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This commit is contained in:
Tim Lorsbach
2025-10-29 19:46:20 +01:00
parent 13ed86a780
commit 138846d84d
35 changed files with 477 additions and 108 deletions
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5
epdb/admin.py
View File

@ -1,11 +1,11 @@
from django.contrib import admin
from django.conf import settings as s
from .models import (
User,
UserPackagePermission,
Group,
GroupPackagePermission,
Package,
MLRelativeReasoning,
EnviFormer,
Compound,
@ -24,6 +24,9 @@ from .models import (
)
Package = s.GET_PACKAGE_MODEL()
class UserAdmin(admin.ModelAdmin):
list_display = ["username", "email", "is_active"]

5
epdb/legacy_api.py
View File

@ -1,5 +1,6 @@
from typing import List, Dict, Optional, Any
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.http import HttpResponse
from django.shortcuts import redirect
@ -10,7 +11,6 @@ from .logic import PackageManager, UserManager, SettingManager
from .models import (
Compound,
CompoundStructure,
Package,
User,
UserPackagePermission,
Rule,
@ -23,6 +23,9 @@ from .models import (
)
Package = s.GET_PACKAGE_MODEL()
def _anonymous_or_real(request):
if request.user.is_authenticated and not request.user.is_anonymous:
return request.user

3
epdb/logic.py
View File

@ -11,7 +11,6 @@ from pydantic import ValidationError
from epdb.models import (
User,
Package,
UserPackagePermission,
GroupPackagePermission,
Permission,
@ -33,6 +32,8 @@ from utilities.misc import PackageImporter, PackageExporter
logger = logging.getLogger(__name__)
Package = s.GET_PACKAGE_MODEL()
class EPDBURLParser:
UUID_PATTERN = r"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"

24
epdb/management/commands/create_ml_models.py
View File

@ -2,7 +2,9 @@ from django.conf import settings as s
from django.core.management.base import BaseCommand
from django.db import transaction
from epdb.models import MLRelativeReasoning, EnviFormer, Package
from epdb.models import EnviFormer, MLRelativeReasoning
Package = s.GET_PACKAGE_MODEL()
class Command(BaseCommand):
@ -75,11 +77,13 @@ class Command(BaseCommand):
return packages
# Iteratively create models in options["model_names"]
print(f"Creating models: {options['model_names']}\n"
f"Data packages: {options['data_packages']}\n"
f"Rule Packages (only for MLRR): {options['rule_packages']}\n"
f"Eval Packages: {options['eval_packages']}\n"
f"Threshold: {options['threshold']:.2f}")
print(
f"Creating models: {options['model_names']}\n"
f"Data packages: {options['data_packages']}\n"
f"Rule Packages (only for MLRR): {options['rule_packages']}\n"
f"Eval Packages: {options['eval_packages']}\n"
f"Threshold: {options['threshold']:.2f}"
)
data_packages = decode_packages(options["data_packages"])
eval_packages = decode_packages(options["eval_packages"])
rule_packages = decode_packages(options["rule_packages"])
@ -90,10 +94,10 @@ class Command(BaseCommand):
pack,
data_packages=data_packages,
eval_packages=eval_packages,
threshold=options['threshold'],
threshold=options["threshold"],
name=f"EnviFormer - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
description=f"EnviFormer transformer trained on {options['data_packages']} "
f"evaluated on {options['eval_packages']}.",
f"evaluated on {options['eval_packages']}.",
)
elif model_name == "mlrr":
model = MLRelativeReasoning.create(
@ -101,10 +105,10 @@ class Command(BaseCommand):
rule_packages=rule_packages,
data_packages=data_packages,
eval_packages=eval_packages,
threshold=options['threshold'],
threshold=options["threshold"],
name=f"ECC - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
description=f"ML Relative Reasoning trained on {options['data_packages']} with rules from "
f"{options['rule_packages']} and evaluated on {options['eval_packages']}.",
f"{options['rule_packages']} and evaluated on {options['eval_packages']}.",
)
else:
raise ValueError(f"Cannot create model of type {model_name}, unknown model type")

