fix handling of taxonomy and way it is skipped

backend/scripts/populate_db/import_igc_data.py

@@ -55,6 +55,8 @@ class ImportIGCGenes(object):
         """
         phylum = gene_dict.pop(self.PHYLUM_COL)
         genus = gene_dict.pop(self.GENUS_COL)
+        if self.skip_tax:
+            return gene_dict
         resp_dict = {}
         if genus != unknown_val:
             resp_dict = self.metagenedb_taxonomy_api.get_all(params={'name': genus, 'rank': 'genus'})
@@ -81,10 +83,7 @@ class ImportIGCGenes(object):
         gene_dict['gene_name'] = gene_dict['gene_id']
         gene_dict['gene_id'] = slugify(gene_dict['gene_id'])
         gene_dict['functions'] = gene_dict.pop('kegg_ko')
-        if gene_dict.get('taxonomy', None) == 'unknown' or self.skip_tax:
-            gene_dict.pop('taxonomy')
-        else:
-            gene_dict = self._select_taxonomy(gene_dict)
+        gene_dict = self._select_taxonomy(gene_dict)
         if self.skip_functions or 'unknown' in gene_dict['functions']:
             gene_dict.pop('functions')
         return gene_dict

backend/scripts/populate_db/test_import_igc_data.py

@@ -76,23 +76,10 @@ class TestCleanGene(TestCase):
         self.gene_dict = {
             'gene_id': 'gene.01',
             'length': 135,
-            'taxonomy': 'Taxo',
             'kegg_ko': ['K00001']
         }
 
     def test_clean_gene(self):
-        expected_gene_dict = {
-            'gene_id': 'gene-01',
-            'gene_name': 'gene.01',
-            'length': 135,
-            'taxonomy': 'Taxo',
-            'functions': ['K00001']
-        }
-        test_gene_dict = self.import_igc_genes._clean_gene(self.gene_dict)
-        self.assertDictEqual(test_gene_dict, expected_gene_dict)
-
-    def test_clean_gene_skip_taxo(self):
-        self.import_igc_genes.skip_tax = True
         expected_gene_dict = {
             'gene_id': 'gene-01',
             'gene_name': 'gene.01',
@@ -108,7 +95,6 @@ class TestCleanGene(TestCase):
             'gene_id': 'gene-01',
             'gene_name': 'gene.01',
             'length': 135,
-            'taxonomy': 'Taxo',
         }
         test_gene_dict = self.import_igc_genes._clean_gene(self.gene_dict)
         self.assertDictEqual(test_gene_dict, expected_gene_dict)