Mercurial > repos > prog > lcmsmatching

annotate BiodbFactory.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
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1 # vi: fdm=marker
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3 ##########################
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4 # CLASS DECLARATION {{{1 #
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5 ##########################
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7 BiodbFactory <- methods::setRefClass("BiodbFactory", contains = 'BiodbObject', fields = list(.useragent = "character",
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8 .conn = "list",
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9 .cache.dir = "character",
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10 .cache.mode = "character",
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11 .debug = "logical",
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12 .chunk.size = "integer",
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13 .use.env.var = "logical"))
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15 ###############
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16 # CONSTRUCTOR #
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17 ###############
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19 BiodbFactory$methods( initialize = function(useragent = NA_character_, cache.dir = NA_character_, cache.mode = BIODB.CACHE.READ.WRITE, debug = FALSE, chunk.size = NA_integer_, use.env.var = FALSE, ...) {
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21 .useragent <<- useragent
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22 .conn <<- list()
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23 .cache.dir <<- cache.dir
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24 .cache.mode <<- cache.mode
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25 .debug <<- debug
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26 .chunk.size <<- as.integer(chunk.size)
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27 .use.env.var <<- use.env.var
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29 callSuper(...) # calls super-class initializer with remaining parameters
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30 })
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32 #######################
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33 # PRINT DEBUG MESSAGE #
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34 #######################
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36 BiodbFactory$methods( .print.debug.msg = function(msg) {
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37 if (.self$.debug)
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38 .print.msg(msg = msg, class = class(.self))
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39 })
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41 ##################
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42 # GET USER AGENT #
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43 ##################
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44
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45 BiodbFactory$methods( getUserAgent = function() {
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46 return(.self$.useragent)
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47 })
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49 ##################
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50 # SET USER AGENT #
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51 ##################
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52
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53 BiodbFactory$methods( setUserAgent = function(useragent) {
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54 "Set useragent of BiodbFactory."
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55 .useragent <<- useragent
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56 })
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57
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58 ###############
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59 # CREATE CONN #
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60 ###############
0
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61
1
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62 BiodbFactory$methods( createConn = function(class, url = NA_character_, token = NA_character_) {
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63 " Create connection to databases useful for metabolomics."
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64 if (class %in% names(.self$.conn))
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65 stop(paste0('A connection of type ', class, ' already exists. Please use method getConn() to access it.'))
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66
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67 # Use environment variables
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68 if (.self$.use.env.var) {
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69 if (is.na(url))
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70 url <- .biodb.get.env.var(c(class, 'URL'))
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71 if (is.na(token))
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72 token <- .biodb.get.env.var(c(class, 'TOKEN'))
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73 }
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74
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75 # Create connection instance
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76 conn <- switch(class,
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77 chebi = ChebiConn$new(useragent = .self$.useragent, debug = .self$.debug),
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78 kegg = KeggConn$new(useragent = .self$.useragent, debug = .self$.debug),
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79 pubchemcomp = PubchemConn$new(useragent = .self$.useragent, db = BIODB.PUBCHEMCOMP, debug = .self$.debug),
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80 pubchemsub = PubchemConn$new(useragent = .self$.useragent, db = BIODB.PUBCHEMSUB, debug = .self$.debug),
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81 hmdb = HmdbConn$new(useragent = .self$.useragent, debug = .self$.debug),
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82 chemspider = ChemspiderConn$new(useragent = .self$.useragent, debug = .self$.debug, token = token),
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83 enzyme = EnzymeConn$new(useragent = .self$.useragent, debug = .self$.debug),
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84 lipidmaps = LipidmapsConn$new(useragent = .self$.useragent, debug = .self$.debug),
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85 mirbase = MirbaseConn$new(useragent = .self$.useragent, debug = .self$.debug),
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86 ncbigene = NcbigeneConn$new(useragent = .self$.useragent, debug = .self$.debug),
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87 ncbiccds = NcbiccdsConn$new(useragent = .self$.useragent, debug = .self$.debug),
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88 uniprot = UniprotConn$new(useragent = .self$.useragent, debug = .self$.debug),
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89 massbank = MassbankConn$new(useragent = .self$.useragent, url = url, debug = .self$.debug),
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90 massfiledb = MassFiledbConn$new(file = url, debug = .self$.debug),
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91 peakforest = PeakforestConn$new(useragent = .self$.useragent, debug = .self$.debug),
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92 NULL)
0
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93
1
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94 # Unknown class
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95 if (is.null(conn))
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96 stop(paste0("Unknown r-biodb class \"", class,"\"."))
