disease.query

Provides query handler class, which receives and responses to user search queries.

exception disease.query.InvalidParameterException

Exception for invalid parameter args provided by the user.

class disease.query.QueryHandler(database)

Class for normalizer management. Stores reference to database instance and normalizes query input.

__init__(database)

Initialize QueryHandler instance. Requires a created database object to initialize. The most straightforward way to do this is via the create_db() method:

>>> from disease.query import QueryHandler
>>> from disease.database import create_db
>>> q = QueryHandler(create_db())

We’ll generally call create_db without any arguments in code examples, for the sake of brevity. See the create_db() API description for more details.

Parameters:

database (AbstractDatabase) – storage backend to search against

normalize(query)

Return normalized concept for query.

Use to retrieve normalized disease concept records:

>>> from disease.query import QueryHandler
>>> from disease.database import create_db
>>> q = QueryHandler(create_db())
>>> result = q.normalize("NSCLC")
>>> result.normalized_id
'ncit:C2926'

Parameters:

query (str) – String to find normalized concept for

Return type:

NormalizationService

Returns:

Normalized disease concept

search(query_str, incl='', excl='')

Return highest match for each source.

>>> from disease.query import QueryHandler
>>> from disease.database import create_db
>>> q = QueryHandler(create_db())
>>> result = q.search("NSCLC")
>>> result.source_matches["Mondo"].records[0].concept_id
'mondo:0005233'

Parameters:

• query_str (str) – query, a string, to search for

• incl (str) – str containing comma-separated names of sources to use. Will exclude all other sources. Case-insensitive.

• excl (str) – str containing comma-separated names of source to exclude. Will include all other source. Case-insensitive.

Returns:

dict containing all matches found in sources.

Return type:

dict

Raises:

InvalidParameterException – if both incl and excl args are provided, or if invalid source names are given.