4
epdb/management/commands/load_enviformer.py
View File

@ -8,7 +8,9 @@ from django.conf import settings as s
from django.core.management.base import BaseCommand
from django.db import transaction
from epdb.models import EnviFormer, Package
from epdb.models import EnviFormer
Package = s.GET_PACKAGE_MODEL()
class Command(BaseCommand):

11
epdb/management/commands/localize_urls.py
View File

@ -1,8 +1,8 @@
from django.apps import apps
from django.conf import settings as s
from django.core.management.base import BaseCommand
from django.db.models import F, Value, TextField, JSONField
from django.db.models.functions import Replace, Cast
from django.db.models import F, JSONField, TextField, Value
from django.db.models.functions import Cast, Replace
from epdb.models import EnviPathModel
@ -23,10 +23,13 @@ class Command(BaseCommand):
)
def handle(self, *args, **options):
Package = s.GET_PACKAGE_MODEL()
print("Localizing urls for Package")
Package.objects.update(url=Replace(F("url"), Value(options["old"]), Value(options["new"])))
MODELS = [
"User",
"Group",
"Package",
"Compound",
"CompoundStructure",
"Pathway",

190
epdb/migrations/0010_alter_userpackagepermission_package_and_more.py Normal file
View File

@ -0,0 +1,190 @@
# Generated by Django 5.2.7 on 2025-10-29 13:32
import django.db.models.deletion
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0009_joblog"),
("public", "0001_initial"),
]
operations = [
migrations.AlterField(
model_name="userpackagepermission",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Permission on",
),
),
migrations.AlterField(
model_name="grouppackagepermission",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Permission on",
),
),
migrations.AlterField(
model_name="epmodel",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="rule",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="compound",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="scenario",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="pathway",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="reaction",
name="package",
field=models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to="public.package",
verbose_name="Package",
),
),
migrations.AlterField(
model_name="user",
name="default_package",
field=models.ForeignKey(
null=True,
on_delete=django.db.models.deletion.SET_NULL,
to="public.package",
verbose_name="Default Package",
),
),
migrations.AlterField(
model_name="enviformer",
name="data_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_data_packages",
to="public.package",
verbose_name="Data Packages",
),
),
migrations.AlterField(
model_name="enviformer",
name="eval_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_eval_packages",
to="public.package",
verbose_name="Evaluation Packages",
),
),
migrations.AlterField(
model_name="enviformer",
name="rule_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_rule_packages",
to="public.package",
verbose_name="Rule Packages",
),
),
migrations.AlterField(
model_name="mlrelativereasoning",
name="data_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_data_packages",
to="public.package",
verbose_name="Data Packages",
),
),
migrations.AlterField(
model_name="mlrelativereasoning",
name="eval_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_eval_packages",
to="public.package",
verbose_name="Evaluation Packages",
),
),
migrations.AlterField(
model_name="mlrelativereasoning",
name="rule_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_rule_packages",
to="public.package",
verbose_name="Rule Packages",
),
),
migrations.AlterField(
model_name="rulebasedrelativereasoning",
name="data_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_data_packages",
to="public.package",
verbose_name="Data Packages",
),
),
migrations.AlterField(
model_name="rulebasedrelativereasoning",
name="eval_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_eval_packages",
to="public.package",
verbose_name="Evaluation Packages",
),
),
migrations.AlterField(
model_name="rulebasedrelativereasoning",
name="rule_packages",
field=models.ManyToManyField(
related_name="%(app_label)s_%(class)s_rule_packages",
to="public.package",
verbose_name="Rule Packages",
),
),
migrations.AlterField(
model_name="setting",
name="rule_packages",
field=models.ManyToManyField(
blank=True,
related_name="setting_rule_packages",
to="public.package",
verbose_name="Setting Rule Packages",
),
),
migrations.DeleteModel(
name="Package",
),
]

