diff --git a/backend/src/monarch_py/cli.py b/backend/src/monarch_py/cli.py index d303f4024..831a277c3 100644 --- a/backend/src/monarch_py/cli.py +++ b/backend/src/monarch_py/cli.py @@ -120,6 +120,12 @@ def associations( "-d", help="Whether to exclude associations with subject/object as ancestors", ), + compact: bool = typer.Option( + False, + "--compact", + "-C", + help="Whether to return a compact representation of the associations", + ), limit: int = typer.Option(20, "--limit", "-l", help="The number of associations to return"), offset: int = typer.Option(0, "--offset", help="The offset of the first association to be retrieved"), fmt: str = typer.Option( diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py index a7c5e2fff..097509c87 100644 --- a/backend/src/monarch_py/datamodels/model.py +++ b/backend/src/monarch_py/datamodels/model.py @@ -176,6 +176,17 @@ class Association(ConfiguredBaseModel): ) +class CompactAssociation(ConfiguredBaseModel): + + category: Optional[str] = Field(None) + subject: str = Field(...) + subject_label: Optional[str] = Field(None, description="""The name of the subject entity""") + predicate: str = Field(...) + object: str = Field(...) + object_label: Optional[str] = Field(None, description="""The name of the object entity""") + negated: Optional[bool] = Field(None) + + class AssociationCountList(ConfiguredBaseModel): """ Container class for a list of association counts @@ -538,6 +549,16 @@ class AssociationResults(Results): total: int = Field(..., description="""total number of items matching a query""") +class CompactAssociationResults(Results): + + items: List[CompactAssociation] = Field( + default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""" + ) + limit: int = Field(..., description="""number of items to return in a response""") + offset: int = Field(..., description="""offset into the total number of items""") + total: int = Field(..., description="""total number of items matching a query""") + + class AssociationTableResults(Results): items: List[DirectionalAssociation] = Field( @@ -745,6 +766,7 @@ class SemsimSearchResult(ConfiguredBaseModel): # Model rebuild # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model Association.model_rebuild() +CompactAssociation.model_rebuild() AssociationCountList.model_rebuild() AssociationTypeMapping.model_rebuild() DirectionalAssociation.model_rebuild() @@ -760,6 +782,7 @@ class SemsimSearchResult(ConfiguredBaseModel): NodeHierarchy.model_rebuild() Results.model_rebuild() AssociationResults.model_rebuild() +CompactAssociationResults.model_rebuild() AssociationTableResults.model_rebuild() CategoryGroupedAssociationResults.model_rebuild() EntityResults.model_rebuild() diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml index 15bd79d06..1a6471c5a 100644 --- a/backend/src/monarch_py/datamodels/model.yaml +++ b/backend/src/monarch_py/datamodels/model.yaml @@ -115,6 +115,22 @@ classes: slot_usage: items: range: Association + CompactAssociation: + slots: + - category + - subject + - subject_label + - predicate + - object + - object_label + - negated + CompactAssociationResults: + is_a: Results + slots: + - items + slot_usage: + items: + range: CompactAssociation AssociationTableResults: is_a: Results slots: @@ -281,7 +297,6 @@ classes: slot_usage: items: range: SearchResult - TextAnnotationResult: slots: - text diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py index b4d28f029..0bf171c0f 100644 --- a/backend/src/monarch_py/implementations/solr/solr_implementation.py +++ b/backend/src/monarch_py/implementations/solr/solr_implementation.py @@ -5,6 +5,7 @@ import requests from monarch_py.datamodels.model import ( Association, + CompactAssociation, AssociationCountList, AssociationResults, AssociationTableResults, @@ -240,9 +241,10 @@ def get_associations( entity: List[str] = None, direct: bool = False, q: str = None, + compact: bool = False, offset: int = 0, limit: int = 20, - ) -> AssociationResults: + ) -> Union[AssociationResults, CompactAssociation]: """Retrieve paginated association records, with filter options Args: @@ -254,6 +256,7 @@ def get_associations( object_closure: Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None entity: Filter to only associations where the specified entities are the subject or the object. Defaults to None. q: Query string to search within matches. Defaults to None. + compact: Return compact results with fewer fields. Defaults to False. offset: Result offset, for pagination. Defaults to 0. limit: Limit results to specified number. Defaults to 20. @@ -262,17 +265,17 @@ def get_associations( """ solr = SolrService(base_url=self.base_url, core=core.ASSOCIATION) query = build_association_query( - category=[c.value for c in category] if category else None, - predicate=[p.value for p in predicate] if predicate else None, + category=[c.value for c in category] if category else [], + predicate=[p.value for p in predicate] if predicate else [], subject=[subject] if isinstance(subject, str) else subject, object=[object] if isinstance(object, str) else object, entity=[entity] if isinstance(entity, str) else