Author: tlinnet
Date: Thu Nov 27 13:33:44 2014
New Revision: 26781
URL: http://svn.gna.org/viewcvs/relax?rev=26781&view=rev
Log:
Added initial systemtest of nmrglue, which is a version test.
This is to test, that import nmrglue is functional.
Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to
nmrglue, to read .ft2 files and process them.
Modified:
branches/nmrglue/test_suite/system_tests/nmrglue.py
Modified: branches/nmrglue/test_suite/system_tests/nmrglue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/nmrglue.py?rev=26781&r1=26780&r2=26781&view=diff
==============================================================================
--- branches/nmrglue/test_suite/system_tests/nmrglue.py (original)
+++ branches/nmrglue/test_suite/system_tests/nmrglue.py Thu Nov 27 13:33:44
2014
@@ -1,6 +1,7 @@
##############################################################################
#
#
# Copyright (C) 2011-2014 Edward d'Auvergne
#
+# Copyright (C) 2014 Troels E. Linnet
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -24,13 +25,14 @@
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
-from pipe_control.mol_res_spin import spin_loop
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
+from extern import nmrglue
class Nmrglue(SystemTestCase):
- """TestCase class for the Bruker Dynamics Center files."""
+ """TestCase class for the functionality of the external module nmrglue.
+ This is from U{Task #7873<https://gna.org/task/index.php?7873>}: Write
wrapper function to nmrglue, to read .ft2 files and process them."""
def setUp(self):
"""Set up for all the functional tests."""
@@ -39,79 +41,12 @@
self.interpreter.pipe.create('mf', 'mf')
- def test_bug_22411_T1_read_fail(self):
- """Test catching U{bug #22411<https://gna.org/bugs/?22411>}, the
failure in reading a Bruker DC T1 file as submitted by Olena Dobrovolska."""
+ def test_version(self):
+ """Test version of nmrglue."""
- # The data path.
- path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'bruker_files'
+ # Test version.
+ ng_vers = nmrglue.__version__
+ print("Version of nmrglue is %s"%ng_vers)
- # Create a data pipe, read the sequence, and read the Bruker DC file
to trigger the bug.
- self.interpreter.pipe.create('bug_22411', 'mf')
- self.interpreter.sequence.read(file='bug_22411_T1_sequence',
dir=path, res_num_col=2, res_name_col=1)
- self.interpreter.bruker.read(ri_id='T1', file='bug_22411_T1.txt',
dir=path)
-
-
- def test_bruker_read_noe(self):
- """Test the reading of a DC NOE file."""
-
- # Read the sequence data.
- self.interpreter.sequence.read(file="seq", dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'bruker_files', res_num_col=2,
res_name_col=1)
-
- # The ID string.
- ri_id = 'NOE_600'
-
- # Read the DC file.
- self.interpreter.bruker.read(ri_id=ri_id, file="testNOE.txt",
dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'bruker_files')
-
- # Check the data pipe structures.
- self.assertEqual(cdp.ri_ids, [ri_id])
- self.assertEqual(cdp.spectrometer_frq[ri_id], 600.13*1e6)
- self.assertEqual(cdp.ri_type[ri_id], 'NOE')
-
- # The NOE values and errors.
