view LipidmapsConn.R @ 3:f61ce21ed17c draft

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

#####################
# CLASS DECLARATION #
#####################

LipidmapsConn <- methods::setRefClass("LipidmapsConn", contains = "RemotedbConn")

###############
# 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), ...)
})

##########################
# GET ENTRY CONTENT TYPE #
##########################

LipidmapsConn$methods( getEntryContentType = function() {
	return(BIODB.CSV)
})

#####################
# GET ENTRY CONTENT #
#####################

LipidmapsConn$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.LIPIDMAPS, x, content.type = BIODB.CSV)), FUN.VALUE = '')

	return(content)
})

################
# CREATE ENTRY #
################

LipidmapsConn$methods( createEntry = function(content, drop = TRUE) {
	return(createLipidmapsEntryFromCsv(content, drop = drop))
})