Mercurial > repos > prog > lcmsmatching

annotate BiodbEntry.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 45e985cd8e9e
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1 #############
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2 # CONSTANTS #
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3 #############
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5 BIODB.BASIC.CLASSES <- c('character', 'integer', 'double', 'logical')
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7 ########################
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8 # ENTRY ABSTRACT CLASS #
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9 ########################
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11 BiodbEntry <- methods::setRefClass("BiodbEntry", fields = list(.fields ='list', .factory = "ANY"))
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13 ###############
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14 # CONSTRUCTOR #
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15 ###############
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17 BiodbEntry$methods( initialize = function(...) {
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19 .fields <<- list()
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20 .factory <<- NULL
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22 callSuper(...) # calls super-class initializer with remaining parameters
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23 })
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25 ###################
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26 # SET FIELD VALUE #
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27 ###################
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29 BiodbEntry$methods( setFieldValue = function(field, value) {
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31 class = .self$getFieldClass(field)
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33 # Secific case to handle objects.
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34 if ( class ==" object" & !(isS4(value) & methods::is(value, "refClass")))
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35 stop(paste0('Cannot set a non RC instance to field "', field, '" in BiodEntry.'))
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1
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37 # Check cardinality
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38 if (class != 'data.frame' && .self$getFieldCardinality(field) == BIODB.CARD.ONE && length(value) > 1)
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39 stop(paste0('Cannot set more that one value to single value field "', field, '" in BiodEntry.'))
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1
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41 # Check value class
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42 value <- switch(class,
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43 'character' = as.character(value),
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44 'double' = as.double(value),
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45 'integer' = as.integer(value),
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46 'logical' = as.logical(value),
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47 value)
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48 # TODO check value class
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50 .self$.fields[[field]] <- value
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51 })
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53 ###################
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54 # GET FIELD NAMES #
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55 ###################
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57 BiodbEntry$methods( getFieldNames = function(field) {
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58 return(names(.self$.fields))
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59 })
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61 #############
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62 # HAS FIELD #
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63 #############
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65 BiodbEntry$methods( hasField = function(field) {
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66 return(field %in% names(.self$.fields))
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67 })
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69 ###################
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70 # GET FIELD CLASS #
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71 ###################
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73 BiodbEntry$methods( getFieldClass = function(field) {
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75 if ( ! field %in% BIODB.FIELDS[['name']])
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76 stop(paste0('Unknown field "', field, '" in BiodEntry.'))
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78 field.class <- BIODB.FIELDS[which(field == BIODB.FIELDS[['name']]), 'class']
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80 return(field.class)
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81 })
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83 #########################
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84 # FIELD HAS BASIC CLASS #
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85 #########################
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87 BiodbEntry$methods( fieldHasBasicClass = function(field) {
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88 return(.self$getFieldClass(field) %in% BIODB.BASIC.CLASSES)
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89 })
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90
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91 #########################
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92 # GET FIELD CARDINALITY #
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93 #########################
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94
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95 BiodbEntry$methods( getFieldCardinality = function(field) {
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96
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97 if ( ! field %in% BIODB.FIELDS[['name']])
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98 stop(paste0('Unknown field "', field, '" in BiodEntry.'))
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99
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100 field.card <- BIODB.FIELDS[which(field == BIODB.FIELDS[['name']]), 'cardinality']
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101
1
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102 return(field.card)
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103 })
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104
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105 ###################
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106 # GET FIELD VALUE #
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107 ###################
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108
1
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109 BiodbEntry$methods( getFieldValue = function(field, compute = TRUE) {
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110
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111 if ( ! field %in% BIODB.FIELDS[['name']])
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112 stop(paste0('Unknown field "', field, '" in BiodEntry.'))
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113
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114 if (field %in% names(.self$.fields))
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115 return(.self$.fields[[field]])
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116 else if (compute && .self$.compute.field(field))
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117 return(.self$.fields[[field]])
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118
1
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119 # Return NULL or NA
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120 class = .self$getFieldClass(field)
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121 return(if (class %in% BIODB.BASIC.CLASSES) as.vector(NA, mode = class) else NULL)
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122 })
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123
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124 #################
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125 # COMPUTE FIELD #
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126 ##################
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127
1
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128 BiodbEntry$methods( .compute.field = function(field) {
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129
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130 if ( ! is.null(.self$.factory) && field %in% names(BIODB.FIELD.COMPUTING)) {
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131 for (db in BIODB.FIELD.COMPUTING[[field]]) {
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132 db.id <- .self$getField(paste0(db, 'id'))
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133 if ( ! is.na(db.id)) {
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134 db.entry <- .self$.factory$createEntry(db, id = db.id)
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135 if ( ! is.null(db.entry)) {
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136 .self$setField(field, db.entry$getField(field))
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137 return(TRUE)
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138 }
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139 }
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140 }
1
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141 }
0
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142
1
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143 return(FALSE)
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144 })
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145
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146 ############################
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147 # GET FIELDS AS DATA FRAME #
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148 ############################
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149 ###TODO add a limiting option to get some fields.
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150 BiodbEntry$methods( getFieldsAsDataFrame = function() {
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151 df <- data.frame()
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152 # Loop on all fields
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153 for (f in names(.self$.fields))
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154
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155 # If field class is a basic type
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156 if (.self$getFieldClass(f) %in% c('character', 'logical', 'integer', 'double') &
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157 length(.self$getFieldValue(f)) == 1)
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158 df[1, f] <- .self$getFieldValue(f)
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159
1
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160 return(df)
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161 })
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162
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163 ###########
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164 # FACTORY #
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165 ###########
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166
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167 BiodbEntry$methods( setFactory = function(factory) {
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168 is.null(factory) || inherits(factory, "BiodbFactory") || stop("The factory instance must inherit from BiodbFactory class.")
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169 .factory <<- factory
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170 })
0
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171
1
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172 ##############
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173 # DEPRECATED #
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174 ##############
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175
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176 BiodbEntry$methods( getField = function(field) {
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177 return(.self$getFieldValue(field))
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178 })
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179
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180 BiodbEntry$methods( setField = function(field, value) {
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181 .self$setFieldValue(field, value)
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182 })