Include post-mapped hgvs in variants data csv

Author: sallybg

src/mavedb/lib/score_sets.py

@@ -25,7 +25,6 @@
 from mavedb.lib.mave.utils import is_csv_null
 from mavedb.lib.validation.constants.general import null_values_list
 from mavedb.lib.validation.utilities import is_null as validate_is_null
-from mavedb.lib.variants import get_hgvs_from_post_mapped, is_hgvs_g, is_hgvs_p
 from mavedb.models.contributor import Contributor
 from mavedb.models.controlled_keyword import ControlledKeyword
 from mavedb.models.doi_identifier import DoiIdentifier
@@ -444,6 +443,8 @@ def get_score_set_variants_as_csv(
     if include_post_mapped_hgvs:
         columns.append("post_mapped_hgvs_g")
         columns.append("post_mapped_hgvs_p")
+        columns.append("post_mapped_hgvs_c")
+        columns.append("post_mapped_hgvs_at_assay_level")
         columns.append("vep_functional_consequence")
 
     if include_custom_columns:
@@ -566,17 +567,13 @@ def variant_to_csv_row(
         elif column_key == "accession":
             value = str(variant.urn)
         elif column_key == "post_mapped_hgvs_g":
-            hgvs_str = get_hgvs_from_post_mapped(mapping.post_mapped) if mapping and mapping.post_mapped else None
-            if hgvs_str is not None and is_hgvs_g(hgvs_str):
-                value = hgvs_str
-            else:
-                value = ""
+            value = str(mapping.hgvs_g) if mapping and mapping.hgvs_g else ""
         elif column_key == "post_mapped_hgvs_p":
-            hgvs_str = get_hgvs_from_post_mapped(mapping.post_mapped) if mapping and mapping.post_mapped else None
-            if hgvs_str is not None and is_hgvs_p(hgvs_str):
-                value = hgvs_str
-            else:
-                value = ""
+            value = str(mapping.hgvs_p) if mapping and mapping.hgvs_p else ""
+        elif column_key == "post_mapped_hgvs_c":
+            value = str(mapping.hgvs_c) if mapping and mapping.hgvs_c else ""
+        elif column_key == "post_mapped_hgvs_at_assay_level":
+            value = str(mapping.hgvs_assay_level) if mapping and mapping.hgvs_assay_level else ""
         elif column_key == "vep_functional_consequence":
             vep_functional_consequence = mapping.vep_functional_consequence if mapping else None
             if vep_functional_consequence is not None: