def open_gui(self):
"""Open a Molmol pipe."""
# Test that the Molmol binary exists.
test_binary('molmol')
# Python 2.3 and earlier.
if Popen == None:
raise RelaxError("The subprocess module is not available in this version of Python.")
# Open Molmol as a pipe.
self.molmol = Popen(['molmol', '-f', '-'], stdin=PIPE).stdin
# Execute the command history.
if len(self.command_history) > 0:
self.exec_cmd(self.command_history, store_command=0)
return
# Wait a little while for Molmol to initialise.
sleep(2)
# Test if the PDB file has been loaded.
if hasattr(cdp, 'structure'):
self.open_pdb()
# Run InitAll to remove everything from Molmol.
else:
self.molmol.write("InitAll yes\n")
def open_gui(self):
"""Open a Molmol pipe."""
# Test that the Molmol binary exists.
test_binary('molmol')
# Python 2.3 and earlier.
if Popen == None:
raise RelaxError(
"The subprocess module is not available in this version of Python."
)
# Open Molmol as a pipe.
self.molmol = Popen(['molmol', '-f', '-'], stdin=PIPE).stdin
# Execute the command history.
if len(self.command_history) > 0:
self.exec_cmd(self.command_history, store_command=0)
return
# Wait a little while for Molmol to initialise.
sleep(2)
# Test if the PDB file has been loaded.
if hasattr(cdp, 'structure'):
self.open_pdb()
# Run InitAll to remove everything from Molmol.
else:
self.molmol.write("InitAll yes\n")
def open_gui(self):
"""Open the PyMOL GUI."""
# Use the PyMOL python modules.
if self.exec_mode == 'module':
# Open the GUI.
pymol.finish_launching()
self.open = True
# Otherwise execute PyMOL on the command line.
if self.exec_mode == 'external':
# Test that the PyMOL binary exists.
test_binary('pymol')
# Python 2.3 and earlier.
if Popen == None:
raise RelaxError("The subprocess module is not available in this version of Python.")
# Open PyMOL as a pipe.
self.pymol = Popen(['pymol', '-qpK'], stdin=PIPE).stdin
# Execute the command history.
if len(self.command_history) > 0:
self.exec_cmd(self.command_history, store_command=0)
return
# Test if the PDB file has been loaded.
if hasattr(cdp, 'structure'):
self.open_pdb()
def open_gui(self):
"""Open the PyMOL GUI."""
# Use the PyMOL python modules.
if self.exec_mode == 'module':
# Open the GUI.
pymol.finish_launching()
self.open = True
# Otherwise execute PyMOL on the command line.
if self.exec_mode == 'external':
# Test that the PyMOL binary exists.
test_binary('pymol')
# Python 2.3 and earlier.
if Popen == None:
raise RelaxError(
"The subprocess module is not available in this version of Python."
)
# Open PyMOL as a pipe.
self.pymol = Popen(['pymol', '-qpK'], stdin=PIPE).stdin
# Execute the command history.
if len(self.command_history) > 0:
self.exec_cmd(self.command_history, store_command=0)
return
# Test if the PDB file has been loaded.
if hasattr(cdp, 'structure'):
self.open_pdb()
def run(file_prefix="map", dir="dx", dx_exe="dx", vp_exec=True):
"""Execute OpenDX.
@keyword file_prefix: The file prefix for all the created files.
@type file_prefix: str
@keyword dir: The directory to place the files into.
@type dir: str or None
@keyword dx_exe: The path to the OpenDX executable file. This can be changed if the
binary 'dx' is not located in the system path.
@type dx_exe: str
@keyword vp_exec: If True, then the OpenDX visual program will be launched.
@type vp_exec: bool
"""
# Text for changing to the directory dir.
dir_text = ""
if dir != None:
dir_text = " -directory " + dir
# Text for executing OpenDX.
execute_text = ""
if vp_exec:
execute_text = " -execute"
# Test the binary file string corresponds to a valid executable.
test_binary(dx_exe)
# Run OpenDX.
system(dx_exe + dir_text + " -program " + file_prefix + ".net" + execute_text + " &")
def run(file_prefix="map", dir="dx", dx_exe="dx", vp_exec=True):
"""Execute OpenDX.
@keyword file_prefix: The file prefix for all the created files.
@type file_prefix: str
@keyword dir: The directory to place the files into.
