def _generate_udf_statements(
command_id: str,
context_id: str,
func_name: str,
positional_args: List[UDFArgument],
keyword_args: Dict[str, UDFArgument],
):
allowed_func_name = func_name.replace(".", "_") # A dot is not an allowed character
udf_name = _create_udf_name(allowed_func_name, command_id, context_id)
result_table_name = create_table_name(
"table", command_id, context_id, node_config.identifier
)
gen_pos_args, gen_kw_args = _convert_udf2udfgen_args(positional_args, keyword_args)
udf_creation_stmt, udf_execution_stmt = generate_udf_application_queries(
func_name, gen_pos_args, gen_kw_args
)
udf_creation_stmt = udf_creation_stmt.substitute(udf_name=udf_name)
udf_execution_stmt = udf_execution_stmt.substitute(
table_name=result_table_name,
udf_name=udf_name,
node_id=node_config.identifier,
)
return udf_creation_stmt, udf_execution_stmt, result_table_name
def create_view(
context_id: str,
command_id: str,
table_name: str,
columns: List[str],
filters_json: str,
) -> str:
"""
Creates a view of a table with specific columns and filters to the DB.
Parameters
----------
context_id : str
The id of the experiment
command_id : str
The id of the command that the view
table_name : str
The name of the table
columns : List[str]
A list of column names
filters_json : str(dict)
A Jquery filters object
Returns
------
str
The name of the created view
"""
view_name = create_table_name("view", command_id, context_id,
node_config.identifier)
views.create_view(view_name=view_name,
table_name=table_name,
columns=columns)
return view_name
def create_merge_table(context_id: str, command_id: str,
table_names: List[str]) -> str:
"""
Parameters
----------
context_id : str
The id of the experiment
command_id : str
The id of the command that the merge table
table_names: List[str]
Its a list of names of the tables to be merged
Returns
------
str
The name(string) of the created merge table in lower case.
"""
validate_tables_can_be_merged(table_names)
schema = common_actions.get_table_schema(table_names[0])
merge_table_name = create_table_name("merge", command_id, context_id,
node_config.identifier)
table_info = TableInfo(merge_table_name, schema)
merge_tables.create_merge_table(table_info)
merge_tables.add_to_merge_table(merge_table_name, table_names)
return merge_table_name
def create_pathology_view(
context_id: str,
command_id: str,
pathology: str,
datasets: List[str],
columns: List[str],
filters_json: str,
) -> str:
# TODO We need to add the filters
"""
Creates a MIP specific view of a pathology with specific columns, filters and datasets to the DB.
Parameters
----------
context_id : str
The id of the experiment
command_id : str
The id of the command that the view
pathology : str
The pathology data table on which the view will be created
datasets : List[str]
A list of dataset names
columns : List[str]
A list of column names
filters_json : str(dict)
A Jquery filters object
Returns
------
str
The name of the created view
"""
view_name = create_table_name("view", command_id, context_id,
node_config.identifier)
columns.insert(0, DATA_TABLE_PRIMARY_KEY)
views.create_view(
view_name=view_name,
table_name=f"{pathology}_data",
columns=columns,
datasets=datasets,
)
return view_name
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