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$SRA_IDS_SE = c('sra_ids_se', 'i', '1', 'character')
args_list$SRA_IDS_PE = c('sra_ids_pe', 'p', '1', 'character')
args_list$FORMAT = c('format', 'f', '1', 'character')
args_list$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$bdss_client_rmd) %>%
  (function(x) {
    gsub('SRA_IDS_SE', opt$sra_ids_se, x)
  }) %>%
  (function(x) {
    gsub('SRA_IDS_PE', opt$sra_ids_pe, x)
  }) %>%
  (function(x) {
    gsub('FORMAT', opt$format, 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=============================