do not erase kegg while linking eggnog for virgo

backend/metagenedb/apps/catalog/management/commands/commons/handle_functions.py

@@ -9,6 +9,7 @@ logger = logging.getLogger(__name__)
 
 
 class HandleFunctions:
+    FUN_SOURCE_TO_DELETE = ['kegg', 'eggnog']  # links to get rid of everytime
 
     def _build_function_mapping(self, source):
         logger.info("Building local mapping for %s function...", source)
@@ -67,11 +68,15 @@ class HandleFunctions:
                 mapping.append(GeneFunction(gene=genes[gene_id], function=function))
         return mapping
 
+    def _delete_previous_annotations(self, genes):
+        for function_source in self.FUN_SOURCE_TO_DELETE:
+            GeneFunction.objects.filter(gene__in=genes.values(), function__source=function_source).delete()
+
     def link_genes_to_functions(self, functions):
         cleaned_functions = self._clean_functions(functions)
         genes = Gene.objects.in_bulk(cleaned_functions.keys(), field_name='gene_id')
         # Get all link with corresponding genes & Delete them
-        GeneFunction.objects.filter(gene__in=genes.values()).delete()
+        self._delete_previous_annotations(genes)
         # Generate table for bulk_create of function <-> gene and create it
         GeneFunction.objects.bulk_create(
             self._generate_gene_function_mapping(cleaned_functions, genes)

backend/metagenedb/apps/catalog/management/commands/import_virgo_eggnog.py

@@ -19,6 +19,8 @@ class ImportVirgoGeneEggNOGAnnotation(BaseImportGenes, HandleFunctions):
     SOURCE = 'virgo'
     PARSER = VirgoEggNOGLineParser
 
+    FUN_SOURCE_TO_DELETE = ['eggnog']
+
     def _clean_functions(self, functions, unknown_val='unknown'):
         """
         Get rid of functions that are not in the db or entitled unknown

backend/metagenedb/apps/catalog/management/commands/import_virgo_kegg.py

@@ -19,6 +19,8 @@ class ImportVirgoGeneKeggAnnotation(BaseImportGenes, HandleFunctions):
     SOURCE = 'virgo'
     PARSER = VirgoKEGGLineParser
 
+    FUN_SOURCE_TO_DELETE = ['kegg']
+
     def _clean_functions(self, functions, unknown_val='unknown'):
         """
         Get rid of functions that are not in the db or entitled unknown