diff PubchemCompound.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/PubchemCompound.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,71 @@
+if ( ! exists('PubchemCompound')) { # Do not load again if already loaded
+
+	source('BiodbEntry.R')
+
+	#####################
+	# CLASS DECLARATION #
+	#####################
+
+	PubchemCompound <- setRefClass("PubchemCompound", contains = "BiodbEntry")
+
+	###########
+	# FACTORY #
+	###########
+
+	createPubchemCompoundFromXml <- function(contents, drop = TRUE) {
+
+		library(XML)
+
+		compounds <- list()
+
+		# Set XML namespace
+		ns <- c(pubchem = "http://pubchem.ncbi.nlm.nih.gov/pug_view")
+
+		# Define xpath expressions
+		xpath.expr <- character()
+		xpath.expr[[RBIODB.ACCESSION]] <- "//pubchem:RecordType[text()='CID']/../pubchem:RecordNumber"
+		xpath.expr[[RBIODB.INCHI]] <- "//pubchem:Name[text()='InChI']/../pubchem:StringValue"
+		xpath.expr[[RBIODB.INCHIKEY]] <- "//pubchem:Name[text()='InChI Key']/../pubchem:StringValue"
+
+		for (content in contents) {
+
+			# Create instance
+			compound <- PubchemCompound$new()
+
+			# Parse XML
+			xml <-  xmlInternalTreeParse(content, asText = TRUE)
+
+			# Unknown compound
+			fault <- xpathSApply(xml, "/pubchem:Fault", xmlValue, namespaces = ns)
+			if (length(fault) == 0) {
+
+				# Test generic xpath expressions
+				for (field in names(xpath.expr)) {
+					v <- xpathSApply(xml, xpath.expr[[field]], xmlValue, namespaces = ns)
+					if (length(v) > 0)
+						compound$setField(field, v)
+				}
+
+				# Get name
+				name <- NA_character_
+				tryCatch( { name <- xpathSApply(xml, "//pubchem:Name[text()='IUPAC Name']/../pubchem:StringValue", xmlValue, namespaces = ns) }, warning = function(w) {})
+				if (is.na(name))
+					tryCatch( { name <- xpathSApply(xml, "//pubchem:Name[text()='Record Title']/../pubchem:StringValue", xmlValue, namespaces = ns) }, warning = function(w) {})
+				if ( ! is.na(name))
+					compound$setField(RBIODB.NAME, name)
+
+			}
+
+			compounds <- c(compounds, compound)
+		}
+
+		# Replace elements with no accession id by NULL
+		compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x)
+
+		# If the input was a single element, then output a single object
+		if (drop && length(contents) == 1)
+			compounds <- compounds[[1]]
+	
+		return(compounds)
+	}
+}