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()