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[Enhancement] Swappable Packages (#216)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#216
Reviewed-by: liambrydon <lbry121@aucklanduni.ac.nz>
Reviewed-by: Tobias O <tobias.olenyi@envipath.com>
This commit is contained in:
jebus
2025-11-14 21:42:39 +13:00
parent d584791ee8
commit a8554c903c
22 changed files with 239 additions and 179 deletions
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16
envipath/settings.py
View File

@ -49,9 +49,23 @@ INSTALLED_APPS = [
"oauth2_provider",
# Custom
"epdb",
"migration",
# "migration",
]
TENANT = os.environ.get("TENANT", "public")
if TENANT != "public":
INSTALLED_APPS.append(TENANT)
EPDB_PACKAGE_MODEL = os.environ.get("EPDB_PACKAGE_MODEL", "epdb.Package")
def GET_PACKAGE_MODEL():
from django.apps import apps
return apps.get_model(EPDB_PACKAGE_MODEL)
AUTHENTICATION_BACKENDS = [
"django.contrib.auth.backends.ModelBackend",
]

4
envipath/urls.py
View File

@ -23,12 +23,14 @@ from .api import api_v1, api_legacy
urlpatterns = [
path("", include("epdb.urls")),
path("", include("migration.urls")),
path("admin/", admin.site.urls),
path("api/v1/", api_v1.urls),
path("api/legacy/", api_legacy.urls),
path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
]
if "migrations" in s.INSTALLED_APPS:
urlpatterns.append(path("", include("migration.urls")))
if s.MS_ENTRA_ENABLED:
urlpatterns.append(path("", include("epauth.urls")))

30
epdb/admin.py
View File

@ -1,29 +1,31 @@
from django.conf import settings as s
from django.contrib import admin
from .models import (
User,
UserPackagePermission,
Group,
GroupPackagePermission,
Package,
MLRelativeReasoning,
EnviFormer,
Compound,
CompoundStructure,
SimpleAmbitRule,
ParallelRule,
Reaction,
Pathway,
Node,
Edge,
Scenario,
Setting,
EnviFormer,
ExternalDatabase,
ExternalIdentifier,
Group,
GroupPackagePermission,
JobLog,
License,
MLRelativeReasoning,
Node,
ParallelRule,
Pathway,
Reaction,
Scenario,
Setting,
SimpleAmbitRule,
User,
UserPackagePermission,
)
Package = s.GET_PACKAGE_MODEL()
class UserAdmin(admin.ModelAdmin):
list_display = ["username", "email", "is_active"]

8
epdb/apps.py
View File

@ -1,4 +1,9 @@
import logging
from django.apps import AppConfig
from django.conf import settings
logger = logging.getLogger(__name__)
class EPDBConfig(AppConfig):
@ -7,3 +12,6 @@ class EPDBConfig(AppConfig):
def ready(self):
import epdb.signals # noqa: F401
model_name = getattr(settings, "EPDB_PACKAGE_MODEL", "epdb.Package")
logger.info(f"Using Package model: {model_name}")

4
epdb/context_processors.py
View File

@ -5,7 +5,7 @@ Context processors automatically make variables available to all templates.
"""
from .logic import PackageManager
from .models import Package
from django.conf import settings as s
def package_context(request):
@ -20,7 +20,7 @@ def package_context(request):
reviewed_package_qs = PackageManager.get_reviewed_packages()
unreviewed_package_qs = Package.objects.none()
unreviewed_package_qs = s.GET_PACKAGE_MODEL().objects.none()
# Only get user-specific packages if user is authenticated
if current_user.is_authenticated:

