start script to create light db

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

+from collections import OrderedDict
+
 from factory import DjangoModelFactory, fuzzy
 from faker import Factory
 
@@ -25,44 +27,47 @@ class DbGenerator:
         self.created_ids = set()  # store already created IDs to skip them
 
     def generate_db_from_tree(self, tree):
+        """
+        Tree need to be an OrderedDict from higher to lower level
+        """
         for rank, desc in tree.items():
             if desc['tax_id'] not in self.created_ids:
-                TaxonomyFactory.create(
+                self.last_tax = TaxonomyFactory.create(
                     tax_id=desc['tax_id'],
                     name=desc['name'],
                     rank=rank,
+                    parent=getattr(self, "last_tax", None)
                 )
             self.created_ids.add(desc['tax_id'])
+        self.last_tax.build_hierarchy()
 
 
 def _generate_lactobacillus_db(db_generator):
     """
     Generate db with few ranks corresponding to Lactobacillus genus
     """
-    tree = {
-        "class": {"name": "Bacilli", "tax_id": "91061"},
-        "genus": {"name": "Lactobacillus", "tax_id": "1578"},
-        "order": {"name": "Lactobacillales", "tax_id": "186826"},
-        "family": {"name": "Lactobacillaceae", "tax_id": "33958"},
-        "phylum": {"name": "Firmicutes", "tax_id": "1239"},
-        "no_rank": {"name": "cellular organisms", "tax_id": "131567"},
-        "superkingdom": {"name": "Bacteria", "tax_id": "2"},
-        "species_group": {"name": "Lactobacillus casei group", "tax_id": "655183"}
-    }
+    tree = OrderedDict()
+    tree['no_rank'] = {"name": "root", "tax_id": "1"}
+    tree["superkingdom"] = {"name": "Bacteria", "tax_id": "2"}
+    tree["phylum"] = {"name": "Firmicutes", "tax_id": "1239"}
+    tree["class"] = {"name": "Bacilli", "tax_id": "91061"}
+    tree["order"] = {"name": "Lactobacillales", "tax_id": "186826"}
+    tree["family"] = {"name": "Lactobacillaceae", "tax_id": "33958"}
+    tree["genus"] = {"name": "Lactobacillus", "tax_id": "1578"}
+    tree["species_group"] = {"name": "Lactobacillus casei group", "tax_id": "655183"}
     db_generator.generate_db_from_tree(tree)
 
 
 def _generate_escherichia_db(db_generator):
-    tree = {
-        "class": {"name": "Gammaproteobacteria", "tax_id": "1236"},
-        "genus": {"name": "Escherichia", "tax_id": "561"},
-        "order": {"name": "Enterobacterales", "tax_id": "91347"},
-        "family": {"name": "Enterobacteriaceae", "tax_id": "543"},
-        "phylum": {"name": "Proteobacteria", "tax_id": "1224"},
-        "no_rank": {"name": "cellular organisms", "tax_id": "131567"},
-        "species": {"name": "Escherichia coli", "tax_id": "562"},
-        "superkingdom": {"name": "Bacteria", "tax_id": "2"}
-    }
+    tree = OrderedDict()
+    tree["no_rank"] = {"name": "root", "tax_id": "1"}
+    tree["superkingdom"] = {"name": "Bacteria", "tax_id": "2"}
+    tree["phylum"] = {"name": "Proteobacteria", "tax_id": "1224"}
+    tree["class"] = {"name": "Gammaproteobacteria", "tax_id": "1236"}
+    tree["order"] = {"name": "Enterobacterales", "tax_id": "91347"}
+    tree["family"] = {"name": "Enterobacteriaceae", "tax_id": "543"}
+    tree["genus"] = {"name": "Escherichia", "tax_id": "561"}
+    tree["species"] = {"name": "Escherichia coli", "tax_id": "562"}
     db_generator.generate_db_from_tree(tree)
 
 

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

+import logging
+
+from django.core.management.base import BaseCommand
+
+from metagenedb.apps.catalog.factory.taxonomy import generate_simple_db as gen_tax_db
+from metagenedb.apps.catalog.models import (
+    Gene, KeggOrthology, Taxonomy
+)
+
+logging.basicConfig(format='[%(asctime)s] %(levelname)s:%(name)s:%(message)s')
+logger = logging.getLogger(__name__)
+
+
+def create_functions_db():
+    KeggOrthology.objects.all().delete()
+    keggs_to_create = {
+        "K03556": {
+            'name': 'malT',
+            'long_name': "LuxR family transcriptional regulator, maltose regulon positive regulatory protein"
+        },
+        "K02229": {
+            'name': "cobG",
+            'long_name': 'precorrin-3B synthase [EC:1.14.13.83]'
+        }
+    }
+    for kegg_id, values in keggs_to_create.items():
+        KeggOrthology(
+            function_id=kegg_id,
+            name=values.get('name'),
+            long_name=values.get('long_name')
+        ).save()
+
+
+def create_taxonomy_db():
+    Taxonomy.objects.all().delete()
+    gen_tax_db()
+
+
+def create_genes_db():
+    pass
+
+
+def create_small_db():
+    create_functions_db()
+    create_taxonomy_db()
+    create_genes_db()
+
+
+class Command(BaseCommand):
+    help = 'Create a light DB with random items to illustrate functionnalities of the application.'
+
+    def set_logger_level(self, verbosity):
+        if verbosity > 2:
+            logger.setLevel(logging.DEBUG)
+        elif verbosity > 1:
+            logger.setLevel(logging.INFO)
+
+    def handle(self, *args, **options):
+        self.set_logger_level(int(options['verbosity']))
+        create_small_db()