def migrate_dataset(
organization_id: int,
dataset_ids: Optional[List[int]] = None,
remove_existing: bool = False,
environment: str = "dev",
jumpbox: Optional[str] = "non-prod",
smoke_test: bool = True,
remap_ids: bool = False,
): # TODO does this need node IDs?
if dataset_ids is None and remove_existing:
raise Exception(
f"Cannot remove existing data from Neo4j while migrating the entire organization {organization_id}"
)
elif dataset_ids is None and remap_ids:
raise Exception(f"Can only remap IDs for a single dataset")
elif dataset_ids is None:
entire_organization = True
else:
entire_organization = False
settings = SSMParameters(environment)
with SSHTunnel(
remote_host=settings.postgres_host,
remote_port=settings.postgres_port,
local_port=7777,
jumpbox=jumpbox,
) as postgres_tunnel, SSHTunnel(
remote_host=settings.neo4j_host,
remote_port=settings.neo4j_port,
local_port=8888,
jumpbox=jumpbox,
) as neo4j_tunnel:
engine, factory = migrate_db.get_postgres(
f"postgresql://{settings.postgres_user}:{settings.postgres_password}@{postgres_tunnel.host}:{postgres_tunnel.port}/{settings.postgres_db}"
)
neo4j = Database(
uri=f"bolt://{neo4j_tunnel.host}:{neo4j_tunnel.port}",
user=settings.neo4j_user,
password=settings.neo4j_password,
max_connection_lifetime=300,
)
bf_database = PennsieveDatabase(engine, factory, organization_id)
# 1) Get the target datasets for the migration
if dataset_ids is None:
dataset_ids = bf_database.get_dataset_ids(organization_id)
for dataset_id in dataset_ids:
print(f"Migrating dataset {dataset_id}")
partitioned_db = PartitionedDatabase(
neo4j,
organization_id=organization_id,
dataset_id=dataset_id,
user_id=0)
# 3) Lock dataset in Pennsieve DB
bf_database.lock_dataset(organization_id, dataset_id)
print(f"Got dataset {dataset_id}")
try:
# 4) Export data to S3 from Neptune
export_from_neptune(
settings,
postgres_tunnel=postgres_tunnel,
organization_id=organization_id,
dataset_id=dataset_id,
jumpbox=jumpbox,
smoke_test=smoke_test,
)
# 5) Import into Neo4j from S3
import_to_neo4j.load(
dataset=f"{organization_id}/{dataset_id}",
bucket=settings.export_bucket,
db=partitioned_db,
cutover=True,
remove_existing=remove_existing,
smoke_test=smoke_test,
remap_ids=remap_ids,
)
finally:
# Whatever happens, unlock the dataset
bf_database.unlock_dataset(organization_id, dataset_id)
# 6) Sanity check that all datasets in the organization have been
# migrated, then mark the organization as migrated.
if entire_organization:
print("Validating migration....")
for dataset_id in bf_database.get_dataset_ids(organization_id):
partitioned_db = PartitionedDatabase(
neo4j,
organization_id=organization_id,
dataset_id=dataset_id,
user_id=0,
)
neo4j.toggle_service_for_organization(
organization_id=organization_id)
print("Done.")
def test_rewrite_ids_and_import(neo4j):
"""
Test that UUIDs are remapped to the exact correct place with a manually
defined remapping.
