import unittest import utils import os from io import StringIO TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..')) utils.set_search_paths(TOPDIR) import ihm import ihm.report import ihm.reference import ihm.location import ihm.representation import ihm.protocol import ihm.analysis import ihm.restraint import ihm.geometry import ihm.model class Tests(unittest.TestCase): def test_report(self): """Test System.report()""" sio = StringIO() s = ihm.System(title='test system') s.report(sio) def test_entities(self): """Test report_entities""" sio = StringIO() s = ihm.System(title='test system') e = ihm.Entity("ACG") a = ihm.AsymUnit(e, "my asym") a.id = 'A' s.asym_units.append(a) s.entities.append(e) r = ihm.report.Reporter(s, sio) # Should warn about missing references self.assertWarns(ihm.report.MissingDataWarning, r.report_entities) uniprot = ihm.reference.UniProtSequence( db_code='testcode', accession='testacc', sequence='CCCG') e.references.append(uniprot) r.report_entities() def test_asyms(self): """Test report_asyms""" sio = StringIO() s = ihm.System(title='test system') e = ihm.Entity("ACG") s.entities.append(e) a = ihm.AsymUnit(e, "my asym") s.asym_units.append(a) r = ihm.report.Reporter(s, sio) r.report_asyms() def test_representations(self): """Test report_representations""" sio = StringIO() s = ihm.System(title='test system') e = ihm.Entity("ACGT") s.entities.append(e) a = ihm.AsymUnit(e, "my asym") s.asym_units.append(a) s1 = ihm.representation.ResidueSegment( a(1, 2), starting_model=None, rigid=False, primitive='sphere') s2 = ihm.representation.FeatureSegment( a(3, 4), starting_model=None, rigid=True, primitive='other', count=3) r1 = ihm.representation.Representation((s1, s2), name='foo') s.orphan_representations.append(r1) r = ihm.report.Reporter(s, sio) # Test report of representation without ID r.report_representations() # Test report of representation with ID r1._id = 42 r.report_representations() def test_citations(self): """Test report_citations""" sio = StringIO() s = ihm.System(title='test system') c = ihm.Citation(pmid="foo", title="bar", journal="j", volume=1, page_range=(10, 20), year=2023, authors=["foo", "bar"], doi="test") s.citations.append(c) r = ihm.report.Reporter(s, sio) r.report_citations() def test_software(self): """Test report_software""" sio = StringIO() s = ihm.System(title='test system') soft = ihm.Software(name='foo', version='1.0', classification='1', description='2', location='3') s.software.append(soft) r = ihm.report.Reporter(s, sio) # Should warn about missing citation self.assertWarns(ihm.report.MissingDataWarning, r.report_software) c = ihm.Citation(pmid="foo", title="bar", journal="j", volume=1, page_range=(10, 20), year=2023, authors=["foo", "bar"], doi="test") soft.citation = c soft.version = None r.report_software() def test_databases(self): """Test report_databases""" sio = StringIO() s = ihm.System(title='test system') s.locations.append( ihm.location.BMRBLocation('27600', version='foo', details='bar')) s.locations.append( ihm.location.FileLocation(repo='mydoi', path='a')) r = ihm.report.Reporter(s, sio) r.report_databases() def test_files(self): """Test report_files""" sio = StringIO() s = ihm.System(title='test system') repo = ihm.location.Repository(doi='1.2.3.4') s.locations.append( ihm.location.BMRBLocation('27600', version='foo', details='bar')) s.locations.append( ihm.location.FileLocation(repo=repo, path='a')) r = ihm.report.Reporter(s, sio) r.report_files() def test_files_local(self): """Test report_files with local files""" sio = StringIO() s = ihm.System(title='test system') s.locations.append( ihm.location.BMRBLocation('27600', version='foo', details='bar')) s.locations.append( ihm.location.FileLocation(repo=None, path='.')) r = ihm.report.Reporter(s, sio) # Should warn about local files self.assertWarns(ihm.report.LocalFilesWarning, r.report_files) def test_protocols(self): """Test report_protocols""" sio = StringIO() s = ihm.System(title='test system') prot = ihm.protocol.Protocol(name='foo') prot.steps.append(ihm.protocol.Step( assembly='foo', dataset_group='bar', method='baz', num_models_begin=0, num_models_end=42)) analysis = ihm.analysis.Analysis() analysis.steps.append(ihm.analysis.ClusterStep( feature='RMSD', num_models_begin=42, num_models_end=5)) prot.analyses.append(analysis) s.orphan_protocols.append(prot) r = ihm.report.Reporter(s, sio) r.report_protocols() def test_restraints(self): """Test report_restraints""" sio = StringIO() s = ihm.System(title='test system') dist = ihm.restraint.UpperBoundDistanceRestraint(42.0) geom = ihm.geometry.XAxis(name='foo', description='bar') rsr = ihm.restraint.GeometricRestraint( dataset='foo', geometric_object=geom, feature='feat', distance=dist) s.restraints.append(rsr) r = ihm.report.Reporter(s, sio) r.report_restraints() def test_models(self): """Test report_models""" sio = StringIO() s = ihm.System(title='test system') sg = ihm.model.StateGroup() state = ihm.model.State(name='foo') mg = ihm.model.ModelGroup(name='bar') m = ihm.model.Model(assembly='foo', protocol='bar', representation='baz') mg.append(m) state.append(mg) sg.append(state) s.state_groups.append(sg) r = ihm.report.Reporter(s, sio) r.report_models() def test_ensembles(self): """Test report_ensembles""" sio = StringIO() s = ihm.System(title='test system') e = ihm.Entity("ACG") a = ihm.AsymUnit(e, "my asym") a.id = 'A' s.asym_units.append(a) s.entities.append(e) e1 = ihm.model.Ensemble(model_group=None, num_models=10) e2 = ihm.model.Ensemble(model_group=None, num_models=5, precision=1.0, name='test ensemble') mg = ihm.model.ModelGroup(name='bar') e3 = ihm.model.Ensemble(model_group=mg, num_models=1, file='file') e3.densities.append(ihm.model.LocalizationDensity( file='foo', asym_unit=a(1, 2))) s.ensembles.extend((e1, e2, e3)) r = ihm.report.Reporter(s, sio) r.report_ensembles() # Should warn about extra models but no external file e4 = ihm.model.Ensemble(model_group=mg, num_models=1) s.ensembles.append(e4) self.assertWarns(ihm.report.MissingFileWarning, r.report_ensembles) if __name__ == '__main__': unittest.main()