Show association selection as association category (#733)

Change up association table category count outputs to be based on the association category, rather than counterpart category. This can potentially be simplified by just generating labels from the association categories, but for now this PR is going to make a smaller change. Downstream, the UI needs a minor shift in the "sentence" structure of the association table heading/controls.
monarch-initiative · Jun 4, 2024 · 79ff82b · 79ff82b
1 parent a9d9d64
commit 79ff82b
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Showing 21 changed files with 190 additions and 191 deletions.
diff --git a/backend/src/monarch_py/implementations/solr/solr_query_utils.py b/backend/src/monarch_py/implementations/solr/solr_query_utils.py
@@ -52,14 +52,11 @@ def build_association_query(
             query.add_filter_query(" OR ".join([f'object:"{o}" OR object_closure:"{o}"' for o in object]))
     if entity:
         if direct:
-            query.add_filter_query(" OR ".join([f'subject:"{escape(e)}" OR object:"{escape(e)}"' for e in entity]))
+            query.add_filter_query(" OR ".join([f'subject:"{e}" OR object:"{e}"' for e in entity]))
         else:
             query.add_filter_query(
                 " OR ".join(
-                    [
-                        f'subject:"{escape(e)}" OR subject_closure:"{escape(e)}" OR object:"{escape(e)}" OR object_closure:"{escape(e)}"'
-                        for e in entity
-                    ]
+                    [f'subject:"{e}" OR subject_closure:"{e}" OR object:"{e}" OR object_closure:"{e}"' for e in entity]
                 )
             )
     if q:
@@ -91,12 +88,7 @@ def build_association_table_query(
         ]
 
     query = build_association_query(
-        entity=entity,
-        category=[category],
-        q=q,
-        sort=sort,
-        offset=offset,
-        limit=limit,
+        entity=entity, category=[category], q=q, sort=sort, offset=offset, limit=limit, direct=False
     )
     return query
 

diff --git a/backend/src/monarch_py/utils/association_type_mappings.yaml b/backend/src/monarch_py/utils/association_type_mappings.yaml
@@ -1,38 +1,38 @@
-- subject_label: Diseases
-  object_label: Phenotypes
+- subject_label: Disease to Phenotype
+  object_label: Phenotype to Disease
   category: "biolink:DiseaseToPhenotypicFeatureAssociation"
-- subject_label: Genes
-  object_label: Phenotypes
+- subject_label: Gene to Phenotype
+  object_label: Phenotype to Gene
   category: "biolink:GeneToPhenotypicFeatureAssociation"
 - subject_label: Interactions
   object_label: Interactions
   symmetric: true
   category: "biolink:PairwiseGeneToGeneInteraction"
-- subject_label: Genes
-  object_label: Pathways
+- subject_label: Gene to Pathway
+  object_label: Pathway to Gene
   category: "biolink:GeneToPathwayAssociation"
-- subject_label: Genes
-  object_label: Anatomy
+- subject_label: Gene Expression
+  object_label: Gene Expression
   category: "biolink:GeneToExpressionSiteAssociation"
 - subject_label: Orthologs
   object_label: Orthologs
   symmetric: true
   category: "biolink:GeneToGeneHomologyAssociation"
-- subject_label: Chemicals
-  object_label: Pathways
+- subject_label: Chemical to Pathway
+  object_label: Pathway to Chemical
   category: "biolink:ChemicalToPathwayAssociation"
-- subject_label: Genes
-  object_label: Molecular Functions
+- subject_label: Gene to Molecular Function
+  object_label: Molecular Function to Gene
   category: "biolink:MacromolecularMachineToMolecularActivityAssociation"
-- subject_label: Genes
-  object_label: Cellular Components
+- subject_label: Gene to Cellular Component
+  object_label: Cellular Component to Gene
   category: "biolink:MacromolecularMachineToCellularComponentAssociation"
-- subject_label: Genes
-  object_label: Biological Processes
+- subject_label: Gene to Biological Process
+  object_label: Biological Process to Gene
   category: "biolink:MacromolecularMachineToBiologicalProcessAssociation"
-- subject_label: Causal Genes
-  object_label: Causal Diseases
+- subject_label: Causal Gene
+  object_label: Causal Disease
   category: "biolink:CausalGeneToDiseaseAssociation"
-- subject_label: "Correlated Genes"
-  object_label: "Correlated Diseases"
+- subject_label: Correlated Gene
+  object_label: Correlated Disease
   category: "biolink:CorrelatedGeneToDiseaseAssociation"
diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py
@@ -5,8 +5,12 @@
 def association_counts():
     return {
         "items": [
-            {"label": "Phenotypes", "count": 3932, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"},
-            {"label": "Causal Genes", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation"},
-            {"label": "Correlated Genes", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation"},
+            {
+                "label": "Phenotype to Disease",
+                "count": 3932,
+                "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
+            },
+            {"label": "Causal Gene", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation"},
+            {"label": "Correlated Gene", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation"},
         ]
     }
diff --git a/backend/tests/fixtures/association_counts_query.py b/backend/tests/fixtures/association_counts_query.py
@@ -37,7 +37,7 @@ def association_counts_query():
             '(category:"biolink:CorrelatedGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")',
         ],
         "filter_queries": [
-            'subject:"MONDO\\:0020121" OR subject_closure:"MONDO\\:0020121" OR object:"MONDO\\:0020121" OR object_closure:"MONDO\\:0020121"'
+            'subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121" OR object:"MONDO:0020121" OR object_closure:"MONDO:0020121"'
         ],
         "query_fields": None,
         "def_type": "edismax",