"""
dataset_id = 60000
dataset_node_id = "N:dataset:b1154216-d1d7-4484-ad18-81b58fb65484"
organization_id = 5
organization_node_id = "N:organization:c905919f-56f5-43ae-9c2a-8d5d542c133b"
user_id = 114
user_node_id = "N:user:028058b9-dd8d-4f24-a187-ea56830b379f"
db = PartitionedDatabase(
db=neo4j,
organization_id=OrganizationId(organization_id),
dataset_id=DatasetId(dataset_id),
user_id=user_node_id,
organization_node_id=organization_node_id,
dataset_node_id=dataset_node_id,
)
REMAPPING = {
"0b4b3615-9eaf-425d-9727-bcac29686fd5":
"aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa",
"7b17c60d-ca2a-4cf5-a4ff-a52bbc32ff17":
"bbbbbbbb-bbbb-bbbb-bbbb-bbbbbbbbbbbb",
"e507b3ef-ade4-4672-83b4-f3f0774fb282":
"cccccccc-cccc-cccc-cccc-cccccccccccc",
"bf858cb5-ae51-4fcf-ad74-b1887946f70f":
"dddddddd-dddd-dddd-dddd-dddddddddddd",
"a99b09f5-caa6-4282-aa0e-cf56bde89254":
"eeeeeeee-eeee-eeee-eeee-eeeeeeeeeeee",
"42fa4eb9-51cc-4c59-b550-ac24d6d5024a":
"ffffffff-ffff-ffff-ffff-ffffffffffff",
"ecb71447-b684-c589-abda-b673c38edefc":
"00000000-0000-0000-0000-000000000000",
"e2b71447-e29d-11c3-24c6-f2ebffd1486a":
"11111111-1111-1111-1111-111111111111",
"c8b71de8-cd9c-cc3f-67fe-4e30968d4e50":
"22222222-2222-2222-2222-222222222222",
"2e754729-684a-4c45-960f-348d68737d4d":
"33333333-3333-3333-3333-333333333333",
"175ff55b-b44d-4381-bd59-d4dbc0b9c5f0":
"44444444-4444-4444-4444-444444444444",
"ccf200d3-e77f-4d9e-bed3-f1f28860152f":
"55555555-5555-5555-5555-555555555555",
"443e141b-f59c-419f-82c1-eed97925b04d":
"66666666-6666-6666-6666-666666666666",
"d0b71de9-21f9-3557-edda-ad278dd81dc0":
"77777777-7777-7777-7777-777777777777",
"aeb7476e-55f6-7924-5e43-a83cfa7e4cef":
"88888888-8888-8888-8888-888888888888",
"fa3daedd-1761-4730-be7d-bb5de8e1261c":
"99999999-9999-9999-9999-999999999999",
"00b71de7-b42f-1fe9-a83f-824452fe966e":
"aaaaaaaa-aaaa-aaaa-aaaa-bbbbbbbbbbbb",
"460591a0-8079-4979-a860-c3a4b18a32ad":
"aaaaaaaa-aaaa-aaaa-aaaa-cccccccccccc",
}
def generate_new_id(old_id):
new_id = REMAPPING.get(old_id, None)
if new_id is None:
return old_id
return new_id
load(
dataset=f"{organization_id}/{dataset_id}",
bucket="dev-neptune-export-use1",
db=db,
use_cache=False,
smoke_test=False,
remap_ids=True,
generate_new_id=generate_new_id,
)
# Models
patient = db.get_model("patient")
assert patient == Model(
name="patient",
display_name="Patient",
description="",
count=2,
id="aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa",
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-01T20:01:27.027Z"),
updated_at=iso8601.parse("2019-11-01T20:01:27.027Z"),
template_id=None,
)
assert sorted(db.get_properties(patient), key=lambda p: p.index) == [
ModelProperty(
id="bbbbbbbb-bbbb-bbbb-bbbb-bbbbbbbbbbbb",
name="name",
display_name="Name",
description="",
index=0,
locked=False,
model_title=True,
required=False,
data_type=dt.String(),
default=True,
default_value=None,
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-01T20:01:37.633Z"),
updated_at=iso8601.parse("2019-11-11T15:11:17.383Z"),
),
ModelProperty(
id="cccccccc-cccc-cccc-cccc-cccccccccccc",
name="dob",
display_name="DOB",
description="",
index=1,
locked=False,
model_title=False,
required=False,
data_type=dt.Date(),
default=False,
default_value=None,
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-11T15:11:17.383Z"),
updated_at=iso8601.parse("2019-11-11T15:11:17.383Z"),
),
]
bicycle = db.get_model("bicycle")
assert bicycle.name == "bicycle"
assert bicycle.display_name == "Bicycle"
assert bicycle.id == "dddddddd-dddd-dddd-dddd-dddddddddddd"
assert bicycle.count == 1
assert bicycle.template_id == None
properties = sorted(db.get_properties(bicycle), key=lambda p: p.index)
assert len(properties) == 2
brand = properties[0]
assert brand.name == "brand"
