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1 ##============ Sink warnings and errors to a file ==============
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2 ## use the sink() function to wrap all code within it.
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3 ##==============================================================
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4 zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/r_rendering.log.txt'))
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5 sink(zz)
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6 sink(zz, type = 'message')
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7
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8 #============== preparation ====================================
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9 # import libraries
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10 #------------------------------------------------------------------
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11 # ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
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12 #------------------------------------------------------------------
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13 library('getopt')
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14 library('rmarkdown')
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15 library('htmltools')
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16 #------------------------------------------------------------------
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17 options(stringsAsFactors = FALSE)
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18
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19
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20 # define two helper functions
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21 #-----: helper function 1
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22 #' \code{getopt_specification_matrix} returns a getopt specification matrix.
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23 #'
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24 #' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
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25 #' The first column are short flags, the second column are argument masks, the third column
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26 #' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
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27 #' @param gtg_name the name of a running GTG.
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28 getopt_specification_matrix = function(specification_file,
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29 gtg_name = 'gtg',
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30 tool_dir = Sys.getenv('TOOL_INSTALL_DIR')) {
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31 df = read.csv(
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32 paste0(tool_dir, '/', specification_file),
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33 header = TRUE,
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34 stringsAsFactors = FALSE
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35 )
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36 # check if there are duplicated short flags
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37 short_flags = df[, 1]
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38 if (length(unique(short_flags)) < length(short_flags)) {
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39 cat('----Duplicated short flags found ----\n')
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40 cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
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41 stop('Duplicated short flags are not allowed.')
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42 }
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43
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44 # use short flags to generate long flags
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45 long_flags = paste0('X_', df[, 1])
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46
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47 # specification matrix
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48 df2 = data.frame(
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49 long_flags = long_flags,
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50 short_flags = df[, 1],
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51 argument_mask = df[, 2],
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52 data_type = df[, 3]
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53 )
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54
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55 as.matrix(df2)
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56 }
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57
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58 #-----: helper function 2
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59 #' \code{file_tree} generate file tree of a directory in the format of HTML lists.
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60 #'
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61 #' @param dir the path to the directory for generating the file tree.
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62 #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
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63 # define a recursive function to build html string of the file tree
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64 file_tree = function(dir = '.') {
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65 # get the OUTPUT_DIR folder data: dataset_NUMBER_files
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66 report_files_path = Sys.getenv('REPORT_FILES_PATH')
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67 output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
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68
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69 files = list.files(path = dir,
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70 recursive = FALSE,
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71 full.names = TRUE)
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72 # files also include directorys, need to remove directorys
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73 files = files[!dir.exists(files)]
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74 dirs = list.dirs(path = dir,
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75 recursive = FALSE,
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76 full.names = TRUE)
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77 tags$ul({
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78 if (length(files) > 0) {
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79 lapply(files, function(x) {
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80 path_end = tail(strsplit(x, '/')[[1]], 1)
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81 href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
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82 li_item = tags$li(tags$a(path_end, href = href_path))
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83 li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}')
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84 li_item
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85 })
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86 }
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87 },
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88 {
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89 if (length(dirs) > 0) {
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90 lapply(dirs, function(x) {
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91 path_end = tail(strsplit(x, '/')[[1]], 1)
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92 # hide vakata-jstree-3.3.5 folder
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93 if (!(path_end %in% c('vakata-jstree-3.3.5', 'rmarkdown_report_files', 'site_libs'))) {
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94 # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
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95 li_item = tags$li(path_end, file_tree(x))
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96 li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
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97 li_item
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98 }
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99 })
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100 }
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101 })
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102 }
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103 #----------------- end of help functions -------------------------
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104
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105
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106 # import getopt specification matrix from a csv file
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107 opt = getopt(getopt_specification_matrix('getopt.csv',
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108 tool_dir = Sys.getenv('TOOL_INSTALL_DIR')))
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109 # define environment variables for all input values. this is useful when we
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110 # want to use input values by other programming language in r markdown
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111 do.call(Sys.setenv, opt[-1])
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112 # add current job working directory
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113 Sys.setenv(JOB_WORKING_DIR=getwd())
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114 #===============================================================
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115
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116
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117 #======================== render Rmd files =========================
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118 # copy jstree javascript library to tool output directory
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119 file.copy(
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120 from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
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121 to = Sys.getenv('REPORT_FILES_PATH'),
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122 recursive = TRUE
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123 )
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124
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125 # if '_site.yml' file exists, this tool is assumed to render a website.
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126 # otherwise, it renders a single html.
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127 if (file.exists(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/_site.yml'))) {
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128 # render a website
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129 system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
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130 system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}')
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131 render_site(input = Sys.getenv('REPORT_FILES_PATH'))
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132 } else {
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133 # render a single html
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134 system(command = 'cp -r ${TOOL_INSTALL_DIR}/rmarkdown_report.Rmd ${REPORT_FILES_PATH}')
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135 # add a few lines to 'rmarkdown_report.Rmd' to generate file tree outputs
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136 jstree_lines = '
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137 ## Outputs
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138
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139 ```{r, echo=FALSE}
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140 tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\')))
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141 ```'
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142 write(
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143 x = jstree_lines,
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144 append = TRUE,
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145 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd')
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146 )
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147 render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd'))
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148 }
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149 #===============================================================
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150
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151
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152 #============== expose outputs to galaxy history ===============
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153 system(command = 'sh ${TOOL_INSTALL_DIR}/galaxy_outputs.sh')
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154 #===============================================================
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155
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156
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157 ##--------end of code rendering .Rmd templates----------------
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158 sink()
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159 ##=========== End of sinking output=============================
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