Adds xref to searched fields, plus test (#681)

Adds xref to searched fields, and an integration test to confirm it
monarch-initiative · Apr 23, 2024 · 5173608 · 5173608
1 parent ac4e7b4
commit 5173608
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Showing 9 changed files with 199 additions and 198 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
@@ -294,7 +294,7 @@ def entity_query_fields():
     """
     Fields and boosts used for entity search, includes autocomplete fields and expands upon them beyond pure name fields
     """
-    return f"{autocomplete_query_fields()} description_t"
+    return f"{autocomplete_query_fields()} description_t xref"
 
 
 def association_search_query_fields():

diff --git a/backend/tests/fixtures/autocomplete_query.py b/backend/tests/fixtures/autocomplete_query.py
@@ -12,7 +12,7 @@ def autocomplete_query():
         "facet_fields": [],
         "facet_queries": [],
         "filter_queries": [],
-        "query_fields": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac description_t",
+        "query_fields": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac description_t xref",
         "def_type": "edismax",
         "q_op": "AND",
         "mm": "100%",

diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py
@@ -5,13 +5,13 @@
 def autocomplete_response():
     return {
         "responseHeader": {
-            "QTime": 1,
+            "QTime": 0,
             "params": {
                 "mm": "100%",
                 "q": "fanc",
                 "defType": "edismax",
                 "facet_min_count": "1",
-                "qf": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac description_t",
+                "qf": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac description_t xref",
                 "start": "0",
                 "q.op": "AND",
                 "boost": 'product(if(termfreq(category,"biolink:PhenotypicFeature"),1.1,1),if(termfreq(category,"biolink:Disease"),1.3,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),1.1,1),if(termfreq(deprecated,"true"),0.1,1))',

diff --git a/backend/tests/fixtures/search_query.py b/backend/tests/fixtures/search_query.py
@@ -12,7 +12,7 @@ def search_query():
         "facet_fields": [],
         "facet_queries": [],
         "filter_queries": ["name:*"],
-        "query_fields": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac description_t",
+        "query_fields": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac description_t xref",
         "def_type": "edismax",
         "q_op": "AND",
         "mm": "100%",

diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py
@@ -5,13 +5,13 @@
 def search_response():
     return {
         "responseHeader": {
-            "QTime": 3,
+            "QTime": 2,
             "params": {
                 "mm": "100%",
                 "q": "fanconi",
                 "defType": "edismax",
                 "facet_min_count": "1",
-                "qf": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac description_t",
+                "qf": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac description_t xref",
                 "start": "0",
                 "q.op": "AND",
                 "boost": 'product(if(termfreq(category,"biolink:PhenotypicFeature"),1.1,1),if(termfreq(category,"biolink:Disease"),1.3,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),1.1,1),if(termfreq(deprecated,"true"),0.1,1))',

diff --git a/backend/tests/integration/test_solr_search.py b/backend/tests/integration/test_solr_search.py
@@ -20,6 +20,7 @@
         # Failing because we don't have synonyms coming in from Phenio (!)
         #        "AD16",
         "symphalangism, C. S. Lewis type",
+        "OMIM:301045",  # Confirmation that we load & search xrefs for Mondo
     ],
 )
 def test_search_query_has_some_results(query: str):

diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json
@@ -1,12 +1,12 @@
 {
   "subject_termset": {
-    "MP:0002169": {
-      "id": "MP:0002169",
-      "label": "no abnormal phenotype detected (MPO)"
-    },
     "MP:0010771": {
       "id": "MP:0010771",
       "label": "integument phenotype (MPO)"
+    },
+    "MP:0002169": {
+      "id": "MP:0002169",
+      "label": "no abnormal phenotype detected (MPO)"
     }
   },
   "object_termset": {
@@ -77,16 +77,16 @@
     "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,
       "similarity": {
         "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",
@@ -95,10 +95,10 @@
         "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
       },
       "score_metric": "ancestor_information_content"
     }