assert brand.id == "eeeeeeee-eeee-eeee-eeee-eeeeeeeeeeee"
color = properties[1]
assert color.name == "color"
assert color.data_type == dt.Array(
items=dt.String(),
enum=["purple", "blue", "orange", "green", "yellow", "red"])
assert color.id == "ffffffff-ffff-ffff-ffff-ffffffffffff"
# Records
patients = db.get_all_records("patient")
alice = Record(
id=UUID("00000000-0000-0000-0000-000000000000"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-01T20:01:58.537Z"),
updated_at=iso8601.parse("2019-11-11T15:37:02.165Z"),
values={
"name": "Alice",
"dob": neotime.DateTime(year=2004, month=5, day=5,
tzinfo=pytz.UTC),
},
)
bob = Record(
id=UUID("11111111-1111-1111-1111-111111111111"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-01T20:02:21.113Z"),
updated_at=iso8601.parse("2019-11-01T20:02:21.113Z"),
values={
"name":
"Bob",
# Embedded linked property
"mother":
RecordStub(id=UUID("00000000-0000-0000-0000-000000000000"),
title="Alice"),
},
)
assert sorted(patients.results,
key=lambda x: x.values["name"]) == [alice, bob]
assert db.get_all_records("bicycle").results == [
Record(
id=UUID("22222222-2222-2222-2222-222222222222"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-05T13:47:02.841Z"),
updated_at=iso8601.parse("2019-11-11T15:12:28.042Z"),
values={
"brand": "Bianchi",
"color": ["red", "blue"]
},
)
]
# Model relationships
with db.transaction() as tx:
assert list(
db.get_outgoing_model_relationships_tx(tx,
patient,
one_to_many=True)
) == [
ModelRelationship(
id="33333333-3333-3333-3333-333333333333",
type="RIDES",
name="rides_c83d5af0-ffd2-11e9-b8f0-1b1d6297ff8c",
display_name="Rides",
description="",
from_="aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa",
to="dddddddd-dddd-dddd-dddd-dddddddddddd",
one_to_many=True,
index=None,
created_at=iso8601.parse("2019-11-05T13:47:17.981Z"),
updated_at=iso8601.parse("2019-11-05T13:47:17.981Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
assert list(
db.get_outgoing_model_relationships_tx(tx,
bicycle,
one_to_many=True)
) == [
ModelRelationship(
id="44444444-4444-4444-4444-444444444444",
type="BELONGS_TO",
name="belongs_to",
display_name="Belongs To",
description="",
from_="dddddddd-dddd-dddd-dddd-dddddddddddd",
to="aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa",
one_to_many=True,
index=None,
created_at=iso8601.parse("2019-11-21T16:47:36.918Z"),
updated_at=iso8601.parse("2019-11-21T16:47:36.918Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
# Model relationship stubs contain no "to" and "from" models, eg. belongs_to
assert list(db.get_model_relationship_stubs_tx(tx)) == [
ModelRelationshipStub(
id="55555555-5555-5555-5555-555555555555",
name="belongs_to",
display_name="Belongs To",
description="",
type="BELONGS_TO",
created_at=iso8601.parse("2019-11-05T13:44:38.598Z"),
updated_at=iso8601.parse("2019-11-05T13:44:38.598Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
# Duplicate @RELATED_TO relationships are created
assert len(db.get_model_relationships_tx(tx, one_to_many=True)) == 2
# Record relationships
assert list(db.get_outgoing_record_relationships_tx(tx, alice)) == [
RecordRelationship(
id="77777777-7777-7777-7777-777777777777",
from_="00000000-0000-0000-0000-000000000000",
to="22222222-2222-2222-2222-222222222222",
type="RIDES",
name="rides_c83d5af0-ffd2-11e9-b8f0-1b1d6297ff8c",
model_relationship_id="33333333-3333-3333-3333-333333333333",
display_name="Rides",
one_to_many=True,
created_at=iso8601.parse("2019-11-05T13:47:46.032Z"),
updated_at=iso8601.parse("2019-11-05T13:47:46.032Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
assert list(
db.get_outgoing_record_relationships_tx(
tx, "22222222-2222-2222-2222-222222222222", one_to_many=True)
) == [
RecordRelationship(
id="88888888-8888-8888-8888-888888888888",
