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

Fixes #77

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

envipath/api.py

@@ -1,7 +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()
 
-api.add_router("/", epdb_app_router)
+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/settings.py

@@ -43,6 +43,7 @@ INSTALLED_APPS = [
     'django.contrib.staticfiles',
     # 3rd party
     'django_extensions',
+    'oauth2_provider',
     # Custom
     'epdb',
     'migration',
@@ -60,8 +61,13 @@ MIDDLEWARE = [
     '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')
 
@@ -260,6 +266,8 @@ 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,
@@ -273,14 +281,14 @@ DEFAULT_RF_MODEL_PARAMS = {
     'num_chains': 10,
 }
 
-DEFAULT_DT_MODEL_PARAMS = {
+DEFAULT_MODEL_PARAMS = {
     'base_clf': DecisionTreeClassifier(
         criterion='entropy',
         max_depth=3,
         min_samples_split=5,
-        min_samples_leaf=5,
+        # min_samples_leaf=5,
         max_features='sqrt',
-        class_weight='balanced',
+        # class_weight='balanced',
         random_state=42
     ),
     'num_chains': 10,
@@ -306,9 +314,36 @@ 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

@@ -17,11 +17,13 @@ Including another URLconf
 from django.contrib import admin
 from django.urls import include, path
 
-from .api import api
+from .api import api_v1, api_legacy
 
 urlpatterns = [
     path("", include("epdb.urls")),
     path("", include("migration.urls")),
     path("admin/", admin.site.urls),
-    path("api/", api.urls),
+    path("api/v1/", api_v1.urls),
+    path("api/legacy/", api_legacy.urls),
+    path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
 ]

epdb/admin.py

@@ -1,40 +1,105 @@
 from django.contrib import admin
 
-from .models import User, Group, UserPackagePermission, GroupPackagePermission, Setting, SimpleAmbitRule, Scenario
+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 GroupAdmin(admin.ModelAdmin):
-    pass
-
-
 class UserPackagePermissionAdmin(admin.ModelAdmin):
     pass
 
 
+class GroupAdmin(admin.ModelAdmin):
+    pass
+
+
 class GroupPackagePermissionAdmin(admin.ModelAdmin):
     pass
 
 
-class SettingAdmin(admin.ModelAdmin):
+class EPAdmin(admin.ModelAdmin):
+    search_fields = ['name', 'description']
+
+
+class PackageAdmin(EPAdmin):
+    pass
+
+class MLRelativeReasoningAdmin(EPAdmin):
     pass
 
 
-class SimpleAmbitRuleAdmin(admin.ModelAdmin):
+class CompoundAdmin(EPAdmin):
     pass
 
 
-class ScenarioAdmin(admin.ModelAdmin):
+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(Group, GroupAdmin)
 admin.site.register(UserPackagePermission, UserPackagePermissionAdmin)
+admin.site.register(Group, GroupAdmin)
 admin.site.register(GroupPackagePermission, GroupPackagePermissionAdmin)
-admin.site.register(Setting, SettingAdmin)
+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/apps.py

@@ -4,3 +4,6 @@ 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/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/logic.py

@@ -1,6 +1,7 @@
 import re
 import logging
-from typing import Union, List, Optional, Set, Dict
+import json
+from typing import Union, List, Optional, Set, Dict, Any
 
 from django.contrib.auth import get_user_model
 from django.db import transaction
@@ -13,6 +14,132 @@ from utilities.chem import FormatConverter
 logger = logging.getLogger(__name__)
 
 
+class EPDBURLParser:
+
+    UUID_PATTERN = r'[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}'
+
+    MODEL_PATTERNS = {
+        'epdb.User': re.compile(rf'^.*/user/{UUID_PATTERN}'),
+        'epdb.Group': re.compile(rf'^.*/group/{UUID_PATTERN}'),
+        'epdb.Package': re.compile(rf'^.*/package/{UUID_PATTERN}'),
+        'epdb.Compound': re.compile(rf'^.*/package/{UUID_PATTERN}/compound/{UUID_PATTERN}'),
+        'epdb.CompoundStructure': re.compile(rf'^.*/package/{UUID_PATTERN}/compound/{UUID_PATTERN}/structure/{UUID_PATTERN}'),
+        'epdb.Rule': re.compile(rf'^.*/package/{UUID_PATTERN}/(?:simple-ambit-rule|simple-rdkit-rule|parallel-rule|sequential-rule|rule)/{UUID_PATTERN}'),
+        'epdb.Reaction': re.compile(rf'^.*/package/{UUID_PATTERN}/reaction/{UUID_PATTERN}$'),
+        'epdb.Pathway': re.compile(rf'^.*/package/{UUID_PATTERN}/pathway/{UUID_PATTERN}'),
+        'epdb.Node': re.compile(rf'^.*/package/{UUID_PATTERN}/pathway/{UUID_PATTERN}/node/{UUID_PATTERN}'),
+        'epdb.Edge': re.compile(rf'^.*/package/{UUID_PATTERN}/pathway/{UUID_PATTERN}/edge/{UUID_PATTERN}'),
+        'epdb.Scenario': re.compile(rf'^.*/package/{UUID_PATTERN}/scenario/{UUID_PATTERN}'),
+        'epdb.EPModel': re.compile(rf'^.*/package/{UUID_PATTERN}/model/{UUID_PATTERN}'),
+        'epdb.Setting': re.compile(rf'^.*/setting/{UUID_PATTERN}'),
+    }
+
+    def __init__(self, url: str):
+        self.url = url
+        self._matches = {}
+        self._analyze_url()
+
+    def _analyze_url(self):
+        for model_path, pattern in self.MODEL_PATTERNS.items():
+            match = pattern.findall(self.url)
+            if match:
+                self._matches[model_path] = match[0]
+
+    def _get_model_class(self, model_path: str):
+        try:
+            from django.apps import apps
+            app_label, model_name = model_path.split('.')[-2:]
+            return apps.get_model(app_label, model_name)
+        except (ImportError, LookupError, ValueError):
+            raise ValueError(f"Model {model_path} does not exist!")
+
+    def _get_object_by_url(self, model_path: str, url: str):
+        model_class = self._get_model_class(model_path)
+        return model_class.objects.get(url=url)
+
+    def is_package_url(self) -> bool:
+        return bool(re.compile(rf'^.*/package/{self.UUID_PATTERN}$').findall(self.url))
+
+    def contains_package_url(self):
+        return bool(self.MODEL_PATTERNS['epdb.Package'].findall(self.url)) and not self.is_package_url()
+
+    def is_user_url(self) -> bool:
+        return bool(self.MODEL_PATTERNS['epdb.User'].findall(self.url))
+
+    def is_group_url(self) -> bool:
+        return bool(self.MODEL_PATTERNS['epdb.Group'].findall(self.url))
+
+    def is_setting_url(self) -> bool:
+        return bool(self.MODEL_PATTERNS['epdb.Setting'].findall(self.url))
+
+    def get_object(self) -> Optional[Any]:
+        # Define priority order from most specific to least specific
+        priority_order = [
+            # 3rd level
+            'epdb.CompoundStructure',
+            'epdb.Node',
+            'epdb.Edge',
+            # 2nd level
+            'epdb.Compound',
+            'epdb.Rule',
+            'epdb.Reaction',
+            'epdb.Scenario',
+            'epdb.EPModel',
+            'epdb.Pathway',
+            # 1st level
+            'epdb.Package',
+            'epdb.Setting',
+            'epdb.Group',
+            'epdb.User',
+        ]
+
+        for model_path in priority_order:
+            if model_path in self._matches:
+                url = self._matches[model_path]
+                return self._get_object_by_url(model_path, url)
+
+        raise ValueError(f"No object found for URL {self.url}")
+
+    def get_objects(self) -> List[Any]:
+        """
+        Get all Django model objects along the URL path in hierarchical order.
+        Returns objects from parent to child (e.g., Package -> Compound -> Structure).
+        """
+        objects = []
+
+        hierarchy_order = [
+            # 1st level
+            'epdb.Package',
+            'epdb.Setting',
+            'epdb.Group',
+            'epdb.User',
+            # 2nd level
+            'epdb.Compound',
+            'epdb.Rule',
+            'epdb.Reaction',
+            'epdb.Scenario',
+            'epdb.EPModel',
+            'epdb.Pathway',
+            # 3rd level
+            'epdb.CompoundStructure',
+            'epdb.Node',
+            'epdb.Edge',
+        ]
+
+        for model_path in hierarchy_order:
+            if model_path in self._matches:
+                url = self._matches[model_path]
+                objects.append(self._get_object_by_url(model_path, url))
+
+        return objects
+
+    def __str__(self) -> str:
+        return f"EPDBURLParser(url='{self.url}')"
+
+    def __repr__(self) -> str:
+        return f"EPDBURLParser(url='{self.url}', matches={list(self._matches.keys())})"
+
+
 class UserManager(object):
     user_pattern = re.compile(r".*/user/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}")
 
@@ -62,7 +189,7 @@ class UserManager(object):
 
     @staticmethod
     def get_user_by_id(user, user_uuid: str):
-        if user.uuid != user_uuid and not user.is_superuser:
+        if str(user.uuid) != user_uuid and not user.is_superuser:
             raise ValueError("Getting user failed!")
         return get_user_model().objects.get(uuid=user_uuid)
 
@@ -183,6 +310,25 @@ class PackageManager(object):
             return True
         return False
 
+    @staticmethod
+    def administrable(user, package):
+        if UserPackagePermission.objects.filter(package=package, user=user, permission=Permission.ALL[0]).exists() or \
+                GroupPackagePermission.objects.filter(package=package, group__in=GroupManager.get_groups(user), permission=Permission.ALL[0]).exists() or \
+                user.is_superuser:
+            return True
+        return False
+
+    # @staticmethod
+    # def get_package_permission(user: 'User', package: Union[str, 'Package']):
+    #     if PackageManager.administrable(user, package):
+    #         return Permission.ALL[0]
+    #     elif PackageManager.writable(user, package):
+    #         return Permission.WRITE[0]
+    #     elif PackageManager.readable(user, package):
+    #         return Permission.READ[0]
+    #     else:
+    #         return None
+
     @staticmethod
     def has_package_permission(user: 'User', package: Union[str, 'Package'], permission: str):
 
@@ -339,7 +485,7 @@ class PackageManager(object):
 
     @staticmethod
     @transaction.atomic
-    def import_package(data: dict, owner: User, keep_ids=False):
+    def import_package(data: dict, owner: User, keep_ids=False, add_import_timestamp=True):
         from uuid import UUID, uuid4
         from datetime import datetime
         from collections import defaultdict
@@ -349,7 +495,12 @@ class PackageManager(object):
 
         pack = Package()
         pack.uuid = UUID(data['id'].split('/')[-1]) if keep_ids else uuid4()
+
+        if add_import_timestamp:
             pack.name = '{} - {}'.format(data['name'], datetime.now().strftime('%Y-%m-%d %H:%M'))
+        else:
+            pack.name = data['name']
+
         pack.reviewed = True if data['reviewStatus'] == 'reviewed' else False
         pack.description = data['description']
         pack.save()
@@ -402,11 +553,13 @@ class PackageManager(object):
 
                 try:
                     res = AdditionalInformationConverter.convert(name, addinf_data)
+                    res_cls_name = res.__class__.__name__
+                    ai_data = json.loads(res.model_dump_json())
+                    ai_data['uuid'] = f"{uuid4()}"
+                    new_add_inf[res_cls_name].append(ai_data)
                 except:
                     logger.error(f"Failed to convert {name} with {addinf_data}")
 
-                new_add_inf[name].append(res.model_dump_json())
-
             scen.additional_information = new_add_inf
             scen.save()
 
@@ -890,9 +1043,10 @@ class SearchManager(object):
 
 class SNode(object):
 
-    def __init__(self, smiles: str, depth: int):
+    def __init__(self, smiles: str, depth: int, app_domain_assessment: dict = None):
         self.smiles = smiles
         self.depth = depth
+        self.app_domain_assessment = app_domain_assessment
 
     def __hash__(self):
         return hash(self.smiles)
@@ -1035,7 +1189,7 @@ class SPathway(object):
     def depth(self):
         return max([v.depth for v in self.smiles_to_node.values()])
 
-    def _get_nodes_for_depth(self, depth: int):
+    def _get_nodes_for_depth(self, depth: int) -> List[SNode]:
         if depth == 0:
             return self.root_nodes
 
@@ -1046,7 +1200,7 @@ class SPathway(object):
 
         return sorted(res, key=lambda x: x.smiles)
 
-    def _get_edges_for_depth(self, depth: int):
+    def _get_edges_for_depth(self, depth: int) -> List[SEdge]:
         res = []
         for e in self.edges:
             for n in e.educts:
@@ -1071,15 +1225,44 @@ class SPathway(object):
         new_tp = False
         if substrates:
             for sub in substrates:
+
+                if sub.app_domain_assessment is None:
+                    if self.prediction_setting.model:
+                        if self.prediction_setting.model.app_domain:
+                            app_domain_assessment = self.prediction_setting.model.app_domain.assess(sub.smiles)[0]
+
+                            if self.persist is not None:
+                                n = self.snode_persist_lookup[sub]
+
+                                assert n.id is not None, "Node has no id! Should have been saved already... aborting!"
+                                node_data = n.simple_json()
+                                node_data['image'] = f"{n.url}?image=svg"
+                                app_domain_assessment['assessment']['node'] = node_data
+
+                                n.kv['app_domain_assessment'] = app_domain_assessment
+                                n.save()
+
+                            sub.app_domain_assessment = app_domain_assessment
+
+
                 candidates = self.prediction_setting.expand(self, sub)
+                # candidates is a List of PredictionResult. The length of the List is equal to the number of rules
                 for cand_set in candidates:
                     if cand_set:
                         new_tp = True
+                        # cand_set is a PredictionResult object that can consist of multiple candidate reactions
                         for cand in cand_set:
                             cand_nodes = []
+                            # candidate reactions can have multiple fragments
                             for c in cand:
                                 if c not in self.smiles_to_node:
-                                    self.smiles_to_node[c] = SNode(c, sub.depth + 1)
+                                    # For new nodes do an AppDomain Assessment if an AppDomain is attached
+                                    app_domain_assessment = None
+                                    if self.prediction_setting.model:
+                                        if self.prediction_setting.model.app_domain:
+                                            app_domain_assessment = self.prediction_setting.model.app_domain.assess(c)[0]
+
+                                    self.smiles_to_node[c] = SNode(c, sub.depth + 1, app_domain_assessment)
 
                                 node = self.smiles_to_node[c]
                                 cand_nodes.append(node)
@@ -1092,18 +1275,30 @@ class SPathway(object):
         if len(substrates) == 0 or from_node is not None:
             self.done = True
 
-        # Check if we need to write back data to database
+        # Check if we need to write back data to the database
         if new_tp and self.persist:
             self._sync_to_pathway()
-            # call save to update internal modified field
+            # call save to update the internal modified field
             self.persist.save()
 
-    def _sync_to_pathway(self):
+    def _sync_to_pathway(self) -> None:
         logger.info("Updating Pathway with SPathway")
 
         for snode in self.smiles_to_node.values():
             if snode not in self.snode_persist_lookup:
                 n = Node.create(self.persist, snode.smiles, snode.depth)
+
+                if snode.app_domain_assessment is not None:
+                    app_domain_assessment = snode.app_domain_assessment
+
+                    assert n.id is not None, "Node has no id! Should have been saved already... aborting!"
+                    node_data = n.simple_json()
+                    node_data['image'] = f"{n.url}?image=svg"
+                    app_domain_assessment['assessment']['node'] = node_data
+
+                    n.kv['app_domain_assessment'] = app_domain_assessment
+                    n.save()
+
                 self.snode_persist_lookup[snode] = n
 
         for sedge in self.edges:
@@ -1125,7 +1320,6 @@ class SPathway(object):
                 self.sedge_persist_lookup[sedge] = e
 
         logger.info("Update done!")
-        pass
 
     def to_json(self):
         nodes = []

epdb/management/commands/bootstrap.py

@@ -5,7 +5,7 @@ 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
+from epdb.models import UserSettingPermission, MLRelativeReasoning, EnviFormer, Permission, User, ExternalDatabase
 
 
 class Command(BaseCommand):
@@ -58,7 +58,7 @@ class Command(BaseCommand):
         return anon, admin, g, jebus
 
     def import_package(self, data, owner):
-        return PackageManager.import_package(data, owner, keep_ids=True)
+        return PackageManager.import_package(data, owner, keep_ids=True, add_import_timestamp=False)
 
     def create_default_setting(self, owner, packages):
         s = SettingManager.create_setting(
@@ -74,6 +74,76 @@ class Command(BaseCommand):
 
         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
@@ -117,17 +187,17 @@ class Command(BaseCommand):
 
         # Create RR
         ml_model = MLRelativeReasoning.create(
-            pack,
-            'ECC - BBD - T0.5',
-            'ML Relative Reasoning',
-            [mapping['EAWAG-BBD']],
-            [mapping['EAWAG-BBD']],
-            [],
-            0.5
+            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',
         )
 
-        X, y = ml_model.build_dataset()
-        ml_model.build_model(X, y)
+        ml_model.build_dataset()
+        ml_model.build_model()
         # ml_model.evaluate_model()
 
         # If available create EnviFormerModel

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

@@ -1,7 +1,7 @@
 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):
@@ -17,5 +17,8 @@ class LoginRequiredMiddleware:
         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

@@ -31,8 +31,8 @@ def send_registration_mail(user_pk: int):
 @shared_task(queue='model')
 def build_model(model_pk: int):
     mod = EPModel.objects.get(id=model_pk)
-    X, y = mod.build_dataset()
-    mod.build_model(X, y)
+    mod.build_dataset()
+    mod.build_model()
 
 
 @shared_task(queue='model')
@@ -58,7 +58,7 @@ def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_
                 spw.predict_step(from_depth=level)
                 level += 1
 
-                # break in case we are in incremental model
+                # break in case we are in incremental mode
                 if limit != -1:
                     if level >= limit:
                         break

epdb/urls.py

@@ -76,5 +76,7 @@ urlpatterns = [
     re_path(r'^indigo/dearomatize$', v.dearomatize, name='indigo_dearomatize'),
     re_path(r'^indigo/layout$', v.layout, name='indigo_layout'),
 
-    re_path(r'^depict$', v.depict, name='depict')
+    re_path(r'^depict$', v.depict, name='depict'),
+
+    path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
 ]

epdb/views.py

@@ -7,10 +7,13 @@ from django.contrib.auth import get_user_model
 from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, HttpResponseBadRequest
 from django.shortcuts import render, redirect
 from django.views.decorators.csrf import csrf_exempt
+from envipy_additional_information import NAME_MAPPING
+from oauth2_provider.decorators import protected_resource
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
-from .logic import GroupManager, PackageManager, UserManager, SettingManager, SearchManager
+from utilities.misc import HTMLGenerator
+from .logic import GroupManager, PackageManager, UserManager, SettingManager, SearchManager, EPDBURLParser
 from .models import Package, GroupPackagePermission, Group, CompoundStructure, Compound, Reaction, Rule, Pathway, Node, \
     EPModel, EnviFormer, MLRelativeReasoning, RuleBaseRelativeReasoning, Scenario, SimpleAmbitRule, APIToken, \
     UserPackagePermission, Permission, License, User, Edge
@@ -44,6 +47,7 @@ def login(request):
 
     if request.method == 'GET':
         context['title'] = 'enviPath'
+        context['next'] = request.GET.get('next', '')
         return render(request, 'login.html', context)
 
     elif request.method == 'POST':
@@ -57,7 +61,7 @@ def login(request):
             username = request.POST.get('username')
             password = request.POST.get('password')
 
-            # Get email for username and check if account is active
+            # Get email for username and check if the account is active
             try:
                 temp_user = get_user_model().objects.get(username=username)
 
@@ -77,6 +81,10 @@ def login(request):
 
             if user is not None:
                 login(request, user)
+
+                if next := request.POST.get('next'):
+                    return redirect(next)
+
                 return redirect(s.SERVER_URL)
             else:
                 context['message'] = "Login failed!"
@@ -103,7 +111,10 @@ def login(request):
             else:
                 context['message'] = "Account has been created! You'll receive a mail to activate your account shortly."
             return render(request, 'login.html', context)
-
+        else:
+            return HttpResponseBadRequest()
+    else:
+        return HttpResponseNotAllowed(['GET', 'POST'])
 
 def logout(request):
     if request.method == 'POST':
@@ -136,7 +147,7 @@ def editable(request, user):
                  f"{s.SERVER_URL}/group", f"{s.SERVER_URL}/search"]:
         return True
     else:
-        print(f"Unknown url: {url}")
+        logger.debug(f"Unknown url: {url}")
         return False
 
 
@@ -144,6 +155,12 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
     current_user = _anonymous_or_real(request)
     can_edit = editable(request, current_user)
 
