[Bugfix] Added Missing Paper in Cite Modal (#87)

Fixes #77

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#87

.env-example

@@ -0,0 +1,19 @@
+# settings.py
+EP_DATA_DIR=
+ALLOWED_HOSTS=
+DEBUG=
+LOG_LEVEL=
+ENVIFORMER_PRESENT=
+FLAG_CELERY_PRESENT=
+SERVER_URL=
+PLUGINS_ENABLED=
+# DB
+POSTGRES_SERVICE_NAME=
+POSTGRES_DB=
+POSTGRES_USER=
+POSTGRES_PASSWORD=
+POSTGRES_PORT=
+# MAIL
+EMAIL_HOST_USER=
+EMAIL_HOST_PASSWORD=
+

.gitignore

@@ -1,176 +1,7 @@
-# ---> Python
+*.pyc
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-cover/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
 db.sqlite3
-db.sqlite3-journal
+.idea/
-
+static/admin/
-# Flask stuff:
+static/django_extensions/
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# UV
-#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#uv.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
-.pdm.toml
-.pdm-python
-.pdm-build/
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
 .env
-.venv
+debug.log
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
-
-# Ruff stuff:
-.ruff_cache/
-
-# PyPI configuration file
-.pypirc
-

.python-version

@@ -0,0 +1 @@
+3.10

envipath/__init__.py

@@ -0,0 +1,5 @@
+# This will make sure the app is always imported when
+# Django starts so that shared_task will use this app.
+from .celery import app as celery_app
+
+__all__ = ('celery_app',)

envipath/api.py

@@ -0,0 +1,14 @@
+from epdb.api import router as epdb_app_router
+from epdb.legacy_api import router as epdb_legacy_app_router
+from ninja import NinjaAPI
+
+api = NinjaAPI()
+
+from ninja import NinjaAPI
+
+api_v1 = NinjaAPI(title="API V1 Docs", urls_namespace="api-v1")
+api_legacy = NinjaAPI(title="Legacy API Docs", urls_namespace="api-legacy")
+
+# Add routers
+api_v1.add_router("/", epdb_app_router)
+api_legacy.add_router("/", epdb_legacy_app_router)

envipath/asgi.py

@@ -0,0 +1,16 @@
+"""
+ASGI config for envipath project.
+
+It exposes the ASGI callable as a module-level variable named ``application``.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/4.2/howto/deployment/asgi/
+"""
+
+import os
+
+from django.core.asgi import get_asgi_application
+
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'envipath.settings')
+
+application = get_asgi_application()

envipath/celery.py

@@ -0,0 +1,27 @@
+import os
+
+from celery import Celery
+from celery.signals import setup_logging
+
+# Set the default Django settings module for the 'celery' program.
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'envipath.settings')
+
+app = Celery('envipath')
+
+# Using a string here means the worker doesn't have to serialize
+# the configuration object to child processes.
+# - namespace='CELERY' means all celery-related configuration keys
+#   should have a `CELERY_` prefix.
+app.config_from_object('django.conf:settings', namespace='CELERY')
+
+
+@setup_logging.connect
+def config_loggers(*args, **kwargs):
+    from logging.config import dictConfig
+    from django.conf import settings
+
+    dictConfig(settings.LOGGING)
+
+
+# Load task modules from all registered Django apps.
+app.autodiscover_tasks()

envipath/settings.py

@@ -0,0 +1,349 @@
+"""
+Django settings for envipath project.
+
+Generated by 'django-admin startproject' using Django 4.2.17.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/4.2/topics/settings/
+
+For the full list of settings and their values, see
+https://docs.djangoproject.com/en/4.2/ref/settings/
+"""
+import os
+from pathlib import Path
+
+from dotenv import load_dotenv
+from envipy_plugins import Classifier, Property, Descriptor
+from sklearn.ensemble import RandomForestClassifier
+from sklearn.tree import DecisionTreeClassifier
+
+# Build paths inside the project like this: BASE_DIR / 'subdir'.
+BASE_DIR = Path(__file__).resolve().parent.parent
+
+load_dotenv(BASE_DIR / '.env', override=False)
+
+# Quick-start development settings - unsuitable for production
+# See https://docs.djangoproject.com/en/4.2/howto/deployment/checklist/
+
+# SECURITY WARNING: keep the secret key used in production secret!
+SECRET_KEY = '7!VTW`aZqg/UBLsM.P=m)2]lWqg>{+:xUgG1"WO@bCyaHR2Up8XW&g<*3.F4l2gi9c.E3}dHyA0D`&z?u#U%^7HYbj],eP"g_MS|3BNMD[mI>s#<i/%2ngZ~Oy+/w&@]'
+
+# SECURITY WARNING: don't run with debug turned on in production!
+DEBUG = os.environ.get('DEBUG', 'False') == 'True'
+ALLOWED_HOSTS = os.environ['ALLOWED_HOSTS'].split(',')
+
+# Application definition
+
+INSTALLED_APPS = [
+    'django.contrib.admin',
+    'django.contrib.auth',
+    'django.contrib.contenttypes',
+    'django.contrib.sessions',
+    'django.contrib.messages',
+    'django.contrib.staticfiles',
+    # 3rd party
+    'django_extensions',
+    'oauth2_provider',
+    # Custom
+    'epdb',
+    'migration',
+]
+
+AUTHENTICATION_BACKENDS = [
+    "django.contrib.auth.backends.ModelBackend",
+]
+
+MIDDLEWARE = [
+    'django.middleware.security.SecurityMiddleware',
+    'django.contrib.sessions.middleware.SessionMiddleware',
+    'django.middleware.common.CommonMiddleware',
+    'django.middleware.csrf.CsrfViewMiddleware',
+    'django.contrib.auth.middleware.AuthenticationMiddleware',
+    'django.contrib.messages.middleware.MessageMiddleware',
+    'django.middleware.clickjacking.XFrameOptionsMiddleware',
+    'oauth2_provider.middleware.OAuth2TokenMiddleware',
+]
+
+OAUTH2_PROVIDER = {
+    "PKCE_REQUIRED": False,  # Accept PKCE requests but dont require them
+}
+
+if os.environ.get('REGISTRATION_MANDATORY', False) == 'True':
+    MIDDLEWARE.append('epdb.middleware.login_required_middleware.LoginRequiredMiddleware')
+
+ROOT_URLCONF = 'envipath.urls'
+
+TEMPLATES = [
+    {
+        'BACKEND': 'django.template.backends.django.DjangoTemplates',
+        'DIRS': (os.path.join(BASE_DIR, 'templates'),),
+        'APP_DIRS': True,
+        'OPTIONS': {
+            'context_processors': [
+                'django.template.context_processors.debug',
+                'django.template.context_processors.request',
+                'django.contrib.auth.context_processors.auth',
+                'django.contrib.messages.context_processors.messages',
+            ],
+        },
+    },
+]
+
+WSGI_APPLICATION = 'envipath.wsgi.application'
+
+# Database
+# https://docs.djangoproject.com/en/4.2/ref/settings/#databases
+
+DATABASES = {
+    "default": {
+        "ENGINE": "django.db.backends.postgresql",
+        "USER": os.environ['POSTGRES_USER'],
+        "NAME": os.environ['POSTGRES_DB'],
+        "PASSWORD": os.environ['POSTGRES_PASSWORD'],
+        "HOST": os.environ['POSTGRES_SERVICE_NAME'],
+        "PORT": os.environ['POSTGRES_PORT']
+    }
+}
+
+# Password validation
+# https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
+
+AUTH_PASSWORD_VALIDATORS = [
+    {
+        'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator',
+    },
+    {
+        'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator',
+    },
+    {
+        'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator',
+    },
+    {
+        'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator',
+    },
+]
+
+# Internationalization
+# https://docs.djangoproject.com/en/4.2/topics/i18n/
+
+LANGUAGE_CODE = 'en-us'
+
+TIME_ZONE = 'UTC'
+
+USE_I18N = True
+
+USE_TZ = True
+
+
+
+# Default primary key field type
+# https://docs.djangoproject.com/en/4.2/ref/settings/#default-auto-field
+
+DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField'
+
+# EMAIL
+EMAIL_BACKEND = 'django.core.mail.backends.smtp.EmailBackend'
+EMAIL_USE_TLS = True
+EMAIL_HOST = 'mail.gandi.net'
+EMAIL_HOST_USER = os.environ['EMAIL_HOST_USER']
+EMAIL_HOST_PASSWORD = os.environ['EMAIL_HOST_PASSWORD']
+EMAIL_PORT = 587
+
+AUTH_USER_MODEL = "epdb.User"
+ADMIN_APPROVAL_REQUIRED = os.environ.get('ADMIN_APPROVAL_REQUIRED', 'False') == 'True'
+
+# # SESAME
+# SESAME_MAX_AGE = 300
+# # TODO set to "home"
+# LOGIN_REDIRECT_URL = "/"
+LOGIN_URL = '/login/'
+
+SERVER_URL = os.environ.get('SERVER_URL', 'http://localhost:8000')
+
+CSRF_TRUSTED_ORIGINS = [SERVER_URL]
+
+AMBIT_URL = 'http://localhost:9001'
+DEFAULT_VALUES = {
+    'description': 'no description'
+}
+
+EP_DATA_DIR = os.environ['EP_DATA_DIR']
+MODEL_DIR = os.path.join(EP_DATA_DIR, 'models')
+if not os.path.exists(MODEL_DIR):
+    os.mkdir(MODEL_DIR)
+
+STATIC_DIR = os.path.join(EP_DATA_DIR, 'static')
+if not os.path.exists(STATIC_DIR):
+    os.mkdir(STATIC_DIR)
+
+LOG_DIR = os.path.join(EP_DATA_DIR, 'log')
+if not os.path.exists(LOG_DIR):
+    os.mkdir(LOG_DIR)
+
+PLUGIN_DIR = os.path.join(EP_DATA_DIR, 'plugins')
+if not os.path.exists(PLUGIN_DIR):
+    os.mkdir(PLUGIN_DIR)
+
+# Set this as our static root dir
+STATIC_ROOT = STATIC_DIR
+
+STATIC_URL = '/static/'
+
+# Where the sources are stored...
+STATICFILES_DIRS = (
+    BASE_DIR / 'static',
+)
+
+FIXTURE_DIRS = (
+        BASE_DIR / 'fixtures',
+)
+
+# Logging
+LOGGING = {
+    "version": 1,
+    "disable_existing_loggers": True,
+    "formatters": {
+        "simple": {
+            'format': '[%(asctime)s] %(levelname)s %(module)s - %(message)s',
+            'datefmt': '%Y-%m-%d %H:%M:%S',
+        },
+    },
+    "handlers": {
+        "console": {
+            "level": "INFO",
+            "class": "logging.StreamHandler",
+            "formatter": "simple",
+        },
+        "file": {
+            "level": "DEBUG",  # Or higher
+            "class": "logging.FileHandler",
+            "filename": os.path.join(LOG_DIR, "debug.log"),
+            "formatter": "simple"
+        },
+    },
+    "loggers": {
+        # For everything under epdb/ loaded via getlogger(__name__)
+        "epdb": {
+            "handlers": ["file"],  # "console",
+            "propagate": True,
+            "level": os.environ.get('LOG_LEVEL', 'INFO')
+        },
+        # For everything under envipath/ loaded via getlogger(__name__)
+        'envipath': {
+            'handlers': ['file', 'console'],
+            'propagate': True,
+            'level': os.environ.get('LOG_LEVEL', 'INFO')
+        },
+        # For everything under utilities/ loaded via getlogger(__name__)
+        'utilities': {
+            'handlers': ['file', 'console'],
+            'propagate': True,
+            'level': os.environ.get('LOG_LEVEL', 'INFO')
+        },
+    },
+}
+
+# Flags
+ENVIFORMER_PRESENT = os.environ.get('ENVIFORMER_PRESENT', 'False') == 'True'
+if ENVIFORMER_PRESENT:
+    print("Loading enviFormer")
+    device = os.environ.get('ENVIFORMER_DEVICE', 'cpu')
+    from enviformer import load
+    ENVIFORMER_INSTANCE = load(device=device)
+    print("loaded")
+
+
+# If celery is not present set always eager to true which will cause delayed tasks to block until finished
+FLAG_CELERY_PRESENT = os.environ.get('FLAG_CELERY_PRESENT', 'False') == 'True'
+if not FLAG_CELERY_PRESENT:
+    CELERY_TASK_ALWAYS_EAGER = True
+
+# Celery Configuration Options
+CELERY_TIMEZONE = "Europe/Berlin"
+# Celery Configuration
+CELERY_BROKER_URL = 'redis://localhost:6379/0'  # Use Redis as message broker
+CELERY_RESULT_BACKEND = 'redis://localhost:6379/1'
+CELERY_ACCEPT_CONTENT = ['json']
+CELERY_TASK_SERIALIZER = 'json'
+
+MODEL_BUILDING_ENABLED = os.environ.get('MODEL_BUILDING_ENABLED', 'False') == 'True'
+APPLICABILITY_DOMAIN_ENABLED = os.environ.get('APPLICABILITY_DOMAIN_ENABLED', 'False') == 'True'
+DEFAULT_RF_MODEL_PARAMS = {
+    'base_clf': RandomForestClassifier(
+        n_estimators=100,
+        max_features='log2',
+        random_state=42,
+        criterion='entropy',
+        ccp_alpha=0.0,
+        max_depth=3,
+        min_samples_leaf=1
+    ),
+    'num_chains': 10,
+}
+
+DEFAULT_MODEL_PARAMS = {
+    'base_clf': DecisionTreeClassifier(
+        criterion='entropy',
+        max_depth=3,
+        min_samples_split=5,
+        # min_samples_leaf=5,
+        max_features='sqrt',
+        # class_weight='balanced',
+        random_state=42
+    ),
+    'num_chains': 10,
+}
+
+DEFAULT_MAX_NUMBER_OF_NODES = 30
+DEFAULT_MAX_DEPTH = 5
+DEFAULT_MODEL_THRESHOLD = 0.25
+
+# Loading Plugins
+PLUGINS_ENABLED = os.environ.get('PLUGINS_ENABLED', 'False') == 'True'
+if PLUGINS_ENABLED:
+    from utilities.plugin import discover_plugins
+    CLASSIFIER_PLUGINS = discover_plugins(_cls=Classifier)
+    PROPERTY_PLUGINS = discover_plugins(_cls=Property)
+    DESCRIPTOR_PLUGINS = discover_plugins(_cls=Descriptor)
+else:
+    CLASSIFIER_PLUGINS = {}
+    PROPERTY_PLUGINS = {}
+    DESCRIPTOR_PLUGINS = {}
+
+SENTRY_ENABLED = os.environ.get('SENTRY_ENABLED', 'False') == 'True'
+if SENTRY_ENABLED:
+    import sentry_sdk
+
+    def before_send(event, hint):
+        # Check if was a handled exception by one of our loggers
+        if event.get('logger'):
+            for log_path in LOGGING.get('loggers').keys():
+                if event['logger'].startswith(log_path):
+                    return None
+
+        return event
+
+    sentry_sdk.init(
+        dsn=os.environ.get('SENTRY_DSN'),
+        # Add data like request headers and IP for users,
+        # see https://docs.sentry.io/platforms/python/data-management/data-collected/ for more info
+        send_default_pii=True,
+        environment=os.environ.get('SENTRY_ENVIRONMENT', 'development'),
+        before_send=before_send,
+    )
+
+# compile into digestible flags
+FLAGS = {
+    'MODEL_BUILDING': MODEL_BUILDING_ENABLED,
+    'CELERY': FLAG_CELERY_PRESENT,
+    'PLUGINS': PLUGINS_ENABLED,
+    'SENTRY': SENTRY_ENABLED,
+    'ENVIFORMER': ENVIFORMER_PRESENT,
+    'APPLICABILITY_DOMAIN': APPLICABILITY_DOMAIN_ENABLED,
+}
+
+LOGIN_EXEMPT_URLS = [
+    '/api/legacy/',
+    '/o/token/',
+    '/o/userinfo/',
+]

envipath/urls.py

@@ -0,0 +1,29 @@
+"""
+URL configuration for envipath project.
+
+The `urlpatterns` list routes URLs to views. For more information please see:
+    https://docs.djangoproject.com/en/4.2/topics/http/urls/
+Examples:
+Function views
+    1. Add an import:  from my_app import views
+    2. Add a URL to urlpatterns:  path('', views.home, name='home')
+Class-based views
+    1. Add an import:  from other_app.views import Home
+    2. Add a URL to urlpatterns:  path('', Home.as_view(), name='home')
+Including another URLconf
+    1. Import the include() function: from django.urls import include, path
+    2. Add a URL to urlpatterns:  path('blog/', include('blog.urls'))
+"""
+from django.contrib import admin
+from django.urls import include, path
+
+from .api import api_v1, api_legacy
+
+urlpatterns = [
+    path("", include("epdb.urls")),
+    path("", include("migration.urls")),
+    path("admin/", admin.site.urls),
+    path("api/v1/", api_v1.urls),
+    path("api/legacy/", api_legacy.urls),
+    path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
+]

