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import utils
import os
import unittest
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
utils.set_search_paths(TOPDIR)
import ihm.dataset
import ihm.location
import ihm.geometry
def _make_test_file(fname):
with open(fname, 'w') as fh:
fh.write('contents')
class Tests(unittest.TestCase):
def test_dataset(self):
"""Test Dataset base class"""
loc = ihm.location.PDBLocation('1abc', version='foo', details='bar')
d = ihm.dataset.Dataset(loc)
self.assertIsNone(d.details)
self.assertEqual(len(d.parents), 0)
l2 = ihm.location.PDBLocation('1xyz', version='foo', details='bar')
d2 = ihm.dataset.Dataset(l2, details='foo')
self.assertEqual(d2.details, 'foo')
d.parents.append(d2)
self.assertEqual(len(d.parents), 1)
self.assertNotEqual(d, d2)
l3 = ihm.location.PDBLocation('1cde', version='foo', details='bar')
d3 = ihm.dataset.Dataset(l3, details='bar')
t = ihm.geometry.Transformation(
rot_matrix=[[-0.64, 0.09, 0.77], [0.76, -0.12, 0.64],
[0.15, 0.99, 0.01]],
tr_vector=[1., 2., 3.])
td = ihm.dataset.TransformedDataset(d3, transform=t)
d.parents.append(td)
self.assertEqual(len(d.parents), 2)
def test_dataset_allow_duplicates(self):
"""Test Dataset base class with allow_duplicates=True"""
loc = ihm.location.PDBLocation('1abc', version='foo', details='bar')
d = ihm.dataset.Dataset(loc)
d._allow_duplicates = True
self.assertEqual(d._eq_vals(), id(d))
d2 = ihm.dataset.Dataset(loc)
d2._allow_duplicates = True
self.assertNotEqual(d, d2)
def test_add_primary_no_parents(self):
"""Test add_primary() method, no parents"""
l1 = ihm.location.PDBLocation('1abc', version='foo', details='bar')
d1 = ihm.dataset.Dataset(l1)
l2 = ihm.location.PDBLocation('1xyz', version='foo', details='bar')
d2 = ihm.dataset.Dataset(l2)
d1.add_primary(d2)
self.assertEqual(d1.parents, [d2])
def test_add_primary_one_parent(self):
"""Test add_primary() method, one parent"""
l1 = ihm.location.PDBLocation('1abc', version='foo', details='bar')
d1 = ihm.dataset.Dataset(l1)
l2 = ihm.location.PDBLocation('1xyz', version='foo', details='bar')
d2 = ihm.dataset.Dataset(l2)
l3 = ihm.location.PDBLocation('2def', version='foo', details='bar')
d3 = ihm.dataset.Dataset(l3)
d1.parents.append(d2)
d1.add_primary(d3)
self.assertEqual(d1.parents, [d2])
self.assertEqual(d2.parents, [d3])
def test_add_primary_two_parents(self):
"""Test add_primary() method, two parents"""
l1 = ihm.location.PDBLocation('1abc', version='foo', details='bar')
d1 = ihm.dataset.Dataset(l1)
l2 = ihm.location.PDBLocation('1xyz', version='foo', details='bar')
d2 = ihm.dataset.Dataset(l2)
l3 = ihm.location.PDBLocation('2def', version='foo', details='bar')
d3 = ihm.dataset.Dataset(l3)
_ = ihm.location.PDBLocation('2ghi', version='foo', details='bar')
d4 = ihm.dataset.Dataset(l3)
d1.parents.extend((d2, d3))
self.assertRaises(ValueError, d1.add_primary, d4)
def test_cxms_dataset(self):
"""Test CXMSDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.CXMSDataset(loc)
self.assertEqual(d.data_type, 'Crosslinking-MS data')
def test_hdx_dataset(self):
"""Test HDXDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.HDXDataset(loc)
self.assertEqual(d.data_type, 'H/D exchange data')
def test_mass_spec_dataset(self):
"""Test MassSpecDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.MassSpecDataset(loc)
self.assertEqual(d.data_type, 'Mass Spectrometry data')
def test_em_density_dataset(self):
"""Test EMDensityDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.EMDensityDataset(loc)
self.assertEqual(d.data_type, '3DEM volume')
def test_pdb_dataset(self):
"""Test PDBDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.PDBDataset(loc)
self.assertEqual(d.data_type, 'Experimental model')
def test_comp_model_dataset(self):
"""Test ComparativeModelDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.ComparativeModelDataset(loc)
self.assertEqual(d.data_type, 'Comparative model')
def test_int_model_dataset(self):
"""Test IntegrativeModelDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.IntegrativeModelDataset(loc)
self.assertEqual(d.data_type, 'Integrative model')
def test_de_novo_model_dataset(self):
