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annotate MsPeakForestDb.R @ 3:abfba8eb1c8d draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c
author prog
date Tue, 14 Mar 2017 12:35:23 -0400
parents 9a0288561ba3
children 1ba222315fd5
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1 if ( ! exists('MsPeakForestDb')) { # Do not load again if already loaded
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3 library(methods)
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4 source('MsDb.R')
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5 source(file.path('UrlRequestScheduler.R'))
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7 #####################
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8 # CLASS DECLARATION #
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9 #####################
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11 MsPeakForestDb <- setRefClass("MsPeakForestDb", contains = "MsDb", fields = list(.url = "character", .url.scheduler = "ANY", .token = "character"))
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13 ###############
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14 # CONSTRUCTOR #
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15 ###############
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17 MsPeakForestDb$methods( initialize = function(url = NA_character_, useragent = NA_character_, token = NA_character_, ...) {
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19 # Check URL
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20 if (is.null(url) || is.na(url))
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21 stop("No URL defined for new MsPeakForestDb instance.")
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23 if (substring(url, nchar(url) - 1, 1) == '/')
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24 url <- substring(url, nchar(url) - 1)
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25 .url <<- url
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26 .url.scheduler <<- UrlRequestScheduler$new(n = 3, useragent = useragent)
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27 .self$.url.scheduler$setVerbose(1L)
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28 .token <<- token
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30 callSuper(...)
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31 })
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33 ###########
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34 # GET URL #
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35 ###########
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37 MsPeakForestDb$methods( .get.url = function(url, params = NULL, ret.type = 'json') {
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39 res <- NULL
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41 # Add url prefix
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42 if (substring(url, 1, 1) == '/')
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43 url <- substring(url, 2)
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44 url <- paste(.self$.url, url, sep = '/')
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46 # Add token
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47 if ( ! is.na(.self$.token))
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48 params <- c(params, token = .self$.token)
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49 param.str <- if (is.null(params)) '' else paste('?', vapply(names(params), function(p) paste(p, params[[p]], sep = '='), FUN.VALUE = ''), collapse = '&', sep = '')
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50
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51 # Get URL
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52 content <- .self$.url.scheduler$getUrl(url = url, params = params)
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53
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54 if (ret.type == 'json') {
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55
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56 library(RJSONIO)
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57
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58 res <- fromJSON(content, nullValue = NA)
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59
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60 if (class(res) == 'list' && 'success' %in% names(res) && res$success == FALSE) {
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61 param.str <- if (is.null(params)) '' else paste('?', vapply(names(params), function(p) paste(p, params[[p]], sep = '='), FUN.VALUE = ''), collapse = '&', sep = '')
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62 stop(paste0("Failed to run web service. URL was \"", url, param.str, "\"."))
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63 }
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64 } else {
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65 if (ret.type == 'integer') {
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66 if (grepl('^[0-9]+$', content, perl = TRUE))
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67 res <- as.integer(content)
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68 else {
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69 library(RJSONIO)
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70 res <- fromJSON(content, nullValue = NA)
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71 }
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72 }
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73 }
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75 return(res)
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76 })
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78 ####################
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79 # GET MOLECULE IDS #
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80 ####################
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82 MsPeakForestDb$methods( getMoleculeIds = function() {
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83
1
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84 ids <- as.character(.self$.get.url(url = 'compounds/all/ids'))
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86 return(ids)
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87 })
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88
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89 ####################
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90 # GET NB MOLECULES #
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91 ####################
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92
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93 MsPeakForestDb$methods( getNbMolecules = function() {
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94
1
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95 n <- .self$.get.url(url = 'compounds/all/count', ret.type = 'integer')
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96
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97 return(n)
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98 })
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99
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100 ###############################
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101 # GET CHROMATOGRAPHIC COLUMNS #
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102 ###############################
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103
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104 MsPeakForestDb$methods( getChromCol = function(molid = NULL) {
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105
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106 # Set URL
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107 params <- NULL
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108 if ( ! is.null(molid))
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109 params <- list(molids = paste(molid, collapse = ','))
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110
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111 # Call webservice
1
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112 wscols <- .self$.get.url(url = 'metadata/lc/list-code-columns', params = params)
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113
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114 # Build data frame
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115 cols <- data.frame(id = character(), title = character())
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116 for(id in names(wscols))
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117 cols <- rbind(cols, data.frame(id = id, title = wscols[[id]]$name, stringsAsFactors = FALSE))
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118
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119 return(cols)
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120 })
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121
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122 #######################
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123 # GET RETENTION TIMES #
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124 #######################
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125
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126 MsPeakForestDb$methods( getRetentionTimes = function(molid, col = NA_character_) {
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127
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128 if (is.null(molid) || is.na(molid) || length(molid) != 1)
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129 stop("The parameter molid must consist only in a single value.")