+    parser = EPDBURLParser(request.build_absolute_uri(request.path))
+
+    url_contains_package = False
+    if parser.contains_package_url() or parser.is_package_url():
+        url_contains_package = True
+
     if for_user:
         current_user = for_user
 
@@ -154,11 +171,12 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
             'server_url': s.SERVER_URL,
             'user': current_user,
             'can_edit': can_edit,
+            'url_contains_package': url_contains_package,
             'readable_packages': PackageManager.get_all_readable_packages(current_user, include_reviewed=True),
             'writeable_packages': PackageManager.get_all_writeable_packages(current_user),
             'available_groups': GroupManager.get_groups(current_user),
             'available_settings': SettingManager.get_all_settings(current_user),
-            'enabled_features': [],
+            'enabled_features': s.FLAGS,
             'debug': s.DEBUG,
         },
     }
@@ -196,6 +214,41 @@ def breadcrumbs(first_level_object=None, second_level_namespace=None, second_lev
     return bread
 
 
+def set_scenarios(current_user, attach_object, scenario_urls: List[str]):
+    scens = []
+    for scenario_url in scenario_urls:
+        package = PackageManager.get_package_by_url(current_user, scenario_url)
+        scen = Scenario.objects.get(package=package, uuid=scenario_url.split('/')[-1])
+        scens.append(scen)
+
+    attach_object.set_scenarios(scens)
+
+
+def copy_object(current_user, target_package: 'Package', source_object_url: str):
+    # Ensures that source is readable
+    source_package = PackageManager.get_package_by_url(current_user, source_object_url)
+
+    parser = EPDBURLParser(source_object_url)
+
+    # if the url won't contain a package or is a plain package
+    if not parser.contains_package_url():
+        raise ValueError(f"Object {source_object_url} can't be copied!")
+
+    # Gets the most specific object
+    source_object = parser.get_object()
+
+    if hasattr(source_object, 'copy'):
+        mapping = dict()
+        copy = source_object.copy(target_package, mapping)
+
+        if s.DEBUG:
+            for k, v in mapping.items():
+                logger.debug(f"Mapping {k.url} to {v.url}")
+
+        return copy
+
+    raise ValueError(f"Object {source_object} can't be copied!")
+
 def index(request):
     context = get_base_context(request)
     context['title'] = 'enviPath - Home'
@@ -424,8 +477,7 @@ def scenarios(request):
         if request.GET.get('all'):
             return JsonResponse({
                 "objects": [
-                    {"name": pw.name, "url": pw.url, "reviewed": True}
-                    for pw in reviewed_scenario_qs
+                    {"name": s.name, "url": s.url, "reviewed": True} for s in reviewed_scenario_qs
                 ]
             })
 
@@ -505,6 +557,7 @@ def search(request):
                 packages = PackageManager.get_reviewed_packages()
 
             search_result = SearchManager.search(packages, searchterm, mode)
+
             return JsonResponse(search_result, safe=False)
 
         context = get_base_context(request)
@@ -530,6 +583,7 @@ def search(request):
                 packages = PackageManager.get_reviewed_packages()
 
             context['search_result'] = SearchManager.search(packages, searchterm, mode)
+            context['search_result']['searchterm'] = searchterm
 
         return render(request, 'search.html', context)
 
@@ -572,15 +626,21 @@ def package_models(request, package_uuid):
         context['model_types'] = {
             'ML Relative Reasoning': 'ml-relative-reasoning',
             'Rule Based Relative Reasoning': 'rule-based-relative-reasoning',
-            'EnviFormer': 'enviformer',
         }
 
+        if s.FLAGS.get('ENVIFORMER', False):
+            context['model_types']['EnviFormer'] = 'enviformer'
+
+        if s.FLAGS.get('PLUGINS', False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
                 context['model_types'][v.display()] = k
 
         return render(request, 'collections/objects_list.html', context)
 
     elif request.method == 'POST':
+
+        log_post_params(request)
+
         name = request.POST.get('model-name')
         description = request.POST.get('model-description')
 
@@ -603,14 +663,25 @@ def package_models(request, package_uuid):
             data_package_objs = [PackageManager.get_package_by_url(current_user, p) for p in data_packages]
             eval_packages_objs = [PackageManager.get_package_by_url(current_user, p) for p in eval_packages]
 
+            # App Domain related parameters
+            build_ad = request.POST.get('build-app-domain', False) == 'on'
+            num_neighbors = request.POST.get('num-neighbors', 5)
+            reliability_threshold = request.POST.get('reliability-threshold', 0.5)
+            local_compatibility_threshold = request.POST.get('local-compatibility-threshold', 0.5)
+
             mod = MLRelativeReasoning.create(
-                current_package,
-                name,
-                description,
-                rule_package_objs,
-                data_package_objs,
-                eval_packages_objs,
-                threshold
+                package=current_package,
+                name=name,
+                description=description,
+                rule_packages=rule_package_objs,
+                data_packages=data_package_objs,
+                eval_packages=eval_packages_objs,
+                threshold=threshold,
+                # fingerprinter=fingerprinter,
+                build_app_domain=build_ad,
+                app_domain_num_neighbours=num_neighbors,
+                app_domain_reliability_threshold=reliability_threshold,
+                app_domain_local_compatibility_threshold=local_compatibility_threshold,
             )
 
             from .tasks import build_model
@@ -646,7 +717,7 @@ def package_model(request, package_uuid, model_uuid):
                 if len(pr) > 0:
                     products = []
                     for prod_set in pr.product_sets:
-                        print(f"Checking {prod_set}")
+                        logger.debug(f"Checking {prod_set}")
                         products.append(tuple([x for x in prod_set]))
 
                     res.append({
@@ -657,6 +728,12 @@ def package_model(request, package_uuid, model_uuid):
 
             return JsonResponse(res, safe=False)
 
+        elif request.GET.get('app-domain-assessment', False):
+            smiles = request.GET['smiles']
+            stand_smiles = FormatConverter.standardize(smiles)
+            app_domain_assessment = current_model.app_domain.assess(stand_smiles)[0]
+            return JsonResponse(app_domain_assessment, safe=False)
+
         context = get_base_context(request)
         context['title'] = f'enviPath - {current_package.name} - {current_model.name}'
 
@@ -665,12 +742,13 @@ def package_model(request, package_uuid, model_uuid):
         context['breadcrumbs'] = breadcrumbs(current_package, 'model', current_model)
 
         context['model'] = current_model
+        context['current_object'] = current_model
         
         return render(request, 'objects/model.html', context)
 
     elif request.method == 'POST':
         if hidden := request.POST.get('hidden', None):
-            if hidden == 'delete-model':
+            if hidden == 'delete':
                 current_model.delete()
                 return redirect(current_package.url + '/model')
             else:
@@ -696,8 +774,6 @@ def package(request, package_uuid):
         context['breadcrumbs'] = breadcrumbs(current_package)
 
         context['package'] = current_package
-        # context['package_group'] = GroupPackagePermission.objects.filter(package=current_package,
-        #                                                                  permission=GroupPackagePermission.ALL)
 
         user_perms = UserPackagePermission.objects.filter(package=current_package)
         users = get_user_model().objects.exclude(
@@ -716,14 +792,24 @@ def package(request, package_uuid):
 
     elif request.method == 'POST':
 
-        if s.DEBUG:
-            for k, v in request.POST.items():
-                logger.debug(f"{k}\t{v}")
+        log_post_params(request)
 
         if hidden := request.POST.get('hidden', None):
-            if hidden == 'delete-package':
+            if hidden == 'delete':
                 logger.debug(current_package.delete())
                 return redirect(s.SERVER_URL + '/package')
+            elif hidden == 'publish-package':
+                for g in Group.objects.filter(public=True):
+                    PackageManager.update_permissions(current_user, current_package, g, Permission.READ[0])
+                return redirect(current_package.url)
+            elif hidden == 'copy':
+                object_to_copy = request.POST.get('object_to_copy')
+
+                if not object_to_copy:
+                    return error(request, 'Invalid target package.', 'Please select a target package.')
+
+                copied_object = copy_object(current_user, current_package, object_to_copy)
+                return JsonResponse({'success': copied_object.url})
             else:
                 return HttpResponseBadRequest()
 
@@ -855,17 +941,24 @@ def package_compound(request, package_uuid, compound_uuid):
         context['breadcrumbs'] = breadcrumbs(current_package, 'compound', current_compound)
 
         context['compound'] = current_compound
+        context['current_object'] = current_compound
 
         return render(request, 'objects/compound.html', context)
 
     elif request.method == 'POST':
         if hidden := request.POST.get('hidden', None):
-            if hidden == 'delete-compound':
+            if hidden == 'delete':
                 current_compound.delete()
                 return redirect(current_package.url + '/compound')
             else:
                 return HttpResponseBadRequest()
 
+        selected_scenarios = request.POST.getlist('selected-scenarios')
+
+        if selected_scenarios:
+            set_scenarios(current_user, current_compound, selected_scenarios)
+            return redirect(current_compound.url)
+
         new_compound_name = request.POST.get('compound-name')
         new_compound_description = request.POST.get('compound-description')
 
@@ -897,6 +990,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
 
         context['meta']['current_package'] = current_package
         context['object_type'] = 'structure'
+        context['breadcrumbs'] = breadcrumbs(current_package, 'compound', current_compound, 'structure')
 
         reviewed_compound_structure_qs = CompoundStructure.objects.none()
         unreviewed_compound_structure_qs = CompoundStructure.objects.none()
@@ -936,12 +1030,45 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
         context['title'] = f'enviPath - {current_package.name} - {current_compound.name} - {current_structure.name}'
 
         context['meta']['current_package'] = current_package
-        context['object_type'] = 'compound'
+        context['object_type'] = 'structure'
 
         context['compound_structure'] = current_structure
+        context['current_object'] = current_structure
+        context['breadcrumbs'] = breadcrumbs(current_package, 'compound', current_compound, 'structure', current_structure)
 
         return render(request, 'objects/compound_structure.html', context)
 
+    elif request.method == 'POST':
+
+        if hidden := request.POST.get('hidden', None):
+            if hidden == 'delete':
+                # Check if we have to delete the compound as no structure is left
+                if len(current_structure.compound.structures.all()) == 1:
+                    # This will delete the structure as well
+                    current_compound.delete()
+                    return redirect(current_package.url + '/compound')
+                else:
+                    if current_structure.normalized_structure:
+                        current_compound.delete()
+                        return redirect(current_package.url + '/compound')
+                    else:
+                        if current_compound.default_structure == current_structure:
+                            current_structure.delete()
+                            current_compound.default_structure = current_compound.structures.all().first()
+                            return redirect(current_compound.url + '/structure')
+                        else:
+                            current_structure.delete()
+                            return redirect(current_compound.url + '/structure')
+            else:
+                return HttpResponseBadRequest()
+
+        selected_scenarios = request.POST.getlist('selected-scenarios')
+
+        if selected_scenarios:
+            set_scenarios(current_user, current_structure, selected_scenarios)
+            return redirect(current_structure.url)
+
+        return HttpResponseBadRequest()
     else:
         return HttpResponseNotAllowed(['GET', ])
 
@@ -1022,6 +1149,24 @@ def package_rule(request, package_uuid, rule_uuid):
 
     if request.method == 'GET':
         context = get_base_context(request)
+
+        if smiles := request.GET.get('smiles', False):
+            stand_smiles = FormatConverter.standardize(smiles)
+            res = current_rule.apply(stand_smiles)
+            if len(res) > 1:
+                logger.info(f"Rule {current_rule.uuid} returned multiple product sets on {smiles}, picking the first one.")
+
+            smirks = f"{stand_smiles}>>{'.'.join(sorted(res[0]))}"
+            # Usually the functional groups are a mapping of fg -> count
+            # As we are doing it on the fly here fake a high count to ensure that its properly highlighted
+            educt_functional_groups = {x: 1000 for x in current_rule.reactants_smarts}
+            product_functional_groups = {x: 1000 for x in current_rule.products_smarts}
+            return HttpResponse(
+                IndigoUtils.smirks_to_svg(smirks, False, 0, 0,
+                                          educt_functional_groups=educt_functional_groups,
+                                          product_functional_groups=product_functional_groups),
+                content_type='image/svg+xml')
+
         context['title'] = f'enviPath - {current_package.name} - {current_rule.name}'
 
         context['meta']['current_package'] = current_package
@@ -1029,6 +1174,8 @@ def package_rule(request, package_uuid, rule_uuid):
         context['breadcrumbs'] = breadcrumbs(current_package, 'rule', current_rule)
 
         context['rule'] = current_rule
+        context['current_object'] = current_rule
+
         if isinstance(current_rule, SimpleAmbitRule):
             return render(request, 'objects/simple_rule.html', context)
         else:  # isinstance(current_rule, ParallelRule) or isinstance(current_rule, SequentialRule):
@@ -1036,12 +1183,18 @@ def package_rule(request, package_uuid, rule_uuid):
 
     elif request.method == 'POST':
         if hidden := request.POST.get('hidden', None):
-            if hidden == 'delete-rule':
+            if hidden == 'delete':
                 current_rule.delete()
                 return redirect(current_package.url + '/rule')
             else:
                 return HttpResponseBadRequest()
 
+        selected_scenarios = request.POST.getlist('selected-scenarios')
+
+        if selected_scenarios:
+            set_scenarios(current_user, current_rule, selected_scenarios)
+            return redirect(current_rule.url)
+
         rule_name = request.POST.get('rule-name', '').strip()
         rule_description = request.POST.get('rule-description', '').strip()
 
@@ -1127,17 +1280,24 @@ def package_reaction(request, package_uuid, reaction_uuid):
         context['breadcrumbs'] = breadcrumbs(current_package, 'reaction', current_reaction)
 
         context['reaction'] = current_reaction
+        context['current_object'] = current_reaction
 
         return render(request, 'objects/reaction.html', context)
 
     elif request.method == 'POST':
         if hidden := request.POST.get('hidden', None):
-            if hidden == 'delete-reaction':
+            if hidden == 'delete':
                 current_reaction.delete()
                 return redirect(current_package.url + '/reaction')
             else:
                 return HttpResponseBadRequest()
 
+        selected_scenarios = request.POST.getlist('selected-scenarios')
+
+        if selected_scenarios:
+            set_scenarios(current_user, current_reaction, selected_scenarios)
+            return redirect(current_reaction.url)
+
         new_reaction_name = request.POST.get('reaction-name')
         new_reaction_description = request.POST.get('reaction-description')
 
@@ -1195,8 +1355,8 @@ def package_pathways(request, package_uuid):
 
         log_post_params(request)
 
-        name = request.POST.get('name', 'Pathway ' + str(Pathway.objects.filter(package=current_package).count()))
-        description = request.POST.get('description', s.DEFAULT_VALUES['description'])
+        name = request.POST.get('name')
+        description = request.POST.get('description')
         pw_mode = request.POST.get('predict', 'predict')
         smiles = request.POST.get('smiles')
 
@@ -1217,7 +1377,14 @@ def package_pathways(request, package_uuid):
             return error(request, "Pathway prediction failed!",
                          f'Pathway prediction failed as received mode "{pw_mode}" is none of {modes}')
 
+        prediction_setting = request.POST.get('prediction-setting', None)
+        if prediction_setting:
+            prediction_setting = SettingManager.get_setting_by_url(current_user, prediction_setting)
+        else:
+            prediction_setting = current_user.prediction_settings()
+
         pw = Pathway.create(current_package, stand_smiles, name=name, description=description)
+
         # set mode
         pw.kv.update({'mode': pw_mode})
         pw.save()
@@ -1230,12 +1397,11 @@ def package_pathways(request, package_uuid):
             if pw_mode == 'incremental':
                 limit = 1
 
-            pred_setting = current_user.prediction_settings()
-            pw.setting = pred_setting
+            pw.setting = prediction_setting
             pw.save()
 
             from .tasks import predict
-            predict.delay(pw.pk, pred_setting.pk, limit=limit)
+            predict.delay(pw.pk, prediction_setting.pk, limit=limit)
 
         return redirect(pw.url)
 
@@ -1254,6 +1420,14 @@ def package_pathway(request, package_uuid, pathway_uuid):
         if request.GET.get("last_modified", False):
             return JsonResponse({'modified': current_pathway.modified.strftime('%Y-%m-%d %H:%M:%S')})
 
+        if request.GET.get("download", False) == "true":
+            filename = f"{current_pathway.name.replace(' ', '_')}_{current_pathway.uuid}.csv"
+            csv_pw = current_pathway.to_csv()
+            response = HttpResponse(csv_pw, content_type='text/csv')
+            response['Content-Disposition'] = f'attachment; filename="{filename}"'
+
+            return response
+
         context = get_base_context(request)
         context['title'] = f'enviPath - {current_package.name} - {current_pathway.name}'
 
@@ -1262,6 +1436,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
         context['breadcrumbs'] = breadcrumbs(current_package, 'pathway', current_pathway)
 
         context['pathway'] = current_pathway
+        context['current_object'] = current_pathway
 
         context['breadcrumbs'] = [
             {'Home': s.SERVER_URL},
@@ -1276,12 +1451,18 @@ def package_pathway(request, package_uuid, pathway_uuid):
 
     elif request.method == 'POST':
         if hidden := request.POST.get('hidden', None):
-            if hidden == 'delete-pathway':
+            if hidden == 'delete':
                 current_pathway.delete()
                 return redirect(current_package.url + '/pathway')
             else:
                 return HttpResponseBadRequest()
 
+        selected_scenarios = request.POST.getlist('selected-scenarios')
+
+        if selected_scenarios:
+            set_scenarios(current_user, current_pathway, selected_scenarios)
+            return redirect(current_pathway.url)
+
         pathway_name = request.POST.get('pathway-name')
         pathway_description = request.POST.get('pathway-description')
 
@@ -1402,19 +1583,33 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
         ]
 
         context['node'] = current_node
+        context['current_object'] = current_node
+
+        context['app_domain_assessment_data'] = json.dumps(current_node.get_app_domain_assessment_data())
 
         return render(request, 'objects/node.html', context)
 
     elif request.method == 'POST':
-        if s.DEBUG:
-            for k, v in request.POST.items():
-                print(k, v)
+
+        log_post_params(request)
 
         if hidden := request.POST.get('hidden', None):
-            if hidden == 'delete-node':
-                current_node.delete()
-                return redirect(current_pathway.url)
+            if hidden == 'delete':
 
+                # pre_delete signal will take care of edge deletion
+                current_node.delete()
+
+                return redirect(current_pathway.url)
+            else:
+                return HttpResponseBadRequest()
+
+        selected_scenarios = request.POST.getlist('selected-scenarios')
+
+        if selected_scenarios:
+            set_scenarios(current_user, current_node, selected_scenarios)
+            return redirect(current_node.url)
+
+        return HttpResponseBadRequest()
     else:
         return HttpResponseNotAllowed(['GET', 'POST'])
 
@@ -1463,6 +1658,8 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
 
     elif request.method == 'POST':
 
+        log_post_params(request)
+
         edge_name = request.POST.get('edge-name')
         edge_description = request.POST.get('edge-description')
         edge_substrates = request.POST.getlist('edge-substrates')
@@ -1499,22 +1696,30 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
             'title'] = f'enviPath - {current_package.name} - {current_pathway.name} - {current_edge.edge_label.name}'
 
         context['meta']['current_package'] = current_package
-        context['object_type'] = 'reaction'
+        context['object_type'] = 'edge'
         context['breadcrumbs'] = breadcrumbs(current_package, 'pathway', current_pathway, 'edge', current_edge)
         context['edge'] = current_edge
+        context['current_object'] = current_edge
 
         return render(request, 'objects/edge.html', context)
 
     elif request.method == 'POST':
-        if s.DEBUG:
-            for k, v in request.POST.items():
-                print(k, v)
+
+        log_post_params(request)
 
         if hidden := request.POST.get('hidden', None):
-            if hidden == 'delete-edge':
+            if hidden == 'delete':
                 current_edge.delete()
                 return redirect(current_pathway.url)
 
+        selected_scenarios = request.POST.getlist('selected-scenarios')
+
+        if selected_scenarios:
+            set_scenarios(current_user, current_edge, selected_scenarios)
+            return redirect(current_edge.url)
+
+        return HttpResponseBadRequest()
+
     else:
         return HttpResponseNotAllowed(['GET', 'POST'])
 
@@ -1525,12 +1730,18 @@ def package_scenarios(request, package_uuid):
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
 
     if request.method == 'GET':
+
+        if 'application/json' in request.META.get('HTTP_ACCEPT') and not request.GET.get('all', False):
+            scens = Scenario.objects.filter(package=current_package).order_by('name')
+            res = [{'name': s.name, 'url': s.url, 'uuid': s.uuid} for s in scens]
+            return JsonResponse(res, safe=False)
+
         context = get_base_context(request)
         context['title'] = f'enviPath - {current_package.name} - Scenarios'
 
         context['meta']['current_package'] = current_package
         context['object_type'] = 'scenario'
-        context['breadcrumbs'] = breadcrumbs(current_package, 'pathway')
+        context['breadcrumbs'] = breadcrumbs(current_package, 'scenario')
 
         reviewed_scenario_qs = Scenario.objects.none()
         unreviewed_scenario_qs = Scenario.objects.none()
@@ -1551,8 +1762,57 @@ def package_scenarios(request, package_uuid):
         context['reviewed_objects'] = reviewed_scenario_qs
         context['unreviewed_objects'] = unreviewed_scenario_qs
 