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97
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98 # Register new class
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99 .self$.conn[[class]] <- conn
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100
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101 return (.self$.conn[[class]])
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102 })
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103
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104 ############
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105 # GET CONN #
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106 ############
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107
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108 BiodbFactory$methods( getConn = function(class) {
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109 "Get connection to a database."
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110
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111 if ( ! class %in% names(.self$.conn))
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112 .self$createConn(class)
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113
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114 return (.self$.conn[[class]])
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115 })
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116
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117 ################
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118 # CREATE ENTRY #
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119 ################
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120
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121 BiodbFactory$methods( createEntry = function(class, id = NULL, content = NULL, drop = TRUE) {
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122 "Create Entry from a database by id."
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123
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124 is.null(id) && is.null(content) && stop("One of id or content must be set.")
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125 ! is.null(id) && ! is.null(content) && stop("id and content cannot be both set.")
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126
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127 # Debug
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128 .self$.print.debug.msg(paste0("Creating ", if (is.null(id)) length(content) else length(id), " entries from ", if (is.null(id)) "contents" else paste("ids", paste(if (length(id) > 10) id[1:10] else id, collapse = ", ")), "..."))
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129
1
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130 # Get content
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131 if ( ! is.null(id))
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132 content <- .self$getEntryContent(class, id)
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133 conn <- .self$getConn(class)
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134 entry <- conn$createEntry(content = content, drop = drop)
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135
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136 # Set factory
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137 .self$.print.debug.msg(paste0("Setting factory reference into entries..."))
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138 for (e in c(entry))
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139 if ( ! is.null(e))
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140 e$setFactory(.self)
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141
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142 return(entry)
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143 })
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144
1
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145 ########################
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146 # GET CACHE FILE PATHS #
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147 ########################
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148
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149 BiodbFactory$methods( .get.cache.file.paths = function(class, id) {
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150
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151 # Get extension
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152 ext <- .self$getConn(class)$getEntryContentType()
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153
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154 # Set filenames
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155 filenames <- vapply(id, function(x) { if (is.na(x)) NA_character_ else paste0(class, '-', x, '.', ext) }, FUN.VALUE = '')
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156
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157 # set file paths
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158 file.paths <- vapply(filenames, function(x) { if (is.na(x)) NA_character_ else file.path(.self$.cache.dir, x) }, FUN.VALUE = '')
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159
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160 # Create cache dir if needed
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161 if ( ! is.na(.self$.cache.dir) && ! file.exists(.self$.cache.dir))
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162 dir.create(.self$.cache.dir)
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163
1
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164 return(file.paths)
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165 })
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166
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167 ###########################
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168 # LOAD CONTENT FROM CACHE #
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169 ###########################
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170
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171 BiodbFactory$methods( .load.content.from.cache = function(class, id) {
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172
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173 content <- NULL
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174
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175 # Read contents from files
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176 file.paths <- .self$.get.cache.file.paths(class, id)
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177 content <- lapply(file.paths, function(x) { if (is.na(x)) NA_character_ else ( if (file.exists(x)) paste(readLines(x), collapse = "\n") else NULL )} )
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178
1
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179 return(content)
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180 })
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181
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182 ############################
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183 # IS CACHE READING ENABLED #
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184 ############################
0
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185
1
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186 BiodbFactory$methods( .is.cache.reading.enabled = function() {
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187 return( ! is.na(.self$.cache.dir) && .self$.cache.mode %in% c(BIODB.CACHE.READ.ONLY, BIODB.CACHE.READ.WRITE))
