def Rmarkdown(script=None,
input=None,
output=None,
args='{input:r}, output_file={output:ar}',
**kwargs):
'''Convert input file to output using Rmarkdown
The input can be specified in three ways:
1. instant script, which is assumed to be in md format
Rmarkdown: output='report.html'
script
2. one or more input files. The format is determined by extension of input file
Rmarkdown(input, output='report.html')
3. input file specified by command line option `-r` .
Rmarkdown(output='report.html')
If no output is specified, it is assumed to be in html format
and is written to standard output.
You can specify more options using the args parameter of the action. The default value
of args is `${input!r} --output ${output!ar}'
'''
if not R_library('rmarkdown').target_exists():
raise RuntimeError('Library rmarkdown does not exist')
input = sos_targets(collect_input(script, input))
output = sos_targets(output)
if len(output) == 0:
write_to_stdout = True
output = sos_targets(
tempfile.NamedTemporaryFile(mode='w+t',
suffix='.html',
delete=False).name)
else:
write_to_stdout = False
#
ret = 1
try:
# render(input, output_format = NULL, output_file = NULL, output_dir = NULL,
# output_options = NULL, intermediates_dir = NULL,
# runtime = c("auto", "static", "shiny"),
# clean = TRUE, params = NULL, knit_meta = NULL, envir = parent.frame(),
# run_Rmarkdown = TRUE, quiet = FALSE, encoding = getOption("encoding"))
cmd = interpolate(f'Rscript -e "rmarkdown::render({args})"', {
'input': input,
'output': output
})
env.logger.trace(f'Running command "{cmd}"')
if env.config['run_mode'] == 'interactive':
# need to catch output and send to python output, which will in trun be hijacked by SoS notebook
p = subprocess.Popen(cmd,
shell=True,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE)
#pid = p.pid
out, err = p.communicate()
sys.stdout.write(out.decode())
sys.stderr.write(err.decode())
ret = p.returncode
else:
p = subprocess.Popen(cmd, shell=True)
#pid = p.pid
ret = p.wait()
except Exception as e:
env.logger.error(e)
if ret != 0:
temp_file = os.path.join('.sos', f'{"Rmarkdown"}_{os.getpid()}.md')
shutil.copyfile(str(input), temp_file)
cmd = interpolate(f'Rscript -e "rmarkdown::render({args})"', {
'input': input,
'output': sos_targets(temp_file)
})
raise RuntimeError(
f'Failed to execute script. Please use command \n"{cmd}"\nunder {os.getcwd()} to test it.'
)
if write_to_stdout:
with open(str(output[0])) as out:
sys.stdout.write(out.read())
else:
env.logger.info(f'Report saved to {output}')
def Rmarkdown(script=None, input=None, output=None, args="${input!r}, output_file=${output!ar}", **kwargs):
"""Convert input file to output using Rmarkdown
The input can be specified in three ways:
1. instant script, which is assumed to be in md format
Rmarkdown: output='report.html'
script
2. one or more input files. The format is determined by extension of input file
Rmarkdown(input, output='report.html')
3. input file specified by command line option `-r` .
Rmarkdown(output='report.html')
If no output is specified, it is assumed to be in html format
and is written to standard output.
You can specify more options using the args parameter of the action. The default value
of args is `${input!r} --output ${output!ar}'
"""
if not R_library("rmarkdown").exists():
raise UnknownTarget(R_library("rmarkdown"))
input_file = collect_input(script, input)
write_to_stdout = False
if output is None:
write_to_stdout = True
output_file = tempfile.NamedTemporaryFile(mode="w+t", suffix=".html", delete=False).name
elif isinstance(output, str):
output_file = output
else:
raise RuntimeError("A filename is expected, {} provided".format(output))
#
ret = 1
try:
# render(input, output_format = NULL, output_file = NULL, output_dir = NULL,
# output_options = NULL, intermediates_dir = NULL,
# runtime = c("auto", "static", "shiny"),
# clean = TRUE, params = NULL, knit_meta = NULL, envir = parent.frame(),
# run_Rmarkdown = TRUE, quiet = FALSE, encoding = getOption("encoding"))
cmd = interpolate(
'Rscript -e "rmarkdown::render({})"'.format(args), "${ }", {"input": input_file, "output": output_file}
)
env.logger.trace('Running command "{}"'.format(cmd))
if env.run_mode == "interactive":
# need to catch output and send to python output, which will in trun be hijacked by SoS notebook
p = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
pid = p.pid
env.register_process(p.pid, "Runing {}".format(input_file))
out, err = p.communicate()
sys.stdout.write(out.decode())
sys.stderr.write(err.decode())
ret = p.returncode
else:
p = subprocess.Popen(cmd, shell=True)
pid = p.pid
env.register_process(pid, "Runing {}".format(input_file))
ret = p.wait()
except Exception as e:
env.logger.error(e)
finally:
env.deregister_process(p.pid)
if ret != 0:
temp_file = os.path.join(".sos", "{}_{}.md".format("Rmarkdown", os.getpid()))
shutil.copyfile(input_file, temp_file)
cmd = interpolate(
'Rscript -e "rmarkdown::render({})"'.format(args), "${ }", {"input": input_file, "output": output_file}
)
raise RuntimeError(
'Failed to execute script. Please use command \n"{}"\nunder {} to test it.'.format(cmd, os.getcwd())
)
if write_to_stdout:
with open(output_file) as out:
sys.stdout.write(out.read())
else:
env.logger.info("Report saved to {}".format(output_file))