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comparison rmarkdown_report_render.R @ 0:803f4888f36a draft

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planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
author mingchen0919
date Thu, 13 Dec 2018 22:46:23 -0500
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-1:000000000000 0:803f4888f36a
1 ##============ Sink warnings and errors to a file ==============
2 ## use the sink() function to wrap all code within it.
3 ##==============================================================
4 zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt'))
5 sink(zz)
6 sink(zz, type = 'message')
7
8 #============== preparation ====================================
9 # import libraries
10 #------------------------------------------------------------------
11 # ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
12 #------------------------------------------------------------------
13 library('getopt')
14 library('rmarkdown')
15 library('htmltools')
16 library(knitr)
17 #------------------------------------------------------------------
18 options(stringsAsFactors = FALSE)
19
20
21 # define two helper functions
22 #-----: helper function 1
23 #' \code{getopt_specification_matrix} returns a getopt specification matrix.
24 #'
25 #' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
26 #' The first column are short flags, the second column are argument masks, the third column
27 #' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
28 #' @param gtg_name the name of a running GTG.
29 getopt_specification_matrix = function(specification_file,
30 gtg_name = 'gtg',
31 tool_dir = Sys.getenv('TOOL_INSTALL_DIR')) {
32 df = read.csv(
33 paste0(tool_dir, '/', specification_file),
34 header = TRUE,
35 stringsAsFactors = FALSE
36 )
37 # check if there are duplicated short flags
38 short_flags = df[, 1]
39 if (length(unique(short_flags)) < length(short_flags)) {
40 cat('----Duplicated short flags found ----\n')
41 cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
42 stop('Duplicated short flags are not allowed.')
43 }
44
45 # use short flags to generate long flags
46 long_flags = paste0('X_', df[, 1])
47
48 # specification matrix
49 df2 = data.frame(
50 long_flags = long_flags,
51 short_flags = df[, 1],
52 argument_mask = df[, 2],
53 data_type = df[, 3]
54 )
55
56 as.matrix(df2)
57 }
58
59 #-----: helper function 2
60 #' \code{file_tree} generate file tree of a directory in the format of HTML lists.
61 #'
62 #' @param dir the path to the directory for generating the file tree.
63 #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
64 # define a recursive function to build html string of the file tree
65 file_tree = function(dir = '.') {
66 # get the OUTPUT_DIR folder data: dataset_NUMBER_files
67 report_files_path = Sys.getenv('REPORT_FILES_PATH')
68 output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
69
70 files = list.files(path = dir,
71 recursive = FALSE,
72 full.names = TRUE)
73 # files also include directorys, need to remove directorys
74 files = files[!dir.exists(files)]
75 dirs = list.dirs(path = dir,
76 recursive = FALSE,
77 full.names = TRUE)
78 tags$ul({
79 if (length(files) > 0) {
80 lapply(files, function(x) {
81 path_end = tail(strsplit(x, '/')[[1]], 1)
82 href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
83 li_item = tags$li(tags$a(path_end, href = href_path))
84 li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}')
85 li_item
86 })
87 }
88 },
89 {
90 if (length(dirs) > 0) {
91 lapply(dirs, function(x) {
92 path_end = tail(strsplit(x, '/')[[1]], 1)
93 # hide vakata-jstree-3.3.5 folder
94 if (!(path_end %in% c('vakata-jstree-3.3.5', 'rmarkdown_report_files', 'site_libs'))) {
95 # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
96 li_item = tags$li(path_end, file_tree(x))
97 li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
98 li_item
99 }
100 })
101 }
102 })
103 }
104 #----------------- end of help functions -------------------------
105
106
107 # import getopt specification matrix from a csv file
108 opt = getopt(getopt_specification_matrix('command-line-arguments.csv',
109 tool_dir = Sys.getenv('TOOL_INSTALL_DIR')))
110 # define environment variables for all input values. this is useful when we
111 # want to use input values by other programming language in r markdown
112 do.call(Sys.setenv, opt[-1])
113 #===============================================================
114
115
116 #======================== render Rmd files =========================
117 # copy jstree javascript library to tool output directory
118 file.copy(
119 from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
120 to = Sys.getenv('REPORT_FILES_PATH'),
121 recursive = TRUE
122 )
123
124 # if '_site.yml' file exists, this tool is assumed to render a website.
125 # otherwise, it renders a single html.
126 if (file.exists(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/_site.yml'))) {
127 # render a website
128 system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
129 system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}')
130 render_site(input = Sys.getenv('REPORT_FILES_PATH'))
131 } else {
132 # render a single html
133 system(command = 'cp -r ${TOOL_INSTALL_DIR}/rmarkdown_report.Rmd ${REPORT_FILES_PATH}')
134 # add a few lines to 'rmarkdown_report.Rmd' to generate file tree outputs
135 jstree_lines = '
136 ## Outputs
137
138 ```{r, echo=FALSE}
139 tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\')))
140 ```'
141 write(
142 x = jstree_lines,
143 append = TRUE,
144 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd')
145 )
146 render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd'))
147 }
148 #===============================================================
149
150
151 #============== expose outputs to galaxy history ===============
152 system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs-to-galaxy-history.sh')
153 #===============================================================
154
155
156 ##--------end of code rendering .Rmd templates----------------
157 sink()
158 ##=========== End of sinking output=============================