diff ChemspiderConn.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/ChemspiderConn.R	Thu Mar 02 08:55:00 2017 -0500
@@ -0,0 +1,92 @@
+#####################
+# CLASS DECLARATION #
+#####################
+
+ChemspiderConn <- methods::setRefClass("ChemspiderConn", contains = "RemotedbConn")
+
+##########################
+# GET ENTRY CONTENT TYPE #
+##########################
+
+ChemspiderConn$methods( getEntryContentType = function() {
+	return(BIODB.XML)
+})
+
+#####################
+# GET ENTRY CONTENT #
+#####################
+
+ChemspiderConn$methods( getEntryContent = function(ids) {
+
+	# Debug
+	.self$.print.debug.msg(paste0("Get entry content(s) for ", length(ids)," id(s)..."))
+
+	URL.MAX.LENGTH <- 2083
+
+	# Initialize return values
+	content <- rep(NA_character_, length(ids))
+
+	# Loop on all
+	n <- 0
+	inc <- NA_integer_
+	while (n < length(ids)) {
+
+		# Get list of accession ids to retrieve
+		accessions <- ids[(n + 1):(if (is.na(inc)) length(ids) else (min(n + inc, length(ids))))]
+
+		# Create URL request
+		x <- get.entry.url(class = BIODB.CHEMSPIDER, accession = accessions, content.type = BIODB.XML, max.length = URL.MAX.LENGTH, base.url = .self$.url, token = .self$.token)
+
+		# Debug
+		.self$.print.debug.msg(paste0("Send URL request for ", x$n," id(s)..."))
+
+		# Send request
+		xmlstr <- .self$.get.url(x$url)
+
+		# Error : "Cannot convert WRONG to System.Int32.\r\nParameter name: type ---> Input string was not in a correct format.\r\n"
+		if (grepl('^Cannot convert .* to System\\.Int32\\.', xmlstr)) {
+			# One of the ids is incorrect
+			if (is.na(inc)) {
+				inc <- 1
+				next
+			}
+			else
+				xmlstr <- NA_character_
+		}
+
+		# Increase number of entries retrieved
+		n <- n + x$n
+
+		# Parse XML and get included XML
+		if ( ! is.na(xmlstr)) {
+			xml <-  xmlInternalTreeParse(xmlstr, asText = TRUE)
+			ns <- c(csns = "http://www.chemspider.com/")
+			returned.ids <- xpathSApply(xml, "//csns:ExtendedCompoundInfo/csns:CSID", xmlValue, namespaces = ns)
+			content[match(returned.ids, ids)] <- vapply(getNodeSet(xml, "//csns:ExtendedCompoundInfo", namespaces = ns), saveXML, FUN.VALUE = '')
+		}
+
+		# Debug
+		.self$.print.debug.msg(paste0("Now ", length(ids) - n," id(s) left to be retrieved..."))
+	}
+
+	return(content)
+})
+
+################
+# CREATE ENTRY #
+################
+
+ChemspiderConn$methods( createEntry = function(content, drop = TRUE) {
+	return(createChemspiderEntryFromXml(content, drop = drop))
+})
+
+############################
+# GET CHEMSPIDER IMAGE URL #
+############################
+
+get.chemspider.image.url <- function(id) {
+
+	url <- paste0('http://www.chemspider.com/ImagesHandler.ashx?w=300&h=300&id=', id)
+
+	return(url)
+}