URL:
<http://gna.org/bugs/?22937>
Summary: Failure of the
Relax_disp.test_estimate_r2eff_err_auto system test on Python 2.5.
Project: relax
Submitted by: bugman
Submitted on: Mon 10 Nov 2014 05:18:21 PM UTC
Category: Test suite
Specific analysis category: None
Priority: 5 - Normal
Severity: 3 - Normal
Status: None
Assigned to: bugman
Originator Name:
Originator Email:
Open/Closed: Open
Release: 3.3.1
Discussion Lock: Any
Operating System: All systems
_______________________________________________________
Details:
Due to a missing newline character at the end of the
test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py
script, the test fails with:
======================================================================
ERROR: Test the user function for estimating R2eff errors from exponential
curve fitting, via the auto_analyses menu.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='relax_disp', pipe_type='relax_disp',
bundle=None)
relax> pipe.create(pipe_name='base pipe', pipe_type='relax_disp',
bundle='relax_disp')
relax>
script(file='/data/relax/relax-trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py',
dir=None)
script =
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py'
----------------------------------------------------------------------------------------------------
###############################################################################
#
#
# Copyright (C) 2013-2014 Troels E. Linnet
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
# This program is free software: you can redistribute it and/or modify
#
# it under the terms of the GNU General Public License as published by
#
# the Free Software Foundation, either version 3 of the License, or
#
# (at your option) any later version.
#
#
#
# This program is distributed in the hope that it will be useful,
#
# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
# GNU General Public License for more details.
#
#
#
# You should have received a copy of the GNU General Public License
#
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
#
#
###############################################################################
# Python module imports.
from os import getcwd, sep
# relax module imports.
from status import Status; status = Status()
#data_path = getcwd()
data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
# Read the spins.
spectrum.read_spins(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')
# Name the isotope for field strength scaling.
spin.isotope(isotope='15N')
# Load the experiments settings file.
expfile = open(data_path+sep+'exp_parameters_sort.txt', 'r')
expfileslines = expfile.readlines()
expfile.close()
# In MHz
yOBS = 81.050
# In ppm
yCAR = 118.078
centerPPM_N15 = yCAR
## Read the chemical shift data.
chemical_shift.read(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')
## The lock power to field, has been found in an calibration experiment.
spin_lock_field_strengths_Hz = {'35': 431.0, '39': 651.2, '41': 800.5, '43':
984.0, '46': 1341.11, '48': 1648.5}
## Apply spectra settings.
for i in range(len(expfileslines)):
line = expfileslines[i]
if line[0] == "#":
continue
else:
# DIRN I deltadof2 dpwr2slock ncyc trim ss sfrq
DIRN = line.split()[0]
I = int(line.split()[1])
deltadof2 = line.split()[2]
dpwr2slock = line.split()[3]
ncyc = int(line.split()[4])
trim = float(line.split()[5])
ss = int(line.split()[6])
set_sfrq = float(line.split()[7])
apod_rmsd = float(line.split()[8])
spin_lock_field_strength = spin_lock_field_strengths_Hz[dpwr2slock]
# Calculate spin_lock time
time_sl = 2*ncyc*trim
# Define file name for peak list.
FNAME = "%s_%s_%s_%s_max_standard.ser"%(I, deltadof2, dpwr2slock,
ncyc)
sp_id = "%s_%s_%s_%s"%(I, deltadof2, dpwr2slock, ncyc)
# Load the peak intensities.
spectrum.read_intensities(file=FNAME, dir=data_path+sep+'peak_lists',
spectrum_id=sp_id, int_method='height')
# Set the peak intensity errors, as defined as the baseplane RMSD.
spectrum.baseplane_rmsd(error=apod_rmsd, spectrum_id=sp_id)
# Set the relaxation dispersion experiment type.
relax_disp.exp_type(spectrum_id=sp_id, exp_type='R1rho')
# Set The spin-lock field strength, nu1, in Hz
relax_disp.spin_lock_field(spectrum_id=sp_id,
field=spin_lock_field_strength)
# Calculating the spin-lock offset in ppm, from offsets values
provided in Hz.
frq_N15_Hz = yOBS * 1E6
offset_ppm_N15 = float(deltadof2) / frq_N15_Hz * 1E6
omega_rf_ppm = centerPPM_N15 + offset_ppm_N15
# Set The spin-lock offset, omega_rf, in ppm.
relax_disp.spin_lock_offset(spectrum_id=sp_id, offset=omega_rf_ppm)
# Set the relaxation times (in s).
relax_disp.relax_time(spectrum_id=sp_id, time=time_sl)
# Set the spectrometer frequency.
spectrometer.frequency(id=sp_id, frq=set_sfrq, units='MHz')
# Read the R1 data
# relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0],
file='R1_fitted_values.txt', dir=data_path, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6,
error_col=7)----------------------------------------------------------------------------------------------------
Traceback (most recent call last):
File "/data/relax/relax-trunk/test_suite/system_tests/relax_disp.py", line
3403, in test_estimate_r2eff_err_auto
self.interpreter.script(file=file, dir=None)
File "/data/relax/relax-trunk/prompt/uf_objects.py", line 226, in __call__
self._backend(*new_args, **uf_kargs)
File "/data/relax/relax-trunk/pipe_control/script.py", line 67, in script
prompt.interpreter.run_script(local=interpreter._locals,
script_file=file_path)
File "/data/relax/relax-trunk/prompt/interpreter.py", line 585, in
run_script
return console.interact(intro, local, script_file,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/data/relax/relax-trunk/prompt/interpreter.py", line 484, in
interact_script
exec_script(script_file, local)
File "/data/relax/relax-trunk/prompt/interpreter.py", line 363, in
exec_script
runpy.run_module(module, globals)
File "/data/python//lib/python2.5/runpy.py", line 88, in run_module
code = loader.get_code(mod_name)
File "/data/python//lib/python2.5/pkgutil.py", line 275, in get_code
self.code = compile(source, self.filename, 'exec')
File
"/data/relax/relax-trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py",
line 107
# relax_data.read(ri_id='R1', ri_type='R1',
frq=cdp.spectrometer_frq_list[0], file='R1_fitted_values.txt', dir=data_path,
mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
^
SyntaxError: invalid syntax
----------------------------------------------------------------------
Ran 432 tests in 902.463s
FAILED (errors=1)
_______________________________________________________
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<http://gna.org/bugs/?22937>
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