def reup_file(object: Any):
thekey = recording_key if recording_key[
'key_field'] in object else sorting_key
if VERBOSE:
print(
f"Executing: object['{thekey['key_field']}'] = kp.store_file(kp.load_file(object['{thekey['key_field']}']), basename={thekey['basename']})"
)
if DRY_RUN: return
# Turns out that kachery doesn't handle big files without manifests all that well. Which was the point of this exercise.
# So let's take advantage of being on the same filesystem to do a little magic.
raw = object[thekey["key_field"]]
print(f'Got raw: {raw}')
if ('sha1dir' in raw):
key_field = object[thekey['key_field']]
sha1dir = key_field.split('/')[2]
print(f'Got dir: {sha1dir}')
kp.load_file(f'sha1://{sha1dir}')
print(f"Fetching hash for file: {key_field}")
reformed_field = trim_dir_annotation(f"{key_field}")
if VERBOSE: print(f"(using reformed field {reformed_field})")
try:
sha1 = ka.get_file_hash(reformed_field)
except:
if FORCE:
print(
f"\t** Trimmed lookup didn't work, falling back to kp.load_file({key_field})"
)
kp.load_file(key_field)
sha1 = ka.get_file_hash(key_field)
else:
print(
f"Error on ka.get_file_hash({reformed_field}) -- aborting")
exit()
else:
#sha1 = '/'.join(raw.split('/')[2:])
sha1 = raw.split('/')[2]
print(f'Got sha1: {sha1}')
src_path = f'/mnt/ceph/users/magland/kachery-storage/sha1/{sha1[0]}{sha1[1]}/{sha1[2]}{sha1[3]}/{sha1[4]}{sha1[5]}/{sha1}'
dest_path = f'/mnt/ceph/users/jsoules/kachery-storage/sha1/{sha1[0]}{sha1[1]}/{sha1[2]}{sha1[3]}/{sha1[4]}{sha1[5]}/{sha1}'
if VERBOSE: print(f"Executing: shutil.copyfile({src_path}, {dest_path})")
if not exists(dest_path):
pathlib.Path('/'.join(dest_path.split('/')[:-1])).mkdir(parents=True,
exist_ok=True)
copyfile(src_path, dest_path)
print("\tCompleted copy operation.")
object[thekey['key_field']] = kp.store_file(
kp.load_file(object[thekey['key_field']]),
basename=f"{thekey['basename']}")
def make(self, key):
print('Computing SHA-1 and storing in kachery...')
nwb_file_abs_path = Nwbfile.get_abs_path(key['nwb_file_name'])
with ka.config(use_hard_links=True):
kachery_path = ka.store_file(nwb_file_abs_path)
key['nwb_file_sha1'] = ka.get_file_hash(kachery_path)
self.insert1(key)
def __init__(self,
*,
recording_directory=None,
timeseries_path=None,
download=False,
samplerate=None,
geom=None,
geom_path=None,
params_path=None):
RecordingExtractor.__init__(self)
if recording_directory:
timeseries_path = recording_directory + '/raw.mda'
geom_path = recording_directory + '/geom.csv'
params_path = recording_directory + '/params.json'
self._timeseries_path = timeseries_path
if params_path:
self._dataset_params = ka.load_object(params_path)
self._samplerate = self._dataset_params['samplerate']
else:
self._dataset_params = dict(samplerate=samplerate)
self._samplerate = samplerate
if download:
path0 = ka.load_file(path=self._timeseries_path)
if not path0:
raise Exception('Unable to realize file: ' +
self._timeseries_path)
self._timeseries_path = path0
self._timeseries = DiskReadMda(self._timeseries_path)
if self._timeseries is None:
raise Exception('Unable to load timeseries: {}'.format(
self._timeseries_path))
X = self._timeseries
if geom is not None:
self._geom = geom
elif geom_path:
geom_path2 = ka.load_file(geom_path)
self._geom = np.genfromtxt(geom_path2, delimiter=',')
else:
self._geom = np.zeros((X.N1(), 2))
if self._geom.shape[0] != X.N1():
# raise Exception(
# 'Incompatible dimensions between geom.csv and timeseries file {} <> {}'.format(self._geom.shape[0], X.N1()))
print(
'WARNING: Incompatible dimensions between geom.csv and timeseries file {} <> {}'
.format(self._geom.shape[0], X.N1()))
self._geom = np.zeros((X.N1(), 2))
self._hash = ka.get_object_hash(
dict(timeseries=ka.get_file_hash(self._timeseries_path),
samplerate=self._samplerate,
geom=_json_serialize(self._geom)))
self._num_channels = X.N1()
self._num_timepoints = X.N2()
for m in range(self._num_channels):
self.set_channel_property(m, 'location', self._geom[m, :])
def make(self, key):
print('Computing SHA-1 and storing in kachery...')
