Author: tlinnet
Date: Wed Aug 20 13:56:47 2014
New Revision: 25088
URL: http://svn.gna.org/viewcvs/relax?rev=25088&view=rev
Log:
Moved the unit test of specific_analyses.relax_disp.checks.check_missing_r1()
from a unit test to a system test.
This is because the unit test involved several functions of relax.
Modified:
trunk/test_suite/system_tests/relax_disp.py
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_checks.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=25088&r1=25087&r2=25088&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Wed Aug 20 13:56:47 2014
@@ -33,6 +33,7 @@
import dep_check
from lib.io import get_file_path
from pipe_control.mol_res_spin import generate_spin_string, return_spin,
spin_loop
+from specific_analyses.relax_disp.checks import check_missing_r1
from specific_analyses.relax_disp.data import generate_r20_key,
get_curve_type, has_r1rho_exp_type, loop_exp_frq, loop_exp_frq_offset_point,
return_grace_file_name_ini, return_param_key_from_data
from specific_analyses.relax_disp.data import INTERPOLATE_DISP,
INTERPOLATE_OFFSET, X_AXIS_DISP, X_AXIS_W_EFF, X_AXIS_THETA, Y_AXIS_R2_R1RHO,
Y_AXIS_R2_EFF
from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_R1RHO, MODEL_B14_FULL,
MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_DPL94_FIT_R1, MODEL_IT99,
MODEL_LM63, MODEL_M61B, MODEL_MP05, MODEL_MP05_FIT_R1, MODEL_NOREX,
MODEL_NOREX_R1RHO, MODEL_NOREX_R1RHO_FIT_R1, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_2SITE_FIT_R1, MODEL_PARAMS, MODEL_R2EFF,
MODEL_TP02, MODEL_TP02_FIT_R1, MODEL_TAP03, MODEL_TAP03_FIT_R1
@@ -691,6 +692,36 @@
self.interpreter.minimise.calculate(verbosity=1)
+ def setup_missing_r1_spins(self):
+ """Function for setting up a few spins for the given pipe."""
+
+ # Path to file.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
+
+ # File with spins.
+ file = open(data_path+sep+'R1_fitted_values.txt')
+ lines = file.readlines()
+ file.close()
+
+ for i, line in enumerate(lines):
+ # Make the string test
+ line_split = line.split()
+
+ if line_split[0] == "#":
+ continue
+
+ mol_name = line_split[0]
+ mol_name = None
+ res_num = int(line_split[1])
+ res_name = line_split[2]
+ spin_num = line_split[3]
+ spin_num = None
+ spin_name = line_split[4]
+
+ # Create the spin.
+ self.interpreter.spin.create(spin_name=spin_name,
spin_num=spin_num, res_name=res_name, res_num=res_num, mol_name=mol_name)
+
+
def setup_tp02_data_to_ns_r1rho_2site(self, clustering=False):
"""Setup data for the test of relaxation dispersion 'NS R1rho
2-site' model fitting against the 'TP02' test data."""
@@ -1319,6 +1350,43 @@
# Assert that the number of columns is equal, plus 1 for "#".
self.assertEqual(nr_split_header, len(line_split_val) + 1)
+
+
+ def test_check_missing_r1(self):
+ """Test of the check_missing_r1() function."""
+
+ # Set up some spins.
+ self.setup_missing_r1_spins()
+
+ # Set variables.
+ exp_type = 'R1rho'
+ frq = 800.1 * 1E6
+
+ spectrum_id='test'
+
+ # Set an experiment type to the pipe.
+ self.interpreter.relax_disp.exp_type(spectrum_id=spectrum_id,
exp_type=exp_type)
+
+ # Set a frequency to loop through.
+ self.interpreter.spectrometer.frequency(id=spectrum_id, frq=frq,
units='Hz')
+
+ # Check R1 for DPL94.
