annotate w4mcorcov_input.R @ 1:0c2ad44b6c9c draft

planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
author eschen42
date Sun, 22 Oct 2017 18:47:57 -0400
parents 23f9fad4edfc
children 50f60f94c034
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1 # read_data_frame - read a w4m data frame, with error handling
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2 # e.g., data_matrix_input_env <- read_data_frame(dataMatrix_in, "data matrix input")
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3 read_data_frame <- function(file_path, kind_string, failure_action = failure_action) {
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4 my.env <- new.env()
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5 my.env$success <- FALSE
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6 my.env$msg <- sprintf("no message reading %s", kind_string)
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7 tryCatch(
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8 expr = {
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9 my.env$data <- utils::read.delim( fill = FALSE, file = file_path )
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10 my.env$success <- TRUE
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11 }
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12 , error = function(e) {
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13 my.env$ msg <- sprintf("%s read failed", kind_string)
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14 }
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15 )
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16 if (!my.env$success) {
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17 failure_action(my.env$msg)
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18 return ( FALSE )
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19 }
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20 return (my.env)
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21 }
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22
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23 # read one of three XCMS data elements: dataMatrix, sampleMetadata, variableMetadata
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24 # returns respectively: matrix, data.frame, data.frame, or FALSE if there is a failure
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25 read_xcms_data_element <- function(xcms_data_in, xcms_data_type, failure_action = stop) {
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26 # note that 'stop' effectively means 'throw'; if 'warning' and 'message' are caught, they mean 'throw' as well
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27 my_failure_action <- function(...) { failure_action("read_xcms_data_element: ", ...) }
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28 # xcms_data_type must be in c("sampleMetadata", "variableMetadata", "dataMatrix")
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29 if ( ! is.character(xcms_data_type) ) {
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30 my_failure_action(sprintf("bad parameter xcms_data_type '%s'", deparse(xcms_data_type)))
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31 return ( FALSE )
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32 }
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33 if ( 1 != length(xcms_data_type)
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34 || ! ( xcms_data_type %in% c("sampleMetadata", "variableMetadata", "dataMatrix") )
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35 ) {
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36 my_failure_action( sprintf("bad parameter xcms_data_type '%s'", xcms_data_type) )
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37 return ( FALSE )
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38 }
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39 if ( is.character(xcms_data_in) ){
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40 # case: xcms_data_in is a path to a file
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41 xcms_data_input_env <- read_data_frame( xcms_data_in, sprintf("%s input", xcms_data_type) )
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42 if (!xcms_data_input_env$success) {
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43 my_failure_action(xcms_data_input_env$msg)
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44 return ( FALSE )
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45 }
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46 return ( xcms_data_input_env$data )
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47 # commenting out pasted code that is not tested here
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48 # } else if ( is.data.frame(xcms_data_in) || is.matrix(xcms_data_in) ) {
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49 # # case: xcms_data_in is a data.frame or matrix
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50 # return(xcms_data_in)
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51 # } else if ( is.list(xcms_data_in) || is.environment(xcms_data_in) ) {
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52 # # NOTE WELL: is.list succeeds for data.frame, so the is.data.frame test must appear before the is.list test
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53 # # case: xcms_data_in is a list
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54 # if ( ! exists(xcms_data_type, where = xcms_data_in) ) {
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55 # my_failure_action(sprintf("%s xcms_data_in is missing member '%s'"), ifelse(is.environment(xcms_data_in),"environment","list"), xcms_data_type)
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56 # return ( FALSE )
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57 # }
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58 # prospect <- getElement(name = xcms_data_type, object = xcms_data_in)
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59 # if ( ! is.data.frame(prospect) && ! is.matrix(prospect) ) {
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60 # utils::str("list - str(prospect)")
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61 # utils::str(prospect)
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62 # if ( is.list(xcms_data_in) ) {
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63 # my_failure_action(sprintf("the first member of xcms_data_in['%s'] is neither a data.frame nor a matrix but is a %s", xcms_data_type, typeof(prospect)))
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64 # } else {
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65 # my_failure_action(sprintf("the first member of xcms_data_in$%s is neither a data.frame nor a matrix but is a %s", xcms_data_type, typeof(prospect)))
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66 # }
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67 # return ( prospect )
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68 # }
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69 # # stop("stopping here for a snapshot")
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70 # return ( prospect )
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71 } else {
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72 # case: xcms_data_in is invalid
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73 my_failure_action( sprintf("xcms_data_in has unexpected type %s", typeof(xcms_data_in)) )
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74 return ( FALSE )
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75 }
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76 }
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77
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78 read_inputs <- function(input_env, failure_action = print) {
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79 if ( ! is.environment(input_env) ) {
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80 failure_action("read_inputs: fatal error - 'input_env' is not an environment")
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81 return ( FALSE )
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82 }
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83
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84 if (!is.null(sampleMetadata_in <- input_env$sampleMetadata_in)) {
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diff changeset
85 # ---
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86 # read in the sample metadata
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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87 read_data_result <- tryCatchFunc(
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88 expr = {
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89 read_xcms_data_element(xcms_data_in = sampleMetadata_in, xcms_data_type = "sampleMetadata")
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diff changeset
90 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
91 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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92 if ( read_data_result$success ) {
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93 smpl_metadata <- read_data_result$value
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94 } else {
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95 failure_action(read_data_result$msg)
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96 return ( FALSE )
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97 }
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98
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99 # extract rownames
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100 rownames(smpl_metadata) <- smpl_metadata[,1]
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101
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102 input_env$smpl_metadata <- smpl_metadata
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103 # ...