28
epdb/legacy_api.py
View File

@ -1,27 +1,30 @@
from typing import List, Dict, Optional, Any
from typing import Any, Dict, List, Optional
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
from ninja import Router, Schema, Field, Form
from ninja import Field, Form, Router, Schema
from utilities.chem import FormatConverter
from .logic import PackageManager, UserManager, SettingManager
from .logic import PackageManager, SettingManager, UserManager
from .models import (
Compound,
CompoundStructure,
Package,
Edge,
Node,
Pathway,
Reaction,
Rule,
Scenario,
SimpleAmbitRule,
User,
UserPackagePermission,
Rule,
Reaction,
Scenario,
Pathway,
Node,
Edge,
SimpleAmbitRule,
)
Package = s.GET_PACKAGE_MODEL()
def _anonymous_or_real(request):
if request.user.is_authenticated and not request.user.is_anonymous:
@ -123,8 +126,7 @@ class SimpleEdge(SimpleObject):
################
@router.post("/", response={200: SimpleUser, 403: Error})
def login(request, loginusername: Form[str], loginpassword: Form[str]):
from django.contrib.auth import authenticate
from django.contrib.auth import login
from django.contrib.auth import authenticate, login
email = User.objects.get(username=loginusername).email
user = authenticate(username=email, password=loginpassword)

63
epdb/logic.py
View File

@ -1,39 +1,40 @@
import re
import logging
import json
from typing import Union, List, Optional, Set, Dict, Any
import logging
import re
from typing import Any, Dict, List, Optional, Set, Union
from uuid import UUID
import nh3
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.db import transaction
from django.conf import settings as s
from pydantic import ValidationError
from epdb.models import (
User,
Package,
UserPackagePermission,
GroupPackagePermission,
Permission,
Group,
Setting,
EPModel,
UserSettingPermission,
Rule,
Pathway,
Node,
Edge,
Compound,
Reaction,
CompoundStructure,
Edge,
EnzymeLink,
EPModel,
Group,
GroupPackagePermission,
Node,
Pathway,
Permission,
Reaction,
Rule,
Setting,
User,
UserPackagePermission,
UserSettingPermission,
)
from utilities.chem import FormatConverter
from utilities.misc import PackageImporter, PackageExporter
from utilities.misc import PackageExporter, PackageImporter
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}"
@ -583,25 +584,27 @@ class PackageManager(object):
def import_legacy_package(
data: dict, owner: User, keep_ids=False, add_import_timestamp=True, trust_reviewed=False
):
from uuid import UUID, uuid4
from datetime import datetime
from collections import defaultdict
from datetime import datetime
from uuid import UUID, uuid4
from envipy_additional_information import AdditionalInformationConverter
from .models import (
Package,
Compound,
CompoundStructure,
SimpleRule,
SimpleAmbitRule,
Edge,
Node,
Package,
ParallelRule,
Pathway,
Reaction,
Scenario,
SequentialRule,
SequentialRuleOrdering,
Reaction,
Pathway,
Node,
Edge,
Scenario,
SimpleAmbitRule,
SimpleRule,
)
from envipy_additional_information import AdditionalInformationConverter
pack = Package()
pack.uuid = UUID(data["id"].split("/")[-1]) if keep_ids else uuid4()

