variant lookup table has sample_type

hail_search/fixtures/GRCh37/SNV_INDEL/lookup.ht/README.txt

@@ -1,3 +1,3 @@
 This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
   Written with version 0.2.128-eead8100a1c1
-  Created at 2024/04/03 17:08:32
+  Created at 2024/08/12 16:34:26

hail_search/fixtures/GRCh38/MITO/lookup.ht/README.txt

@@ -1,3 +1,3 @@
 This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
   Written with version 0.2.128-eead8100a1c1
-  Created at 2024/04/03 15:52:09
+  Created at 2024/08/12 16:46:33

hail_search/fixtures/GRCh38/SNV_INDEL/lookup.ht/README.txt

@@ -1,3 +1,3 @@
 This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
   Written with version 0.2.128-eead8100a1c1
-  Created at 2024/04/03 17:00:55
+  Created at 2024/08/12 17:01:09

hail_search/queries/mito.py

@@ -1,4 +1,4 @@
-import os
+from collections import defaultdict
 
 from aiohttp.web import HTTPNotFound
 import hail as hl
@@ -322,33 +322,30 @@ def _add_project_lookup_data(self, ht, annotation_fields, *args, **kwargs):
                 ).filter(hl.is_defined),
             )).filter(
                 lambda x: x[1].any(hl.is_defined)
-            ).starmap(lambda project_guid, family_indices: (
-                project_guid,
-                hl.dict(family_indices.map(lambda j: (lookup_ht.project_families[project_guid][j], True))),
+            ).starmap(lambda project_key, family_indices: (
+                project_key,
+                hl.dict(family_indices.map(lambda j: (lookup_ht.project_families[project_key][j], True))),
             ))), 1),
         )[0]
 
-        for project_guid, families in variant_projects.items():
-            if os.path.exists(self._get_table_path(f'projects/WES/{project_guid}.ht')):
-                sample_type = 'WES'
-            else:
-                sample_type = 'WGS'
-            for family_guid in families:
-                families[family_guid] = {sample_type: True}
-
         # Variant can be present in the lookup table with only ref calls, so is still not present in any projects
         if not variant_projects:
             raise HTTPNotFound()
 
+        new_variant_projects = defaultdict(lambda: defaultdict(dict))
+        for (project_guid, sample_type), families in variant_projects.items():
+            for family_guid, value in families.items():
+                new_variant_projects[project_guid][family_guid][sample_type] = value
+
         annotation_fields.update({
             'familyGenotypes': lambda r: hl.dict(r.family_entries.map(
                 lambda entries: (entries.first().familyGuid, entries.filter(hl.is_defined).map(self._get_sample_genotype))
             )),
         })
 
-        logger.info(f'Looking up {self.DATA_TYPE} variant in {len(variant_projects)} projects')
+        logger.info(f'Looking up {self.DATA_TYPE} variant in {len(new_variant_projects)} projects')
 
-        return super()._add_project_lookup_data(ht, annotation_fields, project_samples=variant_projects, **kwargs)
+        return super()._add_project_lookup_data(ht, annotation_fields, project_samples=new_variant_projects, **kwargs)
 
     @staticmethod
     def _stat_has_non_ref(s):