def describe_entity(entity: ChebiEntity) -> None: """ Test function to describe a ChEBI entity. Args: entity: a :class:`ChebiEntity` """ name = entity.get_name() out_lines = [] # type: List[str] for other in entity.get_outgoings(): target = ChebiEntity(other.get_target_chebi_id()) out_lines.append( f" ā¢ {name} {other.get_type()} {brief_description(target)}") in_lines = [] # type: List[str] for other in entity.get_incomings(): target = ChebiEntity(other.get_target_chebi_id()) in_lines.append( f" ā¢ {brief_description(target)} {other.get_type()} {name}") lines = ([entity.get_name(), f" āŗ OUTGOING ({len(out_lines)})"] + out_lines + [f" āŗ INCOMING ({len(in_lines)})"] + in_lines) report = "\n".join(lines) log.info(f"{entity.get_id()}:\n{report}")
def conditionclass(request, class_id): class_entity = ChebiEntity('CHEBI:' + str(class_id)) class_name = class_entity.get_name() children = [] for relation in class_entity.get_incomings(): if relation.get_type() == 'has_role': tid = relation.get_target_chebi_id() tid = re.search('(?<=CHEBI:)(\d)*', tid) tid = int(tid.group(0)) children.append(tid) conditiontypes = ConditionType.objects.filter(chebi_id__in=children) datasets = Dataset.objects.filter(conditionset__conditions__type__in=conditiontypes)\ .exclude(paper__latest_data_status__status__name='not relevant').distinct() return render( request, 'conditions/class.html', { 'id': class_id, 'class_name': class_name, 'conditiontypes': conditiontypes, 'papers': datasets, 'DOWNLOAD_PREFIX': settings.DOWNLOAD_PREFIX, 'USER_AUTH': request.user.is_authenticated() })
def data(request, domain, id): file_header = '' if domain == 'papers': paper = get_object_or_404(Paper, pk=id) datasets = paper.dataset_set file_header = u'# Paper: %s (PMID %s)\n' % (paper, paper.pmid) if domain == 'datasets': # datasets = get_object_or_404(Dataset, pk=id) datasets = Dataset.objects.filter(pk=id) dataset = datasets.first() file_header = u'# Paper: %s (PMID %s)\n# Dataset: %s\n' % ( dataset.paper, dataset.paper.pmid, dataset) if domain == 'conditions': conditiontype = get_object_or_404(ConditionType, pk=id) datasets = conditiontype.datasets() file_header = u'# Condition: %s (ID %s)\n' % (conditiontype, conditiontype.id) if domain == 'chebi': chebi_entity = ChebiEntity('CHEBI:' + str(id)) children = [] for relation in chebi_entity.get_incomings(): if relation.get_type() == 'has_role': tid = relation.get_target_chebi_id() tid = int(filter(str.isdigit, tid)) children.append(tid) datasets = Dataset.objects.filter( conditionset__conditions__type__chebi_id__in=children) file_header = u'# Data for conditions annotated as %s (ChEBI:%s)\n' % ( chebi_entity.get_name(), id) if domain == 'phenotypes': phenotype = get_object_or_404(Observable, pk=id) datasets = phenotype.datasets() file_header = u'# Phenotype: %s (ID %s)\n' % (phenotype, phenotype.id) data = Data.objects.filter(dataset_id__in=datasets.values('id')).all() orfs = list(data.values_list('orf', flat=True).distinct()) datasets_ids = list( data.values_list('dataset_id', flat=True).order_by('dataset__paper').distinct()) matrix = [[None] * len(datasets_ids) for i in orfs] for datapoint in data: i = orfs.index(datapoint.orf) j = datasets_ids.index(datapoint.dataset_id) matrix[i][j] = datapoint.value column_headers = '\t' + '\t'.join([ u'%s' % get_object_or_404(Dataset, pk=dataset_id) for dataset_id in datasets_ids ]) + '\n' data_row = [] for i, orf in enumerate(orfs): new_row = orf + '\t' + '\t'.join([str(val) for val in matrix[i]]) print(new_row) data_row.append(new_row) txt3 = '\n'.join(data_row) response = HttpResponse(file_header + column_headers + txt3, content_type='text/plain') response[ 'Content-Disposition'] = 'attachment; filename="%s_%s_%s_data.txt"' % ( settings.DOWNLOAD_PREFIX, domain, id) return response
