def test_create_and_get_remote_table(context_id):
nrclient = NodeRegistryClient()
db = nrclient.get_db_by_node_id(local_node_id)
local_node_monetdb_sock_address = f"{str(db.ip)}:{db.port}"
table_schema = TableSchema([
ColumnInfo("col1", "int"),
ColumnInfo("col2", "real"),
ColumnInfo("col3", "text"),
])
table_name = local_node_create_table.delay(
context_id=context_id,
command_id=str(uuid.uuid1()).replace("-", ""),
schema_json=table_schema.to_json(),
).get()
table_info = TableInfo(table_name, table_schema)
global_node_create_remote_table.delay(
table_info_json=table_info.to_json(),
monetdb_socket_address=local_node_monetdb_sock_address,
).get()
remote_tables = global_node_get_remote_tables.delay(
context_id=context_id).get()
assert table_name in remote_tables
def create_two_column_table(context_id, table_id: int):
table_schema = TableSchema(
[ColumnInfo("col1", "int"),
ColumnInfo("col2", "real")])
table_name = local_node_create_table.delay(
context_id=f"{context_id}_table_{table_id}",
command_id=str(uuid.uuid1()).replace("-", ""),
schema_json=table_schema.to_json(),
).get()
return table_name
def test_sql_injection_create_table_tableschema_name():
with pytest.raises(ValueError):
schema = TableSchema([
ColumnInfo("Robert'); DROP TABLE data; --", "INT"),
ColumnInfo("col2", "real"),
ColumnInfo("col3", "text"),
])
json_schema = schema.to_json()
local_node_create_table.delay(
context_id=context_id,
command_id=str(uuid.uuid1()).replace("-", ""),
schema_json=json_schema,
).get()
def get_table_schema(table_name: str) -> TableSchema:
"""
Retrieves a schema for a specific table name from the monetdb.
Parameters
----------
table_name : str
The name of the table
Returns
------
TableSchema
A schema which is TableSchema object.
"""
schema = MonetDB().execute_and_fetchall(f"""
SELECT columns.name, columns.type
FROM columns
RIGHT JOIN tables
ON tables.id = columns.table_id
WHERE
tables.name = '{table_name}'
AND
tables.system=false
""")
if not schema:
raise TablesNotFound([table_name])
return TableSchema([
ColumnInfo(name, _convert_monet2mip_column_type(table_type))
for name, table_type in schema
])
def test_create_and_find_tables(context_id):
table_schema = TableSchema([
ColumnInfo("col1", "int"),
ColumnInfo("col2", "real"),
ColumnInfo("col3", "text"),
])
table_1_name = local_node_create_table.delay(
context_id=context_id,
command_id=str(uuid.uuid4()).replace("-", ""),
schema_json=table_schema.to_json(),
).get()
tables = local_node_get_tables.delay(context_id=context_id).get()
assert table_1_name in tables
values = [[1, 0.1, "test1"], [2, 0.2, None], [3, 0.3, "test3"]]
local_node_insert_data_to_table.delay(table_name=table_1_name,
values=values).get()
table_data_json = local_node_get_table_data.delay(
table_name=table_1_name).get()
table_data = TableData.from_json(table_data_json)
assert table_data.data == values
assert table_data.schema == table_schema
table_2_name = local_node_create_table.delay(
context_id=context_id,
command_id=str(uuid.uuid4()).replace("-", ""),
schema_json=table_schema.to_json(),
).get()
tables = local_node_get_tables.delay(context_id=context_id).get()
assert table_2_name in tables
values = [[1, 0.1, "test1"], [2, None, "None"], [3, 0.3, None]]
local_node_insert_data_to_table.delay(table_name=table_2_name,
values=values).get()
table_data_json = local_node_get_table_data.delay(
table_name=table_2_name).get()
table_data = TableData.from_json(table_data_json)
assert table_data.data == values
assert table_data.schema == table_schema
table_schema_json = local_node_get_table_schema.delay(
table_name=table_2_name).get()
table_schema_1 = TableSchema.from_json(table_schema_json)
assert table_schema_1 == table_schema
def create_table(self, command_id: str,
schema: TableSchema) -> TableName:
schema_json = schema.to_json()
task_signature = self.__celery_obj.signature(
self.task_signatures_str["create_table"])
result = task_signature.delay(context_id=self.__context_id,
schema_json=schema_json).get()
return TableName(result)
def create_three_column_table_with_data(context_id, table_id: int):
table_schema = TableSchema([
ColumnInfo("col1", "int"),
ColumnInfo("col2", "real"),
ColumnInfo("col3", "text"),
])
table_name = local_node_create_table.delay(
context_id=f"{context_id}_table_{table_id}",
command_id=str(uuid.uuid1()).replace("-", ""),
schema_json=table_schema.to_json(),
).get()
values = [[1, 0.1, "test1"], [2, 0.2, "test2"], [3, 0.3, "test3"]]
local_node_insert_data_to_table.delay(table_name=table_name,
values=values).get()
return table_name
def test_create_view_and_get_view(context_id):
table_schema = TableSchema(
[
ColumnInfo("col1", "int"),
ColumnInfo("col2", "real"),
ColumnInfo("col3", "text"),
]
)
table_name = local_node_create_table.delay(
context_id=context_id,
command_id=str(uuid.uuid4()).replace("-", ""),
schema_json=table_schema.to_json(),
).get()
values = [[1, 0.1, "test1"], [2, 0.2, None], [3, 0.3, "test3"]]
local_node_insert_data_to_table.delay(table_name=table_name, values=values).get()
columns = ["col1", "col3"]
view_name = local_node_create_view.delay(
context_id=context_id,
command_id=str(uuid.uuid1()).replace("-", ""),
