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comparison MsPeakForestDb.R @ 1:45e985cd8e9e draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
author prog
date Tue, 31 Jan 2017 05:27:24 -0500
parents 3afe41d3e9e7
children 9a0288561ba3
comparison
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0:3afe41d3e9e7 1:45e985cd8e9e
6 6
7 ##################### 7 #####################
8 # CLASS DECLARATION # 8 # CLASS DECLARATION #
9 ##################### 9 #####################
10 10
11 MsPeakForestDb <- setRefClass("MsPeakForestDb", contains = "MsDb", fields = list(.url = "character", .url.scheduler = "ANY")) 11 MsPeakForestDb <- setRefClass("MsPeakForestDb", contains = "MsDb", fields = list(.url = "character", .url.scheduler = "ANY", .token = "character"))
12 12
13 ############### 13 ###############
14 # CONSTRUCTOR # 14 # CONSTRUCTOR #
15 ############### 15 ###############
16 16
17 MsPeakForestDb$methods( initialize = function(url = NA_character_, useragent = NA_character_, ...) { 17 MsPeakForestDb$methods( initialize = function(url = NA_character_, useragent = NA_character_, token = NA_character_, ...) {
18 18
19 # Check URL 19 # Check URL
20 if (is.null(url) || is.na(url)) 20 if (is.null(url) || is.na(url))
21 stop("No URL defined for new MsPeakForestDb instance.") 21 stop("No URL defined for new MsPeakForestDb instance.")
22 22
23 if (substring(url, nchar(url) - 1, 1) == '/')
24 url <- substring(url, nchar(url) - 1)
23 .url <<- url 25 .url <<- url
24 .url.scheduler <<- UrlRequestScheduler$new(n = 3, useragent = useragent) 26 .url.scheduler <<- UrlRequestScheduler$new(n = 3, useragent = useragent)
25 .self$.url.scheduler$setVerbose(1L) 27 .self$.url.scheduler$setVerbose(1L)
28 .token <<- token
26 29
27 callSuper(...) 30 callSuper(...)
28 }) 31 })
29 32
30 ########### 33 ###########
33 36
34 MsPeakForestDb$methods( .get.url = function(url, params = NULL, ret.type = 'json') { 37 MsPeakForestDb$methods( .get.url = function(url, params = NULL, ret.type = 'json') {
35 38
36 res <- NULL 39 res <- NULL
37 40
41 # Add url prefix
42 if (substring(url, 1, 1) == '/')
43 url <- substring(url, 2)
44 url <- paste(.self$.url, url, sep = '/')
45
46 # Add token
47 if ( ! is.na(.self$.token))
48 params <- c(params, token = .self$.token)
49 param.str <- if (is.null(params)) '' else paste('?', vapply(names(params), function(p) paste(p, params[[p]], sep = '='), FUN.VALUE = ''), collapse = '&', sep = '')
50
51 # Get URL
38 content <- .self$.url.scheduler$getUrl(url = url, params = params) 52 content <- .self$.url.scheduler$getUrl(url = url, params = params)
39 53
40 if (ret.type == 'json') { 54 if (ret.type == 'json') {
41 55
42 library(RJSONIO) 56 library(RJSONIO)
65 # GET MOLECULE IDS # 79 # GET MOLECULE IDS #
66 #################### 80 ####################
67 81
68 MsPeakForestDb$methods( getMoleculeIds = function() { 82 MsPeakForestDb$methods( getMoleculeIds = function() {
69 83
70 ids <- as.character(.self$.get.url(url = paste0(.self$.url, 'compounds/all/ids'))) 84 ids <- as.character(.self$.get.url(url = 'compounds/all/ids'))
71 85
72 return(ids) 86 return(ids)
73 }) 87 })
74 88
75 #################### 89 ####################
76 # GET NB MOLECULES # 90 # GET NB MOLECULES #
77 #################### 91 ####################
78 92
79 MsPeakForestDb$methods( getNbMolecules = function() { 93 MsPeakForestDb$methods( getNbMolecules = function() {
80 94
81 n <- .self$.get.url(url = paste0(.self$.url, 'compounds/all/count'), ret.type = 'integer') 95 n <- .self$.get.url(url = 'compounds/all/count', ret.type = 'integer')
82 96
83 return(n) 97 return(n)
84 }) 98 })
85 99