class TestChebiEntity(unittest.TestCase): '''COMMENT''' def setUp(self): '''COMMENT''' self.__existing = ChebiEntity('4167') self.__secondary = ChebiEntity('CHEBI:5585') def test_get_non_existing(self): '''COMMENT''' self.assertRaises(ChebiException, ChebiEntity, '-1') def test_get_id_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_id() == 'CHEBI:4167') def test_get_id_secondary(self): '''COMMENT''' self.assertTrue(self.__secondary.get_id() == 'CHEBI:5585') def test_get_formulae_existing(self): '''COMMENT''' this_formula = Formula('C6H12O6', 'KEGG COMPOUND') self.assertTrue(this_formula in self.__existing.get_formulae()) def test_get_formulae_secondary(self): '''COMMENT''' this_formula = Formula('H2O', 'ChEBI') self.assertTrue(this_formula in self.__secondary.get_formulae()) def test_get_formula_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_formula() == 'C6H12O6') def test_get_formula_secondary(self): '''COMMENT''' self.assertTrue(self.__secondary.get_formula() == 'H2O') def test_get_mass_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_mass(), 180.15588) def test_get_mass_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_mass(), 18.01530) def test_get_charge_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_charge(), 0) def test_get_charge_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_charge(), 0) def test_get_charge_secondary2(self): '''COMMENT''' self.assertEquals(-2, ChebiEntity('43474').get_charge()) def test_get_comments_existing(self): '''COMMENT''' this_chebi_entity = ChebiEntity('29044') this_comment = Comment('General', 'General', 'The substituent name \'3-oxoprop-2-enyl\' is ' 'incorrect but is used in various databases.', datetime.datetime.strptime('2005-03-18', '%Y-%M-%d')) self.assertTrue(this_comment in this_chebi_entity.get_comments()) def test_get_comments_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('11505') this_comment = Comment('General', 'General', 'The substituent name \'3-oxoprop-2-enyl\' is ' 'incorrect but is used in various databases.', datetime.datetime.strptime('2005-03-18', '%Y-%M-%d')) self.assertTrue(this_comment in this_chebi_entity.get_comments()) def test_get_source_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_source(), 'KEGG COMPOUND') def test_get_source_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_source(), 'KEGG COMPOUND') def test_get_prnt_id_existing(self): '''COMMENT''' self.assertIsNone(self.__existing.get_parent_id()) def test_get_prnt_id_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_parent_id(), 'CHEBI:15377') def test_get_name_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_name(), 'D-glucopyranose') def test_get_name_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_name(), 'water') def test_get_definition_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_definition(), 'A glucopyranose having D-configuration.') def test_get_definition_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('41140') self.assertEqual(this_chebi_entity.get_definition(), 'D-Glucopyranose with beta configuration at the ' 'anomeric centre.') def test_get_mod_on_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_modified_on() > datetime.datetime.strptime('2014-01-01', '%Y-%M-%d')) def test_get_mod_on_secondary(self): '''COMMENT''' self.assertIsNotNone(self.__secondary.get_modified_on()) def test_get_created_by_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_created_by(), 'CHEBI') def test_get_created_by_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_created_by(), 'ops$mennis') def test_get_star_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_star(), 3) def test_get_star_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_star(), 3) def test_get_db_acc_existing(self): '''COMMENT''' dat_acc = DatabaseAccession('MetaCyc accession', 'D-Glucose', 'MetaCyc') self.assertTrue(dat_acc in self.__existing.get_database_accessions()) def test_get_db_acc_secondary(self): '''COMMENT''' dat_acc = DatabaseAccession('MetaCyc accession', 'WATER', 'MetaCyc') self.assertTrue(dat_acc in self.