Add method to build local mapping for genus and phylum

backend/metagenedb/apps/catalog/factory/taxonomy.py

-from factory import DjangoModelFactory, fuzzy
+from factory import DjangoModelFactory, fuzzy, Faker
 from faker import Factory
 
 from metagenedb.apps.catalog import models
@@ -16,3 +16,4 @@ class TaxonomyFactory(DjangoModelFactory):
 
     rank = fuzzy.FuzzyChoice(SELECTED_RANK)
     tax_id = FuzzyLowerText(prefix='tax-', length=15)
+    name = fuzzy.FuzzyText(length=20)

backend/scripts/populate_db/import_igc_data.py

@@ -34,6 +34,23 @@ class ImportIGCGenes(object):
         self.skip_tax = skip_tax
         self.skip_functions = skip_functions
 
+    def _build_taxo_mapping(self, rank):
+        counter = 1
+        next_page = None
+        mapping = {}
+        while counter == 1 or next_page is not None:
+            current_page = self.metagenedb_taxonomy_api.get_all(params={'page': counter, 'rank': rank})
+            next_page = current_page['next']
+            mapping.update({
+                value['name']: value['tax_id'] for value in current_page['results']
+            })
+            counter += 1
+        return mapping
+
+    def build_mapping(self):
+        self.phylum_mapping = self._build_taxo_mapping("phylum")
+        self.genus_mapping = self._build_taxo_mapping("genus")
+
     def _reset_counters(self):
         self.processed_genes = 0
         self.created_genes = 0
@@ -89,6 +106,8 @@ class ImportIGCGenes(object):
         return gene_dict
 
     def load_annotation_file_to_db_in_chunks(self, chunk_size=1000, test=False):
+        # Build mapping for different phylum and genus
+        self.build_mapping()
         with open(self.annotation_file, 'r') as file:
             while True:
                 chunk_genes = list(islice(file, chunk_size))

backend/scripts/populate_db/test_import_igc_data.py

@@ -116,12 +116,15 @@ class TestCleanGene(TestCase):
 
 class TestSelectTaxonomy(APITestCase):
 
+    @classmethod
+    def setUpTestData(cls):
+        cls.genus_name = 'Genus'
+        cls.phylum_name = 'Phylum'
+        cls.unknown_name = 'unknown'
+        cls.genus = TaxonomyFactory(rank="genus", name=cls.genus_name)
+        cls.phylum = TaxonomyFactory(rank="phylum", name=cls.phylum_name)
+
     def setUp(self):
-        self.genus_name = 'Genus'
-        self.phylum_name = 'Phylum'
-        self.unknown_name = 'unknown'
-        self.genus = TaxonomyFactory(rank="genus", name=self.genus_name)
-        self.phylum = TaxonomyFactory(rank="phylum", name=self.phylum_name)
         self.import_igc_genes = ImportIGCGenes('test', 'test')
         self.api_mock = MetageneDBCatalogTaxonomyAPIMock(self.client)
         self.import_igc_genes.metagenedb_taxonomy_api = self.api_mock
@@ -184,3 +187,27 @@ class TestSelectTaxonomy(APITestCase):
         }
         tested_dict = self.import_igc_genes._select_taxonomy(gene_dict)
         self.assertDictEqual(tested_dict, expected_dict)
+
+
+class TestBuildTaxoMapping(APITestCase):
+
+    @classmethod
+    def setUpTestData(cls):
+        cls.genus_items = TaxonomyFactory.create_batch(200, rank='genus')
+        cls.phylum_items = TaxonomyFactory.create_batch(20, rank='phylum')
+
+    def setUp(self):
+        self.import_igc_genes = ImportIGCGenes('test', 'test')
+        self.api_mock = MetageneDBCatalogTaxonomyAPIMock(self.client)
+        self.import_igc_genes.metagenedb_taxonomy_api = self.api_mock
+
+    def test_build_mapping(self):
+        expected_genus_dict = {
+            item.name: item.tax_id for item in self.genus_items
+        }
+        expected_phylum_dict = {
+            item.name: item.tax_id for item in self.phylum_items
+        }
+        self.import_igc_genes.build_mapping()
+        self.assertDictEqual(self.import_igc_genes.genus_mapping, expected_genus_dict)
+        self.assertDictEqual(self.import_igc_genes.phylum_mapping, expected_phylum_dict)