86 ############################### 100 ###############################
88 ############################### 102 ###############################
89 103
90 MsPeakForestDb$methods( getChromCol = function(molid = NULL) { 104 MsPeakForestDb$methods( getChromCol = function(molid = NULL) {
91 105
92 # Set URL 106 # Set URL
93 url <- paste0(.self$.url, 'metadata/lc/list-code-columns')
94 params <- NULL 107 params <- NULL
95 if ( ! is.null(molid)) 108 if ( ! is.null(molid))
96 params <- list(molids = paste(molid, collapse = ',')) 109 params <- list(molids = paste(molid, collapse = ','))
97 110
98 # Call webservice 111 # Call webservice
99 wscols <- .self$.get.url(url = url, params = params) 112 wscols <- .self$.get.url(url = 'metadata/lc/list-code-columns', params = params)
100 113
101 # Build data frame 114 # Build data frame
102 cols <- data.frame(id = character(), title = character()) 115 cols <- data.frame(id = character(), title = character())
103 for(id in names(wscols)) 116 for(id in names(wscols))
104 cols <- rbind(cols, data.frame(id = id, title = wscols[[id]]$name, stringsAsFactors = FALSE)) 117 cols <- rbind(cols, data.frame(id = id, title = wscols[[id]]$name, stringsAsFactors = FALSE))
116 stop("The parameter molid must consist only in a single value.") 129 stop("The parameter molid must consist only in a single value.")
117 130
118 rt <- list() 131 rt <- list()
119 132
120 # Set URL 133 # Set URL
121 url <- paste0(.self$.url, 'spectra/lcms/search')
122 params <- NULL 134 params <- NULL
123 if ( ! is.null(molid)) 135 if ( ! is.null(molid))
124 params <- list(molids = paste(molid, collapse = ',')) 136 params <- list(molids = paste(molid, collapse = ','))
125 137
126 # Call webservice 138 # Call webservice
127 spectra <- .self$.get.url(url = url, params = params) 139 spectra <- .self$.get.url(url = 'spectra/lcms/search', params = params)
128 if (class(spectra) == 'list' && length(spectra) > 0) { 140 if (class(spectra) == 'list' && length(spectra) > 0) {
129 for (s in spectra) 141 for (s in spectra)
130 if (is.na(col) || s$liquidChromatography$columnCode %in% col) { 142 if (is.na(col) || s$liquidChromatography$columnCode %in% col) {
131 ret.time <- (s$RTmin + s$RTmax) / 2 143 ret.time <- (s$RTmin + s$RTmax) / 2
132 c <- s$liquidChromatography$columnCode 144 c <- s$liquidChromatography$columnCode
158 # Get non NA values 170 # Get non NA values
159 non.na.molid <- molid[ ! is.na(molid)] 171 non.na.molid <- molid[ ! is.na(molid)]
160 172
161 if (length(non.na.molid) > 0) { 173 if (length(non.na.molid) > 0) {
162 # Set URL 174 # Set URL
163 url <- paste0(.self$.url, 'compounds/all/names')
164 params <- c(molids = paste(non.na.molid, collapse = ',')) 175 params <- c(molids = paste(non.na.molid, collapse = ','))
165 176
166 # Call webservice 177 # Call webservice
167 names[ ! is.na(molid)] <- .self$.get.url(url = url, params = params) 178 names[ ! is.na(molid)] <- .self$.get.url(url = 'compounds/all/names', params = params)
168 } 179 }
169 180
170 return(names) 181 return(names)
171 }) 182 })
172 183
185 196
186 if (is.na(n)) 197 if (is.na(n))
187 ids <- c(ids, NA_character_) 198 ids <- c(ids, NA_character_)
188 199
189 else { 200 else {
190 url <- paste0(.self$.url, 'search/compounds/name/', curlEscape(n)) 201 compounds <- .self$.get.url(url = paste0('search/compounds/name/', curlEscape(n)))$compoundNames
191 compounds <- .self$.get.url(url = url)$compoundNames
192 ids <- c(ids, list(vapply(compounds, function(c) as.character(c$compound$id), FUN.VALUE = ''))) 202 ids <- c(ids, list(vapply(compounds, function(c) as.character(c$compound$id), FUN.VALUE = '')))
193 } 203 }
194 } 204 }
195 205
196 return(ids) 206 return(ids)