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188 })
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189
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190 ############################
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191 # IS CACHE WRITING ENABLED #
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192 ############################
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193
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194 BiodbFactory$methods( .is.cache.writing.enabled = function() {
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195 return( ! is.na(.self$.cache.dir) && .self$.cache.mode %in% c(BIODB.CACHE.WRITE.ONLY, BIODB.CACHE.READ.WRITE))
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196 })
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197
1
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198 #########################
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199 # SAVE CONTENT TO CACHE #
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200 #########################
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201
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202 BiodbFactory$methods( .save.content.to.cache = function(class, id, content) {
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203
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204 # Write contents into files
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205 file.paths <- .self$.get.cache.file.paths(class, id)
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206 mapply(function(c, f) { if ( ! is.null(c)) writeLines(c, f) }, content, file.paths)
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207 })
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208
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209 #####################
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210 # GET ENTRY CONTENT #
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211 #####################
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212
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213 BiodbFactory$methods( getEntryContent = function(class, id) {
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214
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215 # Debug
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216 .self$.print.debug.msg(paste0("Get entry content(s) for ", length(id)," id(s)..."))
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217
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218 # Initialize content
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219 if (.self$.is.cache.reading.enabled()) {
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220 content <- .self$.load.content.from.cache(class, id)
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221 missing.ids <- id[vapply(content, is.null, FUN.VALUE = TRUE)]
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222 }
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223 else {
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224 content <- lapply(id, as.null)
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225 missing.ids <- id
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226 }
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227
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228 # Remove duplicates
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229 n.duplicates <- sum(duplicated(missing.ids))
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230 missing.ids <- missing.ids[ ! duplicated(missing.ids)]
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231
1
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232 # Debug
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233 if (any(is.na(id)))
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234 .self$.print.debug.msg(paste0(sum(is.na(id)), " entry ids are NA."))
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235 if (.self$.is.cache.reading.enabled()) {
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236 .self$.print.debug.msg(paste0(sum( ! is.na(id)) - length(missing.ids), " entry content(s) loaded from cache."))
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237 if (n.duplicates > 0)
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238 .self$.print.debug.msg(paste0(n.duplicates, " entry ids, whose content needs to be fetched, are duplicates."))
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239 .self$.print.debug.msg(paste0(length(missing.ids), " entry content(s) need to be fetched."))
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240 }
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241
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242 # Get contents
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243 if (length(missing.ids) > 0) {
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244
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245 # Use connector to get missing contents
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246 conn <- .self$getConn(class)
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247
1
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248 # Divide list of missing ids in chunks (in order to save in cache regularly)
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249 chunks.of.missing.ids = if (is.na(.self$.chunk.size)) list(missing.ids) else split(missing.ids, ceiling(seq_along(missing.ids) / .self$.chunk.size))
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250
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251 # Loop on chunks
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252 missing.contents <- NULL
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253 for (ch.missing.ids in chunks.of.missing.ids) {
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254
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255 ch.missing.contents <- conn$getEntryContent(ch.missing.ids)
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256
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257 # Save to cache
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258 if ( ! is.null(ch.missing.contents) && .self$.is.cache.writing.enabled())
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259 .self$.save.content.to.cache(class, ch.missing.ids, ch.missing.contents)
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260
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261 # Append
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262 missing.contents <- c(missing.contents, ch.missing.contents)
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263
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264 # Debug
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265 if (.self$.is.cache.reading.enabled())
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266 .self$.print.debug.msg(paste0("Now ", length(missing.ids) - length(missing.contents)," id(s) left to be retrieved..."))
0
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267 }
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268
1
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269 # Merge content and missing.contents
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270 content[id %in% missing.ids] <- vapply(id[id %in% missing.ids], function(x) missing.contents[missing.ids %in% x], FUN.VALUE = '')
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271 }
0
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272
1
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273 return(content)
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274 })