Make abstract class an ABC. Add type hints

SACGF · Jan 31, 2025 · 9a6691b · 9a6691b
1 parent 09a4bca
commit 9a6691b
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 2 deletions.
diff --git a/upload/vcf/abstract_bulk_vcf_processor.py b/upload/vcf/abstract_bulk_vcf_processor.py
@@ -1,3 +1,4 @@
+import abc
 import os
 
 import cyvcf2
@@ -10,7 +11,7 @@
 from upload.vcf.sql_copy_files import write_sql_copy_csv
 
 
-class AbstractBulkVCFProcessor:
+class AbstractBulkVCFProcessor(abc.ABC):
     """ The minimum a VCF processor needs to do is
         set max_variant_id and insert multi-allelics so we know what was normalised """
 
@@ -29,6 +30,14 @@ def __init__(self, upload_step, preprocess_vcf_import_info, batch_size=settings.
         self.modified_imported_variants = []
         self.variant_pk_lookup = VariantPKLookup(upload_step.genome_build)
 
+    @abc.abstractmethod
+    def process_entry(self, variant: cyvcf2.Variant):
+        pass
+
+    @abc.abstractmethod
+    def finish(self):
+        pass
+
     @property
     def genome_build(self):
         return self.upload_pipeline.genome_build

diff --git a/upload/vcf/bulk_minimal_vcf_processor.py b/upload/vcf/bulk_minimal_vcf_processor.py
@@ -26,7 +26,7 @@ def get_vcf_importer_version():
                                                             code_git_hash=Git(settings.BASE_DIR).hash)
         return vcf_importer
 
-    def process_entry(self, variant):
+    def process_entry(self, variant: cyvcf2.Variant):
         ref, alt, svlen = vcf_get_ref_alt_svlen(variant)
         variant_coordinate = VariantCoordinate(chrom=variant.CHROM, position=variant.POS, ref=ref, alt=alt, svlen=svlen)
         variant_hash = self.variant_pk_lookup.get_variant_coordinate_hash(variant_coordinate)