Author: bugman
Date: Tue May 22 12:27:15 2012
New Revision: 16374
URL: http://svn.gna.org/viewcvs/relax?rev=16374&view=rev
Log:
Converted the bmrb_rw.py system test script to use the new prompt
self._execute_uf() method.
The GUI test framework will need slight modification to use this script
directly still.
Modified:
branches/uf_redesign/test_suite/system_tests/scripts/bmrb_rw.py
Modified: branches/uf_redesign/test_suite/system_tests/scripts/bmrb_rw.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/system_tests/scripts/bmrb_rw.py?rev=16374&r1=16373&r2=16374&view=diff
==============================================================================
--- branches/uf_redesign/test_suite/system_tests/scripts/bmrb_rw.py (original)
+++ branches/uf_redesign/test_suite/system_tests/scripts/bmrb_rw.py Tue May
22 12:27:15 2012
@@ -8,8 +8,6 @@
from status import Status; status = Status()
-system_test_asdfsda
-
# Missing temp file (allow this script to run outside of the system test
framework).
state_file = 'devnull'
if not hasattr(ds, 'tmpfile'):
@@ -19,50 +17,51 @@
state_file = 'temp_bmrb_state'
# Create the data pipe.
-pipe.create(pipe_name='results', pipe_type='mf')
+self._execute_uf(uf_name='pipe.create', pipe_name='results', pipe_type='mf')
# Read the results.
-results.read(file='final_results_trunc_1.3', dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP')
+self._execute_uf(uf_name='results.read', file='final_results_trunc_1.3',
dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP')
# Play with the data.
-deselect.all()
-spin.copy(spin_from=':9', spin_to=':9@NE')
-select.spin(':9')
-select.spin(':10')
-select.spin(':11')
-spin.name(name='N')
-spin.element(element='N')
-molecule.name(name='OMP')
-molecule.type(type='protein')
-bmrb.thiol_state(state='reduced')
+self._execute_uf(uf_name='deselect.all')
+self._execute_uf(uf_name='spin.copy', spin_from=':9', spin_to=':9@NE')
+self._execute_uf(uf_name='select.spin', spin_id=':9')
+self._execute_uf(uf_name='select.spin', spin_id=':10')
+self._execute_uf(uf_name='select.spin', spin_id=':11')
+self._execute_uf(uf_name='spin.name', name='N')
+self._execute_uf(uf_name='spin.element', element='N')
+self._execute_uf(uf_name='molecule.name', name='OMP')
+self._execute_uf(uf_name='molecule.type', type='protein')
+self._execute_uf(uf_name='bmrb.thiol_state', state='reduced')
# Display the data (as a test).
-relax_data.display(ri_id='R1_800')
+self._execute_uf(uf_name='relax_data.display', ri_id='R1_800')
# Temperature control and peak intensity type.
ri_ids = ['R1_600', 'R2_600', 'NOE_600', 'R1_800', 'R2_800', 'NOE_800']
for i in range(6):
- relax_data.temp_calibration(ri_id=ri_ids[i], method='methanol')
- relax_data.temp_control(ri_id=ri_ids[i], method='single fid
interleaving')
- relax_data.peak_intensity_type(ri_id=ri_ids[i], type='height')
+ self._execute_uf(uf_name='relax_data.temp_calibration', ri_id=ri_ids[i],
method='methanol')
+ self._execute_uf(uf_name='relax_data.temp_control', ri_id=ri_ids[i],
method='single fid interleaving')
+ self._execute_uf(uf_name='relax_data.peak_intensity_type',
ri_id=ri_ids[i], type='height')
# Set up some BMRB information.
-bmrb.software_select('NMRPipe')
-bmrb.software_select('Sparky', version='3.106')
-bmrb.citation(cite_id='test', authors=[["Edward", "d'Auvergne", "E.", "J."],
["Paul", "Gooley", "P.", "R."]], doi="10.1039/b702202f",
pubmed_id="17579774", full_citation="d'Auvergne E. J., Gooley P. R. (2007).
