def run_matlab(**kwargs):
"""Run Matlab program with log file
"""
run = RunProgramDirective(kwargs)
try:
run.error_check('matlab')
run.changedir = True
# Get option
option = run.option
if not run.option:
if run.osname.startswith('win'):
option = metadata.default_options['matlabwin']
else:
option = metadata.default_options['matlabunix']
# Get executable
executable = run.executable
if not run.executable:
executable = metadata.default_executables['matlab']
program = run.program_name
default_log = os.path.join(run.program_path, run.program_name + '.log')
command = metadata.commands['matlab'] % (executable, program,
run.program_name + '.log',
option)
run.execute_run(command)
run.move_log(default_log)
except:
add_error_to_log(run.makelog)
def run_rinstall(**kwargs):
"""Install R package
"""
run = RunRPackageDirective(kwargs)
try:
run.error_check('rinstall')
# Get option
option = run.option
if not run.option:
option = metadata.default_options['rinstall']
# Get executable
executable = run.executable
if not run.executable:
executable = metadata.default_executables['rinstall']
command = metadata.commands['rinstall'] % (executable, option,
run.lib, run.package)
run.execute_run(command)
except:
add_error_to_log(run.makelog)
def run_rbatch(**kwargs):
"""Run R batch program with log file
"""
run = RunProgramDirective(kwargs)
try:
run.error_check('rbatch')
# Get option
option = run.option
if not run.option:
option = metadata.default_options['rbatch']
if run.changedir:
program = '"' + run.program + '"'
default_log = os.path.join(run.program_path,
run.program_name + '.Rout')
else:
program = '"' + os.path.join(run.program_path, run.program) + '"'
default_log = os.path.join(os.getcwd(), run.program_name + '.Rout')
# Get executable
executable = run.executable
if not run.executable:
executable = metadata.default_executables['rbatch']
command = metadata.commands['rbatch'] % (executable, option, program,
run.program_name + '.Rout')
run.execute_run(command)
run.move_log(default_log)
except:
add_error_to_log(run.makelog)
def run_lyx(**kwargs):
"""Run Lyx export to Pdf
"""
run = RunProgramDirective(kwargs)
try:
run.error_check('lyx')
if run.changedir:
program = '"' + run.program + '"'
else:
program = '"' + run.program_full + '"'
# Get executable
executable = run.executable
if not run.executable:
executable = metadata.default_executables['lyx']
command = metadata.commands['lyx'] % (executable, program, run.option)
run.execute_run(command)
# Move PDF output
pdfname = os.path.join(run.program_path, run.program_name + '.pdf')
pdfout = run.pdfout
if '.pdf' not in pdfout:
pdfout = os.path.join(pdfout, run.program_name + '.pdf')
if os.path.abspath(pdfname) != os.path.abspath(pdfout):
shutil.copy2(pdfname, pdfout)
os.remove(pdfname)
except:
add_error_to_log(run.makelog)
def run_mathematica(**kwargs):
"""Run Mathematica program
"""
run = RunProgramDirective(kwargs)
try:
run.error_check('math')
if run.changedir:
program = '"' + run.program + '"'
else:
program = '"' + run.program_full + '"'
# Get option
option = run.option
if not run.option:
option = metadata.default_options['math']
# Get executable
executable = run.executable
if not run.executable:
if run.osname.startswith('darwin'):
executable = metadata.default_executables['mathunix']
else:
executable = metadata.default_executables['mathnonunix']
command = metadata.commands['math'] % (executable, program, option)
run.execute_run(command)
except:
add_error_to_log(run.makelog)
def run_command(**kwargs):
"""Run a Shell command
"""
run = RunCommandDirective(kwargs)
try:
run.error_check('other')
run.execute_run(run.command)
except:
add_error_to_log(run.makelog)
def run_sas(**kwargs):
"""Run SAS script
"""
run = RunProgramDirective(kwargs)
try:
run.error_check('sas')
# Get option
option = run.option
if not run.option:
if run.osname != 'posix':
option = metadata.default_options['saswin']
# Get executable
executable = run.executable
if not run.executable:
executable = metadata.default_executables['sas']
# Get log, lst, and program
if run.changedir:
program = '"' + run.program + '"'
default_log = os.path.join(run.program_path,