@type dir: str or None
@keyword dx_exe: The path to the OpenDX executable file. This can be changed if the
binary 'dx' is not located in the system path.
@type dx_exe: str
@keyword vp_exec: If True, then the OpenDX visual program will be launched.
@type vp_exec: bool
"""
# Text for changing to the directory dir.
dir_text = ""
if dir != None:
dir_text = " -directory " + dir
# Text for executing OpenDX.
execute_text = ""
if vp_exec:
execute_text = " -execute"
# Test the binary file string corresponds to a valid executable.
test_binary(dx_exe)
# Run OpenDX.
system(dx_exe + dir_text + " -program " + file_prefix + ".net" +
execute_text + " &")
def view(file=None, dir=None, grace_exe='xmgrace'):
"""Execute Grace.
@keyword file: The name of the file to open in Grace.
@type file: str
@keyword dir: The optional directory containing the file.
@type dir: str
@keyword grace_exe: The name of the Grace executable file. This should be located within the
system path.
@type grace_exe: str
"""
# Test the binary file string corresponds to a valid executable.
test_binary(grace_exe)
# File path.
file_path = get_file_path(file, dir)
# Run Grace.
system(grace_exe + " \"" + file_path + "\" &")
def __init__(self, methodName='runTest'):
"""Skip the tests if the subprocess module is not available (Python 2.3 and earlier).
@keyword methodName: The name of the test.
@type methodName: str
"""
# Execute the base class method.
super(Palmer, self).__init__(methodName)
# Missing module.
if not dep_check.subprocess_module:
# Store in the status object.
status.skipped_tests.append([methodName, 'subprocess', self._skip_type])
# Test for the presence of the Modelfree4 binary (skip the test if not present).
try:
test_binary('modelfree4')
except:
status.skipped_tests.append([methodName, "Art Palmer's Modelfree4 software", self._skip_type])
def __init__(self, methodName='runTest'):
"""Skip the tests if the subprocess module is not available (Python 2.3 and earlier).
@keyword methodName: The name of the test.
@type methodName: str
"""
# Execute the base class method.
super(Dasha, self).__init__(methodName)
# Missing module.
if not dep_check.subprocess_module:
# Store in the status object.
status.skipped_tests.append([methodName, 'subprocess', self._skip_type])
# Test for the presence of the Dasha binary (skip the test if not present).
try:
test_binary('dasha')
except:
status.skipped_tests.append([methodName, 'Dasha model-free software', self._skip_type])
def view(file=None, dir=None, grace_exe='xmgrace'):
"""Execute Grace.
@keyword file: The name of the file to open in Grace.
@type file: str
@keyword dir: The optional directory containing the file.
@type dir: str
@keyword grace_exe: The name of the Grace executable file. This should be located within the
system path.
@type grace_exe: str
"""
# Test the binary file string corresponds to a valid executable.
test_binary(grace_exe)
# File path.
file_path = get_file_path(file, dir)
# Run Grace.
system(grace_exe + " \"" + file_path + "\" &")
def catia_execute(file='Fit.catia', dir=None, binary=None):
"""Create the CATIA input files.
@keyword file: The main CATIA execution file.
@type file: str
@keyword dir: The optional directory to place the files into. If None, then the files will be placed into the current directory.
@type dir: str or None
@keyword binary: The name of the CATIA binary file. This can include the path to the binary.
@type binary: str
"""
# The current directory.
orig_dir = getcwd()
# Test the binary file string corresponds to a valid executable.
test_binary(binary)
# The directory.
if dir == None:
dir = orig_dir
if not access(dir, F_OK):
raise RelaxDirError('CATIA', dir)
# Change to the directory with the CATIA input files.
chdir(dir)
# Catch failures and return to the correct directory.
try:
# Execute CATIA.
cmd = binary + ' < Fit.catia'
pipe = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE, close_fds=False)
# Close the pipe.
pipe.stdin.close()
# Write to stdout.
for line in pipe.stdout.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stdout.write(line)
# Write to stderr.
for line in pipe.stderr.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stderr.write(line)
# Failure.
except:
# Change back to the original directory.
chdir(orig_dir)
# Reraise the error.
raise
# Change back to the original directory.
chdir(orig_dir)
def cpmgfit_execute(dir=None, binary='cpmgfit', force=False):
"""Execute CPMGFit for each spin input file.
@keyword dir: The directory where the input files are located. If None, this defaults to the dispersion model name in lowercase.
