comparison MsPeakForestDb.R @ 6:b8f70d8216b3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty

5:18254e8d1b72

if ( ! exists('MsPeakForestDb')) { # Do not load again if already loaded

	library(methods)
	source('MsDb.R')
	source(file.path('UrlRequestScheduler.R'))

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

		url <- paste(.self$.url, url, sep = '/')

		# Add token
		if ( ! is.na(.self$.token))
			params <- c(params, token = .self$.token)
				param.str <- if (is.null(params)) '' else paste('?', vapply(names(params), function(p) paste(p, params[[p]], sep = '='), FUN.VALUE = ''), collapse = '&', sep = '')

		# Get URL
		content <- .self$.url.scheduler$getUrl(url = url, params = params)

		if (ret.type == 'json') {

		if ( ! is.null(rt.low) && ! is.null(rt.high)) {

			rt.res <- data.frame(MSDB.TAG.MOLID = character(), MSDB.TAG.COL = character(), MSDB.TAG.COLRT = numeric())

			if (nrow(results) > 0) {
				# Build URL for rt search
				url <- paste0('spectra/lcms/range-rt-min/', rt.low, '/', rt.high)
				params <- NULL
				if ( ! is.null(col))
					params <- c(columns = paste(col, collapse = ','))

				# Run query
				rtspectra <- .self$.get.url(url = url, params = params)


				# Get compound/molecule IDs
				for (x in rtspectra)
					if (all(c('listOfCompounds', 'liquidChromatography') %in% names(x))) {
						molids <- vapply(x$listOfCompounds, function(c) if ('id' %in% names(c) && ! is.null(c$id)) as.character(c$id) else NA_character_, FUN.VALUE = '')

							rtmin <- if ('RTmin' %in% names(x) && ! is.null(x$RTmin)) as.double(x$RTmin) else NA_real_
							rtmax <- if ('RTmax' %in% names(x) && ! is.null(x$RTmax)) as.double(x$RTmax) else NA_real_
							colrt <- (rtmin + rtmax) / 2
							rt.res <- rbind(rt.res, data.frame(MSDB.TAG.MOLID = molids,
				                                   	   	   	   MSDB.TAG.COL = col,
				                                   	   	   	   MSDB.TAG.COLRT = colrt,
					                                   	   	   stringsAsFactors = FALSE))
						}
					}
			}	

6:b8f70d8216b3

if ( ! exists('MsPeakForestDb')) { # Do not load again if already loaded

	library(methods)
	source('MsDb.R')
	source('UrlRequestScheduler.R')

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

		url <- paste(.self$.url, url, sep = '/')

		# Add token
		if ( ! is.na(.self$.token))
			params <- c(params, token = .self$.token)

		# Get URL
		content <- .self$.url.scheduler$getUrl(url = url, params = params)

		if (ret.type == 'json') {

		if ( ! is.null(rt.low) && ! is.null(rt.high)) {

			rt.res <- data.frame(MSDB.TAG.MOLID = character(), MSDB.TAG.COL = character(), MSDB.TAG.COLRT = numeric())

			if (nrow(results) > 0) {

				# Build URL for rt search
				url <- paste0('spectra/lcms/range-rt-min/', rt.low / 60, '/', rt.high / 60)
				params <- NULL
				if ( ! is.null(col))
					params <- c(columns = paste(col, collapse = ','))

				# Run query
				rtspectra <- .self$.get.url(url = url, params = params)

				# Get compound/molecule IDs
				for (x in rtspectra)
					if (all(c('listOfCompounds', 'liquidChromatography') %in% names(x))) {
						molids <- vapply(x$listOfCompounds, function(c) if ('id' %in% names(c) && ! is.null(c$id)) as.character(c$id) else NA_character_, FUN.VALUE = '')

							rtmin <- if ('RTmin' %in% names(x) && ! is.null(x$RTmin)) as.double(x$RTmin) else NA_real_
							rtmax <- if ('RTmax' %in% names(x) && ! is.null(x$RTmax)) as.double(x$RTmax) else NA_real_
							colrt <- (rtmin + rtmax) / 2
							rt.res <- rbind(rt.res, data.frame(MSDB.TAG.MOLID = molids,
				                                   	   	   	   MSDB.TAG.COL = col,
				                                   	   	   	   MSDB.TAG.COLRT = colrt * 60,
					                                   	   	   stringsAsFactors = FALSE))
						}
					}
			}