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adjusted migration
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Browse Source 
Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

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This commit is contained in:
Tim Lorsbach
2026-03-06 15:15:08 +01:00
parent 9d70db2ca2
commit 54056c654d
63 changed files with 2657 additions and 2871 deletions
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71
epdb/legacy_api.py
View File

@ -1,17 +1,22 @@
import hashlib
from collections import defaultdict
from typing import Any, Dict, List, Optional
import jwt
import requests
import nh3
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.http import HttpResponse, JsonResponse
from django.shortcuts import redirect
from ninja import Field, Form, Query, Router, Schema
from ninja.errors import HttpError
from ninja.security import HttpBearer
from ninja.security import SessionAuth
from utilities.chem import FormatConverter
from utilities.misc import PackageExporter
from .logic import (
EPDBURLParser,
GroupManager,
@ -59,7 +64,46 @@ def _anonymous_or_real(request):
return get_user_model().objects.get(username="anonymous")
router = Router(auth=SessionAuth(csrf=False))
def validate_token(token: str) -> dict:
TENANT_ID = s.MS_ENTRA_TENANT_ID
CLIENT_ID = s.MS_ENTRA_CLIENT_ID
# Fetch Microsoft's public keys
jwks_uri = f"https://login.microsoftonline.com/{TENANT_ID}/discovery/v2.0/keys"
jwks = requests.get(jwks_uri).json()
header = jwt.get_unverified_header(token)
public_key = jwt.algorithms.RSAAlgorithm.from_jwk(
next(k for k in jwks["keys"] if k["kid"] == header["kid"])
)
claims = jwt.decode(
token,
public_key,
algorithms=["RS256"],
audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
issuer=f"https://sts.windows.net/{TENANT_ID}/",
)
return claims
class MSBearerTokenAuth(HttpBearer):
def authenticate(self, request, token):
if token is None:
return None
claims = validate_token(token)
if not User.objects.filter(uuid=claims['oid']).exists():
return None
request.user = User.objects.get(uuid=claims['oid'])
return request.user
router = Router(auth=MSBearerTokenAuth())
class Error(Schema):
@ -153,21 +197,6 @@ class SimpleModel(SimpleObject):
identifier: str = "relative-reasoning"
################
# Login/Logout #
################
@router.post("/", response={200: SimpleUser, 403: Error}, auth=None)
def login(request, loginusername: Form[str], loginpassword: Form[str]):
from django.contrib.auth import authenticate, login
email = User.objects.get(username=loginusername).email
user = authenticate(username=email, password=loginpassword)
if user:
login(request, user)
return user
else:
return 403, {"message": "Invalid username and/or password"}
########
# User #
@ -1929,13 +1958,16 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
educts = []
products = []
subclasses = CompoundStructure.__subclasses__()
if e.edgeAsSmirks:
for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
educts.append(
Node.objects.get(
pathway=pw,
default_node_label=CompoundStructure.objects.get(
default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
get(
compound__package=p, smiles=stand_ed
).compound.default_structure,
)
@ -1946,7 +1978,8 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
products.append(
Node.objects.get(
pathway=pw,
default_node_label=CompoundStructure.objects.get(
default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
get(
compound__package=p, smiles=stand_pr
).compound.default_structure,
)

80
epdb/logic.py
View File

@ -7,6 +7,7 @@ import nh3
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.db import transaction
from django.db.models import QuerySet
from pydantic import ValidationError
from epdb.models import (
@ -364,6 +365,14 @@ class PackageManager(object):
groups = GroupManager.get_groups(user)
# EDIT START
if package.classification_level == Package.Classification.SECRET:
if package.data_pool not in groups:
return False
# EDIT END
perms = {"all": ["all"], "write": ["all", "write"], "read": ["all", "write", "read"]}
valid_perms = perms.get(permission)
@ -406,6 +415,7 @@ class PackageManager(object):
try:
p = Package.objects.get(uuid=package_id)
if PackageManager.readable(user, p):
p = PackageManager.check_package_classification(user, p)
return p
else:
# FIXME: use custom exception to be translatable to 403 in API
@ -415,6 +425,37 @@ class PackageManager(object):
except Package.DoesNotExist:
raise ValueError("Package with ID {} does not exist!".format(package_id))
# EDIT START
@staticmethod
def check_package_classification(user, pack: Package):
if pack.classification_level == Package.Classification.SECRET:
if pack.data_pool.user_member.filter(id=user.id).exists():
return pack
raise ValueError("Package is secret and not accessible to user!")
else:
return pack
@staticmethod
def check_package_classifications(user, package_qs: QuerySet[Package]):
non_secret = package_qs.exclude(classification_level=Package.Classification.SECRET)
secret = package_qs.filter(classification_level=Package.Classification.SECRET)
# TODO we should be able to do via the db
accessible_secret = []
for s_package in secret:
if s_package.data_pool.user_member.filter(id=user.id).exists():
accessible_secret.append(s_package.pk)
# Cannot combine a unique query with a non-unique query -> we have to call distinct
return Package.objects.filter(pk__in=accessible_secret).distinct() | non_secret.distinct()
# EDIT END
@staticmethod
def get_all_readable_packages(user, include_reviewed=False):
# UserPermission only exists if at least read is granted...
@ -441,6 +482,10 @@ class PackageManager(object):
qs = qs.distinct()
# EDIT START
qs = PackageManager.check_package_classifications(user, qs)
# EDIT END
return qs
@staticmethod
@ -487,11 +532,11 @@ class PackageManager(object):
qs = qs.distinct()
return qs
# EDIT START
qs = PackageManager.check_package_classifications(user, qs)
# EDIT END
@staticmethod
def get_packages():
return Package.objects.all()
return qs
@staticmethod
@transaction.atomic
@ -596,6 +641,25 @@ class PackageManager(object):
else:
pack.reviewed = False
# EDIT START
if data.get("classification"):
if data["classification"] == "INTERNAL":
pack.classification = Package.Classification.RESTRICTED
elif data["classification"] == "RESTRICTED":
pack.classification = Package.Classification.RESTRICTED
elif data["classification"] == "SECRET":
pack.classification = Package.Classification.SECRET
if not "datapool" in data:
raise ValueError("Missing datapool in package")
g = Group.objects.get(uuid=data["datapool"].split('/')[-1])
pack.data_pool = g
else:
raise ValueError(f"Invalid classification {data['classification']}")
# EDIT END
pack.description = data["description"]
pack.save()
@ -681,7 +745,13 @@ class PackageManager(object):
default_structure = None
for structure in compound["structures"]:
struc = CompoundStructure()
if structure.get("pesLink"):
from bayer.models import PESStructure
struc = PESStructure()
struc.pes_link = structure["pesLink"]
else:
struc = CompoundStructure()
# struc.object_url = Command.get_id(structure, keep_ids)
struc.compound = comp
struc.uuid = UUID(structure["id"].split("/")[-1]) if keep_ids else uuid4()

