cycquery.omop.OMOPQuerier

class OMOPQuerier(database, user, password, dbms='postgresql', host='localhost', port=5432, schema_name='omop')

Bases: DatasetQuerier

OMOP querier.

Methods

get_table	Get a table and possibly map columns to have standard names.
list_columns	List columns in a table.
list_custom_tables	List custom tables methods provided by the dataset API.
list_schemas	List schemas in the database to query.
list_tables	List table methods that can be queried using the database.
map_concept_ids_to_name	Map concept IDs in a source table to concept names from concept table.
measurement	Query OMOP measurement table.
observation	Query OMOP observation table.
person	Query OMOP person table.
visit_detail	Query OMOP visit_detail table.
visit_occurrence	Query OMOP visit_occurrence table.

get_table(schema_name, table_name, cast_timestamp_cols=True)

Get a table and possibly map columns to have standard names.

Standardizing column names allows for columns to be recognized in downstream processing.

Parameters:

• schema_name (str) – Name of schema in the database.

• table_name (str) – Name of table in the database.

• cast_timestamp_cols (bool) – Whether to cast timestamp columns to datetime.

Returns:

Table with mapped columns.

Return type:

sqlalchemy.sql.selectable.Subquery

list_columns(schema_name, table_name)

List columns in a table.

Parameters:

• schema_name (str) – Name of schema in the database.

• table_name (str) – Name of table in the database.

Returns:

List of column names.

Return type:

List[str]

list_custom_tables()

List custom tables methods provided by the dataset API.

Returns:

List of custom table names.

Return type:

List[str]

list_schemas()

List schemas in the database to query.

Returns:

List of schema names.

Return type:

List[str]

list_tables(schema_name=None)

List table methods that can be queried using the database.

Parameters:

schema_name (Optional[str]) – Name of schema in the database.

Returns:

List of table names.

Return type:

List[str]

map_concept_ids_to_name(src_table, src_cols, dst_cols=None)

Map concept IDs in a source table to concept names from concept table.

For each concept ID column with a name like somecol_concept_ID, the mapped concept name column will be named somecol_concept_name. If dst_cols is specified, the mapped concept name column will be named according to the corresponding name in dst_cols.

Parameters:

• src_table (Union[Subquery, QueryInterface]) – Source table with concept IDs.

• src_cols (Union[str, List[str]]) – Column name(s) to consider as concept IDs for mapping.

• dst_cols (Union[str, List[str], None]) – Column name(s) to assign for the mapped concept name columns.

Returns:

Query with mapped columns from concept table.

Return type:

cycquery.interface.QueryInterface

measurement()

Query OMOP measurement table.

Returns:

Constructed query, wrapped in an interface object.

Return type:

cycquery.interface.QueryInterface

observation()

Query OMOP observation table.

Returns:

Constructed query, wrapped in an interface object.

Return type:

cycquery.interface.QueryInterface

person()

Query OMOP person table.

Returns:

Constructed query, wrapped in an interface object.

Return type:

cycquery.interface.QueryInterface

visit_detail()

Query OMOP visit_detail table.

Returns:

Constructed query, wrapped in an interface object.

Return type:

cycquery.interface.QueryInterface

visit_occurrence()

Query OMOP visit_occurrence table.

Returns:

Constructed query, wrapped in an interface object.

Return type:

cycquery.interface.QueryInterface