Author: bugman
Date: Fri Sep 7 09:29:57 2012
New Revision: 17476
URL: http://svn.gna.org/viewcvs/relax?rev=17476&view=rev
Log:
Created the test_bug_20152_read_dc_file() GUI test for catching bug #20152
(https://gna.org/bugs/?20152).
This includes truncated data taken from the bug report (with data for only
the first 3 residues).
Added:
trunk/test_suite/shared_data/bruker_files/T1_demo_1UBQ_H_trunc.txt
(with props)
trunk/test_suite/shared_data/structures/1UBQ_H_trunc.pdb
Modified:
trunk/test_suite/gui_tests/bruker.py
Modified: trunk/test_suite/gui_tests/bruker.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/bruker.py?rev=17476&r1=17475&r2=17476&view=diff
==============================================================================
--- trunk/test_suite/gui_tests/bruker.py (original)
+++ trunk/test_suite/gui_tests/bruker.py Fri Sep 7 09:29:57 2012
@@ -22,11 +22,20 @@
# Module docstring.
"""GUI tests for the Bruker Dynamics Center support."""
+# Python module imports.
+from os import sep
# relax module imports.
+from data import Relax_data_store; ds = Relax_data_store()
import dep_check
+from generic_fns.mol_res_spin import spin_loop
+from status import Status; status = Status()
from test_suite.gui_tests.base_classes import GuiTestCase
from test_suite import system_tests
+
+# relax GUI imports.
+from gui.interpreter import Interpreter; interpreter = Interpreter()
+from gui.string_conv import str_to_gui
class Bruker(GuiTestCase, system_tests.bruker.Bruker):
@@ -47,3 +56,86 @@
# Create a data pipe.
self.interpreter.pipe.create('mf', 'mf')
+
+
+ def test_bug_20152_read_dc_file(self):
+ """Test the reading of a DC file, catching bug #20152
(https://gna.org/bugs/?20152)."""
+
+ # Simulate the new analysis wizard.
+ self.app.gui.analysis.menu_new(None)
+ page = self.app.gui.analysis.new_wizard.wizard.get_page(0)
+ page.select_mf(None)
+ page.analysis_name.SetValue(str_to_gui("Model-free test"))
+ self.app.gui.analysis.new_wizard.wizard._go_next(None)
+ page = self.app.gui.analysis.new_wizard.wizard.get_page(1)
+ self.app.gui.analysis.new_wizard.wizard._go_next(None)
+
+ # Get the data.
+ analysis_type, analysis_name, pipe_name, pipe_bundle =
self.app.gui.analysis.new_wizard.get_data()
+
+ # Set up the analysis.
+ self.app.gui.analysis.new_analysis(analysis_type=analysis_type,
analysis_name=analysis_name, pipe_name=pipe_name, pipe_bundle=pipe_bundle)
+
+ # Alias the analysis.
+ analysis = self.app.gui.analysis.get_page_from_name("Model-free
test")
+
+ # Change the results directory.
+ analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir))
+
+ # Launch the spin viewer window.
+ self.app.gui.show_tree()
+
+ # Spin loading wizard: Initialisation.
+ self.app.gui.spin_viewer.load_spins_wizard()
+
+ # Spin loading wizard: The PDB file.
+ page = self.app.gui.spin_viewer.wizard.get_page(0)
+ page.selection = 'new pdb'
+ self.app.gui.spin_viewer.wizard._go_next()
+ page =
self.app.gui.spin_viewer.wizard.get_page(self.app.gui.spin_viewer.wizard._current_page)
+ page.uf_args['file'].SetValue(str_to_gui(status.install_path + sep +
'test_suite' + sep + 'shared_data' + sep + 'structures' + sep +
'1UBQ_H_trunc.pdb'))
+ self.app.gui.spin_viewer.wizard._go_next()
+ interpreter.flush() # Required because of the asynchronous uf
call.
+
+ # Spin loading wizard: The spin loading.
+ self.app.gui.spin_viewer.wizard._go_next()
+ interpreter.flush() # Required because of the asynchronous uf
call.
