--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bdss_client_sra_render.R	Tue Oct 17 14:09:01 2017 -0400
@@ -0,0 +1,90 @@
+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=============================
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