Mercurial > repos > mingchen0919 > aurora_fastqc

annotate rmarkdown_report_render.R @ 0:0aeed70b3bc5 draft default tip

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author mingchen0919
date Fri, 14 Dec 2018 00:38:44 -0500
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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 library('plyr')
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17 library('dplyr')
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18 library('stringr')
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19 library('DT')
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20 library('reshape2')
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21 library('plotly')
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22 #------------------------------------------------------------------
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23 options(stringsAsFactors = FALSE)
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24
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25
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26 # define two helper functions
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27 #-----: helper function 1
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28 #' \code{getopt_specification_matrix} returns a getopt specification matrix.
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29 #'
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30 #' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
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31 #' The first column are short flags, the second column are argument masks, the third column
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32 #' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
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33 #' @param gtg_name the name of a running GTG.
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34 getopt_specification_matrix = function(specification_file,
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35 gtg_name = 'gtg',
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36 tool_dir = Sys.getenv('TOOL_INSTALL_DIR')) {
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37 df = read.csv(
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38 paste0(tool_dir, '/', specification_file),
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39 header = TRUE,
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40 stringsAsFactors = FALSE
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41 )
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42 # check if there are duplicated short flags
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43 short_flags = df[, 1]
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44 if (length(unique(short_flags)) < length(short_flags)) {
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45 cat('----Duplicated short flags found ----\n')
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46 cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
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47 stop('Duplicated short flags are not allowed.')
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48 }
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49
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50 # use short flags to generate long flags
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51 long_flags = paste0('X_', df[, 1])
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52
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53 # specification matrix
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54 df2 = data.frame(
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55 long_flags = long_flags,
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56 short_flags = df[, 1],
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57 argument_mask = df[, 2],
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58 data_type = df[, 3]
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59 )
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60
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61 as.matrix(df2)
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62 }
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63
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64 #-----: helper function 2
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65 #' \code{file_tree} generate file tree of a directory in the format of HTML lists.
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66 #'
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67 #' @param dir the path to the directory for generating the file tree.
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68 #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
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69 # define a recursive function to build html string of the file tree
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70 file_tree = function(dir = '.') {
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71 # get the OUTPUT_DIR folder data: dataset_NUMBER_files
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72 report_files_path = Sys.getenv('REPORT_FILES_PATH')
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73 output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
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74
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75 files = list.files(path = dir,
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76 recursive = FALSE,
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77 full.names = TRUE)
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78 # files also include directorys, need to remove directorys
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79 files = files[!dir.exists(files)]
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80 dirs = list.dirs(path = dir,
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81 recursive = FALSE,
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82 full.names = TRUE)
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83 tags$ul({
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84 if (length(files) > 0) {
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85 lapply(files, function(x) {
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86 path_end = tail(strsplit(x, '/')[[1]], 1)
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87 href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
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88 li_item = tags$li(tags$a(path_end, href = href_path))
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89 li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}')
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90 li_item
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91 })
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92 }
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93 },
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94 {
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95 if (length(dirs) > 0) {
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96 lapply(dirs, function(x) {
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97 path_end = tail(strsplit(x, '/')[[1]], 1)
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98 # hide vakata-jstree-3.3.5 folder
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99 if ( !(path_end %in% c('vakata-jstree-3.3.5', 'rmarkdown_report_files', 'site_libs'))) {
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100 # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
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101 li_item = tags$li(path_end, file_tree(x))
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102 li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
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103 li_item
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104 }
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105 })
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106 }
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107 })
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108 }
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109 #----------------- end of help functions -------------------------
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110
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111
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112 # import getopt specification matrix from a csv file
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113 opt = getopt(getopt_specification_matrix('command-line-arguments.csv',
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114 tool_dir = Sys.getenv('TOOL_INSTALL_DIR')))
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115 # define environment variables for all input values. this is useful when we
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116 # want to use input values by other programming language in r markdown
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117 do.call(Sys.setenv, opt[-1])
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118 #===============================================================
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119
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120
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121 #======================== render Rmd files =========================
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122 # copy jstree javascript library to tool output directory
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123 file.copy(
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124 from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
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125 to = Sys.getenv('REPORT_FILES_PATH'),
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126 recursive = TRUE
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127 )
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128
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129 # if '_site.yml' file exists, this tool is assumed to render a website.
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130 # otherwise, it renders a single html.
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131 if (file.exists(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/_site.yml'))) {
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132 # render a website
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133 system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
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134 system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}')
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135 render_site(input = Sys.getenv('REPORT_FILES_PATH'))
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136 } else {
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137 # render a single html
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138 system(command = 'cp -r ${TOOL_INSTALL_DIR}/rmarkdown_report.Rmd ${REPORT_FILES_PATH}')
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139 # add a few lines to 'rmarkdown_report.Rmd' to generate file tree outputs
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140 jstree_lines =
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141 '
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142 ## Outputs
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143
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144 ```{r, echo=FALSE}
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145 tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\')))
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146 ```
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147 '
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148 write(
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149 x = jstree_lines,
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150 append = TRUE,
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151 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd')
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152 )
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153 render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd'))
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154 }
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155 #===============================================================
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156
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157
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158 #============== expose outputs to galaxy history ===============
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159 system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs-to-galaxy-history.sh')
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160 #===============================================================
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161
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162
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163 ##--------end of code rendering .Rmd templates----------------
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164 sink()
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165 ##=========== End of sinking output=============================