@type dir: str or None
@keyword binary: The name of the CPMGFit binary file. This can include the path to the binary.
@type binary: str
@keyword force: A flag which if True will cause any pre-existing files to be overwritten by CPMGFit.
@type force: bool
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Test if the experiment type has been set.
if not hasattr(cdp, 'exp_type'):
raise RelaxError("The relaxation dispersion experiment type has not been specified.")
# Test if the model has been set.
if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been specified.")
# The directory.
if dir != None and not access(dir, F_OK):
raise RelaxDirError('CPMGFit', dir)
# Loop over each spin.
for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
# Translate the model.
function = translate_model(spin.model)
# The spin input file name.
file_in = dir + sep + spin_file_name(spin_id=spin_id)
if not access(file_in, F_OK):
raise RelaxFileError("spin input", file_in)
# The spin output file name.
file_out = dir + sep + spin_file_name(spin_id=spin_id, output=True)
# Test the binary file string corresponds to a valid executable.
test_binary(binary)
# Execute CPMGFit.
cmd = "%s -grid -xmgr -f %s | tee %s\n" % (binary, file_in, file_out)
print("\n\n%s" % cmd)
pipe = Popen(cmd, shell=True, stdout=PIPE, stderr=PIPE, close_fds=True)
# Write to stderr.
for line in pipe.stderr.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stderr.write(line)
# Write to stdout.
for line in pipe.stdout.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stdout.write(line)
def execute(dir, force, binary):
"""Execute Modelfree4.
BUG: Control-C during execution causes the cwd to stay as dir.
@param dir: The optional directory where the script is located.
@type dir: str or None
@param force: A flag which if True will cause any pre-existing files to be overwritten by
Modelfree4.
@type force: bool
@param binary: The name of the Modelfree4 binary file. This can include the path to the
binary.
@type binary: str
"""
# Check for the diffusion tensor.
if not hasattr(cdp, 'diff_tensor'):
raise RelaxNoTensorError('diffusion')
# The current directory.
orig_dir = getcwd()
# The directory.
if dir == None:
dir = pipes.cdp_name()
if not access(dir, F_OK):
raise RelaxDirError('Modelfree4', dir)
# Change to this directory.
chdir(dir)
# Catch failures and return to the correct directory.
try:
# Python 2.3 and earlier.
if Popen == None:
raise RelaxError("The subprocess module is not available in this version of Python.")
# Test if the 'mfin' input file exists.
if not access('mfin', F_OK):
raise RelaxFileError('mfin input', 'mfin')
# Test if the 'mfdata' input file exists.
if not access('mfdata', F_OK):
raise RelaxFileError('mfdata input', 'mfdata')
# Test if the 'mfmodel' input file exists.
if not access('mfmodel', F_OK):
raise RelaxFileError('mfmodel input', 'mfmodel')
# Test if the 'mfpar' input file exists.
if not access('mfpar', F_OK):
raise RelaxFileError('mfpar input', 'mfpar')
# Test if the 'PDB' input file exists.
if cdp.diff_tensor.type != 'sphere':
pdb = cdp.structure.structural_data[0].mol[0].file_name
if not access(pdb, F_OK):
raise RelaxFileError('PDB', pdb)
else:
pdb = None
# Remove the file 'mfout' and '*.out' if the force flag is set.
if force:
for file in listdir(getcwd()):
if search('out$', file) or search('rotate$', file):
remove(file)
# Test the binary file string corresponds to a valid executable.
test_binary(binary)
# Execute Modelfree4.
if pdb:
cmd = binary + ' -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out -s ' + pdb
else:
cmd = binary + ' -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out'
pipe = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE, close_fds=False)
# Close the pipe.
pipe.stdin.close()
# Write to stdout.
for line in pipe.stdout.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stdout.write(line)
# Write to stderr.
for line in pipe.stderr.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stderr.write(line)
# Failure.
except:
# Change back to the original directory.
chdir(orig_dir)
# Reraise the error.
raise
# Change back to the original directory.
chdir(orig_dir)
def test_dasha(self):
"""Test a complete model-free analysis using the program 'Dasha'."""
