diff ChebiEntry.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/ChebiEntry.R	Thu Mar 02 08:55:00 2017 -0500
@@ -0,0 +1,57 @@
+#####################
+# CLASS DECLARATION #
+#####################
+
+ChebiEntry <- methods::setRefClass("ChebiEntry", contains = "BiodbEntry")
+
+###########
+# FACTORY #
+###########
+
+createChebiEntryFromHtml <- function(contents, drop = TRUE) {
+
+	entries <- list()
+
+	# Define xpath expressions
+	xpath.expr <- character()
+#		xpath.expr[[BIODB.ACCESSION]] <- "//b[starts-with(., 'CHEBI:')]"
+	xpath.expr[[BIODB.INCHI]] <- "//td[starts-with(., 'InChI=')]"
+	xpath.expr[[BIODB.INCHIKEY]] <- "//td[text()='InChIKey']/../td[2]"
+
+	for (content in contents) {
+
+		# Create instance
+		entry <- ChebiEntry$new()
+
+		if ( ! is.null(content) && ! is.na(content)) {
+		
+			# Parse HTML
+			xml <-  XML::htmlTreeParse(content, asText = TRUE, useInternalNodes = TRUE)
+
+			# Test generic xpath expressions
+			for (field in names(xpath.expr)) {
+				v <- XML::xpathSApply(xml, xpath.expr[[field]], XML::xmlValue)
+				if (length(v) > 0)
+					entry$setField(field, v)
+			}
+		
+			# Get accession
+			accession <- XML::xpathSApply(xml, "//b[starts-with(., 'CHEBI:')]", XML::xmlValue)
+			if (length(accession) > 0) {
+				accession <- sub('^CHEBI:([0-9]+)$', '\\1', accession, perl = TRUE)
+				entry$setField(BIODB.ACCESSION, accession)
+			}
+		}
+
+		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)
+}