envipath/wsgi.py

@@ -0,0 +1,16 @@
+"""
+WSGI config for envipath project.
+
+It exposes the WSGI callable as a module-level variable named ``application``.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/4.2/howto/deployment/wsgi/
+"""
+
+import os
+
+from django.core.wsgi import get_wsgi_application
+
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'envipath.settings')
+
+application = get_wsgi_application()

epdb/admin.py

@@ -0,0 +1,105 @@
+from django.contrib import admin
+
+from .models import (
+    User,
+    UserPackagePermission,
+    Group,
+    GroupPackagePermission,
+    Package,
+    MLRelativeReasoning,
+    Compound,
+    CompoundStructure,
+    SimpleAmbitRule,
+    ParallelRule,
+    Reaction,
+    Pathway,
+    Node,
+    Edge,
+    Scenario,
+    Setting
+)
+
+
+class UserAdmin(admin.ModelAdmin):
+    pass
+
+
+class UserPackagePermissionAdmin(admin.ModelAdmin):
+    pass
+
+
+class GroupAdmin(admin.ModelAdmin):
+    pass
+
+
+class GroupPackagePermissionAdmin(admin.ModelAdmin):
+    pass
+
+
+class EPAdmin(admin.ModelAdmin):
+    search_fields = ['name', 'description']
+
+
+class PackageAdmin(EPAdmin):
+    pass
+
+class MLRelativeReasoningAdmin(EPAdmin):
+    pass
+
+
+class CompoundAdmin(EPAdmin):
+    pass
+
+
+class CompoundStructureAdmin(EPAdmin):
+    pass
+
+
+class SimpleAmbitRuleAdmin(EPAdmin):
+    pass
+
+
+class ParallelRuleAdmin(EPAdmin):
+    pass
+
+
+class ReactionAdmin(EPAdmin):
+    pass
+
+
+class PathwayAdmin(EPAdmin):
+    pass
+
+
+class NodeAdmin(EPAdmin):
+    pass
+
+
+class EdgeAdmin(EPAdmin):
+    pass
+
+
+class ScenarioAdmin(EPAdmin):
+    pass
+
+
+class SettingAdmin(EPAdmin):
+    pass
+
+
+admin.site.register(User, UserAdmin)
+admin.site.register(UserPackagePermission, UserPackagePermissionAdmin)
+admin.site.register(Group, GroupAdmin)
+admin.site.register(GroupPackagePermission, GroupPackagePermissionAdmin)
+admin.site.register(Package, PackageAdmin)
+admin.site.register(MLRelativeReasoning, MLRelativeReasoningAdmin)
+admin.site.register(Compound, CompoundAdmin)
+admin.site.register(CompoundStructure, CompoundStructureAdmin)
+admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)
+admin.site.register(ParallelRule, ParallelRuleAdmin)
+admin.site.register(Reaction, ReactionAdmin)
+admin.site.register(Pathway, PathwayAdmin)
+admin.site.register(Node, NodeAdmin)
+admin.site.register(Edge, EdgeAdmin)
+admin.site.register(Setting, SettingAdmin)
+admin.site.register(Scenario, ScenarioAdmin)

epdb/api.py

@@ -0,0 +1,108 @@
+from typing import List
+
+from django.contrib.auth import get_user_model
+from ninja import Router, Schema, Field
+from ninja.errors import HttpError
+from ninja.pagination import paginate
+from ninja.security import HttpBearer
+
+from .logic import PackageManager
+from .models import User, Compound, APIToken
+
+
+class BearerTokenAuth(HttpBearer):
+    def authenticate(self, request, token):
+        for token_obj in APIToken.objects.select_related("user").all():
+            if token_obj.check_token(token) and token_obj.is_valid():
+                return token_obj.user
+        raise HttpError(401, "Invalid or expired token")
+
+
+def _anonymous_or_real(request):
+    if request.user.is_authenticated and not request.user.is_anonymous:
+        return request.user
+    return get_user_model().objects.get(username='anonymous')
+
+
+router = Router(auth=BearerTokenAuth())
+
+
+class UserSchema(Schema):
+    email: str
+    username: str
+    id: str = Field(None, alias="url")
+
+
+class PackageIn(Schema):
+    name: str
+    description: str
+
+
+class PackageOut(Schema):
+    id: str = Field(None, alias="url")
+    name: str
+    reviewed: bool
+    compound_links: str = None
+
+    @staticmethod
+    def resolve_compound_links(obj):
+        return f"{obj.url}/compound"
+
+
+class Error(Schema):
+    message: str
+
+
+class CompoundSchema(Schema):
+    name: str = Field(None, alias="name")
+    id: str = Field(None, alias="url")
+    smiles: str = Field(None, alias="default_structure.smiles")
+    reviewed: bool = Field(None, alias="package.reviewed")
+
+
+@router.get("/user", response={200: List[UserSchema], 403: Error})
+def get_users(request):
+    return User.objects.all()
+
+
+@router.get("/package", response={200: List[PackageOut], 403: Error})
+def get_packages(request):
+    return PackageManager.get_all_readable_packages(request.user, include_reviewed=True)
+
+
+@router.post("/package", response=PackageOut)
+def create_package(request, package: PackageIn):
+    user = request.auth
+    name = package.name.strip()
+    description = package.description.strip()
+
+    p = PackageManager.create_package(user, name, description=description)
+    return p
+
+
+@router.get("/package/{uuid:package_uuid}", response={200: PackageOut, 403: Error})
+def get_package(request, package_uuid):
+    try:
+        return PackageManager.get_package_by_id(request.auth, package_id=package_uuid)
+    except ValueError:
+        return 403, {'message': f'Getting Package with id  {package_uuid} failed due to insufficient rights!'}
+
+
+@router.get("/compound", response={200: List[CompoundSchema], 403: Error})
+@paginate
+def get_compounds(request):
+    qs = Compound.objects.none()
+    for p in PackageManager.get_reviewed_packages():
+        qs |= Compound.objects.filter(package=p)
+    return qs
+
+
+@router.get("/package/{uuid:package_uuid}/compound", response={200: List[CompoundSchema], 403: Error})
+@paginate
+def get_package_compounds(request, package_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.auth, package_uuid)
+        return Compound.objects.filter(package=p)
+    except ValueError:
+        return 403, {
+            'message': f'Getting Compounds for Package with id  {package_uuid} failed due to insufficient rights!'}

epdb/apps.py

@@ -0,0 +1,9 @@
+from django.apps import AppConfig
+
+
+class EPDBConfig(AppConfig):
+    default_auto_field = 'django.db.models.BigAutoField'
+    name = 'epdb'
+
+    def ready(self):
+        import epdb.signals  # noqa: F401

epdb/forms.py

@@ -0,0 +1,5 @@
+from django import forms
+
+
+class EmailLoginForm(forms.Form):
+    email = forms.EmailField()

