diff MirbaseConn.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/MirbaseConn.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,66 @@
+if ( ! exists('MirbaseConn')) { # Do not load again if already loaded
+
+	source('BiodbConn.R')
+	source('MirbaseCompound.R')
+
+	#####################
+	# CLASS DECLARATION #
+	#####################
+
+	MirbaseConn <- setRefClass("MirbaseConn", contains = "BiodbConn")
+
+	##########################
+	# GET ENTRY CONTENT TYPE #
+	##########################
+
+	MirbaseConn$methods( getEntryContentType = function(type) {
+		return(RBIODB.HTML)
+	})
+
+	#####################
+	# GET ENTRY CONTENT #
+	#####################
+	
+	MirbaseConn$methods( getEntryContent = function(type, id) {
+
+		if (type == RBIODB.COMPOUND) {
+
+			# Initialize return values
+			content <- rep(NA_character_, length(id))
+
+			# Request
+			content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(RBIODB.MIRBASE, x, content.type = RBIODB.HTML)), FUN.VALUE = '')
+
+			return(content)
+		}
+
+		return(NULL)
+	})
+
+	################
+	# CREATE ENTRY #
+	################
+	
+	MirbaseConn$methods( createEntry = function(type, content, drop = TRUE) {
+		return(if (type == RBIODB.COMPOUND) createMirbaseCompoundFromHtml(content, drop = drop) else NULL)
+	})
+
+	###################
+	# FIND ACCESSIONS #
+	###################
+
+	MirbaseConn$methods(
+		findAccessions = function(name) {
+
+			# Get HTML
+			htmlstr <- .self$.scheduler$getUrl('http://www.mirbase.org/cgi-bin/query.pl', params = c(terms = name, submit = 'Search'))
+
+			# Parse HTML
+			xml <-  htmlTreeParse(htmlstr, asText = TRUE, useInternalNodes = TRUE)
+
+			# Get accession number
+			acc <- unlist(xpathSApply(xml, "//a[starts-with(.,'MIMAT')]", xmlValue))
+
+			return(acc)
+	})
+}