from_="22222222-2222-2222-2222-222222222222",
to="11111111-1111-1111-1111-111111111111",
type="BELONGS_TO",
name="belongs_to",
model_relationship_id="44444444-4444-4444-4444-444444444444",
display_name="Belongs To",
one_to_many=True,
created_at=iso8601.parse("2019-11-21T16:47:36.938Z"),
updated_at=iso8601.parse("2019-11-21T16:47:36.938Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
# Linked properties
assert list(
db.get_outgoing_model_relationships_tx(tx,
patient,
one_to_many=False)
) == [
ModelRelationship(
id="66666666-6666-6666-6666-666666666666",
type="MOTHER",
name="mother",
display_name="Mother",
description="",
from_="aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa",
to="aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa",
one_to_many=False,
index=1,
created_at=iso8601.parse("2019-11-05T13:43:38.341Z"),
updated_at=iso8601.parse("2019-11-05T13:43:38.341Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
# Duplicate @RELATED_TO relationships are created for linked properties
assert len(db.get_model_relationships_tx(tx, one_to_many=False)) == 1
assert list(
db.get_outgoing_record_relationships_tx(tx, bob, one_to_many=False)
) == [
RecordRelationship(
id="99999999-9999-9999-9999-999999999999",
from_="11111111-1111-1111-1111-111111111111",
to="00000000-0000-0000-0000-000000000000",
type="MOTHER",
model_relationship_id="66666666-6666-6666-6666-666666666666",
name="mother",
display_name="Mother",
one_to_many=False,
created_at=iso8601.parse("2019-11-05T13:43:54.116Z"),
updated_at=iso8601.parse("2019-11-05T13:43:54.116Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
assert db.get_package_proxies_for_record(alice, limit=10, offset=0) == (
1,
[
PackageProxy(
id="aaaaaaaa-aaaa-aaaa-aaaa-bbbbbbbbbbbb",
proxy_instance_id="aaaaaaaa-aaaa-aaaa-aaaa-cccccccccccc",
package_id=184418,
package_node_id=
"N:package:b493794a-1c86-4c18-9fb9-dfdf236b1fe3",
relationship_type="belongs_to",
created_at=iso8601.parse("2019-11-05T13:44:38.748Z"),
updated_at=iso8601.parse("2019-11-05T13:44:38.748Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
],
)
# Packages link directly to dataset node
assert db.count_packages() == 1
def test_fix_multiple_mismatched_model_relationships(neo4j):
"""
Case when a record relationship has a schemaRelationshipId that does not
match the (from)-[relationship]->(to) triple of the relationship, but a
compatible model relationship does exist in the dataset.
In this case, an extra model relationship (id =
`4ea7d9e6-b2ae-487c-981c-8202e37343f9`) connects
(bike)-[rides_c83d5af0-ffd2-11e9-b8f0-1b1d6297ff8c]->(bike) and the record
relationship (person)-[rides]->(bike) incorrectly uses this
schemaRelationshipId.
AND
Another record relationship, with the same relationship type, also claiming
the same schemaRelationshipId, but actually connecting different models.
This corrupted data is from old versions of the graph-ingest tool.
"""
dataset_id = 50000
dataset_node_id = "N:dataset:b1154216-d1d7-4484-ad18-81b58fb65484"
organization_id = 5
organization_node_id = "N:organization:c905919f-56f5-43ae-9c2a-8d5d542c133b"
user_id = 114
user_node_id = "N:user:028058b9-dd8d-4f24-a187-ea56830b379f"
db = PartitionedDatabase(
db=neo4j,
organization_id=OrganizationId(organization_id),
dataset_id=DatasetId(dataset_id),
user_id=user_node_id,
organization_node_id=organization_node_id,
dataset_node_id=dataset_node_id,
)
load(
dataset=f"{organization_id}/{dataset_id}",
bucket="dev-neptune-export-use1",
db=db,
use_cache=False,
smoke_test=False,
)
with db.transaction() as tx:
assert list(
db.get_outgoing_record_relationships_tx(
tx, "ecb71447-b684-c589-abda-b673c38edefc")
) == [
RecordRelationship(
id="d0b71de9-21f9-3557-edda-ad278dd81dc0",
from_="ecb71447-b684-c589-abda-b673c38edefc",
