def generate_DB_file_with_some_runs(version=VERSION):
"""
Generate a .db-file with a handful of runs with some interdependent
parameters
"""
# This function will run often on CI and re-generate the .db-files
# That should ideally be a deterministic action
# (although this hopefully plays no role)
np.random.seed(0)
vNfixturepath = os.path.join(utils.fixturepath, f'version{version}')
os.makedirs(vNfixturepath, exist_ok=True)
path = os.path.join(vNfixturepath, 'some_runs.db')
if os.path.exists(path):
os.remove(path)
from qcodes.dataset.sqlite_base import connect
from qcodes.dataset.measurements import Measurement
from qcodes.dataset.experiment_container import Experiment
from qcodes import Parameter
connect(path)
exp = Experiment(path_to_db=path,
name='experiment_1',
sample_name='no_sample_1')
# Now make some parameters to use in measurements
params = []
for n in range(5):
params.append(
Parameter(f'p{n}',
label=f'Parameter {n}',
unit=f'unit {n}',
set_cmd=None,
get_cmd=None))
# Set up an experiment
meas = Measurement(exp)
meas.register_parameter(params[0])
meas.register_parameter(params[1])
meas.register_parameter(params[2], basis=(params[0], ))
meas.register_parameter(params[3], basis=(params[1], ))
meas.register_parameter(params[4], setpoints=(params[2], params[3]))
# Make a number of identical runs
for _ in range(10):
with meas.run() as datasaver:
for x in np.random.rand(10):
for y in np.random.rand(10):
z = np.random.rand()
datasaver.add_result((params[0], 0), (params[1], 1),
(params[2], x), (params[3], y),
(params[4], z))
def test_cannot_connect_to_newer_db():
conn = connect(qc.config["core"]["db_location"],
qc.config["core"]["db_debug"])
current_version = get_user_version(conn)
set_user_version(conn, current_version + 1)
conn.close()
err_msg = f'is version {current_version + 1} but this version of QCoDeS ' \
f'supports up to version {current_version}'
with pytest.raises(RuntimeError, match=err_msg):
conn = connect(qc.config["core"]["db_location"],
qc.config["core"]["db_debug"])
def generate_empty_DB_file():
"""
Generate the bare minimal DB file with no runs
"""
import qcodes.dataset.sqlite_base as sqlite_base
v0fixturepath = os.path.join(utils.fixturepath, 'version1')
os.makedirs(v0fixturepath, exist_ok=True)
path = os.path.join(v0fixturepath, 'empty.db')
if os.path.exists(path):
os.remove(path)
sqlite_base.connect(path)
def generate_upgraded_v2_runs():
"""
Generate some runs by upgradeing from v2 db. This
is needed since the bug we want to test against is in
the v2 to v3 upgrade and not in v3 it self.
This requires the v2 generation to be run before this one
"""
import qcodes.dataset.sqlite_base as sqlite_base
v2fixture_path = os.path.join(utils.fixturepath, 'version2',
'some_runs.db')
v3fixturepath = os.path.join(utils.fixturepath, 'version3',
'some_runs_upgraded_2.db')
shutil.copy2(v2fixture_path, v3fixturepath)
sqlite_base.connect(v3fixturepath)
def generate_empty_DB_file(version=VERSION):
"""
Generate an empty DB file with no runs
"""
import qcodes.dataset.sqlite_base as sqlite_base
vNfixturepath = os.path.join(utils.fixturepath, f'version{version}')
os.makedirs(vNfixturepath, exist_ok=True)
path = os.path.join(vNfixturepath, 'empty.db')
if os.path.exists(path):
os.remove(path)
sqlite_base.connect(path)
def two_empty_temp_db_connections():
"""
Yield the paths of two empty files. Meant for use with the
test_database_copy_paste
"""
with tempfile.TemporaryDirectory() as tmpdirname:
source_path = os.path.join(tmpdirname, 'source.db')
target_path = os.path.join(tmpdirname, 'target.db')
source_conn = connect(source_path)
target_conn = connect(target_path)
try:
yield (source_conn, target_conn)
finally:
source_conn.close()
target_conn.close()
def load_by_counter(counter: int,
exp_id: int,
conn: Optional[ConnectionPlus] = None) -> DataSet:
"""
Load a dataset given its counter in a given experiment
Lookup is performed in the database file that is specified in the config.
Args:
counter: counter of the dataset within the given experiment
exp_id: id of the experiment where to look for the dataset
conn: connection to the database to load from. If not provided, a
connection to the DB file specified in the config is made
Returns:
dataset of the given counter in the given experiment
"""
conn = conn or connect(get_DB_location())
sql = """
SELECT run_id
FROM
runs
WHERE
result_counter= ? AND
exp_id = ?