-        return render(request, 'collections/objects_list.html', context)
+        from envipy_additional_information import SLUDGE_ADDITIONAL_INFORMATION, SOIL_ADDITIONAL_INFORMATION, \
+            SEDIMENT_ADDITIONAL_INFORMATION
+        context['scenario_types'] = {
+            'Soil Data': {
+                'name': 'soil',
+                'widgets': [HTMLGenerator.generate_html(ai, prefix=f'soil_{0}') for ai in
+                            [x for s in SOIL_ADDITIONAL_INFORMATION.values() for x in s]]
+            },
+            'Sludge Data': {
+                'name': 'sludge',
+                'widgets': [HTMLGenerator.generate_html(ai, prefix=f'sludge_{0}') for ai in
+                            [x for s in SLUDGE_ADDITIONAL_INFORMATION.values() for x in s]]
+            },
+            'Water-Sediment System Data': {
+                'name': 'sediment',
+                'widgets': [HTMLGenerator.generate_html(ai, prefix=f'sediment_{0}') for ai in
+                            [x for s in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in s]]
+            }
+        }
 
+        context['sludge_additional_information'] = SLUDGE_ADDITIONAL_INFORMATION
+        context['soil_additional_information'] = SOIL_ADDITIONAL_INFORMATION
+        context['sediment_additional_information'] = SEDIMENT_ADDITIONAL_INFORMATION
+
+        return render(request, 'collections/objects_list.html', context)
+    elif request.method == 'POST':
+
+        log_post_params(request)
+
+        scenario_name = request.POST.get('scenario-name')
+        scenario_description = request.POST.get('scenario-description')
+        scenario_date_year = request.POST.get('scenario-date-year')
+        scenario_date_month = request.POST.get('scenario-date-month')
+        scenario_date_day = request.POST.get('scenario-date-day')
+
+        scenario_date = scenario_date_year
+        if scenario_date_month is not None and scenario_date_month.strip() != '':
+            scenario_date += f'-{int(scenario_date_month):02d}'
+            if scenario_date_day is not None and scenario_date_day.strip() != '':
+                scenario_date += f'-{int(scenario_date_day):02d}'
+
+        scenario_type = request.POST.get('scenario-type')
+
+        additional_information = HTMLGenerator.build_models(request.POST.dict())
+        additional_information = [x for s in additional_information.values() for x in s]
+
+        s = Scenario.create(current_package, name=scenario_name, description=scenario_description,
+                            scenario_date=scenario_date, scenario_type=scenario_type,
+                            additional_information=additional_information)
+
+        return redirect(s.url)
     else:
         return HttpResponseNotAllowed(['GET', ])
 
@@ -1573,10 +1833,63 @@ def package_scenario(request, package_uuid, scenario_uuid):
 
         context['scenario'] = current_scenario
 
+        available_add_infs = []
+        for add_inf in NAME_MAPPING.values():
+            available_add_infs.append({
+                'display_name': add_inf.property_name(None),
+                'name': add_inf.__name__,
+                'widget': HTMLGenerator.generate_html(add_inf, prefix=f'{0}')
+            })
+        context['available_additional_information'] = available_add_infs
+
+        context['update_widgets'] = [HTMLGenerator.generate_html(ai, prefix=f'{i}') for i, ai in enumerate(current_scenario.get_additional_information())]
+
         return render(request, 'objects/scenario.html', context)
 
+    elif request.method == 'POST':
+
+        log_post_params(request)
+
+        if hidden := request.POST.get('hidden', None):
+
+            if hidden == 'delete':
+                current_scenario.delete()
+                return redirect(current_package.url + '/scenario')
+            elif hidden == 'delete-additional-information':
+                uuid = request.POST.get('uuid')
+                current_scenario.remove_additional_information(uuid)
+                return redirect(current_scenario.url)
+            elif hidden == 'delete-all-additional-information':
+                current_scenario.additional_information = dict()
+                current_scenario.save()
+                return redirect(current_scenario.url)
+            elif hidden == 'set-additional-information':
+                ais = HTMLGenerator.build_models(request.POST.dict())
+
+                if s.DEBUG:
+                    logger.info(ais)
+
+                current_scenario.set_additional_information(ais)
+                return redirect(current_scenario.url)
+            elif hidden == 'add-additional-information':
+                ais = HTMLGenerator.build_models(request.POST.dict())
+
+                if len(ais.keys()) != 1:
+                    raise ValueError('Only one additional information field can be added at a time.')
+
+                ai = list(ais.values())[0][0]
+
+                if s.DEBUG:
+                    logger.info(ais)
+
+                current_scenario.add_additional_information(ai)
+                return redirect(current_scenario.url)
             else:
-        return HttpResponseNotAllowed(['GET', ])
+                return HttpResponseBadRequest()
+        else:
+            return HttpResponseBadRequest()
+    else:
+        return HttpResponseNotAllowed(['GET', 'POST'])
 
 
 ##############
@@ -1587,7 +1900,6 @@ def users(request):
         context = get_base_context(request)
         context['title'] = f'enviPath - Users'
 
-        context['meta']['current_package'] = context['meta']['user'].default_package
         context['object_type'] = 'user'
         context['breadcrumbs'] = [
             {'Home': s.SERVER_URL},
@@ -1611,27 +1923,27 @@ def user(request, user_uuid):
         if str(current_user.uuid) != user_uuid and not current_user.is_superuser:
             return HttpResponseBadRequest()
 
-        user = UserManager.get_user_by_id(current_user, user_uuid)
+        requested_user = UserManager.get_user_by_id(current_user, user_uuid)
 
-        context = get_base_context(request)
+        context = get_base_context(request, for_user=requested_user)
         context['title'] = f'enviPath - User'
 
         context['object_type'] = 'user'
         context['breadcrumbs'] = [
             {'Home': s.SERVER_URL},
             {'User': s.SERVER_URL + '/user'},
-            {current_user.username: current_user.url}
+            {current_user.username: requested_user.url}
         ]
 
-        context['user'] = user
+        context['user'] = requested_user
 
         model_qs = EPModel.objects.none()
-        for p in PackageManager.get_all_readable_packages(current_user, include_reviewed=True):
+        for p in PackageManager.get_all_readable_packages(requested_user, include_reviewed=True):
             model_qs |= p.models
 
         context['models'] = model_qs
 
-        context['tokens'] = APIToken.objects.filter(user=current_user)
+        context['tokens'] = APIToken.objects.filter(user=requested_user)
 
         return render(request, 'objects/user.html', context)
 
@@ -1700,8 +2012,6 @@ def user(request, user_uuid):
                 }
             }
 
-            print(setting)
-
         return HttpResponseBadRequest()
 
     else:
@@ -1715,7 +2025,6 @@ def groups(request):
         context = get_base_context(request)
         context['title'] = f'enviPath - Groups'
 
-        context['meta']['current_package'] = context['meta']['user'].default_package
         context['object_type'] = 'group'
         context['breadcrumbs'] = [
             {'Home': s.SERVER_URL},
@@ -1764,12 +2073,10 @@ def group(request, group_uuid):
 
     elif request.method == 'POST':
 
-        if s.DEBUG:
-            for k, v in request.POST.items():
-                print(k, v)
+        log_post_params(request)
 
         if hidden := request.POST.get('hidden', None):
-            if hidden == 'delete-group':
+            if hidden == 'delete':
                 current_group.delete()
                 return redirect(s.SERVER_URL + '/group')
             else:
@@ -1912,3 +2219,16 @@ def depict(request):
         return HttpResponse(IndigoUtils.smirks_to_svg(smirks, query_smirks), content_type='image/svg+xml')
     else:
         return HttpResponseBadRequest()
+
+
+@protected_resource()
+def userinfo(request):
+    user = request.resource_owner
+    res = {
+        "sub": str(user.uuid),
+        "email": user.email,
+        "username": user.username,
+        "name": user.get_full_name() or user.username,
+        "email_verified": user.is_active,
+    }
+    return JsonResponse(res)

migration/views.py

@@ -38,10 +38,8 @@ def migration(request):
                 res = True
 
                 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, preprocess_smiles=True, bracketize=False)
+                    products = FormatConverter.apply(comp['smiles'], smirks)
 
                     all_rdkit_prods = []
                     for ps in products:
@@ -130,7 +128,7 @@ def migration_detail(request, package_uuid, rule_uuid):
             # if comp['smiles'] != 'CC1=C(C(=C(C=N1)CO)C=O)O':
             #     continue
 
-            products = FormatConverter.apply(comp['smiles'], smirks, preprocess_smiles=True, bracketize=False)
+            products = FormatConverter.apply(comp['smiles'], smirks)
 
             all_rdkit_prods = []
             for ps in products:

pyproject.toml

@@ -10,6 +10,7 @@ dependencies = [
     "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",
@@ -29,4 +30,4 @@ dependencies = [
 [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" }
+envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.4"}

static/js/pps.js

@@ -638,3 +638,150 @@ function fillPRCurve(modelUri, onclick){
 
     });
 }
+
+
+function handleAssessmentResponse(depict_url, data) {
+    var inside_app_domain = "<a class='list-group-item'>This compound is " + (data["assessment"]["inside_app_domain"] ? "inside" : "outside") + " the Applicability Domain derived from the chemical (PCA) space constructed using the training data." + "</a>";
+    var functionalGroupsImgSrc = null;
+    var reactivityCentersImgSrc = null;
+
+    if (data['assessment']['node'] !== undefined) {
+        functionalGroupsImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "'>";
+        reactivityCentersImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "'>"
+    } else {
+        functionalGroupsImgSrc = "<img width='400' src=\"" + depict_url + "?smiles=" + encodeURIComponent(data['assessment']['smiles']) + "\">";
+        reactivityCentersImgSrc = "<img width='400' src=\"" + depict_url + "?smiles=" + encodeURIComponent(data['assessment']['smiles']) + "\">"
+    }
+
+    tpl = `<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="app-domain-assessment-functional-groups-link" data-toggle="collapse" data-parent="#app-domain-assessment" href="#app-domain-assessment-functional-groups">Functional Groups Covered by Model</a>
+                </h4>
+            </div>
+            <div id="app-domain-assessment-functional-groups" class="panel-collapse collapse">
+                <div class="panel-body list-group-item">
+                    ${inside_app_domain}
+                    <p></p>
+                    <div id="image-div" align="center">
+                        ${functionalGroupsImgSrc}
+                    </div>
+                </div>
+            </div>
+
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="app-domain-assessment-reactivity-centers-link" data-toggle="collapse" data-parent="#app-domain-assessment" href="#app-domain-assessment-reactivity-centers">Reactivity Centers</a>
+                </h4>
+            </div>
+            <div id="app-domain-assessment-reactivity-centers" class="panel-collapse collapse">
+                <div class="panel-body list-group-item">
+                    <div id="image-div" align="center">
+                        ${reactivityCentersImgSrc}
+                    </div>
+                </div>
+            </div>`
+
+    var transformations = '';
+
+    for (t in data['assessment']['transformations']) {
+        transObj = data['assessment']['transformations'][t];
+        var neighbors = '';
+        for (n in transObj['neighbors']) {
+            neighObj = transObj['neighbors'][n];
+            var neighImg = "<img width='100%' src='" + transObj['rule']['url'] + "?smiles=" + encodeURIComponent(neighObj['smiles']) + "'>";
+            var objLink = `<a class='list-group-item' href="${neighObj['url']}">${neighObj['name']}</a>`
+            var neighPredProb = "<a class='list-group-item'>Predicted probability: " + neighObj['probability'].toFixed(2) + "</a>";
+
+            var pwLinks = '';
+            for (pw in neighObj['related_pathways']) {
+                var pwObj = neighObj['related_pathways'][pw];
+                pwLinks += "<a class='list-group-item' href=" + pwObj['url'] + ">" + pwObj['name'] + "</a>";
+            }
+
+            var expPathways = `
+                    <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                        <h4 class="panel-title">
+                            <a id="transformation-${t}-neighbor-${n}-exp-pathway-link" data-toggle="collapse" data-parent="#transformation-${t}-neighbor-${n}" href="#transformation-${t}-neighbor-${n}-exp-pathway">Experimental Pathways</a>
+                        </h4>
+                    </div>
+                    <div id="transformation-${t}-neighbor-${n}-exp-pathway" class="panel-collapse collapse">
+                        <div class="panel-body list-group-item">
+                            ${pwLinks}
+                        </div>
+                    </div>
+                    `
+
+            if (pwLinks === '') {
+                expPathways = ''
+            }
+
+            neighbors += `
+                    <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                        <h4 class="panel-title">
+                            <a id="transformation-${t}-neighbor-${n}-link" data-toggle="collapse" data-parent="#transformation-${t}" href="#transformation-${t}-neighbor-${n}">Analog Transformation on ${neighObj['name']}</a>
+                        </h4>
+                    </div>
+                    <div id="transformation-${t}-neighbor-${n}" class="panel-collapse collapse">
+                        <div class="panel-body list-group-item">
+                            ${objLink}
+                            ${neighPredProb}
+                            ${expPathways}
+                            <p></p>
+                            <div id="image-div" align="center">
+                                ${neighImg}
+                            </div>
+                        </div>
+                    </div>
+                    `
+        }
+
+        var panelName = null;
+        var objLink = null;
+        if (transObj['is_predicted']) {
+            panelName = `Predicted Transformation by ${transObj['rule']['name']}`;
+            for (e in transObj['edges']) {
+                objLink = `<a class='list-group-item' href="${transObj['edges'][e]['url']}">${transObj['edges'][e]['name']}</a>`
+                break;
+            }
+        } else {
+            panelName = `Potential Transformation by applying ${transObj['rule']['name']}`;
+            objLink = `<a class='list-group-item' href="${transObj['rule']['url']}">${transObj['rule']['name']}</a>`
+        }
+
+        var predProb = "<a class='list-group-item'>Predicted probability: " + transObj['probability'].toFixed(2) + "</a>";
+        var timesTriggered = "<a class='list-group-item'>This rule has triggered " + transObj['times_triggered'] + " times in the training set</a>";
+        var reliability = "<a class='list-group-item'>Reliability: " + transObj['reliability'].toFixed(2) + " (" + (transObj['reliability'] > data['ad_params']['reliability_threshold'] ? "&gt" : "&lt") + " Reliability Threshold of " + data['ad_params']['reliability_threshold'] + ") </a>";
+        var localCompatibility = "<a class='list-group-item'>Local Compatibility: " + transObj['local_compatibility'].toFixed(2) + " (" + (transObj['local_compatibility'] > data['ad_params']['local_compatibilty_threshold'] ? "&gt" : "&lt") + " Local Compatibility Threshold of " + data['ad_params']['local_compatibilty_threshold'] + ")</a>";
+
+        var transImg = "<img width='100%' src='" + transObj['rule']['url'] + "?smiles=" + encodeURIComponent(data['assessment']['smiles']) + "'>";
+
+        var transformation = `
+                    <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                        <h4 class="panel-title">
+                            <a id="transformation-${t}-link" data-toggle="collapse" data-parent="#transformation-${t}" href="#transformation-${t}">${panelName}</a>
+                        </h4>
+                    </div>
+                    <div id="transformation-${t}" class="panel-collapse collapse">
+                        <div class="panel-body list-group-item">
+                            ${objLink}
+                            ${predProb}
+                            ${timesTriggered}
+                            ${reliability}
+                            ${localCompatibility}
+                            <p></p>
+                            <div id="image-div" align="center">
+                                ${transImg}
+                            </div>
+                            <p></p>
+                            ${neighbors}
+                        </div>
+                    </div>
+                `
+        transformations += transformation;
+    }
+
+    res = tpl + transformations;
+
+    $("#appDomainAssessmentResultTable").append(res);
+
+}

static/js/pw.js

@@ -1,5 +1,4 @@
-console.log("loaded")
-
+console.log("loaded pw.js")
 
 function predictFromNode(url) {
     $.post("", {node: url})
@@ -28,61 +27,164 @@ function draw(pathway, elem) {
         const horizontalSpacing = 75; // horizontal space between nodes
         const depthMap = new Map();
 
-        nodes.forEach(node => {
+        // Sort nodes by depth first to minimize crossings
+        const sortedNodes = [...nodes].sort((a, b) => a.depth - b.depth);
+
+        sortedNodes.forEach(node => {
             if (!depthMap.has(node.depth)) {
                 depthMap.set(node.depth, 0);
             }
 
             const nodesInLevel = nodes.filter(n => n.depth === node.depth).length;
-            node.fx = width / 2 + depthMap.get(node.depth) * horizontalSpacing - ((nodesInLevel - 1) * horizontalSpacing) / 2;
-            node.fy = node.depth * levelSpacing + 50;
 
+            // For pseudo nodes, try to position them to minimize crossings
+            if (node.pseudo) {
+                const parentLinks = links.filter(l => l.target.id === node.id);
+                const childLinks = links.filter(l => l.source.id === node.id);
+
+                if (parentLinks.length > 0 && childLinks.length > 0) {
+                    const parentX = parentLinks[0].source.x || (width / 2);
+                    const childrenX = childLinks.map(l => l.target.x || (width / 2));
+                    const avgChildX = childrenX.reduce((sum, x) => sum + x, 0) / childrenX.length;
+
+                    // Position pseudo node between parent and average child position
+                    node.fx = (parentX + avgChildX) / 2;
+                } else {
+                    node.fx = width / 2 + depthMap.get(node.depth) * horizontalSpacing - ((nodesInLevel - 1) * horizontalSpacing) / 2;
+                }
+            } else {
+                node.fx = width / 2 + depthMap.get(node.depth) * horizontalSpacing - ((nodesInLevel - 1) * horizontalSpacing) / 2;
+            }
+
+            node.fy = node.depth * levelSpacing + 50;
             depthMap.set(node.depth, depthMap.get(node.depth) + 1);
         });
     }
 
-    // Funktion für das Update der Positionen
+    // Function to update pseudo node positions based on connected nodes
+    function updatePseudoNodePositions() {
+        nodes.forEach(node => {
+            if (node.pseudo && !node.isDragging) { // Don't auto-update if being dragged
+                const parentLinks = links.filter(l => l.target.id === node.id);
+                const childLinks = links.filter(l => l.source.id === node.id);
+
+                if (parentLinks.length > 0 && childLinks.length > 0) {
+                    const parent = parentLinks[0].source;
+                    const children = childLinks.map(l => l.target);
+
+                    // Calculate optimal position to minimize crossing
+                    const parentX = parent.x;
+                    const parentY = parent.y;
+                    const childrenX = children.map(c => c.x);
+                    const childrenY = children.map(c => c.y);
+                    const avgChildX = d3.mean(childrenX);
+                    const avgChildY = d3.mean(childrenY);
+
+                    // Position pseudo node between parent and average child position
+                    node.fx = (parentX + avgChildX) / 2;
+                    node.fy = (parentY + avgChildY) / 2; // Allow vertical movement too
+                }
+            }
+        });
+    }
+
+
+    // Enhanced ticked function
     function ticked() {
+        // Update pseudo node positions first
+        updatePseudoNodePositions();
+
         link.attr("x1", d => d.source.x)
             .attr("y1", d => d.source.y)
             .attr("x2", d => d.target.x)
             .attr("y2", d => d.target.y);
 
         node.attr("transform", d => `translate(${d.x},${d.y})`);
-
-        nodes.forEach(n => {
-            if (n.pseudo) {
-                // Alle Kinder dieses Pseudonodes finden
-                const childLinks = links.filter(l => l.source.id === n.id);
-                const childNodes = childLinks.map(l => l.target);
-                if (childNodes.length > 0) {
-                    // Durchschnitt der Kinderpositionen berechnen
-                    const avgX = d3.mean(childNodes, d => d.x);
-                    const avgY = d3.mean(childNodes, d => d.y);
-                    n.fx = avgX;
-                    // keep level as is
-                    n.fy = n.y;
-                }
-            }
-        });
-        //simulation.alpha(0.3).restart();
     }
 
     function dragstarted(event, d) {
         if (!event.active) simulation.alphaTarget(0.3).restart();
-        d.fx = d.x; // Setzt die Fixierung auf die aktuelle Position
+        d.fx = d.x;
         d.fy = d.y;
+
+        // Mark if this node is being dragged
+        d.isDragging = true;
+
+        // If dragging a non-pseudo node, mark connected pseudo nodes for update
+        if (!d.pseudo) {
+            markConnectedPseudoNodes(d);
+        }
     }
 
     function dragged(event, d) {
-        d.fx = event.x; // Position direkt an Maus anpassen
+        d.fx = event.x;
         d.fy = event.y;
+
+        // Update connected pseudo nodes in real-time
+        if (!d.pseudo) {
+            updateConnectedPseudoNodes(d);
+        }
     }
 
     function dragended(event, d) {
         if (!event.active) simulation.alphaTarget(0);
-        // Knoten bleibt an der neuen Position und wird nicht zurückgezogen
+
+        // Mark that dragging has ended
+        d.isDragging = false;
+
+        // Final update of connected pseudo nodes
+        if (!d.pseudo) {
+            updateConnectedPseudoNodes(d);
         }
+    }
+
+    // Helper function to mark connected pseudo nodes
+    function markConnectedPseudoNodes(draggedNode) {
+        // Find pseudo nodes connected to this node
+        const connectedPseudos = new Set();
+
+        // Check as parent of pseudo nodes
+        links.filter(l => l.source.id === draggedNode.id && l.target.pseudo)
+            .forEach(l => connectedPseudos.add(l.target));
+
+        // Check as child of pseudo nodes
+        links.filter(l => l.target.id === draggedNode.id && l.source.pseudo)
+            .forEach(l => connectedPseudos.add(l.source));
+
+        return connectedPseudos;
+    }
+
+    // Helper function to update connected pseudo nodes
+    function updateConnectedPseudoNodes(draggedNode) {
+        const connectedPseudos = markConnectedPseudoNodes(draggedNode);
+
+        connectedPseudos.forEach(pseudoNode => {
+            if (!pseudoNode.isDragging) { // Don't update if pseudo node is being dragged
+                const parentLinks = links.filter(l => l.target.id === pseudoNode.id);
+                const childLinks = links.filter(l => l.source.id === pseudoNode.id);
+
+                if (parentLinks.length > 0 && childLinks.length > 0) {
+                    const parent = parentLinks[0].source;
+                    const children = childLinks.map(l => l.target);
+
+                    const parentX = parent.fx || parent.x;
+                    const parentY = parent.fy || parent.y;
+                    const childrenX = children.map(c => c.fx || c.x);
+                    const childrenY = children.map(c => c.fy || c.y);
+                    const avgChildX = d3.mean(childrenX);
+                    const avgChildY = d3.mean(childrenY);
+
+                    // Update pseudo node position - allow both X and Y movement
+                    pseudoNode.fx = (parentX + avgChildX) / 2;
+                    pseudoNode.fy = (parentY + avgChildY) / 2;
+                }
+            }
+        });
+
+        // Restart simulation with lower alpha to smooth the transition
+        simulation.alpha(0.1).restart();
+    }
+
 