201 ################# 211 #################
202 212
203 MsPeakForestDb$methods( getNbPeaks = function(molid = NA_integer_, type = NA_character_) { 213 MsPeakForestDb$methods( getNbPeaks = function(molid = NA_integer_, type = NA_character_) {
204 214
205 # Build URL 215 # Build URL
206 url <- paste0(.self$.url, 'spectra/lcms/count-peaks')
207 params <- NULL 216 params <- NULL
208 if ( ! is.na(type)) 217 if ( ! is.na(type))
209 params <- c(params, mode = if (type == MSDB.TAG.POS) 'pos' else 'neg') 218 params <- c(params, mode = if (type == MSDB.TAG.POS) 'pos' else 'neg')
210 if ( ! is.null(molid) && (length(molid) > 1 || ! is.na(molid))) 219 if ( ! is.null(molid) && (length(molid) > 1 || ! is.na(molid)))
211 params <- c(params, molids = paste(molid, collapse = ',')) 220 params <- c(params, molids = paste(molid, collapse = ','))
212 221
213 # Run request 222 # Run request
214 n <- .self$.get.url(url = url, params = params, ret.type = 'integer') 223 n <- .self$.get.url(url = 'spectra/lcms/count-peaks', params = params, ret.type = 'integer')
215 224
216 return(sum(n)) 225 return(sum(n))
217 }) 226 })
218 227
219 ################# 228 #################
220 # GET MZ VALUES # 229 # GET MZ VALUES #
221 ################# 230 #################
222 231
223 MsPeakForestDb$methods( getMzValues = function(mode = NULL) { 232 MsPeakForestDb$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
224
225 # Build URL
226 url <- paste0(.self$.url, 'spectra/lcms/peaks/list-mz')
227 233
228 # Query params 234 # Query params
229 params <- NULL 235 params <- NULL
230 if ( ! is.null(mode)) 236 if ( ! is.null(mode))
231 params <- c(params, mode = if (mode == MSDB.TAG.POS) 'positive' else 'negative') 237 params <- c(params, mode = if (mode == MSDB.TAG.POS) 'positive' else 'negative')
232 238
233 # Get MZ valuels 239 # Get MZ valuels
234 mz <- .self$.get.url(url = url, params = params) 240 mz <- .self$.get.url(url = 'spectra/lcms/peaks/list-mz', params = params)
241
242 # Apply cut-off
243 if ( ! is.na(max.results))
244 mz <- mz[1:max.results]
235 245
236 return(mz) 246 return(mz)
237 }) 247 })
238 248
239 ############################## 249 ##############################
241 ############################## 251 ##############################
242 252
243 MsPeakForestDb$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) { 253 MsPeakForestDb$methods( .do.search.for.mz.rt.bounds = function(mode, mz.low, mz.high, rt.low = NULL, rt.high = NULL, col = NULL, attribs = NULL, molids = NULL) {
244 254
245 # Build URL for mz search 255 # Build URL for mz search
246 url <- paste0(.self$.url, 'spectra/lcms/peaks/get-range/', mz.low, '/', mz.high) 256 url <- paste0('spectra/lcms/peaks/get-range/', mz.low, '/', mz.high)
247 257
248 # Get spectra 258 # Get spectra
249 spectra <- .self$.get.url(url = url) 259 spectra <- .self$.get.url(url = url)
250 260
251 # Build result data frame 261 # Build result data frame
263 273
264 rt.res <- data.frame(MSDB.TAG.MOLID = character(), MSDB.TAG.COL = character(), MSDB.TAG.COLRT = numeric()) 274 rt.res <- data.frame(MSDB.TAG.MOLID = character(), MSDB.TAG.COL = character(), MSDB.TAG.COLRT = numeric())
265 275
266 if (nrow(results) > 0) { 276 if (nrow(results) > 0) {
267 # Build URL for rt search 277 # Build URL for rt search
268 url <- paste0(.self$.url, 'spectra/lcms/range-rt-min/', rt.low, '/', rt.high) 278 url <- paste0('spectra/lcms/range-rt-min/', rt.low, '/', rt.high)
269 params <- NULL 279 params <- NULL
270 if ( ! is.null(col)) 280 if ( ! is.null(col))
271 params <- c(columns = paste(col, collapse = ',')) 281 params <- c(columns = paste(col, collapse = ','))
272 282
273 # Run query 283 # Run query