594
epdb/migrations/0001_initial.py
View File

@ -1,594 +0,0 @@
# Generated by Django 5.2.1 on 2025-07-22 20:58
import datetime
import django.contrib.auth.models
import django.contrib.auth.validators
import django.contrib.postgres.fields
import django.db.models.deletion
import django.utils.timezone
import model_utils.fields
import uuid
from django.conf import settings
from django.db import migrations, models
class Migration(migrations.Migration):
initial = True
dependencies = [
('auth', '0012_alter_user_first_name_max_length'),
('contenttypes', '0002_remove_content_type_name'),
]
operations = [
migrations.CreateModel(
name='Compound',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
],
),
migrations.CreateModel(
name='EPModel',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
),
migrations.CreateModel(
name='Permission',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
],
),
migrations.CreateModel(
name='License',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('link', models.URLField(verbose_name='link')),
('image_link', models.URLField(verbose_name='Image link')),
],
),
migrations.CreateModel(
name='Rule',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
),
migrations.CreateModel(
name='User',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('password', models.CharField(max_length=128, verbose_name='password')),
('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
('email', models.EmailField(max_length=254, unique=True)),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
],
options={
'verbose_name': 'user',
'verbose_name_plural': 'users',
'abstract': False,
},
managers=[
('objects', django.contrib.auth.models.UserManager()),
],
),
migrations.CreateModel(
name='APIToken',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('hashed_key', models.CharField(max_length=128, unique=True)),
('created', models.DateTimeField(auto_now_add=True)),
('expires_at', models.DateTimeField(blank=True, default=datetime.datetime(2025, 10, 20, 20, 58, 48, 351675, tzinfo=datetime.timezone.utc), null=True)),
('name', models.CharField(blank=True, help_text='Optional name for the token', max_length=100)),
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
],
),
migrations.CreateModel(
name='CompoundStructure',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('smiles', models.TextField(verbose_name='SMILES')),
('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
('normalized_structure', models.BooleanField(default=False)),
('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='compound',
name='default_structure',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
),
migrations.CreateModel(
name='Edge',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
),
migrations.CreateModel(
name='EnviFormer',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
('threshold', models.FloatField(default=0.5)),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='PluginModel',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='RuleBaseRelativeReasoning',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='Group',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(verbose_name='Group name')),
('public', models.BooleanField(default=False, verbose_name='Public Group')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('group_member', models.ManyToManyField(related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='user',
name='default_group',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
),
migrations.CreateModel(
name='Node',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('depth', models.IntegerField(verbose_name='Node depth')),
('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='edge',
name='end_nodes',
field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
),
migrations.AddField(
model_name='edge',
name='start_nodes',
field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
),
migrations.CreateModel(
name='Package',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='epmodel',
name='package',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
),
migrations.AddField(
model_name='compound',
name='package',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
),
migrations.AddField(
model_name='user',
name='default_package',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.package', verbose_name='Default Package'),
),
migrations.CreateModel(
name='SequentialRule',
fields=[
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.rule',),
),
migrations.CreateModel(
name='SimpleRule',
fields=[
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.rule',),
),
migrations.AddField(
model_name='rule',
name='package',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
),
migrations.AddField(
model_name='rule',
name='polymorphic_ctype',
field=models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype'),
),
migrations.CreateModel(
name='Pathway',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='node',
name='pathway',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
),
migrations.AddField(
model_name='edge',
name='pathway',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
),
migrations.CreateModel(
name='Reaction',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='edge',
name='edge_label',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
),
migrations.CreateModel(
name='Scenario',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('scenario_date', models.CharField(default='No date', max_length=256)),
('scenario_type', models.CharField(default='Not specified', max_length=256)),
('additional_information', models.JSONField(verbose_name='Additional Information')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
('parent', models.ForeignKey(default=None, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.scenario')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='rule',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='reaction',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='pathway',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='node',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='edge',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='compoundstructure',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='compound',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.CreateModel(
name='Setting',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('public', models.BooleanField(default=False)),
('global_default', models.BooleanField(default=False)),
('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to='epdb.package', verbose_name='Setting Rule Packages')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='pathway',
name='setting',
field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Setting'),
),
migrations.AddField(
model_name='user',
name='default_setting',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
),
migrations.CreateModel(
name='MLRelativeReasoning',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
('threshold', models.FloatField(default=0.5)),
('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
('data_packages', models.ManyToManyField(related_name='data_packages', to='epdb.package', verbose_name='Data Packages')),
('eval_packages', models.ManyToManyField(related_name='eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
('rule_packages', models.ManyToManyField(related_name='rule_packages', to='epdb.package', verbose_name='Rule Packages')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='ApplicabilityDomain',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('num_neighbours', models.FloatField(default=5)),
('reliability_threshold', models.FloatField(default=0.5)),
('local_compatibilty_threshold', models.FloatField(default=0.5)),
('model', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning')),
],
options={
'abstract': False,
},
),
migrations.CreateModel(
name='SimpleAmbitRule',
fields=[
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
('smirks', models.TextField(verbose_name='SMIRKS')),
('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.simplerule',),
),
migrations.CreateModel(
name='SimpleRDKitRule',
fields=[
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.simplerule',),
),
migrations.CreateModel(
name='SequentialRuleOrdering',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('order_index', models.IntegerField()),
('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
],
),
migrations.AddField(
model_name='sequentialrule',
name='simple_rules',
field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
),
migrations.CreateModel(
name='ParallelRule',
fields=[
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.rule',),
),
migrations.AlterUniqueTogether(
name='compound',
unique_together={('uuid', 'package')},
),
migrations.CreateModel(
name='GroupPackagePermission',
fields=[
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
],
options={
'unique_together': {('package', 'group')},
},
bases=('epdb.permission',),
),
migrations.CreateModel(
name='UserPackagePermission',
fields=[
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
],
options={
'unique_together': {('package', 'user')},
},
bases=('epdb.permission',),
),
migrations.CreateModel(
name='UserSettingPermission',
fields=[
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
],
options={
'unique_together': {('setting', 'user')},
},
bases=('epdb.permission',),
),
]