+ check_missing_r1_return = check_missing_r1(model=MODEL_DPL94)
+ self.assertEqual(check_missing_r1_return, True)
+
+ # Check R1 for R2eff.
+ check_missing_r1_return = check_missing_r1(model=MODEL_R2EFF)
+ self.assertEqual(check_missing_r1_return, False)
+
+ # The path to the data files.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
+
+ # Now load some R1 data.
+ self.interpreter.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)
+
+ # Check R1.
+ check_missing_r1_return = check_missing_r1(model=MODEL_DPL94)
+ self.assertEqual(check_missing_r1_return, False)
def test_cpmg_synthetic_b14_to_ns3d_cluster(self):
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_checks.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_checks.py?rev=25088&r1=25087&r2=25088&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_checks.py
(original)
+++ trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_checks.py
Wed Aug 20 13:56:47 2014
@@ -24,91 +24,13 @@
from os import sep
# relax module imports.
-from data_store import Relax_data_store; ds = Relax_data_store()
-from pipe_control import mol_res_spin, pipes, relax_data, spectrometer, state
-from specific_analyses.relax_disp.checks import check_missing_r1, get_times
-from specific_analyses.relax_disp.data import set_exp_type
-from specific_analyses.relax_disp.variables import MODEL_DPL94, MODEL_R2EFF
-from status import Status; status = Status()
+from pipe_control import state
+from specific_analyses.relax_disp.checks import get_times
from test_suite.unit_tests.base_classes import UnitTestCase
class Test_checks(UnitTestCase):
"""Unit tests for the functions of the
specific_analyses.relax_disp.checks module."""
-
- def setUp(self):
- """Setup some structures for the unit tests."""
-
- # Create a dispersion data pipe.
- ds.add(pipe_name='orig', pipe_type='relax_disp')
-
-
- def set_up_spins(self, pipe_name=None):
- """Function for setting up a few spins for the given pipe."""
-
- # Alias the pipe.
- pipe = pipes.get_pipe(pipe_name)
-
- # Path to file.
- data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
-
- # File with spins.
- file = open(data_path+sep+'R1_fitted_values.txt')
- lines = file.readlines()
- file.close()
-
- for i, line in enumerate(lines):
- # Make the string test
- line_split = line.split()
-
- if line_split[0] == "#":
- continue
-
- mol_name = line_split[0]
- mol_name = None
- res_num = int(line_split[1])
- res_name = line_split[2]
- spin_num = line_split[3]
- spin_num = None
- spin_name = line_split[4]
-
- # Create the spin.
- mol_res_spin.create_spin(spin_num=spin_num, spin_name=spin_name,
res_num=res_num, res_name=res_name, mol_name=mol_name, pipe=pipe_name)
-
-
- def test_check_missing_r1(self):
- """Unit test of the check_missing_r1() function."""
-
- # Set up some spins.
- self.set_up_spins(pipe_name='orig')
-
- # Set variables.
- exp_type = 'R1rho'
- frq = 800.1 * 1E6
-
- # Set an experiment type to the pipe.
- set_exp_type(spectrum_id='test', exp_type=exp_type)
-
- # Set a frequency to loop through.
- spectrometer.set_frequency(id='test', frq=frq, units='Hz')
-
- # Check R1 for DPL94.
- check_missing_r1_return = check_missing_r1(model=MODEL_DPL94)
- self.assertEqual(check_missing_r1_return, True)
-
- # Check R1 for R2eff.
- check_missing_r1_return = check_missing_r1(model=MODEL_R2EFF)
- self.assertEqual(check_missing_r1_return, False)
-
- # The path to the data files.
- data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
-
- # Now load some 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)
-
- # Check R1.
- check_missing_r1_return = check_missing_r1(model=MODEL_DPL94)
- self.assertEqual(check_missing_r1_return, False)
def test_get_times_cpmg(self):
r25088 - in /trunk/test_suite: system_tests/relax_disp.py unit_tests/_specific_analyses/_relax_disp/test_checks.py