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",

63
epdb/models.py
View File

@ -2,40 +2,41 @@ import abc
import hashlib
import json
import logging
import math
import os
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 Any, Dict, List, Optional, Set, Tuple, Union
from uuid import uuid4
import math
import joblib
import nh3
import numpy as np
from django.conf import settings as s
from django.contrib.auth.models import AbstractUser
from django.contrib.contenttypes.fields import GenericRelation, GenericForeignKey
from django.contrib.contenttypes.fields import GenericForeignKey, GenericRelation
from django.contrib.contenttypes.models import ContentType
from django.contrib.postgres.fields import ArrayField
from django.db import models, transaction
from django.db.models import JSONField, Count, Q, QuerySet
from django.db.models import Count, JSONField, Q, QuerySet
from django.utils import timezone
from django.utils.functional import cached_property
from envipy_additional_information import EnviPyModel
from model_utils.models import TimeStampedModel
from polymorphic.models import PolymorphicModel
from sklearn.metrics import precision_score, recall_score, jaccard_score
from sklearn.metrics import jaccard_score, precision_score, recall_score
from sklearn.model_selection import ShuffleSplit
from utilities.chem import FormatConverter, ProductSet, PredictionResult, IndigoUtils
from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
from utilities.ml import (
RuleBasedDataset,
ApplicabilityDomainPCA,
EnsembleClassifierChain,
RelativeReasoning,
EnviFormerDataset,
Dataset,
EnsembleClassifierChain,
EnviFormerDataset,
RelativeReasoning,
RuleBasedDataset,
)
logger = logging.getLogger(__name__)
@ -44,8 +45,6 @@ logger = logging.getLogger(__name__)
##########################
# User/Groups/Permission #
##########################
class User(AbstractUser):
email = models.EmailField(unique=True)
uuid = models.UUIDField(
@ -53,7 +52,10 @@ 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.EPDB_PACKAGE_MODEL,
verbose_name="Default Package",
null=True,
on_delete=models.SET_NULL,
)
default_group = models.ForeignKey(
"Group",
@ -243,7 +245,7 @@ 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.EPDB_PACKAGE_MODEL, verbose_name="Permission on", on_delete=models.CASCADE
)
class Meta:
@ -259,7 +261,7 @@ 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.EPDB_PACKAGE_MODEL, verbose_name="Permission on", on_delete=models.CASCADE
)
class Meta:
@ -728,10 +730,13 @@ class Package(EnviPathModel):
rules = sorted(rules, key=lambda x: x.url)
return rules
class Meta:
swappable = "EPDB_PACKAGE_MODEL"
class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
default_structure = models.ForeignKey(
"CompoundStructure",
@ -781,7 +786,7 @@ 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")
@ -1061,7 +1066,7 @@ 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.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
# # https://github.com/django-polymorphic/django-polymorphic/issues/229
@ -1167,7 +1172,7 @@ class SimpleAmbitRule(SimpleRule):
@staticmethod
@transaction.atomic
def create(
package: Package,
package: "Package",
name: str = None,
description: str = None,
smirks: str = None,
@ -1241,7 +1246,7 @@ class SimpleAmbitRule(SimpleRule):
@property
def related_reactions(self):
qs = Package.objects.filter(reviewed=True)
qs = s.GET_PACKAGE_MODEL().objects.filter(reviewed=True)
return self.reaction_rule.filter(package__in=qs).order_by("name")
@property
@ -1333,7 +1338,7 @@ 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.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
educts = models.ManyToManyField(
"epdb.CompoundStructure", verbose_name="Educts", related_name="reaction_educts"
@ -1355,7 +1360,7 @@ 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,
@ -1514,7 +1519,7 @@ 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.EPDB_PACKAGE_MODEL, 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
@ -2076,7 +2081,7 @@ 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.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
def _url(self):
@ -2085,17 +2090,17 @@ class EPModel(PolymorphicModel, EnviPathModel):
class PackageBasedModel(EPModel):
rule_packages = models.ManyToManyField(
"Package",
s.EPDB_PACKAGE_MODEL,
verbose_name="Rule Packages",
related_name="%(app_label)s_%(class)s_rule_packages",
)
data_packages = models.ManyToManyField(
"Package",
s.EPDB_PACKAGE_MODEL,
verbose_name="Data Packages",
related_name="%(app_label)s_%(class)s_data_packages",
)
eval_packages = models.ManyToManyField(
"Package",
s.EPDB_PACKAGE_MODEL,
verbose_name="Evaluation Packages",
related_name="%(app_label)s_%(class)s_eval_packages",
)
@ -3400,7 +3405,7 @@ class PluginModel(EPModel):
class Scenario(EnviPathModel):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.EPDB_PACKAGE_MODEL, 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(
@ -3555,7 +3560,7 @@ class Setting(EnviPathModel):
)
rule_packages = models.ManyToManyField(
"Package",
s.EPDB_PACKAGE_MODEL,
verbose_name="Setting Rule Packages",
related_name="setting_rule_packages",
blank=True,

5
epdb/tasks.py
View File

@ -6,14 +6,17 @@ from uuid import uuid4
from celery import shared_task
from celery.utils.functional import LRUCache
from django.conf import settings as s
from django.utils import timezone
from epdb.logic import SPathway
from epdb.models import Edge, EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User
from epdb.models import Edge, EPModel, JobLog, Node, Pathway, Rule, Setting, User
logger = logging.getLogger(__name__)
ML_CACHE = LRUCache(3) # Cache the three most recent ML models to reduce load times.
Package = s.GET_PACKAGE_MODEL()
def get_ml_model(model_pk: int):
if model_pk not in ML_CACHE:

