cycquery.gemini.GEMINIQuerier¶

class GEMINIQuerier(dbms, user='', password='', host='', port=None, database='', schemas=None)[source]¶

GEMINI dataset querier.

Methods

`care_units`	Query care unit data, fetches transfer info from multiple tables.
`diagnoses`	Query diagnosis data.
`get_table`	Get a table and possibly map columns to have standard names.
`imaging`	Query imaging reports data.
`ip_admin`	Query GEMINI patient encounters.
`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.
`room_transfer`	Query room transfer data.

care_units()[source]¶

Query care unit data, fetches transfer info from multiple tables.

diagnoses()[source]¶

Query diagnosis data.

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

Query imaging reports data.

Query GEMINI patient encounters.

list_columns(schema_name, table_name)¶

List columns in a table.

Parameters:

Returns:

List of column names.

Return type:

List[str]

list_custom_tables()¶

List custom tables methods provided by the dataset API.

list_schemas()¶

List schemas in the database to query.

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]

room_transfer()[source]¶

Query room transfer data.