Mercurial > repos > prog > lcmsmatching

annotate PeakforestConn.R @ 3:f61ce21ed17c draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 476a081c0da66822f4e77070f5ce59d9f14511f4-dirty
author prog
date Thu, 02 Mar 2017 11:07:56 -0500
parents 20d69a062da3
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20d69a062da3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
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1 #####################
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2 # CLASS DECLARATION #
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3 #####################
20d69a062da3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
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4 #'A class to connect to peakforest
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5 #'@export
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6 #'@field .url An urel to the database
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7 PeakforestConn <- methods::setRefClass("PeakforestConn", contains = c("RemotedbConn","MassdbConn"), fields = list( .url = "character" )) # TODO Inherits also from MassdbConn
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9 ##########################
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10 # GET ENTRY CONTENT TYPE #
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11 ##########################
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13 PeakforestConn$methods( getEntryContentType = function(type) {
20d69a062da3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
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14 return(BIODB.JSON)
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15 })
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17 #####################
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18 # GET ENTRY CONTENT #
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19 #####################
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21 PeakforestConn$methods( getEntryContent = function(id) {
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24 # Initialize return values
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25 content <- rep(NA_character_, length(id))
20d69a062da3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
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26 # Request
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28 url <- get.entry.url(BIODB.PEAKFOREST, id[i], BIODB.JSON,token = .self$.token)
20d69a062da3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
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29 jsonstr <- .self$.get.url(url)
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30 if(startsWith("<html>", jsonstr) ){
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31 next
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32 }
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34 return(content)
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35 })
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38 ##########################################
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39 # SEARCH FOR SPECTRA IN GIVEN MASS RANGE #
20d69a062da3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
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40 ##########################################
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42 PeakforestConn$methods( searchMzRange = function(mzmin, mzmax, rtype = c("object","spec","peak")){
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44 rtype <- match.arg(rtype)
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45 if(mzmin>mzmax){
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46 stop("mzmin shloud be inferior to mzmax in searchMzRange.")
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47 }
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49 url <- paste0("https://rest.peakforest.org/spectra/lcms/peaks/get-range/",mzmin,"/",mzmax)
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51 contents <- .self$.get.url(url)
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53 jsontree <- fromJSON(contents)
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55 ###No match form the output.
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56 if( length(jsontree)==0 ) return(NULL)
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58 # Getting a list of all the id.
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59 lid <- sapply(jsontree,function(x){
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60 x$source$id
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61 })
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62
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63 # Returning the content for all the spectra
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64 contents <- .self$getEntryContent(lid)
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66 entries <- .self$createEntry(contents)
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67
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68 # Checking the return type
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69 if( rtype=="object" ){
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70 return( entries )
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71 }
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72
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73 ### XXXX See if we don't want to reduce the output and factorize this shit.
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74 toreturn <- NULL
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75 if( rtype=="spec" ){
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76 toreturn <- sapply(entries,function(x){
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77 x$getFieldsAsDataFrame()
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78 })
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79 }
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80 if( rtype=="peak" ){
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81 toreturn <- lapply(entries,function(x){
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82 temp <- as.data.frame( x$getFieldValue( BIODB.PEAKS ))
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83 temp$accession = x$getFieldValue( BIODB.ACCESSION)
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84 return(temp)
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85
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86 })
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87 }
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88 ###Trying to convert in data.frame
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89 if(!is.data.frame(toreturn)){
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90 temp <- colnames(toreturn[[1]])
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91 toreturn <- do.call("rbind.fill",toreturn)
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92 colnames(toreturn) <- temp
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93 }
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94
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95 return(toreturn)
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96 })
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97
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98
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99 #################################################
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100 # SEARCH FOR SPECTRA IN A TOLERANCE AROUND A MZ #
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101 #################################################
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102
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103 PeakforestConn$methods( searchMzTol = function(mz, tol, tolunit=BIODB.MZTOLUNIT.VALS,
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104 rtype = c("object","spec","peak")){
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105
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106 rtype <- match.arg(rtype)
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107 tolunit <- match.arg(tolunit)
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108
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109 if( tolunit == BIODB.MZTOLUNIT.PPM){
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110 tol <- tol * mz * 10^-6
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111 }
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112
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113 mzmin <- mz - tol
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114 mzmax <- mz + tol
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115
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116 return(.self$searchMzRange(mzmin, mzmax, rtype = rtype))
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117
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118 })
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119
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120 ##################################################
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121 # SEARCH FOR MSMS SPECTRA PRECUSOR AROUND A MASS #
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122 ##################################################
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123
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124
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125 PeakforestConn$methods(
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126 searchSpecPrecTol = function(mz,
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127 tol,
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128 tolunit = "plain",
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129 mode = NULL) {
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130 #TODO handle the units
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131 #tolunit <- match.arg(tolunit)
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132
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133 strmode <- ''
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134
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135 if (!is.null(mode)) {
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136 if (mode %in% c(BIODB.MSMODE.NEG, BIODB.MSMODE.POS)) {
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137 strmode <- paste0('?polarity=', mode)
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138 }
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139
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140 }
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141
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142 if (tolunit == BIODB.MZTOLUNIT.PPM) {
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143 tol <- tol * mz * 10 ^ -6
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144 }
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145
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146 ##Request which return peak and not spectra.
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147 url <-
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148 paste0(
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149 "https://rest.peakforest.org/spectra/lcms/search-naive/",
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150 mz,
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151 "/",
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152 tol,
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153 strmode
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154 )
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155 contents <- .self$.get.url(url)
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156 entries <- .self$createReducedEntry(contents, drop = TRUE)
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157 return(entries)
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158 }
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159 )
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160
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161
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162 ################
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163 # CREATE ENTRY #
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164 ################
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165
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166 # Creates a Spectrum instance from file content.
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167 # content A file content, downloaded from the public database.
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168 # RETURN A spectrum instance.
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169 PeakforestConn$methods( createEntry = function(content, drop = TRUE) {
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170 return(createPeakforestSpectraFromJSON(content, drop = drop))
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171 })
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172
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173 PeakforestConn$methods( createReducedEntry = function(content , drop = TRUE){
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174 entries <- createReducedSpectraFromJSON(content, drop = drop)
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175 return(entries)
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176 })