def parameter_test_helper(ds: DataSet,
toplevel_names: Sequence[str],
expected_names: Dict[str, Sequence[str]],
expected_shapes: Dict[str, Sequence[Tuple[int, ...]]],
expected_values: Dict[str, Sequence[np.ndarray]],
start: Optional[int] = None,
end: Optional[int] = None):
"""
A helper function to compare the data we actually read out of a given
dataset with the expected data.
Args:
ds: the dataset in question
toplevel_names: names of the toplevel parameters of the dataset
expected_names: names of the parameters expected to be loaded for a
given parameter as a sequence indexed by the parameter.
expected_shapes: expected shapes of the parameters loaded. The shapes
should be stored as a tuple per parameter in a sequence containing
all the loaded parameters for a given requested parameter.
expected_values: expected content of the data arrays stored in a
sequenceexpected_names:
"""
data = ds.get_parameter_data(*toplevel_names, start=start, end=end)
dataframe = ds.get_data_as_pandas_dataframe(*toplevel_names,
start=start,
end=end)
all_data = ds.get_parameter_data(start=start, end=end)
all_dataframe = ds.get_data_as_pandas_dataframe(start=start, end=end)
all_parameters = list(all_data.keys())
assert set(data.keys()).issubset(set(all_parameters))
assert list(data.keys()) == list(dataframe.keys())
assert len(data.keys()) == len(toplevel_names)
assert len(dataframe.keys()) == len(toplevel_names)
verify_data_dict(data, dataframe, toplevel_names, expected_names,
expected_shapes, expected_values)
verify_data_dict(all_data, all_dataframe, toplevel_names, expected_names,
expected_shapes, expected_values)
# Now lets remove a random element from the list
# We do this one by one until there is only one element in the list
subset_names = copy(all_parameters)
while len(subset_names) > 1:
elem_to_remove = random.randint(0, len(subset_names) - 1)
name_removed = subset_names.pop(elem_to_remove)
expected_names.pop(name_removed)
expected_shapes.pop(name_removed)
expected_values.pop(name_removed)
subset_data = ds.get_parameter_data(*subset_names,
start=start, end=end)
subset_dataframe = ds.get_data_as_pandas_dataframe(*subset_names,
start=start,
end=end)
verify_data_dict(subset_data, subset_dataframe, subset_names,
expected_names, expected_shapes, expected_values)
def ds_to_datadicts(ds: DataSet) -> Dict[str, DataDict]:
"""
Make DataDicts from a qcodes DataSet.
:param ds: qcodes dataset
:returns: dictionary with one item per dependent.
key: name of the dependent
value: DataDict containing that dependent and its
axes.
"""
ret = {}
pdata = ds.get_parameter_data()
for p, spec in ds.paramspecs.items():
if spec.depends_on != '':
axes = spec.depends_on_ # .split(', ')
data = dict()
data[p] = dict(unit=spec.unit, axes=axes, values=pdata[p][p])
for ax in axes:
axspec = ds.paramspecs[ax]
data[ax] = dict(unit=axspec.unit, values=pdata[p][ax])
ret[p] = DataDict(**data)
ret[p].validate()
return ret
def test_correct_experiment_routing(two_empty_temp_db_connections,
some_interdeps):
"""
Test that existing experiments are correctly identified AND that multiple
insertions of the same runs don't matter (run insertion is idempotent)
"""
source_conn, target_conn = two_empty_temp_db_connections
source_exp_1 = Experiment(conn=source_conn)
# make 5 runs in first experiment
exp_1_run_ids = []
for _ in range(5):
source_dataset = DataSet(conn=source_conn, exp_id=source_exp_1.exp_id)
exp_1_run_ids.append(source_dataset.run_id)
source_dataset.set_interdependencies(some_interdeps[1])
source_dataset.mark_started()
for val in range(10):
source_dataset.add_results(
[{name: val
for name in some_interdeps[1].names}])
source_dataset.mark_completed()
# make a new experiment with 1 run
source_exp_2 = Experiment(conn=source_conn)
ds = DataSet(conn=source_conn, exp_id=source_exp_2.exp_id, name="lala")
exp_2_run_ids = [ds.run_id]
ds.set_interdependencies(some_interdeps[1])
ds.mark_started()
for val in range(10):
ds.add_results([{name: val for name in some_interdeps[1].names}])
ds.mark_completed()
source_path = path_to_dbfile(source_conn)
target_path = path_to_dbfile(target_conn)