epdb/legacy_api.py

@@ -0,0 +1,739 @@
+from typing import List, Dict, Optional, Any
+
+from django.contrib.auth import get_user_model
+from django.http import HttpResponse
+from ninja import Router, Schema, Field, Form
+
+from utilities.chem import FormatConverter
+from .logic import PackageManager
+from .models import Compound, CompoundStructure, Package, User, UserPackagePermission, Rule, Reaction, Scenario, Pathway
+
+
+def _anonymous_or_real(request):
+    if request.user.is_authenticated and not request.user.is_anonymous:
+        return request.user
+    return get_user_model().objects.get(username='anonymous')
+
+
+# router = Router(auth=SessionAuth())
+router = Router()
+
+
+class Error(Schema):
+    message: str
+
+
+class SimpleObject(Schema):
+    id: str = Field(None, alias="url")
+    name: str = Field(None, alias="name")
+    reviewStatus: bool = Field(None, alias="package.reviewed")
+
+
+################
+# Login/Logout #
+################
+class SimpleUser(Schema):
+    id: str = Field(None, alias="url")
+    identifier: str = 'user'
+    name: str = Field(None, alias='username')
+    email: str = Field(None, alias='email')
+
+
+@router.post("/", response={200: SimpleUser, 403: Error})
+def login(request, loginusername: Form[str], loginpassword: Form[str], hiddenMethod: Form[str]):
+    from django.contrib.auth import authenticate
+    from django.contrib.auth import 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 or password'}
+
+
+class SimpleGroup(Schema):
+    id: str
+    identifier: str = 'group'
+    name: str
+
+
+###########
+# Package #
+###########
+class SimplePackage(SimpleObject):
+    identifier: str = 'package'
+    reviewStatus: bool = Field(None, alias="reviewed")
+
+
+class PackageSchema(Schema):
+    description: str = Field(None, alias="description")
+    id: str = Field(None, alias="url")
+    links: List[Dict[str, List[str | int]]] = Field([], alias="links")
+    name: str = Field(None, alias="name")
+    primaryGroup: Optional[SimpleGroup] = None
+    readers: List[Dict[str, str]] = Field([], alias="readers")
+    reviewComment: str = Field(None, alias="review_comment")
+    reviewStatus: str = Field(None, alias="review_status")
+    writers: List[Dict[str, str]] = Field([], alias="writers")
+
+    @staticmethod
+    def resolve_links(obj: Package):
+        return [
+            {
+                'Pathways': [
+                    f'{obj.url}/pathway', obj.pathways.count()
+                ]
+            }, {
+                'Rules': [
+                    f'{obj.url}/rule', obj.rules.count()
+                ]
+            }, {
+                'Compounds': [
+                    f'{obj.url}/compound', obj.compounds.count()
+                ]
+            }, {
+                'Reactions': [
+                    f'{obj.url}/reaction', obj.reactions.count()
+                ]
+            }, {
+                'Relative Reasoning': [
+                    f'{obj.url}/relative-reasoning', obj.models.count()
+                ]
+            }, {
+                'Scenarios': [
+                    f'{obj.url}/scenario', obj.scenarios.count()
+                ]
+            }
+        ]
+
+    @staticmethod
+    def resolve_readers(obj: Package):
+        users = User.objects.filter(
+            id__in=UserPackagePermission.objects.filter(
+                package=obj,
+                permission=UserPackagePermission.READ[0]
+            ).values_list('user', flat=True)
+        ).distinct()
+
+        return [{u.id: u.name} for u in users]
+
+    @staticmethod
+    def resolve_writers(obj: Package):
+        users = User.objects.filter(
+            id__in=UserPackagePermission.objects.filter(
+                package=obj,
+                permission=UserPackagePermission.WRITE[0]
+            ).values_list('user', flat=True)
+        ).distinct()
+
+        return [{u.id: u.name} for u in users]
+
+    @staticmethod
+    def resolve_review_comment(obj):
+        return ""
+
+    @staticmethod
+    def resolve_review_status(obj):
+        return 'reviewed' if obj.reviewed else 'unreviewed'
+
+
+class PackageWrapper(Schema):
+    package: List['PackageSchema']
+
+
+@router.get("/package", response={200: PackageWrapper, 403: Error})
+def get_packages(request):
+    return {'package': PackageManager.get_all_readable_packages(request.user, include_reviewed=True)}
+
+
+@router.get("/package/{uuid:package_uuid}", response={200: PackageSchema, 403: Error})
+def get_package(request, package_uuid):
+    try:
+        return PackageManager.get_package_by_id(request.user, package_uuid)
+    except ValueError:
+        return 403, {
+            'message': f'Getting Package with id {package_uuid} failed due to insufficient rights!'}
+
+
+################################
+# Compound / CompoundStructure #
+################################
+class SimpleCompound(SimpleObject):
+    identifier: str = 'compound'
+
+
+class CompoundPathwayScenario(Schema):
+    scenarioId: str
+    scenarioName: str
+    scenarioType: str
+
+
+class CompoundSchema(Schema):
+    aliases: List[str] = Field([], alias="aliases")
+    description: str = Field(None, alias="description")
+    externalReferences: Dict[str, List[str]] = Field(None, alias="external_references")
+    id: str = Field(None, alias="url")
+    halflifes: List[Dict[str, str]] = Field([], alias="halflifes")
+    identifier: str = 'compound'
+    imageSize: int = 600
+    name: str = Field(None, alias="name")
+    pathwayScenarios: List[CompoundPathwayScenario] = Field([], alias="pathway_scenarios")
+    pathways: List['SimplePathway'] = Field([], alias="related_pathways")
+    pubchemCompoundReferences: List[str] = Field([], alias="pubchem_compound_references")
+    reactions: List['SimpleReaction'] = Field([], alias="related_reactions")
+    reviewStatus: str = Field(False, alias="review_status")
+    scenarios: List['SimpleScenario'] = Field([], alias="scenarios")
+    structures: List['CompoundStructureSchema'] = []
+
+    @staticmethod
+    def resolve_review_status(obj: CompoundStructure):
+        return 'reviewed' if obj.package.reviewed else 'unreviewed'
+
+    @staticmethod
+    def resolve_external_references(obj: Compound):
+        # TODO
+        return {}
+
+    @staticmethod
+    def resolve_structures(obj: Compound):
+        return CompoundStructure.objects.filter(compound=obj)
+
+    @staticmethod
+    def resolve_halflifes(obj: Compound):
+        return []
+
+    @staticmethod
+    def resolve_pubchem_compound_references(obj: Compound):
+        return []
+
+    @staticmethod
+    def resolve_pathway_scenarios(obj: Compound):
+        return [
+            {
+                'scenarioId': 'https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/scenario/cd8350cd-4249-4111-ba9f-4e2209338501',
+                'scenarioName': 'Fritz, R. & Brauner, A. (1989) - (00004)',
+                'scenarioType': 'Soil'
+            }
+        ]
+
+
+class CompoundWrapper(Schema):
+    compound: List['SimpleCompound']
+
+
+class SimpleCompoundStructure(SimpleObject):
+    identifier: str = 'structure'
+    reviewStatus: bool = Field(None, alias="compound.package.reviewed")
+
+
+class CompoundStructureSchema(Schema):
+    InChI: str = Field(None, alias="inchi")
+    aliases: List[str] = Field([], alias="aliases")
+    canonicalSmiles: str = Field(None, alias="canonical_smiles")
+    charge: int = Field(None, alias="charge")
+    description: str = Field(None, alias="description")
+    externalReferences: Dict[str, List[str]] = Field(None, alias="external_references")
+    formula: str = Field(None, alias="formula")
+    halflifes: List[Dict[str, str]] = Field([], alias="halflifes")
+    id: str = Field(None, alias="url")
+    identifier: str = 'structure'
+    imageSize: int = 600
+    inchikey: str = Field(None, alias="inchikey")
+    isDefaultStructure: bool = Field(None, alias="is_default_structure")
+    mass: float = Field(None, alias="mass")
+    name: str = Field(None, alias="name")
+    pathways: List['SimplePathway'] = Field([], alias="related_pathways")
+    pubchemCompoundReferences: List[str] = Field([], alias="pubchem_compound_references")
+    reactions: List['SimpleReaction'] = Field([], alias="related_reactions")
+    reviewStatus: str = Field(None, alias="review_status")
+    scenarios: List['SimpleScenario'] = Field([], alias="scenarios")
+    smiles: str = Field(None, alias="smiles")
+
+    @staticmethod
+    def resolve_review_status(obj: CompoundStructure):
+        return 'reviewed' if obj.compound.package.reviewed else 'unreviewed'
+
+    @staticmethod
+    def resolve_inchi(obj: CompoundStructure):
+        return FormatConverter.InChI(obj.smiles)
+
+    @staticmethod
+    def resolve_charge(obj: CompoundStructure):
+        print(obj.smiles)
+        print(FormatConverter.charge(obj.smiles))
+        return FormatConverter.charge(obj.smiles)
+
+    @staticmethod
+    def resolve_formula(obj: CompoundStructure):
+        return FormatConverter.formula(obj.smiles)
+
+    @staticmethod
+    def resolve_mass(obj: CompoundStructure):
+        return FormatConverter.mass(obj.smiles)
+
+    @staticmethod
+    def resolve_external_references(obj: CompoundStructure):
+        # TODO
+        return {}
+
+    @staticmethod
+    def resolve_halflifes(obj: CompoundStructure):
+        return []
+
+    @staticmethod
+    def resolve_pubchem_compound_references(obj: CompoundStructure):
+        return []
+
+    @staticmethod
+    def resolve_pathway_scenarios(obj: CompoundStructure):
+        return [
+            {
+                'scenarioId': 'https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/scenario/cd8350cd-4249-4111-ba9f-4e2209338501',
+                'scenarioName': 'Fritz, R. & Brauner, A. (1989) - (00004)',
+                'scenarioType': 'Soil'
+            }
+        ]
+
+
+class CompoundStructureWrapper(Schema):
+    structure: List['SimpleCompoundStructure']
+
+
+@router.get("/compound", response={200: CompoundWrapper, 403: Error})
+def get_compounds(request):
+    qs = Compound.objects.none()
+    for p in PackageManager.get_reviewed_packages():
+        qs |= Compound.objects.filter(package=p)
+    return {'compound': qs}
+
+
+@router.get("/package/{uuid:package_uuid}/compound", response={200: CompoundWrapper, 403: Error})
+def get_package_compounds(request, package_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return {'compound': Compound.objects.filter(package=p).prefetch_related('package')}
+    except ValueError:
+        return 403, {
+            'message': f'Getting Compounds for Package with id {package_uuid} failed due to insufficient rights!'}
+
+
+@router.get("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}", response={200: CompoundSchema, 403: Error})
+def get_package_compound(request, package_uuid, compound_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return Compound.objects.get(package=p, uuid=compound_uuid)
+    except ValueError:
+        return 403, {
+            'message': f'Getting Compound with id {compound_uuid} failed due to insufficient rights!'}
+
+
+@router.get("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure",
+            response={200: CompoundStructureWrapper, 403: Error})
+def get_package_compound_structures(request, package_uuid, compound_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return {'structure': Compound.objects.get(package=p, uuid=compound_uuid).structures.all()}
+    except ValueError:
+        return 403, {
+            'message': f'Getting CompoundStructures for Compound with id {compound_uuid} failed due to insufficient rights!'}
+
+
+@router.get("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/{uuid:structure_uuid}",
+            response={200: CompoundStructureSchema, 403: Error})
+def get_package_compound_structure(request, package_uuid, compound_uuid, structure_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return CompoundStructure.objects.get(uuid=structure_uuid,
+                                             compound=Compound.objects.get(package=p, uuid=compound_uuid))
+    except ValueError:
+        return 403, {
+            'message': f'Getting CompoundStructure with id {structure_uuid} failed due to insufficient rights!'}
+
+
+#########
+# Rules #
+#########
+class SimpleRule(SimpleObject):
+    identifier: str = 'rule'
+
+    @staticmethod
+    def resolve_url(obj: Rule):
+        return obj.url.replace('-ambit-', '-').replace('-rdkit-', '-')
+
+
+class RuleWrapper(Schema):
+    rule: List['SimpleRule']
+
+
+class SimpleRuleSchema(Schema):
+    aliases: List[str] = Field([], alias="aliases")
+    description: str = Field(None, alias="description")
+    ecNumbers: List[Dict[str, str]] = Field([], alias="ec_numbers")
+    engine: str = 'ambit'
+    id: str = Field(None, alias="url")
+    identifier: str = Field(None, alias="identifier")
+    isCompositeRule: bool = False
+    name: str = Field(None, alias="name")
+    pathways: List['SimplePathway'] = Field([], alias="related_pathways")
+    productFilterSmarts: str = Field("", alias="product_filter_smarts")
+    productSmarts: str = Field(None, alias="products_smarts")
+    reactantFilterSmarts: str = Field("", alias="reactant_filter_smarts")
+    reactantSmarts: str = Field(None, alias="reactants_smarts")
+    reactions: List['SimpleReaction'] = Field([], alias="related_reactions")
+    reviewStatus: str = Field(None, alias="review_status")
+    scenarios: List['SimpleScenario'] = Field([], alias="scenarios")
+    smirks: str = Field("", alias="smirks")
+    # TODO
+    transformations: str = Field("", alias="transformations")
+
+    @staticmethod
+    def resolve_url(obj: Rule):
+        return obj.url.replace('-ambit-', '-').replace('-rdkit-', '-')
+
+    @staticmethod
+    def resolve_identifier(obj: Rule):
+        if 'simple-rule' in obj.url:
+            return 'simple-rule'
+        if 'simple-ambit-rule' in obj.url:
+            return 'simple-rule'
+        elif 'parallel-rule' in obj.url:
+            return 'parallel-rule'
+        elif 'sequential-rule' in obj.url:
+            return 'sequential-rule'
+        else:
+            return None
+
+    @staticmethod
+    def resolve_review_status(obj: Rule):
+        return 'reviewed' if obj.package.reviewed else 'unreviewed'
+
+    @staticmethod
+    def resolve_product_filter_smarts(obj: Rule):
+        return obj.product_filter_smarts if obj.product_filter_smarts else ''
+
+    @staticmethod
+    def resolve_reactant_filter_smarts(obj: Rule):
+        return obj.reactant_filter_smarts if obj.reactant_filter_smarts else ''
+
+
+class CompositeRuleSchema(Schema):
+    aliases: List[str] = Field([], alias="aliases")
+    description: str = Field(None, alias="description")
+    ecNumbers: List[Dict[str, str]] = Field([], alias="ec_numbers")
+    id: str = Field(None, alias="url")
+    identifier: str = Field(None, alias="identifier")
+    isCompositeRule: bool = True
+    name: str = Field(None, alias="name")
+    pathways: List['SimplePathway'] = Field([], alias="related_pathways")
+    productFilterSmarts: str = Field("", alias="product_filter_smarts")
+    reactantFilterSmarts: str = Field("", alias="reactant_filter_smarts")
+    reactions: List['SimpleReaction'] = Field([], alias="related_reactions")
+    reviewStatus: str = Field(None, alias="review_status")
+    scenarios: List['SimpleScenario'] = Field([], alias="scenarios")
+    simpleRules: List['SimpleRule'] = Field([], alias="simple_rules")
+
+    @staticmethod
+    def resolve_ec_numbers(obj: Rule):
+        return []
+
+    @staticmethod
+    def resolve_url(obj: Rule):
+        return obj.url.replace('-ambit-', '-').replace('-rdkit-', '-')
+
+    @staticmethod
+    def resolve_identifier(obj: Rule):
+        if 'simple-rule' in obj.url:
+            return 'simple-rule'
+        if 'simple-ambit-rule' in obj.url:
+            return 'simple-rule'
+        elif 'parallel-rule' in obj.url:
+            return 'parallel-rule'
+        elif 'sequential-rule' in obj.url:
+            return 'sequential-rule'
+        else:
+            return None
+
+    @staticmethod
+    def resolve_review_status(obj: Rule):
+        return 'reviewed' if obj.package.reviewed else 'unreviewed'
+
+    @staticmethod
+    def resolve_product_filter_smarts(obj: Rule):
+        return obj.product_filter_smarts if obj.product_filter_smarts else ''
+
+    @staticmethod
+    def resolve_reactant_filter_smarts(obj: Rule):
+        return obj.reactant_filter_smarts if obj.reactant_filter_smarts else ''
+
+
+@router.get("/rule", response={200: RuleWrapper, 403: Error})
+def get_rules(request):
+    qs = Rule.objects.none()
+    for p in PackageManager.get_reviewed_packages():
+        qs |= Rule.objects.filter(package=p)
+    return {'rule': qs}
+
+
+@router.get("/package/{uuid:package_uuid}/rule", response={200: RuleWrapper, 403: Error})
+def get_package_rules(request, package_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return {'rule': Rule.objects.filter(package=p).prefetch_related('package')}
+    except ValueError:
+        return 403, {
+            'message': f'Getting Rules for Package with id {package_uuid} failed due to insufficient rights!'}
+
+
+@router.get("/package/{uuid:package_uuid}/rule/{uuid:rule_uuid}",
+            response={200: SimpleRuleSchema | CompositeRuleSchema, 403: Error})
+def get_package_rule(request, package_uuid, rule_uuid):
+    return _get_package_rule(request, package_uuid, rule_uuid)
+
+
+@router.get("/package/{uuid:package_uuid}/simple-rule/{uuid:rule_uuid}",
+            response={200: SimpleRuleSchema | CompositeRuleSchema, 403: Error})
+def get_package_simple_rule(request, package_uuid, rule_uuid):
+    return _get_package_rule(request, package_uuid, rule_uuid)
+
+
+@router.get("/package/{uuid:package_uuid}/parallel-rule/{uuid:rule_uuid}",
+            response={200: SimpleRuleSchema | CompositeRuleSchema, 403: Error})
+def get_package_parallel_rule(request, package_uuid, rule_uuid):
+    return _get_package_rule(request, package_uuid, rule_uuid)
+
+
+def _get_package_rule(request, package_uuid, rule_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return Rule.objects.get(package=p, uuid=rule_uuid)
+    except ValueError:
+        return 403, {
+            'message': f'Getting Rule with id {rule_uuid} failed due to insufficient rights!'}
+
+
+# POST
+@router.post("/package/{uuid:package_uuid}/rule/{uuid:rule_uuid}", response={200: str | Any, 403: Error})
+def post_package_rule(request, package_uuid, rule_uuid, compound: Form[str] = None):
+    return _post_package_rule(request, package_uuid, rule_uuid, compound=compound)
+
+
+@router.post("/package/{uuid:package_uuid}/simple-rule/{uuid:rule_uuid}", response={200: str | Any, 403: Error})
+def post_package_simple_rule(request, package_uuid, rule_uuid, compound: Form[str] = None):
+    return _post_package_rule(request, package_uuid, rule_uuid, compound=compound)
+
+
+@router.post("/package/{uuid:package_uuid}/parallel-rule/{uuid:rule_uuid}", response={200: str | Any, 403: Error})
+def post_package_parallel_rule(request, package_uuid, rule_uuid, compound: Form[str] = None):
+    return _post_package_rule(request, package_uuid, rule_uuid, compound=compound)
+
+
+def _post_package_rule(request, package_uuid, rule_uuid, compound: Form[str]):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        r = Rule.objects.get(package=p, uuid=rule_uuid)
+
+        if compound is not None:
+            if not compound.split():
+                return 400, {'message': 'Compound is empty'}
+
+            product_sets = r.apply(compound)
+
+            res = []
+            for p_set in product_sets:
+                for product in p_set:
+                    res.append(product)
+
+            return HttpResponse('\n'.join(res), content_type="text/plain")
+
+        return r
+
+    except ValueError:
+        return 403, {
+            'message': f'Getting Rule with id {rule_uuid} failed due to insufficient rights!'}
+
+
+############
+# Reaction #
+############
+class SimpleReaction(SimpleObject):
+    identifier: str = 'reaction'
+
+
+class ReactionWrapper(Schema):
+    reaction: List['SimpleReaction']
+
+
+class ReactionCompoundStructure(Schema):
+    compoundName: str = Field(None, alias="name")
+    id: str = Field(None, alias="url")
+    smiles: str = Field(None, alias="smiles")
+
+
+class ReactionSchema(Schema):
+    aliases: List[str] = Field([], alias="aliases")
+    description: str = Field(None, alias="description")
+    ecNumbers: List[Dict[str, str]] = Field([], alias="ec_numbers")
+    educts: List['ReactionCompoundStructure'] = Field([], alias="educts")
+    id: str = Field(None, alias="url")
+    identifier: str = 'reaction'
+    medlineRefs: List[str] = Field([], alias="medline_references")
+    multistep: bool = Field(None, alias="multi_step")
+    name: str = Field(None, alias="name")
+    pathways: List['SimplePathway'] = Field([], alias="related_pathways")
+    products: List['ReactionCompoundStructure'] = Field([], alias="products")
+    references: List[Dict[str, List[str]]] = Field([], alias="references")
+    reviewStatus: str = Field(None, alias="review_status")
+    scenarios: List['SimpleScenario'] = Field([], alias="scenarios")
+    smirks: str = Field("", alias="smirks")
+
+    @staticmethod
+    def resolve_smirks(obj: Reaction):
+        return obj.smirks()
+
+    @staticmethod
+    def resolve_ec_numbers(obj: Reaction):
+        # TODO fetch via scenario EnzymeAI
+        return []
+
+    @staticmethod
+    def resolve_references(obj: Reaction):
+        # TODO
+        return []
+
+    @staticmethod
+    def resolve_medline_references(obj: Reaction):
+        # TODO
+        return []
+
+    @staticmethod
+    def resolve_review_status(obj: Rule):
+        return 'reviewed' if obj.package.reviewed else 'unreviewed'
+
+
+@router.get("/reaction", response={200: ReactionWrapper, 403: Error})
+def get_reactions(request):
+    qs = Reaction.objects.none()
+    for p in PackageManager.get_reviewed_packages():
+        qs |= Reaction.objects.filter(package=p)
+    return {'reaction': qs}
+
+
+@router.get("/package/{uuid:package_uuid}/reaction", response={200: ReactionWrapper, 403: Error})
+def get_package_reactions(request, package_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return {'reaction': Reaction.objects.filter(package=p).prefetch_related('package')}
+    except ValueError:
+        return 403, {
+            'message': f'Getting Reactions for Package with id {package_uuid} failed due to insufficient rights!'}
+
+
+@router.get("/package/{uuid:package_uuid}/reaction/{uuid:reaction_uuid}", response={200: ReactionSchema, 403: Error})
+def get_package_reaction(request, package_uuid, reaction_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return Reaction.objects.get(package=p, uuid=reaction_uuid)
+    except ValueError:
+        return 403, {
+            'message': f'Getting Reaction with id {reaction_uuid} failed due to insufficient rights!'}
+
+
+############
+# Scenario #
+############
+class SimpleScenario(SimpleObject):
+    identifier: str = 'scenario'
+
+
+class ScenarioWrapper(Schema):
+    scenario: List['SimpleScenario']
+
+
+class ScenarioSchema(Schema):
+    aliases: List[str] = Field([], alias="aliases")
+    collection: Dict['str', List[Dict[str, Any]]] = Field([], alias="collection")
+    collectionID: Optional[str] = None
+    description: str = Field(None, alias="description")
+    id: str = Field(None, alias="url")
+    identifier: str = 'scenario'
+    linkedTo: List[Dict[str, str]] = Field({}, alias="linked_to")
+    name: str = Field(None, alias="name")
+    pathways: List['SimplePathway'] = Field([], alias="related_pathways")
+    relatedScenarios: List[Dict[str, str]] = Field([], alias="related_scenarios")
+    reviewStatus: str = Field(None, alias="review_status")
+    scenarios: List['SimpleScenario'] = Field([], alias="scenarios")
+    type: str = Field(None, alias="scenario_type")
+
+    @staticmethod
+    def resolve_collection(obj: Scenario):
+        return obj.additional_information
+
+    @staticmethod
+    def resolve_review_status(obj: Rule):
+        return 'reviewed' if obj.package.reviewed else 'unreviewed'
+
+
+@router.get("/scenario", response={200: ScenarioWrapper, 403: Error})
+def get_scenarios(request):
+    qs = Scenario.objects.none()
+    for p in PackageManager.get_reviewed_packages():
+        qs |= Scenario.objects.filter(package=p)
+    return {'scenario': qs}
+
+
+@router.get("/package/{uuid:package_uuid}/scenario", response={200: ScenarioWrapper, 403: Error})
+def get_package_scenarios(request, package_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return {'scenario': Scenario.objects.filter(package=p).prefetch_related('package')}
+    except ValueError:
+        return 403, {
+            'message': f'Getting Scenarios for Package with id {package_uuid} failed due to insufficient rights!'}
+
+
+@router.get("/package/{uuid:package_uuid}/scenario/{uuid:scenario_uuid}", response={200: ScenarioSchema, 403: Error})
+def get_package_scenario(request, package_uuid, scenario_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return Scenario.objects.get(package=p, uuid=scenario_uuid)
+    except ValueError:
+        return 403, {
+            'message': f'Getting Scenario with id {scenario_uuid} failed due to insufficient rights!'}
+
+
+###########
+# Pathway #
+###########
+class SimplePathway(SimpleObject):
+    identifier: str = 'pathway'
+
+class PathwayWrapper(Schema):
+    pathway: List['SimplePathway']
+
+@router.get("/pathway", response={200: PathwayWrapper, 403: Error})
+def get_pathways(request):
+    qs = Pathway.objects.none()
+    for p in PackageManager.get_reviewed_packages():
+        qs |= Pathway.objects.filter(package=p)
+    return {'pathway': qs}
+
+
+@router.get("/package/{uuid:package_uuid}/pathway", response={200: PathwayWrapper, 403: Error})
+def get_package_pathways(request, package_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return {'pathway': Pathway.objects.filter(package=p).prefetch_related('package')}
+    except ValueError:
+        return 403, {
+            'message': f'Getting Pathways for Package with id {package_uuid} failed due to insufficient rights!'}
+
+
+# @router.get("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}", response={200: Pathway, 403: Error})
+# def get_package_pathway(request, package_uuid, pathway_uuid):
+#     try:
+#         p = PackageManager.get_package_by_id(request.user, package_uuid)
+#         return Pathway.objects.get(package=p, uuid=pathway_uuid)
+#     except ValueError:
+#         return 403, {
+#             'message': f'Getting Pathway with id {pathway_uuid} failed due to insufficient rights!'}