"""
c = transaction(conn, sql, counter, exp_id)
run_id = one(c, 'run_id')
d = DataSet(conn=conn, run_id=run_id)
return d
def load_by_guid(guid: str, conn: Optional[ConnectionPlus] = None) -> DataSet:
"""
Load a dataset by its GUID
If no connection is provided, lookup is performed in the database file that
is specified in the config.
Args:
guid: guid of the dataset
conn: connection to the database to load from
Returns:
dataset with the given guid
Raises:
NameError: if no run with the given GUID exists in the database
RuntimeError: if several runs with the given GUID are found
"""
conn = conn or connect(get_DB_location())
# this function raises a RuntimeError if more than one run matches the GUID
run_id = get_runid_from_guid(conn, guid)
if run_id == -1:
raise NameError(f'No run with GUID: {guid} found in database.')
return DataSet(run_id=run_id, conn=conn)
def load_or_create_experiment(
experiment_name: str,
sample_name: Optional[str] = None,
conn: Optional[ConnectionPlus] = None) -> Experiment:
"""
Find and return an experiment with the given name and sample name,
or create one if not found.
Args:
experiment_name: Name of the experiment to find or create
sample_name: Name of the sample
conn: Connection to the database. If not supplied, a new connection
to the DB file specified in the config is made
Returns:
The found or created experiment
"""
conn = conn or connect(get_DB_location())
try:
experiment = load_experiment_by_name(experiment_name,
sample_name,
conn=conn)
except ValueError as exception:
if "Experiment not found" in str(exception):
experiment = new_experiment(experiment_name,
sample_name,
conn=conn)
else:
raise exception
return experiment
def load_experiment_by_name(
name: str,
sample: Optional[str] = None,
conn: Optional[ConnectionPlus] = None) -> Experiment:
"""
Try to load experiment with the specified name.
Nothing stops you from having many experiments with the same name and
sample_name. In that case this won't work. And warn you.
Args:
name: the name of the experiment
sample: the name of the sample
conn: connection to the database. If not supplied, a new connection
to the DB file specified in the config is made
Returns:
the requested experiment
Raises:
ValueError if the name is not unique and sample name is None.
"""
conn = conn or connect(get_DB_location())
if sample:
sql = """
SELECT
*
FROM
experiments
WHERE
sample_name = ? AND
name = ?
"""
c = transaction(conn, sql, sample, name)
else:
sql = """
SELECT
*
FROM
experiments
WHERE
name = ?
"""
c = transaction(conn, sql, name)
rows = c.fetchall()
if len(rows) == 0:
raise ValueError("Experiment not found")
elif len(rows) > 1:
_repr = []
for row in rows:
s = (f"exp_id:{row['exp_id']} ({row['name']}-{row['sample_name']})"
f" started at ({row['start_time']})")
_repr.append(s)
_repr_str = "\n".join(_repr)
raise ValueError(f"Many experiments matching your request"
f" found:\n{_repr_str}")
else:
e = Experiment(exp_id=rows[0]['exp_id'], conn=conn)
return e
def __init__(self, path_to_db: str, run_id: Optional[int]=None,
conn=None) -> None:
"""
Create a new DataSet object. The object can either be intended
to hold a new run or and old run.
Args:
path_to_db: path to the sqlite file on disk
run_id: provide this when loading an existing run, leave it
as None when creating a new run
conn: connection to the DB
"""
# TODO: handle fail here by defaulting to
# a standard db
self.path_to_db = path_to_db
if conn is None:
self.conn = connect(self.path_to_db)
else:
self.conn = conn
self.run_id = run_id
self._debug = False
self.subscribers: Dict[str, _Subscriber] = {}
if run_id:
self._completed = completed(self.conn, self.run_id)
def get_runs_from_db(path: str,
start: int = 0,
stop: Union[None, int] = None,
get_structure: bool = False):
"""
Get a db 'overview' dictionary from the db located in `path`.
`start` and `stop` refer to indices of the runs in the db that we want
to have details on; if `stop` is None, we'll use runs until the end.
if `get_structure` is True, include info on the run data structure
in the return dict.
"""
conn = connect(path)
runs = get_runs(conn)
if stop is None:
stop = len(runs)
runs = runs[start:stop]
overview = {}
for run in runs:
run_id = run['run_id']
overview[run_id] = get_ds_info(conn,
run_id,
get_structure=get_structure)
return overview
def load_by_counter(counter, exp_id):
"""
Load a dataset given its counter in one experiment
Args:
counter: Counter of the dataset
exp_id: Experiment the dataset belongs to
Returns:
the dataset
"""
conn = connect(get_DB_location())
sql = """
SELECT run_id
FROM
runs
WHERE
result_counter= ? AND
exp_id = ?