to="c8b71de8-cd9c-cc3f-67fe-4e30968d4e50",
type="RIDES",
name="rides_c83d5af0-ffd2-11e9-b8f0-1b1d6297ff8c",
model_relationship_id="2e754729-684a-4c45-960f-348d68737d4d",
display_name="Rides",
one_to_many=True,
created_at=iso8601.parse("2019-11-05T13:47:46.032Z"),
updated_at=iso8601.parse("2019-11-05T13:47:46.032Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
assert sorted(
db.get_outgoing_record_relationships_tx(
tx, "c8b71de8-cd9c-cc3f-67fe-4e30968d4e50", one_to_many=True),
key=lambda r: r.type,
) == [
RecordRelationship(
id="aeb7476e-55f6-7924-5e43-a83cfa7e4cef",
from_="c8b71de8-cd9c-cc3f-67fe-4e30968d4e50",
to="e2b71447-e29d-11c3-24c6-f2ebffd1486a",
type="BELONGS_TO",
name="belongs_to",
model_relationship_id="175ff55b-b44d-4381-bd59-d4dbc0b9c5f0",
display_name="Belongs To",
one_to_many=True,
created_at=iso8601.parse("2019-11-21T16:47:36.938Z"),
updated_at=iso8601.parse("2019-11-21T16:47:36.938Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
),
RecordRelationship(
id="83227fcd-ec4d-47e6-a3a9-4c9fbba4a2f3",
from_="c8b71de8-cd9c-cc3f-67fe-4e30968d4e50",
to="e2b71447-e29d-11c3-24c6-f2ebffd1486a",
type="RIDES",
name="rides_c83d5af0-ffd2-11e9-b8f0-1b1d6297ff8c",
model_relationship_id="92b6a32f-0597-4a7a-944b-27b39998283e",
display_name="Rides",
one_to_many=True,
created_at=iso8601.parse("2019-11-05T13:47:46.032Z"),
updated_at=iso8601.parse("2019-11-05T13:47:46.032Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
),
]
def test_fix_nonexistent_model_relationships(neo4j):
"""
Case when a record relationship has a schemaRelationshipId that does not
exist, but a model relationhip (d0b71de9-21f9-3557-edda-ad278dd81dc0) is
defined that matches the (from)-[relationship]->(to) triple of the
relationship.
This corrupted data is from old versions of the graph-ingest tool.
"""
dataset_id = 30000
dataset_node_id = "N:dataset:b1154216-d1d7-4484-ad18-81b58fb65484"
organization_id = 5
organization_node_id = "N:organization:c905919f-56f5-43ae-9c2a-8d5d542c133b"
user_id = 114
user_node_id = "N:user:028058b9-dd8d-4f24-a187-ea56830b379f"
db = PartitionedDatabase(
db=neo4j,
organization_id=OrganizationId(organization_id),
dataset_id=DatasetId(dataset_id),
user_id=user_node_id,
organization_node_id=organization_node_id,
dataset_node_id=dataset_node_id,
)
load(
dataset=f"{organization_id}/{dataset_id}",
bucket="dev-neptune-export-use1",
db=db,
use_cache=False,
smoke_test=False,
)
with db.transaction() as tx:
assert list(
db.get_outgoing_record_relationships_tx(
tx, "ecb71447-b684-c589-abda-b673c38edefc")
) == [
RecordRelationship(
id="d0b71de9-21f9-3557-edda-ad278dd81dc0",
from_="ecb71447-b684-c589-abda-b673c38edefc",
to="c8b71de8-cd9c-cc3f-67fe-4e30968d4e50",
type="RIDES",
name="rides_c83d5af0-ffd2-11e9-b8f0-1b1d6297ff8c",
model_relationship_id="2e754729-684a-4c45-960f-348d68737d4d",
display_name="Rides",
one_to_many=True,
created_at=iso8601.parse("2019-11-05T13:47:46.032Z"),
updated_at=iso8601.parse("2019-11-05T13:47:46.032Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
assert list(
db.get_outgoing_record_relationships_tx(
tx, "c8b71de8-cd9c-cc3f-67fe-4e30968d4e50", one_to_many=True)
) == [
RecordRelationship(
id="aeb7476e-55f6-7924-5e43-a83cfa7e4cef",
from_="c8b71de8-cd9c-cc3f-67fe-4e30968d4e50",
to="e2b71447-e29d-11c3-24c6-f2ebffd1486a",
type="BELONGS_TO",
name="belongs_to",
model_relationship_id="175ff55b-b44d-4381-bd59-d4dbc0b9c5f0",
display_name="Belongs To",
one_to_many=True,
created_at=iso8601.parse("2019-11-21T16:47:36.938Z"),
updated_at=iso8601.parse("2019-11-21T16:47:36.938Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
def test_loader(neo4j):
dataset_id = 29233
dataset_node_id = "N:dataset:b1154216-d1d7-4484-ad18-81b58fb65484"
organization_id = 5
organization_node_id = "N:organization:c905919f-56f5-43ae-9c2a-8d5d542c133b"
