diff bdss_client_render.R @ 17:246cb7315673 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty

--- a/bdss_client_render.R	Wed Oct 11 15:06:20 2017 -0400
+++ b/bdss_client_render.R	Sat Oct 14 12:12:10 2017 -0400
@@ -1,93 +1,82 @@
-##======= Handle arguments from command line ========
-# setup R error handline to go to stderr
-options(show.error.messages=FALSE,
-        error=function(){
-          cat(geterrmessage(), file=stderr())
-          quit("no", 1, F)
-        })
-
-# we need that to not crash galaxy with an UTF8 error on German LC settings.
-loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
-
-# suppress warning
-options(warn = -1)
-
-options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
-args = commandArgs(trailingOnly=TRUE)
-
-suppressPackageStartupMessages({
-  library(getopt)
-  library(tools)
-})
-
-#/////////////////////// SINK WARNINGS AND ERRORS TO A FILE FOR DEBUGGING ///////////
+##============ 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')
-
-# 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.
-##------- 1. input data ---------------------
-spec_list=list()
-spec_list$URLS = c('urls', 'i', '1', 'character')
-spec_list$ECHO = c('echo', 'e', '1', 'character')
-##--------2. output report and outputs --------------
-spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
-spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character')
-spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
-##--------3. Rmd templates in the tool directory ----------
-spec_list$bdss_client_sra_se_RMD = c('bdss_client_sra_se_rmd', 't', '1', 'character')
-
-spec = t(as.data.frame(spec_list))
-opt = getopt(spec)
-
-#------ Load libraries ---------
-library(rmarkdown)
-library(htmltools)
-library(dplyr)
-library(RCurl)
+##---------below is the code for rendering .Rmd templates-----
 
-#----- 1. create the report directory ------------------------
-dir.create(opt$output_dir)
-
-#----- 2. generate Rmd files with Rmd templates --------------
-#   a. templates without placeholder variables:
-#         copy templates from tool directory to the working directory.
-#   b. templates with placeholder variables:
-#         substitute variables with user input values and place them in the working directory.
-
-#----- 01 bdss_client_sra_se.Rmd -----------------------
-readLines(opt$bdss_client_sra_se_rmd) %>%
-  (function(x) {
-    gsub('URLS', opt$urls, x)
-  }) %>%
-  (function(x) {
-    gsub('ECHO', opt$echo, x)
-  }) %>%
-  (function(x) {
-    gsub('OUTPUT_DIR', opt$output_dir, x)
-  }) %>%
-  (function(x) {
-    fileConn = file('bdss_client_sra_se.Rmd')
-    writeLines(x, con=fileConn)
-    close(fileConn)
-  })
-
-#------ 3. render all Rmd files --------
-render('bdss_client_sra_se.Rmd', output_file = opt$report_html)
+  ##=============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: loading libraries=====================
+  ##
+  ##===========================================================
+  library(rmarkdown)
+  library(htmltools)
+  library(dplyr)
+  library(RCurl)
+  
+  ##=======STEP 3: create report directory (optional)==========
+  ##
+  ##===========================================================
+  dir.create(opt$report_dir)
+  
+  ##=STEP 4: replace placeholders in .Rmd with argument values=
+  ##
+  ##===========================================================
+  #++ need to replace placeholders with args values one by one+
+  #----- 01 bdss_client.Rmd -----------------------
+  readLines(opt$bdss_client_rmd) %>%
+    (function(x) {
+      gsub('URLS', opt$urls, x)
+    }) %>%
+    (function(x) {
+      gsub('ECHO', opt$echo, x)
+    }) %>%
+    (function(x) {
+      gsub('REPORT_DIR', opt$report_dir, x)
+    }) %>%
+    (function(x) {
+      fileConn = file('bdss_client.Rmd')
+      writeLines(x, con=fileConn)
+      close(fileConn)
+    })
+  
+  ##=============STEP 5: render .Rmd templates=================
+  ##
+  ##===========================================================
+  render('bdss_client.Rmd', output_file = opt$report_html)
 
 
-#-------4. manipulate outputs -----------------------------
-
-
-
-
-
+##--------end of code rendering .Rmd templates----------------
 sink()
-#/////////// END OF SINK OUTPUT ///////////////////////////
\ No newline at end of file
+##=========== End of sinking output=============================
\ No newline at end of file