diff BiodbConn.R @ 0:e66bb061af06 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 3529b25417f8e1a5836474c9adec4b696d35099d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BiodbConn.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,78 @@
+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) {
+		return( ! is.null(.self$getEntryContentType(type)))
+	})
+
+	##########################
+	# GET ENTRY CONTENT TYPE #
+	##########################
+
+	BiodbConn$methods( getEntryContentType = function(type) {
+		stop("Method getEntryContentType() is not implemented in concrete class.")
+	})
+
+	#############
+	# GET ENTRY #
+	#############
+
+	BiodbConn$methods( getEntry = function(type, id, drop = TRUE) {
+		content <- .self$getEntryContent(type, id)
+		return(.self$createEntry(type, content, drop = drop))
+	})
+
+	#####################
+	# GET ENTRY CONTENT #
+	#####################
+	
+	# Download entry content from the public database.
+	# type      The entry type.
+	# id        The ID of the enttry to get.
+	# RETURN    An entry content downloaded from database.
+	BiodbConn$methods( getEntryContent = function(type, id) {
+		stop("Method getCompound() is not implemented in concrete class.")
+	})
+	
+	#############################
+	# CREATE ENTRY FROM CONTENT #
+	#############################
+	
+	# Creates a Compound instance from file content.
+	# 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.")
+	})
+}