biothings.web.services

biothings.web.services.query

A Programmatic Query API supporting Biothings Query Syntax.

From an architecture perspective, biothings.web.query is one of the data services, built on top of the biothings.web.connections layer, however, due to the complexity of the module, it is escalated one level in organization to simplify the overall folder structure. The features are available in biothings.web.services.query namespace via import.

biothings.web.services.health

class biothings.web.services.health.DBHealth(client)[source]

Bases: object

check(**kwargs)[source]
class biothings.web.services.health.ESHealth(client, payload=None)[source]

Bases: biothings.web.services.health.DBHealth

async async_check(verbose=False)[source]
check()[source]
class biothings.web.services.health.MongoHealth(client)[source]

Bases: biothings.web.services.health.DBHealth

check(**kwargs)[source]
class biothings.web.services.health.SQLHealth(client)[source]

Bases: biothings.web.services.health.DBHealth

check(**kwargs)[source]

biothings.web.services.metadata

class biothings.web.services.metadata.BiothingHubMeta(**metadata)[source]

Bases: biothings.web.services.metadata.BiothingMetaProp

to_dict()[source]
class biothings.web.services.metadata.BiothingLicenses(licenses)[source]

Bases: biothings.web.services.metadata.BiothingMetaProp

to_dict()[source]
class biothings.web.services.metadata.BiothingMappings(properties)[source]

Bases: biothings.web.services.metadata.BiothingMetaProp

to_dict()[source]
class biothings.web.services.metadata.BiothingMetaProp[source]

Bases: object

to_dict()[source]
class biothings.web.services.metadata.BiothingsESMetadata(indices, client)[source]

Bases: biothings.web.services.metadata.BiothingsMetadata

refresh(biothing_type=None)[source]
property types
update(biothing_type, info, count)[source]

Read ES index mappings for the corresponding biothing_type, Populate datasource info and field properties from mappings.

class biothings.web.services.metadata.BiothingsMetadata[source]

Bases: object

get_licenses(biothing_type)[source]
get_mappings(biothing_type)[source]
get_metadata(biothing_type)[source]
async refresh(biothing_type)[source]
class biothings.web.services.metadata.BiothingsMongoMetadata(collections, client)[source]

Bases: biothings.web.services.metadata.BiothingsMetadata

get_licenses(biothing_type)[source]
get_mappings(biothing_type)[source]
async refresh(biothing_type)[source]
property types
class biothings.web.services.metadata.BiothingsSQLMetadata(tables, client)[source]

Bases: biothings.web.services.metadata.BiothingsMetadata

async refresh(biothing_type)[source]
property types

biothings.web.services.namespace

class biothings.web.services.namespace.BiothingsDBProxy[source]

Bases: object

Provide database-agnostic access to common biothings service components, for single database application.

configure(db)[source]
class biothings.web.services.namespace.BiothingsNamespace(config)[source]

Bases: object

biothings.web.services.namespace.load_class(kls)[source]