def test_upgrade_provenance(self):
ts = msprime.simulate(10)
for record_text in old_provenance_examples:
record = json.loads(record_text)
prov = msprime.Provenance(timestamp='2018-08-25T14:59:13',
record=json.dumps(record))
is_slim, version = pyslim.slim_provenance_version(prov)
self.assertTrue(is_slim)
if 'file_version' in record:
self.assertEqual(version, "0.1")
else:
self.assertEqual(version, record['slim']['file_version'])
tables = ts.dump_tables()
tables.provenances.add_row(json.dumps(record))
pyslim.upgrade_slim_provenance(tables) # modifies the tables
new_ts = tables.tree_sequence()
self.assertEqual(new_ts.num_provenances, 3)
is_slim, version = pyslim.slim_provenance_version(
new_ts.provenance(2))
self.assertTrue(is_slim)
self.assertEqual(version, "0.4")
new_record = json.loads(new_ts.provenance(2).record)
if 'model_type' in record:
self.assertEqual(record['model_type'],
new_record['parameters']['model_type'])
self.assertEqual(record['generation'],
new_record['slim']["generation"])
else:
self.assertEqual(record['parameters']['model_type'],
new_record['parameters']['model_type'])
self.assertEqual(record['slim']['generation'],
new_record['slim']["generation"])
def test_upgrade_provenance(self):
ts = msprime.sim_ancestry(10)
for record_text in old_provenance_examples:
record = json.loads(record_text)
prov = tskit.Provenance(id=0,
timestamp='2018-08-25T14:59:13',
record=json.dumps(record))
is_slim, version = pyslim.slim_provenance_version(prov)
assert is_slim
if 'file_version' in record:
assert version == "0.1"
else:
assert version == record['slim']['file_version']
tables = ts.dump_tables()
tables.provenances.add_row(json.dumps(record))
pyslim.upgrade_slim_provenance(tables) # modifies the tables
new_ts = tables.tree_sequence()
assert new_ts.num_provenances == 3
is_slim, version = pyslim.slim_provenance_version(
new_ts.provenance(2))
assert is_slim
assert version == "0.4"
new_record = json.loads(new_ts.provenance(2).record)
if 'model_type' in record:
assert record['model_type'] == new_record['parameters'][
'model_type']
assert record['generation'] == new_record['slim']["generation"]
else:
assert record['parameters']['model_type'] == new_record[
'parameters']['model_type']
assert record['slim']['generation'] == new_record['slim'][
"generation"]
def test_get_all_provenances(self):
for ts in self.get_slim_examples(WF=True):
rts = self.run_msprime_restart(ts)
provenances = rts.slim_provenances
self.assertEqual(len(provenances), 2)
self.assertEqual(ts.slim_provenance, provenances[0])
# mrts = pyslim.SlimTreeSequence(msprime.mutate(rts, rate=0.001))
j = 0
for p in rts.provenances():
is_slim, _ = pyslim.slim_provenance_version(p)
if is_slim:
sp = pyslim.parse_provenance(p)
self.assertEqual(provenances[j], sp)
j += 1
else:
with self.assertRaises(ValueError):
pyslim.parse_provenance(p)
def test_get_all_provenances(self, recipe, helper_functions, tmp_path):
ts = recipe["ts"]
rts = helper_functions.run_msprime_restart(ts, tmp_path, WF=True)
provenances = rts.slim_provenances
assert len(provenances) == 2
with pytest.warns(Warning):
last_prov = ts.slim_provenance
assert last_prov == provenances[0]
# mrts = pyslim.SlimTreeSequence(msprime.mutate(rts, rate=0.001))
j = 0
for p in rts.provenances():
is_slim, _ = pyslim.slim_provenance_version(p)
if is_slim:
sp = pyslim.parse_provenance(p)
assert provenances[j] == sp
j += 1
else:
with pytest.raises(ValueError):
pyslim.parse_provenance(p)