annotate NcbigeneConn.R @ 3:f61ce21ed17c draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 476a081c0da66822f4e77070f5ce59d9f14511f4-dirty

#####################
# 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))
})