def data_for_specimen_id(specimen_id, passed_only):
name, roi_id, specimen_id = lq.get_specimen_info_from_lims_by_id(specimen_id)
nwb_path = lq.get_nwb_path_from_lims(roi_id)
if len(nwb_path) == 0: # could not find an NWB file
logging.debug("No NWB file for {:d}".format(specimen_id))
return {"error": {"type": "no_nwb", "details": ""}}
# Check if NWB has lab notebook information, or if additional hdf5 file is needed
ontology = StimulusOntology(ju.read(StimulusOntology.DEFAULT_STIMULUS_ONTOLOGY_FILE))
h5_path = None
with h5py.File(nwb_path, "r") as h5:
if "general/labnotebook" not in h5:
h5_path = lq.get_igorh5_path_from_lims(roi_id)
try:
data_set = AibsDataSet(nwb_file=nwb_path, h5_file=h5_path, ontology=ontology)
except Exception as detail:
logging.warn("Exception when processing specimen {:d}".format(specimen_id))
logging.warn(detail)
# return {"error": {"type": "dataset", "details": traceback.format_exc(limit=1)}}
return {}
try:
lsq_sweep_numbers = categorize_iclamp_sweeps(data_set, ontology.long_square_names)
ssq_sweep_numbers = categorize_iclamp_sweeps(data_set, ontology.short_square_names)
ramp_sweep_numbers = categorize_iclamp_sweeps(data_set, ontology.ramp_names)
except Exception as detail:
logging.warn("Exception when processing specimen {:d}".format(specimen_id))
logging.warn(detail)
# return {"error": {"type": "sweep_table", "details": traceback.format_exc(limit=1)}}
return {}
try:
result = extract_features(data_set, ramp_sweep_numbers, ssq_sweep_numbers, lsq_sweep_numbers)
except Exception as detail:
logging.warn("Exception when processing specimen {:d}".format(specimen_id))
logging.warn(detail)
# return {"error": {"type": "processing", "details": traceback.format_exc(limit=1)}}
return {}
result["specimen_id"] = specimen_id
return result
def lims_nwb_information(specimen_id):
_, roi_id, _ = lq.get_specimen_info_from_lims_by_id(specimen_id)
if roi_id is None:
logging.warning(
"No ephys ROI result found for {:d}".format(specimen_id))
return {
"error": {
"type": "no_ephys_roi_result",
"details": "roi ID was None"
}
}, None
nwb_path = lq.get_nwb_path_from_lims(roi_id)
if (nwb_path is None) or (len(nwb_path)
== 0): # could not find an NWB file
logging.warning("No NWB file for {:d}".format(specimen_id))
return {"error": {"type": "no_nwb", "details": "empty nwb path"}}, None
# Check if NWB has lab notebook information, or if additional hdf5 file is needed
h5_path = None
try:
with h5py.File(nwb_path, "r") as h5:
if "general/labnotebook" not in h5:
try:
h5_path = lq.get_igorh5_path_from_lims(roi_id)
except Exception as detail:
logging.warning(
"Exception when loading h5 file for {:d}".format(
specimen_id))
logging.warning(detail)
return {
"error": {
"type": "dataset",
"details": traceback.format_exc(limit=None)
}
}, None
except:
logging.warning("Could not open NWB file for {:d}".format(specimen_id))
return {"error": {"type": "no_nwb", "details": ""}}, None
return nwb_path, h5_path
def test_get_nwb_path_from_lims():
ephys_roi_result = 500844779
result = lq.get_nwb_path_from_lims(ephys_roi_result)
assert result == "/allen/programs/celltypes/production/mousecelltypes/prod589/Ephys_Roi_Result_500844779/500844779.nwb"