diff ChemspiderEntry.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/ChemspiderEntry.R	Thu Mar 02 08:55:00 2017 -0500
@@ -0,0 +1,103 @@
+#####################
+# CLASS DECLARATION #
+#####################
+
+ChemspiderEntry <- methods::setRefClass("ChemspiderEntry", contains = "BiodbEntry")
+
+############################
+# CREATE COMPOUND FROM XML #
+############################
+
+createChemspiderEntryFromXml <- function(contents, drop = TRUE) {
+
+	entries <- list()
+
+	# Define xpath expressions
+	xpath.expr <- character()
+	xpath.expr[[BIODB.ACCESSION]]    	<- "//CSID"
+	xpath.expr[[BIODB.FORMULA]]      	<- "//MF"
+	xpath.expr[[BIODB.NAME]]         	<- "//CommonName"
+	xpath.expr[[BIODB.AVERAGE.MASS]] 	<- "//AverageMass"
+	xpath.expr[[BIODB.INCHI]]           <- "//InChI"
+	xpath.expr[[BIODB.INCHIKEY]]       	<- "//InChIKey"
+	xpath.expr[[BIODB.SMILES]]          <- "//SMILES"
+
+	for (content in contents) {
+
+		# Create instance
+		entry <- ChemspiderEntry$new()
+
+		if ( ! is.null(content) && ! is.na(content) && content != 'NA') {
+		
+			# Parse XML
+			xml <-  XML::xmlInternalTreeParse(content, asText = TRUE)
+
+			# Test generic xpath expressions
+			for (field in names(xpath.expr)) {
+				v <- XML::xpathSApply(xml, xpath.expr[[field]], XML::xmlValue)
+				if (length(v) > 0)
+					entry$setField(field, v)
+			}
+		}
+
+		entries <- c(entries, entry)
+	}
+
+	# Replace elements with no accession id by NULL
+	entries <- lapply(entries, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x)
+
+	# If the input was a single element, then output a single object
+	if (drop && length(contents) == 1)
+		entries <- entries[[1]]
+
+	return(entries)
+}
+
+#############################
+# CREATE COMPOUND FROM HTML #
+#############################
+
+createChemspiderEntryFromHtml <- function(contents, drop = TRUE) {
+
+	entries <- list()
+
+	# Define xpath expressions
+	xpath.expr <- character()
+
+	for (content in contents) {
+
+		# Create instance
+		entry <- ChemspiderEntry$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$setField(field, v)
+			}
+		
+			# Get accession
+			accession <- XML::xpathSApply(xml, "//li[starts-with(., 'ChemSpider ID')]", XML::xmlValue)
+			if (length(accession) > 0) {
+				accession <- sub('^ChemSpider ID([0-9]+)$', '\\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)
+}