     // t -> ref to "this" from d3
     function nodeClick(event, node, t) {
@@ -140,10 +242,19 @@ function draw(pathway, elem) {
         });
     }
 
-
     function node_popup(n) {
         popupContent = "<a href='" + n.url + "'>" + n.name + "</a><br>";
         popupContent += "Depth " + n.depth + "<br>"
+
+        if (appDomainViewEnabled) {
+            if (n.app_domain != null) {
+                popupContent += "This compound is " + (n.app_domain['inside_app_domain'] ? "inside" : "outside") + " the Applicability Domain derived from the chemical (PCA) space constructed using the training data." + "<br>"
+                if (n.app_domain['uncovered_functional_groups']) {
+                    popupContent += "Compound contains functional groups not covered by the training set  <br>"
+                }
+            }
+        }
+
         popupContent += "<img src='" + n.image + "' width='" + 20 * nodeRadius + "'><br>"
         if (n.scenarios.length > 0) {
             popupContent += '<b>Half-lives and related scenarios:</b><br>'
@@ -162,12 +273,23 @@ function draw(pathway, elem) {
 
     function edge_popup(e) {
         popupContent = "<a href='" + e.url + "'>" + e.name + "</a><br>";
+
+        if (e.app_domain) {
+            adcontent = "<p>";
+            if (e.app_domain["times_triggered"]) {
+                adcontent += "This rule triggered " + e.app_domain["times_triggered"] + " times in the training set<br>";
+            }
+            adcontent += "Reliability " + e.app_domain["reliability"].toFixed(2) + " (" + (e.app_domain["reliability"] > e.app_domain["reliability_threshold"] ? "&gt" : "&lt") + " Reliability Threshold of " + e.app_domain["reliability_threshold"] + ")<br>";
+            adcontent += "Local Compatibility " + e.app_domain["local_compatibility"].toFixed(2) + " (" + (e.app_domain["local_compatibility"] > e.app_domain["local_compatibility_threshold"] ? "&gt" : "&lt") + " Local Compatibility Threshold of " + e.app_domain["local_compatibility_threshold"] + ")<br>";
+            adcontent += "</p>";
+            popupContent += adcontent;
+        }
+
         popupContent += "<img src='" + e.image + "' width='" + 20 * nodeRadius + "'><br>"
         if (e.reaction_probability) {
             popupContent += '<b>Probability:</b><br>' + e.reaction_probability.toFixed(3) + '<br>';
         }
 
-
         if (e.scenarios.length > 0) {
             popupContent += '<b>Half-lives and related scenarios:</b><br>'
             for (var s of e.scenarios) {
@@ -233,13 +355,12 @@ function draw(pathway, elem) {
         .enter().append("line")
         // Check if target is pseudo and draw marker only if not pseudo
         .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-        // .on("mouseover", (event, d) => {
-        //     tooltip.style("visibility", "visible")
-        //         .text(`Link: ${d.source.id} → ${d.target.id}`)
-        //         .style("top", `${event.pageY + 5}px`)
-        //         .style("left", `${event.pageX + 5}px`);
-        // })
-        // .on("mouseout", () => tooltip.style("visibility", "hidden"));
+        .attr("marker-end", d => d.target.pseudo ? '' : 'url(#arrow)')
+
+    // add element to links array
+    link.each(function (d) {
+        d.el = this;  // attach the DOM element to the data object
+    });
 
     pop_add(link, "Reaction", edge_popup);
 
@@ -255,20 +376,10 @@ function draw(pathway, elem) {
         .on("click", function (event, d) {
             d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
         })
-        // .on("mouseover", (event, d) => {
-        //     if (d.pseudo) {
-        //         return
-        //     }
-        //     tooltip.style("visibility", "visible")
-        //         .text(`Node: ${d.id} Depth: ${d.depth}`)
-        //         .style("top", `${event.pageY + 5}px`)
-        //         .style("left", `${event.pageX + 5}px`);
-        // })
-        // .on("mouseout", () => tooltip.style("visibility", "hidden"));
 
     // Kreise für die Knoten hinzufügen
     node.append("circle")
-        // make radius "invisible"
+        // make radius "invisible" for pseudo nodes
         .attr("r", d => d.pseudo ? 0.01 : nodeRadius)
         .style("fill", "#e8e8e8");
 
@@ -280,5 +391,10 @@ function draw(pathway, elem) {
         .attr("width", nodeRadius * 2)
         .attr("height", nodeRadius * 2);
 
+    // add element to nodes array
+    node.each(function (d) {
+        d.el = this;  // attach the DOM element to the data object
+    });
+
     pop_add(node, "Compound", node_popup);
 }

templates/actions/collections/model.html

@@ -1,4 +1,4 @@
-{% if meta.can_edit %}
+{% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
     <li>
         <a role="button" data-toggle="modal" data-target="#new_model_modal">
             <span class="glyphicon glyphicon-plus"></span> New Model</a>

templates/actions/collections/scenario.html

@@ -1,6 +1,6 @@
 {% if meta.can_edit %}
     <li>
-        <a role="button" data-toggle="modal" data-target="#new_pathway_modal">
+        <a role="button" data-toggle="modal" data-target="#new_scenario_modal">
             <span class="glyphicon glyphicon-plus"></span> New Scenario</a>
     </li>
 {% endif %}

templates/actions/objects/compound.html

@@ -8,7 +8,17 @@
             <i class="glyphicon glyphicon-plus"></i> Add Structure</a>
     </li>
     <li>
-        <a class="button" data-toggle="modal" data-target="#delete_compound_modal">
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
+    </li>
+{% endif %}
+    <li>
+        <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
+    </li>
+{% if meta.can_edit %}
+    <li>
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
     </li>
 {% endif %}

templates/actions/objects/compound_structure.html

@@ -4,7 +4,11 @@
             <i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a>
     </li>
     <li>
-        <a class="button" data-toggle="modal" data-target="#delete_compound_structure_modal">
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
+    </li>
+    <li>
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a>
     </li>
 {% endif %}

templates/actions/objects/edge.html

@@ -0,0 +1,10 @@
+{% if meta.can_edit %}
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
+    </li>
+    <li>
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
+            <i class="glyphicon glyphicon-trash"></i> Delete Edge</a>
+    </li>
+{% endif %}

templates/actions/objects/group.html

@@ -1,10 +1,10 @@
 {% if meta.can_edit %}
-    <li>
-        <a role="button" data-toggle="modal" data-target="#delete_group_modal">
-            <i class="glyphicon glyphicon-trash"></i> Delete Group</a>
-    </li>
     <li>
     <a role="button" data-toggle="modal" data-target="#edit_group_member_modal">
             <i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#generic_delete_modal">
+            <i class="glyphicon glyphicon-trash"></i> Delete Group</a>
+    </li>
 {% endif %}

templates/actions/objects/model.html

@@ -1,6 +1,6 @@
 {% if meta.can_edit %}
     <li>
-        <a class="button" data-toggle="modal" data-target="#delete_model_modal">
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Model</a>
     </li>
 {% endif %}

templates/actions/objects/node.html

@@ -4,7 +4,11 @@
             <i class="glyphicon glyphicon-edit"></i> Edit Node</a>
     </li>
     <li>
-        <a class="button" data-toggle="modal" data-target="#delete_node_modal">
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
+    </li>
+    <li>
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Node</a>
     </li>
 {% endif %}

templates/actions/objects/package.html

@@ -7,12 +7,16 @@
         <a role="button" data-toggle="modal" data-target="#edit_package_permissions_modal">
             <i class="glyphicon glyphicon-user"></i> Edit Permissions</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#publish_package_modal">
+            <i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_license_modal">
             <i class="glyphicon glyphicon-duplicate"></i> License</a>
     </li>
     <li>
-        <a class="button" data-toggle="modal" data-target="#delete_package_modal">
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Package</a>
     </li>
 {% endif %}

templates/actions/objects/pathway.html

@@ -8,9 +8,24 @@
             <i class="glyphicon glyphicon-plus"></i> Add Reaction</a>
     </li>
     <li role="separator" class="divider"></li>
+{% endif %}
+    <li>
+        <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
+    </li>
+    <li>
+        <a class="button" data-toggle="modal" data-target="#download_pathway_modal">
+            <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway</a>
+    </li>
+{% if meta.can_edit %}
+    <li role="separator" class="divider"></li>
     <li>
         <a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
-            <i class="glyphicon glyphicon-plus"></i> Edit Pathway</a>
+            <i class="glyphicon glyphicon-edit"></i> Edit Pathway</a>
+    </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
     </li>
     {#    <li>#}
     {#        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
@@ -26,7 +41,7 @@
             <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
     </li>
     <li>
-        <a class="button" data-toggle="modal" data-target="#delete_pathway_modal">
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Pathway</a>
     </li>
 {% endif %}

templates/actions/objects/reaction.html

@@ -4,7 +4,17 @@
             <i class="glyphicon glyphicon-edit"></i> Edit Reaction</a>
     </li>
     <li>
-        <a class="button" data-toggle="modal" data-target="#delete_reaction_modal">
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
+    </li>
+{% endif %}
+    <li>
+        <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
+    </li>
+{% if meta.can_edit %}
+    <li>
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
     </li>
 {% endif %}

templates/actions/objects/rule.html

@@ -3,4 +3,18 @@
         <a role="button" data-toggle="modal" data-target="#edit_rule_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Rule</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
+    </li>
+{% endif %}
+    <li>
+        <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
+    </li>
+{% if meta.can_edit %}
+    <li>
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
+            <i class="glyphicon glyphicon-trash"></i> Delete Rule</a>
+    </li>
 {% endif %}

templates/actions/objects/scenario.html

@@ -1,2 +1,14 @@
 {% if meta.can_edit %}
+    <li>
+        <a class="button" data-toggle="modal" data-target="#add_additional_information_modal">
+            <i class="glyphicon glyphicon-trash"></i> Add Additional Information</a>
+    </li>
+    <li>
+        <a class="button" data-toggle="modal" data-target="#update_scenario_additional_information_modal">
+            <i class="glyphicon glyphicon-trash"></i> Set Additional Information</a>
+    </li>
+    <li>
+        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
+            <i class="glyphicon glyphicon-trash"></i> Delete Scenario</a>
+    </li>
 {% endif %}

templates/actions/objects/user.html

@@ -16,7 +16,7 @@
 {#            <i class="glyphicon glyphicon-console"></i> Manage API Token</a>#}
 {#    </li>#}
     <li>
-        <a role="button" data-toggle="modal" data-target="#delete_user_modal">
+        <a role="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Account</a>
     </li>
 {% endif %}

templates/collections/objects_list.html

@@ -2,14 +2,8 @@
 {% load static %}
 {% block content %}
 
-{% if reviewed_objects.count > 50 or unreviewed_objects.count > 50  %}
     {% if object_type != 'package' %}
-<div id="load-remaining-button-div">
-    <button class="btn btn-secondary btn-lg btn-block" type="button" id="load-remaining">Load all {% if reviewed_objects.count > 0 %} {{ reviewed_objects.count }} {% else %} {{ unreviewed_objects.count }} {% endif %} {{ object_type }}s
-    </button>
-    <p></p>
-    <div id="load-all-loading"></div>
-    <p></p>
+        <div>
             <div id="load-all-error" style="display: none;">
                 <div class="alert alert-danger" role="alert">
                     <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
@@ -18,11 +12,11 @@
                 </div>
             </div>
 
-    <input type="text" id="object-search" class="form-control" placeholder="Search by name" style="display: none;">
+            <input type="text" id="object-search" class="form-control" placeholder="Search by name"
+                   style="display: none;">
             <p></p>
         </div>
     {% endif %}
-{% endif %}
 
 {% block action_modals %}
 {% if object_type == 'package' %}
@@ -248,21 +242,34 @@
         </ul>
         {% endif %}
     </div>
+    <style>
+        .spinner-widget {
+            position: fixed; /* stays in place on scroll */
+            bottom: 20px; /* distance from bottom */
+            right: 20px; /* distance from right */
+            z-index: 9999; /* above most elements */
+            width: 60px; /* adjust to gif size */
+            height: 60px;
+        }
+
+        .spinner-widget img {
+            width: 100%;
+            height: auto;
+        }
+    </style>
+    {% if object_type != 'package' %}
+        <div id="load-all-loading" class="spinner-widget">
+            <img id="loading-gif" src="{% static '/images/wait.gif' %}" alt="Loading...">
+        </div>
+    {% endif %}
 </div>
     <script>
         $(function () {
 
-            $('#modal-form-delete-submit').on('click', function (e) {
-                e.preventDefault();
-                $('#modal-form-delete').submit();
-            });
-
             $('#object-search').show();
 
-            if ($('#load-remaining').length) {
-                $('#load-remaining').on('click', function () {
-
-                    makeLoadingGif("#load-all-loading", "{% static '/images/wait.gif' %}");
+            {% if object_type != 'package' %}
+                setTimeout(function () {
                     $('#load-all-error').hide();
 
                     $.getJSON('?all=true', function (resp) {
@@ -272,20 +279,26 @@
                         for (o in resp.objects) {
                             obj = resp.objects[o];
                             if (obj.reviewed) {
-                                $('#ReviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + '</a>');
+                                $('#ReviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + ' <span class="glyphicon glyphicon-star" aria-hidden="true" style="float:right" data-toggle="tooltip" data-placement="top" title="" data-original-title="Reviewed"></span></a>');
                             } else {
                                 $('#UnreviewedContent').append('<a class="list-group-item" href="' + obj.url + '">' + obj.name + '</a>');
                             }
                         }
 
-                        $('#load-all-loading').empty();
+                        $('#load-all-loading').hide();
                         $('#load-remaining').hide();
                     }).fail(function (resp) {
-                        $('#load-all-loading').empty();
+                        $('#load-all-loading').hide();
                         $('#load-all-error').show();
                     });
+
+                }, 2500);
+            {% endif %}
+
+            $('#modal-form-delete-submit').on('click', function (e) {
+                e.preventDefault();
+                $('#modal-form-delete').submit();
             });
-            }
 
             $('#object-search').on('keyup', function () {
                 let query = $(this).val().toLowerCase();

templates/framework.html

@@ -3,7 +3,12 @@
 {% load static %}
 <head>
     <title>{{ title }}</title>
-
+    <style>
+        html, body {
+            height: 100%; /* ensure body fills viewport */
+            overflow-x: hidden; /* prevent horizontal scroll */
+        }
+    </style>
     {# TODO use bundles from bootstrap 3.3.7 #}
     <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
     <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
@@ -51,7 +56,7 @@
             (function () {
                 var u = "//matomo.envipath.com/";
                 _paq.push(['setTrackerUrl', u + 'matomo.php']);
-                _paq.push(['setSiteId', '7']);
+                _paq.push(['setSiteId', '10']);
                 var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
                 g.async = true;
                 g.src = u + 'matomo.js';
@@ -83,21 +88,26 @@
         <!-- Collect the nav links, forms, and other content for toggling -->
         <div class="collapse navbar-collapse collapse-framework navbar-collapse-framework" id="navbarCollapse">
             <ul class="nav navbar-nav navbar-nav-framework">
-                <li class="dropdown">
-                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>
-                    <ul role="menu" class="dropdown-menu">
                 <li>
                     <a class="button" data-toggle="modal" data-target="#predict_modal">
-                                <i class="	glyphicon glyphicon-tag"></i> Predict Pathway
+                        Predict Pathway
                     </a>
                 </li>
-                        <li>
-                            <a class="button" data-toggle="modal" data-target="#batch_predict_modal">
-                                <i class="	glyphicon glyphicon-tags"></i> Batch Prediction
-                            </a>
-                        </li>
-                    </ul>
-                </li>
+{#                <li class="dropdown">#}
+{#                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
+{#                    <ul role="menu" class="dropdown-menu">#}
+{#                        <li>#}
+{#                            <a class="button" data-toggle="modal" data-target="#predict_modal">#}
+{#                                <i class="	glyphicon glyphicon-tag"></i> Predict Pathway#}
+{#                            </a>#}
+{#                        </li>#}
+{#                        <li>#}
+{#                            <a class="button" data-toggle="modal" data-target="#batch_predict_modal">#}
+{#                                <i class="	glyphicon glyphicon-tags"></i> Batch Prediction#}
+{#                            </a>#}
+{#                        </li>#}
+{#                    </ul>#}
+{#                </li>#}
                 <li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li>
                 <li><a href="{{ meta.server_url }}/search" id="searchLink">Search</a></li>
                 <li><a href="{{ meta.server_url }}/model" id="modelLink">Modelling</a></li>
@@ -119,7 +129,7 @@
             </ul>
 
             <ul class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework">
-                {#                <li><a href="{{ meta.server_url }}/search" id="searchLink">Search</a></li>#}
+                <li><a href="https://community.envipath.org/" id="communityLink">Community</a></li>
                 <li class="dropdown">
                     <a data-toggle="dropdown" class="dropdown-toggle" href="#">Info <b class="caret"></b></a>
                     <ul role="menu" class="dropdown-menu">
@@ -192,6 +202,23 @@
     {% endif %}
     {% block content %}
     {% endblock content %}
+    {% if meta.url_contains_package and meta.current_package.license %}
+        <p></p>
+        <div class="panel-group" id="license_accordion">
+            <div class="panel panel-default list-group-item" style="background-color:#f5f5f5">
+                <div class="panel-title">
+                    <a data-toggle="collapse" data-parent="#licence_accordion" href="#license">License</a>
+                </div>
+            </div>
+            <div id="license" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    <a target="_blank" href="{{ meta.current_package.license.link }}">
+                        <img src="{{ meta.current_package.license.image_link }}">
+                    </a>
+                </div>
+            </div>
+        </div>
+    {% endif %}
 </div>
 
 <!-- FOOTER -->

templates/index/index.html

@@ -143,6 +143,14 @@
         }
 
         $(function () {
+
+            $('#index-form').on("keydown", function (e) {
+                if (e.key === "Enter") {
+                    e.preventDefault();
+                    goButtonClicked();
+                }
+            });
+
             // Code that should be executed once DOM is ready goes here
             $('#dropdown-predict').on('click', actionDropdownClicked);
             $('#dropdown-search').on('click', actionDropdownClicked);

templates/login.html

@@ -30,7 +30,7 @@
 
         .center-button {
             position: absolute;
-            top: 50%;
+            top: 70%;
             left: 50%;
             transform: translate(-50%, -50%);
             z-index: 1;
@@ -38,7 +38,7 @@
 
