management command to create sources

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

+import logging
+
+from django.core.management.base import BaseCommand
+from django.db.utils import IntegrityError
+
+from metagenedb.apps.catalog.models import Source
+
+logging.basicConfig(format='[%(asctime)s] %(levelname)s:%(name)s:%(message)s')
+logger = logging.getLogger()
+
+ITEMS_TO_CREATE = [
+    {
+        'name': 'Virgo',
+        'url': 'https://virgo.igs.umaryland.edu/',
+        'doi': '10.1038/s41467-020-14677-3'
+    },
+    {
+        'name': 'IGC-9.9M',
+        'url': 'https://db.cngb.org/microbiome/genecatalog/genecatalog_human/',
+        'doi': '10.1038/nbt.2942'
+    },
+]
+
+
+def create_all_sources():
+    items_to_create = ITEMS_TO_CREATE
+    for item in items_to_create:
+        new_entry = Source(**item)
+        try:
+            new_entry.save()
+        except IntegrityError:
+            logger.info("%s already exists.", item['name'])
+
+
+class Command(BaseCommand):
+    help = 'Create gene sources (Virgo and IGC 9.9M at the moment).'
+
+    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_all_sources()