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