comparison BiodbConn.R @ 1:253d531a0193 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b

0:e66bb061af06

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

	source(file.path('UrlRequestScheduler.R'), chdir = TRUE)
	source('biodb-common.R')

	#####################
	# CLASS DECLARATION #
	#####################
	
	BiodbConn <- setRefClass("BiodbConn", fields = list(.scheduler = "UrlRequestScheduler"))

	###############
	# CONSTRUCTOR #
	###############

	BiodbConn$methods( initialize = function(useragent = NA_character_, scheduler = NULL, ...) {

		# Check useragent
		! is.null(useragent) && ! is.na(useragent) || stop("You must specify a valid useragent.")

		# Set scheduler
		if (is.null(scheduler))
			scheduler <- UrlRequestScheduler$new(n = 3)
		inherits(scheduler, "UrlRequestScheduler") || stop("The scheduler instance must inherit from UrlRequestScheduler class.")
		scheduler$setUserAgent(useragent) # set agent
		.scheduler <<- scheduler
	
		callSuper(...) # calls super-class initializer with remaining parameters
	})
	
	######################
	# HANDLES ENTRY TYPE #
	######################

	BiodbConn$methods( handlesEntryType = function(type) {

	# GET ENTRY CONTENT #
	#####################
	
	# Download entry content from the public database.
	# type      The entry type.
	# id        The ID of the enttry to get.
	# RETURN    An entry content downloaded from database.
	BiodbConn$methods( getEntryContent = function(type, id) {
		stop("Method getCompound() is not implemented in concrete class.")
	})
	

	# content       A file content, downloaded from the public database.
	# RETURN        A compound instance.
	BiodbConn$methods( createEntry = function(type, content, drop = TRUE) {
		stop("Method createEntry() is not implemented in concrete class.")
	})
}

1:253d531a0193

if ( ! exists('BiodbConn')) {

	source('biodb-common.R')

	#####################
	# CLASS DECLARATION #
	#####################
	
	BiodbConn <- setRefClass("BiodbConn", fields = list( .debug = "logical" ))

	###############
	# CONSTRUCTOR #
	###############

	BiodbConn$methods( initialize = function(debug = FALSE, ...) {
		.debug <<- debug
	})

	#######################
	# PRINT DEBUG MESSAGE #
	#######################

	BiodbConn$methods( .print.debug.msg = function(msg) {
		if (.self$.debug)
			.print.msg(msg = msg, class = class(.self))
	})

	######################
	# HANDLES ENTRY TYPE #
	######################

	BiodbConn$methods( handlesEntryType = function(type) {

	# GET ENTRY CONTENT #
	#####################
	
	# Download entry content from the public database.
	# type      The entry type.
	# id        The ID of the entry to get.
	# RETURN    An entry content downloaded from database.
	BiodbConn$methods( getEntryContent = function(type, id) {
		stop("Method getCompound() is not implemented in concrete class.")
	})
	

	# content       A file content, downloaded from the public database.
	# RETURN        A compound instance.
	BiodbConn$methods( createEntry = function(type, content, drop = TRUE) {
		stop("Method createEntry() is not implemented in concrete class.")
	})

	#################
	# GET ENTRY IDS #
	#################
	
	# Get a list of IDs of all entries contained in this database.
	BiodbConn$methods( getEntryIds = function(type) {
		stop("Method getEntryIds() is not implemented in concrete class.")
	})

	##################
	# GET NB ENTRIES #
	##################
	
	# Get the number of entries contained in this database.
	BiodbConn$methods( getNbEntries = function(type) {
		stop("Method getNbEntries() is not implemented in concrete class.")
	})
}