- noe = [0.70140000000000002, 0.72260000000000002,
0.78410000000000002, 0.71389999999999998, 0.72219999999999995,
0.73450000000000004, 0.65800000000000003, 0.61319999999999997,
0.64359999999999995, 0.55810000000000004, 0.64349999999999996,
0.72719999999999996, 0.76690000000000003, 0.78159999999999996,
0.78320000000000001, 0.71179999999999999, 0.73529999999999995, 0.7339,
0.76639999999999997, 0.79600000000000004, 0.76980000000000004,
0.76090000000000002, 0.77000000000000002, 0.76839999999999997, 0.746,
0.75119999999999998, 0.7258, 0.76139999999999997, 0.75970000000000004,
0.76270000000000004, 0.71899999999999997, 0.7752, 0.78710000000000002,
0.75270000000000004, 0.75860000000000005, 0.73709999999999998,
0.76649999999999996, 0.78059999999999996, 0.77710000000000001,
0.74419999999999997, 0.71909999999999996, 0.73429999999999995,
0.69320000000000004, 0.60419999999999996, 0.71460000000000001,
0.73599999999999999, 0.78359999999999996, 0.79749999999999999,
0.75949999999999995, 0.76659999999999995, 0.77559999999999996,
0.73729999999999996, 0.73080000000000001, 0.78420000000000001,
0.70409999999999995, 0.6069, 0.79710000000000003, 0.74829999999999997,
0.72860000000000003, 0.73939999999999995, 0.751, 0.73150000000000004, 0.7238,
0.72529999999999994, 0.7218, 0.62980000000000003, 0.3004,
0.15970000000000001, -0.41570000000000001, -1.3540000000000001]
-
- noe_err = [0.0071371999999999998, 0.0071482999999999998,
0.0090542000000000001, 0.0073617999999999999, 0.0071636,
0.0067083000000000004, 0.0067882000000000003, 0.0076052000000000003,
0.0046737000000000003, 0.0047003000000000001, 0.0061779000000000001,
0.0087358000000000002, 0.0064637999999999996, 0.0084919999999999995,
0.0067708000000000004, 0.0064495999999999998, 0.0079068000000000003,
0.0059157999999999997, 0.0053657000000000002, 0.0088774000000000006,
0.0096562999999999996, 0.0078910000000000004, 0.0066074000000000003,
0.0091068, 0.0079459000000000005, 0.0088655999999999995,
0.0071831000000000004, 0.0069040999999999998, 0.0070117000000000001,
0.0065712000000000001, 0.0063590000000000001, 0.0054622999999999998,
0.0061237000000000002, 0.0058399999999999997, 0.0072487000000000003,
0.0082611999999999998, 0.010810999999999999, 0.010808999999999999,
0.010059999999999999, 0.0091409999999999998, 0.012137999999999999,
0.0063179999999999998, 0.0080087000000000005, 0.0067654999999999998,
0.0090647000000000002, 0.0085708999999999994, 0.0071379,
0.0088193999999999998, 0.010037000000000001, 0.0074373,
0.0059819000000000001, 0.0065192999999999996, 0.006594,
0.0057096999999999998, 0.0078305000000000007, 0.0062278999999999998,
0.0053839999999999999, 0.0085550000000000001, 0.0064421000000000001,
0.0066708000000000002, 0.0089885, 0.0095670000000000009,
0.0073683999999999998, 0.0092160000000000002, 0.0079343999999999994,
0.0059852999999999998, 0.0039353000000000001, 0.0040734999999999999,
0.0060822000000000003, 0.0067099000000000004]
-
- # Loop over the spins.
- i = 0
- for spin in spin_loop():
- # Check the R1 value and error.
- self.assertAlmostEqual(spin.ri_data[ri_id], noe[i])
- self.assertAlmostEqual(spin.ri_data_err[ri_id], noe_err[i])
-
- # Increment the data index.
- i += 1
-
-
- def test_bruker_read_r1(self):
- """Test the reading of a DC R1 file."""
-
- # Read the sequence data.
- self.interpreter.sequence.read(file="seq", dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'bruker_files', res_num_col=2,
res_name_col=1)
-
- # The ID string.
- ri_id = 'NOE_600'
-
- # Read the DC file.
- self.interpreter.bruker.read(ri_id=ri_id, file="testT1.txt",
dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'bruker_files')
-
- # Check the data pipe structures.
- self.assertEqual(cdp.ri_ids, [ri_id])
- self.assertEqual(cdp.spectrometer_frq[ri_id], 600.13*1e6)
- self.assertEqual(cdp.ri_type[ri_id], 'R1')
-
- # The R1 values and errors.