__secondary.get_database_accessions()) def test_get_inchi_existing(self): '''COMMENT''' inchi = 'InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/' + \ 'h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1' self.assertEqual(self.__existing.get_inchi(), inchi) def test_get_inchi_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_inchi(), 'InChI=1S/H2O/h1H2') def test_get_inchi_key_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_inchi_key(), 'WQZGKKKJIJFFOK-GASJEMHNSA-N') def test_get_inchi_key_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_inchi_key(), 'XLYOFNOQVPJJNP-UHFFFAOYSA-N') def test_get_smiles_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_smiles(), 'OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O') def test_get_smiles_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_smiles(), '[H]O[H]') def test_get_mol_existing(self): '''COMMENT''' chebi_id = 73938 this_chebi_entity = ChebiEntity(str(chebi_id)) self.assertEqual(this_chebi_entity.get_mol(), _read_mol_file(chebi_id)) def test_get_mol_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_mol(), _read_mol_file(15377)) def test_get_mol_file_existing(self): '''COMMENT''' chebi_id = 73938 self.__get_mol_file(chebi_id, chebi_id) def test_get_mol_file_secondary(self): '''COMMENT''' read_id = 15377 retrieved_id = 42857 self.__get_mol_file(read_id, retrieved_id) def test_get_names_existing(self): '''COMMENT''' this_name = Name('Grape sugar', 'SYNONYM', 'KEGG COMPOUND', False, 'en') self.assertTrue(this_name in self.__existing.get_names()) def test_get_names_secondary(self): '''COMMENT''' this_name = Name('eau', 'SYNONYM', 'ChEBI', False, 'fr') self.assertTrue(this_name in self.__secondary.get_names()) def test_get_references_existing(self): '''COMMENT''' this_chebi_entity = ChebiEntity('15347') this_reference = Reference('WO2006008754', 'Patent', '', 'NOVEL INTERMEDIATES FOR LINEZOLID ' 'AND RELATED COMPOUNDS') self.assertTrue(this_reference in this_chebi_entity.get_references()) def test_get_references_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('22182') this_reference = Reference('WO2006008754', 'Patent', '', 'NOVEL INTERMEDIATES FOR LINEZOLID ' 'AND RELATED COMPOUNDS') self.assertTrue(this_reference in this_chebi_entity.get_references()) def test_get_cmp_orig_existing(self): '''COMMENT''' this_compound_origin = CompoundOrigin('H**o sapiens', 'NCBI:9606', None, None, None, None, 'DOI', '10.1038/nbt.2488', None) self.assertTrue(this_compound_origin in self.__existing.get_compound_origins()) def test_get_cmp_orig_secondary(self): '''COMMENT''' this_compound_origin = CompoundOrigin('H**o sapiens', 'NCBI:9606', None, None, None, None, 'DOI', '10.1038/nbt.2488', None) self.assertTrue(this_compound_origin in self.__secondary.get_compound_origins()) def test_get_out_existing(self): '''COMMENT''' this_relation = Relation('is_a', '17634', 'C') self.assertTrue(this_relation in self.__existing.get_outgoings()) def test_get_out_secondary(self): '''COMMENT''' this_relation = Relation('has_role', 'CHEBI:48360', 'C') self.assertTrue(this_relation in self.__secondary.get_outgoings()) def test_get_in_existing(self): '''COMMENT''' this_relation = Relation('has_functional_parent', 'CHEBI:15866', 'C') self.assertTrue(this_relation in self.__existing.get_incomings()) def test_get_in_secondary(self): '''COMMENT''' this_relation = Relation('is_conjugate_acid_of', '29412', 'C') self.assertTrue(this_relation in self.__secondary.get_incomings()) def __get_mol_file(self, read_id, retrieved_id): '''COMMENT''' mol_read = _read_mol_file(read_id) this_chebi_entity = ChebiEntity(str(retrieved_id)) textfile_retrieved = open(this_chebi_entity.get_mol_filename(), 'r') mol_retrieved = textfile_retrieved.read() textfile_retrieved.close() self.assertEquals(mol_read, mol_retrieved)