59
epdb/views.py
View File

@ -1,58 +1,60 @@
import json
import logging
from typing import List, Dict, Any
from typing import Any, Dict, List
import nh3
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
from oauth2_provider.decorators import protected_resource
import nh3
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,
)
logger = logging.getLogger(__name__)
Package = s.GET_PACKAGE_MODEL()
def log_post_params(request):
if s.DEBUG:
@ -83,8 +85,7 @@ 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").strip()
if username != request.POST.get("username"):
@ -872,7 +873,7 @@ 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)
@ -2409,9 +2410,9 @@ 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"] = {

32
migration/views.py
View File

@ -1,24 +1,21 @@
import gzip
import json
import logging
import os.path
from datetime import datetime
from django.conf import settings as s
from django.http import HttpResponseNotAllowed
from django.shortcuts import render
from epdb.logic import PackageManager
from epdb.models import Rule, SimpleAmbitRule, Package, CompoundStructure
from epdb.views import get_base_context, _anonymous_or_real
from utilities.chem import FormatConverter
from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize
from epdb.models import CompoundStructure, Rule, SimpleAmbitRule
from epdb.views import get_base_context
from utilities.chem import FormatConverter
logger = logging.getLogger(__name__)
Package = s.GET_PACKAGE_MODEL()
def normalize_smiles(smiles):
m1 = Chem.MolFromSmiles(smiles)
@ -59,9 +56,7 @@ def run_both_engines(SMILES, SMIRKS):
set(
[
normalize_smiles(str(x))
for x in FormatConverter.sanitize_smiles(
[str(s) for s in all_rdkit_prods]
)[0]
for x in FormatConverter.sanitize_smiles([str(s) for s in all_rdkit_prods])[0]
]
)
)
@ -85,8 +80,7 @@ def migration(request):
url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
)
ALL_SMILES = [
cs.smiles
for cs in CompoundStructure.objects.filter(compound__package=BBD)
cs.smiles for cs in CompoundStructure.objects.filter(compound__package=BBD)
]
RULES = SimpleAmbitRule.objects.filter(package=BBD)
@ -142,9 +136,7 @@ def migration(request):
)
for r in migration_status["results"]:
r["detail_url"] = r["detail_url"].replace(
"http://localhost:8000", s.SERVER_URL
)
r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
context.update(**migration_status)
@ -152,8 +144,6 @@ def migration(request):
def migration_detail(request, package_uuid, rule_uuid):
current_user = _anonymous_or_real(request)
if request.method == "GET":
context = get_base_context(request)
@ -235,9 +225,7 @@ def compare(request):
context["smirks"] = (
"[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O"
)
context["smiles"] = (
"C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
)
context["smiles"] = "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
return render(request, "compare.html", context)
elif request.method == "POST":

17
tests/test_enviformer.py
View File

@ -1,10 +1,15 @@
from collections import defaultdict
from datetime import datetime
from tempfile import TemporaryDirectory
from django.conf import settings as s
from django.test import TestCase, tag
from epdb.logic import PackageManager
from epdb.models import User, EnviFormer, Package, Setting
from epdb.tasks import predict_simple, predict
from epdb.models import EnviFormer, Setting, User
from epdb.tasks import predict, predict_simple
Package = s.GET_PACKAGE_MODEL()
def measure_predict(mod, pathway_pk=None):
@ -68,11 +73,15 @@ class EnviFormerTest(TestCase):
# Test pathway prediction
times = [measure_predict(mods[1], self.BBD_SUBSET.pathways[0].pk) for _ in range(5)]
print(f"First pathway prediction took {times[0]} seconds, subsequent ones took {times[1:]}")
print(
f"First pathway prediction took {times[0]} seconds, subsequent ones took {times[1:]}"
)
# Test eviction by performing three prediction with every model, twice.
times = defaultdict(list)
for _ in range(2): # Eviction should cause the second iteration here to have to reload the models
for _ in range(
2
): # Eviction should cause the second iteration here to have to reload the models
for mod in mods:
for _ in range(3):
times[mod.pk].append(measure_predict(mod))

