Author: bugman
Date: Fri Oct 22 19:21:54 2010
New Revision: 11653
URL: http://svn.gna.org/viewcvs/relax?rev=11653&view=rev
Log:
The restoration of the data from BMRB files into data pipes is now fully
tested in the system tests.
Modified:
branches/bmrb/test_suite/system_tests/bmrb.py
Modified: branches/bmrb/test_suite/system_tests/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/bmrb.py?rev=11653&r1=11652&r2=11653&view=diff
==============================================================================
--- branches/bmrb/test_suite/system_tests/bmrb.py (original)
+++ branches/bmrb/test_suite/system_tests/bmrb.py Fri Oct 22 19:21:54 2010
@@ -22,6 +22,8 @@
# Python module imports.
import __main__
+import inspect
+from numpy import ndarray
from os import remove, sep
from re import search
import sys
@@ -59,24 +61,16 @@
"""Check that all data has been successfully restored from the BMRB
files."""
# Print out.
- print "\n\nComparing data pipe contents:\n"
+ print("\n\nComparing data pipe contents:")
+
+ # Blacklists (data that is not restored, and relaxation data which
has been reordered).
+ blacklist_spin = ['name'] + ['attached_proton', 'element',
'equation', 'fixed', 'heteronuc_type', 'nucleus', 'proton_type',
'relax_sim_data', 'select', 'xh_vect'] + ['local_tm', 'local_tm_err',
'model', 'params', 'rex', 'rex_err', 's2', 's2_err', 's2f', 's2f_err', 's2s',
's2s_err', 'te', 'te_err', 'tf', 'tf_err', 'ts', 'ts_err'] + ['r', 'r_err',
'csa', 'csa_err'] + ['chi2', 'chi2_sim', 'f_count', 'g_count', 'h_count',
'iter', 'warning'] + ['frq', 'frq_labels', 'noe_r1_table', 'remap_table',
'ri_labels', 'relax_data', 'relax_error']
+ blacklist_diff = []
+ blacklist_global = ['diff_tensor', 'exp_info', 'hybrid_pipes',
'mol', 'sim_number', 'sim_state'] + ['frq', 'frq_labels', 'noe_r1_table',
'remap_table', 'ri_labels']
# The data pipes.
old_pipe = ds[old_pipe_name]
new_pipe = ds[new_pipe_name]
-
- # The global data structures.
- names = dir(old_pipe)
- for name in names:
- # Skip special names.
- if search('^__', name):
- continue
-
- # Print out.
- print "Object: %s" % name
-
- # Check.
- self.assert_(hasattr(new_pipe, name))
# The molecule data structure.
self.assertEqual(len(old_pipe.mol), len(new_pipe.mol))
@@ -95,27 +89,128 @@
# The spin data structure.
self.assertEqual(len(old_pipe.mol[i].res[j].spin),
len(new_pipe.mol[i].res[j].spin))
for k in range(len(old_pipe.mol[i].res[j].spin)):
- # Check the attributes.
- names = dir(old_pipe.mol[i].res[j].spin[k])
- for name in names:
- # Skip special names.
- if search('^__', name):
- continue
-
- # Print out.
- print "Spin object: %s" % name
-
- # Does it exist?
- self.assert_(hasattr(new_pipe.mol[i].res[j].spin[k],
name))
-
- # Get the objects.
- obj_old = getattr(old_pipe.mol[i].res[j].spin[k],
name)
- obj_new = getattr(new_pipe.mol[i].res[j].spin[k],
name)
-
- # Compare values.
- self.assertEqual(obj_old, obj_new)
-
-
+ # Skip deselected spins.
+ if not old_pipe.mol[i].res[j].spin[k].select:
+ continue
+
+ # Check the containers.
+ self.data_cont_comp(label='Spin',
cont_old=old_pipe.mol[i].res[j].spin[k],
cont_new=new_pipe.mol[i].res[j].spin[k], blacklist=blacklist_spin)
+ if hasattr(old_pipe.mol[i].res[j].spin[k], 'ri_labels'):
+ self.data_ri_comp(label='Global',
cont_old=old_pipe.mol[i].res[j].spin[k],
cont_new=new_pipe.mol[i].res[j].spin[k])
+
+ # The diffusion tensor.
+ self.assert_(hasattr(new_pipe, 'diff_tensor'))
+ self.data_cont_comp(label='Diff tensor',
cont_old=old_pipe.diff_tensor, cont_new=new_pipe.diff_tensor, prec=4,
blacklist=blacklist_diff)
+
+ # The global data structures.
