Fix clinvar crdq field names

Author: bpblanken

v03_pipeline/lib/reference_data/queries.py

@@ -33,7 +33,7 @@ def clinvar_path_variants(
     clinvar_field = 'clinvar_mito' if dataset_type == DatasetType.MITO else 'clinvar'
     ht = ht.select_globals()
     ht = ht.select(
-        pathogenic=(
+        is_pathogenic=(
             (
                 ht[clinvar_field].pathogenicity_id
                 >= CLINVAR_PATHOGENICITIES_LOOKUP[CLINVAR_PATH_RANGE[0]]
@@ -43,7 +43,7 @@ def clinvar_path_variants(
                 <= CLINVAR_PATHOGENICITIES_LOOKUP[CLINVAR_PATH_RANGE[1]]
             )
         ),
-        likely_pathogenic=(
+        is_likely_pathogenic=(
             (
                 ht[clinvar_field].pathogenicity_id
                 >= CLINVAR_PATHOGENICITIES_LOOKUP[CLINVAR_LIKELY_PATH_RANGE[0]]
@@ -54,7 +54,7 @@ def clinvar_path_variants(
             )
         ),
     )
-    return ht.filter(ht.pathogenic | ht.likely_pathogenic)
+    return ht.filter(ht.is_pathogenic | ht.is_likely_pathogenic)
 
 
 def gnomad_coding_and_noncoding_variants(

v03_pipeline/lib/tasks/reference_data/updated_cached_reference_dataset_query_test.py

@@ -187,8 +187,8 @@ def test_clinvar(
         def _clinvar_path_variants(table, **_: Any):
             table = table.select_globals()
             return table.select(
-                pathogenic=False,
-                likely_pathogenic=True,
+                is_pathogenic=False,
+                is_likely_pathogenic=True,
             )
 
         mock_crdq_query.side_effect = _clinvar_path_variants
@@ -215,8 +215,8 @@ def _clinvar_path_variants(table, **_: Any):
                         reference_genome='GRCh38',
                     ),
                     alleles=['A', 'C'],
-                    pathogenic=False,
-                    likely_pathogenic=True,
+                    is_pathogenic=False,
+                    is_likely_pathogenic=True,
                 ),
             ],
         )

v03_pipeline/var/test/reference_data/test_clinvar_path_variants_crdq.ht/.README.txt.crc

@@ -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 2024/03/04 17:48:25
+  Written with version 0.2.120-f00f916faf78
+  Created at 2024/03/15 15:45:48