45
epdb/models.py
View File

@ -7,7 +7,7 @@ import secrets
from abc import abstractmethod
from collections import defaultdict
from datetime import datetime
from typing import Union, List, Optional, Dict, Tuple, Set, Any
from typing import Union, List, Optional, Dict, Tuple, Set, Any, TYPE_CHECKING
from uuid import uuid4
import math
import joblib
@ -32,6 +32,8 @@ from utilities.ml import Dataset, ApplicabilityDomainPCA, EnsembleClassifierChai
logger = logging.getLogger(__name__)
if TYPE_CHECKING:
Package = s.GET_PACKAGE_MODEL()
##########################
# User/Groups/Permission #
@ -45,7 +47,10 @@ class User(AbstractUser):
)
url = models.TextField(blank=False, null=True, verbose_name="URL", unique=True)
default_package = models.ForeignKey(
"epdb.Package", verbose_name="Default Package", null=True, on_delete=models.SET_NULL
s.PACKAGE_IMPLEMENTATION,
verbose_name="Default Package",
null=True,
on_delete=models.SET_NULL,
)
default_group = models.ForeignKey(
"Group",
@ -235,7 +240,7 @@ class UserPackagePermission(Permission):
)
user = models.ForeignKey("User", verbose_name="Permission to", on_delete=models.CASCADE)
package = models.ForeignKey(
"epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
s.PACKAGE_IMPLEMENTATION, verbose_name="Permission on", on_delete=models.CASCADE
)
class Meta:
@ -251,7 +256,7 @@ class GroupPackagePermission(Permission):
)
group = models.ForeignKey("Group", verbose_name="Permission to", on_delete=models.CASCADE)
package = models.ForeignKey(
"epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
s.PACKAGE_IMPLEMENTATION, verbose_name="Permission on", on_delete=models.CASCADE
)
class Meta:
@ -651,7 +656,7 @@ class License(models.Model):
image_link = models.URLField(blank=False, null=False, verbose_name="Image link")
class Package(EnviPathModel):
class AbstractPackage(EnviPathModel):
reviewed = models.BooleanField(verbose_name="Reviewstatus", default=False)
license = models.ForeignKey(
"epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
@ -719,10 +724,13 @@ class Package(EnviPathModel):
rules = sorted(rules, key=lambda x: x.url)
return rules
class Meta:
abstract = True
class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
default_structure = models.ForeignKey(
"CompoundStructure",
@ -772,7 +780,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
@staticmethod
@transaction.atomic
def create(
package: Package, smiles: str, name: str = None, description: str = None, *args, **kwargs
package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
) -> "Compound":
if smiles is None or smiles.strip() == "":
raise ValueError("SMILES is required")
@ -1050,7 +1058,7 @@ class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
# # https://github.com/django-polymorphic/django-polymorphic/issues/229
@ -1156,7 +1164,7 @@ class SimpleAmbitRule(SimpleRule):
@staticmethod
@transaction.atomic
def create(
package: Package,
package: "Package",
name: str = None,
description: str = None,
smirks: str = None,
@ -1222,6 +1230,7 @@ class SimpleAmbitRule(SimpleRule):
@property
def related_reactions(self):
Package = s.GET_PACKAGE_MODEL()
qs = Package.objects.filter(reviewed=True)
return self.reaction_rule.filter(package__in=qs).order_by("name")
@ -1314,7 +1323,7 @@ class SequentialRuleOrdering(models.Model):
class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
educts = models.ManyToManyField(
"epdb.CompoundStructure", verbose_name="Educts", related_name="reaction_educts"
@ -1336,7 +1345,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
@staticmethod
@transaction.atomic
def create(
package: Package,
package: "Package",
name: str = None,
description: str = None,
educts: Union[List[str], List[CompoundStructure]] = None,
@ -1496,7 +1505,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
setting = models.ForeignKey(
"epdb.Setting", verbose_name="Setting", on_delete=models.CASCADE, null=True, blank=True
@ -2052,7 +2061,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
class EPModel(PolymorphicModel, EnviPathModel):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
def _url(self):
@ -2061,17 +2070,17 @@ class EPModel(PolymorphicModel, EnviPathModel):
class PackageBasedModel(EPModel):
rule_packages = models.ManyToManyField(
"Package",
s.PACKAGE_IMPLEMENTATION,
verbose_name="Rule Packages",
related_name="%(app_label)s_%(class)s_rule_packages",
)
data_packages = models.ManyToManyField(
"Package",
s.PACKAGE_IMPLEMENTATION,
verbose_name="Data Packages",
related_name="%(app_label)s_%(class)s_data_packages",
)
eval_packages = models.ManyToManyField(
"Package",
s.PACKAGE_IMPLEMENTATION,
verbose_name="Evaluation Packages",
related_name="%(app_label)s_%(class)s_eval_packages",
)
@ -3439,7 +3448,7 @@ class PluginModel(EPModel):
class Scenario(EnviPathModel):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
scenario_date = models.CharField(max_length=256, null=False, blank=False, default="No date")
scenario_type = models.CharField(
@ -3590,7 +3599,7 @@ class Setting(EnviPathModel):
)
rule_packages = models.ManyToManyField(
"Package",
s.PACKAGE_IMPLEMENTATION,
verbose_name="Setting Rule Packages",
related_name="setting_rule_packages",
blank=True,

