External References (#50)

Fix for #24

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#50

epdb/management/commands/bootstrap.py

@@ -5,7 +5,7 @@ from django.core.management.base import BaseCommand
 from django.db import transaction
 
 from epdb.logic import UserManager, GroupManager, PackageManager, SettingManager
-from epdb.models import UserSettingPermission, MLRelativeReasoning, EnviFormer, Permission, User
+from epdb.models import UserSettingPermission, MLRelativeReasoning, EnviFormer, Permission, User, ExternalDatabase
 
 
 class Command(BaseCommand):
@@ -74,6 +74,76 @@ class Command(BaseCommand):
 
         return s
 
+    def populate_common_external_databases(self):
+        """
+        Helper function to populate common external databases.
+        This can be called from a Django management command.
+        """
+        databases = [
+            {
+                'name': 'PubChem Compound',
+                'full_name': 'PubChem Compound Database',
+                'description': 'Chemical database of small organic molecules',
+                'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
+                'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'
+            },
+            {
+                'name': 'PubChem Substance',
+                'full_name': 'PubChem Substance Database',
+                'description': 'Database of chemical substances',
+                'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
+                'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/substance/{id}'
+            },
+            {
+                'name': 'ChEBI',
+                'full_name': 'Chemical Entities of Biological Interest',
+                'description': 'Dictionary of molecular entities',
+                'base_url': 'https://www.ebi.ac.uk/chebi',
+                'url_pattern': 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}'
+            },
+            {
+                'name': 'RHEA',
+                'full_name': 'RHEA Reaction Database',
+                'description': 'Comprehensive resource of biochemical reactions',
+                'base_url': 'https://www.rhea-db.org',
+                'url_pattern': 'https://www.rhea-db.org/rhea/{id}'
+            },
+            {
+                'name': 'CAS',
+                'full_name': 'Chemical Abstracts Service Registry',
+                'description': 'Registry of chemical substances',
+                'base_url': 'https://www.cas.org',
+                'url_pattern': None  # CAS doesn't have a free public URL pattern
+            },
+            {
+                'name': 'KEGG Reaction',
+                'full_name': 'KEGG Reaction Database',
+                'description': 'Database of biochemical reactions',
+                'base_url': 'https://www.genome.jp',
+                'url_pattern': 'https://www.genome.jp/entry/reaction+{id}'
+            },
+            {
+                'name': 'MetaCyc',
+                'full_name': 'MetaCyc Metabolic Pathway Database',
+                'description': 'Database of metabolic pathways and enzymes',
+                'base_url': 'https://metacyc.org',
+                'url_pattern': None
+            },
+            {
+                'name': 'UniProt',
+                'full_name': 'MetaCyc Metabolic Pathway Database',
+                'description': 'UniProt is a freely accessible database of protein sequence and functional information',
+                'base_url': 'https://www.uniprot.org',
+                'url_pattern': 'https://www.uniprot.org/uniprotkb?query="{id}"'
+            }
+        ]
+
+        for db_info in databases:
+            ExternalDatabase.objects.get_or_create(
+                name=db_info['name'],
+                defaults=db_info
+            )
+
     @transaction.atomic
     def handle(self, *args, **options):
         # Create users