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130
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131 rt <- list()
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132
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133 # Set URL
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134 params <- NULL
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135 if ( ! is.null(molid))
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136 params <- list(molids = paste(molid, collapse = ','))
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137
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138 # Call webservice
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139 spectra <- .self$.get.url(url = 'spectra/lcms/search', params = params)
0
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140 if (class(spectra) == 'list' && length(spectra) > 0) {
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141 for (s in spectra)
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142 if (is.na(col) || s$liquidChromatography$columnCode %in% col) {
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143 ret.time <- (s$RTmin + s$RTmax) / 2
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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144 c <- s$liquidChromatography$columnCode
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145 if (c %in% names(rt)) {
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146 if ( ! ret.time %in% rt[[c]])
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147 rt[[c]] <- c(rt[[c]], ret.time)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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148 } else
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149 rt[[c]] <- ret.time
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150 }
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151 }
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152
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153 return(rt)
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154 })
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155
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156 #####################
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157 # GET MOLECULE NAME #
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158 #####################
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159
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160 MsPeakForestDb$methods( getMoleculeName = function(molid) {
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161
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162 library(RJSONIO)
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163
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164 if (is.null(molid))
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165 return(NA_character_)
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166
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167 # Initialize names
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168 names <- as.character(molid)
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169
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170 # Get non NA values
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171 non.na.molid <- molid[ ! is.na(molid)]
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172
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173 if (length(non.na.molid) > 0) {
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174 # Set URL
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175 params <- c(molids = paste(non.na.molid, collapse = ','))
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176
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177 # Call webservice
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178 names[ ! is.na(molid)] <- .self$.get.url(url = 'compounds/all/names', params = params)
0
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179 }
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180
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181 return(names)
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182 })
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183
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184 ################
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185 # FIND BY NAME #
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186 ################
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187
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188 MsPeakForestDb$methods( findByName = function(name) {
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189
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190 if (is.null(name))
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191 return(NA_character_)
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192
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193 ids <- list()
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194
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195 for (n in name) {
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196
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197 if (is.na(n))
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198 ids <- c(ids, NA_character_)
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199
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200 else {
1
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201 compounds <- .self$.get.url(url = paste0('search/compounds/name/', curlEscape(n)))$compoundNames
0
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202 ids <- c(ids, list(vapply(compounds, function(c) as.character(c$compound$id), FUN.VALUE = '')))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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203 }
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204 }
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205
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206 return(ids)
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207 })
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208
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209 #################
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210 # GET NB PEAKS #
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211 #################
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212
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213 MsPeakForestDb$methods( getNbPeaks = function(molid = NA_integer_, type = NA_character_) {
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214
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215 # Build URL
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216 params <- NULL
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217 if ( ! is.na(type))
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218 params <- c(params, mode = if (type == MSDB.TAG.POS) 'pos' else 'neg')
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219 if ( ! is.null(molid) && (length(molid) > 1 || ! is.na(molid)))
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220 params <- c(params, molids = paste(molid, collapse = ','))
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221
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222 # Run request
1
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223 n <- .self$.get.url(url = 'spectra/lcms/count-peaks', params = params, ret.type = 'integer')
0
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224
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225 return(sum(n))
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226 })
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227
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228 #################
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229 # GET MZ VALUES #
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230 #################
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231
1
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232 MsPeakForestDb$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
0
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233
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234 # Query params
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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235 params <- NULL
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236 if ( ! is.null(mode))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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237 params <- c(params, mode = if (mode == MSDB.TAG.POS) 'positive' else 'negative')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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238