user_id = 114
user_node_id = "N:user:028058b9-dd8d-4f24-a187-ea56830b379f"
db = PartitionedDatabase(
db=neo4j,
organization_id=OrganizationId(organization_id),
dataset_id=DatasetId(dataset_id),
user_id=user_node_id,
organization_node_id=organization_node_id,
dataset_node_id=dataset_node_id,
)
load(
dataset=f"{organization_id}/{dataset_id}",
bucket="dev-neptune-export-use1",
db=db,
use_cache=False,
smoke_test=False,
)
# Models
patient = db.get_model("patient")
assert patient == Model(
name="patient",
display_name="Patient",
description="",
count=2,
id="0b4b3615-9eaf-425d-9727-bcac29686fd5",
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-01T20:01:27.027Z"),
updated_at=iso8601.parse("2019-11-01T20:01:27.027Z"),
template_id=None,
)
assert sorted(db.get_properties(patient), key=lambda p: p.index) == [
ModelProperty(
id="7b17c60d-ca2a-4cf5-a4ff-a52bbc32ff17",
name="name",
display_name="Name",
description="",
index=0,
locked=False,
model_title=True,
required=False,
data_type=dt.String(),
default=True,
default_value=None,
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-01T20:01:37.633Z"),
updated_at=iso8601.parse("2019-11-11T15:11:17.383Z"),
),
ModelProperty(
id="e507b3ef-ade4-4672-83b4-f3f0774fb282",
name="dob",
display_name="DOB",
description="",
index=1,
locked=False,
model_title=False,
required=False,
data_type=dt.Date(),
default=False,
default_value=None,
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-11T15:11:17.383Z"),
updated_at=iso8601.parse("2019-11-11T15:11:17.383Z"),
),
]
bicycle = db.get_model("bicycle")
assert bicycle.name == "bicycle"
assert bicycle.display_name == "Bicycle"
assert bicycle.id == "bf858cb5-ae51-4fcf-ad74-b1887946f70f"
assert bicycle.count == 1
assert bicycle.template_id == None
properties = sorted(db.get_properties(bicycle), key=lambda p: p.index)
assert len(properties) == 2
brand = properties[0]
assert brand.name == "brand"
color = properties[1]
assert color.name == "color"
assert color.data_type == dt.Array(
items=dt.String(),
enum=["purple", "blue", "orange", "green", "yellow", "red"])
# Records
patients = db.get_all_records("patient")
alice = Record(
id=UUID("ecb71447-b684-c589-abda-b673c38edefc"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-01T20:01:58.537Z"),
updated_at=iso8601.parse("2019-11-11T15:37:02.165Z"),
values={
"name": "Alice",
"dob": neotime.DateTime(year=2004, month=5, day=5,
tzinfo=pytz.UTC),
},
)
bob = Record(
id=UUID("e2b71447-e29d-11c3-24c6-f2ebffd1486a"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-01T20:02:21.113Z"),
updated_at=iso8601.parse("2019-11-01T20:02:21.113Z"),
values={
"name":
"Bob",
# Embedded linked property
"mother":
RecordStub(id=UUID("ecb71447-b684-c589-abda-b673c38edefc"),
title="Alice"),
},
)
assert sorted(patients.results,
key=lambda x: x.values["name"]) == [alice, bob]
assert db.get_all_records("bicycle").results == [
Record(
id=UUID("c8b71de8-cd9c-cc3f-67fe-4e30968d4e50"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
created_at=iso8601.parse("2019-11-05T13:47:02.841Z"),
updated_at=iso8601.parse("2019-11-11T15:12:28.042Z"),
values={
"brand": "Bianchi",
"color": ["red", "blue"]
},
)
]
# Model relationships
with db.transaction() as tx:
assert list(
db.get_outgoing_model_relationships_tx(tx,
patient,
one_to_many=True)
) == [
ModelRelationship(
id="2e754729-684a-4c45-960f-348d68737d4d",
type="RIDES",
name="rides_c83d5af0-ffd2-11e9-b8f0-1b1d6297ff8c",
display_name="Rides",
description="",
from_="0b4b3615-9eaf-425d-9727-bcac29686fd5",
to="bf858cb5-ae51-4fcf-ad74-b1887946f70f",
one_to_many=True,
index=None,
created_at=iso8601.parse("2019-11-05T13:47:17.981Z"),
updated_at=iso8601.parse("2019-11-05T13:47:17.981Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
