use the file.full_path method and fix arguments

Clinical-Genomics · Oct 15, 2024 · 3e592c8 · 3e592c8
1 parent 97560f2
commit 3e592c8
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/cg/meta/upload/gt.py b/cg/meta/upload/gt.py
@@ -1,7 +1,7 @@
 import logging
 from pathlib import Path
 
-from housekeeper.store.models import File, Version
+from housekeeper.store.models import File
 
 from cg.apps.gt import GenotypeAPI
 from cg.apps.housekeeper.hk import HousekeeperAPI
@@ -196,14 +196,15 @@ def _is_variant_file(genotype_file: File):
             FileExtensions.VCF_GZ
         ) or genotype_file.full_path.endswith(FileExtensions.BCF)
 
+    @staticmethod
     def _sort_genotype_files(hk_genotype_files: list[File]) -> File | None:
         """
         Take a list of files and only keep files finishing with .bcf or .vcf.gz
         Returns a single remaining file or raises ValueError if more than one file remains.
         """
         allowed_extensions = (FileExtensions.BCF, FileExtensions.VCF_GZ)
         filtered_files = [
-            file for file in hk_genotype_files if str(file).endswith(allowed_extensions)
+            file for file in hk_genotype_files if file.full_path.endswith(allowed_extensions)
         ]
         if len(filtered_files) > 1:
             raise ValueError(

diff --git a/tests/cli/upload/test_cli_upload_genotype.py b/tests/cli/upload/test_cli_upload_genotype.py
@@ -9,7 +9,6 @@
 from cg.models.cg_config import CGConfig
 from cg.store.store import Store
 
-
 def test_upload_genotype(
     upload_context: CGConfig,
     case_id: str,