1020
epdb/migrations/0001_squashed_0003_applicabilitydomain_url_compound_url_and_more.py
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128
epdb/migrations/0002_externaldatabase_alter_apitoken_options_and_more.py
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@ -1,128 +0,0 @@
# Generated by Django 5.2.1 on 2025-08-25 18:07
import django.db.models.deletion
import django.utils.timezone
import model_utils.fields
import uuid
from django.conf import settings
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('contenttypes', '0002_remove_content_type_name'),
('epdb', '0001_initial'),
]
operations = [
migrations.CreateModel(
name='ExternalDatabase',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
('description', models.TextField(blank=True, verbose_name='Description')),
('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
],
options={
'verbose_name': 'External Database',
'verbose_name_plural': 'External Databases',
'db_table': 'epdb_external_database',
'ordering': ['name'],
},
),
migrations.AlterModelOptions(
name='apitoken',
options={'ordering': ['-created'], 'verbose_name': 'API Token', 'verbose_name_plural': 'API Tokens'},
),
migrations.AlterModelOptions(
name='edge',
options={},
),
migrations.RemoveField(
model_name='edge',
name='polymorphic_ctype',
),
migrations.AddField(
model_name='apitoken',
name='is_active',
field=models.BooleanField(default=True, help_text='Whether this token is active'),
),
migrations.AddField(
model_name='apitoken',
name='modified',
field=model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified'),
),
migrations.AddField(
model_name='applicabilitydomain',
name='functional_groups',
field=models.JSONField(blank=True, default=dict, null=True),
),
migrations.AddField(
model_name='mlrelativereasoning',
name='app_domain',
field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
),
migrations.AlterField(
model_name='apitoken',
name='created',
field=model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created'),
),
migrations.AlterField(
model_name='apitoken',
name='expires_at',
field=models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True),
),
migrations.AlterField(
model_name='apitoken',
name='hashed_key',
field=models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True),
),
migrations.AlterField(
model_name='apitoken',
name='name',
field=models.CharField(help_text='Descriptive name for this token', max_length=100),
),
migrations.AlterField(
model_name='apitoken',
name='user',
field=models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL),
),
migrations.AlterField(
model_name='applicabilitydomain',
name='num_neighbours',
field=models.IntegerField(default=5),
),
migrations.AlterModelTable(
name='apitoken',
table='epdb_api_token',
),
migrations.CreateModel(
name='ExternalIdentifier',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
('object_id', models.IntegerField()),
('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
],
options={
'verbose_name': 'External Identifier',
'verbose_name_plural': 'External Identifiers',
'db_table': 'epdb_external_identifier',
'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
},
),
]

228
epdb/migrations/0003_applicabilitydomain_url_compound_url_and_more.py
View File

@ -1,228 +0,0 @@
# Generated by Django 5.2.1 on 2025-08-26 17:05
from django.db import migrations, models
def populate_url(apps, schema_editor):
MODELS = [
'User',
'Group',
'Package',
'Compound',
'CompoundStructure',
'Pathway',
'Edge',
'Node',
'Reaction',
'SimpleAmbitRule',
'SimpleRDKitRule',
'ParallelRule',
'SequentialRule',
'Scenario',
'Setting',
'MLRelativeReasoning',
'EnviFormer',
'ApplicabilityDomain',
]
for model in MODELS:
obj_cls = apps.get_model("epdb", model)
for obj in obj_cls.objects.all():
obj.url = assemble_url(obj)
if obj.url is None:
raise ValueError(f"Could not assemble url for {obj}")
obj.save()
def assemble_url(obj):
from django.conf import settings as s
match obj.__class__.__name__:
case 'User':
return '{}/user/{}'.format(s.SERVER_URL, obj.uuid)
case 'Group':
return '{}/group/{}'.format(s.SERVER_URL, obj.uuid)
case 'Package':
return '{}/package/{}'.format(s.SERVER_URL, obj.uuid)
case 'Compound':
return '{}/compound/{}'.format(obj.package.url, obj.uuid)
case 'CompoundStructure':
return '{}/structure/{}'.format(obj.compound.url, obj.uuid)
case 'SimpleAmbitRule':
return '{}/simple-ambit-rule/{}'.format(obj.package.url, obj.uuid)
case 'SimpleRDKitRule':
return '{}/simple-rdkit-rule/{}'.format(obj.package.url, obj.uuid)
case 'ParallelRule':
return '{}/parallel-rule/{}'.format(obj.package.url, obj.uuid)
case 'SequentialRule':
return '{}/sequential-rule/{}'.format(obj.compound.url, obj.uuid)
case 'Reaction':
return '{}/reaction/{}'.format(obj.package.url, obj.uuid)
case 'Pathway':
return '{}/pathway/{}'.format(obj.package.url, obj.uuid)
case 'Node':
return '{}/node/{}'.format(obj.pathway.url, obj.uuid)
case 'Edge':
return '{}/edge/{}'.format(obj.pathway.url, obj.uuid)
case 'MLRelativeReasoning':
return '{}/model/{}'.format(obj.package.url, obj.uuid)
case 'EnviFormer':
return '{}/model/{}'.format(obj.package.url, obj.uuid)
case 'ApplicabilityDomain':
return '{}/model/{}/applicability-domain/{}'.format(obj.model.package.url, obj.model.uuid, obj.uuid)
case 'Scenario':
return '{}/scenario/{}'.format(obj.package.url, obj.uuid)
case 'Setting':
return '{}/setting/{}'.format(s.SERVER_URL, obj.uuid)
case _:
raise ValueError(f"Unknown model {obj.__class__.__name__}")
class Migration(migrations.Migration):
dependencies = [
('epdb', '0002_externaldatabase_alter_apitoken_options_and_more'),
]
operations = [
migrations.AddField(
model_name='applicabilitydomain',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='compound',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='compoundstructure',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='edge',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='epmodel',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='group',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='node',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='package',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='pathway',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='reaction',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='rule',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='scenario',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='setting',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.AddField(
model_name='user',
name='url',
field=models.TextField(null=True, unique=False, verbose_name='URL'),
),
migrations.RunPython(populate_url, reverse_code=migrations.RunPython.noop),
migrations.AlterField(
model_name='applicabilitydomain',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='compound',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='compoundstructure',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='edge',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='epmodel',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='group',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='node',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='package',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='pathway',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='reaction',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='rule',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='scenario',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='setting',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
migrations.AlterField(
model_name='user',
name='url',
field=models.TextField(null=True, unique=True, verbose_name='URL'),
),
]

55
epdb/migrations/0004_alter_mlrelativereasoning_options_and_more.py
View File

@ -1,55 +0,0 @@
# Generated by Django 5.2.1 on 2025-09-09 09:21
import django.db.models.deletion
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('epdb', '0001_squashed_0003_applicabilitydomain_url_compound_url_and_more'),
]
operations = [
migrations.AlterModelOptions(
name='mlrelativereasoning',
options={},
),
migrations.AlterField(
model_name='mlrelativereasoning',
name='data_packages',
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.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='epdb.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='epdb.package', verbose_name='Rule Packages'),
),
migrations.CreateModel(
name='RuleBasedRelativeReasoning',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
('threshold', models.FloatField(default=0.5)),
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
('min_count', models.IntegerField(default=10)),
('max_count', models.IntegerField(default=0)),
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages')),
('eval_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
('rule_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages')),
],
options={
'abstract': False,
},
bases=('epdb.epmodel',),
),
migrations.DeleteModel(
name='RuleBaseRelativeReasoning',
),
]

