From b0d07e703bde7d823602a93a4f1e7c621ef72a25 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Wed, 8 Jul 2026 19:31:10 -0700 Subject: [PATCH 01/12] feat(associations): show all remaining fields in the details modal (#1348) Enrich the association details modal (SectionAssociationDetails.vue) to surface the fields it previously hid: knowledge level, the nested retrieval-source provenance chain (e.g. MEDIC's infores:medic <- infores:dailymed/FDA), aggregator knowledge source, original predicate, qualifiers, frequency data, FDA adverse event level, and negated. Extract the sources JSON parsing into a tested util (parseRetrievalSources). Claude-Session: https://claude.ai/code/session_018c9UddtKsKtm35YNrxHWuL --- .../pages/node/SectionAssociationDetails.vue | 157 ++++++++++++++++++ frontend/src/util/retrievalSources.ts | 26 +++ frontend/unit/retrievalSources.test.ts | 41 +++++ 3 files changed, 224 insertions(+) create mode 100644 frontend/src/util/retrievalSources.ts create mode 100644 frontend/unit/retrievalSources.test.ts diff --git a/frontend/src/pages/node/SectionAssociationDetails.vue b/frontend/src/pages/node/SectionAssociationDetails.vue index bc0c193ac..23822313e 100644 --- a/frontend/src/pages/node/SectionAssociationDetails.vue +++ b/frontend/src/pages/node/SectionAssociationDetails.vue @@ -48,6 +48,14 @@ + + {{ startCase(association.knowledge_level) }} + + {{ association.primary_knowledge_source }} @@ -79,6 +87,42 @@ + + +
+ {{ formatRole(source.resource_role) }}: + {{ source.resource_id }} + + ← {{ source.upstream_resource_ids.join(", ") }} + +
+ + + + + + {{ agg }} + + + {{ association.provided_by_link?.id || association.provided_by }} @@ -97,6 +141,61 @@ + + {{ association.original_predicate }} + + + + +
+ {{ qualifier.label }}: {{ qualifier.value }} +
+ + + + + +
+ Count: {{ association.has_count }} +
+
+ Total: {{ association.has_total }} +
+
+ Percentage: {{ association.has_percentage }} +
+
+ Quotient: {{ association.has_quotient }} +
+ + + + + {{ association.FDA_adverse_event_level }} + + + + Yes + + import { computed, onMounted, watch } from "vue"; +import { startCase } from "lodash"; import type { DirectionalAssociation, Node } from "@/api/model"; import AppDetail from "@/components/AppDetail.vue"; import AppDetails from "@/components/AppDetails.vue"; @@ -127,6 +227,7 @@ import AppPredicateBadge from "@/components/AppPredicateBadge.vue"; import { useSourceVersions } from "@/composables/use-source-versions"; import { scrollTo } from "@/router"; import { getAgentTypeMeta } from "@/util/agentType"; +import { parseRetrievalSources } from "@/util/retrievalSources"; type Props = { /** current node */ @@ -148,6 +249,47 @@ const sourceVersion = computed(() => props.association ? versionForEdge(props.association) : null, ); +/** parse the nested retrieval-source provenance chain (JSON-encoded) */ +const retrievalSources = computed(() => + parseRetrievalSources(props.association?.sources), +); + +/** humanize a retrieval-source role, e.g. "primary_knowledge_source" */ +const formatRole = (role?: string) => (role ? startCase(role) : "Source"); + +/** present qualifier values, preferring labels over raw ids */ +const qualifierRows = computed(() => { + const a = props.association; + const rows: { label: string; value: string }[] = []; + if (!a) return rows; + const add = (label: string, value?: string | null) => { + if (value) rows.push({ label, value }); + }; + add("Frequency", a.frequency_qualifier_label || a.frequency_qualifier); + add("Onset", a.onset_qualifier_label || a.onset_qualifier); + add("Sex", a.sex_qualifier_label || a.sex_qualifier); + add("Stage", a.stage_qualifier_label || a.stage_qualifier); + add( + "Disease context", + a.disease_context_qualifier_label || a.disease_context_qualifier, + ); + add("Object specialization", a.object_specialization_qualifier); + (a.qualifiers ?? []).forEach((qualifier) => add("Qualifier", qualifier)); + return rows; +}); + +/** whether any frequency/count representation is present */ +const hasFrequencyData = computed(() => { + const a = props.association; + return ( + a != null && + (a.has_count != null || + a.has_total != null || + a.has_percentage != null || + a.has_quotient != null) + ); +}); + /** scroll details section into view */ async function scrollIntoView() { scrollTo("#association-details"); @@ -186,4 +328,19 @@ onMounted(scrollIntoView); color: $gray; font-size: 0.9em; } + +.retrieval-source { + display: flex; + flex-wrap: wrap; + align-items: baseline; + gap: 0 0.5em; +} + +.retrieval-source .role { + color: $gray; +} + +.retrieval-source .upstream { + color: $gray; +} diff --git a/frontend/src/util/retrievalSources.ts b/frontend/src/util/retrievalSources.ts new file mode 100644 index 000000000..2d49423cc --- /dev/null +++ b/frontend/src/util/retrievalSources.ts @@ -0,0 +1,26 @@ +export type RetrievalSource = { + resource_id?: string; + resource_role?: string; + upstream_resource_ids?: string[]; +}; + +/** + * Parse the `sources` field of an association into a flat list of + * retrieval-source records. Each entry may be a JSON-encoded string holding an + * array of records (as the API serializes it); malformed entries are skipped. + */ +export const parseRetrievalSources = ( + sources?: string[] | null, +): RetrievalSource[] => { + const out: RetrievalSource[] = []; + for (const entry of sources ?? []) { + try { + const parsed = typeof entry === "string" ? JSON.parse(entry) : entry; + if (Array.isArray(parsed)) out.push(...parsed); + else if (parsed) out.push(parsed); + } catch { + /* skip