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104 } else {
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105 failure_action("read_inputs: fatal error - 'sampleMetadata_in' is missing from 'input_env'")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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106 return ( FALSE )
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107 }
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108
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109 if (!is.null(variableMetadata_in <- input_env$variableMetadata_in)) {
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110 # ---
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111 # read in the variable metadata
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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112 read_data_result <- tryCatchFunc(
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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113 expr = {
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114 read_xcms_data_element(xcms_data_in = variableMetadata_in, xcms_data_type = "variableMetadata")
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115 }
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116 )
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117 if ( read_data_result$success ) {
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118 vrbl_metadata <- read_data_result$value
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119 } else {
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120 failure_action(read_data_result$msg)
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121 return (FALSE)
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122 }
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123
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124
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125 # extract rownames (using make.names to handle degenerate feature names)
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126 err.env <- new.env()
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127 err.env$success <- FALSE
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128 err.env$msg <- "no message setting vrbl_metadata rownames"
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129 tryCatch(
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130 expr = {
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131 rownames(vrbl_metadata) <- make.names( vrbl_metadata[,1], unique = TRUE )
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132 vrbl_metadata[,1] <- rownames(vrbl_metadata)
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133 err.env$success <- TRUE
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134 }
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135 , error = function(e) {
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136 err.env$ msg <- sprintf("failed to set rownames for vrbl_metadata read because '%s'", e$message)
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137 }
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138 )
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139 if (!err.env$success) {
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140 failure_action(err.env$msg)
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141 return ( FALSE )
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142 }
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143
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144 input_env$vrbl_metadata <- vrbl_metadata
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145 # ...
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146 } else {
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147 failure_action("read_inputs: fatal error - 'variableMetadata_in' is missing from 'input_env'")
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148 return ( FALSE )
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149 }
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150
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151 if (!is.null(dataMatrix_in <- input_env$dataMatrix_in)) {
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152 # ---
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153 # read in the data matrix
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154 read_data_result <- tryCatchFunc(
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155 expr = {
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156 read_xcms_data_element(xcms_data_in = dataMatrix_in, xcms_data_type = "dataMatrix")
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157 }
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158 )
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159 if ( read_data_result$success ) {
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160 data_matrix <- read_data_result$value
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161 } else {
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162 failure_action(read_data_result$msg)
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163 return (FALSE)
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164 }
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165
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166 if ( ! is.matrix(data_matrix) ) {
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167 # extract rownames (using make.names to handle degenerate feature names)
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168 err.env <- new.env()
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169 err.env$success <- FALSE
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170 err.env$msg <- "no message setting data_matrix rownames"
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171 tryCatch(
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172 expr = {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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173 rownames(data_matrix) <- make.names( data_matrix[,1], unique = TRUE )
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174 err.env$success <- TRUE
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175 }
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176 , error = function(e) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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177 err.env$msg <- sprintf("failed to set rownames for data_matrix read because '%s'", e$message)
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178 }
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179 )
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180 if (!err.env$success) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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181 failure_action(err.env$msg)
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182 return ( FALSE )
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183 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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184
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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185 # remove rownames column
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186 data_matrix <- data_matrix[,2:ncol(data_matrix)]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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187
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188 # convert data_matrix to matrix from data.frame
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189 data_matrix <- as.matrix(data_matrix)
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190 }
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191
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192 input_env$data_matrix <- data_matrix
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193 # ...
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194 } else {
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195 failure_action("read_inputs: fatal error - 'dataMatrix_in' is missing from 'input_env'")
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196 return ( FALSE )
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197 }
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198
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199 return ( TRUE )
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200 }
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201