# Test for the presence of the Dasha binary (skip the test if not present).
try:
test_binary('dasha')
except:
return
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'dasha.py')
# Check the global data.
self.assertEqual(len(cdp.ri_ids), 3)
for ri_id in cdp.ri_ids:
self.assertEqual(cdp.spectrometer_frq[ri_id], 600000000.0)
self.assertEqual(cdp.ri_type['R1_600'], 'R1')
self.assertEqual(cdp.ri_type['R2_600'], 'R2')
self.assertEqual(cdp.ri_type['NOE_600'], 'NOE')
# The spin data.
select = [True, True, False, False]
fixed = [False, False, False, False]
isotope = ['15N', '15N', '15N', '15N']
model = ['m3', 'm3', 'm3', 'm3']
equation = ['mf_orig', 'mf_orig', 'mf_orig', 'mf_orig']
params = [['s2', 'rex'], ['s2', 'rex'], ['s2', 'rex'], ['s2', 'rex']]
s2 = [0.71510, 0.64359, None, None]
s2f = [None, None, None, None]
s2s = [None, None, None, None]
local_tm = [None, None, None, None]
te = [None, None, None, None]
tf = [None, None, None, None]
ts = [None, None, None, None]
rex_scale = 1.0 / (2.0 * pi * cdp.spectrometer_frq[cdp.ri_ids[0]]) ** 2
rex = [4.32701*rex_scale, 4.29432*rex_scale, None, None]
csa = [-172e-6, -172e-6, -172e-6, -172e-6]
chi2 = [1.9657, 0.63673, None, None]
ri_data = [{'R1_600': 1.0, 'R2_600': 15.0, 'NOE_600': 0.9},
{'R1_600': 0.9, 'R2_600': 13.9, 'NOE_600': 0.79},
{'R2_600': 12.0, 'NOE_600': 0.6},
None]
ri_data_err = [{'R1_600': 0.05, 'R2_600': 0.5, 'NOE_600': 0.05},
{'R1_600': 0.05, 'R2_600': 0.8, 'NOE_600': 0.05},
{'R2_600': 0.5, 'NOE_600': 0.05},
None]
# Check the spin data.
i = 0
for spin in spin_loop():
# Protons.
if spin.isotope == '1H':
self.assertEqual(spin.select, False)
continue
# Check the data.
self.assertEqual(spin.select, select[i])
self.assertEqual(spin.fixed, fixed[i])
self.assertEqual(spin.isotope, isotope[i])
self.assertEqual(spin.model, model[i])
self.assertEqual(spin.equation, equation[i])
self.assertEqual(spin.params, params[i])
self.assertEqual(spin.s2, s2[i])
self.assertEqual(spin.s2f, s2f[i])
self.assertEqual(spin.s2s, s2s[i])
self.assertEqual(spin.local_tm, local_tm[i])
self.assertEqual(spin.te, te[i])
self.assertEqual(spin.tf, tf[i])
self.assertEqual(spin.ts, ts[i])
self.assertEqual(spin.rex, rex[i])
self.assertAlmostEqual(spin.csa, csa[i])
self.assertEqual(spin.chi2, chi2[i])
if ri_data[i] == None:
self.assert_(not hasattr(spin, 'ri_data'))
else:
for ri_id in cdp.ri_ids:
if ri_id in ri_data[i].keys():
self.assertEqual(spin.ri_data[ri_id], ri_data[i][ri_id])
# Increment the spin index.
i += 1
# Check the interatomic data.
r = [1.02e-10, 1.02e-10, 1.02e-10, 1.02e-10]
i = 0
for interatom in interatomic_loop():
self.assertAlmostEqual(interatom.r, r[i])
i += 1
def execute(dir, force, binary):
"""Execute Dasha.
@param dir: The optional directory where the script is located.
@type dir: str or None
@param force: A flag which if True will cause any pre-existing files to be overwritten by Dasha.
@type force: bool
@param binary: The name of the Dasha binary file. This can include the path to the binary.
@type binary: str
"""
# Test the binary file string corresponds to a valid executable.
test_binary(binary)
# The current directory.
orig_dir = getcwd()
# The directory.
if dir == None:
dir = pipes.cdp_name()
if not access(dir, F_OK):
raise RelaxDirError('Dasha', dir)
# Change to this directory.
chdir(dir)
# Catch failures and return to the correct directory.
try:
# Test if the 'dasha_script' script file exists.
if not access('dasha_script', F_OK):
raise RelaxFileError('dasha script', 'dasha_script')
# Python 2.3 and earlier.
if Popen == None:
raise RelaxError("The subprocess module is not available in this version of Python.")