"""
c = transaction(conn, sql, counter, exp_id)
run_id = one(c, 'run_id')
conn.close()
d = DataSet(get_DB_location(), run_id=run_id)
return d
def test_tabels_exists(empty_temp_db):
print(qc.config["core"]["db_location"])
conn = connect(qc.config["core"]["db_location"], qc.config["core"]["db_debug"])
cursor = conn.execute("select sql from sqlite_master where type = 'table'")
expected_tables = ['experiments', 'runs', 'layouts', 'dependencies']
for row, expected_table in zip(cursor, expected_tables):
assert expected_table in row['sql']
conn.close()
def test_path_to_dbfile():
with tempfile.TemporaryDirectory() as tempdir:
tempdb = os.path.join(tempdir, 'database.db')
conn = mut.connect(tempdb)
try:
assert path_to_dbfile(conn) == tempdb
finally:
conn.close()
def toggle_debug(self):
"""
Toggle debug mode, if debug mode is on
all the queries made are echoed back.
"""
self._debug = not self._debug
self.conn.close()
self.conn = connect(self.path_to_db, self._debug)
def shadow_conn(path_to_db: str):
"""
Simple context manager to create a connection for testing and
close it on exit
"""
conn = mut.connect(path_to_db)
yield conn
conn.close()
def test_connect():
conn = connect(':memory:')
assert isinstance(conn, sqlite3.Connection)
assert isinstance(conn, ConnectionPlus)
assert False is conn.atomic_in_progress
assert sqlite3.Row is conn.row_factory
def load_last_experiment() -> Experiment:
"""
Load last experiment
Returns:
last experiment
"""
conn = connect(get_DB_location())
return Experiment(exp_id=get_last_experiment(conn))
def __init__(self,
path_to_db: Optional[str] = None,
exp_id: Optional[int] = None,
name: Optional[str] = None,
sample_name: Optional[str] = None,
format_string: str = "{}-{}-{}",
conn: Optional[ConnectionPlus] = None) -> None:
"""
Create or load an experiment. If exp_id is None, a new experiment is
created. If exp_id is not None, an experiment is loaded.
Args:
path_to_db: The path of the database file to create in/load from.
If a conn is passed together with path_to_db, an exception is
raised
exp_id: The id of the experiment to load
name: The name of the experiment to create. Ignored if exp_id is
not None
sample_name: The sample name for this experiment. Ignored if exp_id
is not None
format_string: The format string used to name result-tables.
Ignored if exp_id is not None.
conn: connection to the database. If not supplied, the constructor
first tries to use path_to_db to figure out where to connect to.
If path_to_db is not supplied either, a new connection
to the DB file specified in the config is made
"""
if path_to_db is not None and conn is not None:
raise ValueError('Received BOTH conn and path_to_db. Please '
'provide only one or the other.')
self._path_to_db = path_to_db or get_DB_location()
self.conn = conn or connect(self.path_to_db, get_DB_debug())
max_id = len(get_experiments(self.conn))
if exp_id is not None:
if exp_id not in range(1, max_id + 1):
raise ValueError('No such experiment in the database')
self._exp_id = exp_id
else:
# it is better to catch an invalid format string earlier than later
try:
# the sqlite_base will try to format
# (name, exp_id, run_counter)
format_string.format("name", 1, 1)
except Exception as e:
raise ValueError("Invalid format string. Can not format "
"(name, exp_id, run_counter)") from e
log.info("creating new experiment in {}".format(self.path_to_db))
name = name or f"experiment_{max_id+1}"
sample_name = sample_name or "some_sample"
self._exp_id = ne(self.conn, name, sample_name, format_string)
def __init__(self, path_to_db: str, conn=None) -> None:
# TODO: handle fail here by defaulting to
# a standard db
self.path_to_db = path_to_db
if conn is None:
self.conn = connect(self.path_to_db)
else:
self.conn = conn
self._debug = False
def load_last_experiment() -> Experiment:
"""
Load last experiment (from database file from config)
Returns:
last experiment
"""
last_exp_id = get_last_experiment(connect(get_DB_location()))
if last_exp_id is None:
raise ValueError('There are no experiments in the database file')
return Experiment(exp_id=last_exp_id)
def test_database_upgrade(empty_temp_db):
connection = connect(qc.config["core"]["db_location"],
qc.config["core"]["db_debug"])
userversion = get_user_version(connection)
if userversion != 0:
