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

Parameters:

Name	Type	Description	Default
entity	str	The entity ID to get association counts for.	required
entity_category	Optional[str]	The biolink category of the entity (e.g. 'biolink:Gene'). If the entity is a gene, ortholog associations will also be counted.	None

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
facet_fields	Optional[List[str]]	List of fields to include facet counts for. Defaults to None.	None
facet_queries	Optional[List[str]]	List of queries to include facet counts for. Defaults to None.	None
filter_queries	Optional[List[str]]	List of queries to filter results by. 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_case_phenotype_matrix

Fetch case-phenotype matrix for a disease.

Execution flow: 1. Query for case-disease associations to get case list and count 2. Check count against limit, raise error if exceeded 3. Query for case-phenotype associations with JOIN (includes facets) 4. Build and return matrix response

Parameters:

Name	Type	Description	Default
disease_id	str	MONDO disease ID (e.g., "MONDO:0007078")	required
direct_only	bool	If True, only cases with exactly this disease	True
limit	int	Maximum number of cases allowed	200

Returns:

Type	Description
CasePhenotypeMatrixResponse	CasePhenotypeMatrixResponse with complete matrix data

Raises:

Type	Description
ValueError	If case count exceeds limit

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_entity_grid

Fetch entity grid for any supported grid type.

This is a generic 2-hop query that works for multiple grid types: - case-phenotype: Disease -> Case × Phenotype - disease-phenotype: Gene -> Disease × Phenotype - ortholog-phenotype: Gene -> Ortholog × Phenotype

Execution flow: 1. Get grid configuration for the specified type 2. Query for column entities (first hop) 3. Check count against limit 4. Query for row associations via JOIN (second hop, includes facets) 5. Build and return grid response

Parameters:

Name	Type	Description	Default
context_id	str	The context entity ID (e.g., disease ID, gene ID)	required
grid_type	str	The type of grid to generate	required
direct_only	bool	If True, only direct associations; if False, use closure	True
limit	int	Maximum number of column entities allowed	200

Returns:

Type	Description
EntityGridResponse	EntityGridResponse with complete grid data

Raises:

Type	Description
ValueError	If column count exceeds limit or grid type is unknown

get_generic_entity_grid

Fetch generic entity grid with configurable association categories.

This method allows specifying association categories directly, enabling flexible grid construction without predefined configurations.

Parameters:

Name	Type	Description	Default
context_id	str	The context entity ID (e.g., gene ID, disease ID)	required
column_assoc_categories	List[str]	List of association category values for context -> column	required
row_assoc_categories	List[str]	List of association category values for column -> row	required
row_grouping	str	How to group rows ("histopheno" or "none")	'histopheno'
group_columns_by_category	bool	If True, sort columns by their source association category	False
direct_only	bool	If True, only direct associations; if False, use closure	True
limit	int	Maximum number of column entities	500

Returns:

Type	Description
EntityGridResponse	EntityGridResponse with complete grid data

Raises:

Type	Description
ValueError	If column count exceeds limit or configuration is invalid

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

Grounds a single entity

Parameters:

Name	Type	Description	Default
text	str	Text to ground	required

Returns:

Name	Type	Description
Entity	List[Entity]	Dataclass representing a single 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