# Execute Dasha.
pipe = Popen(binary, shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE, close_fds=False)
# Get the contents of the script and pump it into Dasha.
script = open('dasha_script')
lines = script.readlines()
script.close()
for line in lines:
# Encode to a Python 3 byte array.
if hasattr(line, 'encode'):
line = line.encode()
# Write out.
pipe.stdin.write(line)
# Close the pipe.
pipe.stdin.close()
# Write to stdout.
for line in pipe.stdout.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stdout.write(line)
# Write to stderr.
for line in pipe.stderr.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stderr.write(line)
# Failure.
except:
# Change back to the original directory.
chdir(orig_dir)
# Reraise the error.
raise
# Change back to the original directory.
chdir(orig_dir)
# Print some blank lines (aesthetics)
sys.stdout.write("\n\n")
def execute(dir, force, binary):
"""Execute Modelfree4.
BUG: Control-C during execution causes the cwd to stay as dir.
@param dir: The optional directory where the script is located.
@type dir: str or None
@param force: A flag which if True will cause any pre-existing files to be overwritten by
Modelfree4.
@type force: bool
@param binary: The name of the Modelfree4 binary file. This can include the path to the
binary.
@type binary: str
"""
# Check for the diffusion tensor.
if not hasattr(cdp, 'diff_tensor'):
raise RelaxNoTensorError('diffusion')
# The current directory.
orig_dir = getcwd()
# The directory.
if dir == None:
dir = pipes.cdp_name()
if not access(dir, F_OK):
raise RelaxDirError('Modelfree4', dir)
# Change to this directory.
chdir(dir)
# Catch failures and return to the correct directory.
try:
# Python 2.3 and earlier.
if Popen == None:
raise RelaxError(
"The subprocess module is not available in this version of Python."
)
# Test if the 'mfin' input file exists.
if not access('mfin', F_OK):
raise RelaxFileError('mfin input', 'mfin')
# Test if the 'mfdata' input file exists.
if not access('mfdata', F_OK):
raise RelaxFileError('mfdata input', 'mfdata')
# Test if the 'mfmodel' input file exists.
if not access('mfmodel', F_OK):
raise RelaxFileError('mfmodel input', 'mfmodel')
# Test if the 'mfpar' input file exists.
if not access('mfpar', F_OK):
raise RelaxFileError('mfpar input', 'mfpar')
# Test if the 'PDB' input file exists.
if cdp.diff_tensor.type != 'sphere':
pdb = cdp.structure.structural_data[0].mol[0].file_name
if not access(pdb, F_OK):
raise RelaxFileError('PDB', pdb)
else:
pdb = None
# Remove the file 'mfout' and '*.out' if the force flag is set.
if force:
for file in listdir(getcwd()):
if search('out$', file) or search('rotate$', file):
remove(file)
# Test the binary file string corresponds to a valid executable.
test_binary(binary)
# Execute Modelfree4.
if pdb:
cmd = binary + ' -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out -s ' + pdb
else:
cmd = binary + ' -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out'
pipe = Popen(cmd,
shell=True,
stdin=PIPE,
stdout=PIPE,
stderr=PIPE,
close_fds=False)
out, err = pipe.communicate()
# Close the pipe.
pipe.stdin.close()
# Write to stdout.
if out:
# Decode Python 3 byte arrays.
if hasattr(out, 'decode'):
out = out.decode()
# Write.
sys.stdout.write(out)
# Write to stderr.
if err:
# Decode Python 3 byte arrays.
if hasattr(err, 'decode'):
err = err.decode()
# Write.
sys.stderr.write(err)
# Catch errors.
if pipe.returncode == -signal.SIGSEGV:
raise RelaxError(
"Modelfree4 return code 11 (Segmentation fault).\n")
elif pipe.returncode:
raise RelaxError("Modelfree4 return code %s.\n" % pipe.returncode)
# Failure.
except:
# Change back to the original directory.
chdir(orig_dir)
# Reraise the error.
raise
# Change back to the original directory.
chdir(orig_dir)
def cpmgfit_execute(dir=None, binary='cpmgfit', force=False):
"""Execute CPMGFit for each spin input file.
@keyword dir: The directory where the input files are located. If None, this defaults to the dispersion model name in lowercase.
@type dir: str or None
@keyword binary: The name of the CPMGFit binary file. This can include the path to the binary.
@type binary: str
@keyword force: A flag which if True will cause any pre-existing files to be overwritten by CPMGFit.
