def test_construct_currect_rundesciber_from_v0(some_paramspecs):
pgroup1 = some_paramspecs[1]
interdeps = InterDependencies(pgroup1['ps1'], pgroup1['ps2'],
pgroup1['ps3'], pgroup1['ps4'],
pgroup1['ps6'])
v0 = RunDescriberV0Dict(interdependencies=interdeps._to_dict(), version=0)
rds1 = RunDescriber._from_dict(v0)
rds2 = from_dict_to_current(v0)
expected_v2_dict = RunDescriberV2Dict(
interdependencies=interdeps._to_dict(),
interdependencies_=old_to_new(interdeps)._to_dict(),
version=2)
assert DeepDiff(rds1._to_dict(), expected_v2_dict, ignore_order=True) == {}
assert DeepDiff(rds2._to_dict(), expected_v2_dict, ignore_order=True) == {}
def test_convert_v0_to_newer(some_paramspecs):
pgroup1 = some_paramspecs[1]
interdeps = InterDependencies(pgroup1['ps1'], pgroup1['ps2'],
pgroup1['ps3'], pgroup1['ps4'],
pgroup1['ps6'])
v0 = RunDescriberV0Dict(interdependencies=interdeps._to_dict(), version=0)
v1 = v0_to_v1(v0)
v2 = v0_to_v2(v0)
_assert_dicts_are_related_as_expected(v0, v1, v2)
def upgrade_2_to_3(conn: ConnectionPlus) -> None:
"""
Perform the upgrade from version 2 to version 3
Insert a new column, run_description, to the runs table and fill it out
for exisitng runs with information retrieved from the layouts and
dependencies tables represented as the json output of a RunDescriber
object
"""
no_of_runs_query = "SELECT max(run_id) FROM runs"
no_of_runs = one(atomic_transaction(conn, no_of_runs_query), 'max(run_id)')
no_of_runs = no_of_runs or 0
# If one run fails, we want the whole upgrade to roll back, hence the
# entire upgrade is one atomic transaction
with atomic(conn) as conn:
sql = "ALTER TABLE runs ADD COLUMN run_description TEXT"
transaction(conn, sql)
result_tables = _2to3_get_result_tables(conn)
layout_ids_all = _2to3_get_layout_ids(conn)
indeps_all = _2to3_get_indeps(conn)
deps_all = _2to3_get_deps(conn)
layouts = _2to3_get_layouts(conn)
dependencies = _2to3_get_dependencies(conn)
pbar = tqdm(range(1, no_of_runs + 1))
pbar.set_description("Upgrading database")
for run_id in pbar:
if run_id in layout_ids_all:
result_table_name = result_tables[run_id]
layout_ids = list(layout_ids_all[run_id])
if run_id in indeps_all:
independents = tuple(indeps_all[run_id])
else:
independents = ()
if run_id in deps_all:
dependents = tuple(deps_all[run_id])
else:
dependents = ()
paramspecs = _2to3_get_paramspecs(conn, layout_ids, layouts,
dependencies, dependents,
independents,
result_table_name)
interdeps = InterDependencies(*paramspecs.values())
desc_dict = {'interdependencies': interdeps._to_dict()}
json_str = json.dumps(desc_dict)
else:
desc_dict = {
'interdependencies': InterDependencies()._to_dict()
}
json_str = json.dumps(desc_dict)
sql = f"""
UPDATE runs
SET run_description = ?
WHERE run_id == ?
"""
cur = conn.cursor()
cur.execute(sql, (json_str, run_id))
log.debug(f"Upgrade in transition, run number {run_id}: OK")
def upgrade_3_to_4(conn: ConnectionPlus) -> None:
"""
Perform the upgrade from version 3 to version 4. This really
repeats the version 3 upgrade as it originally had two bugs in
the inferred annotation. inferred_from was passed incorrectly
resulting in the parameter being marked inferred_from for each char
in the inferred_from variable and inferred_from was not handled
correctly for parameters that were neither dependencies nor dependent on
other parameters. Both have since been fixed so rerun the upgrade.
"""
no_of_runs_query = "SELECT max(run_id) FROM runs"
no_of_runs = one(atomic_transaction(conn, no_of_runs_query), 'max(run_id)')
no_of_runs = no_of_runs or 0
# If one run fails, we want the whole upgrade to roll back, hence the
# entire upgrade is one atomic transaction
with atomic(conn) as conn:
result_tables = _2to3_get_result_tables(conn)
layout_ids_all = _2to3_get_layout_ids(conn)
indeps_all = _2to3_get_indeps(conn)
deps_all = _2to3_get_deps(conn)
layouts = _2to3_get_layouts(conn)
dependencies = _2to3_get_dependencies(conn)
pbar = tqdm(range(1, no_of_runs + 1), file=sys.stdout)
pbar.set_description("Upgrading database; v3 -> v4")
for run_id in pbar:
if run_id in layout_ids_all:
result_table_name = result_tables[run_id]
layout_ids = list(layout_ids_all[run_id])
if run_id in indeps_all:
independents = tuple(indeps_all[run_id])
else:
independents = ()
if run_id in deps_all:
dependents = tuple(deps_all[run_id])
else:
dependents = ()
paramspecs = _2to3_get_paramspecs(conn, layout_ids, layouts,
dependencies, dependents,
independents,
result_table_name)
interdeps = InterDependencies(*paramspecs.values())
desc_dict = {'interdependencies': interdeps._to_dict()}
json_str = json.dumps(desc_dict)
else:
desc_dict = {
'interdependencies': InterDependencies()._to_dict()
}
json_str = json.dumps(desc_dict)
sql = f"""
UPDATE runs
SET run_description = ?
WHERE run_id == ?
"""
cur = conn.cursor()
cur.execute(sql, (json_str, run_id))
log.debug(f"Upgrade in transition, run number {run_id}: OK")