# This relationship can be created in the Python client with the following:
#
# >>> patient = ds.models()["patient"]
# >>> bike = ds.models()["bicycle"]
# >>> bob = patient.get_all()[1]
# >>> bianchi = bike.get_all()[0]
# >>> bianchi.relate_to(bob, relationship_type="belongs_to")
#
# This reuses the `belongs_to` name even though that is disallowed through
# the frontend. This means that the `belongs_to` CSV contains relationships
# between proxy packages and records, *and* between records and records.
assert list(
db.get_outgoing_model_relationships_tx(tx,
bicycle,
one_to_many=True)
) == [
ModelRelationship(
id="175ff55b-b44d-4381-bd59-d4dbc0b9c5f0",
type="BELONGS_TO",
name="belongs_to",
display_name="Belongs To",
description="",
from_="bf858cb5-ae51-4fcf-ad74-b1887946f70f",
to="0b4b3615-9eaf-425d-9727-bcac29686fd5",
one_to_many=True,
index=None,
created_at=iso8601.parse("2019-11-21T16:47:36.918Z"),
updated_at=iso8601.parse("2019-11-21T16:47:36.918Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
# Model relationship stubs contain no "to" and "from" models, eg. belongs_to
assert list(db.get_model_relationship_stubs_tx(tx)) == [
ModelRelationshipStub(
id="ccf200d3-e77f-4d9e-bed3-f1f28860152f",
name="belongs_to",
display_name="Belongs To",
description="",
type="BELONGS_TO",
created_at=iso8601.parse("2019-11-05T13:44:38.598Z"),
updated_at=iso8601.parse("2019-11-05T13:44:38.598Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
# Duplicate @RELATED_TO relationships are created
assert len(db.get_model_relationships_tx(tx, one_to_many=True)) == 2
# Record relationships
assert list(db.get_outgoing_record_relationships_tx(tx, alice)) == [
RecordRelationship(
id="d0b71de9-21f9-3557-edda-ad278dd81dc0",
from_="ecb71447-b684-c589-abda-b673c38edefc",
to="c8b71de8-cd9c-cc3f-67fe-4e30968d4e50",
type="RIDES",
name="rides_c83d5af0-ffd2-11e9-b8f0-1b1d6297ff8c",
model_relationship_id="2e754729-684a-4c45-960f-348d68737d4d",
display_name="Rides",
one_to_many=True,
created_at=iso8601.parse("2019-11-05T13:47:46.032Z"),
updated_at=iso8601.parse("2019-11-05T13:47:46.032Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
assert list(
db.get_outgoing_record_relationships_tx(
tx, "c8b71de8-cd9c-cc3f-67fe-4e30968d4e50", one_to_many=True)
) == [
RecordRelationship(
id="aeb7476e-55f6-7924-5e43-a83cfa7e4cef",
from_="c8b71de8-cd9c-cc3f-67fe-4e30968d4e50",
to="e2b71447-e29d-11c3-24c6-f2ebffd1486a",
type="BELONGS_TO",
name="belongs_to",
model_relationship_id="175ff55b-b44d-4381-bd59-d4dbc0b9c5f0",
display_name="Belongs To",
one_to_many=True,
created_at=iso8601.parse("2019-11-21T16:47:36.938Z"),
updated_at=iso8601.parse("2019-11-21T16:47:36.938Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
# Linked properties
assert list(
db.get_outgoing_model_relationships_tx(tx,
patient,
one_to_many=False)
) == [
ModelRelationship(
id="443e141b-f59c-419f-82c1-eed97925b04d",
type="MOTHER",
name="mother",
display_name="Mother",
description="",
from_="0b4b3615-9eaf-425d-9727-bcac29686fd5",
to="0b4b3615-9eaf-425d-9727-bcac29686fd5",
one_to_many=False,
index=1,
created_at=iso8601.parse("2019-11-05T13:43:38.341Z"),
updated_at=iso8601.parse("2019-11-05T13:43:38.341Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
# Duplicate @RELATED_TO relationships are created for linked properties
assert len(db.get_model_relationships_tx(tx, one_to_many=False)) == 1
assert list(
db.get_outgoing_record_relationships_tx(tx, bob, one_to_many=False)
) == [
RecordRelationship(
id="fa3daedd-1761-4730-be7d-bb5de8e1261c",
from_="e2b71447-e29d-11c3-24c6-f2ebffd1486a",
to="ecb71447-b684-c589-abda-b673c38edefc",
type="MOTHER",
model_relationship_id="443e141b-f59c-419f-82c1-eed97925b04d",
name="mother",
display_name="Mother",
one_to_many=False,
created_at=iso8601.parse("2019-11-05T13:43:54.116Z"),
updated_at=iso8601.parse("2019-11-05T13:43:54.116Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
]
assert db.get_package_proxies_for_record(alice, limit=10, offset=0) == (
1,
[
PackageProxy(
id="00b71de7-b42f-1fe9-a83f-824452fe966e",
proxy_instance_id="460591a0-8079-4979-a860-c3a4b18a32ad",
package_id=184418,
package_node_id=
"N:package:b493794a-1c86-4c18-9fb9-dfdf236b1fe3",
relationship_type="belongs_to",
created_at=iso8601.parse("2019-11-05T13:44:38.748Z"),
updated_at=iso8601.parse("2019-11-05T13:44:38.748Z"),
created_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
updated_by="N:user:06080380-fb56-46eb-8c70-f24112aff878",
)
],
)
# Packages link directly to dataset node
assert db.count_packages() == 1
def test_rewrite_ids_randomly_and_import(neo4j):
"""
Test that UUIDs are remapped using the default random remapper.