diff --git 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": 2,
+            "QTime": 1,
             "params": {
                 "facet.query": [
                     '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
@@ -39,7 +39,7 @@ def association_counts_response():
                 "facet_min_count": "1",
                 "start": "0",
                 "q.op": "AND",
-                "fq": 'subject:"MONDO\\:0020121" OR subject_closure:"MONDO\\:0020121" OR object:"MONDO\\:0020121" OR object_closure:"MONDO\\:0020121"',
+                "fq": 'subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121" OR object:"MONDO:0020121" OR object_closure:"MONDO:0020121"',
                 "rows": "20",
                 "facet": "true",
             },

diff --git a/backend/tests/fixtures/association_query_direct.py b/backend/tests/fixtures/association_query_direct.py
@@ -24,7 +24,7 @@ def association_query_direct():
             "object_taxon:NCBITaxon\\:2222",
             "subject:TEST\\:0000001",
             "object:TEST\\:0000002",
-            'subject:"TEST\\:0000005" OR object:"TEST\\:0000005"',
+            'subject:"TEST:0000005" OR object:"TEST:0000005"',
         ],
         "query_fields": "subject subject_label^2 subject_label_t subject_closure subject_closure_label subject_closure_label_t predicate predicate_t object object_label^2 object_label_t object_closure object_closure_label object_closure_label_t publications has_evidence primary_knowledge_source aggregator_knowledge_source provided_by ",
         "def_type": "edismax",

diff --git a/backend/tests/fixtures/association_query_indirect.py b/backend/tests/fixtures/association_query_indirect.py
@@ -24,7 +24,7 @@ def association_query_indirect():
             "object_taxon:NCBITaxon\\:2222",
             'subject:"TEST:0000001" OR subject_closure:"TEST:0000001"',
             'object:"TEST:0000002" OR object_closure:"TEST:0000002"',
-            'subject:"TEST\\:0000005" OR subject_closure:"TEST\\:0000005" OR object:"TEST\\:0000005" OR object_closure:"TEST\\:0000005"',
+            'subject:"TEST:0000005" OR subject_closure:"TEST:0000005" OR object:"TEST:0000005" OR object_closure:"TEST:0000005"',
         ],
         "query_fields": "subject subject_label^2 subject_label_t subject_closure subject_closure_label subject_closure_label_t predicate predicate_t object object_label^2 object_label_t object_closure object_closure_label object_closure_label_t publications has_evidence primary_knowledge_source aggregator_knowledge_source provided_by ",
         "def_type": "edismax",

diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py
@@ -13,7 +13,7 @@ def association_response():
                 "facet_min_count": "1",
                 "start": "0",
                 "q.op": "AND",
-                "fq": 'subject:"MONDO\\:0020121" OR subject_closure:"MONDO\\:0020121" OR object:"MONDO\\:0020121" OR object_closure:"MONDO\\:0020121"',
+                "fq": 'subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121" OR object:"MONDO:0020121" OR object_closure:"MONDO:0020121"',
                 "rows": "20",
                 "facet": "true",
             },

diff --git a/backend/tests/fixtures/association_table_response.py b/backend/tests/fixtures/association_table_response.py
@@ -5,7 +5,7 @@
 def association_table_response():
     return {
         "responseHeader": {
-            "QTime": 1,
+            "QTime": 0,
             "params": {
                 "mm": "100%",
                 "q": "*:*",
@@ -15,7 +15,7 @@ def association_table_response():
                 "q.op": "AND",
                 "fq": [
                     "category:biolink\\:DiseaseToPhenotypicFeatureAssociation",
-                    'subject:"MONDO\\:0020121" OR subject_closure:"MONDO\\:0020121" OR object:"MONDO\\:0020121" OR object_closure:"MONDO\\:0020121"',
+                    'subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121" OR object:"MONDO:0020121" OR object_closure:"MONDO:0020121"',
                 ],
                 "sort": "frequency_computed_sortable_float desc, evidence_count desc, subject_label asc, predicate asc, object_label asc, primary_knowledge_source asc",
                 "rows": "5",

diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py
@@ -5,7 +5,7 @@
 def autocomplete_response():
     return {
         "responseHeader": {
-            "QTime": 1,
+            "QTime": 0,
             "params": {
                 "mm": "100%",
                 "q": "fanc",

diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py
@@ -66,9 +66,13 @@ def node():
             "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#",
         },
         "association_counts": [
-            {"label": "Phenotypes", "count": 3932, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"},
-            {"label": "Causal Genes", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation"},
-            {"label": "Correlated Genes", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation"},
+            {
+                "label": "Phenotype to Disease",
+                "count": 3932,
+                "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
+            },
+            {"label": "Causal Gene", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation"},
+            {"label": "Correlated Gene", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation"},
         ],
         "node_hierarchy": {
             "super_classes": [