18
epdb/migrations/0005_alter_group_group_member.py
View File

@ -1,18 +0,0 @@
# Generated by Django 5.2.1 on 2025-09-11 06:21
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('epdb', '0004_alter_mlrelativereasoning_options_and_more'),
]
operations = [
migrations.AlterField(
model_name='group',
name='group_member',
field=models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member'),
),
]

23
epdb/migrations/0006_mlrelativereasoning_multigen_eval_and_more.py
View File

@ -1,23 +0,0 @@
# Generated by Django 5.2.1 on 2025-09-18 06:42
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('epdb', '0005_alter_group_group_member'),
]
operations = [
migrations.AddField(
model_name='mlrelativereasoning',
name='multigen_eval',
field=models.BooleanField(default=False),
),
migrations.AddField(
model_name='rulebasedrelativereasoning',
name='multigen_eval',
field=models.BooleanField(default=False),
),
]

53
epdb/migrations/0007_alter_enviformer_options_enviformer_app_domain_and_more.py
View File

@ -1,53 +0,0 @@
# Generated by Django 5.2.1 on 2025-10-07 08:19
import django.db.models.deletion
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('epdb', '0006_mlrelativereasoning_multigen_eval_and_more'),
]
operations = [
migrations.AlterModelOptions(
name='enviformer',
options={},
),
migrations.AddField(
model_name='enviformer',
name='app_domain',
field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
),
migrations.AddField(
model_name='enviformer',
name='data_packages',
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages'),
),
migrations.AddField(
model_name='enviformer',
name='eval_packages',
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages'),
),
migrations.AddField(
model_name='enviformer',
name='eval_results',
field=models.JSONField(blank=True, default=dict, null=True),
),
migrations.AddField(
model_name='enviformer',
name='model_status',
field=models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL'),
),
migrations.AddField(
model_name='enviformer',
name='multigen_eval',
field=models.BooleanField(default=False),
),
migrations.AddField(
model_name='enviformer',
name='rule_packages',
field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages'),
),
]

64
epdb/migrations/0008_enzymelink.py
View File

@ -1,64 +0,0 @@
# Generated by Django 5.2.7 on 2025-10-10 06:58
import django.db.models.deletion
import django.utils.timezone
import model_utils.fields
import uuid
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0007_alter_enviformer_options_enviformer_app_domain_and_more"),
]
operations = [
migrations.CreateModel(
name="EnzymeLink",
fields=[
(
"id",
models.BigAutoField(
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
),
),
(
"created",
model_utils.fields.AutoCreatedField(
default=django.utils.timezone.now, editable=False, verbose_name="created"
),
),
(
"modified",
model_utils.fields.AutoLastModifiedField(
default=django.utils.timezone.now, editable=False, verbose_name="modified"
),
),
(
"uuid",
models.UUIDField(
default=uuid.uuid4, unique=True, verbose_name="UUID of this object"
),
),
("name", models.TextField(default="no name", verbose_name="Name")),
(
"description",
models.TextField(default="no description", verbose_name="Descriptions"),
),
("url", models.TextField(null=True, unique=True, verbose_name="URL")),
("kv", models.JSONField(blank=True, default=dict, null=True)),
("ec_number", models.TextField(verbose_name="EC Number")),
("classification_level", models.IntegerField(verbose_name="Classification Level")),
("linking_method", models.TextField(verbose_name="Linking Method")),
("edge_evidence", models.ManyToManyField(to="epdb.edge")),
("reaction_evidence", models.ManyToManyField(to="epdb.reaction")),
(
"rule",
models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="epdb.rule"),
),
],
options={
"abstract": False,
},
),
]

66
epdb/migrations/0009_joblog.py
View File

@ -1,66 +0,0 @@
# Generated by Django 5.2.7 on 2025-10-27 09:39
import django.db.models.deletion
import django.utils.timezone
import model_utils.fields
from django.conf import settings
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0008_enzymelink"),
]
operations = [
migrations.CreateModel(
name="JobLog",
fields=[
(
"id",
models.BigAutoField(
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
),
),
(
"created",
model_utils.fields.AutoCreatedField(
default=django.utils.timezone.now, editable=False, verbose_name="created"
),
),
(
"modified",
model_utils.fields.AutoLastModifiedField(
default=django.utils.timezone.now, editable=False, verbose_name="modified"
),
),
("task_id", models.UUIDField(unique=True)),
("job_name", models.TextField()),
(
"status",
models.CharField(
choices=[
("INITIAL", "Initial"),
("SUCCESS", "Success"),
("FAILURE", "Failure"),
("REVOKED", "Revoked"),
("IGNORED", "Ignored"),
],
default="INITIAL",
max_length=20,
),
),
("done_at", models.DateTimeField(blank=True, default=None, null=True)),
("task_result", models.TextField(blank=True, default=None, null=True)),
(
"user",
models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL
),
),
],
options={
"abstract": False,
},
),
]

18
epdb/migrations/0010_license_cc_string.py
View File

@ -1,18 +0,0 @@
# Generated by Django 5.2.7 on 2025-11-11 14:11
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0009_joblog"),
]
operations = [
migrations.AddField(
model_name="license",
name="cc_string",
field=models.TextField(default="by-nc-sa", verbose_name="CC string"),
preserve_default=False,
),
]

59
epdb/migrations/0011_auto_20251111_1413.py
View File

@ -1,59 +0,0 @@
# Generated by Django 5.2.7 on 2025-11-11 14:13
import re
from django.contrib.postgres.aggregates import ArrayAgg
from django.db import migrations
from django.db.models import Min
def set_cc(apps, schema_editor):
License = apps.get_model("epdb", "License")
# For all existing licenses extract cc_string from link
for license in License.objects.all():
pattern = r"/licenses/([^/]+)/4\.0"
match = re.search(pattern, license.link)
if match:
license.cc_string = match.group(1)
license.save()
else:
raise ValueError(f"Could not find license for {license.link}")
# Ensure we have all licenses
cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
for cc_string in cc_strings:
if not License.objects.filter(cc_string=cc_string).exists():
new_license = License()
new_license.cc_string = cc_string
new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
new_license.save()
# As we might have existing Licenses representing the same License,
# get min pk and all pks as a list
license_lookup_qs = License.objects.values("cc_string").annotate(
lowest_pk=Min("id"), all_pks=ArrayAgg("id", order_by=("id",))
)
license_lookup = {
row["cc_string"]: (row["lowest_pk"], row["all_pks"]) for row in license_lookup_qs
}
Packages = apps.get_model("epdb", "Package")
for k, v in license_lookup.items():
# Set min pk to all packages pointing to any of the duplicates
Packages.objects.filter(pk__in=v[1]).update(license_id=v[0])
# remove the min pk from "other" pks as we use them for deletion
v[1].remove(v[0])
# Delete redundant License objects
License.objects.filter(pk__in=v[1]).delete()
class Migration(migrations.Migration):
dependencies = [
("epdb", "0010_license_cc_string"),
]
operations = [migrations.RunPython(set_cc)]