class TestChebiEntity(unittest.TestCase): '''COMMENT''' def setUp(self): '''COMMENT''' self.__existing = ChebiEntity('4167') self.__secondary = ChebiEntity('CHEBI:5585') def test_get_non_existing(self): '''COMMENT''' self.assertRaises(ChebiException, ChebiEntity, '-1') def test_get_id_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_id() == 'CHEBI:4167') def test_get_id_secondary(self): '''COMMENT''' self.assertTrue(self.__secondary.get_id() == 'CHEBI:5585') def test_get_formulae_existing(self): '''COMMENT''' this_formula = Formula('C6H12O6', 'KEGG COMPOUND') self.assertTrue(this_formula in self.__existing.get_formulae()) def test_get_formulae_secondary(self): '''COMMENT''' this_formula = Formula('H2O', 'ChEBI') self.assertTrue(this_formula in self.__secondary.get_formulae()) def test_get_formula_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_formula() == 'C6H12O6') def test_get_formula_secondary(self): '''COMMENT''' self.assertTrue(self.__secondary.get_formula() == 'H2O') def test_get_mass_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_mass(), 180.15588) def test_get_mass_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_mass(), 18.01530) def test_get_charge_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_charge(), 0) def test_get_charge_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_charge(), 0) def test_get_charge_secondary2(self): '''COMMENT''' self.assertEquals(-2, ChebiEntity('43474').get_charge()) def test_get_comments_existing(self): '''COMMENT''' this_chebi_entity = ChebiEntity('29044') this_comment = Comment( 'General', 'General', 'The substituent name \'3-oxoprop-2-enyl\' is ' 'incorrect but is used in various databases.', datetime.datetime.strptime('2005-03-18', '%Y-%M-%d')) self.assertTrue(this_comment in this_chebi_entity.get_comments()) def test_get_comments_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('11505') this_comment = Comment( 'General', 'General', 'The substituent name \'3-oxoprop-2-enyl\' is ' 'incorrect but is used in various databases.', datetime.datetime.strptime('2005-03-18', '%Y-%M-%d')) self.assertTrue(this_comment in this_chebi_entity.get_comments()) def test_get_source_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_source(), 'KEGG COMPOUND') def test_get_source_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_source(), 'KEGG COMPOUND') def test_get_prnt_id_existing(self): '''COMMENT''' self.assertIsNone(self.__existing.get_parent_id()) def test_get_prnt_id_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_parent_id(), 'CHEBI:15377') def test_get_name_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_name(), 'D-glucopyranose') def test_get_name_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_name(), 'water') def test_get_definition_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_definition(), 'A glucopyranose having D-configuration.') def test_get_definition_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('41140') self.assertEqual( this_chebi_entity.get_definition(), 'D-Glucopyranose with beta configuration at the ' 'anomeric centre.') def test_get_mod_on_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_modified_on() > datetime.datetime.strptime('2014-01-01', '%Y-%M-%d')) def test_get_mod_on_secondary(self): '''COMMENT''' self.assertIsNotNone(self.__secondary.get_modified_on()) def test_get_created_by_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_created_by(), 'CHEBI') def test_get_created_by_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_created_by(), 'ops$mennis') def test_get_star_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_star(), 3) def test_get_star_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_star(), 3) def test_get_db_acc_existing(self): '''COMMENT''' dat_acc = DatabaseAccession('MetaCyc accession', 'D-Glucose', 'MetaCyc') self.assertTrue(dat_acc in self.__existing.get_database_accessions()) def test_get_db_acc_secondary(self): '''COMMENT''' dat_acc = DatabaseAccession('MetaCyc accession', 'WATER', 'MetaCyc') self.assertTrue(dat_acc in self.