table_name=table_name,
columns=columns,
filters_json="filters_json",
).get()
views = local_node_get_views.delay(context_id=context_id).get()
assert view_name in views
view_intended_schema = TableSchema(
[
ColumnInfo("col1", "int"),
ColumnInfo("col3", "text"),
]
)
schema_result_json = local_node_get_view_schema.delay(table_name=view_name).get()
assert view_intended_schema == TableSchema.from_json(schema_result_json)
view_data_json = local_node_get_view_data.delay(table_name=view_name).get()
view_data = TableData.from_json(view_data_json)
assert all(
len(columns) == len(view_intended_schema.columns) for columns in view_data.data
)
assert view_data.schema == view_intended_schema
def test_create_pathology_view_and_get_view(context_id):
columns = [
"dataset",
"age_value",
"gcs_motor_response_scale",
"pupil_reactivity_right_eye_result",
]
datasets = ["dummy_tbi"]
pathology = "tbi"
view_name = local_node_create_pathology_view.delay(
context_id=context_id,
command_id=str(uuid.uuid1()).replace("-", ""),
pathology=pathology,
datasets=datasets,
columns=columns,
filters_json="filters_json",
).get()
views = local_node_get_views.delay(context_id=context_id).get()
assert view_name in views
schema = TableSchema(
[
ColumnInfo("row_id", "int"),
ColumnInfo("dataset", "text"),
ColumnInfo("age_value", "int"),
ColumnInfo("gcs_motor_response_scale", "text"),
ColumnInfo("pupil_reactivity_right_eye_result", "text"),
]
)
schema_result_json = local_node_get_view_schema.delay(table_name=view_name).get()
assert schema == TableSchema.from_json(schema_result_json)
view_data_json = local_node_get_view_data.delay(table_name=view_name).get()
view_data = TableData.from_json(view_data_json)
assert all(len(columns) == len(schema.columns) for columns in view_data.data)
assert view_data.schema == schema
view_schema_json = local_node_get_view_schema.delay(table_name=view_name).get()
view_schema = TableSchema.from_json(view_schema_json)
assert view_schema == schema
def create_table(context_id: str, command_id: str, schema_json: str) -> str:
"""
Parameters
----------
context_id : str
The id of the experiment
command_id : str
The id of the command that the table
schema_json : str(TableSchema)
A TableSchema object in a jsonified format
Returns
------
str
The name of the created table in lower case
"""
schema_object = TableSchema.from_json(schema_json)
table_name = create_table_name(
"table", command_id, context_id, node_config.identifier
)
table_info = TableInfo(table_name, schema_object)
tables.create_table(table_info)
return table_name
def get_table_schema(self, table_name: TableName):
task_signature = self.__celery_obj.signature(
self.task_signatures_str["get_table_schema"])
result = task_signature.delay(
table_name=table_name.full_table_name).get()
return TableSchema.from_json(result)
def test_create_merge_table_with_remote_tables(context_id):
local_node_1_data = node_catalog.get_node(local_node_1_id)
local_node_2_data = node_catalog.get_node(local_node_2_id)
schema = TableSchema([
ColumnInfo("col1", "int"),
ColumnInfo("col2", "real"),
ColumnInfo("col3", "text"),
])
# Create local tables
local_node_1_table_name = local_node_1_create_table.delay(
context_id=context_id,
command_id=str(uuid.uuid1()).replace("-", ""),
schema_json=schema.to_json(),
).get()
local_node_2_table_name = local_node_2_create_table.delay(
context_id=context_id,
command_id=str(uuid.uuid1()).replace("-", ""),
schema_json=schema.to_json(),
).get()
# Insert data into local tables
values = [[1, 0.1, "test1"], [2, 0.2, "test2"], [3, 0.3, "test3"]]
local_node_1_insert_data_to_table.delay(table_name=local_node_1_table_name,
values=values).get()
local_node_2_insert_data_to_table.delay(table_name=local_node_2_table_name,
values=values).get()
# Create remote tables
table_info_local_1 = TableInfo(local_node_1_table_name, schema)
table_info_local_2 = TableInfo(local_node_2_table_name, schema)
local_node_1_monetdb_sock_address = (
f"{local_node_1_data.monetdbIp}:{local_node_1_data.monetdbPort}")
local_node_2_monetdb_sock_address = (
f"{local_node_2_data.monetdbIp}:{local_node_2_data.monetdbPort}")
global_node_create_remote_table.delay(
table_info_json=table_info_local_1.to_json(),
monetdb_socket_address=local_node_1_monetdb_sock_address,
).get()
global_node_create_remote_table.delay(
table_info_json=table_info_local_2.to_json(),
monetdb_socket_address=local_node_2_monetdb_sock_address,
).get()
remote_tables = global_node_get_remote_tables.delay(
context_id=context_id).get()
assert local_node_1_table_name in remote_tables
assert local_node_2_table_name in remote_tables
# Create merge table
merge_table_name = global_node_create_merge_table.delay(
context_id=context_id,
command_id=str(uuid.uuid1()).replace("-", ""),
table_names=remote_tables,
).get()
# Validate merge table exists
merge_tables = global_node_get_merge_tables.delay(
context_id=context_id).get()
assert merge_table_name in merge_tables
# Validate merge table row count
table_data_json = global_node_get_merge_table_data.delay(
table_name=merge_table_name).get()
table_data = TableData.from_json(table_data_json)
row_count = len(table_data.data)
assert row_count == 6