enviPy-bayer/epdb/management/commands/bootstrap.py

import json

from django.conf import settings as s
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, ExternalDatabase


class Command(BaseCommand):

    def create_users(self):

        if not User.objects.filter(email='anon@lorsba.ch').exists():
            anon = UserManager.create_user("anonymous", "anon@lorsba.ch", "SuperSafe", is_active=True,
                                           add_to_group=False, set_setting=False)
        else:
            anon = User.objects.get(email='anon@lorsba.ch')

        if not User.objects.filter(email='admin@lorsba.ch').exists():
            admin = UserManager.create_user("admin", "admin@lorsba.ch", "SuperSafe", is_active=True, add_to_group=False,
                                            set_setting=False)
            admin.is_staff = True
            admin.is_superuser = True
            admin.save()
        else:
            admin = User.objects.get(email='admin@lorsba.ch')

        g = GroupManager.create_group(admin, 'enviPath Users', 'All enviPath Users')
        g.public = True
        g.save()

        g.user_member.add(anon)
        g.save()

        anon.default_group = g
        anon.save()

        admin.default_group = g
        admin.save()

        if not User.objects.filter(email='jebus@lorsba.ch').exists():
            jebus = UserManager.create_user("jebus", "jebus@lorsba.ch", "SuperSafe", is_active=True, add_to_group=False,
                                            set_setting=False)
            jebus.is_staff = True
            jebus.is_superuser = True
            jebus.save()
        else:
            jebus = User.objects.get(email='jebus@lorsba.ch')

        g.user_member.add(jebus)
        g.save()

        jebus.default_group = g
        jebus.save()

        return anon, admin, g, jebus

    def import_package(self, data, owner):
        return PackageManager.import_package(data, owner, keep_ids=True, add_import_timestamp=False)

    def create_default_setting(self, owner, packages):
        s = SettingManager.create_setting(
            owner,
            name='Global Default Setting',
            description='Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8',
            max_nodes=30,
            max_depth=5,
            rule_packages=packages,
            model=None,
            model_threshold=None
        )

        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
        anon, admin, g, jebus = self.create_users()

        # Import Packages
        packages = [
            'EAWAG-BBD.json',
            'EAWAG-SOIL.json',
            'EAWAG-SLUDGE.json',
            'EAWAG-SEDIMENT.json',
        ]

        mapping = {}
        for p in packages:
            print(f"Importing {p}...")
            package_data = json.loads(open(s.BASE_DIR / 'fixtures' / 'packages' / '2025-07-18' / p).read())
            imported_package = self.import_package(package_data, admin)
            mapping[p.replace('.json', '')] = imported_package

        setting = self.create_default_setting(admin, [mapping['EAWAG-BBD']])
        setting.public = True
        setting.save()
        setting.make_global_default()

        for u in [anon, jebus]:
            u.default_setting = setting
            u.save()

            usp = UserSettingPermission()
            usp.user = u
            usp.setting = setting
            usp.permission = Permission.READ[0]
            usp.save()

        # Create Model Package
        pack = PackageManager.create_package(admin, "Public Prediction Models",
                                             "Package to make Prediction Models publicly available")
        pack.reviewed = True
        pack.save()

        # Create RR
        ml_model = MLRelativeReasoning.create(
            package=pack,
            rule_packages=[mapping['EAWAG-BBD']],
            data_packages=[mapping['EAWAG-BBD']],
            eval_packages=[],
            threshold=0.5,
            name='ECC - BBD - T0.5',
            description='ML Relative Reasoning',
        )

        ml_model.build_dataset()
        ml_model.build_model()
        # ml_model.evaluate_model()

        # If available create EnviFormerModel
        if s.ENVIFORMER_PRESENT:
            enviFormer_model = EnviFormer.create(pack, 'EnviFormer - T0.5', 'EnviFormer Model with Threshold 0.5', 0.5)