entity, subject_closure=subject_closure, object_closure=object_closure, - subject_category=[c.value for c in subject_category] if subject_category else None, + subject_category=[c.value for c in subject_category] if subject_category else [], subject_namespace=[subject_namespace] if isinstance(subject_namespace, str) else subject_namespace, subject_taxon=[subject_taxon] if isinstance(subject_taxon, str) else subject_taxon, - object_category=[c.value for c in object_category] if object_category else None, + object_category=[c.value for c in object_category] if object_category else [], object_taxon=[object_taxon] if isinstance(object_taxon, str) else object_taxon, object_namespace=[object_namespace] if isinstance(object_namespace, str) else object_namespace, direct=direct, @@ -281,7 +284,8 @@ def get_associations( limit=limit, ) query_result = solr.query(query) - associations = parse_associations(query_result, offset, limit) + + associations = parse_associations(query_result, compact, offset, limit) return associations def get_histopheno(self, subject_closure: str = None) -> HistoPheno: diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py index b5d676dc9..47626fff2 100644 --- a/backend/src/monarch_py/implementations/solr/solr_parsers.py +++ b/backend/src/monarch_py/implementations/solr/solr_parsers.py @@ -5,6 +5,8 @@ from monarch_py.datamodels.model import ( Association, + CompactAssociation, + CompactAssociationResults, AssociationCount, AssociationCountList, AssociationDirectionEnum, @@ -33,26 +35,44 @@ def parse_associations( query_result: SolrQueryResult, + compact: bool = False, offset: int = 0, limit: int = 20, ) -> AssociationResults: associations = [] - for doc in query_result.response.docs: - try: - association = Association(**doc) - except ValidationError: - logger.error(f"Validation error for {doc}") - raise ValidationError - association.provided_by_link = get_provided_by_link(association.provided_by) if association.provided_by else [] - association.has_evidence_links = ( - get_links_for_field(association.has_evidence) if association.has_evidence else [] - ) - association.publications_links = ( - get_links_for_field(association.publications) if association.publications else [] - ) - associations.append(association) total = query_result.response.num_found - return AssociationResults(items=associations, limit=limit, offset=offset, total=total) + if compact: + associations = [ + CompactAssociation( + category=doc.get("category"), + subject=doc.get("subject"), + subject_label=doc.get("subject_label"), + predicate=doc.get("predicate"), + object=doc.get("object"), + object_label=doc.get("object_label"), + negated=doc.get("negated"), + ) + for doc in query_result.response.docs + ] + return CompactAssociationResults(items=associations, limit=limit, offset=offset, total=total) + else: + for doc in query_result.response.docs: + try: + association = Association(**doc) + except ValidationError: + logger.error(f"Validation error for {doc}") + raise ValidationError + association.provided_by_link = ( + get_provided_by_link(association.provided_by) if association.provided_by else [] + ) + association.has_evidence_links = ( + get_links_for_field(association.has_evidence) if association.has_evidence else [] + ) + association.publications_links = ( + get_links_for_field(association.publications) if association.publications else [] + ) + associations.append(association) + return AssociationResults(items=associations, limit=limit, offset=offset, total=total) def parse_association_counts(query_result: SolrQueryResult, entity: str) -> AssociationCountList: @@ -88,7 +108,6 @@ def parse_association_counts(query_result: SolrQueryResult, entity: str) -> Asso def parse_entity(solr_document: Dict) -> Entity: try: entity = Entity(**solr_document) - entity.uri = converter.expand(entity.id) except ValidationError: logger.error(f"Validation error for {solr_document}") diff --git a/backend/src/monarch_py/implementations/sql/sql_implementation.py b/backend/src/monarch_py/implementations/sql/sql_implementation.py index 7b2bed105..0f05b8800 100644 --- a/backend/src/monarch_py/implementations/sql/sql_implementation.py +++ b/backend/src/monarch_py/implementations/sql/sql_implementation.py @@ -1,11 +1,19 @@ from dataclasses import dataclass -from typing import List +from typing import List, Union import pystow from loguru import logger from pydantic import ValidationError -from monarch_py.datamodels.model import Association, AssociationResults, Entity, Node, NodeHierarchy +from monarch_py.datamodels.model import ( + Association, + CompactAssociation, + CompactAssociationResults, + AssociationResults, + Entity, + Node, + NodeHierarchy, +) from monarch_py.interfaces.association_interface import AssociationInterface from monarch_py.interfaces.entity_interface import EntityInterface from monarch_py.service.curie_service import converter @@ -168,9 +176,10 @@ def get_associations( object_closure: str = None, entity: List[str] = None, direct: bool = None, + compact: bool = False, offset: int = 0, limit: int = 20, - ) -> AssociationResults: + ) -> Union[AssociationResults, CompactAssociationResults]: """Retrieve paginated association