epdb/management/commands/bootstrap.py

@@ -0,0 +1,205 @@
+import json
+
+from django.conf import settings as s
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.logic import UserManager, GroupManager, PackageManager, SettingManager
+from epdb.models import UserSettingPermission, MLRelativeReasoning, EnviFormer, Permission, User, ExternalDatabase
+
+
+class Command(BaseCommand):
+
+    def create_users(self):
+
+        if not User.objects.filter(email='anon@lorsba.ch').exists():
+            anon = UserManager.create_user("anonymous", "anon@lorsba.ch", "SuperSafe", is_active=True,
+                                           add_to_group=False, set_setting=False)
+        else:
+            anon = User.objects.get(email='anon@lorsba.ch')
+
+        if not User.objects.filter(email='admin@lorsba.ch').exists():
+            admin = UserManager.create_user("admin", "admin@lorsba.ch", "SuperSafe", is_active=True, add_to_group=False,
+                                            set_setting=False)
+            admin.is_staff = True
+            admin.is_superuser = True
+            admin.save()
+        else:
+            admin = User.objects.get(email='admin@lorsba.ch')
+
+        g = GroupManager.create_group(admin, 'enviPath Users', 'All enviPath Users')
+        g.public = True
+        g.save()
+
+        g.user_member.add(anon)
+        g.save()
+
+        anon.default_group = g
+        anon.save()
+
+        admin.default_group = g
+        admin.save()
+
+        if not User.objects.filter(email='jebus@lorsba.ch').exists():
+            jebus = UserManager.create_user("jebus", "jebus@lorsba.ch", "SuperSafe", is_active=True, add_to_group=False,
+                                            set_setting=False)
+            jebus.is_staff = True
+            jebus.is_superuser = True
+            jebus.save()
+        else:
+            jebus = User.objects.get(email='jebus@lorsba.ch')
+
+        g.user_member.add(jebus)
+        g.save()
+
+        jebus.default_group = g
+        jebus.save()
+
+        return anon, admin, g, jebus
+
+    def import_package(self, data, owner):
+        return PackageManager.import_package(data, owner, keep_ids=True, add_import_timestamp=False)
+
+    def create_default_setting(self, owner, packages):
+        s = SettingManager.create_setting(
+            owner,
+            name='Global Default Setting',
+            description='Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8',
+            max_nodes=30,
+            max_depth=5,
+            rule_packages=packages,
+            model=None,
+            model_threshold=None
+        )
+
+        return s
+
+    def populate_common_external_databases(self):
+        """
+        Helper function to populate common external databases.
+        This can be called from a Django management command.
+        """
+        databases = [
+            {
+                'name': 'PubChem Compound',
+                'full_name': 'PubChem Compound Database',
+                'description': 'Chemical database of small organic molecules',
+                'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
+                'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'
+            },
+            {
+                'name': 'PubChem Substance',
+                'full_name': 'PubChem Substance Database',
+                'description': 'Database of chemical substances',
+                'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
+                'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/substance/{id}'
+            },
+            {
+                'name': 'ChEBI',
+                'full_name': 'Chemical Entities of Biological Interest',
+                'description': 'Dictionary of molecular entities',
+                'base_url': 'https://www.ebi.ac.uk/chebi',
+                'url_pattern': 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}'
+            },
+            {
+                'name': 'RHEA',
+                'full_name': 'RHEA Reaction Database',
+                'description': 'Comprehensive resource of biochemical reactions',
+                'base_url': 'https://www.rhea-db.org',
+                'url_pattern': 'https://www.rhea-db.org/rhea/{id}'
+            },
+            {
+                'name': 'CAS',
+                'full_name': 'Chemical Abstracts Service Registry',
+                'description': 'Registry of chemical substances',
+                'base_url': 'https://www.cas.org',
+                'url_pattern': None  # CAS doesn't have a free public URL pattern
+            },
+            {
+                'name': 'KEGG Reaction',
+                'full_name': 'KEGG Reaction Database',
+                'description': 'Database of biochemical reactions',
+                'base_url': 'https://www.genome.jp',
+                'url_pattern': 'https://www.genome.jp/entry/reaction+{id}'
+            },
+            {
+                'name': 'MetaCyc',
+                'full_name': 'MetaCyc Metabolic Pathway Database',
+                'description': 'Database of metabolic pathways and enzymes',
+                'base_url': 'https://metacyc.org',
+                'url_pattern': None
+            },
+            {
+                'name': 'UniProt',
+                'full_name': 'MetaCyc Metabolic Pathway Database',
+                'description': 'UniProt is a freely accessible database of protein sequence and functional information',
+                'base_url': 'https://www.uniprot.org',
+                'url_pattern': 'https://www.uniprot.org/uniprotkb?query="{id}"'
+            }
+        ]
+
+        for db_info in databases:
+            ExternalDatabase.objects.get_or_create(
+                name=db_info['name'],
+                defaults=db_info
+            )
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        # Create users
+        anon, admin, g, jebus = self.create_users()
+
+        # Import Packages
+        packages = [
+            'EAWAG-BBD.json',
+            'EAWAG-SOIL.json',
+            'EAWAG-SLUDGE.json',
+            'EAWAG-SEDIMENT.json',
+        ]
+
+        mapping = {}
+        for p in packages:
+            print(f"Importing {p}...")
+            package_data = json.loads(open(s.BASE_DIR / 'fixtures' / 'packages' / '2025-07-18' / p).read())
+            imported_package = self.import_package(package_data, admin)
+            mapping[p.replace('.json', '')] = imported_package
+
+        setting = self.create_default_setting(admin, [mapping['EAWAG-BBD']])
+        setting.public = True
+        setting.save()
+        setting.make_global_default()
+
+        for u in [anon, jebus]:
+            u.default_setting = setting
+            u.save()
+
+            usp = UserSettingPermission()
+            usp.user = u
+            usp.setting = setting
+            usp.permission = Permission.READ[0]
+            usp.save()
+
+        # Create Model Package
+        pack = PackageManager.create_package(admin, "Public Prediction Models",
+                                             "Package to make Prediction Models publicly available")
+        pack.reviewed = True
+        pack.save()
+
+        # Create RR
+        ml_model = MLRelativeReasoning.create(
+            package=pack,
+            rule_packages=[mapping['EAWAG-BBD']],
+            data_packages=[mapping['EAWAG-BBD']],
+            eval_packages=[],
+            threshold=0.5,
+            name='ECC - BBD - T0.5',
+            description='ML Relative Reasoning',
+        )
+
+        ml_model.build_dataset()
+        ml_model.build_model()
+        # ml_model.evaluate_model()
+
+        # If available create EnviFormerModel
+        if s.ENVIFORMER_PRESENT:
+            enviFormer_model = EnviFormer.create(pack, 'EnviFormer - T0.5', 'EnviFormer Model with Threshold 0.5', 0.5)

epdb/management/commands/import_package.py

@@ -0,0 +1,27 @@
+from django.core.management.base import BaseCommand
+
+from epdb.logic import PackageManager
+from epdb.models import *
+
+
+class Command(BaseCommand):
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--data',
+            type=str,
+            help='Path of the Package to import.',
+            required=True,
+        )
+        parser.add_argument(
+            '--owner',
+            type=str,
+            help='Username of the desired Owner.',
+            required=True,
+        )
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        owner = User.objects.get(username=options['owner'])
+        package_data = json.load(open(options['data']))
+        PackageManager.import_package(package_data, owner)

epdb/management/commands/localize_urls.py

@@ -0,0 +1,50 @@
+from django.apps import apps
+from django.core.management.base import BaseCommand
+
+from django.db.models import F, Value
+from django.db.models.functions import Replace
+
+
+class Command(BaseCommand):
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--old',
+            type=str,
+            help='Old Host, most likely https://envipath.org/',
+            required=True,
+        )
+        parser.add_argument(
+            '--new',
+            type=str,
+            help='New Host, most likely http://localhost:8000/',
+            required=True,
+        )
+
+    def handle(self, *args, **options):
+        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)
+            print(f"Localizing urls for {model}")
+            obj_cls.objects.update(
+                url=Replace(F('url'), Value(options['old']), Value(options['new']))
+            )

epdb/middleware/login_required_middleware.py

@@ -0,0 +1,24 @@
+from django.conf import settings
+from django.shortcuts import redirect
+from django.urls import reverse
+from urllib.parse import quote
+
+class LoginRequiredMiddleware:
+    def __init__(self, get_response):
+        self.get_response = get_response
+        self.exempt_urls = [
+                               reverse('login'),
+                               reverse('logout'),
+                               reverse('admin:login'),
+                               reverse('admin:index'),
+                           ] + getattr(settings, 'LOGIN_EXEMPT_URLS', [])
+
+    def __call__(self, request):
+        if not request.user.is_authenticated:
+            path = request.path_info
+            if not any(path.startswith(url) for url in self.exempt_urls):
+                if request.method == 'GET':
+                    if request.get_full_path() and request.get_full_path() != '/':
+                        return redirect(f"{settings.LOGIN_URL}?next={quote(request.get_full_path())}")
+                return redirect(settings.LOGIN_URL)
+        return self.get_response(request)

epdb/migrations/0001_initial.py

@@ -0,0 +1,594 @@
+# 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',),
+        ),
+    ]

epdb/migrations/0002_externaldatabase_alter_apitoken_options_and_more.py

@@ -0,0 +1,128 @@
+# 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')},
+            },
+        ),
+    ]

epdb/migrations/0003_applicabilitydomain_url_compound_url_and_more.py

@@ -0,0 +1,228 @@
+# 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'),
+        ),
+    ]

epdb/signals.py

@@ -0,0 +1,20 @@
+from django.db import transaction
+from django.db.models.signals import pre_delete
+from django.dispatch import receiver
+
+from epdb.models import Node, Edge
+
+
+@receiver(pre_delete, sender=Node)
+@transaction.atomic
+def delete_orphan_edges(sender, instance, **kwargs):
+    # check if the node that is about to be deleted is the only start node
+    for edge in Edge.objects.filter(start_nodes=instance):
+        if edge.start_nodes.count() == 1:
+            edge.delete()
+
+    # same for end_nodes
+    for edge in Edge.objects.filter(end_nodes=instance):
+        # check if the node that is about to be deleted is the only start node
+        if edge.end_nodes.count() == 1:
+            edge.delete()

epdb/tasks.py

@@ -0,0 +1,81 @@
+import logging
+from typing import Optional
+
+from celery.signals import worker_process_init
+from celery import shared_task
+from epdb.models import Pathway, Node, Edge, EPModel, Setting
+from epdb.logic import SPathway
+
+from utilities.chem import FormatConverter
+
+logger = logging.getLogger(__name__)
+
+
+@shared_task(queue='background')
+def mul(a, b):
+    return a * b
+
+
+@shared_task(queue='predict')
+def predict_simple(model_pk: int, smiles: str):
+    mod = EPModel.objects.get(id=model_pk)
+    res = mod.predict(smiles)
+    return res
+
+
+@shared_task(queue='background')
+def send_registration_mail(user_pk: int):
+    pass
+
+
+@shared_task(queue='model')
+def build_model(model_pk: int):
+    mod = EPModel.objects.get(id=model_pk)
+    mod.build_dataset()
+    mod.build_model()
+
+
+@shared_task(queue='model')
+def evaluate_model(model_pk: int):
+    mod = EPModel.objects.get(id=model_pk)
+    mod.evaluate_model()
+
+
+@shared_task(queue='predict')
+def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_pk: Optional[int] = None) -> Pathway:
+    pw = Pathway.objects.get(id=pw_pk)
+    setting = Setting.objects.get(id=pred_setting_pk)
+
+    pw.kv.update(**{'status': 'running'})
+    pw.save()
+
+    try:
+        # regular prediction
+        if limit is not None:
+            spw = SPathway(prediction_setting=setting, persist=pw)
+            level = 0
+            while not spw.done:
+                spw.predict_step(from_depth=level)
+                level += 1
+
+                # break in case we are in incremental mode
+                if limit != -1:
+                    if level >= limit:
+                        break
+
+        elif node_pk is not None:
+            n = Node.objects.get(id=node_pk, pathway=pw)
+            spw = SPathway.from_pathway(pw)
+            spw.predict_step(from_node=n)
+        else:
+            raise ValueError("Neither limit nor node_pk given!")
+
+
+
+    except Exception as e:
+        pw.kv.update({'status': 'failed'})
+        pw.save()
+        raise e
+
+    pw.kv.update(**{'status': 'completed'})
+    pw.save()

epdb/templatetags/envipytags.py

@@ -0,0 +1,7 @@
+from django import template
+
+register = template.Library()
+
+@register.filter
+def classname(obj):
+    return obj.__class__.__name__

epdb/tests.py

@@ -0,0 +1,3 @@
+from django.test import TestCase
+
+# Create your tests here.

epdb/urls.py

@@ -0,0 +1,82 @@
+from django.urls import path, re_path
+
+from . import views as v
+# from sesame.views import LoginView
+
+UUID = '[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}'
+
+urlpatterns = [
+    # Sesame
+    # path("login/", v.EmailLoginView.as_view(), name="email_login"),
+    # path("login/auth/", LoginView.as_view(), name="login"),
+
+    # Home
+    re_path(r'^$', v.index, name='index'),
+
+    re_path(r'^login', v.login, name='login'),
+    re_path(r'^logout', v.logout, name='logout'),
+
+    # Top level urls
+    re_path(r'^package$', v.packages, name='packages'),
+    re_path(r'^compound$', v.compounds, name='compounds'),
+    re_path(r'^rule$', v.rules, name='rules'),
+    re_path(r'^reaction$', v.reactions, name='reactions'),
+    re_path(r'^pathway$', v.pathways, name='pathways'),
+    re_path(r'^scenario$', v.scenarios, name='scenarios'),
+    re_path(r'^model$', v.models, name='model'),
+    re_path(r'^user$', v.users, name='users'),
+    re_path(r'^group$', v.groups, name='groups'),
+    re_path(r'^search$', v.search, name='search'),
+
+
+    # User Detail
+    re_path(rf'^user/(?P<user_uuid>{UUID})', v.user, name='user'),
+    # Group Detail
+    re_path(rf'^group/(?P<group_uuid>{UUID})$', v.group, name='group_detail'),
+
+    # "in package" urls
+    re_path(rf'^package/(?P<package_uuid>{UUID})$', v.package, name='package_detail'),
+    # Compound
+    re_path(rf'^package/(?P<package_uuid>{UUID})/compound$', v.package_compounds, name='package compound list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})$', v.package_compound, name='package compound detail'),
+    # Compound Structure
+    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure$', v.package_compound_structures, name='package compound structure list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure/(?P<structure_uuid>{UUID})$', v.package_compound_structure, name='package compound structure detail'),
+    # Rule
+    re_path(rf'^package/(?P<package_uuid>{UUID})/rule$', v.package_rules, name='package rule list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+    # Reaction
+    re_path(rf'^package/(?P<package_uuid>{UUID})/reaction$', v.package_reactions, name='package reaction list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/reaction/(?P<reaction_uuid>{UUID})$', v.package_reaction, name='package reaction detail'),
+    # # Pathway
+    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway$', v.package_pathways, name='package pathway list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})$', v.package_pathway, name='package pathway detail'),
+    # Pathway Nodes
+    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$', v.package_pathway_nodes, name='package pathway node list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node/(?P<node_uuid>{UUID})$', v.package_pathway_node, name='package pathway node detail'),
+    # Pathway Edges
+    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge$', v.package_pathway_edges, name='package pathway edge list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$', v.package_pathway_edge, name='package pathway edge detail'),
+    # Scenario
+    re_path(rf'^package/(?P<package_uuid>{UUID})/scenario$', v.package_scenarios, name='package scenario list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/scenario/(?P<scenario_uuid>{UUID})$', v.package_scenario, name='package scenario detail'),
+    # Model
+    re_path(rf'^package/(?P<package_uuid>{UUID})/model$', v.package_models, name='package model list'),
+    re_path(rf'^package/(?P<package_uuid>{UUID})/model/(?P<model_uuid>{UUID})$', v.package_model,name='package model detail'),
+
+    re_path(r'^setting$', v.settings, name='settings'),
+    re_path(rf'^setting/(?P<setting_uuid>{UUID})', v.setting, name='setting'),
+
+    re_path(r'^indigo/info$', v.indigo, name='indigo_info'),
+    re_path(r'^indigo/aromatize$', v.aromatize, name='indigo_aromatize'),
+    re_path(r'^indigo/dearomatize$', v.dearomatize, name='indigo_dearomatize'),
+    re_path(r'^indigo/layout$', v.layout, name='indigo_layout'),
+
+    re_path(r'^depict$', v.depict, name='depict'),
+
+    path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
+]

manage.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+"""Django's command-line utility for administrative tasks."""
+import os
+import sys
+
+
+def main():
+    """Run administrative tasks."""
+    os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'envipath.settings')
+    try:
+        from django.core.management import execute_from_command_line
+    except ImportError as exc:
+        raise ImportError(
+            "Couldn't import Django. Are you sure it's installed and "
+            "available on your PYTHONPATH environment variable? Did you "
+            "forget to activate a virtual environment?"
+        ) from exc
+    execute_from_command_line(sys.argv)
+
+
+if __name__ == '__main__':
+    main()

migration/admin.py

@@ -0,0 +1,3 @@
+from django.contrib import admin
+
+# Register your models here.

