Mercurial > repos > mingchen0919 > aurora_skewer
view rmarkdown_report_render.R @ 0:0358f6f78adf draft
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author | mingchen0919 |
---|---|
date | Fri, 14 Dec 2018 00:40:15 -0500 |
parents | |
children |
line wrap: on
line source
##============ Sink warnings and errors to a file ============== ## use the sink() function to wrap all code within it. ##============================================================== zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt')) sink(zz) sink(zz, type = 'message') #============== preparation ==================================== # import libraries #------------------------------------------------------------------ # ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES #------------------------------------------------------------------ library('getopt') library('rmarkdown') library('htmltools') #------------------------------------------------------------------ options(stringsAsFactors = FALSE) # define two helper functions #-----: helper function 1 #' \code{getopt_specification_matrix} returns a getopt specification matrix. #' #' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data. #' The first column are short flags, the second column are argument masks, the third column #' is data types. The fourth column are variable names used in the tool XML. These three columns are required. #' @param gtg_name the name of a running GTG. getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_INSTALL_DIR')) { df = read.csv( paste0(tool_dir, '/', specification_file), header = TRUE, stringsAsFactors = FALSE ) # check if there are duplicated short flags short_flags = df[, 1] if (length(unique(short_flags)) < length(short_flags)) { cat('----Duplicated short flags found ----\n') cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n') stop('Duplicated short flags are not allowed.') } # use short flags to generate long flags long_flags = paste0('X_', df[, 1]) # specification matrix df2 = data.frame( long_flags = long_flags, short_flags = df[, 1], argument_mask = df[, 2], data_type = df[, 3] ) as.matrix(df2) } #-----: helper function 2 #' \code{file_tree} generate file tree of a directory in the format of HTML lists. #' #' @param dir the path to the directory for generating the file tree. #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files. # define a recursive function to build html string of the file tree file_tree = function(dir = '.') { # get the OUTPUT_DIR folder data: dataset_NUMBER_files report_files_path = Sys.getenv('REPORT_FILES_PATH') output_dir = tail(strsplit(report_files_path, '/')[[1]], 1) files = list.files(path = dir, recursive = FALSE, full.names = TRUE) # files also include directorys, need to remove directorys files = files[!dir.exists(files)] dirs = list.dirs(path = dir, recursive = FALSE, full.names = TRUE) tags$ul({ if (length(files) > 0) { lapply(files, function(x) { path_end = tail(strsplit(x, '/')[[1]], 1) href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2] li_item = tags$li(tags$a(path_end, href = href_path)) li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}') li_item }) } }, { if (length(dirs) > 0) { lapply(dirs, function(x) { path_end = tail(strsplit(x, '/')[[1]], 1) # hide vakata-jstree-3.3.5 folder if (!(path_end %in% c('vakata-jstree-3.3.5', 'rmarkdown_report_files', 'site_libs'))) { # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2] li_item = tags$li(path_end, file_tree(x)) li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}') li_item } }) } }) } #----------------- end of help functions ------------------------- # import getopt specification matrix from a csv file opt = getopt(getopt_specification_matrix('command-line-arguments.csv', tool_dir = Sys.getenv('TOOL_INSTALL_DIR'))) # define environment variables for all input values. this is useful when we # want to use input values by other programming language in r markdown do.call(Sys.setenv, opt[-1]) #=============================================================== #======================== render Rmd files ========================= # copy jstree javascript library to tool output directory file.copy( from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'), to = Sys.getenv('REPORT_FILES_PATH'), recursive = TRUE ) # if '_site.yml' file exists, this tool is assumed to render a website. # otherwise, it renders a single html. if (file.exists(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/_site.yml'))) { # render a website system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}') system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}') render_site(input = Sys.getenv('REPORT_FILES_PATH')) } else { # render a single html system(command = 'cp -r ${TOOL_INSTALL_DIR}/rmarkdown_report.Rmd ${REPORT_FILES_PATH}') # add a few lines to 'rmarkdown_report.Rmd' to generate file tree outputs jstree_lines = ' ## Outputs ```{r, echo=FALSE} tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\'))) ```' write( x = jstree_lines, append = TRUE, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd') ) render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd')) } #=============================================================== #============== expose outputs to galaxy history =============== system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs-to-galaxy-history.sh') #=============================================================== ##--------end of code rendering .Rmd templates---------------- sink() ##=========== End of sinking output=============================