run.program_name + '.log')
default_lst = os.path.join(run.program_path,
run.program_name + '.lst')
else:
program = '"' + os.path.join(run.program_path, run.program) + '"'
default_log = os.path.join(os.getcwd(), run.program_name + '.log')
default_lst = os.path.join(os.getcwd(), run.program_name + '.lst')
if run.osname == 'posix':
command = metadata.commands['sas'] % (executable, option, program)
else:
command = metadata.commands['sas'] % (executable, program, option)
run.execute_run(command)
run.move_log(default_log)
run.move_lst(default_lst)
except:
add_error_to_log(run.makelog)
def run_stata(**kwargs):
"""Run Stata program with log file
"""
run = RunProgramDirective(kwargs)
try:
run.error_check('stata')
# Set option
option = run.option
if not option:
if run.osname.startswith('win'):
option = metadata.default_options['statawin']
else:
option = metadata.default_options['stataunix']
# Set executable
executable = run.executable
if not executable:
if run.osname.startswith('win'):
executable = metadata.default_executables['statawin']
elif run.osname.startswith('linux'):
executable = metadata.default_executables['statalinux']
else:
executable = metadata.default_executables['statamac']
# Set default_log
if run.changedir:
program = '"' + run.program + '"'
default_log = os.path.join(run.program_path,
run.program_name + '.log')
else:
program = '"' + os.path.join(run.program_path, run.program) + '"'
default_log = os.path.join(os.getcwd(), run.program_name + '.log')
command = metadata.commands['stata'] % (executable, option, program)
run.execute_run(command)
run.move_log(default_log)
except:
add_error_to_log(run.makelog)
def run_stcmd(**kwargs):
"""Run StatTransfer .stcmd program
"""
run = RunProgramDirective(kwargs)
try:
run.error_check('stcmd')
if run.changedir:
program = '"' + run.program + '"'
else:
program = '"' + run.program_full + '"'
# Get executable
executable = run.executable
if not run.executable:
executable = metadata.default_executables['st']
command = metadata.commands['st'] % (executable, program)
run.execute_run(command)
except:
add_error_to_log(run.makelog)
def run_perl(**kwargs):
"""Run Perl program
"""
run = RunProgramDirective(kwargs)
try:
run.error_check('perl')
if run.changedir:
program = '"' + run.program + '"'
else:
program = '"' + run.program_full + '"'
# Get executable
executable = run.executable
if not run.executable:
executable = metadata.default_executables['perl']
command = metadata.commands['perl'] % (executable, run.option,
program, run.args)
run.execute_run(command)
except:
add_error_to_log(run.makelog)
def run_tex(**kwargs):
"""Run latexmk to convert .tex to .pdf
"""
run = RunProgramDirective(kwargs)
try:
run.error_check('tex')
run.changedir = True
# Get executable
executable = run.executable
if not run.executable:
executable = metadata.default_executables['tex']
# Get option
option = run.option
if not run.option:
option = metadata.default_options['tex']
option = option + ' -output-directory=temp'
prog_tex = run.program_name + metadata.extensions['tex']
prog_tilde_tex = run.program_name + '_tilde' + \
metadata.extensions['tex']
file_path = os.path.join(run.program_path, prog_tex)
file_path_tilde = os.path.join(run.program_path, prog_tilde_tex)
add_tilde(file_path, file_path_tilde)
check_for_multiple_periods(file_path_tilde, run.makelog)
program = '"' + prog_tilde_tex + '"'
command = metadata.commands['tex'] % (executable, option, program)
run.execute_run(command)
out_dir = metadata.settings['output_dir']
print(os.path.abspath(out_dir))
try:
shutil.copy2(file_path_tilde, out_dir)
os.remove(file_path_tilde)
except:
pass
pdf_tilde = os.path.join(run.program_path, 'temp',
run.program_name + '_tilde.pdf')
pdf = os.path.join(run.program_path, 'temp', run.program_name + '.pdf')
os.rename(pdf_tilde, pdf)
try:
shutil.copy2(pdf, out_dir)
except:
print('error')
shutil.rmtree(os.path.join(run.program_path, 'temp'))
except:
add_error_to_log(run.makelog)
try:
prog_tilde_tex = run.program_name + '_tilde' + \
metadata.extensions['tex']
file_path_tilde = os.path.join(run.program_path, prog_tilde_tex)
os.remove(file_path_tilde)
except OSError:
pass