inspectomop.inspector.Inspector¶

class inspectomop.inspector.Inspector(connection_url)¶

Creates an Inspector object which can be used to run OMOP data queries

Parameters:	connection_url (string) – A connection url of form ‘dialect+driver://username:password@host:port/database’. The driver can be any currently supported by sqlalchemy (sqlite, mysql, postgresql, etc.).

connection_url¶

Type:	str

Notes

SQLite DBs require an additional ‘/’ as in ‘sqlite:///foo.db’ for a relative path and ‘sqlite:////abs/path/to/foo.db’ for an absolute path.

See http://docs.sqlalchemy.org/en/latest/core/engines.html for more information about connection URLs and supported dialects.

Examples

>>> import inspectomop as iomop
>>> connection_url = 'sqlite:///:memory:'
>>> iomop.Inspector(connection_url)

__init__(connection_url)¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(connection_url)	Initialize self.
`attach_sqlite_db`(db_file, schema_name)	For SQLite backends, attaches an additional sqlite database file.
`execute`(statement)	Executes an SQL query on the OMOP CDM.
`table_info`(table_name)	Return a Pandas DataFrame describing the fields and properties of a table.

Attributes

`clinical_tables`	A dictionary containing all of the `Clinical` OMOP CDM tables in the connected database.
`connection_url`	password@host:port/database’ used to specify the dialect, location, etc.
`derived_elements_tables`	A dictionary containing all of the `Derived Elements` OMOP CDM tables in the connected database.
`engine`	A convenience hook to the underlying sqlalchemy engine.
`health_economics_tables`	A dictionary containing all of the `Health Economics` OMOP CDM tables in the connected database.
`health_system_tables`	A dictionary containing all of the `Health System` OMOP CDM tables in the connected database.
`metadata_tables`	A dictionary containing all of the `MetaData` OMOP CDM tables in the connected database.
`tables`	A dictionary containing all OMOP CDM tables in the connected database.
`vocabularies_tables`	A dictionary containing all of the `Vocabularies` OMOP CDM tables in the connected database.