analysis_file_abs_path = AnalysisNwbfile().get_abs_path(key['analysis_file_name'])
with ka.config(use_hard_links=True):
kachery_path = ka.store_file(analysis_file_abs_path)
key['analysis_file_sha1'] = ka.get_file_hash(kachery_path)
self.insert1(key)
#TODO: load from kachery and fetch_nwb
def patch_recording_geom(recording, geom_fname):
print(f'PATCHING geom for recording: {recording["name"]}')
geom_info = ka.get_file_info(geom_fname)
x = recording['directory']
y = ka.store_dir(x).replace('sha1dir://', 'sha1://')
obj = ka.load_object(y)
obj['files']['geom.csv'] = dict(size=geom_info['size'],
sha1=geom_info['sha1'])
x2 = ka.store_object(obj)
recording['directory'] = 'sha1dir://' + ka.get_file_hash(x2) + '.patched'
def main():
test1()
f = kp.load_feed('feed://' + os.environ['FEED_ID'])
N1 = 10000
N2 = 1000
a = kp.store_npy(np.meshgrid(np.arange(N1), np.arange(N2))[0])
sf = f.get_subfeed('sf1')
sf.append_message({'a': a, 'N1': N1, 'N2': N2})
# test invalid manifest
b = kp.store_npy(np.meshgrid(np.arange(N1 + 1), np.arange(N2))[0])
invalid_manifest = kp.store_object({'invalid': True})
b_invalid_manifest = b.split('?')[0] + '?manifest=' + ka.get_file_hash(
invalid_manifest)
sf.append_message({'b_invalid_manifest': b_invalid_manifest})
def hash(self):
return ka.get_object_hash(
dict(firings=ka.get_file_hash(self._firings_path),
samplerate=self._sampling_frequency))
def handle_message(self, msg):
type0 = msg.get('type')
if type0 == 'reportClientInfo':
print('reported client info:', msg)
self._feed_uri = msg['clientInfo']['feedUri']
self._workspace_name = msg['clientInfo']['workspaceName']
self._readonly = msg['clientInfo']['readOnly']
if not self._feed_uri:
self._feed_uri = 'feed://' + self._default_feed_id
# self._feed_uri = kp.create_feed(feed_name='labbox-ephys-default').get_uri()
# assert self._feed_uri.startswith('sha1://'), 'For now, feedUri must start with sha1://'
self._feed = kp.load_feed(self._feed_uri)
for key in ['recordings', 'sortings']:
self._subfeed_positions[key] = 0
subfeed_name = dict(key=key,
workspaceName=self._workspace_name)
subfeed = self._feed.get_subfeed(subfeed_name)
messages = subfeed.get_next_messages(wait_msec=10)
for m in messages:
if 'action' in m:
self._send_message({
'type': 'action',
'action': m['action']
})
else:
print(f'WARNING: No action in message for {key}')
self._subfeed_positions[
key] = self._subfeed_positions[key] + len(messages)
self._send_message({'type': 'reportInitialLoadComplete'})
if self._feed:
qm = self._queued_document_action_messages
self._queued_document_action_messages = []
for m in qm:
self.handle_message(m)
elif type0 == 'appendDocumentAction':
if self._readonly:
print(
'Cannot append document action. This is a readonly feed.')
