def expt_data_set(specimen_id):
sql = """
select wkf.storage_directory || wkf.filename from well_known_files wkf
join specimens sp on sp.ephys_roi_result_id = wkf.attachable_id
where sp.id = %s
and wkf.well_known_file_type_id = %s
"""
results = lims_utils.query(sql, (specimen_id, NWB_DOWNLOAD_TYPE_ID))
nwb_path = results[0][0]
return NwbDataSet(nwb_path)
def collect_exp_var(ids):
sql = """
select sp.id, nmr.explained_variance_ratio from specimens sp
join neuronal_models nm on nm.specimen_id = sp.id
join neuronal_model_runs nmr on nmr.neuronal_model_id = nm.id
where sp.id = any(%s)
and nm.neuronal_model_template_id = %s
"""
exp_var_data = {}
for model_type, nmt_id in NEURONAL_MODEL_TEMPLATES.iteritems():
results = lims_utils.query(sql, (list(ids), nmt_id))
exp_var_data[model_type] = dict(results)
return exp_var_data
def query_cells():
q = """
SELECT n.specimen_id, donors.full_genotype FROM neuron_reconstructions n
JOIN well_known_files f ON n.id = f.attachable_id
JOIN specimens on specimens.id=n.specimen_id
left join donors on specimens.donor_id=donors.id
where
donors.full_genotype is not null
and n.manual
and not n.superseded
and f.well_known_file_type_id = 303941301
"""
cells = lims_utils.query(q, ())
return cells
def collect_virtual_experiments(ids):
sql = """
select sp.id, wkf.storage_directory || wkf.filename from specimens sp
join neuronal_models nm on nm.specimen_id = sp.id
join neuronal_model_runs nmr on nmr.neuronal_model_id = nm.id
join well_known_files wkf on wkf.attachable_id = nmr.id
where sp.id = any(%s)
and nm.neuronal_model_template_id = %s
"""
ve_paths = {}
for model_type, nmt_id in NEURONAL_MODEL_TEMPLATES.iteritems():
results = lims_utils.query(sql, (list(ids), nmt_id))
ve_paths[model_type] = dict(results)
return ve_paths