"""
dataset_id = 70000
dataset_node_id = "N:dataset:b1154216-d1d7-4484-ad18-81b58fb65484"
organization_id = 5
organization_node_id = "N:organization:c905919f-56f5-43ae-9c2a-8d5d542c133b"
user_id = 114
user_node_id = "N:user:028058b9-dd8d-4f24-a187-ea56830b379f"
db = PartitionedDatabase(
db=neo4j,
organization_id=OrganizationId(organization_id),
dataset_id=DatasetId(dataset_id),
user_id=user_node_id,
organization_node_id=organization_node_id,
dataset_node_id=dataset_node_id,
)
load(
dataset=f"{organization_id}/{dataset_id}",
bucket="dev-neptune-export-use1",
db=db,
use_cache=False,
smoke_test=False,
remap_ids=True,
)
# Models
patient = db.get_model("patient")
assert patient is not None
assert len(db.get_properties(patient)) == 2
assert patient.id != UUID("0b4b3615-9eaf-425d-9727-bcac29686fd5")
bicycle = db.get_model("bicycle")
assert bicycle is not None
assert len(db.get_properties(bicycle)) == 2
assert bicycle.id != UUID("bf858cb5-ae51-4fcf-ad74-b1887946f70f")
# Records
patients = db.get_all_records("patient")
alice = [r for r in patients if r.values["name"] == "Alice"][0]
assert alice.id != "ecb71447-b684-c589-abda-b673c38edefc"
bob = [r for r in patients if r.values["name"] == "Bob"][0]
assert bob.id != UUID("e2b71447-e29d-11c3-24c6-f2ebffd1486a")
assert len(db.get_all_records("bicycle").results) == 1
bianchi = db.get_all_records("bicycle").results[0]
assert bianchi.id != UUID("c8b71de8-cd9c-cc3f-67fe-4e30968d4e50")
# Model relationships
with db.transaction() as tx:
assert (len(
list(
db.get_outgoing_model_relationships_tx(
tx, patient, one_to_many=True))) == 1)
assert (len(
list(
db.get_outgoing_model_relationships_tx(
tx, bicycle, one_to_many=True))) == 1)
# Model relationship stubs contain no "to" and "from" models, eg. belongs_to
assert len(list(db.get_model_relationship_stubs_tx(tx))) == 1
# Duplicate @RELATED_TO relationships are created
assert len(list(db.get_model_relationships_tx(tx,
one_to_many=True))) == 2
# Record relationships
assert len(list(db.get_outgoing_record_relationships_tx(tx,
alice))) == 1
assert (len(
list(
db.get_outgoing_record_relationships_tx(
tx, bianchi, one_to_many=True))) == 1)
# Linked properties
assert (len(
list(
db.get_outgoing_model_relationships_tx(
tx, patient, one_to_many=False))) == 1)
# Duplicate @RELATED_TO relationships are created for linked properties
assert len(list(db.get_model_relationships_tx(tx,
one_to_many=False))) == 1
assert (len(
list(
db.get_outgoing_record_relationships_tx(
tx, bob, one_to_many=False))) == 1)
assert len(
db.get_package_proxies_for_record(alice, limit=10, offset=0)[1]) == 1
# Packages link directly to dataset node
assert db.count_packages() == 1