forked from enviPath/enviPy
245 lines
8.1 KiB
Python
245 lines
8.1 KiB
Python
import json
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from django.conf import settings as s
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from django.core.management.base import BaseCommand
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from django.db import transaction
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from epdb.logic import UserManager, GroupManager, PackageManager, SettingManager
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from epdb.models import (
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UserSettingPermission,
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MLRelativeReasoning,
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EnviFormer,
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Permission,
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User,
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ExternalDatabase,
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License,
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)
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class Command(BaseCommand):
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def add_arguments(self, parser):
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parser.add_argument(
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"-ol", "--only-licenses", action="store_true", help="Only create licenses."
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)
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def create_users(self):
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# Anonymous User
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if not User.objects.filter(email="anon@envipath.com").exists():
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anon = UserManager.create_user(
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"anonymous",
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"anon@envipath.com",
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"SuperSafe",
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is_active=True,
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add_to_group=False,
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set_setting=False,
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)
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else:
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anon = User.objects.get(email="anon@envipath.com")
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# Admin User
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if not User.objects.filter(email="admin@envipath.com").exists():
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admin = UserManager.create_user(
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"admin",
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"admin@envipath.com",
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"SuperSafe",
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is_active=True,
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add_to_group=False,
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set_setting=False,
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)
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admin.is_staff = True
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admin.is_superuser = True
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admin.save()
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else:
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admin = User.objects.get(email="admin@envipath.com")
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# System Group
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g = GroupManager.create_group(admin, "enviPath Users", "All enviPath Users")
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g.public = True
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g.save()
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g.user_member.add(anon)
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g.save()
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anon.default_group = g
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anon.save()
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admin.default_group = g
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admin.save()
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if not User.objects.filter(email="user0@envipath.com").exists():
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user0 = UserManager.create_user(
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"user0",
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"user0@envipath.com",
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"SuperSafe",
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is_active=True,
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add_to_group=False,
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set_setting=False,
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)
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user0.is_staff = True
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user0.is_superuser = True
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user0.save()
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else:
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user0 = User.objects.get(email="user0@envipath.com")
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g.user_member.add(user0)
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g.save()
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user0.default_group = g
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user0.save()
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return anon, admin, g, user0
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def create_licenses(self):
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"""Create the six default licenses supported by enviPath"""
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cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
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for cc_string in cc_strings:
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new_license = License()
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new_license.cc_string = cc_string
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new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
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new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
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new_license.save()
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def import_package(self, data, owner):
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return PackageManager.import_legacy_package(
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data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
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)
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def create_default_setting(self, owner, packages):
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s = SettingManager.create_setting(
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owner,
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name="Global Default Setting",
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description="Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8",
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max_nodes=30,
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max_depth=5,
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rule_packages=packages,
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model=None,
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model_threshold=None,
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)
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return s
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def populate_common_external_databases(self):
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"""
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Helper function to populate common external databases.
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This can be called from a Django management command.
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"""
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databases = [
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{
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"name": "PubChem Compound",
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"full_name": "PubChem Compound Database",
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"description": "Chemical database of small organic molecules",
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"base_url": "https://pubchem.ncbi.nlm.nih.gov",
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"url_pattern": "https://pubchem.ncbi.nlm.nih.gov/compound/{id}",
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},
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{
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"name": "PubChem Substance",
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"full_name": "PubChem Substance Database",
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"description": "Database of chemical substances",
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"base_url": "https://pubchem.ncbi.nlm.nih.gov",
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"url_pattern": "https://pubchem.ncbi.nlm.nih.gov/substance/{id}",
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},
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{
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"name": "ChEBI",
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"full_name": "Chemical Entities of Biological Interest",
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"description": "Dictionary of molecular entities",
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"base_url": "https://www.ebi.ac.uk/chebi",
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"url_pattern": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}",
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},
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{
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"name": "RHEA",
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"full_name": "RHEA Reaction Database",
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"description": "Comprehensive resource of biochemical reactions",
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"base_url": "https://www.rhea-db.org",
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"url_pattern": "https://www.rhea-db.org/rhea/{id}",
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},
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{
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"name": "KEGG Reaction",
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"full_name": "KEGG Reaction Database",
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"description": "Database of biochemical reactions",
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"base_url": "https://www.genome.jp",
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"url_pattern": "https://www.genome.jp/entry/{id}",
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},
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{
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"name": "UniProt",
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"full_name": "MetaCyc Metabolic Pathway Database",
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"description": "UniProt is a freely accessible database of protein sequence and functional information",
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"base_url": "https://www.uniprot.org",
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"url_pattern": 'https://www.uniprot.org/uniprotkb?query="{id}"',
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},
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]
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for db_info in databases:
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ExternalDatabase.objects.get_or_create(name=db_info["name"], defaults=db_info)
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@transaction.atomic
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def handle(self, *args, **options):
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# Create licenses
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self.create_licenses()
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if options.get("only_licenses", False):
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return
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# Create users
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anon, admin, g, user0 = self.create_users()
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self.populate_common_external_databases()
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# Import Packages
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packages = [
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"EAWAG-BBD.json",
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"EAWAG-SOIL.json",
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"EAWAG-SLUDGE.json",
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"EAWAG-SEDIMENT.json",
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]
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mapping = {}
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for p in packages:
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print(f"Importing {p}...")
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package_data = json.loads(
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open(
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s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
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).read()
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)
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imported_package = self.import_package(package_data, admin)
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mapping[p.replace(".json", "")] = imported_package
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setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])
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setting.public = True
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setting.save()
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setting.make_global_default()
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for u in [anon, user0]:
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u.default_setting = setting
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u.save()
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usp = UserSettingPermission()
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usp.user = u
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usp.setting = setting
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usp.permission = Permission.READ[0]
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usp.save()
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# Create Model Package
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pack = PackageManager.create_package(
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admin,
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"Public Prediction Models",
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"Package to make Prediction Models publicly available",
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)
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pack.reviewed = True
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pack.save()
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# Create RR
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ml_model = MLRelativeReasoning.create(
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package=pack,
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rule_packages=[mapping["EAWAG-BBD"]],
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data_packages=[mapping["EAWAG-BBD"]],
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eval_packages=[],
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threshold=0.5,
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name="ECC - BBD - T0.5",
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description="ML Relative Reasoning",
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)
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ml_model.build_dataset()
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ml_model.build_model()
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# If available, create EnviFormerModel
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if s.ENVIFORMER_PRESENT:
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EnviFormer.create(pack, "EnviFormer - T0.5", "EnviFormer Model with Threshold 0.5", 0.5)
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