13
tests/test_model.py
View File

@ -1,10 +1,13 @@
from tempfile import TemporaryDirectory
import numpy as np
from django.conf import settings as s
from django.test import TestCase
from epdb.logic import PackageManager
from epdb.models import User, MLRelativeReasoning, Package, RuleBasedRelativeReasoning
from epdb.models import MLRelativeReasoning, RuleBasedRelativeReasoning, User
Package = s.GET_PACKAGE_MODEL()
class ModelTest(TestCase):
@ -85,7 +88,7 @@ class ModelTest(TestCase):
mod.build_model()
mod.evaluate_model(True, eval_packages_objs, n_splits=2)
results = mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")
_ = mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")
def test_rbrr(self):
with TemporaryDirectory() as tmpdir:
@ -103,12 +106,12 @@ class ModelTest(TestCase):
threshold=threshold,
min_count=5,
max_count=0,
name='ECC - BBD - 0.5',
description='Created MLRelativeReasoning in Testcase',
name="ECC - BBD - 0.5",
description="Created MLRelativeReasoning in Testcase",
)
mod.build_dataset()
mod.build_model()
mod.evaluate_model(True, eval_packages_objs, n_splits=2)
results = mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")
_ = mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")

8
tests/test_multigen_eval.py
View File

@ -1,8 +1,12 @@
from django.conf import settings as s
from django.test import TestCase
from networkx.utils.misc import graphs_equal
from epdb.logic import PackageManager, SPathway
from epdb.models import Pathway, User, Package
from utilities.ml import multigen_eval, pathway_edit_eval, graph_from_pathway
from epdb.models import Pathway, User
from utilities.ml import graph_from_pathway, multigen_eval, pathway_edit_eval
Package = s.GET_PACKAGE_MODEL()
class MultiGenTest(TestCase):

7
tests/test_simpleambitrule.py
View File

@ -1,9 +1,10 @@
from unittest.mock import patch, MagicMock, PropertyMock
from unittest.mock import MagicMock, PropertyMock, patch
from django.conf import settings as s
from django.test import TestCase
from epdb.logic import PackageManager
from epdb.models import User, SimpleAmbitRule
from epdb.models import SimpleAmbitRule, User
class SimpleAmbitRuleTest(TestCase):
@ -209,7 +210,7 @@ class SimpleAmbitRuleTest(TestCase):
self.assertEqual(rule.products_smarts, expected_products)
@patch("epdb.models.Package.objects")
@patch(f"{s.EPDB_PACKAGE_MODEL.replace('.', '.models.')}.objects")
def test_related_reactions_property(self, mock_package_objects):
"""Test related_reactions property returns correct queryset."""
mock_qs = MagicMock()

6
tests/views/test_model_views.py
View File

@ -1,9 +1,11 @@
from django.conf import settings as s
from django.test import TestCase, override_settings
from django.urls import reverse
from django.conf import settings as s
from epdb.logic import UserManager
from epdb.models import Package, User
from epdb.models import User
Package = s.GET_PACKAGE_MODEL()
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)

9
tests/views/test_package_views.py
View File

@ -5,14 +5,15 @@ from django.urls import reverse
from epdb.logic import UserManager
from epdb.models import (
Package,
UserPackagePermission,
Permission,
GroupPackagePermission,
Group,
GroupPackagePermission,
License,
Permission,
UserPackagePermission,
)
Package = s.GET_PACKAGE_MODEL()
class PackageViewTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]

4
utilities/decorators.py
View File

@ -1,10 +1,12 @@
# decorators.py
from functools import wraps
from django.conf import settings as s
from django.shortcuts import get_object_or_404
from epdb.logic import PackageManager
from epdb.models import Package
Package = s.GET_PACKAGE_MODEL()
# Map HTTP methods to required permissions
DEFAULT_METHOD_PERMISSIONS = {

3
utilities/misc.py
View File

@ -11,6 +11,7 @@ from enum import Enum
from types import NoneType
from typing import Any, Dict, List
from django.conf import settings as s
from django.db import transaction
from envipy_additional_information import NAME_MAPPING, EnviPyModel, Interval
from pydantic import BaseModel, HttpUrl
@ -26,7 +27,6 @@ from epdb.models import (
License,
MLRelativeReasoning,
Node,
Package,
ParallelRule,
Pathway,
PluginModel,
@ -42,6 +42,7 @@ from epdb.models import (
from utilities.chem import FormatConverter
logger = logging.getLogger(__name__)
Package = s.GET_PACKAGE_MODEL()
class HTMLGenerator: