def install_package(service, library_path, package_name, package_path):
r_path = r_config.get_r_path(service)
# check if the R library is installed
def raise_e_path_error(msg):
raise InstallPackageError(package_name, msg)
verify_r_path(r_path, raise_e_path_error)
# dont't install if the package already exists in library
library_package_path = os.path.join(library_path, package_name)
if os.path.exists(library_package_path):
raise InstallPackageError(package_name, 'Already installed')
command = "\"" + r_path + "\" CMD INSTALL -l \"" + library_path + "\" \"" + package_path + "\""
process = subprocess.Popen(
command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True
)
_, output = process.communicate()
# package directory doesn't exists after installation?
if not os.path.exists(library_package_path):
raise InstallPackageError(package_name, output)
def install_package(service, library_path, package_name, package_path):
r_path = r_config.get_r_path(service)
# check if the R library is installed
def raise_e_path_error(msg):
raise InstallPackageError(package_name, msg)
verify_r_path(r_path, raise_e_path_error)
# dont't install if the package already exists in library
library_package_path = os.path.join(library_path, package_name)
if os.path.exists(library_package_path):
raise InstallPackageError(package_name, 'Already installed')
command = "\"" + r_path + "\" CMD INSTALL -l \"" + library_path + "\" \"" + package_path + "\""
process = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
_, output = process.communicate()
# package directory doesn't exists after installation?
if not os.path.exists(library_package_path):
raise InstallPackageError(package_name, output)
def exeute(service, script, library_path, scripts_path):
r_path = r_config.get_r_path(service)
# check if the R library is installed
def raise_e_path_error(msg):
raise RError(msg)
verify_r_path(r_path, raise_e_path_error)
r_output_filename = None
error_path = None
script_path = None
try:
# create r output file
with tempfile.NamedTemporaryFile(delete=False) as f:
r_output_filename = f.name
# create error file
with tempfile.NamedTemporaryFile(delete=False) as f:
error_path = f.name
# create script file
with tempfile.NamedTemporaryFile(delete=False) as f:
script_path = f.name
f.write("""
tryCatch(
{
""")
f.write(script)
f.write("""
},
error=function(err) {
fileConn<-file('""")
f.write(error_path.replace('\\', '\\\\'))
f.write("""')
writeLines(c(conditionMessage(err)), fileConn)
close(fileConn)
})
""")
process = subprocess.Popen(
"\"" + r_path + "\" --vanilla" + " < \"" + script_path + "\" > \"" + r_output_filename + "\"",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True,
cwd=scripts_path,
env={
'R_LIBS_USER': library_path
},
)
std_output, std_error = process.communicate()
if process.returncode:
if std_error is not None and len(std_error) > 0:
output = std_error.strip()
elif std_output is not None and len(std_output) > 0:
output = std_output.strip()
else:
output = None
if output:
raise RError('R exited with code %s: %s' % (process.returncode, output))
else:
raise RError('R exited with code %s' % process.returncode)
with open(error_path) as f:
err = f.read().strip()
if len(err) > 0:
if std_error is not None and len(std_error) > 0:
raise RError('%s, %s' % (err, std_error.strip()))
elif std_output is not None and len(std_output) > 0:
raise RError('%s, %s' % (err, std_output.strip()))
else:
raise RError('%s' % err)
finally:
# delete temp files
if error_path:
os.remove(error_path)
if r_output_filename:
os.remove(r_output_filename)
if script_path:
os.remove(script_path)
def test_get_r_path(self):
service = Service()
r_path = r_config.get_r_path(service)
self.assertTrue(os.path.exists(r_path), 'invalid R path: %s' % r_path)
def exeute(service, script, library_path, scripts_path):
r_path = r_config.get_r_path(service)
# check if the R library is installed
def raise_e_path_error(msg):
raise RError(msg)
verify_r_path(r_path, raise_e_path_error)
r_output_filename = None
error_path = None
script_path = None
try:
# create r output file
with tempfile.NamedTemporaryFile(delete=False) as f:
r_output_filename = f.name
# create error file
with tempfile.NamedTemporaryFile(delete=False) as f:
error_path = f.name
# create script file
with tempfile.NamedTemporaryFile(delete=False) as f:
script_path = f.name
f.write("""
tryCatch(
{
""")
f.write(script)
f.write("""
},
error=function(err) {
fileConn<-file('""")
f.write(error_path.replace('\\', '\\\\'))
f.write("""')
writeLines(c(conditionMessage(err)), fileConn)
close(fileConn)
})
""")
process = subprocess.Popen(
"\"" + r_path + "\" --vanilla" + " < \"" + script_path +
"\" > \"" + r_output_filename + "\"",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True,
cwd=scripts_path,
env={'R_LIBS_USER': library_path},
)
std_output, std_error = process.communicate()
if process.returncode:
if std_error is not None and len(std_error) > 0:
output = std_error.strip()
elif std_output is not None and len(std_output) > 0:
output = std_output.strip()
else:
output = None
if output:
raise RError('R exited with code %s: %s' %
(process.returncode, output))
else:
raise RError('R exited with code %s' % process.returncode)
with open(error_path) as f:
err = f.read().strip()
if len(err) > 0:
if std_error is not None and len(std_error) > 0:
raise RError('%s, %s' % (err, std_error.strip()))
elif std_output is not None and len(std_output) > 0:
raise RError('%s, %s' % (err, std_output.strip()))
else:
raise RError('%s' % err)
finally:
# delete temp files
if error_path:
os.remove(error_path)
if r_output_filename:
os.remove(r_output_filename)
if script_path:
os.remove(script_path)
def test_get_r_path(self):
service = Service()
r_path = r_config.get_r_path(service)
self.assertTrue(os.path.exists(r_path), 'invalid R path: %s' % r_path)
