annotate bdss_client_render.R @ 0:1cc0ed4567e1 draft default tip

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty

library(getopt)
library(rmarkdown)
library(htmltools)
library(dplyr)
library(RCurl)


##============ Sink warnings and errors to a file ==============
## use the sink() function to wrap all code within it.
##==============================================================
zz = file('warnings_and_errors.txt')
sink(zz)
sink(zz, type = 'message')
##---------below is the code for rendering .Rmd templates-----

  ##=============STEP 1: handle command line arguments==========
  ##
  ##============================================================
  # column 1: the long flag name
  # column 2: the short flag alias. A SINGLE character string
  # column 3: argument mask
  #           0: no argument
  #           1: argument required
  #           2: argument is optional
  # column 4: date type to which the flag's argument shall be cast.
  #           possible values: logical, integer, double, complex, character.
  #-------------------------------------------------------------
  #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
  # 1. short flag alias should match the flag in the command section in the XML file.
  # 2. long flag name can be any legal R variable names
  # 3. two names in args_list can have common string but one name should not be a part of another name.
  #    for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
  #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  ##------- 1. input data ---------------------
  args_list=list()
  args_list$URLS = c('urls', 'i', '1', 'character')
  args_list$ECHO = c('echo', 'e', '1', 'character')
  ##--------2. output report and outputs --------------
  args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
  args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
  args_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
  ##--------3. Rmd templates in the tool directory ----------
  args_list$BDSS_CLIENT_RMD = c('bdss_client_rmd', 't', '1', 'character')
  
  opt = getopt(t(as.data.frame(args_list)))
  
  
  ##=======STEP 2: create report directory (optional)==========
  ##
  ##===========================================================
  dir.create(opt$report_dir)
  
  ##=STEP 3: replace placeholders in .Rmd with argument values=
  ##
  ##===========================================================
  #++ need to replace placeholders with args values one by one+
  #----- 01 bdss_client.Rmd -----------------------
  readLines(opt$bdss_client_rmd) %>%
    (function(x) {
      gsub('URLS', opt$urls, x)
    }) %>%
    (function(x) {
      gsub('ECHO', opt$echo, x)
    }) %>%
    (function(x) {
      gsub('REPORT_DIR', opt$report_dir, x)
    }) %>%
    (function(x) {
      fileConn = file('bdss_client.Rmd')
      writeLines(x, con=fileConn)
      close(fileConn)
    })
  
  ##=============STEP 4: render .Rmd templates=================
  ##
  ##===========================================================
  render('bdss_client.Rmd', output_file = opt$report_html)


##--------end of code rendering .Rmd templates----------------
sink()
##=========== End of sinking output=============================