__secondary.get_database_accessions()) def test_get_inchi_existing(self): '''COMMENT''' inchi = 'InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/' + \ 'h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1' self.assertEqual(self.__existing.get_inchi(), inchi) def test_get_inchi_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_inchi(), 'InChI=1S/H2O/h1H2') def test_get_inchi_key_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_inchi_key(), 'WQZGKKKJIJFFOK-GASJEMHNSA-N') def test_get_inchi_key_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_inchi_key(), 'XLYOFNOQVPJJNP-UHFFFAOYSA-N') def test_get_smiles_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_smiles(), 'OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O') def test_get_smiles_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_smiles(), '[H]O[H]') def test_get_mol_existing(self): '''COMMENT''' chebi_id = 73938 this_chebi_entity = ChebiEntity(str(chebi_id)) self.assertEqual(this_chebi_entity.get_mol(), _read_mol_file(chebi_id)) def test_get_mol_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_mol(), _read_mol_file(15377)) def test_get_mol_file_existing(self): '''COMMENT''' chebi_id = 73938 self.__get_mol_file(chebi_id, chebi_id) def test_get_mol_file_secondary(self): '''COMMENT''' read_id = 15377 retrieved_id = 42857 self.__get_mol_file(read_id, retrieved_id) def test_get_names_existing(self): '''COMMENT''' this_name = Name('Grape sugar', 'SYNONYM', 'KEGG COMPOUND', False, 'en') self.assertTrue(this_name in self.__existing.get_names()) def test_get_names_secondary(self): '''COMMENT''' this_name = Name('eau', 'SYNONYM', 'ChEBI', False, 'fr') self.assertTrue(this_name in self.__secondary.get_names()) def test_get_references_existing(self): '''COMMENT''' this_chebi_entity = ChebiEntity('15347') this_reference = Reference( 'WO2006008754', 'Patent', '', 'NOVEL INTERMEDIATES FOR LINEZOLID ' 'AND RELATED COMPOUNDS') self.assertTrue(this_reference in this_chebi_entity.get_references()) def test_get_references_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('22182') this_reference = Reference( 'WO2006008754', 'Patent', '', 'NOVEL INTERMEDIATES FOR LINEZOLID ' 'AND RELATED COMPOUNDS') self.assertTrue(this_reference in this_chebi_entity.get_references()) def test_get_cmp_orig_existing(self): '''COMMENT''' this_compound_origin = CompoundOrigin('H**o sapiens', 'NCBI:9606', None, None, None, None, 'DOI', '10.1038/nbt.2488', None) self.assertTrue( this_compound_origin in self.__existing.get_compound_origins()) def test_get_cmp_orig_secondary(self): '''COMMENT''' this_compound_origin = CompoundOrigin('H**o sapiens', 'NCBI:9606', None, None, None, None, 'DOI', '10.1038/nbt.2488', None) self.assertTrue( this_compound_origin in self.__secondary.get_compound_origins()) def test_get_out_existing(self): '''COMMENT''' this_relation = Relation('is_a', '17634', 'C') self.assertTrue(this_relation in self.__existing.get_outgoings()) def test_get_out_secondary(self): '''COMMENT''' this_relation = Relation('has_role', 'CHEBI:48360', 'C') self.assertTrue(this_relation in self.__secondary.get_outgoings()) def test_get_in_existing(self): '''COMMENT''' this_relation = Relation('has_functional_parent', 'CHEBI:15866', 'C') self.assertTrue(this_relation in self.__existing.get_incomings()) def test_get_in_secondary(self): '''COMMENT''' this_relation = Relation('is_conjugate_acid_of', '29412', 'C') self.assertTrue(this_relation in self.__secondary.get_incomings()) def __get_mol_file(self, read_id, retrieved_id): '''COMMENT''' mol_read = _read_mol_file(read_id) this_chebi_entity = ChebiEntity(str(retrieved_id)) textfile_retrieved = open(this_chebi_entity.get_mol_filename(), 'r') mol_retrieved = textfile_retrieved.read() textfile_retrieved.close() self.assertEquals(mol_read, mol_retrieved)