Mercurial > repos > prog > lcmsmatching

annotate BiodbEntry.R @ 0:3afe41d3e9e7 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
author prog
date Mon, 11 Jul 2016 09:12:03 -0400
parents
children 45e985cd8e9e
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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1 if ( ! exists('BiodbEntry')) { # Do not load again if already loaded
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3 source('biodb-common.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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5 ########################
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6 # ENTRY ABSTRACT CLASS #
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7 ########################
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9 BiodbEntry <- setRefClass("BiodbEntry", fields = list(.fields ='list', .factory = "ANY"))
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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11 ###############
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12 # CONSTRUCTOR #
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13 ###############
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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15 BiodbEntry$methods( initialize = function(...) {
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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17 .fields <<- list()
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18 .factory <<- NULL
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20 callSuper(...) # calls super-class initializer with remaining parameters
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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21 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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23 #############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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24 # SET FIELD #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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25 #############
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27 BiodbEntry$methods( setField = function(field, value) {
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29 class = .self$getFieldClass(field)
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31 # Check cardinality
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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32 if (class != 'data.frame' && .self$getFieldCardinality(field) == RBIODB.CARD.ONE && length(value) > 1)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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33 stop(paste0('Cannot set more that one value to single value field "', field, '" in BiodEntry.'))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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35 # Check value class
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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36 value <- switch(class,
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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37 'character' = as.character(value),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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38 'double' = as.double(value),
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39 'integer' = as.integer(value),
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40 'logical' = as.logical(value),
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41 value)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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42 # TODO check value class
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44 .self$.fields[[field]] <- value
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45 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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47 ###################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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48 # GET FIELD CLASS #
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49 ###################
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51 BiodbEntry$methods( getFieldClass = function(field) {
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53 if ( ! field %in% RBIODB.FIELDS[['name']])
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54 stop(paste0('Unknown field "', field, '" in BiodEntry.'))
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56 field.class <- RBIODB.FIELDS[which(field == RBIODB.FIELDS[['name']]), 'class']
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58 return(field.class)
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59 })
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61 #########################
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62 # GET FIELD CARDINALITY #
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63 #########################
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65 BiodbEntry$methods( getFieldCardinality = function(field) {
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66
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67 if ( ! field %in% RBIODB.FIELDS[['name']])
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68 stop(paste0('Unknown field "', field, '" in BiodEntry.'))
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70 field.card <- RBIODB.FIELDS[which(field == RBIODB.FIELDS[['name']]), 'cardinality']
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72 return(field.card)
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73 })
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75 #############
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76 # GET FIELD #
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77 #############
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79 BiodbEntry$methods( getField = function(field) {
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81 if ( ! field %in% RBIODB.FIELDS[['name']])
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82 stop(paste0('Unknown field "', field, '" in BiodEntry.'))
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83
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84 if (field %in% names(.self$.fields))
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85 return(.self$.fields[[field]])
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86 else if (.self$.compute.field(field))
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87 return(.self$.fields[[field]])
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88
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89 # Return NULL or NA
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90 class = .self$getFieldClass(field)
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91 return(if (class %in% c('character', 'integer', 'double', 'logical')) as.vector(NA, mode = class) else NULL)
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92 })
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93
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94 #################
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95 # COMPUTE FIELD #
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96 ##################
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97
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98 BiodbEntry$methods( .compute.field = function(field) {
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99
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100 if ( ! is.null(.self$.factory) && field %in% names(RBIODB.FIELD.COMPUTING)) {
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101 for (db in RBIODB.FIELD.COMPUTING[[field]]) {
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102 db.id <- .self$getField(paste0(db, 'id'))
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103 if ( ! is.na(db.id)) {
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104 db.compound <- .self$.factory$createEntry(db, type = RBIODB.COMPOUND, id = db.id)
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105 if ( ! is.null(db.compound)) {
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106 .self$setField(field, db.compound$getField(field))
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107 return(TRUE)
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108 }
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109 }
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110 }
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111 }
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112
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113 return(FALSE)
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114 })
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115
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116 ###########
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117 # FACTORY #
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118 ###########
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119
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120 BiodbEntry$methods( setFactory = function(factory) {
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121
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122 is.null(factory) || inherits(factory, "BiodbFactory") || stop("The factory instance must inherit from BiodbFactory class.")
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123 .factory <<- factory
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124 })
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125 }