records, with filter options Args: @@ -182,6 +191,7 @@ def get_associations( object_closure (str, optional): Filter to only associations the specified term ID as an ancestor of the object. Defaults to None. entity (str, optional): Filter to only associations where the specified entity is the subject or the object. Defaults to None. association_type (str, optional): Filter to only associations matching the specified association label. Defaults to None. + compact (bool, optional): Whether to return compact or full association records. Defaults to False. offset (int, optional): Result offset, for pagination. Defaults to 0. limit (int, optional): Limit results to specified number. Defaults to 20. @@ -239,35 +249,56 @@ def get_associations( total = count[f"COUNT(*)"] associations = [] - for row in results: - result = { - "id": row["id"], - "original_subject": row["original_subject"], - "predicate": row["predicate"], - "original_object": row["original_object"], - "category": row["category"], - "aggregator_knowledge_source": row["aggregator_knowledge_source"].split("|"), - "primary_knowledge_source": row["primary_knowledge_source"], - "publications": row["publications"].split("|"), - "qualifiers": row["qualifiers"].split("|"), - "provided_by": row["provided_by"], - "has_evidence": row["has_evidence"].split("|"), - "stage_qualifier": row["stage_qualifier"], - "negated": False if not row["negated"] else True, - "frequency_qualifier": row["frequency_qualifier"], - "onset_qualifier": row["onset_qualifier"], - "sex_qualifier": row["sex_qualifier"], - "subject": row["subject"], - "object": row["object"], - } - # Convert empty strings to null value - for key in result: - result[key] = None if not result[key] else result[key] - try: - associations.append(Association(**result)) - except ValidationError: - logger.error(f"Validation error for {row}") - raise - - results = AssociationResults(items=associations, limit=limit, offset=offset, total=total) - return results + if compact: + for row in results: + result = { + "category": row["category"], + "subject": row["subject"], + "subject_label": row["subject_label"], + "predicate": row["predicate"], + "object": row["object"], + "object_label": row["object_label"], + "negated": False if not row["negated"] else True, + } + # Convert empty strings to null value + for key in result: + result[key] = None if not result[key] else result[key] + try: + associations.append(CompactAssociation(**result)) + except ValidationError: + logger.error(f"Validation error for {row}") + raise + return CompactAssociationResults(items=associations, limit=limit, offset=offset, total=total) + else: + for row in results: + result = { + "id": row["id"], + "original_subject": row["original_subject"], + "predicate": row["predicate"], + "original_object": row["original_object"], + "category": row["category"], + "aggregator_knowledge_source": row["aggregator_knowledge_source"].split("|"), + "primary_knowledge_source": row["primary_knowledge_source"], + "publications": row["publications"].split("|"), + "qualifiers": row["qualifiers"].split("|"), + "provided_by": row["provided_by"], + "has_evidence": row["has_evidence"].split("|"), + "stage_qualifier": row["stage_qualifier"], + "negated": False if not row["negated"] else True, + "frequency_qualifier": row["frequency_qualifier"], + "onset_qualifier": row["onset_qualifier"], + "sex_qualifier": row["sex_qualifier"], + "subject": row["subject"], + "object": row["object"], + } + # Convert empty strings to null value + for key in result: + result[key] = None if not result[key] else result[key] + if isinstance(result[key], list) and len(result[key]) == 1 and not result[key][0]: + result[key] = [] + try: + associations.append(Association(**result)) + except ValidationError: + logger.error(f"Validation error for {row}") + raise + return AssociationResults(items=associations, limit=limit, offset=offset, total=total) diff --git a/backend/src/monarch_py/solr_cli.py b/backend/src/monarch_py/solr_cli.py index 2c7ed866f..ea5ba28db 100644 --- a/backend/src/monarch_py/solr_cli.py +++ b/backend/src/monarch_py/solr_cli.py @@ -148,6 +148,12 @@ def associations( "-d", help="Whether to exclude associations with subject/object as ancestors", ), + compact: bool = typer.Option( + False, + "--compact", + "-C", + help="Whether to return a compact representation of the associations", + ), limit: int = typer.Option(20, "--limit", "-l", help="The number of associations to return"), offset: int = typer.Option(0, "--offset", help="The offset of the first association to be retrieved"), fmt: str = typer.Option( diff --git a/backend/src/monarch_py/sql_cli.py b/backend/src/monarch_py/sql_cli.py index e049c3e51..c10a1b6a5 100644 --- a/backend/src/monarch_py/sql_cli.py +++ b/backend/src/monarch_py/sql_cli.py @@ -89,6 +89,12 @@ def associations( "-d", help="Whether to exclude associations with subject/object as ancestors", ), + compact: bool = typer.Option( + False, + "--compact", + "-C", + help="Whether to return a compact representation of the associations", + ), limit: int = typer.Option(20, "--limit", "-l", help="The number of associations to