Author: semor
Date: Thu Jul 31 16:51:45 2008
New Revision: 7051
URL: http://svn.gna.org/viewcvs/relax?rev=7051&view=rev
Log:
Started to implement system tests for the use of the external program Dasha.
This code is mimicked on the palmer code for testing interaction with
ModelFree4.
Added:
1.3/test_suite/system_tests/dasha.py
1.3/test_suite/system_tests/scripts/dasha.py
Modified:
1.3/test_suite/system_tests/__init__.py
Modified: 1.3/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/__init__.py?rev=7051&r1=7050&r2=7051&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/__init__.py (original)
+++ 1.3/test_suite/system_tests/__init__.py Thu Jul 31 16:51:45 2008
@@ -33,6 +33,7 @@
# relax system/functional test module imports.
from angles import Angles
from consistency_tests import Ct
+from dasha import Dasha
from diffusion_tensor import Diffusion_tensor
from generic import Generic
from jw_mapping import Jw
@@ -50,6 +51,7 @@
__all__ = ['angles',
'consistency_tests',
+ 'dasha'
'diffusion_tensor',
'generic',
'jw_mapping',
@@ -85,6 +87,7 @@
suite_array = []
suite_array.append(TestLoader().loadTestsFromTestCase(Angles))
suite_array.append(TestLoader().loadTestsFromTestCase(Ct))
+ suite_array.append(TestLoader().loadTestsFromTestCase(Dasha))
suite_array.append(TestLoader().loadTestsFromTestCase(Diffusion_tensor))
suite_array.append(TestLoader().loadTestsFromTestCase(Generic))
suite_array.append(TestLoader().loadTestsFromTestCase(Jw))
Added: 1.3/test_suite/system_tests/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/dasha.py?rev=7051&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/dasha.py (added)
+++ 1.3/test_suite/system_tests/dasha.py Thu Jul 31 16:51:45 2008
@@ -1,0 +1,76 @@
+###############################################################################
+#
#
+# Copyright (C) 2008 Sebastien Morin
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax 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 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax 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 relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+# Python module imports.
+import sys
+from os import chdir
+from shutil import rmtree
+from tempfile import mkdtemp
+from unittest import TestCase
+
+# relax module imports.
+from data import Relax_data_store; ds = Relax_data_store()
+from relax_io import test_binary
+
+
+class Dasha(TestCase):
+ """Class for testing various aspects specific to model-free analysis
using the program
+ 'Dasha'.
+ """
+
+
+ def setUp(self):
+ """Set up for all the functional tests."""
+
+ # Create the data pipe.
+ self.relax.interpreter._Pipe.create('dasha', 'mf')
+
+ # Create a temporary directory for Dasha outputs.
+ self.temp_Dasha_dir = mkdtemp()
+
+
+ def tearDown(self):
+ """Reset the relax data storage object."""
+
+ ds.__reset__()
+
+ # Remove the temporary directory created during the execution of the
test_dasha() function.
+ rmtree(self.temp_Dasha_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
+
+ # Move to the temporary directory for Dasha outputs.
+ chdir(self.temp_Dasha_dir)
+
+ # Execute the script.
+ self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/dasha.py')
+
+ # Move back to the base relax directory.
+ chdir(sys.path[-1])
Added: 1.3/test_suite/system_tests/scripts/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/dasha.py?rev=7051&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/dasha.py (added)
+++ 1.3/test_suite/system_tests/scripts/dasha.py Thu Jul 31 16:51:45 2008
@@ -1,0 +1,45 @@
+# Script for model-free analysis using the program Dasha.
+
+# Python module imports.
+import sys
+
+
+# Set the data pipe names (also the names of preset model-free models).
+pipes = ['m1', 'm2', 'm3']
+
+# Loop over the pipes.
+for name in pipes:
+ # Create the data pipe.
+ pipe.create(name, 'mf')
+
+ # Load the sequence.
+ sequence.read(sys.path[-1] +
'/test_suite/system_tests/data/jw_mapping/noe.dat')
+
+ # Load a PDB file.
+ #structure.read_pdb('example.pdb')
+
+ # Load the relaxation data.
+ relax_data.read('R1', '600', 600.0 * 1e6, sys.path[-1] +
'/test_suite/system_tests/data/jw_mapping/R1.dat')
+ relax_data.read('R2', '600', 600.0 * 1e6, sys.path[-1] +
'/test_suite/system_tests/data/jw_mapping/R2.dat')
+ relax_data.read('NOE', '600', 600.0 * 1e6, sys.path[-1] +
'/test_suite/system_tests/data/jw_mapping/noe.dat')
+
+ # Setup other values.
+ diffusion_tensor.init(1e-8, fixed=True)
+ value.set('15N', 'heteronucleus')
+ value.set(1.02 * 1e-10, 'bond_length')
+ value.set(-172 * 1e-6, 'csa')
+
+ # Select the model-free model.
+ model_free.select_model(model=name)
+
+ # Create the Dasha script.
+ dasha.create(algor='NR', force=True)
+
+ # Execute Dasha.
+ dasha.execute()
+
+ # Read the data.
+ dasha.extract()
+
+ # Write the results.
+ results.write(file='results_dasha', force=True)
r7051 - in /1.3/test_suite/system_tests: __init__.py dasha.py scripts/dasha.py