comparison HmdbConn.R @ 2:20d69a062da3 draft

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

1:253d531a0193

if ( ! exists('HmdbConn')) { # Do not load again if already loaded

	source('RemotedbConn.R')
	source('HmdbCompound.R')
	
	#####################
	# CLASS DECLARATION #
	#####################
	
	HmdbConn <- setRefClass("HmdbConn", contains = "RemotedbConn")

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

	HmdbConn$methods( getEntryContentType = function(type) {
		return(BIODB.XML)
	})

	#####################
	# GET ENTRY CONTENT #
	#####################
	
	HmdbConn$methods( getEntryContent = function(type, id) {

		if (type == BIODB.COMPOUND) {

			# Initialize return values
			content <- rep(NA_character_, length(id))

			# Request
			content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(BIODB.HMDB, x, content.type = BIODB.XML)), FUN.VALUE = '')

			return(content)
		}

		return(NULL)
	})
	
	################
	# CREATE ENTRY #
	################
	
	HmdbConn$methods( createEntry = function(type, content, drop = TRUE) {
		return(if (type == BIODB.COMPOUND) createHmdbCompoundFromXml(content, drop = drop) else NULL)
	})
	
} # end of load safe guard

2:20d69a062da3

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

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

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

HmdbConn$methods( getEntryContentType = function() {
	return(BIODB.XML)
})

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

HmdbConn$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.HMDB, x, content.type = BIODB.XML)), FUN.VALUE = '')

	return(content)
})

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

HmdbConn$methods( createEntry = function(content, drop = TRUE) {
	return(createHmdbEntryFromXml(content, drop = drop))
})