def should_import_epochs(self):
expt2 = self.ctx.insertProject("project2","project2",DateTime()).insertExperiment("purpose", DateTime())
protocol2 = self.ctx.insertProtocol("protocol", "description")
epoch_start = DateTime()
epoch = expt2.insertEpoch(Maps.newHashMap(),
Maps.newHashMap(),
epoch_start,
DateTime(),
protocol2,
to_map({}),
to_map({}))
segment = self.block.segments[0]
neoepoch = neo.core.epoch.Epoch(10 * pq.ms, 100 * pq.ms, "epoch1")
segment.epochs.append(neoepoch)
try:
import_timeline_annotations(epoch, segment, epoch_start)
annotations = list(iterable(epoch.getUserTimelineAnnotations(self.ctx.getAuthenticatedUser())))
assert_equals(1, len(annotations))
assert_equals(epoch_start.plusMillis(10).getMillis(), annotations[0].getStart().getMillis())
assert_equals(epoch_start.plusMillis(10).plusMillis(100).getMillis(), annotations[0].getEnd().get().getMillis())
finally:
segment.epochs.remove(neoepoch)
def should_import_events(self):
expt2 = self.ctx.insertProject("project2","project2",DateTime()).insertExperiment("purpose", DateTime())
protocol2 = self.ctx.insertProtocol("protocol", "description")
epoch_start = DateTime()
epoch = expt2.insertEpoch(Maps.newHashMap(),
Maps.newHashMap(),
epoch_start,
DateTime(),
protocol2,
to_map(dict()),
to_map(dict()))
segment = self.block.segments[0]
event_ms = 10
event1 = Event(event_ms * pq.ms, "event1", name = "event1")
segment.events.append(event1)
try:
import_timeline_annotations(epoch, segment, epoch_start)
annotations = list(iterable(epoch.getUserTimelineAnnotations(self.ctx.getAuthenticatedUser())))
assert(epoch_start.plusMillis(event_ms).equals(annotations[0].getStart()))
assert_equals(1, len(annotations))
finally:
segment.events.remove(event1)
def should_use_existing_sources(self):
expt2 = self.ctx.insertProject("project2","project2",DateTime()).insertExperiment("purpose", DateTime())
protocol2 = self.ctx.insertProtocol("protocol", "description")
import_csv(self.ctx,
container_uri=expt2.getURI().toString(),
protocol_uri=protocol2.getURI().toString(),
files=[EXAMPLE_FIELD_DATA_CSV])
expected_source_names = np.unique(self.df.Site)
sources = self.ctx.getTopLevelSources()
assert_equals(len(expected_source_names), len(list(iterable(sources))))
def should_import_event_arrays(self):
expt2 = self.ctx.insertProject("project2","project2",DateTime()).insertExperiment("purpose", DateTime())
protocol2 = self.ctx.insertProtocol("protocol", "description")
epoch_start = DateTime()
epoch = expt2.insertEpoch(Maps.newHashMap(),
Maps.newHashMap(),
epoch_start,
DateTime(),
protocol2,
to_map({}),
to_map({}))
segment = self.block.segments[0]
event_ms = [10, 12]
event_array = EventArray(times=np.array(event_ms) * pq.ms, labels=['event1', 'event2'])
segment.eventarrays.append(event_array)
try:
import_timeline_annotations(epoch, segment, epoch_start)
annotations = list(iterable(epoch.getUserTimelineAnnotations(self.ctx.getAuthenticatedUser())))
assert_equals(2, len(annotations))
event_starts = [a.getStart() for a in annotations]
for ms in event_ms:
found = False
for s in event_starts:
if epoch_start.plusMillis(ms).equals(s):
found = True
if not found:
assert_true(False, "event start time doesn't match")
finally:
segment.eventarrays.remove(event_array)
def should_call_via_main(self):
expt2 = self.ctx.insertProject("project2","project2",DateTime()).insertExperiment("purpose", DateTime())
protocol2 = self.ctx.insertProtocol("protocol", "description")
number_of_days = np.unique(np.asarray(self.df.index)).size
args = ['--timezone=America/New_York',
'--container={}'.format(str(expt2.getURI().toString())),
'--protocol={}'.format(str(protocol2.getURI().toString())),
EXAMPLE_FIELD_DATA_CSV,
]
main(args, dsc=self.dsc)
assert_equals(number_of_days, len(list(iterable(expt2.getEpochGroups()))))
def should_use_existing_site_epoch_when_present(self):
expt2 = self.ctx.insertProject("project2","project2",DateTime()).insertExperiment("purpose", DateTime())
protocol2 = self.ctx.insertProtocol("protocol", "description")
import_csv(self.ctx,
container_uri=expt2.getURI().toString(),
protocol_uri=protocol2.getURI().toString(),
files=[EXAMPLE_FIELD_DATA_CSV])
import_csv(self.ctx,
container_uri=expt2.getURI().toString(),
protocol_uri=protocol2.getURI().toString(),
files=[EXAMPLE_FIELD_DATA_CSV])
self.check_epoch_per_site(expt2)
def _make_day_ends(python_datetime, tzone):
"""Makes a midnight,end-of-day DateTime pair from Python datetime and timezone ID"""
d = DateTime(python_datetime.isoformat(), DateTimeZone.forID(tzone))
return (d.toDateMidnight().toDateTime(), d.plusDays(1).minusSeconds(1))
def make_experiment_fixture(cls):
ctx = cls.dsc.getContext()
project = ctx.insertProject("name", "description", DateTime())
expt = project.insertExperiment("purpose", DateTime())
protocol = ctx.insertProtocol("protocol", "description")
return ctx, expt, protocol
def _make_day_ends(python_datetime, tzone):
"""Makes a midnight,end-of-day DateTime pair from Python datetime and timezone ID"""
d = DateTime(python_datetime.isoformat(), DateTimeZone.forID(tzone))
return (d.toDateMidnight().toDateTime(), d.plusDays(1).minusSeconds(1))