return"), offset: int = typer.Option(0, "--offset", help="The offset of the first association to be retrieved"), fmt: str = typer.Option( @@ -107,6 +113,8 @@ def associations( predicate: A comma-separated list of predicates object: A comma-separated list of objects entity: A comma-separated list of entities + direct: Whether to exclude associations with subject/object as ancestors + compact: Whether to return a compact representation of the associations limit: The number of associations to return offset: The offset of the first association to be retrieved fmt: The format of the output (json, yaml, tsv, table) diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index 4d9cca184..4e3f17c0c 100644 --- a/backend/tests/fixtures/association_counts_response.py +++ b/backend/tests/fixtures/association_counts_response.py @@ -5,7 +5,7 @@ def association_counts_response(): return { "responseHeader": { - "QTime": 5, + "QTime": 7, "params": { "facet.query": [ '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', diff --git a/backend/tests/fixtures/associations_compact.py b/backend/tests/fixtures/associations_compact.py new file mode 100644 index 000000000..bd4c9dc14 --- /dev/null +++ b/backend/tests/fixtures/associations_compact.py @@ -0,0 +1,192 @@ +import pytest + + +@pytest.fixture +def associations_compact(): + return { + "limit": 20, + "offset": 0, + "total": 4627, + "items": [ + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0001371", + "object_label": "Flexion contracture", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0003458", + "object_label": "EMG: myopathic abnormalities", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0003560", + "object_label": "Muscular dystrophy", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0030095", + "object_label": "Reduced muscle collagen VI", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0001220", + "object_label": "Interphalangeal joint contracture of finger", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0001288", + "object_label": "Gait disturbance", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002355", + "object_label": "Difficulty walking", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002460", + "object_label": "Distal muscle weakness", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0003325", + "object_label": "Limb-girdle muscle weakness", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0003731", + "object_label": "Quadriceps muscle weakness", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0006466", + "object_label": "Ankle flexion contracture", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0009058", + "object_label": "Increased muscle lipid content", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0100490", + "object_label": "Camptodactyly of finger", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0000962", + "object_label": "Hyperkeratosis", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0001073", + "object_label": "Cigarette-paper scars", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0001382", + "object_label": "Joint hypermobility", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002086", + "object_label": "Abnormality of the respiratory system", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002515", + "object_label": "Waddling gait", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002791", + "object_label": "Hypoventilation", + "negated": None, + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002938", + "object_label": "Lumbar hyperlordosis", + "negated": None, + }, + ], + } diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py index de36f3a05..bead038c9 100644 --- a/backend/tests/fixtures/histopheno_response.py +++ b/backend/tests/fixtures/histopheno_response.py @@ -5,7 +5,7 @@ def histopheno_response(): return { "responseHeader": { - "QTime": 2, + "QTime": 5, "params": { "facet.query": [ 'object_closure:"HP:0000924"', diff --git a/backend/tests/fixtures/phenotype_explorer_compare.py b/backend/tests/fixtures/phenotype_explorer_compare.py index 033f9c27f..625c9c6fa 100644 --- a/backend/tests/fixtures/phenotype_explorer_compare.py +++ b/backend/tests/fixtures/phenotype_explorer_compare.py @@ -69,8 +69,8 @@ def phenotype_explorer_compare(): "HP:0004325": { "match_source": "HP:0004325", "match_source_label": "Decreased body weight (HPO)", - "match_target": "MP:0002169", - "match_target_label": "no abnormal phenotype detected (MPO)", + "match_target": "MP:0010771", + "match_target_label": "integument phenotype (MPO)", "score": 1.5540019332516637, "match_subsumer": None, "match_subsumer_label": None, @@ -78,7 +78,7 @@ def phenotype_explorer_compare(): "subject_id": "HP:0004325", "subject_label": None, "subject_source": None, - "object_id": "MP:0002169", + "object_id": "MP:0010771", "object_label": None, "object_source": None, "ancestor_id": "UPHENO:0001003", @@ -87,10 +87,10 @@ def phenotype_explorer_compare(): "object_information_content": None, "subject_information_content": None, "ancestor_information_content": 1.5540019332516637, - "jaccard_similarity": 0.23076923076923078, + "jaccard_similarity": 