Solr
SolrImplementation
dataclass
Bases: EntityInterface, AssociationInterface, SearchInterface, GroundingInterface
Implementation of Monarch Interfaces for Solr endpoint
get_association_counts
Get list of association counts for a given entity
get_associations
Retrieve paginated association records, with filter options
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
category |
List[AssociationCategory]
|
Filter to only associations matching the specified categories. Defaults to None. |
None
|
predicate |
List[AssociationPredicate]
|
Filter to only associations matching the specified predicates. Defaults to None. |
None
|
subject |
Optional[List[str]]
|
Filter to only associations matching the specified subjects. Defaults to None. |
None
|
object |
Optional[List[str]]
|
Filter to only associations matching the specified objects. Defaults to None. |
None
|
subject_closure |
Optional[str]
|
Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None |
None
|
object_closure |
Optional[str]
|
Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None |
None
|
entity |
Optional[List[str]]
|
Filter to only associations where the specified entities are the subject or the object. Defaults to None. |
None
|
q |
Optional[str]
|
Query string to search within matches. Defaults to None. |
None
|
compact |
bool
|
Return compact results with fewer fields. Defaults to False. |
False
|
offset |
int
|
Result offset, for pagination. Defaults to 0. |
0
|
limit |
int
|
Limit results to specified number. Defaults to 20. |
20
|
Returns:
| Name | Type | Description |
|---|---|---|
AssociationResults |
Union[AssociationResults, CompactAssociation]
|
Dataclass representing results of an association search. |
get_counterpart_entities
Get a list of entities directly associated with this_entity fetched from associations in the Solr index
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
this_entity |
Entity
|
The entity to get associations for |
required |
entity |
str
|
an entity ID occurring in either the subject or object. Defaults to None. |
None
|
subject |
str
|
an entity ID occurring in the subject. Defaults to None. |
None
|
predicate |
str
|
a predicate value. Defaults to None. |
None
|
object |
str
|
an entity ID occurring in the object. Defaults to None. |
None
|
get_entity
Retrieve a specific entity by exact ID match, with optional extras
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id |
str
|
id of the entity to search for. |
required |
extra |
bool
|
Whether to include association counts and hierarchy in the response. |
required |
Returns:
| Name | Type | Description |
|---|---|---|
Entity |
Optional[Union[Node, Entity]]
|
Dataclass representing results of an entity search. |
Node |
Optional[Union[Node, Entity]]
|
Dataclass representing results of an entity search with extra=True. |
get_histopheno
Get histopheno counts for a given subject_closure
get_multi_entity_associations
Get associations between multiple entities and counterparts of a given category
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
entity |
List[str]
|
List of entity IDs to get associations for |
required |
counterpart_category |
List[str]
|
List of categories of counterpart entity to get associations for. Defaults to None. |
None
|
offset |
int
|
Result offset, for pagination. Defaults to 0. |
0
|
limit |
int
|
Limit results to specified number. Defaults to 20. |
required |
limit_per_group |
int
|
Limit results to specified number per group. Defaults to 20. |
20
|
ground_entity
search
Search for entities by label, with optional filters
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
q |
str
|
Query string. Defaults to ":". |
'*:*'
|
offset |
int
|
Result offset, for pagination. Defaults to 0. |
0
|
limit |
int
|
Limit results to specified number. Defaults to 20. |
20
|
category |
List[str]
|
Filter to only entities matching the specified categories. Defaults to None. |
None
|
in_taxon_label |
List[str]
|
Filter to only entities matching the specified taxon label. Defaults to None. |
None
|
facet_fields |
List[str]
|
List of fields to include facet counts for. Defaults to None. |
None
|
facet_queries |
List[str]
|
List of queries to include facet counts for. Defaults to None. |
None
|
filter_queries |
List[str]
|
List of queries to filter results by. Defaults to None. |
None
|
sort |
str
|
Sort results by the specified field. Defaults to None. |
None
|
Returns:
| Name | Type | Description |
|---|---|---|
SearchResults |
SearchResults
|
Dataclass representing results of a search. |
solr_is_available
Check if the Solr instance is available