         .center-message {
             position: absolute;
-            top: 40%;
+            top: 35%;
             left: 50%;
             transform: translate(-50%, -50%);
             z-index: 1;
@@ -124,6 +124,7 @@
                                         </button>
                                     </div>
                                 </div>
+                                <input type="hidden" name="next" value="{{ next }}" />
                             </fieldset>
                         </form>
                     </div>

templates/modals/cite_modal.html

@@ -3,13 +3,25 @@
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-                <h4>How to cite enviPath</h4>
+                <h3>How to cite enviPath</h3>
             </div>
             <div class="modal-body">
-                <p>
-                    enviPath–The environmental contaminant biotransformation pathway resource. J Wicker, T Lorsbach, M
-                    Gütlein, E Schmid, D Latino, S Kramer, K Fenner. Nucleic Acids Research, gkv1229
-                </p>
+                <ol class="list-group list-group-numbered">
+                    <li class="list-group-item">
+                        Hafner, J., Lorsbach, T., Schmidt, S. <em>et al.</em>
+                        <cite>Advancements in biotransformation pathway prediction: enhancements, datasets, and novel
+                            functionalities in enviPath.</cite>
+                        <a href="https://doi.org/10.1186/s13321-024-00881-6" target="_blank">J Cheminform 16, 93
+                            (2024)</a>
+                    </li>
+                    <li class="list-group-item">
+                        Wicker, J., Lorsbach, T., Gütlein, M., Schmid, E., Latino, D., Kramer, S., Fenner, K.
+                        <cite>enviPath - The environmental contaminant biotransformation pathway resource</cite>
+                        <a href="https://doi.org/10.1093/nar/gkv1229" target="_blank">
+                            Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D502-D508
+                        </a>
+                    </li>
+                </ol>
             </div>
             <div class="modal-footer">
                 <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>

templates/modals/collections/new_model_modal.html

@@ -16,14 +16,14 @@
                     <div class="jumbotron">Create a new Model to
                         limit the number of degradation products in the
                         prediction. You just need to set a name and the packages
-                        you want the object to be based on. If you want to use the
-                        default options suggested by us, simply click Submit,
-                        otherwise click Advanced Options.
+                        you want the object to be based on. There are multiple types of models available.
+                        For additional information have a look at our
+                        <a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki &gt;&gt;</a>
                     </div>
-                    <label for="name">Name</label>
-                    <input id="name" name="model-name" class="form-control" placeholder="Name"/>
-                    <label for="description">Description</label>
-                    <input id="description" name="model-description" class="form-control"
+                    <label for="model-name">Name</label>
+                    <input id="model-name" name="model-name" class="form-control" placeholder="Name"/>
+                    <label for="model-description">Description</label>
+                    <input id="model-description" name="model-description" class="form-control"
                            placeholder="Description"/>
                     <label for="model-type">Model Type</label>
                     <select id="model-type" name="model-type" class="form-control" data-width='100%'>
@@ -35,7 +35,7 @@
                     <!-- ML Based Form-->
                     <div id="ml-relative-reasoning-specific-form">
                         <!-- Rule Packages -->
-                        <label>Rule Packages</label><br>
+                        <label for="ml-relative-reasoning-rule-packages">Rule Packages</label>
                         <select id="ml-relative-reasoning-rule-packages" name="ml-relative-reasoning-rule-packages"
                                 data-actions-box='true' class="form-control" multiple data-width='100%'>
                             <option disabled>Reviewed Packages</option>
@@ -53,7 +53,7 @@
                             {% endfor %}
                         </select>
                         <!-- Data Packages -->
-                        <label>Data Packages</label><br>
+                        <label for="ml-relative-reasoning-data-packages" >Data Packages</label>
                         <select id="ml-relative-reasoning-data-packages" name="ml-relative-reasoning-data-packages"
                                 data-actions-box='true' class="form-control" multiple data-width='100%'>
                             <option disabled>Reviewed Packages</option>
@@ -77,22 +77,24 @@
                                 class="form-control">
                             <option value="MACCS" selected>MACCS Fingerprinter</option>
                         </select>
-                        {% if 'plugins' in meta.enabled_features %}
+                        {% if meta.enabled_features.PLUGINS and additional_descriptors %}
                         <!-- Property Plugins go here -->
-                        <label for="ml-relative-reasoning-additional-fingerprinter">Fingerprinter</label>
-                        <select id="ml-relative-reasoning-additional-fingerprinter"
-                                name="ml-relative-reasoning-additional-fingerprinter"
-                                class="form-control">
+                        <label for="ml-relative-reasoning-additional-fingerprinter">Additional Fingerprinter / Descriptors</label>
+                        <select id="ml-relative-reasoning-additional-fingerprinter" name="ml-relative-reasoning-additional-fingerprinter" class="form-control">
+                            <option disabled selected>Select Additional Fingerprinter / Descriptor</option>
+                        {% for k, v in additional_descriptors.items %}
+                            <option value="{{ v }}">{{ k }}</option>
+                        {% endfor %}
                         </select>
                         {% endif %}
+
                         <label for="ml-relative-reasoning-threshold">Threshold</label>
-                        <input type="number" min="0" , max="1" step="0.05" value="0.5"
+                        <input type="number" min="0" max="1" step="0.05" value="0.5"
                                id="ml-relative-reasoning-threshold"
                                name="ml-relative-reasoning-threshold" class="form-control">
 
                         <!-- Evaluation -->
-
-                        <label>Evaluation Packages</label><br>
+                        <label for="ml-relative-reasoning-evaluation-packages">Evaluation Packages</label>
                         <select id="ml-relative-reasoning-evaluation-packages" name="ml-relative-reasoning-evaluation-packages"
                                 data-actions-box='true' class="form-control" multiple data-width='100%'>
                             <option disabled>Reviewed Packages</option>
@@ -110,6 +112,26 @@
                             {% endfor %}
                         </select>
 
+                    {% if meta.enabled_features.APPLICABILITY_DOMAIN %}
+                        <!-- Build AD? -->
+                        <div class="checkbox">
+                            <label>
+                                <input type="checkbox" id="build-app-domain" name="build-app-domain">Also build an Applicability Domain?
+                            </label>
+                        </div>
+                        <!-- Num Neighbors -->
+                        <label for="num-neighbors">Number of Neighbors</label>
+                        <input id="num-neighbors" name="num-neighbors" type="number" class="form-control" value="5"
+                               step="1" min="0" max="10">
+                        <!-- Local Compatibility -->
+                        <label for="local-compatibility-threshold">Local Compatibility Threshold</label>
+                        <input id="local-compatibility-threshold" name="local-compatibility-threshold" type="number"
+                               class="form-control" value="0.5" step="0.01" min="0" max="1">
+                        <!-- Reliability -->
+                        <label for="reliability-threshold">Reliability Threshold</label>
+                        <input id="reliability-threshold" name="reliability-threshold" type="number"
+                               class="form-control" value="0.5" step="0.01" min="0" max="1">
+                    {% endif %}
                     </div>
                     <!-- Rule Based Based Form-->
                     <div id="rule-based-relative-reasoning-specific-form">
@@ -118,47 +140,9 @@
                     <!-- EnviFormer-->
                     <div id="enviformer-specific-form">
                         <label for="enviformer-threshold">Threshold</label>
-                        <input type="number" min="0" , max="1" step="0.05" value="0.5" id="enviformer-threshold"
+                        <input type="number" min="0" max="1" step="0.05" value="0.5" id="enviformer-threshold"
                                name="enviformer-threshold" class="form-control">
                     </div>
-
-                    {% if 'applicability_domain' in enabled_features %}
-                    <div class="modal-body hide" data-step="3" data-title="Advanced Options II">
-                        <div class="jumbotron">Selection of parameter values for the Applicability Domain process.
-                            Number of Neighbours refers to a requirement on the minimum number of compounds from the
-                            training
-                            dataset that has at least one triggered transformation rule that is common with the compound
-                            being
-                            analyzed.
-                            Reliability Threshold is a requirement on the average tanimoto distance to the set number of
-                            "nearest neighbours" (Number of neighbours with the smallest tanimoto distances).
-                            Local Compatibility Threshold is a requirement on the average F1 score determined from the
-                            number of
-                            nearest neighbours, using their respective precision and recall values computed from the
-                            agreement
-                            between their observed and triggered rules.
-                            You can learn more about it in our wiki!
-                        </div>
-                        <!-- Use AD? -->
-                        <div class="checkbox">
-                            <label>
-                                <input type="checkbox" id="buildAD" name="buildAD">Also build an Applicability Domain?
-                            </label>
-                        </div>
-                        <!-- Num Neighbours -->
-                        <label for="adK">Number of Neighbours</label>
-                        <input id="adK" name="adK" type="number" class="form-control" value="5" step="1" min="0"
-                               max="10">
-                        <!-- F1 Threshold -->
-                        <label for="localCompatibilityThreshold">Local Compatibility Threshold</label>
-                        <input id="localCompatibilityThreshold" name="localCompatibilityThreshold" type="number"
-                               class="form-control" value="0.5" step="0.01" min="0" max="1">
-                        <!-- Percentile Threshold -->
-                        <label for="reliabilityThreshold">Reliability Threshold</label>
-                        <input id="reliabilityThreshold" name="reliabilityThreshold" type="number" class="form-control"
-                               value="0.5" step="0.01" min="0" max="1">
-                    </div>
-                    {% endif %}
                 </form>
             </div>
             <div class="modal-footer">
@@ -179,6 +163,9 @@ $(function() {
     $("#ml-relative-reasoning-rule-packages").selectpicker();
     $("#ml-relative-reasoning-data-packages").selectpicker();
     $("#ml-relative-reasoning-evaluation-packages").selectpicker();
+    if ($('#ml-relative-reasoning-additional-fingerprinter').length > 0) {
+        $("#ml-relative-reasoning-additional-fingerprinter").selectpicker();
+    }
 
     // On change hide all and show only selected
     $("#model-type").change(function() {

templates/modals/collections/new_scenario_modal.html

@@ -1,115 +1,95 @@
-<div class="modal fade" tabindex="-1" id="new_scenario_modal" role="dialog" aria-labelledby="newScenGenMod"
+<div class="modal fade" tabindex="-1" id="new_scenario_modal" role="dialog" aria-labelledby="new_scenario_modal"
      aria-hidden="true">
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
                 <button type="button" class="close" data-dismiss="modal">
-                    <span aria-hidden="true">&times;</span> <span
-                        class="sr-only">Close</span>
+                    <span aria-hidden="true">&times;</span>
+                    <span class="sr-only">Close</span>
                 </button>
-                <h4 class="js-title-step"></h4>
+                <h4 class="modal-title">New Scenario</h4>
             </div>
-            <form id="base-scenario-form" accept-charset="UTF-8" action="" data-remote="true" method="POST">
-                <div class="modal-body hide" data-step="1" data-title="New Scenario - Step 1">
-                    <div class="jumbotron">Please enter name, description,
-                        and date of scenario. Date should be associated to the
-                        data, not the current date. For example, this could
-                        reflect the publishing date of a study. You can leave
-                        all fields but the name empty and fill them in
-                        later.
+            <div class="modal-body">
+                <form id="new_scenario_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/scenario"
+                      data-remote="true" method="post">
+                    {% csrf_token %}
+                    <div class="jumbotron">Please enter name, description, and date of scenario. Date should be
+                        associated to the data, not the current date. For example, this could reflect the publishing
+                        date of a study. You can leave all fields but the name empty and fill them in later.
+                        <a target="_blank" href="https://wiki.envipath.org/index.php/scenario" role="button">wiki
+                            &gt;&gt;</a>
                     </div>
-                    <label for="name">Name</label>
-                    <input id="name" name="studyname" placeholder="Name" class="form-control"/>
-                    <label for="name">Description</label>
-                    <input id="description" name="studydescription" placeholder="Description" class="form-control"/>
+                    <label for="scenario-name">Name</label>
+                    <input id="scenario-name" name="scenario-name" class="form-control" placeholder="Name"/>
+                    <label for="scenario-description">Description</label>
+                    <input id="scenario-description" name="scenario-description" class="form-control"
+                           placeholder="Description"/>
                     <label id="dateField" for="dateYear">Date</label>
                     <table>
                         <tr>
                             <th>
-                                <input type="number" id="dateYear" name="dateYear" class="form-control" placeholder="YYYY">
+                                <input type="number" id="dateYear" name="scenario-date-year" class="form-control"
+                                       placeholder="YYYY">
                             </th>
                             <th>
-                                <input type="number" id="dateMonth" name="dateMonth" min="1" max="12"
+                                <input type="number" id="dateMonth" name="scenario-date-month" min="1" max="12"
                                        class="form-control" placeholder="MM" align="">
                             </th>
                             <th>
-                                <input type="number" id="dateDay" name="dateDay" min="1" max="31" class="form-control"
+                                <input type="number" id="dateDay" name="scenario-date-day" min="1" max="31" class="form-control"
                                        placeholder="DD">
                             </th>
                         </tr>
                     </table>
+                    <label for="scenario-type">Scenario Type</label>
+                    <select id="scenario-type" name="scenario-type" class="form-control" data-width='100%'>
+                        <option value="empty" selected>Empty Scenario</option>
+                        {% for k, v in scenario_types.items %}
+                            <option value="{{ v.name }}">{{ k }}</option>
+                        {% endfor %}
+                    </select>
+
+                    {% for type in scenario_types.values %}
+                        <div id="{{ type.name }}-specific-inputs">
+                            {% for widget in type.widgets %}
+                                {{ widget|safe }}
+                            {% endfor %}
                         </div>
-                <div class="modal-body hide" data-step="2" data-title="New Scenario - Step 2">
-                    <div class="jumbotron">
-                        Do you want to create an empty scenario and fill it
-                        with your own set of attributes, or fill in a
-                        pre-defined set of attributes for soil, sludge or sediment
-                        data?
-                    </div>
-                    <div class="radio">
-                        <label>
-                            <input type="radio" name="type" id="radioEmpty" checked>Empty Scenario
-                        </label>
-                    </div>
-                    <div class="radio">
-                        <label>
-                            <input type="radio" name="type" id="radioSoil" value="soil" >Soil Data
-                        </label>
-                    </div>
-                    <div class="radio">
-                        <label>
-                            <input type="radio" name="type" id="radioSludge" value="sludge">Sludge Data
-                        </label>
-                    </div>
-                    <div class="radio">
-                        <label>
-                            <input type="radio" name="type" id="radioSediment" value="sediment">Water-Sediment System Data
-                        </label>
-                    </div>
-                </div>
-                <div class="modal-body hide" data-step="3" data-title="New Scenario - Step 3">
-                    <div class="jumbotron" id="finaljumbo">
-                        All done! Click Submit!
-                    </div>
-                    <div style="float: left"><button
-                            id="addColumnButton" type="button"
-                            class="btn btn-default">Add
-                        another Scenario
-                    </button></div>
-                    <input type="hidden" name="fullScenario" value="true"/>
-                    {% include "tables/scenario.html" %}
-                </div>
+                    {% endfor %}
+
                 </form>
+            </div>
             <div class="modal-footer">
-                <button type="button" class="btn btn-default js-btn-step pull-left" data-orientation="cancel" data-dismiss="modal"></button>
-                <button type="button" class="btn btn-default js-btn-step" data-orientation="previous"></button>
-                <button type="button" class="btn btn-default js-btn-step"
-                        data-orientation="next" id="nextbutton"></button>
+                <a id="new_scenario_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
             </div>
         </div>
     </div>
 </div>
 
-
-
-<p></p>
-<div id="scenariocontent"></div>
-
-<!--Template index -->
-<script language="javascript">
+<script>
     $(function () {
-
-    // Hide additional columns per default
-    $('.col-2').hide();
-    $('.col-3').hide();
-
-    //TODO just to see modal
-    $('#new_scenario_modal').modalSteps({
-        btnCancelHtml: 'Cancel',
-        btnPreviousHtml: 'Previous',
-        btnNextHtml: 'Next',
-        btnLastStepHtml: 'Submit',
-        disableNextButton: false,
+        // Initially hide all "specific" forms
+        $("div[id$='-specific-inputs']").each(function () {
+            $(this).hide();
         });
+
+        // On change hide all and show only selected
+        $("#scenario-type").change(function () {
+            $("div[id$='-specific-inputs']").each(function () {
+                $(this).hide();
             });
+            val = $('option:selected', this).val();
+            $("#" + val + "-specific-inputs").show();
+        });
+
+        $('#new_scenario_modal_form_submit').on('click', function (e) {
+            e.preventDefault();
+            $('#new_scenario_form').submit();
+        });
+
+    });
+
+
 </script>
+

templates/modals/objects/add_additional_information_modal.html

@@ -0,0 +1,61 @@
+{% load static %}
+<!-- Add Additional Information-->
+<div id="add_additional_information_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+                <h3 class="modal-title">Add Additional Information</h3>
+            </div>
+            <div class="modal-body">
+                <select id="select-additional-information-type" data-actions-box='true' class="form-control" data-width='100%'>
+                    <option selected disabled>Select the type to add</option>
+                    {% for add_inf in available_additional_information %}
+                        <option value="{{ add_inf.name }}">{{ add_inf.display_name }}</option>
+                    {% endfor %}
+                </select>
+                {% for add_inf in available_additional_information %}
+                    <div class="aiform {{ add_inf.name }}" style="display: none;">
+                        <form id="add_{{ add_inf.name }}_add-additional-information-modal-form" accept-charset="UTF-8"
+                              action="" data-remote="true" method="post">
+                            {% csrf_token %}
+                            {{ add_inf.widget|safe }}
+                            <input type="hidden" name="hidden" value="add-additional-information">
+                        </form>
+                    </div>
+                {% endfor %}
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="add-additional-information-modal-submit">Add
+                </button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+$(function() {
+
+    $('#select-additional-information-type').change(function(e){
+        var selectedType = $("#select-additional-information-type :selected").val();
+        $('.aiform').hide();
+        $('.' + selectedType).show();
+    })
+
+    $('#add-additional-information-modal-submit').click(function(e){
+        e.preventDefault();
+
+        var selectedType = $("#select-additional-information-type :selected").val();
+        console.log(selectedType);
+        if (selectedType !== null && selectedType !== undefined && selectedType !== '') {
+            $('.' + selectedType + ' >form').submit();
+        }
+
+    });
+
+});
+
+
+</script>

templates/modals/objects/delete_group_modal.html

@@ -1,38 +0,0 @@
-{% load static %}
-<!-- Delete Group -->
-<div id="delete_group_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h3 class="modal-title">Delete Group</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
-                </button>
-            </div>
-            <div class="modal-body">
-                <div class="alert alert-danger">
-                    Clicking "Delete" will <strong>permanently</strong> delete the Group.
-                    This action can't be undone!
-                </div>
-                <form id="delete-group-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-                    {% csrf_token %}
-                    <input type="hidden" name="hidden" value="delete-group">
-                </form>
-            </div>
-            <div class="modal-footer">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-danger" id="delete-group-modal-submit">Delete</button>
-            </div>
-        </div>
-    </div>
-</div>
-<script>
-    $(function() {
-
-        $('#delete-group-modal-submit').click(function(e){
-            e.preventDefault();
-            $('#delete-group-modal-form').submit();
-        });
-
-    })
-</script>

templates/modals/objects/delete_model_modal.html

@@ -1,35 +0,0 @@
-{% load static %}
-<!-- Delete Model -->
-<div id="delete_model_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h3 class="modal-title">Delete Model</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
-                </button>
-            </div>
-            <div class="modal-body">
-                Deletes the Model.
-                <form id="delete-model-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-                    {% csrf_token %}
-                    <input type="hidden" id="hidden" name="hidden" value="delete-model"/>
-                </form>
-            </div>
-            <div class="modal-footer">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="delete-model-modal-submit">Delete</button>
-            </div>
-        </div>
-    </div>
-</div>
-<script>
-    $(function () {
-
-        $('#delete-model-modal-submit').click(function (e) {
-            e.preventDefault();
-            $('#delete-model-modal-form').submit();
-        });
-
-    })
-</script>

templates/modals/objects/delete_node_modal.html

@@ -1,35 +0,0 @@
-{% load static %}
-<!-- Delete Node -->
-<div id="delete_node_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h3 class="modal-title">Delete Node</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
-                </button>
-            </div>
-            <div class="modal-body">
-                Deletes the Node as well as ingoing and outgoing edges.
-                <form id="delete-node-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-                    {% csrf_token %}
-                    <input type="hidden" id="hidden" name="hidden" value="delete-node"/>
-                </form>
-            </div>
-            <div class="modal-footer">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="delete-node-modal-submit">Delete</button>
-            </div>
-        </div>
-    </div>
-</div>
-<script>
-    $(function () {
-
-        $('#delete-node-modal-submit').click(function (e) {
-            e.preventDefault();
-            $('#delete-node-modal-form').submit();
-        });
-
-    })
-</script>

