def test_adapt_reference(data_pool): """Test that we can map a Reference object to a PyOpenWorm Experiment object.""" r = data_pool.get_reference() reference_adapter = Adapter.create(r) experiment = reference_adapter.get_pow() reference = reference_adapter.get_cw() PyOpenWorm.connect() pyow_dict = { 'authors': experiment.author(), 'doi': experiment.doi(), 'pmid': experiment.pmid(), 'title': experiment.title(), 'url': experiment.uri(), 'year': experiment.year(), } cw_dict = { 'authors': set([reference.authors]), 'doi': reference.doi, 'pmid': reference.PMID, 'title': reference.title, 'url': set([reference.url]), 'year': reference.year } PyOpenWorm.disconnect() assert pyow_dict == cw_dict
def test_adapt_IonChannel(data_pool): """ Test that we can map a IonChannel object to a PyOpenWorm Channel object. """ ic = data_pool.get_ion_channel() ica = Adapter.create(ic) cw_obj = ica.get_cw() pow_obj = ica.get_pow() # parse PMIDs for expression_patterns, # then for descriptions # and finally proteins exp_strings = cw_obj.expression_evidences.split(', ') cw_expression_pmids = set(int(s) for s in exp_strings) desc_strings = cw_obj.description_evidences.split(', ') cw_description_pmids = set(int(s) for s in desc_strings) cw_proteins = set(cw_obj.proteins.split('; ')) cw_dict = { 'channel_name': cw_obj.channel_name, 'description': cw_obj.description, 'description_evidences': cw_obj.description_evidences, 'gene_name': cw_obj.gene_name, 'gene_WB_ID': cw_obj.gene_WB_ID, 'gene_class': cw_obj.gene_class, 'proteins': cw_proteins, 'expression_pattern': cw_obj.expression_pattern, 'expression_evidences': cw_obj.expression_evidences, } # retrieve PMIDs for expression_patterns, # then for descriptions ev = PyOpenWorm.Evidence() ev.asserts(pow_obj.expression_pattern) pow_expression_pmids = set(e.pmid() for e in ev.load()) ev = PyOpenWorm.Evidence() ev.asserts(pow_obj.description) pow_description_pmids = set(e.pmid() for e in ev.load()) pow_dict = { 'channel_name': pow_obj.name(), 'description': pow_obj.description(), 'description_evidences': pow_description_pmids, 'gene_name': pow_obj.gene_name(), 'gene_WB_ID': pow_obj.gene_WB_ID(), 'gene_class': pow_obj.gene_class(), 'proteins': pow_obj.proteins(), 'expression_pattern': pow_obj.expression_pattern(), 'expression_evidences': pow_expression_pmids, } assert pow_dict == cw_dict
def test_adapt_GraphData(data_pool): """ Test that we can map some GraphData to a PyOpenWorm data object. """ graph_data = data_pool.get_graph_data() gda = Adapter.create(graph_data) cw_obj = gda.get_cw() pow_obj = gda.get_pow() PyOpenWorm.connect() assert cw_obj.asarray() == pow_obj.data PyOpenWorm.disconnect()
def test_adapt_PatchClamp(data_pool): """ Test that we can map a PatchClamp object to a PyOpenWorm PatchClamp object. """ pc = data_pool.get_patch_clamp() pca = Adapter.create(pc) cw_obj = pca.get_cw() pow_obj = pca.get_pow() PyOpenWorm.connect() pow_dict = { 'delta_t': pow_obj.delta_t(), 'duration': pow_obj.duration(), 'end_time': pow_obj.end_time(), 'ion_channel': pow_obj.ion_channel(), 'protocol_end': pow_obj.protocol_end(), 'protocol_start': pow_obj.protocol_start(), 'protocol_step': pow_obj.protocol_step(), 'start_time': pow_obj.start_time(), } cw_dict = { 'delta_t': cw_obj.deltat, 'duration': cw_obj.duration, 'end_time': cw_obj.end_time, 'ion_channel': cw_obj.ion_channel, 'protocol_end': cw_obj.protocol_end, 'protocol_start': cw_obj.protocol_start, 'protocol_step': cw_obj.protocol_step, 'start_time': cw_obj.start_time, } PyOpenWorm.disconnect() assert cw_dict == pow_dict