migration/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class MigrationConfig(AppConfig):
+    default_auto_field = 'django.db.models.BigAutoField'
+    name = 'migration'

migration/models.py

@@ -0,0 +1,3 @@
+from django.db import models
+
+# Create your models here.

migration/tests.py

@@ -0,0 +1,3 @@
+from django.test import TestCase
+
+# Create your tests here.

migration/urls.py

@@ -0,0 +1,15 @@
+from django.urls import re_path
+
+from . import views as v
+
+UUID = '[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}'
+
+urlpatterns = [
+    re_path(rf'^migration$', v.migration, name='migration'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/simple-rule/(?P<rule_uuid>{UUID})$',v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+]

migration/views.py

@@ -0,0 +1,199 @@
+import gzip
+import json
+import os.path
+
+from django.conf import settings as s
+from django.shortcuts import render
+
+from epdb.logic import PackageManager
+from epdb.models import Rule
+from epdb.views import get_base_context, _anonymous_or_real
+from utilities.chem import FormatConverter
+
+
+def migration(request):
+    if request.method == 'GET':
+        context = get_base_context(request)
+
+        if os.path.exists(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json') and request.GET.get(
+                "force") is None:
+            migration_status = json.load(open(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json'))
+        else:
+            data = json.load(gzip.open(s.BASE_DIR / 'fixtures' / 'ambit_rules.json.gz', 'rb'))
+
+            results = []
+
+            success = 0
+            error = 0
+            total = 0
+
+            num_keys = len(data.keys())
+            for i, bt_rule_name in enumerate(data.keys()):
+                print(f"{i + 1}/{num_keys}")
+                bt_rule = data[bt_rule_name]
+                smirks = bt_rule['smirks']
+
+                all_prods = set()
+
+                res = True
+
+                for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
+
+                    products = FormatConverter.apply(comp['smiles'], smirks)
+
+                    all_rdkit_prods = []
+                    for ps in products:
+                        for p in ps:
+                            all_rdkit_prods.append(p)
+
+                    all_rdkit_prods = list(set(all_rdkit_prods))
+
+                    ambit_smiles, ambit_errors = FormatConverter.sanitize_smiles(ambit_prod)
+                    rdkit_smiles, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
+
+                    for x in ambit_smiles:
+                        all_prods.add(x)
+
+                    # TODO mode "intersection"
+                    # partial_res = (len(set(ambit_smiles).intersection(set(rdkit_smiles))) > 0) or (len(ambit_smiles) == 0)
+                    # FAILED (failures=37)
+
+                    # TODO mode = "full ambit"
+                    # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
+                    # FAILED (failures=46)
+
+                    # TODO mode = "equality"
+                    partial_res = set(ambit_smiles) == set(rdkit_smiles)
+                    # FAILED (failures=69)
+
+                    res &= partial_res
+
+                results.append(
+                    {
+                        'name': bt_rule_name,
+                        'id': bt_rule['id'].split('/')[-1],
+                        'url': bt_rule['id'],
+                        'status': res,
+                        'detail_url': s.SERVER_URL + '/migration/' + bt_rule['id'].replace('https://envipath.org/', '')
+                    }
+                )
+
+                if res:
+                    success += 1
+                else:
+                    error += 1
+
+                total += 1
+
+            results = sorted(results, key=lambda x: (x['status'], x['name']))
+
+            migration_status = {
+                'results': results,
+                'success': success,
+                'error': error,
+                'total': total
+            }
+
+            json.dump(migration_status, open(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json', 'w'))
+
+        for r in migration_status['results']:
+            r['detail_url'] = r['detail_url'].replace('http://localhost:8000', s.SERVER_URL)
+
+        context.update(**migration_status)
+
+        return render(request, 'migration.html', context)
+
+
+def migration_detail(request, package_uuid, rule_uuid):
+    current_user = _anonymous_or_real(request)
+
+    if request.method == 'GET':
+        context = get_base_context(request)
+
+        p = PackageManager.get_package_by_id(current_user, package_uuid)
+        rule = Rule.objects.get(package=p, uuid=rule_uuid)
+        bt_rule_name = rule.name
+
+        data = json.load(gzip.open(s.BASE_DIR / 'fixtures' / 'ambit_rules.json.gz', 'rb'))
+
+        bt_rule = data[bt_rule_name]
+        smirks = bt_rule['smirks']
+
+        results = []
+
+        res = True
+
+        all_prods = set()
+        for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
+            # if comp['smiles'] != 'CC1=C(C(=C(C=N1)CO)C=O)O':
+            #     continue
+
+            products = FormatConverter.apply(comp['smiles'], smirks)
+
+            all_rdkit_prods = []
+            for ps in products:
+                for p in ps:
+                    all_rdkit_prods.append(p)
+
+            all_rdkit_prods = list(set(all_rdkit_prods))
+
+            ambit_smiles, ambit_errors = FormatConverter.sanitize_smiles(ambit_prod)
+            rdkit_smiles, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
+
+            for x in ambit_smiles:
+                all_prods.add(x)
+
+            # TODO mode "intersection"
+            # partial_res = (len(set(ambit_smiles).intersection(set(rdkit_smiles))) > 0) or (len(ambit_smiles) == 0)
+            # FAILED (failures=37)
+
+            # TODO mode = "full ambit"
+            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
+            # FAILED (failures=46)
+
+            # TODO mode = "equality"
+            partial_res = set(ambit_smiles) == set(rdkit_smiles)
+            # FAILED (failures=69)
+
+            #
+            if len(ambit_smiles) or len(rdkit_smiles):
+                temp = {
+                    'url': comp['id'],
+                    'id': comp['id'].split('/')[-1],
+                    'name': comp['name'],
+                    'initial_smiles': comp['smiles'],
+                    'ambit_smiles': sorted(list(ambit_smiles)),
+                    'rdkit_smiles': sorted(list(rdkit_smiles)),
+                    'status': set(ambit_smiles) == set(rdkit_smiles),
+                }
+
+                if set(ambit_smiles) != set(rdkit_smiles):
+                    detail = f"""
+                        BT: {bt_rule_name}
+                        SMIRKS: {bt_rule['smirks']}
+                        Compound: {comp['smiles']}
+                        Compound URL: {comp['id']}
+                        Num ambit: {len(set(ambit_smiles))}
+                        Num rdkit: {len(set(rdkit_smiles))}
+                        Num Intersection A: {len(set(ambit_smiles).intersection(set(rdkit_smiles)))}
+                        Num Intersection B: {len(set(rdkit_smiles).intersection(set(ambit_smiles)))}
+                        Difference A: {set(ambit_smiles).difference(set(rdkit_smiles))}
+                        Difference B: {set(rdkit_smiles).difference(set(ambit_smiles))}
+                        ambit products: {ambit_smiles}
+                        rdkit products: {rdkit_smiles}
+                        ambit_errors: {ambit_errors}
+                        rdkit_errors: {rdkit_errors}
+                    """
+
+                    temp['detail'] = '\n'.join([x.strip() for x in detail.split('\n')])
+                    # print(detail.strip())
+
+                results.append(temp)
+
+            res &= partial_res
+
+        results = sorted(results, key=lambda x: x['status'])
+        context['results'] = results
+        context['res'] = res
+        context['bt_rule_name'] = bt_rule_name
+        return render(request, 'migration_detail.html', context)

pyproject.toml

@@ -0,0 +1,33 @@
+[project]
+name = "envipy"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "celery>=5.5.2",
+    "django>=5.2.1",
+    "django-extensions>=4.1",
+    "django-model-utils>=5.0.0",
+    "django-ninja>=1.4.1",
+    "django-oauth-toolkit>=3.0.1",
+    "django-polymorphic>=4.1.0",
+    "enviformer",
+    "envipy-additional-information",
+    "envipy-plugins",
+    "epam-indigo>=1.30.1",
+    "gunicorn>=23.0.0",
+    "psycopg2-binary>=2.9.10",
+    "python-dotenv>=1.1.0",
+    "rdkit>=2025.3.2",
+    "redis>=6.1.0",
+    "requests>=2.32.3",
+    "scikit-learn>=1.6.1",
+    "sentry-sdk[django]>=2.32.0",
+    "setuptools>=80.8.0",
+]
+
+[tool.uv.sources]
+enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.0" }
+envipy-plugins = { git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git", rev = "v0.1.0" }
+envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.4"}

static/css/c3.css

@@ -0,0 +1,168 @@
+/*-- Chart --*/
+.c3 svg {
+  font: 10px sans-serif;
+  -webkit-tap-highlight-color: transparent; }
+
+.c3 path, .c3 line {
+  fill: none;
+  stroke: #000;
+  }
+
+.c3 text {
+  -webkit-user-select: none;
+  -moz-user-select: none;
+  user-select: none; }
+
+.c3-legend-item-tile,
+.c3-xgrid-focus,
+.c3-ygrid,
+.c3-event-rect,
+.c3-bars path {
+  shape-rendering: crispEdges; }
+
+.c3-chart-arc path {
+  stroke: #fff; }
+
+.c3-chart-arc text {
+  fill: #fff;
+  font-size: 13px; }
+
+/*-- Axis --*/
+/*-- Grid --*/
+.c3-grid line {
+  stroke: #aaa; }
+
+.c3-grid text {
+  fill: #aaa; }
+
+.c3-xgrid, .c3-ygrid {
+  stroke-dasharray: 3 3; }
+
+/*-- Text on Chart --*/
+.c3-text.c3-empty {
+  fill: #808080;
+  font-size: 2em; }
+
+/*-- Line --*/
+.c3-line {
+  stroke-width: 1px; }
+
+/*-- Point --*/
+.c3-circle._expanded_ {
+  stroke-width: 1px;
+  stroke: white; }
+
+.c3-selected-circle {
+  fill: white;
+  stroke-width: 2px; }
+
+/*-- Bar --*/
+.c3-bar {
+  stroke-width: 0; }
+
+.c3-bar._expanded_ {
+  fill-opacity: 0.75; }
+
+/*-- Focus --*/
+.c3-target.c3-focused {
+  opacity: 1; }
+
+.c3-target.c3-focused path.c3-line, .c3-target.c3-focused path.c3-step {
+  stroke-width: 2px; }
+
+.c3-target.c3-defocused {
+  opacity: 0.3 !important; }
+
+/*-- Region --*/
+.c3-region {
+  fill: steelblue;
+  fill-opacity: .1; }
+
+/*-- Brush --*/
+.c3-brush .extent {
+  fill-opacity: .1; }
+
+/*-- Select - Drag --*/
+/*-- Legend --*/
+.c3-legend-item {
+  font-size: 12px; }
+
+.c3-legend-item-hidden {
+  opacity: 0.15; }
+
+.c3-legend-background {
+  opacity: 0.75;
+  fill: white;
+  stroke: lightgray;
+  stroke-width: 1; }
+
+/*-- Title --*/
+.c3-title {
+  font: 14px sans-serif; }
+
+/*-- Tooltip --*/
+.c3-tooltip-container {
+  z-index: 10; }
+
+.c3-tooltip {
+  border-collapse: collapse;
+  border-spacing: 0;
+  background-color: #fff;
+  empty-cells: show;
+  -webkit-box-shadow: 7px 7px 12px -9px #777777;
+  -moz-box-shadow: 7px 7px 12px -9px #777777;
+  box-shadow: 7px 7px 12px -9px #777777;
+  opacity: 0.9; }
+
+.c3-tooltip tr {
+  border: 1px solid #CCC; }
+
+.c3-tooltip th {
+  background-color: #aaa;
+  font-size: 14px;
+  padding: 2px 5px;
+  text-align: left;
+  color: #FFF; }
+
+.c3-tooltip td {
+  font-size: 13px;
+  padding: 3px 6px;
+  background-color: #fff;
+  border-left: 1px dotted #999; }
+
+.c3-tooltip td > span {
+  display: inline-block;
+  width: 10px;
+  height: 10px;
+  margin-right: 6px; }
+
+.c3-tooltip td.value {
+  text-align: right; }
+
+/*-- Area --*/
+.c3-area {
+  stroke-width: 0;
+  opacity: 0.2; }
+
+/*-- Arc --*/
+.c3-chart-arcs-title {
+  dominant-baseline: middle;
+  font-size: 1.3em; }
+
+.c3-chart-arcs .c3-chart-arcs-background {
+  fill: #e0e0e0;
+  stroke: none; }
+
+.c3-chart-arcs .c3-chart-arcs-gauge-unit {
+  fill: #000;
+  font-size: 16px; }
+
+.c3-chart-arcs .c3-chart-arcs-gauge-max {
+  fill: #777; }
+
+.c3-chart-arcs .c3-chart-arcs-gauge-min {
+  fill: #777; }
+
+.c3-chart-arc .c3-gauge-value {
+  fill: #000;
+  /*  font-size: 28px !important;*/ }

static/css/epp.css

@@ -0,0 +1,126 @@
+
+.mini-submenu{
+  display:none;
+  background-color: rgba(0, 0, 0, 0);
+  border: 1px solid rgba(0, 0, 0, 0.9);
+  border-radius: 4px;
+  padding: 9px;
+  /*position: relative;*/
+  width: 42px;
+
+}
+
+.mini-submenu:hover{
+  cursor: pointer;
+}
+
+.mini-submenu .icon-bar {
+  border-radius: 1px;
+  display: block;
+  height: 2px;
+  width: 22px;
+  margin-top: 3px;
+}
+
+.mini-submenu .icon-bar {
+  background-color: #000;
+}
+
+#slide-submenu{
+  background: rgba(0, 0, 0, 0.45);
+  display: inline-block;
+  padding: 0 8px;
+  border-radius: 4px;
+  cursor: pointer;
+}
+
+#eductsdiv {
+	float:left;
+}
+#agentsdiv {
+	float:left;
+}
+#productsdiv {
+	float:left;
+}
+#actions {
+	float:left;
+}
+
+.modal.fade .modal-dialog {
+  overflow-y: auto;
+  max-height: 800px;
+}
+
+.modal-dialog-multiple {
+  position: relative;
+  overflow: visible;
+  width: 600px;
+  margin: 30px auto;
+  max-height: 800px;
+ }
+
+.modal-element{
+  padding-top: 10px;
+  margin-top: 5px;
+  margin-bottom: 5px;
+
+  border-top: 1px solid #e5e5e5;
+}
+
+.modal-dialog-pps{
+  position: relative;
+  display: table;
+  margin-left: 35%;
+  margin-right: 35%;
+  overflow-y: auto;
+  overflow-x: auto;
+  width: 30%;
+}
+
+.modal-dialog-pps-big{
+  position: relative;
+  display: table;
+  margin-left: 25%;
+  margin-right: 25%;
+  overflow-y: auto;
+  overflow-x: auto;
+  width: 50%;
+}
+
+    @media (max-width: 1220px) {
+    .navbar-header-framework {
+        float: none;
+    }
+    .navbar-left-framework,.navbar-right-framework {
+        float: none !important;
+    }
+    .navbar-toggle-framework {
+        display: block;
+    }
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static/js/epp/epp.js