+
+ # Close the spin viewer window.
+ self.app.gui.spin_viewer.handler_close()
+
+ # Flush the interpreter in preparation for the synchronous user
functions of the peak list wizard.
+ interpreter.flush()
+
+ # The data path.
+ data_path = status.install_path + sep + 'test_suite' + sep +
'shared_data' + sep + 'model_free' + sep + 'sphere' + sep
+
+ # Set up the Bruker DC wizard.
+ analysis.relax_data.wizard_bruker(None)
+
+ # The spectrum.
+ page =
analysis.relax_data.wizard.get_page(analysis.relax_data.page_indices['read'])
+ page.uf_args['ri_id'].SetValue(str_to_gui('r1_700'))
+ page.uf_args['file'].SetValue(str_to_gui(status.install_path + sep +
'test_suite' + sep + 'shared_data' + sep + 'bruker_files' + sep +
'T1_demo_1UBQ_H_trunc.txt'))
+
+ # Next to load the data.
+ analysis.relax_data.wizard._go_next(None)
+ interpreter.flush()
+
+ # Go to the next page (i.e. finish).
+ analysis.wizard._go_next(None)
+
+ # The real data.
+ res_nums = [1, 2, 3]
+ r1 = [None, 0.455962, 0.428882]
+ r1_err = [None, 0.0055642, 0.0040993]
+
+ # Check the data.
+ i = 0
+ for spin_cont, mol_name, res_num, res_name in
spin_loop(full_info=True):
+ # Spin info.
+ self.assertEqual(res_nums[i], res_num)
+
+ # Check the relaxation data and errors.
+ self.assertEqual(r1[i], spin_cont.ri['r1_700'])
+ self.assertEqual(r1_err[i], spin_cont.ri_err['r1_700'])
Added: trunk/test_suite/shared_data/bruker_files/T1_demo_1UBQ_H_trunc.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/bruker_files/T1_demo_1UBQ_H_trunc.txt?rev=17476&view=auto
==============================================================================
--- trunk/test_suite/shared_data/bruker_files/T1_demo_1UBQ_H_trunc.txt (added)
+++ trunk/test_suite/shared_data/bruker_files/T1_demo_1UBQ_H_trunc.txt Fri
Sep 7 09:29:57 2012
@@ -1,0 +1,70 @@
+$##1.0
+
+Project: Dynamic method/T1
+Date: Friday, June 1, 2012 10:31:46 PM
+User: Mengjun Xue
+Computer: MengjunXue
+generated by: Dynamics Center 2.0.6 (2012 Aug/27)
+
+
+SECTION: sample information
+sample name: ubiquitine
+Description/Title: standard demo sample
+Origin: in-house
+Date of preparation: 06 / 2005
+Solvent: D2O
+pH: 7.0
+Sample tube: normal
+Tube diameter (mm): 3
+Concentration (mM): 10.00
+Temperature (K): 308.0
+Weight (Daltons): 8900
+Correlation time (ns): 12.40
+Labelling: 15N
+AminoAcid storage: FASTA file
+AminoAcid file: C:\Users\Mengjun Xue\Desktop\Discussion with
Franzen\tutorial_pdc\ubi_fasta.txt
+ 0 M Q I
+PDB file: C:\Users\Mengjun Xue\Desktop\Discussion with
Franzen\tutorial_pdc\1UBQ_H.pdb
+
+
+SECTION: relevant parameters
+Proton frequency[MHz]: 600.130
+X nucleus frequency[MHz]: 60.811
+
+
+SECTION: integrals
+Mixing time [s]: 0.01000000 0.05000000
0.10000000 0.10000000 0.20000000
0.30000000 0.40000000 0.50000000
0.50000000 0.70000000 1.00000000
1.50000000
+Peak name I0 I1
I2 I3 I4 I5
I6 I7 I8
I9 I10 I11
+ Gln [2] 188221907.00000000 170715850.00000000
155029756.00000000 153590916.00000000 122823911.00000000
99589044.00000000 80386192.00000000 64045596.00000000
63158976.00000000 41739761.00000000 21211820.00000000
7618632.00000000
+ Ile [3] 181874689.00000000 165473246.00000000