templates/modals/objects/delete_package_modal.html

@@ -1,36 +0,0 @@
-{% load static %}
-<!-- Delete Package -->
-<div id="delete_package_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h3 class="modal-title">Delete Package</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
-                </button>
-            </div>
-            <div class="modal-body">
-                  Deleting a Package deletes the very Package
-                  as well as all Objects stored in the Package.
-                <form id="delete-package-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-                    {% csrf_token %}
-                    <input type="hidden" id="hidden" name="hidden" value="delete-package"/>
-                </form>
-            </div>
-            <div class="modal-footer">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="delete-package-modal-submit">Delete</button>
-            </div>
-        </div>
-    </div>
-</div>
-<script>
-$(function() {
-
-    $('#delete-package-modal-submit').click(function(e){
-        e.preventDefault();
-        $('#delete-package-modal-form').submit();
-    });
-
-})
-</script>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -22,7 +22,7 @@
                             <option value="{{ e.url }}">{{ e.edge_label.name }}</option>
                         {% endfor %}
                     </select>
-                    <input type="hidden" id="hidden" name="hidden" value="delete-edge"/>
+                    <input type="hidden" id="hidden" name="hidden" value="delete"/>
                 </form>
                 <p></p>
                 <div id="delete_pathway_edge_image"></div>

templates/modals/objects/delete_pathway_node_modal.html

@@ -22,7 +22,7 @@
                             <option value="{{ n.url }}">{{ n.default_node_label.name }}</option>
                         {% endfor %}
                     </select>
-                    <input type="hidden" id="hidden" name="hidden" value="delete-node"/>
+                    <input type="hidden" id="hidden" name="hidden" value="delete"/>
                 </form>
                 <p></p>
                 <div id="delete_pathway_node_image"></div>

templates/modals/objects/delete_reaction_modal.html

@@ -1,35 +0,0 @@
-{% load static %}
-<!-- Delete Reaction -->
-<div id="delete_reaction_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h3 class="modal-title">Delete Reaction</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
-                </button>
-            </div>
-            <div class="modal-body">
-                Deletes the Reaction.
-                <form id="delete-reaction-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-                    {% csrf_token %}
-                    <input type="hidden" id="hidden" name="hidden" value="delete-reaction"/>
-                </form>
-            </div>
-            <div class="modal-footer">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="delete-reaction-modal-submit">Delete</button>
-            </div>
-        </div>
-    </div>
-</div>
-<script>
-    $(function () {
-
-        $('#delete-reaction-modal-submit').click(function (e) {
-            e.preventDefault();
-            $('#delete-reaction-modal-form').submit();
-        });
-
-    })
-</script>

templates/modals/objects/delete_user_modal.html

@@ -1,38 +0,0 @@
-{% load static %}
-<!-- Delete User -->
-<div id="delete_user_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
-        <div class="modal-content">
-            <div class="modal-header">
-                <h3 class="modal-title">Delete User</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-                    <span aria-hidden="true">&times;</span>
-                </button>
-            </div>
-            <div class="modal-body">
-                <div class="alert alert-danger">
-                    Clicking "Delete" will <strong>permanently</strong> delete the User and associated data.
-                    This action can't be undone!
-                </div>
-                <form id="delete-user-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-                    {% csrf_token %}
-                    <input type="hidden" name="hidden" value="delete-user">
-                </form>
-            </div>
-            <div class="modal-footer">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-danger" id="delete-user-modal-submit">Delete</button>
-            </div>
-        </div>
-    </div>
-</div>
-<script>
-    $(function() {
-
-        $('#delete-user-modal-submit').click(function(e){
-            e.preventDefault();
-            $('#delete-user-modal-form').submit();
-        });
-
-    })
-</script>

templates/modals/objects/download_pathway_modal.html

@@ -1,24 +1,24 @@
 {% load static %}
-<!-- Delete Pathway -->
-<div id="delete_pathway_modal" class="modal" tabindex="-1">
+<!-- Download Pathway -->
+<div id="download_pathway_modal" class="modal" tabindex="-1">
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-                <h3 class="modal-title">Delete Pathway</h3>
+                <h3 class="modal-title">Download Pathway</h3>
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close">
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-                Deletes the Pathway together with all Nodes and Edges.
-                <form id="delete-pathway-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-                    {% csrf_token %}
-                    <input type="hidden" id="hidden" name="hidden" value="delete-pathway"/>
+                By clicking on Download the Pathway will be converted into a CSV and directly downloaded.
+                <form id="download-pathway-modal-form" accept-charset="UTF-8" action="{{ pathway.url }}"
+                      data-remote="true" method="GET">
+                    <input type="hidden" name="download" value="true"/>
                 </form>
             </div>
             <div class="modal-footer">
                 <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="delete-pathway-modal-submit">Delete</button>
+                <button type="button" class="btn btn-primary" id="download-pathway-modal-submit">Download</button>
             </div>
         </div>
     </div>
@@ -26,9 +26,10 @@
 <script>
     $(function () {
 
-        $('#delete-pathway-modal-submit').click(function (e) {
+        $('#download-pathway-modal-submit').click(function (e) {
             e.preventDefault();
-            $('#delete-pathway-modal-form').submit();
+            $('#download-pathway-modal-form').submit();
+            $('#download_pathway_modal').modal('hide');
         });
 
     })

templates/modals/objects/edit_compound_modal.html

@@ -27,7 +27,7 @@
             </div>
             <div class="modal-footer">
                 <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="edit-compound-modal-submit">Create</button>
+                <button type="button" class="btn btn-primary" id="edit-compound-modal-submit">Update</button>
             </div>
         </div>
     </div>

templates/modals/objects/generic_copy_object_modal.html

@@ -0,0 +1,61 @@
+{% load static %}
+<!-- Copy Object -->
+<div id="generic_copy_object_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3 class="modal-title">Copy {{ object_type|capfirst }}</h3>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                <form id="generic-copy-object-modal-form" accept-charset="UTF-8" data-remote="true" method="post">
+                    {% csrf_token %}
+                    <label for="target-package">Select the Target Package you want to copy this {{ object_type }}
+                        into</label>
+                    <select id="target-package" name="target-package" data-actions-box='true' class="form-control"
+                            data-width='100%'>
+                        <option disabled selected>Select Target Package</option>
+                        {% for p in meta.writeable_packages %}
+                            <option value="{{ p.url }}">{{ p.name }}</option>`
+                        {% endfor %}
+                    </select>
+                    <input type="hidden" name="hidden" value="copy">
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="generic-copy-object-modal-form-submit">
+                    Copy
+                </button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+
+        $('#generic-copy-object-modal-form-submit').click(function (e) {
+            e.preventDefault();
+
+            const packageUrl = $('#target-package').find(":selected").val();
+
+            if (packageUrl === 'Select Target Package' || packageUrl === '' || packageUrl === null || packageUrl === undefined) {
+                return;
+            }
+            const formData = {
+                hidden: 'copy',
+                object_to_copy: '{{ current_object.url }}',
+            }
+
+            $.post(packageUrl, formData, function (response) {
+                if (response.success) {
+                    window.location.href = response.success;
+                }
+            });
+
+        });
+
+    })
+</script>

templates/modals/objects/generic_delete_modal.html

@@ -0,0 +1,42 @@
+{% load static %}
+<!-- Delete Object -->
+<div id="generic_delete_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3 class="modal-title">Delete {{ object_type|capfirst }}</h3>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                {% if object_type == 'user' %}
+                    Clicking "Delete" will <strong>permanently</strong> delete the User and associated data.
+                    This action can't be undone!
+                {% else %}
+                    Deletes the {{ object_type|capfirst }}. Related objects that depend on this {{ object_type|capfirst }}
+                    will be deleted as well.
+                {% endif %}
+                <form id="generic-delete-modal-form" accept-charset="UTF-8" action="{{ current_object.url }}"
+                      data-remote="true" method="post">
+                    {% csrf_token %}
+                    <input type="hidden" id="hidden" name="hidden" value="delete"/>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="generic-delete-modal-form-submit">Delete</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+
+        $('#generic-delete-modal-form-submit').click(function (e) {
+            e.preventDefault();
+            $('#generic-delete-modal-form').submit();
+        });
+
+    })
+</script>

templates/modals/objects/generic_set_scenario_modal.html

@@ -0,0 +1,72 @@
+{% load static %}
+<div class="modal fade bs-modal-lg" id="set_scenario_modal" tabindex="-1" aria-labelledby="set_scenario_modal"
+     aria-modal="true" role="dialog">
+    <div class="modal-dialog modal-lg">
+        <div class="modal-content">
+            <div class="modal-header">
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">×</span>
+                </button>
+                <h4 class="modal-title">Set Scenarios for {{ current_object.name }}</h4>
+            </div>
+            <div class="modal-body">
+                <div id="loading_scenario_div" class="text-center"></div>
+                <form id="set_scenario_modal_form" accept-charset="UTF-8" action="{{ current_object.url }}"
+                      data-remote="true" method="post">
+                    {% csrf_token %}
+                    <label for="scenario-select">Scenarios</label>
+                    <select id="scenario-select" name="selected-scenarios" data-actions-box='true' class="form-control"
+                            multiple data-width='100%'>
+                        <option disabled>Select Scenarios</option>
+                    </select>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+                </button>
+                <button type="button" class="btn btn-primary" id="set_scenario_modal_form_submit">Submit</button>
+            </div>
+        </div>
+    </div>
+
+</div>
+<script>
+
+    $(function () {
+        var loaded = false;
+
+        var attachedScenarios = []
+        {% if current_object.scenarios.all %}
+            {% for scen in current_object.scenarios.all %}
+            attachedScenarios.push('{{ scen.url }}')
+            {% endfor %}
+        {% endif %}
+
+        $('#scenario-select').selectpicker();
+
+        $('#set_scenario_modal').on('shown.bs.modal', function () {
+
+            if (!loaded) {
+                makeLoadingGif("#loading_scenario_div", "{% static '/images/wait.gif' %}");
+                $('#loading_scenario_div').append("<p></p><div class='alert alert-info'>Loading Scenarios...</div>");
+
+                $.getJSON("{% url 'package scenario list' meta.current_package.uuid %}").then(function (data) {
+                    for(s in data) {
+                        scenario = data[s]
+                        var selected = attachedScenarios.includes(scenario.url);
+                        $('#scenario-select').append(`<option value="${scenario.url}" ${selected ? 'selected' : ''}>${scenario.name}</option>`);
+                    }
+                    $('#scenario-select').selectpicker('refresh');
+                    $("#loading_scenario_div").empty();
+                });
+                loaded = true;
+            }
+
+            $('#set_scenario_modal_form_submit').on('click', function (e) {
+                e.preventDefault();
+                $('#set_scenario_modal_form').submit();
+            });
+        });
+    });
+
+</script>

templates/modals/objects/publish_package_modal.html

@@ -1,24 +1,24 @@
 {% load static %}
-<!-- Delete Compound -->
-<div id="delete_compound_modal" class="modal" tabindex="-1">
+<!-- Publish a Package -->
+<div id="publish_package_modal" class="modal" tabindex="-1">
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-                <h3 class="modal-title">Delete Compound</h3>
+                <h5 class="modal-title">Publish Package</h5>
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close">
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-                  Deletes the Compound and associated Structures.
-                <form id="delete-compound-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+                <p>Clicking on Publish will make this Package publicly available!</p>
+                <form id="publish-package-modal-form" accept-charset="UTF-8" action="{{ current_package.url }}" data-remote="true" method="post">
                     {% csrf_token %}
-                    <input type="hidden" id="hidden" name="hidden" value="delete-compound"/>
+                    <input type="hidden" name="hidden" value="publish-package">
                 </form>
             </div>
             <div class="modal-footer">
                 <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="delete-compound-modal-submit">Delete</button>
+                <button type="button" class="btn btn-primary" id="publish-package-modal-form-submit">Publish</button>
             </div>
         </div>
     </div>
@@ -26,9 +26,9 @@
 <script>
 $(function() {
 
-    $('#delete-compound-modal-submit').click(function(e){
+    $('#publish-package-modal-form-submit').click(function(e){
         e.preventDefault();
-        $('#delete-compound-modal-form').submit();
+        $('#publish-package-modal-form').submit();
     });
 
 })

templates/modals/objects/update_scenario_additional_information_modal.html

@@ -0,0 +1,39 @@
+{% load static %}
+<!-- Update Scenario Additional Information-->
+<div id="update_scenario_additional_information_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+                <h3 class="modal-title">Update Additional Information</h3>
+            </div>
+            <div class="modal-body">
+                <form id="edit-scenario-additional-information-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+                    {% csrf_token %}
+                    {% for widget in update_widgets %}
+                        {{ widget|safe }}
+                    {% endfor %}
+                <input type="hidden" name="hidden" value="set-additional-information">
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="edit-scenario-additional-information-modal-submit">Update</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+$(function() {
+
+    $('#edit-scenario-additional-information-modal-submit').click(function(e){
+        e.preventDefault();
+        $('#edit-scenario-additional-information-modal-form').submit();
+    });
+
+});
+
+
+</script>

templates/modals/predict_modal.html

@@ -49,6 +49,18 @@
                         <iframe id="predict-modal-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
                                 height="510"></iframe>
                     </div>
+
+                    <label for="prediction-setting">Default Prediction Setting</label>
+                    <select id="prediction-setting" name="prediction-setting" class="form-control"
+                            data-width='100%'>
+                        <option disabled>Select a Setting</option>
+                        {% for s in meta.available_settings %}
+                            <option value="{{ s.url }}"{% if s.id == meta.user.default_setting.id %}selected{% endif %}>
+                                {{ s.name }}{% if s.id == meta.user.default_setting.id %} <i>(User default)</i>{% endif %}
+                            </option>
+                        {% endfor %}
+                    </select>
+
                 </form>
             </div>
             <div class="modal-footer">

templates/objects/composite_rule.html

@@ -4,6 +4,9 @@
 
 {% block action_modals %}
 {% include "modals/objects/edit_rule_modal.html" %}
+{% include "modals/objects/generic_set_scenario_modal.html" %}
+{% include "modals/objects/generic_copy_object_modal.html" %}
+{% include "modals/objects/generic_delete_modal.html" %}
 {% endblock action_modals %}
 
 <div class="panel-group" id="rule-detail">
@@ -49,7 +52,22 @@
             </div>
         </div>
 
-
+        <!-- Scenarios -->
+        {% if rule.scenarios.all %}
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="rule-scenario-link" data-toggle="collapse" data-parent="#rule-detail"
+                       href="#rule-scenario">Scenarios</a>
+                </h4>
+            </div>
+            <div id="rule-scenario" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {% for s in rule.scenarios.all %}
+                        <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                    {% endfor %}
+                </div>
+            </div>
+        {% endif %}
 
         <!-- EC Numbers -->
         <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">

templates/objects/compound.html

@@ -5,7 +5,9 @@
     {% block action_modals %}
         {% include "modals/objects/edit_compound_modal.html" %}
         {% include "modals/objects/add_structure_modal.html" %}
-        {% include "modals/objects/delete_compound_modal.html" %}
+        {% include "modals/objects/generic_set_scenario_modal.html" %}
+        {% include "modals/objects/generic_copy_object_modal.html" %}
+        {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
 
     <div class="panel-group" id="compound-detail">
@@ -134,7 +136,69 @@
                     </div>
                 </div>
             {% endif %}
+
+            <!-- Scenarios -->
+            {% if compound.scenarios.all %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="compound-scenario-link" data-toggle="collapse" data-parent="#compound-detail"
+                           href="#compound-scenario">Scenarios</a>
+                    </h4>
+                </div>
+                <div id="compound-scenario" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for s in compound.scenarios.all %}
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- External Identifiers -->
+            {% if compound.get_external_identifiers %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="compound-external-identifier-link" data-toggle="collapse" data-parent="#compound-detail"
+                           href="#compound-external-identifier">External Identifier</a>
+                    </h4>
+                </div>
+                <div id="compound-external-identifier" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% if compound.get_pubchem_identifiers %}
+                            <div class="panel panel-default panel-heading list-group-item"
+                                 style="background-color:silver">
+                                <h4 class="panel-title">
+                                    <a id="compound-pubchem-identifier-link" data-toggle="collapse"
+                                       data-parent="#compound-external-identifier"
+                                       href="#compound-pubchem-identifier">PubChem Compound Identifier</a>
+                                </h4>
+                            </div>
+                            <div id="compound-pubchem-identifier" class="panel-collapse collapse in">
+                                {% for eid in compound.get_pubchem_identifiers %}
+                                    <a class="list-group-item"
+                                       href="{{ eid.external_url }}">CID{{ eid.identifier_value }}</a>
+                                {% endfor %}
+                            </div>
+                        {% endif %}
+                        {% if compound.get_chebi_identifiers %}
+                            <div class="panel panel-default panel-heading list-group-item"
+                                 style="background-color:silver">
+                                <h4 class="panel-title">
+                                    <a id="compound-chebi-identifier-link" data-toggle="collapse"
+                                       data-parent="#compound-external-identifier"
+                                       href="#compound-chebi-identifier">ChEBI Identifier</a>
+                                </h4>
+                            </div>
+                            <div id="compound-chebi-identifier" class="panel-collapse collapse in">
+                                {% for eid in compound.get_chebi_identifiers %}
+                                    <a class="list-group-item"
+                                       href="{{ eid.external_url }}">CHEBI:{{ eid.identifier_value }}</a>
+                                {% endfor %}
+                            </div>
+                        {% endif %}
+                    </div>
+                </div>
+            {% endif %}
 
         </div>
 

templates/objects/compound_structure.html

@@ -4,6 +4,8 @@
 
 {% block action_modals %}
 {% include "modals/objects/edit_compound_structure_modal.html" %}
+{% include "modals/objects/generic_set_scenario_modal.html" %}
+{% include "modals/objects/generic_delete_modal.html" %}
 {% endblock action_modals %}
 
 <div class="panel-group" id="compound-structure-detail">
@@ -54,6 +56,22 @@
             </div>
         </div>
 
+        {% if compound_structure.scenarios.all %}
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="compound_structure-scenario-link" data-toggle="collapse" data-parent="#compound-structure-detail"
+                       href="#compound-structure-scenario">Scenarios</a>
+                </h4>
+            </div>
+            <div id="compound-structure-scenario" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {% for s in compound_structure.scenarios.all %}
+                        <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                    {% endfor %}
+                </div>
+            </div>
+        {% endif %}
+
         <!-- Reactions -->
 
         <!-- Pathways -->

templates/objects/edge.html

@@ -4,7 +4,8 @@
 
     {% block action_modals %}
 {#        {% include "modals/objects/edit_edge_modal.html" %}#}
-{#        {% include "modals/objects/delete_edge_modal.html" %}#}
+        {% include "modals/objects/generic_set_scenario_modal.html" %}
+        {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
 
     <div class="panel-group" id="edge-detail">
@@ -19,7 +20,7 @@
                         style="padding-right:1em"></span></a>
                     <ul id="actionsList" class="dropdown-menu">
                         {% block actions %}
-{#                            {% include "actions/objects/edge.html" %}#}
+                            {% include "actions/objects/edge.html" %}
                         {% endblock %}
                     </ul>
                 </div>
@@ -103,6 +104,21 @@
                 </div>
             {% endif %}
 
+            {% if edge.scenarios.all %}
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="edge-scenario-link" data-toggle="collapse" data-parent="#edge-detail"
+                       href="#edge-scenario">Scenarios</a>
+                </h4>
+            </div>
+            <div id="edge-scenario" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {% for s in edge.scenarios.all %}
+                        <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                    {% endfor %}
+                </div>
+            </div>
+            {% endif %}
 
     </div>
 {% endblock content %}

templates/objects/group.html

@@ -5,7 +5,7 @@
 {% block action_modals %}
 {% include "modals/objects/edit_group_modal.html" %}
 {% include "modals/objects/edit_group_member_modal.html" %}
-{% include "modals/objects/delete_group_modal.html" %}
+{% include "modals/objects/generic_delete_modal.html" %}
 {% endblock action_modals %}
 
 <div class="panel-group" id="package-detail">

templates/objects/model.html

@@ -4,7 +4,7 @@
 {% block content %}
 
     {% block action_modals %}
-        {% include "modals/objects/delete_model_modal.html" %}
+        {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
 
     <!-- Include required libs -->
@@ -90,6 +90,7 @@
                     </div>
                 </div>
             {% endif %}
+            {% if model.ready_for_prediction %}
                 <!-- Predict Panel -->
                 <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">
@@ -106,11 +107,36 @@
                         <button class="btn btn-default" type="submit" id="predict-button">Predict!</button>
                     </span>
                         </div>
-                    <div id="loading"></div>
+                        <div id="predictLoading"></div>
                         <div id="predictResultTable"></div>
                     </div>
                 </div>
                 <!-- End Predict Panel       -->
+            {% endif %}
+
+            {% if model.app_domain %}
+                <!-- App Domain -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="app-domain-assessment-link" data-toggle="collapse" data-parent="#model-detail"
+                           href="#app-domain-assessment">Applicability Domain Assessment</a>
+                    </h4>
+                </div>
+                <div id="app-domain-assessment" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        <div class="input-group">
+                            <input id="smiles-to-assess" type="text" class="form-control" placeholder="CCN(CC)C(=O)C1=CC(=CC=C1)C">
+                            <span class="input-group-btn">
+                        <button class="btn btn-default" type="submit" id="assess-button">Assess!</button>
+                    </span>
+                        </div>
+                        <div id="appDomainLoading"></div>
+                        <div id="appDomainAssessmentResultTable"></div>
+                    </div>
+                </div>
+                <!-- End App Domain -->
+            {% endif %}
+
             {% if model.model_status == 'FINISHED' %}
                 <!-- Single Gen Curve Panel -->
                 <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
@@ -243,7 +269,7 @@
 
