Suggested changes to indices post consult session

CHANGELOG.md

@@ -52,6 +52,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - New SO terms: `sequence_variant` and `coding_transcript_variant`
 - More MEI specific annotation is shown on the variant page
 - Parse and save MANE transcripts info when updating genes in build 38
+- ClinVar submission can now be downloaded as a json file
 - `Mane Select` and `Mane Plus Clinical` badges on Gene page, when available
 - ClinVar submission can now be downloaded as a json file
 - API endpoint to pin variant
@@ -65,6 +66,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Default loglevel up to INFO, making logs with default start easier to read
 - Add XTR region to PAR region definition
 - Diagnoses can be searched on diagnoses page without waiting for load first
+- Optimised indexes to address slow queries
 ### Fixed
 - Removed log info showing hgnc IDs used in variantS search
 - Maintain Matchmaker Exchange and Beacon submission status when a case is re-uploaded

scout/constants/indexes.py

@@ -30,23 +30,15 @@
         ),
     ],
     "variant": [
-        IndexModel(
-            [
-                ("case_id", ASCENDING),
-                ("category", ASCENDING),
-                ("variant_rank", ASCENDING),
-            ],
-            name="caseid_variantrank",
-            background=True,
-        ),
         IndexModel(
             [
                 ("case_id", ASCENDING),
                 ("category", ASCENDING),
                 ("variant_type", ASCENDING),
-                ("rank_score", DESCENDING),
+                ("variant_rank", ASCENDING),
+                ("hgnc_ids", ASCENDING),
             ],
-            name="caseid_category_varianttype_rankscore",
+            name="caseid_category_varianttype_variantrank_hgncids",
             background=True,
         ),
         IndexModel(
@@ -62,11 +54,11 @@
         ),
         IndexModel(
             [
+                ("variant_id", ASCENDING),
                 ("case_id", ASCENDING),
                 ("category", ASCENDING),
-                ("variant_id", ASCENDING),
             ],
-            name="caseid_variantid",
+            name="variantid_caseid_category",
             background=True,
         ),
         IndexModel(