22
epdb/migrations/0012_node_stereo_removed_pathway_predicted.py
View File

@ -1,22 +0,0 @@
# Generated by Django 5.2.7 on 2025-12-02 13:09
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0011_auto_20251111_1413"),
]
operations = [
migrations.AddField(
model_name="node",
name="stereo_removed",
field=models.BooleanField(default=False),
),
migrations.AddField(
model_name="pathway",
name="predicted",
field=models.BooleanField(default=False),
),
]

25
epdb/migrations/0013_setting_expansion_schema.py
View File

@ -1,25 +0,0 @@
# Generated by Django 5.2.7 on 2025-12-14 11:30
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0012_node_stereo_removed_pathway_predicted"),
]
operations = [
migrations.AddField(
model_name="setting",
name="expansion_schema",
field=models.CharField(
choices=[
("BFS", "Breadth First Search"),
("DFS", "Depth First Search"),
("GREEDY", "Greedy"),
],
default="BFS",
max_length=20,
),
),
]

17
epdb/migrations/0014_rename_expansion_schema_setting_expansion_scheme.py
View File

@ -1,17 +0,0 @@
# Generated by Django 5.2.7 on 2025-12-14 16:02
from django.db import migrations
class Migration(migrations.Migration):
dependencies = [
("epdb", "0013_setting_expansion_schema"),
]
operations = [
migrations.RenameField(
model_name="setting",
old_name="expansion_schema",
new_name="expansion_scheme",
),
]

17
epdb/migrations/0015_user_is_reviewer.py
View File

@ -1,17 +0,0 @@
# Generated by Django 5.2.7 on 2026-01-19 19:26
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0014_rename_expansion_schema_setting_expansion_scheme"),
]
operations = [
migrations.AddField(
model_name="user",
name="is_reviewer",
field=models.BooleanField(default=False),
),
]

179
epdb/migrations/0016_remove_enviformer_model_status_and_more.py
View File

@ -1,179 +0,0 @@
# Generated by Django 5.2.7 on 2026-02-12 09:38
import django.db.models.deletion
from django.conf import settings
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0015_user_is_reviewer"),
]
operations = [
migrations.RemoveField(
model_name="enviformer",
name="model_status",
),
migrations.RemoveField(
model_name="mlrelativereasoning",
name="model_status",
),
migrations.RemoveField(
model_name="rulebasedrelativereasoning",
name="model_status",
),
migrations.AddField(
model_name="epmodel",
name="model_status",
field=models.CharField(
choices=[
("INITIAL", "Initial"),
("INITIALIZING", "Model is initializing."),
("BUILDING", "Model is building."),
(
"BUILT_NOT_EVALUATED",
"Model is built and can be used for predictions, Model is not evaluated yet.",
),
("EVALUATING", "Model is evaluating"),
("FINISHED", "Model has finished building and evaluation."),
("ERROR", "Model has failed."),
],
default="INITIAL",
),
),
migrations.AlterField(
model_name="enviformer",
name="eval_packages",
field=models.ManyToManyField(
blank=True,
related_name="%(app_label)s_%(class)s_eval_packages",
to=settings.EPDB_PACKAGE_MODEL,
verbose_name="Evaluation Packages",
),
),
migrations.AlterField(
model_name="enviformer",
name="rule_packages",
field=models.ManyToManyField(
blank=True,
related_name="%(app_label)s_%(class)s_rule_packages",
to=settings.EPDB_PACKAGE_MODEL,
verbose_name="Rule Packages",
),
),
migrations.AlterField(
model_name="mlrelativereasoning",
name="eval_packages",
field=models.ManyToManyField(
blank=True,
related_name="%(app_label)s_%(class)s_eval_packages",
to=settings.EPDB_PACKAGE_MODEL,
verbose_name="Evaluation Packages",
),
),
migrations.AlterField(
model_name="mlrelativereasoning",
name="rule_packages",
field=models.ManyToManyField(
blank=True,
related_name="%(app_label)s_%(class)s_rule_packages",
to=settings.EPDB_PACKAGE_MODEL,
verbose_name="Rule Packages",
),
),
migrations.AlterField(
model_name="rulebasedrelativereasoning",
name="eval_packages",
field=models.ManyToManyField(
blank=True,
related_name="%(app_label)s_%(class)s_eval_packages",
to=settings.EPDB_PACKAGE_MODEL,
verbose_name="Evaluation Packages",
),
),
migrations.AlterField(
model_name="rulebasedrelativereasoning",
name="rule_packages",
field=models.ManyToManyField(
blank=True,
related_name="%(app_label)s_%(class)s_rule_packages",
to=settings.EPDB_PACKAGE_MODEL,
verbose_name="Rule Packages",
),
),
migrations.CreateModel(
name="PropertyPluginModel",
fields=[
(
"epmodel_ptr",
models.OneToOneField(
auto_created=True,
on_delete=django.db.models.deletion.CASCADE,
parent_link=True,
primary_key=True,
serialize=False,
to="epdb.epmodel",
),
),
("threshold", models.FloatField(default=0.5)),
("eval_results", models.JSONField(blank=True, default=dict, null=True)),
("multigen_eval", models.BooleanField(default=False)),
("plugin_identifier", models.CharField(max_length=255)),
(
"app_domain",
models.ForeignKey(
blank=True,
default=None,
null=True,
on_delete=django.db.models.deletion.SET_NULL,
to="epdb.applicabilitydomain",
),
),
(
"data_packages",
models.ManyToManyField(
blank=True,
related_name="%(app_label)s_%(class)s_data_packages",
to=settings.EPDB_PACKAGE_MODEL,
verbose_name="Data Packages",
),
),
(
"eval_packages",
models.ManyToManyField(
blank=True,
related_name="%(app_label)s_%(class)s_eval_packages",
to=settings.EPDB_PACKAGE_MODEL,
verbose_name="Evaluation Packages",
),
),
(
"rule_packages",
models.ManyToManyField(
blank=True,
related_name="%(app_label)s_%(class)s_rule_packages",
to=settings.EPDB_PACKAGE_MODEL,
verbose_name="Rule Packages",
),
),
],
options={
"abstract": False,
},
bases=("epdb.epmodel",),
),
migrations.AddField(
model_name="setting",
name="property_models",
field=models.ManyToManyField(
blank=True,
related_name="settings",
to="epdb.propertypluginmodel",
verbose_name="Setting Property Models",
),
),
migrations.DeleteModel(
name="PluginModel",
),
]

