Mercurial > repos > prog > lcmsmatching
diff MsPeakForestDb.R @ 1:253d531a0193 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b
| author | prog |
|---|---|
| date | Sat, 03 Sep 2016 17:02:01 -0400 |
| parents | e66bb061af06 |
| children | 20d69a062da3 |
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--- a/MsPeakForestDb.R Tue Jul 12 12:02:37 2016 -0400 +++ b/MsPeakForestDb.R Sat Sep 03 17:02:01 2016 -0400 @@ -8,21 +8,24 @@ # CLASS DECLARATION # ##################### - MsPeakForestDb <- setRefClass("MsPeakForestDb", contains = "MsDb", fields = list(.url = "character", .url.scheduler = "ANY")) + MsPeakForestDb <- setRefClass("MsPeakForestDb", contains = "MsDb", fields = list(.url = "character", .url.scheduler = "ANY", .token = "character")) ############### # CONSTRUCTOR # ############### - MsPeakForestDb$methods( initialize = function(url = NA_character_, useragent = NA_character_, ...) { + MsPeakForestDb$methods( initialize = function(url = NA_character_, useragent = NA_character_, token = NA_character_, ...) { # Check URL if (is.null(url) || is.na(url)) stop("No URL defined for new MsPeakForestDb instance.") + if (substring(url, nchar(url) - 1, 1) == '/') + url <- substring(url, nchar(url) - 1) .url <<- url .url.scheduler <<- UrlRequestScheduler$new(n = 3, useragent = useragent) .self$.url.scheduler$setVerbose(1L) + .token <<- token callSuper(...) }) @@ -35,6 +38,17 @@ res <- NULL + # Add url prefix + if (substring(url, 1, 1) == '/') + url <- substring(url, 2) + url <- paste(.self$.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') { @@ -67,7 +81,7 @@ MsPeakForestDb$methods( getMoleculeIds = function() { - ids <- as.character(.self$.get.url(url = paste0(.self$.url, 'compounds/all/ids'))) + ids <- as.character(.self$.get.url(url = 'compounds/all/ids')) return(ids) }) @@ -78,7 +92,7 @@ MsPeakForestDb$methods( getNbMolecules = function() { - n <- .self$.get.url(url = paste0(.self$.url, 'compounds/all/count'), ret.type = 'integer') + n <- .self$.get.url(url = 'compounds/all/count', ret.type = 'integer') return(n) }) @@ -90,13 +104,12 @@ MsPeakForestDb$methods( getChromCol = function(molid = NULL) { # Set URL - url <- paste0(.self$.url, 'metadata/lc/list-code-columns') params <- NULL if ( ! is.null(molid)) params <- list(molids = paste(molid, collapse = ',')) # Call webservice - wscols <- .self$.get.url(url = url, params = params) + wscols <- .self$.get.url(url = 'metadata/lc/list-code-columns', params = params) # Build data frame cols <- data.frame(id = character(), title = character()) @@ -118,13 +131,12 @@ rt <- list() # Set URL - url <- paste0(.self$.url, 'spectra/lcms/search') params <- NULL if ( ! is.null(molid)) params <- list(molids = paste(molid, collapse = ',')) # Call webservice - spectra <- .self$.get.url(url = url, params = params) + spectra <- .self$.get.url(url = 'spectra/lcms/search', params = params) if (class(spectra) == 'list' && length(spectra) > 0) { for (s in spectra) if (is.na(col) || s$liquidChromatography$columnCode %in% col) { @@ -160,11 +172,10 @@ if (length(non.na.molid) > 0) { # Set URL - url <- paste0(.self$.url, 'compounds/all/names') params <- c(molids = paste(non.na.molid, collapse = ',')) # Call webservice - names[ ! is.na(molid)] <- .self$.get.url(url = url, params = params) + names[ ! is.na(molid)] <- .self$.get.url(url = 'compounds/all/names', params = params) } return(names) @@ -187,8 +198,7 @@ ids <- c(ids, NA_character_) else { - url <- paste0(.self$.url, 'search/compounds/name/', curlEscape(n)) - compounds <- .self$.get.url(url = url)$compoundNames + compounds <- .self$.get.url(url = paste0('search/compounds/name/', curlEscape(n)))$compoundNames ids <- c(ids, list(vapply(compounds, function(c) as.character(c$compound$id), FUN.VALUE = ''))) } } @@ -203,7 +213,6 @@ MsPeakForestDb$methods( getNbPeaks = function(molid = NA_integer_, type = NA_character_) { # Build URL - url <- paste0(.self$.url, 'spectra/lcms/count-peaks') params <- NULL if ( ! is.na(type)) params <- c(params, mode = if (type == MSDB.TAG.POS) 'pos' else 'neg') @@ -211,7 +220,7 @@ params <- c(params, molids = paste(molid, collapse = ',')) # Run request - n <- .self$.get.url(url = url, params = params, ret.type = 'integer') + n <- .self$.get.url(url = 'spectra/lcms/count-peaks', params = params, ret.type = 'integer') return(sum(n)) }) @@ -222,16 +231,13 @@ MsPeakForestDb$methods( getMzValues = function(mode = NULL) { - # Build URL - url <- paste0(.self$.url, 'spectra/lcms/peaks/list-mz') - # Query params params <- NULL if ( ! is.null(mode)) params <- c(params, mode = if (mode == MSDB.TAG.POS) 'positive' else 'negative') # Get MZ valuels - mz <- .self$.get.url(url = url, params = params) + mz <- .self$.get.url(url = 'spectra/lcms/peaks/list-mz', params = params) return(mz) }) @@ -243,7 +249,7 @@ MsPeakForestDb$methods( .do.search.for.mz.rt.bounds = function(mode, mz.low, mz.high, rt.low = NULL, rt.high = NULL, col = NULL, attribs = NULL, molids = NULL) { # Build URL for mz search - url <- paste0(.self$.url, 'spectra/lcms/peaks/get-range/', mz.low, '/', mz.high) + url <- paste0('spectra/lcms/peaks/get-range/', mz.low, '/', mz.high) # Get spectra spectra <- .self$.get.url(url = url) @@ -265,7 +271,7 @@ if (nrow(results) > 0) { # Build URL for rt search - url <- paste0(.self$.url, 'spectra/lcms/range-rt-min/', rt.low, '/', rt.high) + url <- paste0('spectra/lcms/range-rt-min/', rt.low, '/', rt.high) params <- NULL if ( ! is.null(col)) params <- c(columns = paste(col, collapse = ','))