return
if self._feed is None:
self._queued_document_action_messages.append(msg)
else:
subfeed_name = dict(key=msg['key'],
workspaceName=self._workspace_name)
subfeed = self._feed.get_subfeed(subfeed_name)
subfeed.append_message({'action': msg['action']})
elif type0 == 'hitherCreateJob':
functionName = msg['functionName']
kwargs = msg['kwargs']
client_job_id = msg['clientJobId']
try:
outer_job = hi.run(functionName,
**kwargs,
labbox=self._labbox_context)
except Exception as err:
self._send_message({
'type': 'hitherJobError',
'job_id': client_job_id,
'client_job_id': client_job_id,
'error_message': f'Error creating outer job: {str(err)}',
'runtime_info': None
})
return
try:
job_or_result = outer_job.wait()
except Exception as err:
self._send_message({
'type': 'hitherJobError',
'job_id': outer_job._job_id,
'client_job_id': client_job_id,
'error_message': str(err),
'runtime_info': outer_job.get_runtime_info()
})
return
if hasattr(job_or_result, '_job_id'):
job = job_or_result
setattr(job, '_client_job_id', client_job_id)
job_id = job._job_id
self._jobs_by_id[job_id] = job
print(
f'======== Created hither job (2): {job_id} {functionName}'
)
self._send_message({
'type': 'hitherJobCreated',
'job_id': job_id,
'client_job_id': client_job_id
})
else:
result = job_or_result
msg = {
'type':
'hitherJobFinished',
'client_job_id':
client_job_id,
'job_id':
client_job_id,
# 'result': _make_json_safe(result),
'result_sha1':
ka.get_file_hash(ka.store_object(_make_json_safe(result))),
'runtime_info':
outer_job.get_runtime_info()
}
elif type0 == 'hitherCancelJob':
job_id = msg['job_id']
assert job_id, 'Missing job_id'
assert job_id in self._jobs_by_id, f'No job with id: {job_id}'
job = self._jobs_by_id[job_id]
job.cancel()
def iterate(self):
subfeed_watches = {}
if (self._feed_uri
is not None) and (self._feed_uri.startswith('feed://')):
for key in ['recordings', 'sortings']:
subfeed_name = dict(workspaceName=self._workspace_name,
key=key)
subfeed_watches[key] = dict(
feedId=self._feed._feed_id, # fix this
subfeedName=subfeed_name,
position=self._subfeed_positions[key])
for w in self._additional_subfeed_watches:
subfeed_watches[w['watch_name']] = dict(
feedId=w['feed_id'],
subfeedHash=w['subfeed_hash'],
position=self._subfeed_positions[w['watch_name']])
if len(subfeed_watches.keys()) > 0:
messages = kp.watch_for_new_messages(
subfeed_watches=subfeed_watches, wait_msec=100)
for key in messages.keys():
if key in ['recordings', 'sortings']:
for m in messages[key]:
if 'action' in m:
self._send_message({
'type': 'action',
'action': m['action']
})
else:
print(
f'WARNING: no action in feed message for {key}'
)
else:
for m in messages[key]:
self._send_message({
'type': 'subfeedMessage',
'watchName': key,
'message': m
})
self._subfeed_positions[
key] = self._subfeed_positions[key] + len(messages[key])
hi.wait(0)
job_ids = list(self._jobs_by_id.keys())
for job_id in job_ids:
job = self._jobs_by_id[job_id]
status0 = job.get_status()
if status0 == hi.JobStatus.FINISHED:
print(
f'======== Finished hither job: {job_id} {job.get_label()}'
)
result = job.get_result()
runtime_info = job.get_runtime_info()
del self._jobs_by_id[job_id]
msg = {
'type':
'hitherJobFinished',
'client_job_id':
job._client_job_id,
'job_id':
job_id,
# 'result': _make_json_safe(result),
'result_sha1':
ka.get_file_hash(ka.store_object(_make_json_safe(result))),
'runtime_info':
runtime_info
}
self._send_message(msg)
elif status0 == hi.JobStatus.ERROR:
exc = job.get_exception()
runtime_info = job.get_runtime_info()
del self._jobs_by_id[job_id]
msg = {
'type': 'hitherJobError',
'job_id': job_id,
'client_job_id': job._client_job_id,
'error_message': str(exc),
'runtime_info': runtime_info
}
self._send_message(msg)
