annotate MirbaseEntry.R @ 2:20d69a062da3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8

#####################
# CLASS DECLARATION #
#####################

MirbaseEntry <- methods::setRefClass("MirbaseEntry", contains = "BiodbEntry")

###########
# FACTORY #
###########

createMirbaseEntryFromHtml <- function(contents, drop = TRUE) {

	entries <- list()

	# Define fields regex
	xpath.expr <- character()
	xpath.expr[[BIODB.ACCESSION]]  <- "//td[text()='Accession number']/../td[2]"
	xpath.expr[[BIODB.NAME]]       <- "//td[text()='ID']/../td[2]"
	xpath.expr[[BIODB.SEQUENCE]]   <- "//td[text()='Sequence']/..//pre"

	for (html in contents) {

		# Create instance
		entry <- MirbaseEntry$new()
	
		# Parse HTML
		xml <-  XML::htmlTreeParse(html, asText = TRUE, useInternalNodes = TRUE)

		# Test generic xpath expressions
		for (field in names(xpath.expr)) {
			v <- XML::xpathSApply(xml, xpath.expr[[field]], XML::xmlValue)
			if (length(v) > 0)
				entry$setField(field, v)
		}

		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)
}