93
epdb/migrations/0017_additionalinformation.py
View File

@ -1,93 +0,0 @@
# Generated by Django 5.2.7 on 2026-02-20 12:02
import django.db.models.deletion
import uuid
from django.conf import settings
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("contenttypes", "0002_remove_content_type_name"),
("epdb", "0016_remove_enviformer_model_status_and_more"),
]
operations = [
migrations.CreateModel(
name="AdditionalInformation",
fields=[
(
"id",
models.BigAutoField(
auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
),
),
("uuid", models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
("url", models.TextField(null=True, unique=True, verbose_name="URL")),
("kv", models.JSONField(blank=True, default=dict, null=True)),
("type", models.TextField(verbose_name="Additional Information Type")),
("data", models.JSONField(blank=True, default=dict, null=True)),
("object_id", models.PositiveBigIntegerField(blank=True, null=True)),
(
"content_type",
models.ForeignKey(
blank=True,
null=True,
on_delete=django.db.models.deletion.CASCADE,
to="contenttypes.contenttype",
),
),
(
"package",
models.ForeignKey(
on_delete=django.db.models.deletion.CASCADE,
to=settings.EPDB_PACKAGE_MODEL,
verbose_name="Package",
),
),
(
"scenario",
models.ForeignKey(
blank=True,
null=True,
on_delete=django.db.models.deletion.CASCADE,
related_name="scenario_additional_information",
to="epdb.scenario",
),
),
],
options={
"indexes": [
models.Index(fields=["type"], name="epdb_additi_type_394349_idx"),
models.Index(
fields=["scenario", "type"], name="epdb_additi_scenari_a59edf_idx"
),
models.Index(
fields=["content_type", "object_id"], name="epdb_additi_content_44d4b4_idx"
),
models.Index(
fields=["scenario", "content_type", "object_id"],
name="epdb_additi_scenari_ef2bf5_idx",
),
],
"constraints": [
models.CheckConstraint(
condition=models.Q(
models.Q(("content_type__isnull", True), ("object_id__isnull", True)),
models.Q(("content_type__isnull", False), ("object_id__isnull", False)),
_connector="OR",
),
name="ck_addinfo_gfk_pair",
),
models.CheckConstraint(
condition=models.Q(
("scenario__isnull", False),
("content_type__isnull", False),
_connector="OR",
),
name="ck_addinfo_not_both_null",
),
],
},
),
]

132
epdb/migrations/0018_auto_20260220_1203.py
View File

@ -1,132 +0,0 @@
# Generated by Django 5.2.7 on 2026-02-20 12:03
from django.db import migrations
def get_additional_information(scenario):
from envipy_additional_information import registry
from envipy_additional_information.parsers import TypeOfAerationParser
for k, vals in scenario.additional_information.items():
if k == "enzyme":
continue
if k == "SpikeConentration":
k = "SpikeConcentration"
if k == "AerationType":
k = "TypeOfAeration"
for v in vals:
# Per default additional fields are ignored
MAPPING = {c.__name__: c for c in registry.list_models().values()}
try:
inst = MAPPING[k](**v)
except Exception:
if k == "TypeOfAeration":
toa = TypeOfAerationParser()
inst = toa.from_string(v["type"])
# Add uuid to uniquely identify objects for manipulation
if "uuid" in v:
inst.__dict__["uuid"] = v["uuid"]
yield inst
def forward_func(apps, schema_editor):
Scenario = apps.get_model("epdb", "Scenario")
ContentType = apps.get_model("contenttypes", "ContentType")
AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
bulk = []
related = []
ctype = {o.model: o for o in ContentType.objects.all()}
parents = Scenario.objects.prefetch_related(
"compound_set",
"compoundstructure_set",
"reaction_set",
"rule_set",
"pathway_set",
"node_set",
"edge_set",
).filter(parent__isnull=True)
for i, scenario in enumerate(parents):
print(f"{i + 1}/{len(parents)}", end="\r")
if scenario.parent is not None:
related.append(scenario.parent)
continue
for ai in get_additional_information(scenario):
bulk.append(
AdditionalInformation(
package=scenario.package,
scenario=scenario,
type=ai.__class__.__name__,
data=ai.model_dump(mode="json"),
)
)
print("\n", len(bulk))
related = Scenario.objects.prefetch_related(
"compound_set",
"compoundstructure_set",
"reaction_set",
"rule_set",
"pathway_set",
"node_set",
"edge_set",
).filter(parent__isnull=False)
for i, scenario in enumerate(related):
print(f"{i + 1}/{len(related)}", end="\r")
parent = scenario.parent
# Check to which objects this scenario is attached to
for ai in get_additional_information(scenario):
rel_objs = [
"compound",
"compoundstructure",
"reaction",
"rule",
"pathway",
"node",
"edge",
]
for rel_obj in rel_objs:
for o in getattr(scenario, f"{rel_obj}_set").all():
bulk.append(
AdditionalInformation(
package=scenario.package,
scenario=parent,
type=ai.__class__.__name__,
data=ai.model_dump(mode="json"),
content_type=ctype[rel_obj],
object_id=o.pk,
)
)
print("Start creating additional information objects...")
AdditionalInformation.objects.bulk_create(bulk)
print("Done!")
print(len(bulk))
Scenario.objects.filter(parent__isnull=False).delete()
# Call ai save to fix urls
ais = AdditionalInformation.objects.all()
total = ais.count()
for i, ai in enumerate(ais):
print(f"{i + 1}/{total}", end="\r")
ai.save()
class Migration(migrations.Migration):
dependencies = [
("epdb", "0017_additionalinformation"),
]
operations = [
migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
]

739
epdb/migrations/0019_remove_scenario_additional_information_and_more.py
View File