@type force: bool
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Test if the experiment type has been set.
if not hasattr(cdp, 'exp_type'):
raise RelaxError("The relaxation dispersion experiment type has not been specified.")
# Test if the model has been set.
if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been specified.")
# The directory.
if dir != None and not access(dir, F_OK):
raise RelaxDirError('CPMGFit', dir)
# Loop over each spin.
for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
# Translate the model.
function = translate_model(spin.model)
# The spin input file name.
file_in = dir + sep + spin_file_name(spin_id=spin_id)
if not access(file_in, F_OK):
raise RelaxFileError("spin input", file_in)
# The spin output file name.
file_out = dir + sep + spin_file_name(spin_id=spin_id, output=True)
# Test the binary file string corresponds to a valid executable.
test_binary(binary)
# Execute CPMGFit.
cmd = "%s -grid -xmgr -f %s | tee %s\n" % (binary, file_in, file_out)
print("\n\n%s" % cmd)
pipe = Popen(cmd, shell=True, stdout=PIPE, stderr=PIPE, close_fds=True)
# Write to stderr.
for line in pipe.stderr.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stderr.write(line)
# Write to stdout.
for line in pipe.stdout.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stdout.write(line)
def execute(dir, force, binary):
"""Execute Dasha.
@param dir: The optional directory where the script is located.
@type dir: str or None
@param force: A flag which if True will cause any pre-existing files to be overwritten by Dasha.
@type force: bool
@param binary: The name of the Dasha binary file. This can include the path to the binary.
@type binary: str
"""
# Test the binary file string corresponds to a valid executable.
test_binary(binary)
# The current directory.
orig_dir = getcwd()
# The directory.
if dir == None:
dir = pipes.cdp_name()
if not access(dir, F_OK):
raise RelaxDirError('Dasha', dir)
# Change to this directory.
chdir(dir)
# Catch failures and return to the correct directory.
try:
# Test if the 'dasha_script' script file exists.
if not access('dasha_script', F_OK):
raise RelaxFileError('dasha script', 'dasha_script')
# Python 2.3 and earlier.
if Popen == None:
raise RelaxError(
"The subprocess module is not available in this version of Python."
)
# Execute Dasha.
pipe = Popen(binary,
shell=True,
stdin=PIPE,
stdout=PIPE,
stderr=PIPE,
close_fds=False)
# Get the contents of the script and pump it into Dasha.
script = open('dasha_script')
lines = script.readlines()
script.close()
for line in lines:
# Encode to a Python 3 byte array.
if hasattr(line, 'encode'):
line = line.encode()
# Write out.
pipe.stdin.write(line)
# Close the pipe.
pipe.stdin.close()
# Write to stdout.
for line in pipe.stdout.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stdout.write(line)
# Write to stderr.
for line in pipe.stderr.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stderr.write(line)
# Failure.
except:
# Change back to the original directory.
chdir(orig_dir)
# Reraise the error.
raise
# Change back to the original directory.
chdir(orig_dir)
# Print some blank lines (aesthetics)
sys.stdout.write("\n\n")
def catia_execute(file='Fit.catia', dir=None, binary=None):
"""Create the CATIA input files.
@keyword file: The main CATIA execution file.
@type file: str
@keyword dir: The optional directory to place the files into. If None, then the files will be placed into the current directory.
@type dir: str or None
@keyword binary: The name of the CATIA binary file. This can include the path to the binary.
@type binary: str
"""
# The current directory.
orig_dir = getcwd()
# Test the binary file string corresponds to a valid executable.
test_binary(binary)
# The directory.
if dir == None:
dir = orig_dir
if not access(dir, F_OK):
raise RelaxDirError('CATIA', dir)
# Change to the directory with the CATIA input files.
chdir(dir)
# Catch failures and return to the correct directory.
try:
# Execute CATIA.
cmd = binary + ' < Fit.catia'
pipe = Popen(cmd,
shell=True,
stdin=PIPE,
stdout=PIPE,
stderr=PIPE,
close_fds=False)
# Close the pipe.
pipe.stdin.close()
# Write to stdout.
for line in pipe.stdout.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stdout.write(line)
# Write to stderr.
for line in pipe.stderr.readlines():
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
# Write.
sys.stderr.write(line)
# Failure.
except:
# Change back to the original directory.
chdir(orig_dir)
# Reraise the error.
raise
# Change back to the original directory.
chdir(orig_dir)
