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annotate BiodbFactory.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('BiodbFactory')) { # 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 library(methods)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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4 source('ChebiConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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5 source('KeggConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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6 source('PubchemConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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7 source('HmdbConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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8 source('ChemspiderConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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9 source('EnzymeConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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10 source('LipidmapsConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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11 source('MirbaseConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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12 source('NcbigeneConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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13 source('NcbiccdsConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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14 source('UniprotConn.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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15 source('MassbankConn.R')
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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17 #####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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18 # CLASS DECLARATION #
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19 #####################
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21 BiodbFactory <- setRefClass("BiodbFactory", fields = list(.useragent = "character", .conn = "list", .cache.dir = "character"))
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 ###############
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24 # CONSTRUCTOR #
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25 ###############
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27 BiodbFactory$methods( initialize = function(useragent = NA_character_, cache.dir = NA_character_, ...) {
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29 ( ! is.null(useragent) && ! is.na(useragent)) || stop("You must provide a user agent string (e.g.: \"myapp ; my.email@address\").")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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30 .useragent <<- useragent
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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31 .conn <<- list()
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32 .cache.dir <<- cache.dir
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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34 callSuper(...) # calls super-class initializer with remaining parameters
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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35 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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37 ##################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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38 # GET USER AGENT #
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39 ##################
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41 BiodbFactory$methods( getUserAgent = function() {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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42 return(.self$.useragent)
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43 })
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45 ############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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46 # GET CONN #
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47 ############
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49 BiodbFactory$methods( getConn = function(class) {
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51 if ( ! class %in% names(.self$.conn)) {
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52
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53 # Create connection instance
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54 conn <- switch(class,
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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55 chebi = ChebiConn$new(useragent = .self$.useragent),
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56 kegg = KeggConn$new(useragent = .self$.useragent),
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57 pubchem = PubchemConn$new(useragent = .self$.useragent),
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58 hmdb = HmdbConn$new(useragent = .self$.useragent),
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59 chemspider = ChemspiderConn$new(useragent = .self$.useragent),
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60 enzyme = EnzymeConn$new(useragent = .self$.useragent),
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61 lipidmaps = LipidmapsConn$new(useragent = .self$.useragent),
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62 mirbase = MirbaseConn$new(useragent = .self$.useragent),
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63 ncbigene = NcbigeneConn$new(useragent = .self$.useragent),
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64 ncbiccds = NcbiccdsConn$new(useragent = .self$.useragent),
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65 uniprot = UniprotConn$new(useragent = .self$.useragent),
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66 massbank = MassbankConn$new(useragent = .self$.useragent),
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67 NULL)
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68
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69 # Unknown class
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70 if (is.null(conn))
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71 stop(paste0("Unknown r-biodb class \"", class,"\"."))
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72
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73 .self$.conn[[class]] <- conn
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74 }
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75
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76 return (.self$.conn[[class]])
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77 })
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78
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79 ################
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80 # CREATE ENTRY #
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81 ################
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82
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83 BiodbFactory$methods( createEntry = function(class, type, id = NULL, content = NULL, drop = TRUE) {
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84
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85 is.null(id) && is.null(content) && stop("One of id or content must be set.")
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86 ! is.null(id) && ! is.null(content) && stop("id and content cannot be both set.")
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87
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88 # Get content
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89 if ( ! is.null(id))
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90 content <- .self$getEntryContent(class, type, id)
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91
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92 conn <- .self$getConn(class)
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93 entry <- conn$createEntry(type = type, content = content, drop = drop)
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94
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95 # Set factory
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96 for (e in c(entry))
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97 e$setFactory(.self)
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98
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99 return(entry)
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100 })
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101
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102 ########################
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103 # GET CACHE FILE PATHS #
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104 ########################
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105
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106 BiodbFactory$methods( .get.cache.file.paths = function(class, type, id) {
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107
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108 # Get extension
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109 ext <- .self$getConn(class)$getEntryContentType(type)
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110
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111 # Set filenames
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112 filenames <- vapply(id, function(x) paste0(class, '-', type, '-', x, '.', ext), FUN.VALUE = '')
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113
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114 # set file paths
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115 file.paths <- vapply(filenames, function(x) file.path(.self$.cache.dir, x), FUN.VALUE = '')
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116
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117 # Create cache dir if needed
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118 if ( ! is.na(.self$.cache.dir) && ! file.exists(.self$.cache.dir))
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119 dir.create(.self$.cache.dir)
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120
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121 return(file.paths)
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122 })
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123
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124 ###########################
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125 # LOAD CONTENT FROM CACHE #
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126 ###########################
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127
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128 BiodbFactory$methods( .load.content.from.cache = function(class, type, id) {
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129
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130 content <- NULL
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131
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132 # Read contents from files
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133 file.paths <- .self$.get.cache.file.paths(class, type, id)
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134 content <- lapply(file.paths, function(x) { if (file.exists(x)) paste(readLines(x), collapse = "\n") else NULL })
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135
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136 return(content)
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137 })
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138
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139 #########################
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140 # SAVE CONTENT TO CACHE #
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141 #########################
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142
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143 BiodbFactory$methods( .save.content.to.cache = function(class, type, id, content) {
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144
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145 # Write contents into files
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146 file.paths <- .self$.get.cache.file.paths(class, type, id)
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147 mapply(function(c, f) { if ( ! is.null(c)) writeLines(c, f) }, content, file.paths)
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148 })
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149
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150 #####################
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151 # GET ENTRY CONTENT #
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152 #####################
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153
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154 BiodbFactory$methods( getEntryContent = function(class, type, id) {
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155
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156 content <- NULL
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157 # Load from cache
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158 if ( ! is.na(.self$.cache.dir))
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159 content <- .self$.load.content.from.cache(class, type, id)
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160
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161 # Get contents
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162 missing.content.indexes <- vapply(content, is.null, FUN.VALUE = TRUE)
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163 missing.ids <- if (is.null(content)) id else id[missing.content.indexes]
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164 if (length(missing.ids) > 0) {
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165
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166 # Use connector to get missing contents
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167 conn <- .self$getConn(class)
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168 missing.contents <- conn$getEntryContent(type, missing.ids)
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169
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170 # Save to cache
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171 if ( ! is.null(missing.contents) && ! is.na(.self$.cache.dir))
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172 .self$.save.content.to.cache(class, type, missing.ids, missing.contents)
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173
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174 # Merge content and missing.contents
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175 if (is.null(content))
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176 content <- missing.contents
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177 else
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178 content[missing.content.indexes] <- missing.contents
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179 }
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180
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181 return(content)
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182 })
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183 }