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+class Setting {
+  constructor(nameInputId, selectedPackagesId, relativeReasoningSelectId, cutoffInputId, evaluationTypeSelectId,
+              availableTSSelectId, formsId, tableId, summaryTableId) {
+    this.nameInputId = nameInputId;
+    this.selectedPackagesId = selectedPackagesId;
+    this.relativeReasoningSelectId = relativeReasoningSelectId;
+    this.cutoffInputId = cutoffInputId;
+    this.evaluationTypeSelectId = evaluationTypeSelectId;
+    this.availableTSSelectId = availableTSSelectId;
+    this.formsId = formsId;
+    this.tableId = tableId;
+    this.summaryTableId = summaryTableId;
+
+    // General settings
+    this.name = null;
+    this.selectedPackages = [];
+
+    // Relative Reasoning related
+    this.selectedRelativeReasoning = null;
+    this.cutoff = null;
+    this.evaluationType = null;
+
+    // parameters such as { "lowPH": 7, "highPH": 8 }
+    this.tsParams = {};
+  }
+
+  extractName() {
+    var tempName = $('#' + this.nameInputId).val()
+    if (tempName == '') {
+        console.log("Name was empty...");
+        return;
+    }
+    this.name = tempName;
+  }
+
+  extractSelectedPackages() {
+    var selPacks = $("#" + this.selectedPackagesId + " :selected");
+    var ref = this;
+    ref.selectedPackages = [];
+    selPacks.each(function () {
+      var obj = {}
+      obj['id'] = this.value;
+      obj['name'] = this.text;
+      ref.selectedPackages.push(obj);
+    });
+  }
+
+  extractRelativeReasoning() {
+    var tempRR = $('#' + this.relativeReasoningSelectId + " :selected").val()
+    if (tempRR == '') {
+        console.log("RR was empty...");
+        return;
+    }
+    var obj = {}
+    obj['id'] = $('#' + this.relativeReasoningSelectId + " :selected").val()
+    obj['name'] = $('#' + this.relativeReasoningSelectId + " :selected").text()
+    this.selectedRelativeReasoning = obj;
+  }
+
+  extractCutoff() {
+    var tempCutoff = $('#' + this.cutoffInputId).val()
+    if (tempCutoff == '') {
+        console.log("Cutoff was empty...");
+        return;
+    }
+    this.cutoff = tempCutoff;
+  }
+
+  extractEvaluationType() {
+    var tempEvaluationType = $('#' + this.evaluationTypeSelectId).val()
+    if (tempEvaluationType == '') {
+        console.log("EvaluationType was empty...");
+        return;
+    }
+    this.evaluationType = tempEvaluationType;
+  }
+
+  addTruncator() {
+    // triggered by "Add"
+    // will extract values and afterwards updates table + summary
+    var type = $("#" + this.availableTSSelectId + " :selected").val();
+    var text = $("#" + this.availableTSSelectId + " :selected").text();
+    var form = $("#" + type + "_form > :input")
+
+    // flag to check whether at least one input had a valid value
+    var addedValue = false;
+
+    // reference being used in each
+    var ref = this;
+
+    form.each(function() {
+        if(this.value == "" || this.value === "undefined"){
+            console.log(this);
+            console.log("Skipping " + this.name);
+        } else {
+            var obj = {}
+            obj[this.name] = this.value;
+            obj['text'] = text;
+            ref.tsParams[type] = obj
+        }
+    });
+
+    this.updateTable();
+    this.updateSummaryTable();
+  }
+
+  removeTruncator(rowId) {
+    var summary = rowId.startsWith("sum") ? true : false;
+    // plain key
+    var key = rowId.replace(summary ? "sum" : "trunc", "").replace("row", "");
+
+    console.log("Removing " + key);
+
+    // remove the rows
+    $("#trunc"+ key + "row").remove();
+    if($("#sum"+ key + "row").length > 0) {
+        $("#sum"+ key + "row").remove();
+    }
+
+    delete this.tsParams[key];
+  }
+
+  updateTable() {
+    // remove all children
+    $('#'+this.tableId + "Body").empty()
+
+    var innerHTML = "<tr>" +
+                      "<td>Name</td>" +
+                      "<td>Value</td>" +
+                      "<td width='10%'>Action</td>" +
+                    "</tr>";
+
+    for (var x in this.tsParams) {
+      var val = "";
+      for (var y in this.tsParams[x]){
+        if (y == 'text') {
+            continue;
+        }
+        val += this.tsParams[x][y]
+
+      }
+      innerHTML += "<tr id='trunc" + x + "row'>" +
+                     "<td>" + this.tsParams[x]['text'] + "</td>" +
+                     "<td>" + val + "</td>" +
+                     "<td width='10%'>"+
+                       "<button type='button' id='" + x + "button' class='form-control' onclick='s.removeTruncator(\"trunc" + x + "row\")'>Remove</button>" +
+                     "</td>" +
+                   "</tr>";
+    }
+
+    $('#'+this.tableId + "Body").append(innerHTML);
+  }
+
+  packageRows() {
+    var res = '';
+    for(var p in this.selectedPackages) {
+        var obj = this.selectedPackages[p];
+        res += "<tr>" +
+                 "<td>Package</td>" +
+                 "<td>" + obj['name'] + "</td>" +
+                 "<td width='10%'>" +
+                   // "<button type='button' id='relativereasoningbutton' class='form-control' onclick='s.removeTruncator(\"Relative Reasoning\")'>Remove</button>" +
+                 "</td>" +
+               "</tr>";
+    }
+    return res;
+  }
+
+  modelRow() {
+    if(this.selectedRelativeReasoning == null) {
+      return '';
+    }
+    return "<tr>" +
+             "<td>Relative Reasoning</td>" +
+             "<td>" + this.selectedRelativeReasoning['name'] + " " + (this.evaluationType == "singleGen" ? "SG" : "MG") + " with t=" + this.cutoff + " </td>" +
+             "<td width='10%'>" +
+               // "<button type='button' id='relativereasoningbutton' class='form-control' onclick='s.removeTruncator(\"Relative Reasoning\")'>Remove</button>" +
+             "</td>" +
+           "</tr>";
+  }
+
+  updateSummaryTable() {
+    // remove all children
+    $('#'+this.summaryTableId + "Body").empty()
+
+    var innerHTML = "<tr>" +
+                      "<td>Name</td>" +
+                      "<td>Value</td>" +
+                      "<td width='10%'>Action</td>" +
+                    "</tr>";
+
+    innerHTML += this.packageRows();
+    innerHTML += this.modelRow();
+
+    // var innerHTML = ''
+    for (var x in this.tsParams) {
+      var val = "";
+      for (var y in this.tsParams[x]){
+        if (y == 'text') {
+            continue;
+        }
+        val += this.tsParams[x][y]
+
+      }
+      innerHTML += "<tr id='sum" + x + "row'>" +
+                     "<td>" + this.tsParams[x]['text'] + "</td>" +
+                     "<td>" + val + "</td>" +
+                     "<td width='10%'>"+
+                       "<button type='button' id='" + x + "button' class='form-control' onclick='s.removeTruncator(\"sum" + x + "row\")'>Remove</button>" +
+                     "</td>" +
+                   "</tr>";
+    }
+
+    $('#'+this.summaryTableId + "Body").append(innerHTML);
+  }
+
+}

static/js/epp/jquery-bootstrap-modal-steps.js

@@ -0,0 +1 @@
+!function(t){"use strict";t.fn.modalSteps=function(a){var e=this,n=t.extend({btnCancelHtml:"Cancel",btnPreviousHtml:"Previous",btnNextHtml:"Next",btnLastStepHtml:"Complete",disableNextButton:!1,completeCallback:function(){},callbacks:{},getTitleAndStep:function(){}},a),d=function(t){return void 0!==t&&"function"==typeof t&&(t(),!0)};return e.on("show.bs.modal",function(){var a,l,s,i=e.find(".modal-footer"),o=i.find(".js-btn-step[data-orientation=cancel]"),p=i.find(".js-btn-step[data-orientation=previous]"),r=i.find(".js-btn-step[data-orientation=next]"),c=n.callbacks["*"],b=n.callbacks[1];n.disableNextButton&&r.attr("disabled","disabled"),p.attr("disabled","disabled"),function(){var t=n.callbacks["*"];if(void 0!==t&&"function"!=typeof t)throw"everyStepCallback is not a function! I need a function";if("function"!=typeof n.completeCallback)throw"completeCallback is not a function! I need a function";for(var a in n.callbacks)if(n.callbacks.hasOwnProperty(a)){var e=n.callbacks[a];if("*"!==a&&void 0!==e&&"function"!=typeof e)throw"Step "+a+" callback must be a function"}}(),d(c),d(b),o.html(n.btnCancelHtml),p.html(n.btnPreviousHtml),r.html(n.btnNextHtml),a=t("<input>").attr({type:"hidden",id:"actual-step",value:"1"}),e.find("#actual-step").remove(),e.append(a),e.find("[data-step=1]").removeClass("d-none"),r.attr("data-step",2),l=e.find("[data-step=1]").data("title"),s=t("<span>").addClass("label label-success").html(1),e.find(".js-title-step").append(s).append(" "+l),n.getTitleAndStep(a.attr("data-title"),1)}).on("hidden.bs.modal",function(){var t=e.find("#actual-step"),a=e.find(".js-btn-step[data-orientation=next]");e.find("[data-step]").not(e.find(".js-btn-step")).addClass("d-none"),t.not(e.find(".js-btn-step")).remove(),a.attr("data-step",1).html(n.btnNextHtml),e.find(".js-title-step").html("")}),e.find(".js-btn-step").on("click",function(){var a,l,s,i,o=t(this),p=e.find("#actual-step"),r=e.find(".js-btn-step[data-orientation=previous]"),c=e.find(".js-btn-step[data-orientation=next]"),b=e.find(".js-title-step"),f=o.data("orientation"),u=parseInt(p.val()),m=n.callbacks["*"];if(a=e.find("div[data-step]").length,"complete"===o.attr("data-step"))return n.completeCallback(),void e.modal("hide");if("next"===f)l=u+1,r.attr("data-step",u),p.val(l);else{if("previous"!==f)return void e.modal("hide");l=u-1,c.attr("data-step",u),r.attr("data-step",l-1),p.val(u-1)}parseInt(p.val())===a?c.attr("data-step","complete").html(n.btnLastStepHtml):c.attr("data-step",l).html(n.btnNextHtml),n.disableNextButton&&c.attr("disabled","disabled"),e.find("[data-step="+u+"]").not(e.find(".js-btn-step")).addClass("d-none"),e.find("[data-step="+l+"]").not(e.find(".js-btn-step")).removeClass("d-none"),parseInt(r.attr("data-step"))>0?r.removeAttr("disabled"):r.attr("disabled","disabled"),"previous"===f&&c.removeAttr("disabled"),(s=e.find("[data-step="+l+"]")).attr("data-unlock-continue")&&c.removeAttr("disabled"),i=s.attr("data-title");var v=t("<span>").addClass("label label-success").html(l);b.html(v).append(" "+i),n.getTitleAndStep(s.attr("data-title"),l);var h=n.callbacks[p.val()];d(m),d(h)}),this}}(jQuery);

static/js/epp/pathway.js

@@ -0,0 +1,191 @@
+// drawarea
+var svg;
+
+// colors
+var border = "thin solid lightgrey";
+
+
+// nodes
+
+
+// links
+
+// tree
+var compoundSize = 75; // = diameter of nodes of small compounds
+var maxCompoundSize = function(){ return 1.5 * compoundSize }; // limit increased size of larger compounds
+var maxCompoundPopupSize = function(){ return 5 * compoundSize };
+var compoundImageMargin = 0.15;  // compounds images are rectangles, reduce size to fit into nodes
+
+var treeLayoutLinkDistance = function(){ return 2.5 * compoundSize };
+var treeLayoutCharge = -1000; // compounds push each other apart
+var treeLayoutPseudoCharge = treeLayoutCharge * 0.1; // relaxes forces on pseudo nodes
+var treeLayoutLevelGravity = 0.5; // pulls compounds back to their depth level
+var treeLayoutXCenterGravity = 0.03; // pulls compounds to x center
+var treeLayoutLevels = function(){ return treeLayoutLinkDistance() }; // distance between depth levels
+var treeLayoutXInitMargin = function(){ return treeLayoutLinkDistance() }; // initial x-distance between nodes of same depth
+
+
+// Convenience method to check wether a given node is a leaf
+function isLeaf(node) {
+    return node.children.length == 0;
+}
+
+function getMaxNodeDepth(graph) {
+    maxDepth = 0
+    graph.nodes.forEach(function(node, i) {
+        if (node.depth > maxDepth)
+            maxDepth = node.depth;
+    });
+    return maxDepth;
+}
+
+// adds a parents[] and a children[] array for each node set treeSize
+function setChildrenAndParents(graph) {
+    // Init arrays on each node
+    graph.nodes.forEach(function(node, i) {
+        node.parents = []
+        node.children = []
+    });
+
+    // loop through links, determine source and target and populate
+    // their parent/children arrays
+    graph.links.forEach(function(link, j) {
+        source = graph.nodes[link.source];
+        target = graph.nodes[link.target];
+        source.children.push(target);
+        target.parents.push(source);
+    });
+
+    // Recursively traverses the tree to count the nodes that can be reached
+    function count(node) {
+        node.touch = true;
+        c = 1;
+        node.children.forEach(function(child, i) {
+            if (!child.touch) {
+                c += count(child);
+            }
+        });
+        node.count = false;
+        return c;
+    }
+
+    // Check how many nodes can be reached from each given node
+    // by traversing the children property
+    graph.nodes.forEach(function(node, i) {
+        // reset touch on all nodes
+        graph.nodes.forEach(function(n, i) {
+            n.touch = false;
+        });
+        // get count
+        node.downstreamNodeCount = count(node);
+    });
+
+    // determine siblings for each links
+    graph.links.forEach(function(link, j) {
+        p = graph.nodes[link.source].children.length;
+        c = graph.nodes[link.target].parents.length;
+        link.siblings = Math.max(p, c);
+    });
+}
+
+// sets all links to pseudo that are connected to a pseudo node
+function setPseudoLinks(graph) {
+    graph.links.forEach(function(link, j) {
+        if (graph.nodes[link.source].pseudo || graph.nodes[link.target].pseudo) {
+            link.pseudo = true;
+        } else {
+            link.pseudo = false;
+        }
+    });
+}
+
+function redraw() {
+    svg.attr("transform", "translate(" + d3.event.translate + ")" + " scale(" + d3.event.scale + ")");
+}
+
+function reset() {
+    // remove all;
+    svg.selectAll("g.node").remove();
+    svg.selectAll("rect").remove();
+    svg.selectAll("image").remove();
+    svg.selectAll("line").remove();
+    svg.selectAll("marker").remove();
+    svg.selectAll("text").remove();
+    svg.selectAll("g").remove();
+    svg.selectAll("defs").remove();
+    //start(__graph);
+}
+
+function _drawPathway(elem, graph, options) {
+    width = document.getElementById(elem).offsetWidth;
+    height = width * 0.75;
+
+    svg = d3.select("#" + elem)
+            .append("svg")
+            .attr("width", "100%")
+            .attr("height", height)
+            .style("border", border)
+            .attr("inline", "block")
+            .attr("margin", "auto")
+            .attr("pointer-events", "all")
+            .append('svg:g')
+            .call(d3.behavior.zoom().on("zoom", redraw))
+            .attr("preserveAspectRatio", "xMidYMid meet")
+            .append('svg:g');
+
+    // Background rectangle to enable zoom function
+    // even cursor is not on a node or path
+    svg.append('svg:rect')
+        .attr('width', 9 * width)
+        .attr('height', 9 * height)
+        .attr('fill', 'white')
+        .attr("x", -4 * width)
+        .attr("y", -4 * height)
+        .attr("opacity", 0.0);
+
+    setChildrenAndParents(graph)
+    setPseudoLinks(graph)
+    var maxDepths = getMaxNodeDepth(graph);
+
+//    if(options.treeLayout) {
+//
+//    } else {
+//
+//    }
+    force = d3.layout.force()
+                .charge(function(d) {
+                    if (d.pseudo) {
+                        return treeLayoutPseudoCharge;
+                    } else {
+                        return treeLayoutCharge;
+                    }
+                })
+                .gravity(0)
+                .linkDistance(function(d) {
+                    dist = Math.abs(d.target.treeLevel - d.source.treeLevel) * treeLayoutLinkDistance();
+                    if (dist == 0) {
+                        // nodes with depth in brackets: A (0) -> B (1) + C (2)
+                        // then there is a pseudo node that is on the same level as B
+                        dist = 0.5 * treeLayoutLinkDistance();
+                    }
+                    return dist;
+                })
+                .linkStrength(function(d) {
+                    return strength = 1 / d.siblings;
+                })
+                .size([width, height]);
+
+    force.nodes(graph.nodes).links(graph.links).start();
+
+}
+
+function drawPathway(elem, options) {
+
+    d3.json("", function(error, graph) {
+        if (graph) {
+            _drawPathway(elem, graph, options);
+        } else {
+            throw new Error("Graph not defined: " + error);
+        }
+    });
+}