unparseable source entries */ + } + } + return out; +}; diff --git a/frontend/unit/retrievalSources.test.ts b/frontend/unit/retrievalSources.test.ts new file mode 100644 index 000000000..83e9b67ab --- /dev/null +++ b/frontend/unit/retrievalSources.test.ts @@ -0,0 +1,41 @@ +import { expect, test } from "vitest"; +import { parseRetrievalSources } from "@/util/retrievalSources"; + +test("parses a MEDIC-style nested retrieval-source chain", () => { + /** the API serializes `sources` as a list holding one JSON-encoded array */ + const sources = [ + JSON.stringify([ + { + resource_id: "infores:medic", + resource_role: "primary_knowledge_source", + upstream_resource_ids: ["infores:dailymed"], + }, + { + resource_id: "infores:dailymed", + resource_role: "supporting_data_source", + upstream_resource_ids: null, + }, + ]), + ]; + const parsed = parseRetrievalSources(sources); + expect(parsed).toHaveLength(2); + expect(parsed[0].resource_id).toBe("infores:medic"); + expect(parsed[0].resource_role).toBe("primary_knowledge_source"); + expect(parsed[0].upstream_resource_ids).toEqual(["infores:dailymed"]); + expect(parsed[1].resource_role).toBe("supporting_data_source"); +}); + +test("returns empty for missing or empty sources", () => { + expect(parseRetrievalSources(undefined)).toEqual([]); + expect(parseRetrievalSources(null)).toEqual([]); + expect(parseRetrievalSources([])).toEqual([]); +}); + +test("skips unparseable entries without throwing", () => { + const parsed = parseRetrievalSources([ + "not json", + JSON.stringify([{ resource_id: "infores:ctd" }]), + ]); + expect(parsed).toHaveLength(1); + expect(parsed[0].resource_id).toBe("infores:ctd"); +}); From d366da9a7715ed156ec6468d087c881172b9167c Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Thu, 9 Jul 2026 16:35:07 -0700 Subject: [PATCH 02/12] feat(associations): merged MEDIC + CTD drug-indications section (#1348) Replace the hidden single-category "Medical Action" mapping with a merged "drug_indications" section built on the flexible enabler: it combines MEDIC (biolink:treats) and CTD (biolink:treats_or_applied_or_studied_to_treat), which carry different association categories, via the multivalued category criterion (no ingest change needed). Shown as "Indications" on a drug/chemical page and "Treatments" on a disease/phenotype page. Merged filter verified vs api-beta (medic 6619 + ctd 19139 = 25758). Un-hid the section (cleared the now-stale HIDDEN_CATEGORIES entry, since sections key on `key` not category). Fixtures regenerated. The modal field enrichment rides along (cherry-picked). Claude-Session: https://claude.ai/code/session_018c9UddtKsKtm35YNrxHWuL --- .../utils/association_type_mappings.yaml | 21 ++++++++++++++----- backend/tests/fixtures/association_counts.py | 2 +- .../fixtures/association_counts_query.py | 2 +- .../fixtures/association_counts_response.py | 2 +- .../composables/use-association-categories.ts | 5 ++--- 5 files changed, 21 insertions(+), 11 deletions(-) diff --git a/backend/src/monarch_py/utils/association_type_mappings.yaml b/backend/src/monarch_py/utils/association_type_mappings.yaml index 1e4e70d94..ff9c13bc2 100644 --- a/backend/src/monarch_py/utils/association_type_mappings.yaml +++ b/backend/src/monarch_py/utils/association_type_mappings.yaml @@ -80,11 +80,22 @@ category: "biolink:GenotypeToDiseaseAssociation" subject_category: "biolink:Genotype" object_category: "biolink:Disease" -- subject_label: Medical Action - object_label: Medical Action - category: "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation" - # Note: subject_category/object_category omitted - this association uses disease_context_qualifier - # and requires special 1-hop handling that isn't yet implemented in the entity grid +# Drug indications / treatments. Combines MEDIC (biolink:treats, FDA-approved, +# text-mined) and CTD (biolink:treats_or_applied_or_studied_to_treat, curated), +# which carry different association categories, into one section via the +# multivalued category criterion. Shown as "Indications" on a drug/chemical page +# and "Treatments" on a disease/phenotype page. +- key: drug_indications + subject_label: Indications + object_label: Treatments + category: + - "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation" + - "biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation" + subject_category: + - "biolink:ChemicalEntity" + object_category: + - "biolink:Disease" + - "biolink:PhenotypicFeature" - subject_label: Variant to Phenotype object_label: Variant to Phenotype category: "biolink:VariantToPhenotypicFeatureAssociation" diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py index c26f39fd8..4d0c4920f 100644 --- a/backend/tests/fixtures/association_counts.py +++ b/backend/tests/fixtures/association_counts.py @@ -3,4 +3,4 @@ @pytest.fixture def association_counts(): - return {'items': [{'label': 'Disease Model', 'count': 246, 'key': 'biolink:GenotypeToDiseaseAssociation', 'category': 'biolink:GenotypeToDiseaseAssociation', 'count_direct': 14, 'count_with_orthologs': None}, {'label': 'Disease to Phenotype', 'count': 4247, 'key': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Causal Gene', 'count': 133, 'key': 'biolink:CausalGeneToDiseaseAssociation', 'category': 'biolink:CausalGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Correlated Gene', 'count': 156, 'key': 'biolink:CorrelatedGeneToDiseaseAssociation', 'category': 'biolink:CorrelatedGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Variant to Disease', 'count': 701, 'key': 'biolink:VariantToDiseaseAssociation', 