diff HmdbEntry.R @ 2:20d69a062da3 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/HmdbEntry.R	Thu Mar 02 08:55:00 2017 -0500
@@ -0,0 +1,59 @@
+#####################
+# CLASS DECLARATION #
+#####################
+
+HmdbEntry <- methods::setRefClass("HmdbEntry", contains = "BiodbEntry")
+
+###########
+# FACTORY #
+###########
+
+createHmdbEntryFromXml <- function(contents, drop = FALSE) {
+
+	entries <- list()
+
+	# Define xpath expressions
+	xpath.expr <- character()
+	xpath.expr[[BIODB.ACCESSION]]          <- "/metabolite/accession"
+	xpath.expr[[BIODB.KEGG.ID]]            <- "//kegg_id"
+	xpath.expr[[BIODB.NAME]]               <- "/metabolite/name"
+	xpath.expr[[BIODB.FORMULA]]            <- "/metabolite/chemical_formula"
+	xpath.expr[[BIODB.SUPER.CLASS]]        <- "//super_class"
+	xpath.expr[[BIODB.AVERAGE.MASS]]       <- "//average_molecular_weight"
+	xpath.expr[[BIODB.MONOISOTOPIC.MASS]]  <- "//monisotopic_moleculate_weight"
+
+	for (content in contents) {
+
+		# Create instance
+		entry <- HmdbEntry$new()
+
+		if ( ! is.null(content) && ! is.na(content)) {
+
+			# Parse XML
+			xml <-  XML::xmlInternalTreeParse(content, asText = TRUE)
+
+			# An error occured
+			if (length(XML::getNodeSet(xml, "//error")) == 0) {
+
+				# Test generic xpath expressions
+				for (field in names(xpath.expr)) {
+					v <- XML::xpathSApply(xml, xpath.expr[[field]], XML::xmlValue)
+					if (length(v) > 0)
+						entry$setField(field, v)
+				}
+
+			}
+		}
+
+		entries <- c(entries, entry)
+	}
+
+	# Replace elements with no accession id by NULL
+	entries <- lapply(entries, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x)
+
+	# If the input was a single element, then output a single object
+	if (drop && length(contents) == 1)
+		entries <- entries[[1]]
+
+	return(entries)
+}