raise RuntimeError("trying to upgrade from version 0"
" but your database is version"
" {}".format(userversion))
sql = 'ALTER TABLE "runs" ADD COLUMN "quality"'
atomic_transaction(connection, sql)
set_user_version(connection, 1)
def test_tables_exist(empty_temp_db, version):
conn = connect(qc.config["core"]["db_location"],
qc.config["core"]["db_debug"],
version=version)
cursor = conn.execute("select sql from sqlite_master"
" where type = 'table'")
expected_tables = ['experiments', 'runs', 'layouts', 'dependencies']
rows = [row for row in cursor]
assert len(rows) == len(expected_tables)
for row, expected_table in zip(rows, expected_tables):
assert expected_table in row['sql']
conn.close()
def test_runs_table_columns(empty_temp_db):
"""
Ensure that the column names of a pristine runs table are what we expect
"""
colnames = mut.RUNS_TABLE_COLUMNS.copy()
conn = mut.connect(get_DB_location())
query = "PRAGMA table_info(runs)"
cursor = conn.cursor()
for row in cursor.execute(query):
colnames.remove(row['name'])
assert colnames == []
def experiments() -> List[Experiment]:
"""
List all the experiments in the container (database file from config)
Returns:
All the experiments in the container
"""
log.info("loading experiments from {}".format(get_DB_location()))
rows = get_experiments(connect(get_DB_location(), get_DB_debug()))
experiments = []
for row in rows:
experiments.append(load_experiment(row['exp_id']))
return experiments
def experiments() -> List[Experiment]:
"""
List all the experiments in the container
Returns:
All the experiments in the container
"""
log.info("loading experiments from {}".format(DB))
rows = get_experiments(connect(DB, debug_db))
experiments = []
for row in rows:
experiments.append(load_experiment(row['exp_id']))
return experiments
def generate_DB_file_with_empty_runs():
"""
Generate a DB file that holds empty runs and runs with no interdependencies
"""
v2fixturepath = os.path.join(fixturepath, 'version2')
os.makedirs(v2fixturepath, exist_ok=True)
path = os.path.join(v2fixturepath, 'empty_runs.db')
if os.path.exists(path):
os.remove(path)
from qcodes.dataset.sqlite_base import connect
from qcodes.dataset.measurements import Measurement
from qcodes.dataset.experiment_container import Experiment
from qcodes import Parameter
from qcodes.dataset.data_set import DataSet
conn = connect(path)
exp = Experiment(path)
exp._new(name='experiment_1', sample_name='no_sample_1')
# Now make some parameters to use in measurements
params = []
for n in range(5):
params.append(Parameter(f'p{n}', label=f'Parameter {n}',
unit=f'unit {n}', set_cmd=None, get_cmd=None))
# truly empty run, no layouts table, no nothing
dataset = DataSet(path, conn=conn)
dataset._new('empty_dataset', exp_id=exp.exp_id)
# empty run
meas = Measurement(exp)
with meas.run() as datasaver:
pass
# run with no interdeps
meas = Measurement(exp)
for param in params:
meas.register_parameter(param)
with meas.run() as datasaver:
pass
with meas.run() as datasaver:
for _ in range(10):
res = tuple((p, 0.0) for p in params)
datasaver.add_result(*res)
def empty_temp_db():
# create a temp database for testing
with tempfile.TemporaryDirectory() as tmpdirname:
qc.config["core"]["db_location"] = os.path.join(tmpdirname, 'temp.db')
qc.config["core"]["db_debug"] = False
# this is somewhat annoying but these module scope variables
# are initialized at import time so they need to be overwritten
qc.dataset.experiment_container.DB = qc.config["core"]["db_location"]
qc.dataset.data_set.DB = qc.config["core"]["db_location"]
qc.dataset.experiment_container.debug_db = qc.config["core"]["db_debug"]
_c = mut.connect(qc.config["core"]["db_location"],
qc.config["core"]["db_debug"])
mut.init_db(_c)
_c.close()
yield
def test_perform_actual_upgrade_0_to_1():
# we cannot use the empty_temp_db, since that has already called connect
# and is therefore latest version already
connection = connect(':memory:', debug=False, version=0)
assert get_user_version(connection) == 0
guid_table_query = "SELECT guid FROM runs"
with pytest.raises(RuntimeError):
atomic_transaction(connection, guid_table_query)
perform_db_upgrade_0_to_1(connection)
assert get_user_version(connection) == 1
c = atomic_transaction(connection, guid_table_query)
assert len(c.fetchall()) == 0