- r1 = [2.1931556000035091, 2.3314642761386288, 2.3482998309224121,
2.2490812503092488, 2.2794204801371301, 2.2197311905528241,
2.2402487572220018, 1.9682404717478763, 2.0880183244488153,
1.9977625059932875, 2.1644881093845711, 2.2725568309649504,
2.1992861117281328, 2.2794360675168961, 2.0871205875661878,
2.2847272835278019, 2.1080324468354217, 2.2433596554199569,
2.3491493730120321, 2.2750850881822982, 2.4672959916309321,
2.3956227181693608, 2.1334016021846032, 2.3625860867305351,
2.3848078202618042, 2.3269721670859096, 2.4206451987712803,
2.3722597434638315, 2.343270361847809, 2.1927612565399106,
2.2380977959212909, 2.2461360844008094, 1.9912266553564995,
2.2936831964769029, 2.25463891957703, 2.2244169803094609, 2.280408101833904,
2.172312143876578, 2.2795451851446598, 2.266191370796498, 2.1729305009908564,
2.1917183729559486, 2.201809006279559, 2.1141693745652739,
2.2445782213064343, 2.133488082335572, 2.0460023160746217,
2.1921507848995887, 2.2750902642062325, 2.3691236848402144,
2.2981479225891852, 2.377233708223089, 2.2256001887308958,
2.2846020109066898, 2.3422878999749375, 1.973756927886817,
2.1651301459730745, 2.3191578673951914, 2.1891945734244915,
2.1815674998800136, 2.2678668217887572, 2.2465094858863042,
2.248479465761279, 2.3154901661132645, 2.1756630333094011,
2.1637200405913881, 1.8566309574645847, 1.6125599066005301,
1.1626041402658644, 0.76306229106400647]
-
- r1_err = [0.014883089934780979, 0.016303964816225223,
0.020363318742260723, 0.016687709376937879, 0.015718752396670817,
0.014518431475680691, 0.021886132469627697, 0.031556287075440621,
0.013515188095333659, 0.012453357417944776, 0.017587242385253953,
0.019302908234606619, 0.01371059959156644, 0.018437979357718477,
0.011698687778157989, 0.014869218069149722, 0.015737214115414941,
0.01390943018668532, 0.011941067694394526, 0.018293553488398374,
0.02261268912683069, 0.018087051681058786, 0.011598407444726788,
0.020469296587543661, 0.016620045900872408, 0.018909060457610323,
0.016739624643405365, 0.014806679126327058, 0.014476089754057037,
0.013123976098001535, 0.014050407715829098, 0.011838554421252851,
0.010844835351527457, 0.012711044971238742, 0.014752794876103476,
0.018227294017845289, 0.021723973501089892, 0.023441165299977383,
0.020591141498844744, 0.021778249169927173, 0.048387937817301517,
0.014867254858784009, 0.015546891671168217, 0.0142895492367403,
0.019750595476352866, 0.018562225014765673, 0.01329331372822814,
0.017647341591456655, 0.022969665803225174, 0.017861428710653073,
0.013099301992997067, 0.016245795194826523, 0.01547652953130973,
0.012508928370486994, 0.018321615170728861, 0.012861357034233434,
0.0098069239594803376, 0.019462269334464877, 0.015102761537490045,
0.015366805452534153, 0.020263438728953861, 0.020365125023511663,
0.015793641211181965, 0.020435935240713243, 0.014399976749920211,
0.012424600763085578, 0.0098441373116733167, 0.011085457618140082,
0.013079658707916478, 0.0029578895055556633]
-
- # Loop over the spins.
- i = 0
- for spin in spin_loop():
- # Check the R1 value and error.
- self.assertAlmostEqual(spin.ri_data[ri_id], r1[i], 5)
- self.assertAlmostEqual(spin.ri_data_err[ri_id], r1_err[i], 5)
-
- # Increment the data index.
- i += 1
+ # Assert the version to be 0.4.
+ self.assertEqual(ng_vers, '0.4')
r26781 - /branches/nmrglue/test_suite/system_tests/nmrglue.py