@ -1,20 +1,741 @@
# Generated by Django 5.2.7 on 2026-02-23 08:45
# Generated by Django 5.2.7 on 2026-03-06 10:51
from django.db import migrations
import django.contrib.auth.models
import django.contrib.auth.validators
import django.contrib.postgres.fields
import django.db.models.deletion
import django.utils.timezone
import model_utils.fields
import uuid
from django.conf import settings
from django.db import migrations, models
class Migration(migrations.Migration):
initial = True
dependencies = [
("epdb", "0018_auto_20260220_1203"),
('auth', '0012_alter_user_first_name_max_length'),
('contenttypes', '0002_remove_content_type_name'),
migrations.swappable_dependency(settings.EPDB_PACKAGE_MODEL),
]
operations = [
migrations.RemoveField(
model_name="scenario",
name="additional_information",
migrations.CreateModel(
name='ApplicabilityDomain',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('num_neighbours', models.IntegerField(default=5)),
('reliability_threshold', models.FloatField(default=0.5)),
('local_compatibilty_threshold', models.FloatField(default=0.5)),
('functional_groups', models.JSONField(blank=True, default=dict, null=True)),
],
options={
'abstract': False,
},
),
migrations.RemoveField(
model_name="scenario",
name="parent",
migrations.CreateModel(
name='Edge',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
],
options={
'abstract': False,
},
),
migrations.CreateModel(
name='EPModel',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
),
migrations.CreateModel(
name='ExternalDatabase',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
('description', models.TextField(blank=True, verbose_name='Description')),
('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
],
options={
'verbose_name': 'External Database',
'verbose_name_plural': 'External Databases',
'db_table': 'epdb_external_database',
'ordering': ['name'],
},
),
migrations.CreateModel(
name='Permission',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
],
),
migrations.CreateModel(
name='License',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('cc_string', models.TextField(verbose_name='CC string')),
('link', models.URLField(verbose_name='link')),
('image_link', models.URLField(verbose_name='Image link')),
],
),
migrations.CreateModel(
name='Rule',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
),
migrations.CreateModel(
name='User',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('password', models.CharField(max_length=128, verbose_name='password')),
('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
('email', models.EmailField(max_length=254, unique=True)),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('is_reviewer', models.BooleanField(default=False)),
('default_package', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Default Package')),
('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
],
options={
'verbose_name': 'user',
'verbose_name_plural': 'users',
'abstract': False,
},
managers=[
('objects', django.contrib.auth.models.UserManager()),
],
),
migrations.CreateModel(
name='APIToken',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('hashed_key', models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True)),
('expires_at', models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True)),
('name', models.CharField(help_text='Descriptive name for this token', max_length=100)),
('is_active', models.BooleanField(default=True, help_text='Whether this token is active')),
('user', models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL)),
],
options={
'verbose_name': 'API Token',
'verbose_name_plural': 'API Tokens',
'db_table': 'epdb_api_token',
'ordering': ['-created'],
},
),
migrations.CreateModel(
name='Compound',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
],
),
migrations.CreateModel(
name='CompoundStructure',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('smiles', models.TextField(verbose_name='SMILES')),
('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
('normalized_structure', models.BooleanField(default=False)),
('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='compound',
name='default_structure',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
),
migrations.CreateModel(
name='PropertyPluginModel',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
('threshold', models.FloatField(default=0.5)),
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
('multigen_eval', models.BooleanField(default=False)),
('plugin_identifier', models.CharField(max_length=255)),
],
options={
'abstract': False,
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='Group',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('name', models.TextField(verbose_name='Group name')),
('public', models.BooleanField(default=False, verbose_name='Public Group')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('group_member', models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='user',
name='default_group',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
),
migrations.CreateModel(
name='JobLog',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('task_id', models.UUIDField(unique=True)),
('job_name', models.TextField()),
('status', models.CharField(choices=[('INITIAL', 'Initial'), ('SUCCESS', 'Success'), ('FAILURE', 'Failure'), ('REVOKED', 'Revoked'), ('IGNORED', 'Ignored')], default='INITIAL', max_length=20)),
('done_at', models.DateTimeField(blank=True, default=None, null=True)),
('task_result', models.TextField(blank=True, default=None, null=True)),
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
],
options={
'abstract': False,
},
),
migrations.CreateModel(
name='Package',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
],
options={
'swappable': 'EPDB_PACKAGE_MODEL',
},
),
migrations.CreateModel(
name='Node',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('depth', models.IntegerField(verbose_name='Node depth')),
('stereo_removed', models.BooleanField(default=False)),
('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='edge',
name='end_nodes',
field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
),
migrations.AddField(
model_name='edge',
name='start_nodes',
field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
),
migrations.CreateModel(
name='SequentialRule',
fields=[
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.rule',),
),
migrations.CreateModel(
name='SimpleRule',
fields=[
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.rule',),
),
migrations.CreateModel(
name='Pathway',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('predicted', models.BooleanField(default=False)),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='node',
name='pathway',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
),
migrations.AddField(
model_name='edge',
name='pathway',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
),
migrations.CreateModel(
name='Reaction',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
],
options={
'abstract': False,
},
),
migrations.CreateModel(
name='EnzymeLink',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('ec_number', models.TextField(verbose_name='EC Number')),
('classification_level', models.IntegerField(verbose_name='Classification Level')),
('linking_method', models.TextField(verbose_name='Linking Method')),
('edge_evidence', models.ManyToManyField(to='epdb.edge')),
('rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.rule')),
('reaction_evidence', models.ManyToManyField(to='epdb.reaction')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='edge',
name='edge_label',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
),
migrations.CreateModel(
name='Scenario',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('scenario_date', models.CharField(default='No date', max_length=256)),
('scenario_type', models.CharField(default='Not specified', max_length=256)),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='rule',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='reaction',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='pathway',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='node',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='edge',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='compoundstructure',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.AddField(
model_name='compound',
name='scenarios',
field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
),
migrations.CreateModel(
name='Setting',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
('name', models.TextField(default='no name', verbose_name='Name')),
('description', models.TextField(default='no description', verbose_name='Descriptions')),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('public', models.BooleanField(default=False)),
('global_default', models.BooleanField(default=False)),
('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
('expansion_scheme', models.CharField(choices=[('BFS', 'Breadth First Search'), ('DFS', 'Depth First Search'), ('GREEDY', 'Greedy')], default='BFS', max_length=20)),
('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Setting Rule Packages')),
('property_models', models.ManyToManyField(blank=True, related_name='settings', to='epdb.propertypluginmodel', verbose_name='Setting Property Models')),
],
options={
'abstract': False,
},
),
migrations.AddField(
model_name='pathway',
name='setting',
field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Setting'),
),
migrations.AddField(
model_name='user',
name='default_setting',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
),
migrations.CreateModel(
name='EnviFormer',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
('threshold', models.FloatField(default=0.5)),
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
('multigen_eval', models.BooleanField(default=False)),
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
],
options={
'abstract': False,
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='MLRelativeReasoning',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
('threshold', models.FloatField(default=0.5)),
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
('multigen_eval', models.BooleanField(default=False)),
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
],
options={
'abstract': False,
},
bases=('epdb.epmodel',),
),
migrations.AddField(
model_name='applicabilitydomain',
name='model',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning'),
),
migrations.AddField(
model_name='propertypluginmodel',
name='app_domain',
field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
),
migrations.AddField(
model_name='propertypluginmodel',
name='data_packages',
field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages'),
),
migrations.AddField(
model_name='propertypluginmodel',
name='eval_packages',
field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages'),
),
migrations.AddField(
model_name='propertypluginmodel',
name='rule_packages',
field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages'),
),
migrations.CreateModel(
name='RuleBasedRelativeReasoning',
fields=[
('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
('threshold', models.FloatField(default=0.5)),
('eval_results', models.JSONField(blank=True, default=dict, null=True)),
('multigen_eval', models.BooleanField(default=False)),
('min_count', models.IntegerField(default=10)),
('max_count', models.IntegerField(default=0)),
('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
],
options={
'abstract': False,
},
bases=('epdb.epmodel',),
),
migrations.CreateModel(
name='ExternalIdentifier',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
('object_id', models.IntegerField()),
('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
],
options={
'verbose_name': 'External Identifier',
'verbose_name_plural': 'External Identifiers',
'db_table': 'epdb_external_identifier',
'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
},
),
migrations.CreateModel(
name='SimpleAmbitRule',
fields=[
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
('smirks', models.TextField(verbose_name='SMIRKS')),
('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.simplerule',),
),
migrations.CreateModel(
name='SimpleRDKitRule',
fields=[
('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.simplerule',),
),
migrations.CreateModel(
name='SequentialRuleOrdering',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('order_index', models.IntegerField()),
('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
],
),
migrations.AddField(
model_name='sequentialrule',
name='simple_rules',
field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
),
migrations.CreateModel(
name='ParallelRule',
fields=[
('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
],
options={
'abstract': False,
'base_manager_name': 'objects',
},
bases=('epdb.rule',),
),
migrations.AlterUniqueTogether(
name='compound',
unique_together={('uuid', 'package')},
),
migrations.CreateModel(
name='AdditionalInformation',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
('url', models.TextField(null=True, unique=True, verbose_name='URL')),
('kv', models.JSONField(blank=True, default=dict, null=True)),
('type', models.TextField(verbose_name='Additional Information Type')),
('data', models.JSONField(blank=True, default=dict, null=True)),
('object_id', models.PositiveBigIntegerField(blank=True, null=True)),
('content_type', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
('scenario', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='scenario_additional_information', to='epdb.scenario')),
],
options={
'indexes': [models.Index(fields=['type'], name='epdb_additi_type_394349_idx'), models.Index(fields=['scenario', 'type'], name='epdb_additi_scenari_a59edf_idx'), models.Index(fields=['content_type', 'object_id'], name='epdb_additi_content_44d4b4_idx'), models.Index(fields=['scenario', 'content_type', 'object_id'], name='epdb_additi_scenari_ef2bf5_idx')],
'constraints': [models.CheckConstraint(condition=models.Q(models.Q(('content_type__isnull', True), ('object_id__isnull', True)), models.Q(('content_type__isnull', False), ('object_id__isnull', False)), _connector='OR'), name='ck_addinfo_gfk_pair'), models.CheckConstraint(condition=models.Q(('scenario__isnull', False), ('content_type__isnull', False), _connector='OR'), name='ck_addinfo_not_both_null')],
},
),
migrations.CreateModel(
name='GroupPackagePermission',
fields=[
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
],
options={
'unique_together': {('package', 'group')},
},
bases=('epdb.permission',),
),
migrations.CreateModel(
name='UserPackagePermission',
fields=[
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
],
options={
'unique_together': {('package', 'user')},
},
bases=('epdb.permission',),
),
migrations.CreateModel(
name='UserSettingPermission',
fields=[
('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
],
options={
'unique_together': {('setting', 'user')},
},
bases=('epdb.permission',),
),
]