# now copy 2 runs
extract_runs_into_db(source_path, target_path, *exp_1_run_ids[:2])
target_exp1 = Experiment(conn=target_conn, exp_id=1)
assert len(target_exp1) == 2
# copy two other runs, one of them already in
extract_runs_into_db(source_path, target_path, *exp_1_run_ids[1:3])
assert len(target_exp1) == 3
# insert run from different experiment
extract_runs_into_db(source_path, target_path, ds.run_id)
assert len(target_exp1) == 3
target_exp2 = Experiment(conn=target_conn, exp_id=2)
assert len(target_exp2) == 1
# finally insert every single run from experiment 1
extract_runs_into_db(source_path, target_path, *exp_1_run_ids)
# check for idempotency once more by inserting all the runs but in another
# order
with raise_if_file_changed(target_path):
extract_runs_into_db(source_path, target_path, *exp_1_run_ids[::-1])
target_exps = get_experiments(target_conn)
assert len(target_exps) == 2
assert len(target_exp1) == 5
assert len(target_exp2) == 1
# check that all the datasets match up
for run_id in exp_1_run_ids + exp_2_run_ids:
source_ds = DataSet(conn=source_conn, run_id=run_id)
target_ds = load_by_guid(guid=source_ds.guid, conn=target_conn)
assert source_ds.the_same_dataset_as(target_ds)
source_data = source_ds.get_parameter_data(
*source_ds.parameters.split(','))
target_data = target_ds.get_parameter_data(
*target_ds.parameters.split(','))
for outkey, outval in source_data.items():
for inkey, inval in outval.items():
np.testing.assert_array_equal(inval,
target_data[outkey][inkey])
def test_basic_extraction(two_empty_temp_db_connections, some_interdeps):
source_conn, target_conn = two_empty_temp_db_connections
source_path = path_to_dbfile(source_conn)
target_path = path_to_dbfile(target_conn)
type_casters = {
'numeric':
float,
'array': (lambda x: np.array(x)
if hasattr(x, '__iter__') else np.array([x])),
'text':
str
}
source_exp = Experiment(conn=source_conn)
source_dataset = DataSet(conn=source_conn, name="basic_copy_paste_name")
with pytest.raises(RuntimeError) as excinfo:
extract_runs_into_db(source_path, target_path, source_dataset.run_id)
assert error_caused_by(excinfo, ('Dataset not completed. An incomplete '
'dataset can not be copied. The '
'incomplete dataset has GUID: '
f'{source_dataset.guid} and run_id: '
f'{source_dataset.run_id}'))
source_dataset.set_interdependencies(some_interdeps[0])
source_dataset.parent_dataset_links = [
Link(head=source_dataset.guid,
tail=str(uuid.uuid4()),
edge_type='test_link')
]
source_dataset.mark_started()
for value in range(10):
result = {
ps.name: type_casters[ps.type](value)
for ps in some_interdeps[0].paramspecs
}
source_dataset.add_results([result])
source_dataset.add_metadata('goodness', 'fair')
source_dataset.add_metadata('test', True)
source_dataset.mark_completed()
assert source_dataset.run_id == source_dataset.captured_run_id
extract_runs_into_db(source_path, target_path, source_dataset.run_id)
target_exp = Experiment(conn=target_conn, exp_id=1)
length1 = len(target_exp)
assert length1 == 1
# trying to insert the same run again should be a NOOP
with raise_if_file_changed(target_path):
extract_runs_into_db(source_path, target_path, source_dataset.run_id)
assert len(target_exp) == length1
target_dataset = DataSet(conn=target_conn, run_id=1)
# Now make the interesting comparisons: are the target objects the same as
# the source objects?
assert source_dataset.the_same_dataset_as(target_dataset)
source_data = source_dataset.get_parameter_data(
*source_dataset.parameters.split(','))
target_data = target_dataset.get_parameter_data(
*target_dataset.parameters.split(','))
for outkey, outval in source_data.items():
for inkey, inval in outval.items():
np.testing.assert_array_equal(inval, target_data[outkey][inkey])
exp_attrs = [
'name', 'sample_name', 'format_string', 'started_at', 'finished_at'
]
for exp_attr in exp_attrs:
assert getattr(source_exp, exp_attr) == getattr(target_exp, exp_attr)
# trying to insert the same run again should be a NOOP
with raise_if_file_changed(target_path):
extract_runs_into_db(source_path, target_path, source_dataset.run_id)