+ self.data_cont_comp(label='Global', cont_old=old_pipe,
cont_new=new_pipe, blacklist=blacklist_global)
+ if hasattr(old_pipe, 'ri_labels'):
+ self.data_ri_comp(label='Global', cont_old=old_pipe,
cont_new=new_pipe)
+
+
+ def data_cont_comp(self, label=None, cont_old=None, cont_new=None,
prec=7, blacklist=[]):
+ """Compare the contents of the two data containers."""
+
+ # Print a new line.
+ print('')
+
+ # Check the attributes.
+ names = dir(cont_old)
+ for name in names:
+ # Skip special names.
+ if search('^__', name):
+ continue
+
+ # Skip the data store methods.
+ if name in list(cont_old.__class__.__dict__.keys()):
+ continue
+
+ # Simulation data.
+ if search('_sim$', name):
+ continue
+
+ # Blacklisting.
+ if name in blacklist:
+ continue
+
+ # Print out.
+ print("%s object: '%s'" % (label, name))
+
+ # Get the objects.
+ obj_old = getattr(cont_old, name)
+ obj_new = getattr(cont_new, name)
+
+ # Functions and methods.
+ if inspect.isfunction(obj_old) or inspect.ismethod(obj_old):
+ continue
+
+ # Does it exist?
+ self.assert_(hasattr(cont_new, name))
+
+ # Compare lists.
+ if (isinstance(obj_old, list) or isinstance(obj_old, ndarray)):
+ self.assertEqual(len(obj_old), len(obj_new))
+
+ # List of lists (or rank-2 array).
+ if (isinstance(obj_old[0], list) or isinstance(obj_old[0],
ndarray)):
+ for i in range(len(obj_old)):
+ for j in range(len(obj_old[i])):
+ if isinstance(obj_old[i][j], float):
+ self.assertAlmostEqual(obj_old[i][j],
obj_new[i][j], prec)
+ else:
+ self.assertEqual(obj_old[i][j],
obj_new[i][j])
+
+ # Standard list.
+ else:
+ for i in range(len(obj_old)):
+ if isinstance(obj_old[i], float):
+ self.assertAlmostEqual(obj_old[i], obj_new[i],
prec)
+ else:
+ self.assertEqual(obj_old[i], obj_new[i])
+
+ # Compare floats.
+ elif isinstance(obj_old, float):
+ self.assertAlmostEqual(obj_old, obj_new, prec)
+
+ # Compare ints and strings.
+ else:
+ self.assertEqual(obj_old, obj_new)
+
+
+ def data_ri_comp(self, label=None, cont_old=None, cont_new=None, prec=7):
+ """Compare the contents of the two data containers."""
+
+ # Check that the new container has relaxation data.
+ for name in ['frq', 'frq_labels', 'noe_r1_table', 'remap_table',
'ri_labels']:
+ self.assert_(hasattr(cont_new, name))
+
+ # Loop over the original relaxation data.
+ for i in range(cont_old.num_ri):
+ # A flag to make sure the data matches.
+ match = False
+
+ # Loop over the new relaxation data.
+ for j in range(cont_old.num_ri):
+ # Matching relaxation data.
+ if cont_old.ri_labels[i] == cont_new.ri_labels[j] and
cont_old.frq_labels[cont_old.remap_table[i]] ==
cont_new.frq_labels[cont_new.remap_table[j]]:
+ # NOE to R1 checks.
+ if cont_old.noe_r1_table[i] == None:
+ self.assertEqual(cont_new.noe_r1_table[j], None)
+ else:
+
self.assertEqual(cont_old.ri_labels[cont_old.noe_r1_table[i]],
cont_new.ri_labels[cont_new.noe_r1_table[j]])
+
self.assertEqual(cont_old.remap_table[cont_old.noe_r1_table[i]],
cont_new.remap_table[cont_new.noe_r1_table[j]])
+
self.assertEqual(cont_old.frq_labels[cont_old.remap_table[cont_old.noe_r1_table[i]]],
cont_new.frq_labels[cont_new.remap_table[cont_new.noe_r1_table[j]]])
+
+ # Relaxation data checks.
+ if hasattr(cont_old, 'relax_data'):
+ self.assertAlmostEqual(cont_old.relax_data[i],
cont_new.relax_data[j])
+ self.assertAlmostEqual(cont_old.relax_error[i],
cont_new.relax_error[j])
+
+ # Flag.
+ match = True
+
+ # No match.
+ self.assert_(match)
def test_rw_bmrb_3_0_model_free(self):
r11653 - /branches/bmrb/test_suite/system_tests/bmrb.py