	# Request
+	content <- vapply(id, function(x) .self$.get.url(get.entry.url(BIODB.NCBIGENE, x, content.type = BIODB.XML)), FUN.VALUE = '')
+
+	return(content)
+})
+
+################
+# CREATE ENTRY #
+################
+
+NcbigeneConn$methods( createEntry = function(content, drop = TRUE) {
+	return(createNcbigeneEntryFromXml(content, drop = drop))
+})