Re: r25048 - in /trunk: specific_analyses/relax_disp/checks.py test_suite/unit_tests/_specific_analyses/_relax_disp/test_checks.py -- August 18, 2014 - 17:15

Hi Troels,

As the unit test is calling other parts of the relax code, you should
convert it to a system test.  Unit tests should be stand-alone and not
rely on any other parts of the code base for setting up the test.
I.e. if the unit test fails, it can only be because there is a problem
in that function it tests.  In this case, if
mol_res_spin.create_spin() fails, for example, then so does this unit
test.  That should not happen, hence why this is more of a system test
-  it can have multiple points of failure.  To properly set up such a
unit test, you would have to provide dummy data structures with dummy
data, but this is too much effort.

Cheers,

Edward


On 18 August 2014 16:20,  <tlinnet@xxxxxxxxxxxxx> wrote:
> Author: tlinnet
> Date: Mon Aug 18 16:20:33 2014
> New Revision: 25048
>
> URL: http://svn.gna.org/viewcvs/relax?rev=25048&view=rev
> Log:
> Added a "check" function, what will determine if R1 data is missing for a 
> model to analyse.
>
> Also added corresponding unit tests, to test the functionality.
>
> Modified:
>     trunk/specific_analyses/relax_disp/checks.py
>     
> trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_checks.py
>
> Modified: trunk/specific_analyses/relax_disp/checks.py
> URL: 
> http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/checks.py?rev=25048&r1=25047&r2=25048&view=diff
> ==============================================================================
> --- trunk/specific_analyses/relax_disp/checks.py        (original)
> +++ trunk/specific_analyses/relax_disp/checks.py        Mon Aug 18 16:20:33 
> 2014
> @@ -30,7 +30,7 @@
>  from dep_check import C_module_exp_fn
>  from lib.errors import RelaxError, RelaxFuncSetupError, 
> RelaxNoPeakIntensityError
>  import specific_analyses
> -from specific_analyses.relax_disp.variables import EXP_TYPE_LIST_CPMG, 
> EXP_TYPE_LIST_R1RHO
> +from specific_analyses.relax_disp.variables import EXP_TYPE_LIST_CPMG, 
> EXP_TYPE_LIST_R1RHO, MODEL_LIST_R1RHO_W_R1_ONLY
>
>
>  def check_c_modules():
> @@ -178,6 +178,30 @@
>          raise 
> RelaxFuncSetupError(specific_analyses.setup.get_string(function_type))
>
>
> +def check_missing_r1(model=None):
> +    """Check if R1 data is missing for the model.
> +
> +    @keyword model: The model to test for.
> +    @type model:    str
> +    @return:        Return True if R1 data is not available for the model.
> +    @rtype:         bool
> +    """
> +
> +    # Check that the model uses R1 data.
> +    if model in MODEL_LIST_R1RHO_W_R1_ONLY:
> +        # If R1 ids are present.
> +        if hasattr(cdp, 'ri_ids'):
> +            return False
> +
> +        # If not present.
> +        else:
> +            return True
> +
> +    # If model does not need R1.
> +    else:
> +        return False
> +
> +
>  def check_relax_times():
>      """Check if the spectrometer frequencies have been set up.
>
>
> 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=25048&r1=25047&r2=25048&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   
> Mon Aug 18 16:20:33 2014
> @@ -25,8 +25,10 @@
>
>  # relax module imports.
>  from data_store import Relax_data_store; ds = Relax_data_store()
> -from pipe_control import state
> -from specific_analyses.relax_disp.checks import get_times
> +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 test_suite.unit_tests.base_classes import UnitTestCase
>
> @@ -39,6 +41,74 @@
>
>          # 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):
>
>
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