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comparison bdss_client_render.R @ 0:512d008295db draft default tip

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
author mingchen0919
date Tue, 17 Oct 2017 14:09:01 -0400
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-1:000000000000 0:512d008295db
1 library(getopt)
2 library(rmarkdown)
3 library(htmltools)
4 library(dplyr)
5 library(RCurl)
6
7
8 ##============ Sink warnings and errors to a file ==============
9 ## use the sink() function to wrap all code within it.
10 ##==============================================================
11 zz = file('warnings_and_errors.txt')
12 sink(zz)
13 sink(zz, type = 'message')
14 ##---------below is the code for rendering .Rmd templates-----
15
16 ##=============STEP 1: handle command line arguments==========
17 ##
18 ##============================================================
19 # column 1: the long flag name
20 # column 2: the short flag alias. A SINGLE character string
21 # column 3: argument mask
22 # 0: no argument
23 # 1: argument required
24 # 2: argument is optional
25 # column 4: date type to which the flag's argument shall be cast.
26 # possible values: logical, integer, double, complex, character.
27 #-------------------------------------------------------------
28 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
29 # 1. short flag alias should match the flag in the command section in the XML file.
30 # 2. long flag name can be any legal R variable names
31 # 3. two names in args_list can have common string but one name should not be a part of another name.
32 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
33 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
34 ##------- 1. input data ---------------------
35 args_list=list()
36 args_list$URLS = c('urls', 'i', '1', 'character')
37 args_list$ECHO = c('echo', 'e', '1', 'character')
38 ##--------2. output report and outputs --------------
39 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
40 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
41 args_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
42 ##--------3. Rmd templates in the tool directory ----------
43 args_list$BDSS_CLIENT_RMD = c('bdss_client_rmd', 't', '1', 'character')
44
45 opt = getopt(t(as.data.frame(args_list)))
46
47
48 ##=======STEP 2: create report directory (optional)==========
49 ##
50 ##===========================================================
51 dir.create(opt$report_dir)
52
53 ##=STEP 3: replace placeholders in .Rmd with argument values=
54 ##
55 ##===========================================================
56 #++ need to replace placeholders with args values one by one+
57 #----- 01 bdss_client.Rmd -----------------------
58 readLines(opt$bdss_client_rmd) %>%
59 (function(x) {
60 gsub('URLS', opt$urls, x)
61 }) %>%
62 (function(x) {
63 gsub('ECHO', opt$echo, x)
64 }) %>%
65 (function(x) {
66 gsub('REPORT_DIR', opt$report_dir, x)
67 }) %>%
68 (function(x) {
69 fileConn = file('bdss_client.Rmd')
70 writeLines(x, con=fileConn)
71 close(fileConn)
72 })
73
74 ##=============STEP 4: render .Rmd templates=================
75 ##
76 ##===========================================================
77 render('bdss_client.Rmd', output_file = opt$report_html)
78
79
80 ##--------end of code rendering .Rmd templates----------------
81 sink()
82 ##=========== End of sinking output=============================