'category': 'biolink:VariantToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Medical Action', 'count': 6, 'key': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'category': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Cases', 'count': 136, 'key': 'biolink:CaseToDiseaseAssociation', 'category': 'biolink:CaseToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}]} + return {'items': [{'label': 'Disease Model', 'count': 246, 'key': 'biolink:GenotypeToDiseaseAssociation', 'category': 'biolink:GenotypeToDiseaseAssociation', 'count_direct': 14, 'count_with_orthologs': None}, {'label': 'Disease to Phenotype', 'count': 4247, 'key': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Causal Gene', 'count': 133, 'key': 'biolink:CausalGeneToDiseaseAssociation', 'category': 'biolink:CausalGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Correlated Gene', 'count': 156, 'key': 'biolink:CorrelatedGeneToDiseaseAssociation', 'category': 'biolink:CorrelatedGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Variant to Disease', 'count': 701, 'key': 'biolink:VariantToDiseaseAssociation', 'category': 'biolink:VariantToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Treatments', 'count': 6, 'key': 'drug_indications', 'category': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Cases', 'count': 136, 'key': 'biolink:CaseToDiseaseAssociation', 'category': 'biolink:CaseToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}]} diff --git a/backend/tests/fixtures/association_counts_query.py b/backend/tests/fixtures/association_counts_query.py index c55c0ebcc..e27136bc4 100644 --- a/backend/tests/fixtures/association_counts_query.py +++ b/backend/tests/fixtures/association_counts_query.py @@ -3,4 +3,4 @@ @pytest.fixture def association_counts_query(): - return {'q': '*:*', 'rows': 20, 'start': 0, 'facet': True, 'facet_min_count': 1, 'facet_fields': [], 'facet_queries': ['(category:"biolink:DiseaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Disease" AND object_category:"biolink:PhenotypicFeature") AND subject:"MONDO:0020121"', '(category:"biolink:GeneToPhenotypicFeatureAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:PhenotypicFeature") AND subject:"MONDO:0020121"', '(category:"biolink:PairwiseGeneToGeneInteraction" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND subject:"MONDO:0020121"', '(category:"biolink:GeneToPathwayAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Pathway") AND subject:"MONDO:0020121"', '(category:"biolink:GeneToExpressionSiteAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:AnatomicalEntity") AND subject:"MONDO:0020121"', '(category:"biolink:GeneToGeneHomologyAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND subject:"MONDO:0020121"', '(category:"biolink:ChemicalToPathwayAssociation" AND subject_category:"biolink:ChemicalEntity" AND object_category:"biolink:Pathway") AND subject:"MONDO:0020121"', '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:MolecularActivity") AND subject:"MONDO:0020121"', '(category:"biolink:MacromolecularMachineToCellularComponentAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:CellularComponent") AND subject:"MONDO:0020121"', '(category:"biolink:MacromolecularMachineToBiologicalProcessAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:BiologicalProcess") AND subject:"MONDO:0020121"', '(category:"biolink:CausalGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND subject:"MONDO:0020121"', '(category:"biolink:CorrelatedGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND subject:"MONDO:0020121"', '(category:"biolink:VariantToGeneAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Gene") AND subject:"MONDO:0020121"', '(category:"biolink:VariantToDiseaseAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Disease") AND subject:"MONDO:0020121"', '(category:"biolink:GenotypeToPhenotypicFeatureAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:PhenotypicFeature") AND subject:"MONDO:0020121"', '(category:"biolink:GenotypeToDiseaseAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Disease") AND subject:"MONDO:0020121"', '(category:"biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation") AND subject:"MONDO:0020121"', '(category:"biolink:VariantToPhenotypicFeatureAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:PhenotypicFeature") AND subject:"MONDO:0020121"', '(category:"biolink:GenotypeToGeneAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Gene") AND subject:"MONDO:0020121"', '(category:"biolink:GenotypeToVariantAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:SequenceVariant") AND subject:"MONDO:0020121"', '(category:"biolink:CaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:PhenotypicFeature") AND subject:"MONDO:0020121"', '(category:"biolink:CaseToDiseaseAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Disease") AND subject:"MONDO:0020121"', '(category:"biolink:CaseToGeneAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Gene") AND subject:"MONDO:0020121"', '(category:"biolink:DiseaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Disease" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GeneToPhenotypicFeatureAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:PairwiseGeneToGeneInteraction" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GeneToPathwayAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Pathway") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GeneToExpressionSiteAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:AnatomicalEntity") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GeneToGeneHomologyAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:ChemicalToPathwayAssociation" AND