Set theory formulation of the model-free problem and the diffusion seeded
model-free paradigm. Mol. Biosyst., 3(7), 483-494.", title="Set theory
formulation of the model-free problem and the diffusion seeded model-free
paradigm.", status="published", type="journal", journal_abbrev="Mol.
Biosyst.", journal_full="Molecular Biosystems", volume=3, issue=7,
page_first=483, page_last=498, year=2007)
-bmrb.software(name='X', url='http://www.nmr-relax.com', vendor_name='me',
cite_ids=['test'], tasks=['procrastinating', 'nothing much', 'wasting time'])
-bmrb.script(file='noe.py', dir=status.install_path+sep+'sample_scripts',
analysis_type='noe', engine='relax')
-bmrb.script(file='relax_fit.py',
dir=status.install_path+sep+'sample_scripts', analysis_type='relax_fit',
engine='relax')
-bmrb.script(file='dauvergne_protocol.py',
dir=status.install_path+sep+'sample_scripts'+sep+'model_free',
analysis_type='mf', model_selection='AIC', engine='relax', model_elim=True,
universal_solution=True)
+self._execute_uf(uf_name='bmrb.software_select', name='NMRPipe')
+self._execute_uf(uf_name='bmrb.software_select', name='Sparky',
version='3.106')
+
+self._execute_uf(uf_name='bmrb.citation', cite_id='test',
authors=[["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.",
"R."]], doi="10.1039/b702202f", pubmed_id="17579774",
full_citation="d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation
of the model-free problem and the diffusion seeded model-free paradigm. Mol.
Biosyst., 3(7), 483-494.", title="Set theory formulation of the model-free
problem and the diffusion seeded model-free paradigm.", status="published",
type="journal", journal_abbrev="Mol. Biosyst.", journal_full="Molecular
Biosystems", volume=3, issue=7, page_first=483, page_last=498, year=2007)
+self._execute_uf(uf_name='bmrb.software', name='X',
url='http://www.nmr-relax.com', vendor_name='me', cite_ids=['test'],
tasks=['procrastinating', 'nothing much', 'wasting time'])
+self._execute_uf(uf_name='bmrb.script', file='noe.py',
dir=status.install_path+sep+'sample_scripts', analysis_type='noe',
engine='relax')
+self._execute_uf(uf_name='bmrb.script', file='relax_fit.py',
dir=status.install_path+sep+'sample_scripts', analysis_type='relax_fit',
engine='relax')
+self._execute_uf(uf_name='bmrb.script', file='dauvergne_protocol.py',
dir=status.install_path+sep+'sample_scripts'+sep+'model_free',
analysis_type='mf', model_selection='AIC', engine='relax', model_elim=True,
universal_solution=True)
# Write, then read the data to a new data pipe.
-bmrb.write(file=ds.tmpfile, dir=None, version=ds.version, force=True)
-pipe.create(pipe_name='new', pipe_type='mf')
-bmrb.read(file=ds.tmpfile, version=ds.version)
+self._execute_uf(uf_name='bmrb.write', file=ds.tmpfile, dir=None,
version=ds.version, force=True)
+self._execute_uf(uf_name='pipe.create', pipe_name='new', pipe_type='mf')
+self._execute_uf(uf_name='bmrb.read', file=ds.tmpfile, version=ds.version)
# Display tests.
-sequence.display()
-relax_data.display(ri_id='R1_800')
+self._execute_uf(uf_name='sequence.display')
+self._execute_uf(uf_name='relax_data.display', ri_id='R1_800')
# Save the program state.
-state.save(state_file, force=True)
+self._execute_uf(uf_name='state.save', state=state_file, force=True)
r16374 - /branches/uf_redesign/test_suite/system_tests/scripts/bmrb_rw.py