diff LipidmapsEntry.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/LipidmapsEntry.R	Thu Mar 02 08:55:00 2017 -0500
@@ -0,0 +1,64 @@
+#####################
+# CLASS DECLARATION #
+#####################
+
+LipidmapsEntry <- methods::setRefClass("LipidmapsEntry", contains = 'BiodbEntry')
+
+###########
+# FACTORY #
+###########
+
+createLipidmapsEntryFromCsv <- function(contents, drop = TRUE) {
+
+	entries <- list()
+
+	# Mapping column names
+	col2field <- list()
+	col2field[[BIODB.NAME]] <- 'COMMON_NAME'
+	col2field[[BIODB.ACCESSION]] <- 'LM_ID'
+	col2field[[BIODB.KEGG.ID]] <- 'KEGG_ID'
+	col2field[[BIODB.HMDB.ID]] <- 'HMDBID'
+	col2field[[BIODB.MASS]] <- 'MASS'
+	col2field[[BIODB.FORMULA]] <- 'FORMULA'
+	
+	for (text in contents) {
+
+		# Create instance
+		entry <- LipidmapsEntry$new()
+
+		# Split text in lines
+		lines <- split.str(text, sep = "\n", unlist = TRUE)
+
+		# An error occured
+		if ( ! grepl("No record found", lines[[2]])) {
+
+			# Keys on first line
+			keys <- split.str(lines[[1]], unlist = TRUE)
+
+			# Values on second line
+			values <- split.str(lines[[2]], unlist = TRUE)
+			names(values) <- keys[seq(values)]
+
+			# Get field values
+			for (field in names(col2field))
+				if (values[[col2field[[field]]]] != '-')
+					entry$setField(field, values[[col2field[[field]]]])
+
+			# Set names
+			if (values[['SYNONYMS']] != '-') {
+				# TODO
+			}
+		}
+
+		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)
+}