0.24, "cosine_similarity": None, "dice_similarity": None, - "phenodigm_score": 0.5988454147360435, + "phenodigm_score": 0.61070489107293, }, } }, diff --git a/backend/tests/fixtures/phenotype_explorer_search.py b/backend/tests/fixtures/phenotype_explorer_search.py index 904cf8435..4eed8caa6 100644 --- a/backend/tests/fixtures/phenotype_explorer_search.py +++ b/backend/tests/fixtures/phenotype_explorer_search.py @@ -68,8 +68,8 @@ def phenotype_explorer_search(): "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)") }, object_termset={ - "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), + "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), }, subject_best_matches={ "ZP:0018569": BestMatch( @@ -423,12 +423,12 @@ def phenotype_explorer_search(): score=7.234842285670967, similarity=TermSetPairwiseSimilarity( subject_termset={ - "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"), "ZP:0018568": TermInfo(id="ZP:0018568", label="primitive hemopoiesis absent, abnormal (ZPO)"), + "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"), }, object_termset={ - "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), + "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), }, subject_best_matches={ "ZP:0018568": BestMatch( @@ -517,8 +517,8 @@ def phenotype_explorer_search(): "HP:0012378": BestMatch( match_source="HP:0012378", match_source_label="Fatigue (HPO)", - match_target="ZP:0018569", - match_target_label="myeloid cell development absent, abnormal (ZPO)", + match_target="ZP:0018568", + match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", score=1.6836208034928104, match_subsumer=None, match_subsumer_label=None, @@ -526,7 +526,7 @@ def phenotype_explorer_search(): subject_id="HP:0012378", subject_label=None, subject_source=None, - object_id="ZP:0018569", + object_id="ZP:0018568", object_label=None, object_source=None, ancestor_id="UPHENO:0001005", @@ -535,10 +535,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=1.6836208034928104, - jaccard_similarity=0.47058823529411764, + jaccard_similarity=0.4444444444444444, cosine_similarity=None, dice_similarity=None, - phenodigm_score=0.8901079388591847, + phenodigm_score=0.8650294287846346, ), ), }, @@ -622,12 +622,12 @@ def phenotype_explorer_search(): score=7.234842285670967, similarity=TermSetPairwiseSimilarity( subject_termset={ - "ZP:0018568": TermInfo(id="ZP:0018568", label="primitive hemopoiesis absent, abnormal (ZPO)"), "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"), + "ZP:0018568": TermInfo(id="ZP:0018568", label="primitive hemopoiesis absent, abnormal (ZPO)"), }, object_termset={ - "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), + "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), }, subject_best_matches={ "ZP:0018568": BestMatch( @@ -689,8 +689,8 @@ def phenotype_explorer_search(): "HP:0002104": BestMatch( match_source="HP:0002104", match_source_label="Apnea (HPO)", - match_target="ZP:0018568", - match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", + match_target="ZP:0018569", + match_target_label="myeloid cell development absent, abnormal (ZPO)", score=9.08524944639702, match_subsumer=None, match_subsumer_label=None, @@ -698,7 +698,7 @@ def phenotype_explorer_search(): subject_id="HP:0002104", subject_label=None, subject_source=None, - object_id="ZP:0018568", + object_id="ZP:0018569", object_label=None, object_source=None, ancestor_id="UPHENO:0034024", @@ -707,17 +707,17 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=9.08524944639702, - jaccard_similarity=0.3333333333333333, + jaccard_similarity=0.34615384615384615, cosine_similarity=None, dice_similarity=None, - phenodigm_score=1.7402346054863809, + phenodigm_score=1.773384910034319, ), ), "HP:0012378": BestMatch( match_source="HP:0012378", match_source_label="Fatigue (HPO)", - match_target="ZP:0018568", - match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", + match_target="ZP:0018569", + match_target_label="myeloid cell development absent, abnormal (ZPO)", score=1.6836208034928104, match_subsumer=None, match_subsumer_label=None, @@ -725,7 +725,7 @@ def phenotype_explorer_search(): subject_id="HP:0012378", subject_label=None, subject_source=None, - object_id="ZP:0018568", + object_id="ZP:0018569", object_label=None, object_source=None, ancestor_id="UPHENO:0001005", @@ -734,10 +734,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=1.6836208034928104, - jaccard_similarity=0.4444444444444444, + jaccard_similarity=0.47058823529411764, cosine_similarity=None, dice_similarity=None, - phenodigm_score=0.8650294287846346, + phenodigm_score=0.8901079388591847, ), ), }, @@ -814,8 +814,8 @@ def phenotype_explorer_search(): score=7.234842285670967, similarity=TermSetPairwiseSimilarity( subject_termset={ - "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"), "ZP:0018568": TermInfo(id="ZP:0018568", label="primitive hemopoiesis absent, abnormal (ZPO)"), + "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"), }, object_termset={ "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), @@ -881,8 +881,8 @@ def phenotype_explorer_search(): "HP:0002104": BestMatch( match_source="HP:0002104", match_source_label="Apnea (HPO)", - match_target="ZP:0018568", - match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", + match_target="ZP:0018569", + match_target_label="myeloid cell development absent, abnormal (ZPO)", score=9.08524944639702, match_subsumer=None, match_subsumer_label=None, @@ -890,7 +890,7 @@ def phenotype_explorer_search(): subject_id="HP:0002104", subject_label=None, subject_source=None, - object_id="ZP:0018568", + object_id="ZP:0018569", object_label=None, object_source=None, ancestor_id="UPHENO:0034024", @@ -899,17 +899,17 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=9.08524944639702, - jaccard_similarity=0.3333333333333333, + jaccard_similarity=0.34615384615384615, cosine_similarity=None, dice_similarity=None, - phenodigm_score=1.7402346054863809, + phenodigm_score=1.773384910034319, ), ), "HP:0012378": BestMatch( match_source="HP:0012378", match_source_label="Fatigue (HPO)", - match_target="ZP:0018569", - match_target_label="myeloid cell development absent, abnormal (ZPO)", + match_target="ZP:0018568", + match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", score=1.6836208034928104, match_subsumer=None, match_subsumer_label=None, @@ -917,7 +917,7 @@ def phenotype_explorer_search(): subject_id="HP:0012378", subject_label=None, subject_source=None, - object_id="ZP:0018569", + object_id="ZP:0018568", object_label=None, object_source=None, ancestor_id="UPHENO:0001005", @@ -926,10 +926,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=1.6836208034928104, - jaccard_similarity=0.47058823529411764, + jaccard_similarity=0.4444444444444444, cosine_similarity=None, dice_similarity=None, - phenodigm_score=0.8901079388591847, + phenodigm_score=0.8650294287846346, ), ), }, @@ -1009,8 +1009,8 @@ def phenotype_explorer_search(): "ZP:0100294": TermInfo(id="ZP:0100294", label="visual perception absent, abnormal (ZPO)"), }, object_termset={ - "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), + "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), }, subject_best_matches={ "ZP:0000945": BestMatch( @@ -1099,8 +1099,8 @@ def phenotype_explorer_search(): "HP:0012378": BestMatch( match_source="HP:0012378", match_source_label="Fatigue (HPO)", - match_target="ZP:0000945", - match_target_label="pigment cell quality, abnormal (ZPO)", + match_target="ZP:0100294", + match_target_label="visual perception absent, abnormal (ZPO)", score=1.6836208034928104, match_subsumer=None, match_subsumer_label=None, @@ -1108,7 +1108,7 @@ def phenotype_explorer_search(): subject_id="HP:0012378", subject_label=None, subject_source=None, - object_id="ZP:0000945", + object_id="ZP:0100294", object_label=None, object_source=None, ancestor_id="UPHENO:0001005", @@ -1117,10 +1117,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=1.6836208034928104, - jaccard_similarity=0.42105263157894735, + jaccard_similarity=0.4444444444444444, cosine_similarity=None, dice_similarity=None, - phenodigm_score=0.841957819544251, + phenodigm_score=0.8650294287846346, ), ), }, @@ -1284,8 +1284,8 @@ def phenotype_explorer_search(): "HP:0012378": BestMatch( match_source="HP:0012378", match_source_label="Fatigue (HPO)", - match_target="ZP:0015039", - match_target_label="visual behavior absent, abnormal (ZPO)", + match_target="ZP:0001841", + match_target_label="visual behavior quality, abnormal (ZPO)", score=1.6836208034928104, match_subsumer=None, match_subsumer_label=None, @@ -1293,7 +1293,7 @@ def phenotype_explorer_search(): subject_id="HP:0012378", subject_label=None, subject_source=None, - object_id="ZP:0015039", + object_id="ZP:0001841", object_label=None, object_source=None, ancestor_id="UPHENO:0001005", @@ -1302,10 +1302,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=1.6836208034928104, - jaccard_similarity=0.38095238095238093, + jaccard_similarity=0.47058823529411764, cosine_similarity=None, dice_similarity=None, - phenodigm_score=0.8008616320635836, + phenodigm_score=0.8901079388591847, ), ), }, @@ -1401,8 +1401,8 @@ def phenotype_explorer_search(): "ZP:0021445": TermInfo(id="ZP:0021445", label="gill increased amount, abnormal (ZPO)") }, object_termset={ - "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), + "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), }, subject_best_matches={ "ZP:0021445": BestMatch( @@ -1567,8 +1567,8 @@ def phenotype_explorer_search(): "ZP:0003210": TermInfo(id="ZP:0003210", label="whole organism decreased mobility, abnormal (ZPO)") }, object_termset={ - "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), + "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), }, subject_best_matches={ "ZP:0003210": BestMatch( diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index afbd49ce7..c6a98c8b5 100644 --- a/backend/tests/fixtures/search_response.py +++ b/backend/tests/fixtures/search_response.py @@ -5,7 +5,7 @@ def search_response(): return { "responseHeader": { - "QTime": 0, + "QTime": 2, "params": { "mm": "100%", "q": "fanconi", diff --git a/backend/tests/unit/test_solr_parsers.py b/backend/tests/unit/test_solr_parsers.py index 2875371c2..6d2309ce7 100644 --- a/backend/tests/unit/test_solr_parsers.py +++ b/backend/tests/unit/test_solr_parsers.py @@ -20,6 +20,15 @@ def test_parse_associations(association_response, associations): assert parsed == associations, f"Parsed result is not as expected. Difference: {dict_diff(parsed, associations)}" +def test_parse_associations_compact(association_response, associations_compact): + association_response["response"]["numFound"] = association_response["response"].pop("num_found") + solr_response = SolrQueryResult(**association_response) + parsed = parse_associations(solr_response, compact=True).model_dump() + assert ( + parsed == associations_compact + ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, associations_compact)}" + + def test_parse_association_counts(association_counts_response, association_counts, node): association_counts_response["response"]["numFound"] = association_counts_response["response"].pop("num_found") solr_response = SolrQueryResult(**association_counts_response) diff --git a/frontend/fixtures/associations-compact.json b/frontend/fixtures/associations-compact.json new file mode 100644 index 000000000..d27c6b961 --- /dev/null +++ b/frontend/fixtures/associations-compact.json @@ -0,0 +1,187 @@ +{ + "limit": 20, + "offset": 0, + "total": 4627, + "items": [ + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0001371", + "object_label": "Flexion contracture", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0003458", + "object_label": "EMG: myopathic abnormalities", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0003560", + "object_label": "Muscular dystrophy", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0030095", + "object_label": "Reduced muscle collagen VI", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0001220", + "object_label": "Interphalangeal joint contracture of finger", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0001288", + "object_label": "Gait disturbance", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002355", + "object_label": "Difficulty walking", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002460", + "object_label": "Distal muscle weakness", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0003325", + "object_label": "Limb-girdle muscle weakness", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0003731", + "object_label": "Quadriceps muscle weakness", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0006466", + "object_label": "Ankle flexion contracture", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0009058", + "object_label": "Increased muscle lipid content", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0100490", + "object_label": "Camptodactyly of finger", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0000962", + "object_label": "Hyperkeratosis", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0001073", + "object_label": "Cigarette-paper scars", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0001382", + "object_label": "Joint hypermobility", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002086", + "object_label": "Abnormality of the respiratory system", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002515", + "object_label": "Waddling gait", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002791", + "object_label": "Hypoventilation", + "negated": null + }, + { + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008029", + "subject_label": "Bethlem myopathy", + "predicate": "biolink:has_phenotype", + "object": "HP:0002938", + "object_label": "Lumbar hyperlordosis", + "negated": null + } + ] +} diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json index 9f71ec202..d0524b8dc 100644 --- a/frontend/fixtures/phenotype-explorer-compare.json +++ b/frontend/fixtures/phenotype-explorer-compare.json @@ -75,8 +75,8 @@ "HP:0004325": { "match_source": "HP:0004325", "match_source_label": "Decreased body weight (HPO)", - "match_target": "MP:0002169", - "match_target_label": "no abnormal phenotype detected (MPO)", + "match_target": "MP:0010771", + "match_target_label": "integument phenotype (MPO)", "score": 1.5540019332516637, "match_subsumer": null, "match_subsumer_label": null, @@ -84,7 +84,7 @@ "subject_id": "HP:0004325", "subject_label": null, "subject_source": null, - "object_id": "MP:0002169", + "object_id": "MP:0010771", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001003", @@ -93,10 +93,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.5540019332516637, - "jaccard_similarity": 0.23076923076923078, + "jaccard_similarity": 0.24, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.5988454147360435 + "phenodigm_score": 0.61070489107293 } } }, diff --git a/frontend/fixtures/phenotype-explorer-search.json b/frontend/fixtures/phenotype-explorer-search.json index 9c6dcf5e7..4f17a6e50 100644 --- a/frontend/fixtures/phenotype-explorer-search.json +++ b/frontend/fixtures/phenotype-explorer-search.json @@ -1,14 +1,14 @@ { "items": [ - "{\"subject\":{\"id\":\"ZFIN:ZDB-GENE-990415-269\",\"category\":\"biolink:Gene\",\"name\":\"tpma\",\"full_name\":\"alpha-tropomyosin\",\"deprecated\":null,\"description\":null,\"xref\":[\"NCBIGene:30324\",\"ENSEMBL:ENSDARG00000033683\",\"UniProtKB:P13104\",\"PANTHER:PTHR19269\",\"ZFIN:ZDB-GENE-990415-269\"],\"provided_by\":\"alliance_gene_nodes\",\"in_taxon\":\"NCBITaxon:7955\",\"in_taxon_label\":\"Danio