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239 # Get MZ valuels
1
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240 mz <- .self$.get.url(url = 'spectra/lcms/peaks/list-mz', params = params)
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241
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242 # Apply cut-off
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243 if ( ! is.na(max.results))
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244 mz <- mz[1:max.results]
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245
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246 return(mz)
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247 })
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248
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249 ##############################
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250 # DO SEARCH FOR MZ RT BOUNDS #
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251 ##############################
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252
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253 MsPeakForestDb$methods( .do.search.for.mz.rt.bounds = function(mode, mz.low, mz.high, rt.low = NULL, rt.high = NULL, col = NULL, attribs = NULL, molids = NULL) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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254
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255 # Build URL for mz search
1
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256 url <- paste0('spectra/lcms/peaks/get-range/', mz.low, '/', mz.high)
0
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257
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258 # Get spectra
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259 spectra <- .self$.get.url(url = url)
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260
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261 # Build result data frame
3
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262 results <- data.frame(MSDB.TAG.MOLID = character(), MSDB.TAG.MOLNAMES = character(), MSDB.TAG.MOLMASS = numeric(), MSDB.TAG.MZTHEO = numeric(), MSDB.TAG.COMP = character(), MSDB.TAG.ATTR = character(), MSDB.TAG.INCHI = character(), MSDB.TAG.INCHIKEY = character(), MSDB.TAG.CHEBI = character(), MSDB.TAG.HMDB = character(), MSDB.TAG.KEGG = character(), MSDB.TAG.PUBCHEM = character())
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9a0288561ba3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 476a081c0da66822f4e77070f5ce59d9f14511f4-dirty
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263 for (x in spectra) {
9a0288561ba3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 476a081c0da66822f4e77070f5ce59d9f14511f4-dirty
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264 if ('source' %in% names(x) && is.list(x$source))
3
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265 mztheo <- if ('theoricalMass' %in% names(x)) as.numeric(x$theoricalMass) else NA_real_
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266 comp <- if ('composition' %in% names(x)) x$composition else NA_character_
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267 attr <- if ('attribution' %in% names(x)) x$attribution else NA_character_
abfba8eb1c8d planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c
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268 if ('listOfCompounds' %in% names(x$source)) {
abfba8eb1c8d planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c
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269 molids <- vapply(x$source$listOfCompounds, function(c) as.character(c$id), FUN.VALUE = '')
abfba8eb1c8d planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c
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270 molnames <- vapply(x$source$listOfCompounds, function(c) paste(c$names, collapse = MSDB.MULTIVAL.FIELD.SEP), FUN.VALUE = '')
abfba8eb1c8d planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c
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271 mass <- vapply(x$source$listOfCompounds, function(c) as.character(c$averageMass), FUN.VALUE = '')
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272 inchi <- vapply(x$source$listOfCompounds, function(c) as.character(c$inChI), FUN.VALUE = '')
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273 inchikey <- vapply(x$source$listOfCompounds, function(c) as.character(c$inChIKey), FUN.VALUE = '')
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274 chebi <- vapply(x$source$listOfCompounds, function(c) as.character(c$ChEBI), FUN.VALUE = '')
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275 chebi[chebi == 'CHEBI:null'] <- NA_character_
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276 hmdb <- vapply(x$source$listOfCompounds, function(c) as.character(c$HMDB), FUN.VALUE = '')
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277 hmdb[hmdb == 'HMDBnull'] <- NA_character_
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278 kegg <- vapply(x$source$listOfCompounds, function(c) as.character(c$KEGG), FUN.VALUE = '')
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279 pubchem <- vapply(x$source$listOfCompounds, function(c) as.character(c$PubChemCID), FUN.VALUE = '')
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280 if (length(molids) > 0 && length(molids) == length(molnames))
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281 results <- rbind(results, data.frame(MSDB.TAG.MOLID = molids, MSDB.TAG.MOLNAMES = molnames, MSDB.TAG.MOLMASS = mass, MSDB.TAG.MZTHEO = mztheo, MSDB.TAG.COMP = comp, MSDB.TAG.ATTR = attr, MSDB.TAG.INCHI = inchi, MSDB.TAG.INCHIKEY = inchikey, MSDB.TAG.CHEBI = chebi, MSDB.TAG.HMDB = hmdb, MSDB.TAG.KEGG = kegg, MSDB.TAG.PUBCHEM = pubchem, stringsAsFactors = FALSE))
abfba8eb1c8d planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c
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282 }
2
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283 }
0
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284
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285 # RT search
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286 if ( ! is.null(rt.low) && ! is.null(rt.high)) {
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287
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288 rt.res <- data.frame(MSDB.TAG.MOLID = character(), MSDB.TAG.COL = character(), MSDB.TAG.COLRT = numeric())
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290 if (nrow(results) > 0) {
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291 # Build URL for rt search
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292 url <- paste0('spectra/lcms/range-rt-min/', rt.low, '/', rt.high)
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293 params <- NULL
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294 if ( ! is.null(col))
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295 params <- c(columns = paste(col, collapse = ','))
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297 # Run query
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298 rtspectra <- .self$.get.url(url = url, params = params)
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299
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300 # Get compound/molecule IDs
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301 for (x in spectra)
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302 rt.res <- rbind(rt.res, data.frame(MSDB.TAG.MOLID = vapply(x$listOfCompounds, function(c) as.character(c$id), FUN.VALUE = ''),
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303 MSDB.TAG.COL = as.character(x$liquidChromatography$columnCode),
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304 MSDB.TAG.COLRT = (as.numeric(x$RTmin) + as.numeric(x$RTmax)) / 2,
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305 stringsAsFactors = FALSE))
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306 }
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307
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308 # Add retention times and column info
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309 results <- merge(results, rt.res)
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310 }
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311
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312 # Rename columns with proper names
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313 colnames(results) <- vapply(colnames(results), function(s) eval(parse(text=s)), FUN.VALUE = '')
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314
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315 return(results)
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316 })
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317 }