Fixing problem with CNV import (#386)

Closes: #386 Related-Issue: #386 Projected-Results-Impact: none
varfish-org · Mar 11, 2022 · e0bfa14 · e0bfa14
1 parent 2e75c4e
commit e0bfa14
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Showing 2 changed files with 14 additions and 3 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -9,10 +9,13 @@ HEAD (unreleased)
 End-User Summary
 ================
 
+- Fixing problem with CNV import (#386)
+
 Full Change List
 ================
 
 - Adding REST API for generating query shortcuts (#367)
+- Fixing problem with CNV import (#386)
 
 ------
 v1.1.0

diff --git a/importer/models.py b/importer/models.py
@@ -477,7 +477,14 @@ def _clear_old_variant_sets(self, keep_variant_set, table_names):
         )
 
     def _import_table(
-        self, variant_set_info, variant_set, token, path_attr, model_class, default_values=None
+        self,
+        variant_set_info,
+        variant_set,
+        token,
+        path_attr,
+        model_class,
+        default_values=None,
+        no_release=True,
     ):
         default_values = default_values or {}
         before = timezone.now()
@@ -490,7 +497,7 @@ def _import_table(
                     header = inputf.readline().strip()
                     header_arr = header.split("\t")
                     try:
-                        release_idx = header_arr.index("release")
+                        release_idx = None if no_release else header_arr.index("release")
                         case_idx = header_arr.index("case_id")
                         set_idx = header_arr.index("set_id")
                     except ValueError as e:
@@ -511,7 +518,7 @@ def _import_table(
                         if not line:
                             break
                         arr = line.split("\t")
-                        if arr[release_idx] != case_genomebuild:
+                        if release_idx is not None and arr[release_idx] != case_genomebuild:
                             raise RuntimeError(
                                 "Incompatible genome build in %s TSV: %s vs %s from case"
                                 % (token, arr[release_idx], case_genomebuild)
@@ -575,6 +582,7 @@ def _perform_import(self, variant_set, variant_set_info):
                 "SV-gene annotation",
                 "effectfile_set",
                 StructuralVariantGeneAnnotation,
+                no_release=True,
             )
 
     def _post_import(self, variant_set, variant_type):