subject_category:"biolink:ChemicalEntity" AND object_category:"biolink:Pathway") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:MolecularActivity") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToCellularComponentAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:CellularComponent") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToBiologicalProcessAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:BiologicalProcess") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:CausalGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:CorrelatedGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:VariantToGeneAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:VariantToDiseaseAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GenotypeToPhenotypicFeatureAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GenotypeToDiseaseAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:VariantToPhenotypicFeatureAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GenotypeToGeneAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GenotypeToVariantAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:SequenceVariant") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:CaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:CaseToDiseaseAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:CaseToGeneAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:DiseaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Disease" AND object_category:"biolink:PhenotypicFeature") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GeneToPhenotypicFeatureAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:PhenotypicFeature") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:PairwiseGeneToGeneInteraction" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GeneToPathwayAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Pathway") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GeneToExpressionSiteAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:AnatomicalEntity") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GeneToGeneHomologyAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:ChemicalToPathwayAssociation" AND subject_category:"biolink:ChemicalEntity" AND object_category:"biolink:Pathway") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:MolecularActivity") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToCellularComponentAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:CellularComponent") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToBiologicalProcessAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:BiologicalProcess") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:CausalGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:CorrelatedGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:VariantToGeneAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Gene") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:VariantToDiseaseAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Disease") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToPhenotypicFeatureAssociation" AND 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subject_closure:"MONDO:0020121")', '(category:"biolink:VariantToPhenotypicFeatureAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:PhenotypicFeature") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToGeneAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Gene") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToVariantAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:SequenceVariant") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:CaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:PhenotypicFeature") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:CaseToDiseaseAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Disease") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:CaseToGeneAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Gene") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:DiseaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Disease" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GeneToPhenotypicFeatureAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:PairwiseGeneToGeneInteraction" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GeneToPathwayAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Pathway") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GeneToExpressionSiteAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:AnatomicalEntity") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GeneToGeneHomologyAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:ChemicalToPathwayAssociation" AND subject_category:"biolink:ChemicalEntity" AND object_category:"biolink:Pathway") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:MolecularActivity") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToCellularComponentAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:CellularComponent") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToBiologicalProcessAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:BiologicalProcess") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:CausalGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:CorrelatedGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:VariantToGeneAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:VariantToDiseaseAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToPhenotypicFeatureAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToDiseaseAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '((category:"biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation" OR