     <script>
 
-        function handleResponse(data) {
+        function handlePredictionResponse(data) {
             res = "<table class='table table-striped'>"
             res += "<thead>"
             res += "<th scope='col'>#</th>"
@@ -277,9 +303,9 @@
             $("#predictResultTable").append(res);
         }
 
-        function clear() {
-            $("#predictResultTable").removeClass("alert alert-danger");
-            $("#predictResultTable").empty();
+        function clear(divid) {
+            $("#" + divid).removeClass("alert alert-danger");
+            $("#" + divid).empty();
         }
 
         if ($('#predict-button').length > 0) {
@@ -291,32 +317,70 @@
                     "classify": "ILikeCats!"
                 }
 
-                clear();
+                clear("predictResultTable");
 
-                makeLoadingGif("#loading", "{% static '/images/wait.gif' %}");
+                makeLoadingGif("#predictLoading", "{% static '/images/wait.gif' %}");
                 $.ajax({
                     type: 'get',
                     data: data,
                     url: '',
                     success: function (data, textStatus) {
                         try {
-                            $("#loading").empty();
-                            handleResponse(data);
+                            $("#predictLoading").empty();
+                            handlePredictionResponse(data);
                         } catch (error) {
                             console.log("Error");
-                            $("#loading").empty();
+                            $("#predictLoading").empty();
                             $("#predictResultTable").addClass("alert alert-danger");
                             $("#predictResultTable").append("Error while processing request :/");
                         }
                     },
                     error: function (jqXHR, textStatus, errorThrown) {
-                        $("#loading").empty();
+                        $("#predictLoading").empty();
                         $("#predictResultTable").addClass("alert alert-danger");
                         $("#predictResultTable").append("Error while processing request :/");
                     }
                 });
             });
         }
+
+        if ($('#assess-button').length > 0) {
+            $("#assess-button").on("click", function (e) {
+                e.preventDefault();
+
+                data = {
+                    "smiles": $("#smiles-to-assess").val(),
+                    "app-domain-assessment": "ILikeCats!"
+                }
+
+                clear("appDomainAssessmentResultTable");
+
+                makeLoadingGif("#appDomainLoading", "{% static '/images/wait.gif' %}");
+                $.ajax({
+                    type: 'get',
+                    data: data,
+                    url: '',
+                    success: function (data, textStatus) {
+                        try {
+                            $("#appDomainLoading").empty();
+                            handleAssessmentResponse("{% url 'depict' %}", data);
+                            console.log(data);
+                        } catch (error) {
+                            console.log("Error");
+                            $("#appDomainLoading").empty();
+                            $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
+                            $("#appDomainAssessmentResultTable").append("Error while processing request :/");
+                        }
+                    },
+                    error: function (jqXHR, textStatus, errorThrown) {
+                        $("#appDomainLoading").empty();
+                        $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
+                        $("#appDomainAssessmentResultTable").append("Error while processing request :/");
+                    }
+                });
+            });
+        }
+
     </script>
 
 {% endblock content %}

templates/objects/node.html

@@ -4,7 +4,8 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_node_modal.html" %}
-        {% include "modals/objects/delete_node_modal.html" %}
+        {% include "modals/objects/generic_set_scenario_modal.html" %}
+        {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
 
     <div class="panel-group" id="node-detail">
@@ -69,7 +70,34 @@
                 </div>
             </div>
 
+            {% if node.scenarios.all %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="node-scenario-link" data-toggle="collapse" data-parent="#node-detail"
+                           href="#node-scenario">Scenarios</a>
+                    </h4>
+                </div>
+                <div id="node-scenario" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for s in node.scenarios.all %}
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            {% if app_domain_assessment_data %}
+                <div id="appDomainAssessmentResultTable"></div>
+                <script>
+                    $(document).ready(function () {
+                        handleAssessmentResponse("{% url 'depict' %}", {{ app_domain_assessment_data|safe }})
+                    })
+                </script>
+            {% endif %}
+
         </div>
 
     </div>
+
+
 {% endblock content %}

templates/objects/package.html

@@ -5,8 +5,9 @@
 {% block action_modals %}
     {% include "modals/objects/edit_package_modal.html" %}
     {% include "modals/objects/edit_package_permissions_modal.html" %}
+    {% include "modals/objects/publish_package_modal.html" %}
     {% include "modals/objects/set_license_modal.html" %}
-    {% include "modals/objects/delete_package_modal.html" %}
+    {% include "modals/objects/generic_delete_modal.html" %}
 {% endblock action_modals %}
 
 <div class="panel-group" id="package-detail">
@@ -52,23 +53,5 @@
 
     </div>
 
-    {%  if package.license %}
-    <p></p>
-    <div class="panel-group" id="license_accordion">
-        <div class="panel panel-default list-group-item" style="background-color:#f5f5f5">
-            <div class="panel-title">
-                <a data-toggle="collapse" data-parent="#licence_accordion" href="#license">License</a>
-            </div>
-        </div>
-        <div id="license" class="panel-collapse collapse in">
-            <div class="panel-body list-group-item">
-                <a target="_blank" href="{{ package.license.link }}">
-                    <img src="{{ package.license.image_link }}">
-                </a>
-            </div>
-        </div>
-    </div>
-    {% endif %}
-
 </div>
 {% endblock content %}

templates/objects/pathway.html

@@ -4,16 +4,22 @@
 
     <script src="https://d3js.org/d3.v7.min.js"></script>
     <style>
-        svg {
+        #vizdiv {
             width: 100%;
             height: 600px;
+            background: white;
+        }
+
+        #pwsvg {
+            width: 100%;
+            height: 100%;
             color: red;
         }
 
         .link {
             stroke: #999;
             stroke-opacity: 0.6;
-            marker-end: url(#arrow);
+            //marker-end: url(#arrow);
         }
 
         .link_no_arrow {
@@ -31,6 +37,31 @@
             stroke-width: 1.5px;
         }
 
+        .inside_app_domain {
+            fill: green;
+            stroke: green;
+            stroke-width: 1.5px;
+        }
+
+        .outside_app_domain {
+            fill: red;
+            stroke: red;
+            stroke-width: 1.5px;
+        }
+
+        .passes_app_domain {
+            stroke: green;
+            stroke-width: 1.5px;
+            stroke-opacity: 0.6;
+        }
+
+        .fails_app_domain {
+            stroke: red;
+            stroke-width: 1.5px;
+            stroke-opacity: 0.6;
+        }
+
+
         .highlighted {
             stroke: red;
             stroke-width: 3px;
@@ -50,10 +81,13 @@
     {% block action_modals %}
         {% include "modals/objects/add_pathway_node_modal.html" %}
         {% include "modals/objects/add_pathway_edge_modal.html" %}
+        {% include "modals/objects/download_pathway_modal.html" %}
+        {% include "modals/objects/generic_copy_object_modal.html" %}
         {% include "modals/objects/edit_pathway_modal.html" %}
+        {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/delete_pathway_node_modal.html" %}
         {% include "modals/objects/delete_pathway_edge_modal.html" %}
-        {% include "modals/objects/delete_pathway_modal.html" %}
+        {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
 
     <p></p>
@@ -79,8 +113,7 @@
                         <ul class="nav navbar-nav">
                             <li class="dropdown requiresWritePerm">
                                 <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
-                                   aria-haspopup="true"
-                                   aria-expanded="false">
+                                   aria-haspopup="true" aria-expanded="false">
                                     <span class="glyphicon glyphicon-edit"></span>
                                     Edit
                                     <span class="caret"></span></a>
@@ -90,11 +123,26 @@
                                     {% endblock %}
                                 </ul>
                             </li>
+                            {% if pathway.setting.model.app_domain %}
+                            <li class="dropdown">
+                                <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
+                                   aria-haspopup="true" aria-expanded="false">
+                                    <span class="glyphicon glyphicon-eye-open"></span>
+                                    View
+                                    <span class="caret"></span></a>
+                                <ul id="editingList" class="dropdown-menu">
+                                    <li>
+                                        <a class="button" id="app-domain-toggle-button">
+                                            <i id="app-domain-toggle-button" class="glyphicon glyphicon-eye-open"></i> App Domain View</a>
+                                    </li>
+                                </ul>
+                            </li>
+                            {% endif %}
                         </ul>
 
                         <ul class="nav navbar-nav navbar-right">
                             <li>
-                                <a role="button" data-toggle="modal" onclick="goFullscreen('pwcontent')">
+                                <a role="button" data-toggle="modal" onclick="goFullscreen('vizdiv')">
                                     <span class="glyphicon glyphicon-fullscreen"></span>
                                     Fullscreen
                                 </a>
@@ -126,15 +174,23 @@
                     </div>
                 </nav>
                 <div id="vizdiv" >
-                    <svg width="2000" height="2000">
+                    <svg id="pwsvg">
                         {% if debug %}
                             <rect width="100%" height="100%" fill="aliceblue"/>
                         {% endif %}
                         <defs>
                             <marker id="arrow" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
-                                    orient="auto-start-reverse">
+                                    orient="auto-start-reverse" markerUnits="userSpaceOnUse">
                                 <path d="M 0 0 L 10 5 L 0 10 z" fill="#999"/>
                             </marker>
+                            <marker id="arrow_passes_app_domain" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
+                                    orient="auto-start-reverse" markerUnits="userSpaceOnUse">
+                                <path d="M 0 0 L 10 5 L 0 10 z" fill="green"/>
+                            </marker>
+                            <marker id="arrow_fails_app_domain" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
+                                    orient="auto-start-reverse" markerUnits="userSpaceOnUse">
+                                <path d="M 0 0 L 10 5 L 0 10 z" fill="red"/>
+                            </marker>
                         </defs>
                         <g id="zoomable"></g>
                     </svg>
@@ -153,13 +209,29 @@
                 </div>
             </div>
 
+            {% if pathway.scenarios.all %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="pathway-scenario-link" data-toggle="collapse" data-parent="#pathway-detail"
+                           href="#pathway-scenario">Scenarios</a>
+                    </h4>
+                </div>
+                <div id="pathway-scenario" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for s in pathway.scenarios.all %}
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             {% if pathway.setting %}
                 <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">
                         <a id="pathwaySettingLink" data-toggle="collapse" data-parent="#pathwayAccordion"
                            href="#pathwaySetting">Setting</a></h4>
                 </div>
-                <div id="pathwaySetting" class="panel-collapse collapse in">
+                <div id="pathwaySetting" class="panel-collapse collapse">
                     <div class="panel-body list-group-item" id="pathwaySettingContent">
                         <table class="table table-bordered table-hover">
                             <tr style="background-color: rgba(0, 0, 0, 0.08);">
@@ -245,6 +317,8 @@
         </div>
     </div>
     <script>
+        // Globla switch for app domain view
+        var appDomainViewEnabled = false;
 
         function goFullscreen(id) {
             var element = document.getElementById(id);
@@ -266,6 +340,51 @@
             // TODO fix somewhere else...
             var newDesc = transformReferences($('#DescriptionContent')[0].innerText);
             $('#DescriptionContent').html(newDesc);
+
+
+            $('#app-domain-toggle-button').on('click', function () {
+                // glyphicon glyphicon-eye-close
+                // glyphicon glyphicon-eye-open
+                appDomainViewEnabled = !appDomainViewEnabled;
+
+                if (appDomainViewEnabled) {
+                    $('#app-domain-toggle-button > i').removeClass('glyphicon-eye-open');
+                    $('#app-domain-toggle-button > i').addClass('glyphicon-eye-close');
+                    nodes.forEach((x) => {
+                        if(x.app_domain) {
+                            if (x.app_domain.inside_app_domain) {
+                                d3.select(x.el).select("circle").classed("inside_app_domain", true);
+                            } else {
+                                d3.select(x.el).select("circle").classed("outside_app_domain", true);
+                            }
+                        }
+                    });
+                    links.forEach((x) => {
+                        if(x.app_domain) {
+                            if (x.app_domain.passes_app_domain) {
+                                d3.select(x.el).attr("marker-end", d => d.target.pseudo ? "" : "url(#arrow_passes_app_domain)");
+                                d3.select(x.el).classed("passes_app_domain", true);
+                            } else {
+                                d3.select(x.el).attr("marker-end", d => d.target.pseudo ? "" : "url(#arrow_fails_app_domain)");
+                                d3.select(x.el).classed("fails_app_domain", true);
+                            }
+                        }
+                    });
+                } else {
+                    $('#app-domain-toggle-button > i').removeClass('glyphicon-eye-close');
+                    $('#app-domain-toggle-button > i').addClass('glyphicon-eye-open');
+                    nodes.forEach((x) => {
+                        d3.select(x.el).select("circle").classed("inside_app_domain", false);
+                        d3.select(x.el).select("circle").classed("outside_app_domain", false);
+                    });
+                    links.forEach((x) => {
+                        d3.select(x.el).attr("marker-end", d => d.target.pseudo ? "" : "url(#arrow)");
+                        d3.select(x.el).classed("passes_app_domain", false);
+                        d3.select(x.el).classed("fails_app_domain", false);
+                    });
+                }
+            })
+
         });
 
     </script>

templates/objects/reaction.html

@@ -4,7 +4,9 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_reaction_modal.html" %}
-        {% include "modals/objects/delete_reaction_modal.html" %}
+        {% include "modals/objects/generic_set_scenario_modal.html" %}
+        {% include "modals/objects/generic_copy_object_modal.html" %}
+        {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
 
     <div class="panel-group" id="reaction-detail">
@@ -118,9 +120,70 @@
                         {% endfor %}
                     </div>
                 </div>
+            {% endif %}
 
+            {% if reaction.scenarios.all %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="reaction-scenario-link" data-toggle="collapse" data-parent="#reaction-detail"
+                           href="#reaction-scenario">Scenarios</a>
+                    </h4>
+                </div>
+                <div id="reaction-scenario" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for s in reaction.scenarios.all %}
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            <!-- External Identifiers -->
+            {% if reaction.get_external_identifiers %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="reaction-external-identifier-link" data-toggle="collapse" data-parent="#reaction-detail"
+                           href="#reaction-external-identifier">External Identifier</a>
+                    </h4>
+                </div>
+                <div id="reaction-external-identifier" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% if reaction.get_rhea_identifiers %}
+                            <div class="panel panel-default panel-heading list-group-item"
+                                 style="background-color:silver">
+                                <h4 class="panel-title">
+                                    <a id="reaction-rhea-identifier-link" data-toggle="collapse"
+                                       data-parent="#reaction-external-identifier"
+                                       href="#reaction-rhea-identifier">Rhea</a>
+                                </h4>
+                            </div>
+                            <div id="reaction-rhea-identifier" class="panel-collapse collapse in">
+                                {% for eid in reaction.get_rhea_identifiers %}
+                                    <a class="list-group-item"
+                                       href="{{ eid.external_url }}">{{ eid.identifier_value }}</a>
+                                {% endfor %}
+                            </div>
+                        {% endif %}
+                        {% if reaction.get_uniprot_identifiers %}
+                            <div class="panel panel-default panel-heading list-group-item"
+                                 style="background-color:silver">
+                                <h4 class="panel-title">
+                                    <a id="reaction-uniprot-identifier-link" data-toggle="collapse"
+                                       data-parent="#reaction-external-identifier"
+                                       href="#reaction-uniprot-identifier">UniProt</a>
+                                </h4>
+                            </div>
+                            <div id="reaction-uniprot-identifier" class="panel-collapse collapse in">
+                                {% for eid in reaction.get_uniprot_identifiers %}
+                                    <a class="list-group-item"
+                                       href="{{ eid.external_url }}">10 SwissProt entries ({{ eid.identifier_value }})</a>
+                                {% endfor %}
+                            </div>
+                        {% endif %}
+                    </div>
                 </div>
             {% endif %}
 
         </div>
+    </div>
 {% endblock content %}

templates/objects/scenario.html

@@ -3,7 +3,9 @@
 {% block content %}
 
     {% block action_modals %}
-
+        {% include "modals/objects/add_additional_information_modal.html" %}
+        {% include "modals/objects/update_scenario_additional_information_modal.html" %}
+        {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
     <div class="panel-group" id="scenario-detail">
         <div class="panel panel-default">
@@ -24,6 +26,18 @@
             </div>
         </div>
     </div>
+
+    <div class="panel panel-default">
+        <div class="panel-heading">Description</div>
+        <div class="panel-body">
+            {{ scenario.description }}
+            <br>
+            {{ scenario.scenario_type }}
+            <br>
+            Reported {{ scenario.scenario_date }}
+        </div>
+    </div>
+
     <div class="table-responsive">
         <table id="scenario-table" class="table table-bordered table-striped table-hover">
             <tbody>
@@ -31,7 +45,9 @@
                 <th>Property</th>
                 <th>Value</th>
                 <th>Unit</th>
+                {% if meta.can_edit %}
                 <th>Remove</th>
+                {%  endif %}
             </tr>
 
             {% for ai in scenario.get_additional_information %}
@@ -39,10 +55,32 @@
                     <td> {{ ai.property_name|safe }} </td>
                     <td> {{ ai.property_data|safe }} </td>
                     <td> {{ ai.property_unit|safe }} </td>
-                    <td></td>
+                    {% if meta.can_edit %}
+                    <td>
+                        <form action="{% url 'package scenario detail' scenario.package.uuid scenario.uuid %}" method="post">
+                            {% csrf_token %}
+                            <input type="hidden" name="uuid" value="{{ ai.uuid }}">
+                            <input type="hidden" name="hidden" value="delete-additional-information">
+                            <button type="submit" class="btn"><span class="glyphicon glyphicon-minus"></span></button>
+                        </form>
+                    </td>
+                    {%  endif %}
                 </tr>
             {% endfor %}
-
+            {% if meta.can_edit %}
+                <tr>
+                    <td></td>
+                    <td></td>
+                    <td>Delete all</td>
+                    <td>
+                        <form action="{% url 'package scenario detail' scenario.package.uuid scenario.uuid %}" method="post">
+                            {% csrf_token %}
+                            <input type="hidden" name="hidden" value="delete-all-additional-information">
+                            <button type="submit" class="btn"><span class="glyphicon glyphicon-trash"></span></button>
+                        </form>
+                    </td>
+                </tr>
+            {% endif %}
             </tbody>
         </table>
     </div>

templates/objects/simple_rule.html

@@ -4,6 +4,9 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_rule_modal.html" %}
+        {% include "modals/objects/generic_set_scenario_modal.html" %}
+        {% include "modals/objects/generic_copy_object_modal.html" %}
+        {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
 
     <div class="panel-group" id="rule-detail">

templates/objects/user.html

@@ -7,7 +7,7 @@
 {% include "modals/objects/edit_password_modal.html" %}
 {% include "modals/collections/new_prediction_setting_modal.html" %}
 {% include "modals/objects/manage_api_token_modal.html" %}
-{% include "modals/objects/delete_user_modal.html" %}
+{% include "modals/objects/generic_delete_modal.html" %}
 {% endblock action_modals %}
 
 <div class="panel-group" id="user-detail">

templates/search.html

@@ -79,6 +79,10 @@
 
             allEmpty = true;
             for (key in data) {
+                if (key === 'searchterm') {
+                    continue;
+                }
+
                 if (data[key].length < 1) {
                     continue;
                 }
@@ -176,8 +180,16 @@
             $("#selPackages").selectpicker();
             $("#search-button").on("click", search);
 
