diff ChebiCompound.R @ 1:253d531a0193 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b

--- a/ChebiCompound.R	Tue Jul 12 12:02:37 2016 -0400
+++ b/ChebiCompound.R	Sat Sep 03 17:02:01 2016 -0400
@@ -20,9 +20,9 @@
 
 		# Define xpath expressions
 		xpath.expr <- character()
-#		xpath.expr[[RBIODB.ACCESSION]] <- "//b[starts-with(., 'CHEBI:')]"
-		xpath.expr[[RBIODB.INCHI]] <- "//td[starts-with(., 'InChI=')]"
-		xpath.expr[[RBIODB.INCHIKEY]] <- "//td[text()='InChIKey']/../td[2]"
+#		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 (html in contents) {
 
@@ -43,14 +43,14 @@
 			accession <- xpathSApply(xml, "//b[starts-with(., 'CHEBI:')]", xmlValue)
 			if (length(accession) > 0) {
 				accession <- sub('^CHEBI:([0-9]+)$', '\\1', accession, perl = TRUE)
-				compound$setField(RBIODB.ACCESSION, accession)
+				compound$setField(BIODB.ACCESSION, accession)
 			}
 
 			compounds <- c(compounds, compound)
 		}
 
 		# Replace elements with no accession id by NULL
-		compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x)
+		compounds <- lapply(compounds, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x)
 
 		# If the input was a single element, then output a single object
 		if (drop && length(contents) == 1)