category:"biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation") AND subject_category:"biolink:ChemicalEntity" AND (object_category:"biolink:Disease" OR object_category:"biolink:PhenotypicFeature")) AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:VariantToPhenotypicFeatureAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToGeneAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToVariantAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:SequenceVariant") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:CaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:CaseToDiseaseAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:CaseToGeneAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")'], 'filter_queries': ['subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121" OR object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121"'], 'facet_mincount': 1, 'query_fields': None, 'def_type': 'edismax', 'q_op': 'AND', 'mm': '100%', 'boost': None, 'sort': None, 'hl': False} diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index ed8cab2d4..6028472c2 100644 --- a/backend/tests/fixtures/association_counts_response.py +++ b/backend/tests/fixtures/association_counts_response.py @@ -3,4 +3,4 @@ @pytest.fixture def association_counts_response(): - return {'responseHeader': {'QTime': 2, 'params': {'facet.query': ['(category:"biolink:DiseaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Disease" AND object_category:"biolink:PhenotypicFeature") AND subject:"MONDO:0020121"', '(category:"biolink:GeneToPhenotypicFeatureAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:PhenotypicFeature") AND subject:"MONDO:0020121"', '(category:"biolink:PairwiseGeneToGeneInteraction" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND subject:"MONDO:0020121"', '(category:"biolink:GeneToPathwayAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Pathway") AND subject:"MONDO:0020121"', '(category:"biolink:GeneToExpressionSiteAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:AnatomicalEntity") AND subject:"MONDO:0020121"', '(category:"biolink:GeneToGeneHomologyAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND subject:"MONDO:0020121"', '(category:"biolink:ChemicalToPathwayAssociation" AND subject_category:"biolink:ChemicalEntity" AND object_category:"biolink:Pathway") AND subject:"MONDO:0020121"', '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:MolecularActivity") AND subject:"MONDO:0020121"', '(category:"biolink:MacromolecularMachineToCellularComponentAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:CellularComponent") AND subject:"MONDO:0020121"', '(category:"biolink:MacromolecularMachineToBiologicalProcessAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:BiologicalProcess") AND subject:"MONDO:0020121"', '(category:"biolink:CausalGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND subject:"MONDO:0020121"', '(category:"biolink:CorrelatedGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND subject:"MONDO:0020121"', '(category:"biolink:VariantToGeneAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Gene") AND subject:"MONDO:0020121"', '(category:"biolink:VariantToDiseaseAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Disease") AND subject:"MONDO:0020121"', '(category:"biolink:GenotypeToPhenotypicFeatureAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:PhenotypicFeature") AND subject:"MONDO:0020121"', '(category:"biolink:GenotypeToDiseaseAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Disease") AND subject:"MONDO:0020121"', '(category:"biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation") AND subject:"MONDO:0020121"', '(category:"biolink:VariantToPhenotypicFeatureAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:PhenotypicFeature") AND subject:"MONDO:0020121"', '(category:"biolink:GenotypeToGeneAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Gene") AND subject:"MONDO:0020121"', '(category:"biolink:GenotypeToVariantAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:SequenceVariant") AND subject:"MONDO:0020121"', '(category:"biolink:CaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:PhenotypicFeature") AND subject:"MONDO:0020121"', '(category:"biolink:CaseToDiseaseAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Disease") AND subject:"MONDO:0020121"', '(category:"biolink:CaseToGeneAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Gene") AND subject:"MONDO:0020121"', '(category:"biolink:DiseaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Disease" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GeneToPhenotypicFeatureAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:PairwiseGeneToGeneInteraction" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GeneToPathwayAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Pathway") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GeneToExpressionSiteAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:AnatomicalEntity") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GeneToGeneHomologyAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:ChemicalToPathwayAssociation" AND subject_category:"biolink:ChemicalEntity" AND