static/js/jquery-bootstrap-modal-steps.js

@@ -0,0 +1,228 @@
+/* global jQuery */
+
+(function($){
+    'use strict';
+
+    $.fn.modalSteps = function(options){
+        var $modal = this;
+
+        var settings = $.extend({
+            btnCancelHtml: 'Cancel',
+            btnPreviousHtml: 'Previous',
+            btnNextHtml: 'Next',
+            btnLastStepHtml: 'Complete',
+            disableNextButton: false,
+            completeCallback: function(){},
+            callbacks: {}
+        }, options);
+
+
+        var validCallbacks = function(){
+            var everyStepCallback = settings.callbacks['*'];
+
+            if (everyStepCallback !== undefined && typeof(everyStepCallback) !== 'function'){
+                throw 'everyStepCallback is not a function! I need a function';
+            }
+
+            if (typeof(settings.completeCallback) !== 'function') {
+                throw 'completeCallback is not a function! I need a function';
+            }
+
+            for(var step in settings.callbacks){
+                if (settings.callbacks.hasOwnProperty(step)){
+                    var callback = settings.callbacks[step];
+
+                    if (step !== '*' && callback !== undefined && typeof(callback) !== 'function'){
+                        throw 'Step ' + step + ' callback must be a function';
+                    }
+                }
+            }
+        };
+
+        var executeCallback = function(callback){
+            if (callback !== undefined && typeof(callback) === 'function'){
+                callback();
+                return true;
+            }
+            return false;
+        };
+
+        $modal
+            .on('show.bs.modal', function(){
+                var $modalFooter = $modal.find('.modal-footer'),
+                    $btnCancel = $modalFooter.find('.js-btn-step[data-orientation=cancel]'),
+                    $btnPrevious = $modalFooter.find('.js-btn-step[data-orientation=previous]'),
+                    $btnNext = $modalFooter.find('.js-btn-step[data-orientation=next]'),
+                    everyStepCallback = settings.callbacks['*'],
+                    stepCallback = settings.callbacks['1'],
+                    actualStep,
+                    $actualStep,
+                    titleStep,
+                    $titleStepSpan,
+                    nextStep;
+
+                if (settings.disableNextButton){
+                    $btnNext.attr('disabled', 'disabled');
+                }
+                $btnPrevious.attr('disabled', 'disabled');
+
+                validCallbacks();
+                executeCallback(everyStepCallback);
+                executeCallback(stepCallback);
+
+                // Setting buttons
+                $btnCancel.html(settings.btnCancelHtml);
+                $btnPrevious.html(settings.btnPreviousHtml);
+                $btnNext.html(settings.btnNextHtml);
+
+                $actualStep = $('<input>').attr({
+                    'type': 'hidden',
+                    'id': 'actual-step',
+                    'value': '1',
+                });
+
+                $modal.find('#actual-step').remove();
+                $modal.append($actualStep);
+
+                actualStep = 1;
+                nextStep = actualStep + 1;
+
+                $modal.find('[data-step=' + actualStep + ']').removeClass('hide');
+                $btnNext.attr('data-step', nextStep);
+
+                titleStep = $modal.find('[data-step=' + actualStep + ']').data('title');
+                $titleStepSpan = $('<span>')
+                                    .addClass('label label-success')
+                                    .html(actualStep);
+
+                $modal
+                    .find('.js-title-step')
+                    .append($titleStepSpan)
+                    .append(' ' + titleStep);
+            })
+            .on('hidden.bs.modal', function(){
+                var $actualStep = $modal.find('#actual-step'),
+                    $btnNext = $modal.find('.js-btn-step[data-orientation=next]');
+
+                $modal
+                    .find('[data-step]')
+                    .not($modal.find('.js-btn-step'))
+                    .addClass('hide');
+
+                $actualStep
+                    .not($modal.find('.js-btn-step'))
+                    .remove();
+
+                $btnNext
+                    .attr('data-step', 1)
+                    .html(settings.btnNextHtml);
+
+                $modal.find('.js-title-step').html('');
+            });
+
+        $modal.find('.js-btn-step').on('click', function(){
+            var $btn = $(this),
+                $actualStep = $modal.find('#actual-step'),
+                $btnPrevious = $modal.find('.js-btn-step[data-orientation=previous]'),
+                $btnNext = $modal.find('.js-btn-step[data-orientation=next]'),
+                $title = $modal.find('.js-title-step'),
+                orientation = $btn.data('orientation'),
+                actualStep = parseInt($actualStep.val()),
+                everyStepCallback = settings.callbacks['*'],
+                steps,
+                nextStep,
+                $nextStep,
+                newTitle;
+
+            steps = $modal.find('div[data-step]').length;
+
+            // Callback on Complete
+            if ($btn.attr('data-step') === 'complete'){
+                settings.completeCallback();
+                $modal.modal('hide');
+
+                return;
+            }
+
+            // Check the orientation to make logical operations with actualStep/nextStep
+            if (orientation === 'next'){
+                nextStep = actualStep + 1;
+
+                $btnPrevious.attr('data-step', actualStep);
+                $actualStep.val(nextStep);
+
+            } else if (orientation === 'previous'){
+                nextStep = actualStep - 1;
+
+                $btnNext.attr('data-step', actualStep);
+                $btnPrevious.attr('data-step', nextStep - 1);
+
+                $actualStep.val(actualStep - 1);
+
+            } else {
+                $modal.modal('hide');
+                return;
+            }
+
+            if (parseInt($actualStep.val()) === steps){
+                $btnNext
+                    .attr('data-step', 'complete')
+                    .html(settings.btnLastStepHtml);
+            } else {
+                $btnNext
+                    .attr('data-step', nextStep)
+                    .html(settings.btnNextHtml);
+            }
+
+            if (settings.disableNextButton){
+                $btnNext.attr('disabled', 'disabled');
+            }
+
+            // Hide and Show steps
+            $modal
+                .find('[data-step=' + actualStep + ']')
+                .not($modal.find('.js-btn-step'))
+                .addClass('hide');
+
+            $modal
+                .find('[data-step=' + nextStep + ']')
+                .not($modal.find('.js-btn-step'))
+                .removeClass('hide');
+
+            // Just a check for the class of previous button
+            if (parseInt($btnPrevious.attr('data-step')) > 0 ){
+                $btnPrevious.removeAttr('disabled');
+            } else {
+                $btnPrevious.attr('disabled', 'disabled');
+            }
+
+            if (orientation === 'previous'){
+                $btnNext.removeAttr('disabled');
+            }
+
+            // Get the next step
+            $nextStep = $modal.find('[data-step=' + nextStep + ']');
+
+            // Verify if we need to unlock continue btn of the next step
+            if ($nextStep.attr('data-unlock-continue')){
+                $btnNext.removeAttr('disabled');
+            }
+
+            // Set the title of step
+            newTitle = $nextStep.attr('data-title');
+            var $titleStepSpan = $('<span>')
+                                .addClass('label label-success')
+                                .html(nextStep);
+
+            $title
+                .html($titleStepSpan)
+                .append(' ' + newTitle);
+
+            var stepCallback = settings.callbacks[$actualStep.val()];
+            executeCallback(everyStepCallback);
+            executeCallback(stepCallback);
+        });
+
+        return this;
+    };
+}(jQuery));

static/js/ketcher2/DEVNOTES.md

@@ -0,0 +1,57 @@
+## Prerequisites
+
+   Stable [Node.js](https://nodejs.org) version
+
+## Build instructions
+
+    npm install
+    npm start
+
+For production build:
+
+    npm run build
+   
+You could also build only the style with command
+
+    npm run style
+
+## Indigo Service
+
+Ketcher uses Indigo Service for server operations.
+You can use `--api-path` parameter to start with it:
+
+    npm start -- --api-path=<server-url>
+For production build:
+
+    npm run build -- --api-path=<server-url>
+
+You can find the instruction for service installation
+[here](http://lifescience.opensource.epam.com/indigo/service/index.html).
+
+## Tests instructions
+
+You can start tests for input/output `.mol`-files and render.
+
+    npm test
+
+Tests are started for all structures in `test/fixtures` directory.
+
+To start the tests separately:
+
+    npm run test-io
+    npm run test-render
+
+#### Parameters
+
+You can use following parameters to start the tests:
+ - `--fixtures` - for the choice of a specific directory with molecules
+ - `--headless` - for start of the browser in headless mode
+
+```
+npm run test-render -- --fixtures=fixtures/super --headless
+```
+
+If you have added new structures for testing to the `test/fixtures` directory 
+you have to generate `svg` from them for correct render-test with:
+
+    npm run generate-svg    

static/js/ketcher2/LICENSE

@@ -0,0 +1,184 @@
+                               Apache License
+                         Version 2.0, January 2004
+                      http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+    "License" shall mean the terms and conditions for use, reproduction,
+    and distribution as defined by Sections 1 through 9 of this document.
+    "Licensor" shall mean the copyright owner or entity authorized by
+    the copyright owner that is granting the License.
+    "Legal Entity" shall mean the union of the acting entity and all
+    other entities that control, are controlled by, or are under common
+    control with that entity. For the purposes of this definition,
+    "control" means (i) the power, direct or indirect, to cause the
+    direction or management of such entity, whether by contract or
+    otherwise, or (ii) ownership of fifty percent (50%) or more of the
+    outstanding shares, or (iii) beneficial ownership of such entity.
+    "You" (or "Your") shall mean an individual or Legal Entity
+    exercising permissions granted by this License.
+    "Source" form shall mean the preferred form for making modifications,
+    including but not limited to software source code, documentation
+    source, and configuration files.
+    "Object" form shall mean any form resulting from mechanical
+    transformation or translation of a Source form, including but
+    not limited to compiled object code, generated documentation,
+    and conversions to other media types.
+    "Work" shall mean the work of authorship, whether in Source or
+    Object form, made available under the License, as indicated by a
+    copyright notice that is included in or attached to the work
+    (an example is provided in the Appendix below).
+    "Derivative Works" shall mean any work, whether in Source or Object
+    form, that is based on (or derived from) the Work and for which the
+    editorial revisions, annotations, elaborations, or other modifications
+    represent, as a whole, an original work of authorship. For the purposes
+    of this License, Derivative Works shall not include works that remain
+    separable from, or merely link (or bind by name) to the interfaces of,
+    the Work and Derivative Works thereof.
+    "Contribution" shall mean any work of authorship, including
+    the original version of the Work and any modifications or additions
+    to that Work or Derivative Works thereof, that is intentionally
+    submitted to Licensor for inclusion in the Work by the copyright owner
+    or by an individual or Legal Entity authorized to submit on behalf of
+    the copyright owner. For the purposes of this definition, "submitted"
+    means any form of electronic, verbal, or written communication sent
+    to the Licensor or its representatives, including but not limited to
+    communication on electronic mailing lists, source code control systems,
+    and issue tracking systems that are managed by, or on behalf of, the
+    Licensor for the purpose of discussing and improving the Work, but
+    excluding communication that is conspicuously marked or otherwise
+    designated in writing by the copyright owner as "Not a Contribution."
+    "Contributor" shall mean Licensor and any individual or Legal Entity
+    on behalf of whom a Contribution has been received by Licensor and
+    subsequently incorporated within the Work.
+
+ 2. Grant of Copyright License. Subject to the terms and conditions of
+    this License, each Contributor hereby grants to You a perpetual,
+    worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+    copyright license to reproduce, prepare Derivative Works of,
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+ 4. Redistribution. You may reproduce and distribute copies of the
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+
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+    To apply the Apache License to your work, attach the following
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+
+ Copyright 2017 EPAM Systems
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
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+
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+ See the License for the specific language governing permissions and
+ limitations under the License.

static/js/ketcher2/LICENSE-history

@@ -0,0 +1,5 @@
+ Ketcher version 1 was released under GNU Affero General Public License v3.0
+ Ketcher version 2 was re-licensed under Apache License, Version 2.
+
+ Current version is distributed by the terms of the Apache License, Version 2.
+ which is included in the file LICENSE, found at the root of the Ketcher source tree.

static/js/ketcher2/NOTICE

@@ -0,0 +1,19 @@
+ Ketcher
+ Copyright (C) 2017 EPAM Systems
+ This product includes software developed at EPAM Systems, Inc.
+
+ In addition, this product contains dependencies on files licensed under:
+
+ The FreeBSD Documentation License https://www.freebsd.org/copyright/freebsd-doc-license.html
+ The MIT License https://opensource.org/licenses/MIT
+ X11 License http://www.xfree86.org/3.3.6/COPYRIGHT2.html
+ Academic Free License https://opensource.org/licenses/AFL-3.0
+ Apache License, Version 1.0 http://www.apache.org/licenses/LICENSE-1.0
+ Apache License, Version 2.0 http://www.apache.org/licenses/LICENSE-2.0
+ The 2-Clause BSD License https://opensource.org/licenses/BSD-2-Clause
+ The 3-Clause BSD License https://opensource.org/licenses/BSD-3-Clause
+ ISC License (ISC) https://opensource.org/licenses/ISC
+ GNU Lesser General Public License version 2.1 https://opensource.org/licenses/LGPL-2.1
+ The Mozilla Public License https://opensource.org/licenses/MPL-1.0
+ Public Domain https://wiki.creativecommons.org/wiki/Public_domain
+ Unlicense http://unlicense.org/

static/js/ketcher2/README.md

@@ -0,0 +1,35 @@
+# EPAM Ketcher projects
+Copyright (c) 2017 EPAM Systems, Inc
+
+Ketcher is an open-source web-based chemical structure editor incorporating high performance, good portability, light weight, and ability to easily integrate into a custom web-application. Ketcher is designed for chemists, laboratory scientists and technicians who draw structures and reactions.
+
+## KEY FEATURES
+* Fast 2D structure representation that satisfies common chemical drawing standards
+* 3D structure visualization
+* Draw and edit structures using major tools: Atom Tool, Bond Tool, and Template Tool
+* Template library (including custom and user's templates)
+* Add atom and bond basic properties and query features, add aliases and Generic groups
+* Select, modify, and erase connected and unconnected atoms and bonds using Selection Tool, or using Shift key
+* Simple Structure Clean up Tool (checks bonds length, angles and spatial arrangement of atoms) and Advanced Structure Clean up Tool (+ stereochemistry checking and structure layout) 
+* Aromatize/De-aromatize Tool
+* Calculate CIP Descriptors Tool
+* Structure Check Tool
+* MW and Structure Parameters Calculate Tool 
+* Stereochemistry support during editing, loading, and saving chemical structures
+* Storing history of actions, with the ability to rollback to previous state
+* Ability to load and save structures and reactions in MDL Molfile or RXN file format, InChI String, ChemAxon Extended SMILES, ChemAxon Extended CML file formats
+* Easy to use R-Group and S-Group tools (Generic, Multiple group, SRU polymer, peratom, Data S-Group) 
+* Reaction Tool (reaction generating, manual and automatic atom-to-atom mapping) 
+* Flip/Rotate Tool
+* Zoom in/out, hotkeys, cut/copy/paste
+* OCR - ability to recognize structures at pictures (image files) and reproduce them
+* Copy and paste between different chemical editors
+* Settings support (Rendering, Displaying, Debugging)
+* Use of SVG to achieve best quality in-browser chemical structure rendering
+* Languages: JavaScript with third-party libraries
+
+## Build instructions
+Please read [DEVNOTES.md](DEVNOTES.md) for details.
+
+## License
+Please read [LICENSE](LICENSE) and [NOTICE](NOTICE) for details.