5
epdb/migrations/0023_alter_compoundstructure_options_and_more.py
View File

@ -46,4 +46,9 @@ class Migration(migrations.Migration):
name="molfile",
field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
),
migrations.AddField(
model_name="group",
name="secret",
field=models.BooleanField(default=False, verbose_name="Secret Group"),
),
]

24
epdb/models.py
View File

@ -204,6 +204,7 @@ class Group(TimeStampedModel):
name = models.TextField(blank=False, null=False, verbose_name="Group name")
owner = models.ForeignKey("User", verbose_name="Group Owner", on_delete=models.CASCADE)
public = models.BooleanField(verbose_name="Public Group", default=False)
secret = models.BooleanField(verbose_name="Secret Group", default=False)
description = models.TextField(
blank=False, null=False, verbose_name="Descriptions", default="no description"
)
@ -867,18 +868,25 @@ class Compound(
standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
subclasses = CompoundStructure.__subclasses__()
qs = CompoundStructure.objects.filter(smiles=smiles, compound__package=package)
if subclasses:
qs = qs.not_instance_of(*subclasses)
# Check if we find a direct match for a given SMILES
if CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
if qs.exists():
return qs.first().compound
qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
if subclasses:
qs = qs.not_instance_of(*subclasses)
# Check if we can find the standardized one
if CompoundStructure.objects.filter(
smiles=standardized_smiles, compound__package=package
).exists():
if qs.exists():
# TODO should we add a structure?
return CompoundStructure.objects.get(
smiles=standardized_smiles, compound__package=package
).compound
return qs.first().compound
# Generate Compound
c = Compound()

31
epdb/views.py
View File

@ -388,6 +388,9 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
"debug": s.DEBUG,
"external_databases": ExternalDatabase.get_databases(),
"site_id": s.MATOMO_SITE_ID,
# EDIT START
"secret_groups": Group.objects.filter(secret=True),
# EDIT END
},
}
@ -587,10 +590,38 @@ def packages(request):
"package-description", s.DEFAULT_VALUES["description"]
)
# EDIT START
data_pool = None
package_classification = request.POST.get("package-classification")
classification = Package.Classification(int(package_classification))
# For SECRET we'll need a data pool which will be an additional perm check later
if classification == Package.Classification.SECRET:
package_data_pool = request.POST.get("package-data-pool")
if package_data_pool is None:
return error(request, "Invalid data pool.", "Data Pool is required!")
data_pool = GroupManager.get_group_by_url(current_user, package_data_pool)
if data_pool is None:
return error(request, "Invalid data pool.", "Data Pool does not exist or no access!")
if not data_pool.secret:
return error(request, "Invalid data pool.", "Data Pool is not a secret group!")
created_package = PackageManager.create_package(
current_user, package_name, package_description
)
created_package.classification_level = classification
# Set previously determined data pool
if classification == Package.Classification.SECRET:
created_package.data_pool = data_pool
created_package.save()
# EDIT END
return redirect(created_package.url)
elif request.method == "OPTIONS":