object_category:"biolink:Pathway") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:MolecularActivity") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToCellularComponentAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:CellularComponent") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToBiologicalProcessAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:BiologicalProcess") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:CausalGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:CorrelatedGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:VariantToGeneAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:VariantToDiseaseAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GenotypeToPhenotypicFeatureAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GenotypeToDiseaseAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:VariantToPhenotypicFeatureAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GenotypeToGeneAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:GenotypeToVariantAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:SequenceVariant") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:CaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:CaseToDiseaseAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:CaseToGeneAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121")', '(category:"biolink:DiseaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Disease" AND object_category:"biolink:PhenotypicFeature") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GeneToPhenotypicFeatureAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:PhenotypicFeature") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:PairwiseGeneToGeneInteraction" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GeneToPathwayAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Pathway") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GeneToExpressionSiteAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:AnatomicalEntity") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GeneToGeneHomologyAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:ChemicalToPathwayAssociation" AND subject_category:"biolink:ChemicalEntity" AND object_category:"biolink:Pathway") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:MolecularActivity") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToCellularComponentAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:CellularComponent") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:MacromolecularMachineToBiologicalProcessAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:BiologicalProcess") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:CausalGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:CorrelatedGeneToDiseaseAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Disease") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:VariantToGeneAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Gene") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:VariantToDiseaseAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:Disease") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToPhenotypicFeatureAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:PhenotypicFeature") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToDiseaseAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Disease") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:VariantToPhenotypicFeatureAssociation" AND subject_category:"biolink:SequenceVariant" AND object_category:"biolink:PhenotypicFeature") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToGeneAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:Gene") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:GenotypeToVariantAssociation" AND subject_category:"biolink:Genotype" AND object_category:"biolink:SequenceVariant") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:CaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:PhenotypicFeature") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:CaseToDiseaseAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Disease") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:CaseToGeneAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Gene") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', '(category:"biolink:DiseaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Disease" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GeneToPhenotypicFeatureAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:PairwiseGeneToGeneInteraction" AND subject_category:"biolink:Gene" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GeneToPathwayAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:Pathway") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")', '(category:"biolink:GeneToExpressionSiteAssociation" AND subject_category:"biolink:Gene" AND object_category:"biolink:AnatomicalEntity") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR 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disease_context_qualifier_closure:"MONDO:0020121")': 0, '(category:"biolink:CaseToPhenotypicFeatureAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:PhenotypicFeature") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")': 0, '(category:"biolink:CaseToDiseaseAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Disease") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")': 136, '(category:"biolink:CaseToGeneAssociation" AND subject_category:"biolink:Case" AND object_category:"biolink:Gene") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR disease_context_qualifier:"MONDO:0020121" OR disease_context_qualifier_closure:"MONDO:0020121")': 0}}, 'highlighting': {}} diff --git a/frontend/src/composables/use-association-categories.ts