static/js/ketcher2/doc/help.md

@@ -0,0 +1,570 @@
+**Ketcher** is a tool to draw molecular structures and chemical
+reactions.
+
+# Ketcher Overview
+
+**Ketcher** is a tool to draw molecular structures and chemical
+reactions. Ketcher operates in two modes, the Server mode with most
+functions available and the client mode with limited functions
+available.
+
+**Ketcher** consists of the following elements:
+
+ ![](main.png "Main window")
+
+**Note** : Depending on the screen size, some tools on the _Tool
+palette_ can be displayed in expanded or collapsed forms.
+
+Using the _Tool palette_, you can
+
+  * draw and edit a molecule or reaction by clicking on and dragging
+  atoms, bonds, and other elements provided with the buttons on the
+  _Atoms_ toolbar and _Tool palette_;
+
+  * delete any element of the drawing (atom or bond) by clicking on it
+  with the Erase tool;
+
+  * delete the entire molecule or its fragment by a lasso,
+  rectangular, or fragment selection with the Erase tool;
+
+  * draw special structures (see the following sections);
+
+  * select the entire molecule or its fragment in one of the following
+  ways (click on the button to see the list of available options):
+
+    * in the expanded form
+
+      ![](expanded.png "Expanded tool")
+
+    * in the collapsed form
+
+      ![](collapsed.png "Collapsed tool")
+
+To select one atom or bond, click Lasso or Rectangle Selection tool,
+and then click the atom or bond.
+
+To select the entire structure:
+
+  * Select the Fragment Selection tool and then click the object.
+
+  * Select the Lasso or Rectangle Selection tool, and then drag the
+  mouse to select the object.
+
+  * `Ctrl-click` with the Lasso or Rectangle Selection tool.
+
+To select multiple atoms, bonds, structures, or other objects, do one
+of the following:
+
+  * `Shift-click` with the Lasso or Rectangle Selection tool selects
+  some (connected or not) atoms/bonds.
+
+  * With the Lasso or Rectangle Selection tool click and drag the
+  mouse around the atoms, bonds, or structures that you want to
+  select.
+
+**Note** : `Ctrl+Shift-click` with the Lasso or Rectangle Selection tool
+selects several structures.
+
+You can use the buttons of the _Main_ toolbar:
+
+
+ ![](toolbar.png "Tolbar")
+
+  * **Clear Canvas** (1) button to start drawing a new molecule; this
+  command clears the drawing area;
+
+  * **Open…** (2) and **Save As…** (3) buttons to import a molecule
+  from a molecular file or save it to a supported molecular file
+  format;
+
+  * **Undo** / **Redo** (4), **Cut** (5), **Copy** (6), **Paste** (7),
+  **Zoom In** / **Out** (8), and **Scaling** (9) buttons to perform
+  the corresponding actions;
+
+  * **Layout** button (10) to change the position of the structure to
+  work with it with the most convenience;
+
+  * **Clean Up** button (11) to improve the appearance of the
+  structure by assigning them uniform bond lengths and angles.
+
+  * **Aromatize** / **Dearomatize** buttons (12) to mark aromatic
+  structures (to convert a structure to the Aromatic or Kekule
+  presentation);
+
+  * **Calculate CIP** button (13) to determine R/S and E/Z
+  configurations;
+
+  * **Check Structure** button (14) to check the following properties
+  of the structure:
+
+    ![](check.png "Structure Ckeck")
+
+  * **Calculated Values** button (15) to display some properties of
+  the structure:
+
+    ![](analyse.png "Calculated Values")
+
+  * **Recognize Molecule** button (16) to recognize a structure in the
+  image file and load it to the canvas;
+
+  * **3D Viewer** button (17) to open the structure in the
+  three-dimensional Viewer;
+
+  * **Settings** button (18) to make some settings for molecular
+    files:
+    
+    ![](settings.png "Settings")
+
+  * **Help** button (19) to view Help;
+    
+  * **About** button (20) to display version and copyright information
+  of the program.
+
+**Note** : **Layout,** **Clean Up,** **Aromatize** / **Dearomatize,**
+**Calculate CIP,** **Check Structure,** **Calculated Values,**
+**Recognize Molecule** and **3D View** buttons are active only in the
+Server mode.
+
+# 3D Viewer
+
+The structure appears in a modal window after clicking on the **3D
+Viewer** button:
+
+ ![](miew.png "3D Viewer")
+
+You can perform the following actions:
+
+  * Rotate the structure holding the left mouse button;
+
+  * Zoom In/Out the structure;
+
+Ketcher Settings allow to change the appearance of the structure and background coloring.
+
+"Lines" drawing method, "Bright" atom name coloring
+method and "Light" background coloring are default.
+
+# Drawing Atoms
+
+To draw/edit atoms you can:
+
+  * select an atom in the Atoms toolbar and click inside the drawing
+  area;
+
+  * if the desired atom is absent in the toolbar, click on
+  the ![](periodic-table.png) button to invoke the Periodic Table and
+  click on the desired atom (available options: _Single_ – selection
+  of a single atom, _List_ – choose an atom from the list of selected
+  options (To allow one atom from a list of atoms of your choice at
+  that position), _Not List_ - exclude any atom on your list at that
+  position).
+
+    ![](periodic-dialog.png "Periodic Table")
+
+  * add an atom to the existing molecule by selecting an atom in the
+  _Atoms_ toolbar, clicking on an atom in the molecule, and dragging
+  the cursor; the atom will be added with a single bond; vacant
+  valences will be filled with the corresponding number of hydrogen
+  atoms;
+
+  * change an atom by selecting an atom in the _Atoms_ toolbar and
+  clicking on the atom to be changed; in the case a wrong valence thus
+  appears the atom will be underlined in red;
+
+  * change an atom by clicking on an existing atom with the
+  _Selection_ tool and waiting for a couple of seconds for the text
+  box to appear; type another atom symbol in the text box:
+
+    ![](inline-edit.png "Change Atom")
+
+  * change the charge of an atom by selecting the Charge Plus or
+  Charge Minus tool and clicking consecutively on an atom to
+  increase/decrease its charge
+
+    ![](charge.png "Ions")
+
+  * change an atom or its properties by double-clicking on the atom to
+  invoke the Atom Properties dialog (the dialog also provides atom
+  query features):
+
+    ![](atom-dialog.png "Atom Properties")
+
+  * click on the Periodic Table button, open the Extended table and
+  select a corresponding Generic group or Special Node:
+
+    ![](periodic-dialog-ext.png "Generic Groups")
+
+# Drawing Bonds
+
+To draw/edit bonds you can:
+
+  * Click an arrow on the Bond tool ![](bond.png) in the Tools palette
+  to open the drop-down list with the following bond types:
+
+    ![](bonds.png)
+
+    For the full screen format, the Bond tool from the Tools palette
+    splits into three: _Single Bond,__Single Up Bond,_ and _Any
+    Bond_,which include the corresponding bond types:
+
+    ![](bond-types.png)
+
+  * select a bond type from the drop down list and click inside the
+  drawing area; a bond of the selected type will be drawn;
+
+  * click on an atom in the molecule; a bond of the selected type will
+  be added to the atom at the angle of 120 degrees;
+
+  * add a bond to the existing molecule by clicking on an atom in the
+  molecule and dragging the cursor; in this case you can set the angle
+  manually;
+
+  * change the bond type by clicking on it;
+
+  * use the Chain Tool ![](chain.png) to draw consecutive single
+  bonds;
+
+  * change a bond or its properties by double-clicking on the bond to
+  invoke the Bond Properties dialog:
+
+    ![](bond-dialog.png "Bond Properties")
+
+  * clicking on a drawn stereo bond changes its direction.
+
+  * clicking with the Single Bond tool or Chain tool switches the bond type
+  cyclically: Single-Double-Triple-Single.
+
+# Drawing R-Groups
+
+Use the _R-Group_ toolbox ![](rgroup.png) to draw R-groups in Markush
+structures:
+
+ ![](rgroup-types.png)
+
+Selecting the _R-Group_ _Label_ Tool and clicking on an atom in the
+structure invokes the dialog to select the R-Group label for a current
+atom position in the structure:
+
+ ![](rgroup-dialog.png)
+
+Selecting the R-Group label and clicking **OK** converts the structure
+into a Markush structure with the selected R-Group label:
+
+ ![](rgroup-example1.png)
+
+**Note** : You can choose several R-Group labels simultaneously:
+
+ ![](rgroup-example2.png)
+
+Particular chemical fragments that may be substituted for a given
+R-Group form a set of R-Group members. R-Group members can be any
+structural fragment, including functional groups and single atoms or
+atom lists.
+
+To create a set of R-Group members:
+
+  1. Draw a structure to become an R-Group member.
+
+  2. Select the structure using the _R-Group Fragment Tool_ to invoke
+     the R-Group dialog; in this dialog select the label of the
+     R-Group to assign the fragment to.
+
+  3. Click on **OK** to convert the structure into an R-Group member.
+
+An R-Group attachment point is the atom in an R-Group member fragment
+that attaches the fragment to the initial Markush structure.
+
+Selecting the _Attachment Point Tool_ and clicking on an atom in the
+R-Group fragment converts this atom into an attachment point. If the
+R-Group contains more than one attachment point, you can specify one
+of them as primary and the other as secondary. You can select between
+either the primary or secondary attachment point using the dialog that
+appears after clicking on the atom:
+
+ ![](attpoints-dialog.png)
+
+If there are two attachment points on an R-Group member, there must be
+two corresponding attachments (bonds) to the R-Group atom that has the
+same R-Group label. Clicking on **OK** in the above dialog creates the
+attachment point.
+
+Schematically, the entire process of the R-Group member creation can
+be presented as:
+
+ ![](rgroup-example3.png)
+
+ ![](rgroup-example4.png)
+
+# R-Group Logic
+
+**Ketcher** enables one to add logic when using R-Groups. To access
+the R-Group logic:
+
+  1. Create an R-Group member fragment as described above.
+
+  2. Move the cursor over the entire fragment for the green frame to
+     appear, then click inside the fragment. The following dialog
+     appears:
+
+     ![](rlogic-dialog.png)
+
+  3. Specify **Occurrence** to define how many of an R-Group
+     occurs. If an R-Group atom appears several times in the initial
+     structure, you will specify **Occurrence**">n", n
+     being the number of occurrences; if it appears once, you see
+     "R1 > 0".
+
+  4. Specify H at **unoccupied** R-Group sites ( **RestH** ): check or
+     clear the checkbox.
+
+  5. Specify the logical **Condition**. Use the R-Group condition **If
+     R(i) Then** to specify whether the presence of an R-Group is
+     dependent on the presence of another R-Group.
+
+
+# Marking S-Groups
+
+To mark S-Groups, use the _S-Group tool_ ![](sgroup.png) and the
+following dialog that appears after selecting a fragment with this
+tool:
+
+ ![](sgroup-dialog.png "S-Group Dialog")
+
+Available S-Group types:
+
+_Generic_
+
+Generic is a pair of brackets without any labels.
+
+_Multiple group_
+
+A Multiple group indicates a number of replications of a fragment or a part of a
+structure in contracted form.
+
+_SRU Polymer_
+
+The Structural Repeating Unit (SRU) brackets enclose the structural
+repeating of a polymer. You have three available patterns:
+head-to-tail (the default), head-to-head, and either/unknown.
+
+_Superatom_
+
+An abbreviated structure (abbreviation) is all or part of a structure
+(molecule or reaction component) that has been abbreviated to a text
+label. Structures that you abbreviate keep their chemical
+significance, but their underlying structure is hidden. The current
+version can't display contracted structures but correctly
+saves/reads them into/from files.
+
+# Data S-Groups
+
+The _Data S-Groups Tool_ ![](sdata.png) is a separate tool for
+comfortable use with the accustomed set of descriptors (like Attached
+Data in **Marvin** Editor).
+
+You can attach data to an atom, a fragment, a single bond, or a
+group. The defined set of _Names_ and _Values_ is introduced for each
+type of selected elements:
+
+ ![](sdata-dialog.png)
+
+  * Select the appropriate S-Group Field Name.
+
+  * Select or type the appropriate Field Value.
+
+  * Labels can be specified as Absolute, Relative or Attached.
+
+# Changing Structure Display
+
+Use the _Flip/Rotate_ tool ![](transform.png) to change the structure
+display:
+
+ ![](transform-types.png)
+
+For the full screen format, the _Flip/Rotate_ tool is split into
+separate buttons:
+
+ ![](rotate.png)
+
+_Rotate Tool_
+
+This tool allows rotating objects.
+  * If some objects are selected, the tool rotates the selected objects.
+  * If no objects are selected, or all objects are selected, the tool rotates the whole canvas
+  * The default rotation step is 15 degrees. 
+  * Press and hold the Ctrl key for more gradual continuous rotation with 1 degree rotation step
+
+Select any bond on the structure and click Alt+H to rotate the structure so that the selected bond is placed horizontally.
+Select any bond on the structure and click Alt+V to rotate the structure so that the selected bond is placed vertically.
+
+_Flip Tool_
+
+This tool flips the objects horizontally or vertically.
+  * If some objects are selected, the Horizontal Flip tool (or Alt+H) flips the selected objects horizontally
+  * If no objects are selected, or all objects are selected, the Horizontal Flip tool (or Alt+H) flips each structure horizontally
+  * If some objects are selected, the Vertical Flip tool (or Alt+V) flips the selected objects vertically
+  * If no objects are selected, or all objects are selected, the Vertical Flip tool (or Alt+V) flips each structure vertically
+
+# Drawing Reactions
+
+To draw/edit reactions you can
+
+  * draw reagents and products as described above;
+  * use options of the _Reaction Arrow Tool_ ![](reaction.png) to draw an
+  arrow and pluses in the reaction equation and map same atoms in
+  reagents and products.
+
+    ![](reaction-types.png)
+
+**Note** : Reaction Auto-Mapping Tool is available only in the Server
+mode.
+
+# Templates toolbar
+
+You can add templates (rings or other predefined structures) to the
+structure using the _Templates_ toolbar together with the _Custom
+Templates_ button located at the bottom:
+
+ ![](template.png)
+
+To add a ring to the molecule, select a ring from the toolbar and
+click inside the drawing area, or click on an atom or a bond in the
+molecule.
+
+Rules of using templates:
+
+  * Selecting a template and clicking on an atom in the existing
+  structure adds the template to the structure connected with a single
+  bond:
+
+    ![](template-example1.png)
+
+  * Selecting a template and dragging the cursor from an atom in the
+  existing structure adds the template directly to this atom resulting
+  in the fused structure:
+
+    ![](template-example2.png)
+
+  * Dragging the cursor from an atom in the existing structure results
+  in the single bond attachment if the cursor is dragged to more than
+  the bond length; otherwise the fused structure is drawn.
+  * Selecting a template and clicking on a bond in the existing
+  structure created a bond-to-bond fused structure:
+
+    ![](template-example3.png)
+
+  * The bond in the initial structure is replaced with the bond in the
+  template.
+
+  * This procedure doesn't change the length of the bond in the
+  initial structure.
+
+  * Dragging the cursor relative to the initial bond applies the
+  template at the corresponding side of the bond.
+
+**Note** : The added template will be fused by the default attachment
+atom or bond preset in the program.
+
+**Note** : User is able to define the attachment atom and bond by clicking
+the Edit button for template structure.
+
+
+The _Custom Templates_ button ![](template-lib.png)invokes the scrolling
+list of templates available in the program; both built-in and created
+by user:
+
+ ![](template-dialog.png)
+
+
+To create a user template:
+* draw a structure.
+* click the Save as button.
+* click the Save to Templates button.
+* enter a name and define the attachment atom and bond.
+
+# Working with Files
+
+Ketcher supports the following molecular formats that can be entered
+either manually or from files:
+
+  * MDL Molfile or RXN file;
+
+  * Daylight SMILES (Server mode only);
+
+  * Daylight SMARTS (Server mode only);
+
+  * InChi string (Server mode only);
+
+  * CML file (Server mode only).
+
+You can use the **Open…** and **Save As…** buttons of the _Main_
+toolbar to import a molecule from a molecular file or save it to a
+supported molecular file format. The _Open Structure_ dialog enables
+one to either browse for a file (Server mode) or manually input, e.g.,
+the Molfile ctable for the molecule to be imported:
+
+ ![](open.png)
+
+The _Save Structure_ dialog enables one to save the molecular file:
+
+ ![](save.png)
+
+**Note** : In the standalone version only mol/rxn are supported for
+Open and mol/rxn/SMILES for Save.
+
+
+# Hotkeys
+
+You can use keyboard hotkeys (including Numeric keypad) for some
+features/commands of the Editor. To display the hotkeys just place the
+cursor over a toolbar button. If a hotkey is available for the button,
+it will appear in brackets after the description of the button.
+
+| Key | Action |
+| --- | --- |
+| `Esc` | Switching between the Lasso/Rectangle/Fragment Selection tools |
+| `Del` | Delete the selected objects |
+| `0` | Draw Any bond. |
+| `1` | Single / Single Up / Single Down / Single Up/Down bond. Consecutive pressing switches between these types. |
+| `2` | Double / Double Cis/Trans bond |
+| `3` | Draw a triple bond. |
+| `4` | Draw an aromatic bond. |
+| `5` | Charge Plus/Charge Minus |
+| `A` | Draw any atom |
+| `H` | Draw a hydrogen |
+| `C` | Draw a carbon |
+| `N` | Draw a nitrogen |
+| `O` | Draw an oxygen |
+| `S` | Draw a sulfur |
+| `F` | Draw a fluorine |
+| `P` | Draw a phosphorus |
+| `I` | Draw an iodine |
+| `T` | Basic templates. Consecutive pressing switches between different templates |
+| `Shift+t` | Open template library |
+| `Alt+r` | Rotate tool |
+| `Alt+v` | Flip vertically |
+| `Alt+h` | Flip horizontally |
+| `Ctrl+g` | S-Group tool / Data S-Group tool |
+| `Ctrl+d` | Align and select all S-Group data
+| `Ctrl+r` | Switching between the R-Group Label Tool/R-Group Fragment Tool/Attachment Point Tool |
+| `Ctrl+Shift+r`  | R-Group Fragment Tool |
+| `Ctrl+Del` | Clear canvas |
+| `Ctrl+o` | Open |
+| `Ctrl+s` | Save As |
+| `Ctrl+z` | Undo |
+| `Ctrl+Shift+z` | Redo |
+| `Ctrl+x` | Cut selected objects |
+| `Ctrl+c` | Copy selected objects |
+| `Ctrl+v` | Paste selected objects |
+| `+` | Zoom In |
+| `-` | Zoom Out |
+| `Ctrl+l` | Layout |
+| `Ctrl+Shift+l` | Clean Up |
+| `Ctrl+p` | Calculate CIP |
+| `?` | Help |
+
+**Note** : Please, use `Ctrl+V` to paste the selected object in
+Google Chrome and Mozilla Firefox browsers.
+
+**Note 2** : Probably, you have forbidden access to the local storage.
+If you are using IE10 or IE11 and didn't forbid access to local storage 
+intentionally, you can pay attention here: https://stackoverflow.com/a/20848924