147666938.00000000 148524160.00000000 116288129.00000000
92254697.00000000 73753362.00000000 57608294.00000000
58646397.00000000 35733527.00000000 18548893.00000000
6005615.00000000
+
+
+SECTION: integral errors
+Mixing time [s]: 0.01000000 0.05000000
0.10000000 0.10000000 0.20000000
0.30000000 0.40000000 0.50000000
0.50000000 0.70000000 1.00000000
1.50000000
+Peak name I0 I1
I2 I3 I4 I5
I6 I7 I8
I9 I10 I11
+ Gln [2] 897542.47418861 896854.72297723
897490.21067925 878081.13588050 897985.79603740
913382.23030477 888948.93460278 905641.14635477
903540.85559709 912300.24401111 899610.64435054
908895.14915618
+ Ile [3] 897542.47418861 896854.72297723
897490.21067925 878081.13588050 897985.79603740
913382.23030477 888948.93460278 905641.14635477
903540.85559709 912300.24401111 899610.64435054
908895.14915618
+
+
+SECTION: integrals back calculated from fit
+Mixing time [s]: 0.01000000 0.05000000
0.10000000 0.10000000 0.20000000
0.30000000 0.40000000 0.50000000
0.50000000 0.70000000 1.00000000
1.50000000
+Peak name I0 I1
I2 I3 I4 I5
I6 I7 I8
I9 I10 I11
+ Gln [2] 187542336.12504458 171790887.65616792
153948735.65601960 153948735.65601960 123631213.49175845
99284199.27784644 79731905.46172418 64030095.37063183
64030095.37063183 41294114.70297287 21386719.64789395
7143387.41259164
+ Ile [3] 182020644.30116520 165811967.33932748
147565523.64014703 147565523.64014703 116875361.03757486
92568031.34432912 73316055.24803348 58068037.95079300
58068037.95079300 36426150.39432082 18097869.94214024
5640502.21087503
+
+
+SECTION: details
+Fitted function: f(t) = Io * exp (-t/T)
+Random error estimation of data: RMS per spectrum (or trace/plane)
+Systematic error estimation of data: average variance calculation
+Fit parameter Error estimation method: from fit using arbitray y
uncertainties
+Confidence level: 95%
+Used peaks: peaks from C:\Users\Mengjun Xue\Desktop\Discussion with
Franzen\tutorial_pdc\2D-Ref\pdata\1\peaklist.xml
+Used integrals: peak intensities
+Used Mixing time: all values (including replicates) used
+
+
+SECTION: results
+Peak name F1 [ppm] F2 [ppm] Io error T1
[s] error errorScale
+Gln [2] 122.508 8.898 191700886.375809
1056073.6682084 0.455962 0.0055642 2.2281389 null
null
+Ile [3] 114.800 8.280 186314579.684507
816404.5451273 0.428882 0.0040993 2.2281389 null null
Propchange: trunk/test_suite/shared_data/bruker_files/T1_demo_1UBQ_H_trunc.txt
------------------------------------------------------------------------------
svn:eol-style = native
Added: trunk/test_suite/shared_data/structures/1UBQ_H_trunc.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/structures/1UBQ_H_trunc.pdb?rev=17476&view=auto
==============================================================================
--- trunk/test_suite/shared_data/structures/1UBQ_H_trunc.pdb (added)
+++ trunk/test_suite/shared_data/structures/1UBQ_H_trunc.pdb Fri Sep 7
09:29:57 2012
@@ -1,0 +1,4 @@
+ATOM 1 N MET A 1 27.340 24.430 2.614 1.00 9.67
N
+ATOM 9 N GLN A 2 26.335 27.770 3.258 1.00 9.27
N
+ATOM 18 N ILE A 3 26.849 29.656 6.217 1.00 5.87
N
+END
r17476 - in /trunk/test_suite: gui_tests/ shared_data/bruker_files/ shared_data/structures/