comparison ChebiCompound.R @ 1:253d531a0193 draft

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

0:e66bb061af06

		compounds <- list()

		# 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]"

		for (html in contents) {

			# Create instance
			compound <- ChebiCompound$new()

		
			# Get accession
			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)
			}

			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]]
	

1:253d531a0193

		compounds <- list()

		# Define xpath expressions
		xpath.expr <- character()
#		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) {

			# Create instance
			compound <- ChebiCompound$new()

		
			# Get accession
			accession <- xpathSApply(xml, "//b[starts-with(., 'CHEBI:')]", xmlValue)
			if (length(accession) > 0) {
				accession <- sub('^CHEBI:([0-9]+)$', '\\1', accession, perl = TRUE)
				compound$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(BIODB.ACCESSION))) NULL else x)

		# If the input was a single element, then output a single object
		if (drop && length(contents) == 1)
			compounds <- compounds[[1]]