rerio\",\"symbol\":\"tpma\",\"synonym\":[\"TPM1-2 alpha\",\"wu:fb37a09\",\"tm\",\"fb37a09\",\"tropomyosin alpha chain\"],\"uri\":\"https://identifiers.org/zfin/ZDB-GENE-990415-269\",\"namespace\":\"ZFIN\",\"has_phenotype\":[\"ZP:0018569\"],\"has_phenotype_label\":[\"myeloid cell development absent, abnormal\"],\"has_phenotype_closure\":[\"BFO:0000020\",\"UPHENO:0001001\",\"UPHENO:0034024\",\"ZP:0018569\",\"ZP:00000000\",\"UPHENO:0001002\",\"BFO:0000002\",\"UPHENO:0001005\",\"UPHENO:0001003\",\"UPHENO:0078513\",\"ZP:0131284\",\"ZP:0014956\",\"PATO:0000001\",\"BFO:0000001\"],\"has_phenotype_closure_label\":[\"specifically dependent continuant\",\"myeloid cell development absent, abnormal\",\"biological_process quality, abnormal\",\"Zebrafish Phenotype\",\"quality\",\"absent myeloid cell development\",\"Phenotypic abnormality\",\"continuant\",\"abnormal phenotype by ontology source\",\"absent biological_process\",\"entity\",\"phenotype\",\"phenotype by ontology source\",\"hemopoiesis 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(ZPO)\",\"score\":1.6836208034928104,\"match_subsumer\":null,\"match_subsumer_label\":null,\"similarity\":{\"subject_id\":\"HP:0012378\",\"subject_label\":null,\"subject_source\":null,\"object_id\":\"ZP:0001432\",\"object_label\":null,\"object_source\":null,\"ancestor_id\":\"UPHENO:0001005\",\"ancestor_label\":\"abnormal phenotype by ontology source\",\"ancestor_source\":null,\"object_information_content\":null,\"subject_information_content\":null,\"ancestor_information_content\":1.6836208034928104,\"jaccard_similarity\":0.3333333333333333,\"cosine_similarity\":null,\"dice_similarity\":null,\"phenodigm_score\":0.7491374603486355}}},\"average_score\":2.0320941603922114,\"best_score\":2.1482519460253453,\"metric\":\"ancestor_information_content\"}}" ] } diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts index 9834891aa..fc8146a49 100644 --- a/frontend/src/api/model.ts +++ b/frontend/src/api/model.ts @@ -140,6 +140,18 @@ export interface Association { stage_qualifier_closure_label?: string[], }; +export interface CompactAssociation { + category?: string, + subject: string, + /** The name of the subject entity */ + subject_label?: string, + predicate: string, + object: string, + /** The name of the object entity */ + object_label?: string, + negated?: boolean, +}; + export interface AssociationCount extends FacetValue { category?: string, label: string, @@ -165,6 +177,17 @@ export interface AssociationResults extends Results { total: number, }; +export interface CompactAssociationResults extends Results { + /** A collection of items, with the type to be overriden by slot_usage */ + items: CompactAssociation[], + /** number of items to return in a response */ + limit: number, + /** offset into the total number of items */ + offset: number, + /** total number of items matching a query */ + total: number, +}; + export interface AssociationTableResults extends Results { /** A collection of items, with the type to be overriden by slot_usage */ items: DirectionalAssociation[], diff --git a/scripts/generate_fixtures.py b/scripts/generate_fixtures.py index 708e0afd2..bce3dc9d2 100644 --- a/scripts/generate_fixtures.py +++ b/scripts/generate_fixtures.py @@ -9,7 +9,11 @@ from pathlib import Path from monarch_py.api.semsim import _compare, _search -from monarch_py.datamodels.category_enums import AssociationCategory, AssociationPredicate, EntityCategory +from monarch_py.datamodels.category_enums import ( + AssociationCategory, + AssociationPredicate, + EntityCategory, +) from monarch_py.datamodels.model import Association, HistoBin, Node, SearchResult from monarch_py.implementations.solr.solr_implementation import SolrImplementation from monarch_py.implementations.solr.solr_query_utils import ( @@ -253,6 +257,9 @@ def main( if any([backend, frontend, all_fixtures]): print(f"{'-'*120}\n\tGenerating core fixtures...") fixtures["associations"] = si.get_associations(entity=[node_id]) + fixtures["associations-compact"] = si.get_associations( + entity=[node_id], compact=True + ) fixtures["association-counts"] = si.get_association_counts(entity=node_id) fixtures["association-table"] = si.get_association_table( entity=node_id, category=category, offset=0, limit=5 @@ -288,13 +295,13 @@ def main( ) extra_fixtures["association-query-params"] = { "category": [category.value], - "subject": ["TEST:0000001"], + "subject": ["TEST:0000001"], "subject_closure": "TEST:0000003", "subject_category": [EntityCategory.GENE.value], "subject_namespace": "TEST", "subject_taxon": ["NCBITaxon:1111"], "predicate": [AssociationPredicate.CAUSES.value], - "object": ["TEST:0000002"], + "object": ["TEST:0000002"], "object_closure": "TEST:0000004", "object_category": [EntityCategory.DISEASE.value], "object_namespace": "TEST", @@ -302,7 +309,7 @@ def main( "entity": ["TEST:0000005"], "q": "test:q", "offset": 100, - "limit": 100 + "limit": 100, } extra_fixtures["association-query-direct"] = build_association_query( **extra_fixtures["association-query-params"], direct=True