"""Test DeNovoModelDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.DeNovoModelDataset(loc)
self.assertEqual(d.data_type, 'De Novo model')
def test_nmr_dataset(self):
"""Test NMRDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.NMRDataset(loc)
self.assertEqual(d.data_type, 'NMR data')
def test_mutagenesis_dataset(self):
"""Test MutagenesisDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.MutagenesisDataset(loc)
self.assertEqual(d.data_type, 'Mutagenesis data')
def test_em2d_class_dataset(self):
"""Test EM2DClassDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.EM2DClassDataset(loc)
self.assertEqual(d.data_type, '2DEM class average')
def test_em_micrographs_dataset(self):
"""Test EMMicrographsDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.EMMicrographsDataset(loc)
self.assertEqual(d.data_type, 'EM raw micrographs')
def test_sas_dataset(self):
"""Test SASDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.SASDataset(loc)
self.assertEqual(d.data_type, 'SAS data')
def test_fret_dataset(self):
"""Test FRETDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.FRETDataset(loc)
self.assertEqual(d.data_type, 'Single molecule FRET data')
def test_ensemble_fret_dataset(self):
"""Test EnsembleFRETDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.EnsembleFRETDataset(loc)
self.assertEqual(d.data_type, 'Ensemble FRET data')
def test_y2h_dataset(self):
"""Test YeastTwoHybridDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.YeastTwoHybridDataset(loc)
self.assertEqual(d.data_type, 'Yeast two-hybrid screening data')
def test_genetic_dataset(self):
"""Test GeneticInteractionsDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.GeneticInteractionsDataset(loc)
self.assertEqual(
d.data_type, 'Quantitative measurements of genetic interactions')
def test_epr_dataset(self):
"""Test EPRDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.EPRDataset(loc)
self.assertEqual(d.data_type, 'EPR data')
def test_xray_diffraction_dataset(self):
"""Test XRayDiffractionDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.XRayDiffractionDataset(loc)
self.assertEqual(d.data_type, 'X-ray diffraction data')
def test_hydroxyl_radical_footprinting_dataset(self):
"""Test HydroxylRadicalFootprintingDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.HydroxylRadicalFootprintingDataset(loc)
self.assertEqual(d.data_type, 'Hydroxyl radical footprinting data')
def test_dna_footprinting_dataset(self):
"""Test DNAFootprintingDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.DNAFootprintingDataset(loc)
self.assertEqual(d.data_type, 'DNA footprinting data')
def test_predicted_contacts_dataset(self):
"""Test PredictedContactsDataset"""
loc = ihm.location.FileLocation(repo='mydoi', path='a')
d = ihm.dataset.PredictedContactsDataset(loc)
self.assertEqual(d.data_type, 'Predicted contacts')
def test_duplicate_datasets_details(self):
"""Datasets with differing details should be considered duplicates"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
_make_test_file(fname)
l1 = ihm.location.InputFileLocation(fname, details='test details')
_ = ihm.dataset.PDBDataset(l1)
l2 = ihm.location.InputFileLocation(fname, details='other details')
d2 = ihm.dataset.PDBDataset(l2)
self.assertEqual(l1, l2)
d3 = ihm.dataset.PDBDataset(l2, details='other dataset details')
self.assertEqual(d2, d3)
def test_duplicate_locations(self):
"""Datasets with same location should be considered duplicates"""
with utils.temporary_directory() as tmpdir:
fname1 = os.path.join(tmpdir, 'test1.pdb')
fname2 = os.path.join(tmpdir, 'test2.pdb')
_make_test_file(fname1)
_make_test_file(fname2)
loc1 = ihm.location.InputFileLocation(fname1)
loc2 = ihm.location.InputFileLocation(fname2)
# Identical datasets in the same location aren't duplicated
pdb1 = ihm.dataset.PDBDataset(loc1)
pdb2 = ihm.dataset.PDBDataset(loc1)
self.assertEqual(pdb1, pdb2)
# Datasets in different locations are OK
pdb1 = ihm.dataset.PDBDataset(loc1)
pdb2 = ihm.dataset.PDBDataset(loc2)
self.assertNotEqual(pdb1, pdb2)
if __name__ == '__main__':
unittest.main()
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