b/frontend/src/composables/use-association-categories.ts index 906ef6707..6b3da703b 100644 --- a/frontend/src/composables/use-association-categories.ts +++ b/frontend/src/composables/use-association-categories.ts @@ -3,9 +3,8 @@ import { startCase } from "lodash"; import { TRAVERSE_ORTHOLOG_CATEGORIES } from "@/api/associations"; import type { Node } from "@/api/model"; -const HIDDEN_CATEGORIES = new Set([ - "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation", -]); +/** section keys (ac.key) to hide from node pages */ +const HIDDEN_CATEGORIES = new Set([]); export function useAssociationCategories(node: Node) { const options = computed(() => { From 57f5a2be86c64f95829426c1d5931c1749430a54 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Fri, 10 Jul 2026 11:40:52 -0700 Subject: [PATCH 03/12] docs: add medic ingest to the source docs manifest Register monarch-initiative/medic-ingest so `make fetch-docs` generates the /Sources/medic/ page, fixing the association "Provided By" link for MEDIC edges (.../Sources/medic/), which 404s without a manifest entry. Claude-Session: https://claude.ai/code/session_018c9UddtKsKtm35YNrxHWuL --- docs/sources-manifest.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/sources-manifest.yaml b/docs/sources-manifest.yaml index 44125e734..fab869a8f 100644 --- a/docs/sources-manifest.yaml +++ b/docs/sources-manifest.yaml @@ -45,6 +45,9 @@ sources: - repo: monarch-initiative/maxo-annotation-ingest branch: main filename: maxo.md + - repo: monarch-initiative/medic-ingest + branch: main + filename: medic.md - repo: monarch-initiative/mmrrc-ingest branch: main filename: mmrrc.md From 45b06900cb17e18398bcf2a01865119676b534e3 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Fri, 10 Jul 2026 14:04:18 -0700 Subject: [PATCH 04/12] test: update hidden-category test for un-hidden drug indications This PR clears HIDDEN_CATEGORIES to un-hide the drug-indications section, so the "filters out hidden categories" test (which asserted that category is hidden) no longer holds. Update it to assert the category now renders, keyed on `key`. Claude-Session: https://claude.ai/code/session_018c9UddtKsKtm35YNrxHWuL --- frontend/unit/useAssociationCategories.test.ts | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/frontend/unit/useAssociationCategories.test.ts b/frontend/unit/useAssociationCategories.test.ts index e5d6f071b..25ec4fe66 100644 --- a/frontend/unit/useAssociationCategories.test.ts +++ b/frontend/unit/useAssociationCategories.test.ts @@ -9,7 +9,7 @@ type AssocCount = { }; type TestNode = { association_counts?: AssocCount[] }; -const hidden = +const drugIndications = "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"; const causal = "biolink:CausalGeneToDiseaseAssociation"; const genePh = "biolink:GeneToPhenotypicFeatureAssociation"; @@ -31,15 +31,20 @@ describe("useAssociationCategories", () => { ]); }); - it("filters out hidden categories", () => { + it("no longer hides the drug-indication category (now shown, keyed on key)", () => { const node: TestNode = { association_counts: [ - { category: hidden, label: "should hide", count: 1 }, + { + key: "drug_indications", + category: drugIndications, + label: "Treatments", + count: 1, + }, { category: "Y", label: "keep me", count: 2 }, ], }; const { options } = useAssociationCategories(node as any); - expect(options.value.map((o) => o.id)).toEqual(["Y"]); + expect(options.value.map((o) => o.id)).toEqual(["drug_indications", "Y"]); }); it("keeps special order: causal before gene→phenotype", () => { From ee196e8c66c70536bbaf0d49c60777ba160a4e86 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Fri, 10 Jul 2026 15:03:29 -0700 Subject: [PATCH 05/12] feat(associations): predicate filter for the drug-indications section The merged drug-indications section mixes biolink:treats (MEDIC/FDA) and biolink:treats_or_applied_or_studied_to_treat (CTD). Add a per-section "Filter by relationship" dropdown that scopes the table by predicate, mirroring the existing taxon filter: the table facets on predicate, emits the options, and selected predicates become filter_queries. Gated by predicateFilterConfig (currently just drug_indications) and shown only when >1 predicate is present. Verified: /entity/MONDO:0005148/drug_indications = 97, filtered to treats = 46, to treats_or_applied_or_studied_to_treat = 51. Claude-Session: https://claude.ai/code/session_018c9UddtKsKtm35YNrxHWuL --- frontend/src/pages/node/AssociationsTable.vue | 73 +++++++++++++++++-- .../src/pages/node/SectionAssociations.vue | 52 +++++++++++++ frontend/src/util/predicateFilterConfig.ts | 30 ++++++++ frontend/unit/predicateFilterConfig.test.ts | 33 +++++++++ 4 files changed, 180 insertions(+), 8 deletions(-) create mode 100644 frontend/src/util/predicateFilterConfig.ts create mode 100644 frontend/unit/predicateFilterConfig.test.ts diff --git a/frontend/src/pages/node/AssociationsTable.vue b/frontend/src/pages/node/AssociationsTable.vue index 9d4cb52b9..d3d74461d 100644 --- a/frontend/src/pages/node/AssociationsTable.vue +++ b/frontend/src/pages/node/AssociationsTable.vue @@ -232,6 +232,10 @@ import { import { getBreadcrumbs } from "@/pages/node/AssociationsSummary.vue"; import SectionAssociationDetails from "@/pages/node/SectionAssociationDetails.vue"; import { getAgentTypeMeta } from "@/util/agentType"; +import { + formatPredicate, + isPredicateFilterable, +} from "@/util/predicateFilterConfig"; import { taxonFieldFor } from "@/util/taxonFilterConfig"; import { fieldFor } from "@/util/typeConfig"; @@ -246,6 +250,8 @@ type Props = { search: string; /** selected taxon labels to filter by */ taxonFilters?: string[]; + /** selected predicates to filter by */ + predicateFilters?: string[]; }; const props = defineProps(); @@ -264,6 +270,10 @@ const emit = defineEmits<{ e: "taxon-options", options: { id: string; label: string; count: number }[], ): void; + ( + e: "predicate-options", + options: { id: string; label: string; count: number }[], + ): void; }>(); const shouldTraverseOrthologs = computed(() => @@ -273,16 +283,33 @@ const shouldTraverseOrthologs = computed(() => /** the single taxon field to facet/filter on for this category */ const taxonField = computed(() => taxonFieldFor(props.category.id)); -/** facet fields to request when taxon filtering is enabled */ -const facetFields = computed(() => - taxonField.value ? [taxonField.value] : undefined, +/** whether this section offers a predicate filter */ +const predicateFilterable = computed(() => + isPredicateFilterable(props.category.id), ); -/** build filter queries from selected taxon labels */ +/** facet fields to request for the enabled filters */ +const facetFields = computed(() => { + const fields: string[] = []; + if (taxonField.value) fields.push(taxonField.value); + if (predicateFilterable.value) fields.push("predicate"); + return fields.length ? fields : undefined; +}); + +/** build filter queries from the selected taxon and predicate filters */ const filterQueries = computed(() => { - if (!props.taxonFilters?.length || !taxonField.value) return undefined; - const clauses = props.taxonFilters.map((t) => `${taxonField.value}:"${t}"`); - return [clauses.join(" OR ")]; + const queries: string[] = []; + if (props.taxonFilters?.length && taxonField.value) { + queries.push( + props.taxonFilters.map((t) => `${taxonField.value}:"${t}"`).join(" OR "), + ); + } + if (props.predicateFilters?.length) { + queries.push( + props.predicateFilters.map((p) => `predicate:"${p}"`).join(" OR "), + ); + } + return queries.length ? queries : undefined; }); /** track last emitted taxon options to avoid redundant emits */ @@ -313,6 +340,33 @@ function emitTaxonOptions(facetFieldsData?: FacetField[]) { emit("taxon-options", options); } +/** track last emitted predicate options to avoid redundant emits */ +let lastPredicateOptionsKey = ""; + +/** extract predicate options from the predicate facet for this category */ +function emitPredicateOptions(facetFieldsData?: FacetField[]) { + if (!predicateFilterable.value || !facetFieldsData) return; + + /** see emitTaxonOptions: only build options from unfiltered queries */ + if (props.predicateFilters?.length) return; + + const field = facetFieldsData.find((f) => f.label === "predicate"); + const options = (field?.facet_values ?? []) + .filter((fv) => fv.label) + .map((fv) => ({ + id: fv.label, + label: formatPredicate(fv.label), + count: fv.count ?? 0, + })) + .sort((a, b) => b.count - a.count); + + const key = JSON.stringify(options); + if (key === lastPredicateOptionsKey) return; + lastPredicateOptionsKey = key; + + emit("predicate-options", options); +} + function openModal(association: DirectionalAssociation) { selectedAssociation.value = association; showModal.value = true; @@ -606,7 +660,10 @@ watch( props.direct.id === "true" ? directData.value?.facet_fields : allData.value?.facet_fields, - (facetFieldsData) => emitTaxonOptions(facetFieldsData), + (facetFieldsData) => { + emitTaxonOptions(facetFieldsData); + emitPredicateOptions(facetFieldsData); + }, { immediate: true }, ); diff --git a/frontend/src/pages/node/SectionAssociations.vue b/frontend/src/pages/node/SectionAssociations.vue index df79f3b53..61945bf7c 100644 --- a/frontend/src/pages/node/SectionAssociations.vue +++ b/frontend/src/pages/node/SectionAssociations.vue @@ -71,6 +71,24 @@ @change="(value) => onTaxonFilterChange(String(category.id), value)" /> + +
@@ -127,6 +149,7 @@ import { useAssociationCategories } from "@/composables/use-association-categori import AssociationsTable from "@/pages/node/AssociationsTable.vue"; import SectionCasePhenotypeGrid from "@/pages/node/SectionCasePhenotypeGrid.vue"; import SectionPathograph from "@/pages/node/SectionPathograph.vue"; +import { isPredicateFilterable } from "@/util/predicateFilterConfig"; import { sectionTitle } from "@/util/sectionTitles"; import { tabLabel } from "@/util/tabText"; import { isTaxonFilterable } from "@/util/taxonFilterConfig"; @@ -180,6 +203,35 @@ const selectedTaxonLabels = (categoryId: string): string[] => { return selected.map((opt) => opt.id); }; +/** predicate filter state per category (mirrors the taxon filter) */ +const predicateOptionsByCategory = ref>({}); +const selectedPredicatesByCategory = ref>( + {}, +); + +const onPredicateOptions = ( + categoryId: string, + options: { id: string; label: string; count: number }[], +) => { + predicateOptionsByCategory.value[categoryId] = options; +}; + +const onPredicateFilterChange = ( + categoryId: string, + value: MultiSelectOptions, +) => { + selectedPredicatesByCategory.value[categoryId] = value; +}; + +/** selected predicate ids to pass to AssociationsTable (empty = no filter) */ +const selectedPredicateIds = (categoryId: string): string[] => { + const selected = selectedPredicatesByCategory.value[categoryId]; + const allOptions = predicateOptionsByCategory.value[categoryId]; + if (!selected || !allOptions || selected.length === 0) return []; + if (selected.length === allOptions.length) return []; + return selected.map((opt) => opt.id); +}; + const { options: categoryOptions } = useAssociationCategories(props.node); // parent