5
epdb/tasks.py
View File

@ -7,9 +7,12 @@ from uuid import uuid4
from celery import shared_task
from celery.utils.functional import LRUCache
from django.conf import settings as s
from epdb.logic import SPathway
from epdb.models import EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User, Edge
from epdb.models import Edge, EPModel, JobLog, Node, Pathway, Rule, Setting, User
Package = s.GET_PACKAGE_MODEL()
logger = logging.getLogger(__name__)
ML_CACHE = LRUCache(3) # Cache the three most recent ML models to reduce load times.

56
epdb/views.py
View File

@ -1,11 +1,11 @@
import json
import logging
from typing import List, Dict, Any
from typing import Any, Dict, List
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, HttpResponseBadRequest
from django.shortcuts import render, redirect
from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed, JsonResponse
from django.shortcuts import redirect, render
from django.urls import reverse
from django.views.decorators.csrf import csrf_exempt
from envipy_additional_information import NAME_MAPPING
@ -14,42 +14,43 @@ from oauth2_provider.decorators import protected_resource
from utilities.chem import FormatConverter, IndigoUtils
from utilities.decorators import package_permission_required
from utilities.misc import HTMLGenerator
from .logic import (
EPDBURLParser,
GroupManager,
PackageManager,
UserManager,
SettingManager,
SearchManager,
EPDBURLParser,
SettingManager,
UserManager,
)
from .models import (
Package,
GroupPackagePermission,
Group,
CompoundStructure,
APIToken,
Compound,
CompoundStructure,
Edge,
EnviFormer,
EnzymeLink,
EPModel,
ExternalDatabase,
ExternalIdentifier,
Group,
GroupPackagePermission,
JobLog,
License,
MLRelativeReasoning,
Node,
Pathway,
Permission,
Reaction,
Rule,
Pathway,
Node,
EPModel,
EnviFormer,
MLRelativeReasoning,
RuleBasedRelativeReasoning,
Scenario,
SimpleAmbitRule,
APIToken,
UserPackagePermission,
Permission,
License,
User,
Edge,
ExternalDatabase,
ExternalIdentifier,
EnzymeLink,
JobLog,
UserPackagePermission,
)
Package = s.GET_PACKAGE_MODEL()
logger = logging.getLogger(__name__)
@ -82,8 +83,7 @@ def login(request):
return render(request, "static/login.html", context)
elif request.method == "POST":
from django.contrib.auth import authenticate
from django.contrib.auth import login
from django.contrib.auth import authenticate, login
username = request.POST.get("username")
password = request.POST.get("password")
@ -832,7 +832,7 @@ def package_models(request, package_uuid):
request, "Invalid model type.", f'Model type "{model_type}" is not supported."'
)
from .tasks import dispatch, build_model
from .tasks import build_model, dispatch
dispatch(current_user, build_model, mod.pk)
@ -2325,9 +2325,9 @@ def package_scenarios(request, package_uuid):
context["unreviewed_objects"] = unreviewed_scenario_qs
from envipy_additional_information import (
SEDIMENT_ADDITIONAL_INFORMATION,
SLUDGE_ADDITIONAL_INFORMATION,
SOIL_ADDITIONAL_INFORMATION,
SEDIMENT_ADDITIONAL_INFORMATION,
)
context["scenario_types"] = {