+            $("#searchbar").on("keydown", function (e) {
+                if (e.key === "Enter") {
+                    e.preventDefault();
+                    search(e);
+                }
+            });
+
         });
         {% if search_result %}
+            $('#searchbar').val('{{ search_result.searchterm }}')
             handleSearchResponse("results", {{ search_result|safe }});
         {% endif %}
     </script>

templates/tables/scenario.html

@@ -1,72 +0,0 @@
-{% for obj in available_additional_information.types %}
-<div id="table-{{obj.type}}-Div">
-    <table class="table table-bordered table-hover">
-        <tbody>
-        <tr id="{{ obj.type }}GroupRow" style="background-color: rgba(0, 0, 0, 0.08);">
-            <td><p style="font-size:18px">{{obj.title}}</p></td>
-        </tr>
-        <!-- Loop through all AIs and attach the ones without subtype -->
-        {% for ai in available_additional_information.ais %}
-        <tr>
-        {% if obj.type in ai.types and ai.sub_type is not defined %}
-            <td><span title="">{{ ai.name }}</span></td>
-            <!-- #TODO -->
-            {% for c in "1 2 3"|make_list %}
-            <td class="col-{{ c }}">
-                {% for form in ai.forms %}
-                <!-- Build input -->
-                {% if form.type == 'select' %}
-                <select class="form-control" name="{{ form.param_name}}">
-                    <option value="">{{ form.placeholder }}</option>
-                    {% for choice in form.choices %}
-                    <option value="{{ choice.value }}">
-                        {{ choice.name }}
-                    </option>
-                    {% endfor %}
-                </select>
-                {% else %}
-                <input type="{{ form.type }}" name="{{ form.param_name }}" class="form-control" placeholder="{{ form.placeholder|safe }}"/>
-                {% endif %}
-                {% endfor %}
-            </td>
-            {% endfor %}
-        {% endif %}
-        {% endfor %}
-        </tr>
-        {% for subtype in available_additional_information.subtypes %}
-        <tr id="{{ subtype.type }}GroupRow" style="background-color: rgba(0, 0, 0, 0.08);">
-            <td><p style="font-size:18px">{{subtype.title}}</p></td>
-        </tr>
-        <!-- Loop through all AIs and attach the ones with the same subtype -->
-        {% for ai in available_additional_information.ais %}
-        <tr>
-            {% if obj.type in ai.types and subtype.type == ai.sub_type %}
-            <td><span title="">{{ ai.name }}</span></td>
-            <!-- #TODO -->
-            {% for c in "1 2 3"|make_list %}
-            <td class="col-{{ c }}">
-            {% for form in ai.forms %}
-                <!-- Build input -->
-                {% if form.type == 'select' %}
-                <select class="form-control" name="{{ form.param_name }}">
-                    <option value="">{{ form.placeholder }}</option>
-                    {% for choice in form.choices %}
-                    <option value="{{ choice.value }}">
-                        {{ choice.name }}
-                    </option>
-                    {% endfor %}
-                </select>
-                {% else %}
-                <input type="{{ form.type }}" name="{{ form.param_name }}" class="form-control" placeholder="{{ form.placeholder|safe }}">
-                {% endif %}
-            {% endfor %}
-            </td>
-            {% endfor %}
-            {% endif %}
-        </tr>
-        {% endfor %}
-        {% endfor %}
-        </tbody>
-    </table>
-</div>
-{% endfor %}

tests/test_copy_objects.py

@@ -0,0 +1,200 @@
+import json
+
+from django.test import TestCase
+
+from epdb.logic import PackageManager
+from epdb.models import Compound, User, CompoundStructure, Reaction, Rule, MLRelativeReasoning, Pathway
+
+
+class CopyTest(TestCase):
+    fixtures = ["test_fixture.cleaned.json"]
+
+    def setUp(self):
+        pass
+
+    @classmethod
+    def setUpClass(cls):
+        super(CopyTest, cls).setUpClass()
+        cls.user = User.objects.get(username='anonymous')
+        cls.package = PackageManager.create_package(cls.user, 'Source Package', 'No Desc')
+        cls.AFOXOLANER = Compound.create(
+            cls.package,
+            smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
+            name='Afoxolaner',
+            description='Test compound for copying'
+        )
+
+        cls.FOUR_NITROBENZOIC_ACID = Compound.create(
+            cls.package,
+            smiles='[O-][N+](=O)c1ccc(C(=O)[O-])cc1',  # Normalized: O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
+            name='Test Compound',
+            description='Compound with multiple structures'
+        )
+
+        cls.ETHANOL = Compound.create(
+            cls.package,
+            smiles='CCO',
+            name='Ethanol',
+            description='Simple alcohol'
+        )
+        cls.target_package = PackageManager.create_package(cls.user, 'Target Package', 'No Desc')
+
+        cls.reaction_educt = Compound.create(
+            cls.package,
+            smiles='C(CCl)Cl',
+            name='1,2-Dichloroethane',
+            description='Eawag BBD compound c0001'
+        ).default_structure
+
+        cls.reaction_product = Compound.create(
+            cls.package,
+            smiles='C(CO)Cl',
+            name='2-Chloroethanol',
+            description='Eawag BBD compound c0005'
+        ).default_structure
+
+        cls.REACTION = Reaction.create(
+            package=cls.package,
+            name='Eawag BBD reaction r0001',
+            educts=[cls.reaction_educt],
+            products=[cls.reaction_product],
+            multi_step=False
+        )
+
+
+    @classmethod
+    def tearDownClass(cls):
+        pass
+
+    def tearDown(self):
+        pass
+
+
+    def test_compound_copy_basic(self):
+        """Test basic compound copying functionality"""
+        mapping = dict()
+        copied_compound = self.AFOXOLANER.copy(self.target_package, mapping)
+
+        self.assertNotEqual(self.AFOXOLANER.uuid, copied_compound.uuid)
+        self.assertEqual(self.AFOXOLANER.name, copied_compound.name)
+        self.assertEqual(self.AFOXOLANER.description, copied_compound.description)
+        self.assertEqual(copied_compound.package, self.target_package)
+        self.assertEqual(self.AFOXOLANER.package, self.package)
+        self.assertEqual(self.AFOXOLANER.default_structure.smiles, copied_compound.default_structure.smiles)
+
+    def test_compound_copy_with_multiple_structures(self):
+        """Test copying a compound with multiple structures"""
+
+        original_structure_count = self.FOUR_NITROBENZOIC_ACID.structures.count()
+
+        mapping = dict()
+        # Copy the compound
+        copied_compound = self.FOUR_NITROBENZOIC_ACID.copy(self.target_package, mapping)
+
+        # Verify all structures were copied
+        self.assertEqual(copied_compound.structures.count(), original_structure_count)
+
+        # Verify default_structure is properly set
+        self.assertIsNotNone(copied_compound.default_structure)
+        self.assertEqual(
+            copied_compound.default_structure.smiles,
+            self.FOUR_NITROBENZOIC_ACID.default_structure.smiles
+        )
+
+    def test_compound_copy_preserves_aliases(self):
+        """Test that compound copying preserves aliases"""
+        # Create a compound and add aliases
+        original_compound = self.ETHANOL
+
+        # Add aliases if the method exists
+        if hasattr(original_compound, 'add_alias'):
+            original_compound.add_alias('Ethyl alcohol')
+            original_compound.add_alias('Grain alcohol')
+
+        mapping = dict()
+        copied_compound = original_compound.copy(self.target_package, mapping)
+
+        # Verify aliases were copied if they exist
+        if hasattr(original_compound, 'aliases') and hasattr(copied_compound, 'aliases'):
+            original_aliases = original_compound.aliases
+            copied_aliases = copied_compound.aliases
+            self.assertEqual(original_aliases, copied_aliases)
+
+    def test_compound_copy_preserves_external_identifiers(self):
+        """Test that external identifiers are preserved during copying"""
+        original_compound = self.ETHANOL
+
+        # Add external identifiers if the methods exist
+        if hasattr(original_compound, 'add_cas_number'):
+            original_compound.add_cas_number('64-17-5')
+        if hasattr(original_compound, 'add_pubchem_compound_id'):
+            original_compound.add_pubchem_compound_id('702')
+
+        mapping = dict()
+        copied_compound = original_compound.copy(self.target_package, mapping)
+
+        # Verify external identifiers were copied
+        original_ext_ids = original_compound.external_identifiers.all()
+        copied_ext_ids = copied_compound.external_identifiers.all()
+
+        self.assertEqual(original_ext_ids.count(), copied_ext_ids.count())
+
+        # Check that identifier values match
+        original_values = set(ext_id.identifier_value for ext_id in original_ext_ids)
+        copied_values = set(ext_id.identifier_value for ext_id in copied_ext_ids)
+        self.assertEqual(original_values, copied_values)
+
+    def test_compound_copy_structure_properties(self):
+        """Test that structure properties are properly copied"""
+        original_compound = self.ETHANOL
+
+        mapping = dict()
+        copied_compound = original_compound.copy(self.target_package, mapping)
+
+        # Verify structure properties
+        original_structure = original_compound.default_structure
+        copied_structure = copied_compound.default_structure
+
+        self.assertEqual(original_structure.smiles, copied_structure.smiles)
+        self.assertEqual(original_structure.canonical_smiles, copied_structure.canonical_smiles)
+        self.assertEqual(original_structure.inchikey, copied_structure.inchikey)
+        self.assertEqual(original_structure.normalized_structure, copied_structure.normalized_structure)
+
+        # Verify they are different objects
+        self.assertNotEqual(original_structure.uuid, copied_structure.uuid)
+        self.assertEqual(copied_structure.compound, copied_compound)
+
+    def test_reaction_copy_basic(self):
+        """Test basic reaction copying functionality"""
+        mapping = dict()
+        copied_reaction = self.REACTION.copy(self.target_package, mapping)
+
+        self.assertNotEqual(self.REACTION.uuid, copied_reaction.uuid)
+        self.assertEqual(self.REACTION.name, copied_reaction.name)
+        self.assertEqual(self.REACTION.description, copied_reaction.description)
+        self.assertEqual(self.REACTION.multi_step, copied_reaction.multi_step)
+        self.assertEqual(copied_reaction.package, self.target_package)
+        self.assertEqual(self.REACTION.package, self.package)
+        
+        
+    def test_reaction_copy_structures(self):
+        """Test basic reaction copying functionality"""
+        mapping = dict()
+        copied_reaction = self.REACTION.copy(self.target_package, mapping)
+        
+        for orig_educt, copy_educt in zip(self.REACTION.educts.all(), copied_reaction.educts.all()):
+            self.assertNotEqual(orig_educt.uuid, copy_educt.uuid)
+            self.assertEqual(orig_educt.name, copy_educt.name)
+            self.assertEqual(orig_educt.description, copy_educt.description)
+            self.assertEqual(copy_educt.compound.package, self.target_package)
+            self.assertEqual(orig_educt.compound.package, self.package)
+            self.assertEqual(orig_educt.smiles, copy_educt.smiles)
+
+        for orig_product, copy_product in zip(self.REACTION.products.all(), copied_reaction.products.all()):
+            self.assertNotEqual(orig_product.uuid, copy_product.uuid)
+            self.assertEqual(orig_product.name, copy_product.name)
+            self.assertEqual(orig_product.description, copy_product.description)
+            self.assertEqual(copy_product.compound.package, self.target_package)
+            self.assertEqual(orig_product.compound.package, self.package)
+            self.assertEqual(orig_product.smiles, copy_product.smiles)
+

tests/test_dataset.py

@@ -0,0 +1,52 @@
+from django.test import TestCase
+
+from epdb.logic import PackageManager
+from epdb.models import Reaction, Compound, User, Rule
+from utilities.ml import Dataset
+
+
+class DatasetTest(TestCase):
+    fixtures = ["test_fixture.cleaned.json"]
+
+    def setUp(self):
+        self.cs1 = Compound.create(
+            self.package,
+            name='2,6-Dibromohydroquinone',
+            description='http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d6435251-1a54-4327-b4b1-fd6e9a8f4dc9/structure/d8a0225c-dbb5-4e6c-a642-730081c09c5b',
+            smiles='C1=C(C(=C(C=C1O)Br)O)Br',
+        ).default_structure
+
+        self.cs2 = Compound.create(
+            self.package,
+            smiles='O=C(O)CC(=O)/C=C(/Br)C(=O)O',
+        ).default_structure
+
+        self.rule1 = Rule.create(
+            rule_type='SimpleAmbitRule',
+            package=self.package,
+            smirks='[#8:8]([H])-[c:4]1[c:3]([H])[c:2](-[#1,#17,#35:9])[c:1](-[#8:7]([H]))[c:6](-[#1,#17,#35])[c:5]([H])1>>[#8-]-[#6:6](=O)-[#6:5]-[#6:4](=[O:8])\[#6:3]=[#6:2](\[#1,#17,#35:9])-[#6:1](-[#8-])=[O:7]',
+            description='http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/f6a56c0f-a4a0-4ee3-b006-d765b4767cf6'
+        )
+
+        self.reaction1 = Reaction.create(
+            package=self.package,
+            educts=[self.cs1],
+            products=[self.cs2],
+            rules=[self.rule1],
+            multi_step=False
+        )
+
+    @classmethod
+    def setUpClass(cls):
+        super(DatasetGeneratorTest, cls).setUpClass()
+        cls.user = User.objects.get(username='anonymous')
+        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+
+    def test_smoke(self):
+        reactions = [r for r in Reaction.objects.filter(package=self.package)]
+        applicable_rules = [self.rule1]
+
+        ds = Dataset.generate_dataset(reactions, applicable_rules)
+
+        self.assertEqual(len(ds.y()), 1)
+        self.assertEqual(sum(ds.y()[0]), 1)

tests/test_datasetgenerator.py

@@ -1,111 +0,0 @@
-from django.test import TestCase
-
-from epdb.models import ParallelRule
-from utilities.ml import Compound, Reaction, DatasetGenerator
-
-
-class CompoundTest(TestCase):
-
-    def setUp(self):
-        self.c1 = Compound(smiles="CCN(CC)C(=O)C1=CC(=CC=C1)C", uuid='c1')
-        self.c2 = Compound(smiles="CCN(CC)C(=O)C1=CC(=CC=C1)C", uuid='c2')
-
-    def test_compound_eq_ignores_uuid(self):
-        self.assertEqual(self.c1, self.c2)
-
-
-class ReactionTest(TestCase):
-
-    def setUp(self):
-        self.c1 = Compound(smiles="CCN(CC)C(=O)C1=CC(=CC=C1)C")
-        self.c2 = Compound(smiles="CCN(CCO)C(=O)C1=CC(C)=CC=C1")
-        # self.r1 = Rule(uuid="bt0334")
-        # c1 --r1--> c2
-        self.c3_1 = Compound(smiles="CCNC(=O)C1=CC(C)=CC=C1")
-        self.c3_2 = Compound(smiles="CC=O")
-        # self.r2 = Rule(uuid="bt0243")
-        # c1 --r2--> c3_1, c3_2
-
-    def test_reaction_equality_ignores_uuid(self):
-        r1 = Reaction([self.c1], [self.c2], self.r1, uuid="abc")
-        r2 = Reaction([self.c1], [self.c2], self.r1, uuid="xyz")
-        self.assertEqual(r1, r2)
-
-    def test_reaction_inequality_on_data_change(self):
-        r1 = Reaction([self.c1], [self.c2], self.r1)
-        r2 = Reaction([self.c1], [self.c3_1], self.r1)
-        self.assertNotEqual(r1, r2)
-
-    def test_reaction_is_hashable(self):
-        r = Reaction([self.c1], [self.c2], self.r1)
-        reactions = {r}
-        self.assertIn(Reaction([self.c1], [self.c2], self.r1), reactions)
-
-    def test_rule_is_optional(self):
-        r = Reaction([self.c1], [self.c2])
-        self.assertIsNone(r.rule)
-
-    def test_uuid_is_optional(self):
-        r = Reaction([self.c1], [self.c2], self.r1)
-        self.assertIsNone(r.uuid)
-
-    def test_repr_includes_uuid(self):
-        r = Reaction([self.c1], [self.c2], self.r1, uuid="abc")
-        self.assertIn("abc", repr(r))
-
-    def test_reaction_equality_with_multiple_compounds_different_ordering(self):
-        r1 = Reaction([self.c1], [self.c3_1, self.c3_2], self.r2)
-        r2 = Reaction([self.c1], [self.c3_2, self.c3_1], self.r2)
-
-        self.assertEqual(r1, r2, "Reaction equality should not rely on list order")
-
-
-class RuleTest(TestCase):
-
-    def setUp(self):
-        pass
-        # self.r1 = Rule(uuid="bt0334")
-        # self.r2 = Rule(uuid="bt0243")
-
-
-class DatasetGeneratorTest(TestCase):
-    fixtures = ['bootstrap.json']
-
-    def setUp(self):
-        self.c1 = Compound(smiles="CCN(CC)C(=O)C1=CC(=CC=C1)C")
-        self.c2 = Compound(smiles="CCN(CCO)C(=O)C1=CC(C)=CC=C1")
-        self.c3_1 = Compound(smiles="CCNC(=O)C1=CC(C)=CC=C1")
-        self.c3_2 = Compound(smiles="CC=O")
-
-        # self.r1 = Rule(uuid="bt0334") # trig
-        # self.r2 = Rule(uuid="bt0243") # trig
-        # self.r3 = Rule(uuid="bt0003") # no trig
-
-        self.reaction1 = Reaction([self.c1], [self.c2], self.r3)
-        self.reaction2 = Reaction([self.c1], [self.c3_1, self.c3_2], self.r2)
-
-
-
-
-    def test_test(self):
-        compounds = [
-            self.c1,
-            self.c2,
-            self.c3_1,
-            self.c3_2,
-        ]
-
-        reactions = [
-            self.reaction1,
-            self.reaction2,
-        ]
-
-        applicable_rules = [
-            # Rule('bt0334', ParallelRule.objects.get(name='bt0334')),
-            # Rule('bt0243', ParallelRule.objects.get(name='bt0243')),
-            # Rule('bt0003', ParallelRule.objects.get(name='bt0003')),
-        ]
-
-        ds = DatasetGenerator.generate_dataset(compounds, reactions, applicable_rules)
-
-        self.assertIsNotNone(ds)

tests/test_model.py

@@ -0,0 +1,55 @@
+import json
+
+from django.test import TestCase
+
+from epdb.logic import PackageManager
+from epdb.models import Compound, User, CompoundStructure, Reaction, Rule, MLRelativeReasoning
+
+
+class ModelTest(TestCase):
+    fixtures = ["test_fixture.cleaned.json"]
+
+    def setUp(self):
+        pass
+
+    @classmethod
+    def setUpClass(cls):
+        super(ModelTest, cls).setUpClass()
+        cls.user = User.objects.get(username='anonymous')
+        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+        bbd_data = json.load(open('fixtures/packages/2025-07-18/EAWAG-BBD.json'))
+        cls.BBD = PackageManager.import_package(bbd_data, cls.user)
+
+    @classmethod
+    def tearDownClass(cls):
+        pass
+
+    def tearDown(self):
+        pass
+
+    def test_smoke(self):
+        threshold = float(0.5)
+
+        # get Package objects from urls
+        rule_package_objs = [self.BBD]
+        data_package_objs = [self.BBD]
+        eval_packages_objs = []
+
+        mod = MLRelativeReasoning.create(
+            self.package,
+            rule_package_objs,
+            data_package_objs,
+            eval_packages_objs,
+            threshold,
+            'ECC - BBD - 0.5',
+            'Created MLRelativeReasoning in Testcase',
+        )
+        ds = mod.load_dataset()
+
+        mod.build_model()
+        print("Model built!")
+        mod.evaluate_model()
+        print("Model Evaluated")
+
+        results = mod.predict('CCN(CC)C(=O)C1=CC(=CC=C1)C')
+        print(results)

tests/test_ruleapplication.py

@@ -19,9 +19,8 @@ class RuleApplicationTest(TestCase):
 
     @classmethod
     def tearDownClass(cls):
-        from collections import Counter
-        # print(Counter(cls.error_smiles))
-        pass
+        print(f"\nTotal Errors across Rules {len(cls.error_smiles)}")
+        # print(cls.error_smiles)
 
     def tearDown(self):
         print(f"\nTotal errors {self.total_errors}")
@@ -36,7 +35,7 @@ class RuleApplicationTest(TestCase):
         for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
 
             smi = comp['smiles']
-            products = FormatConverter.apply(smi, smirks, preprocess_smiles=True, bracketize=False)
+            products = FormatConverter.apply(smi, smirks)
 
             all_rdkit_prods = []
             for ps in products:
@@ -53,15 +52,15 @@ class RuleApplicationTest(TestCase):
 
             # TODO mode "intersection"
             # partial_res = (len(set(ambit_smiles).intersection(set(rdkit_smiles))) > 0) or (len(ambit_smiles) == 0)
-            # FAILED (failures=42)
+            # FAILED (failures=33)
 
             # TODO mode = "full ambit"
             # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
-            # FAILED (failures=52)
+            # FAILED (failures=44)
 
             # TODO mode = "equality"
             partial_res = set(ambit_smiles) == set(rdkit_smiles)
-            # FAILED (failures=71)
+            # FAILED (failures=64)
 
             if len(ambit_smiles) and not partial_res:
                 print(f"""

utilities/chem.py

@@ -8,10 +8,12 @@ from indigo import Indigo, IndigoException, IndigoObject
 from indigo.renderer import IndigoRenderer
 from rdkit import Chem
 from rdkit import RDLogger
-from rdkit.Chem import MACCSkeys
+from rdkit.Chem import MACCSkeys, Descriptors
 from rdkit.Chem import rdChemReactions
 from rdkit.Chem.Draw import rdMolDraw2D
 from rdkit.Chem.MolStandardize import rdMolStandardize
+from rdkit.Chem.rdmolops import GetMolFrags
+from rdkit.Contrib.IFG import ifg
 
 logger = logging.getLogger(__name__)
 RDLogger.DisableLog('rdApp.*')
@@ -65,6 +67,18 @@ class PredictionResult(object):
 
 class FormatConverter(object):
 
+    @staticmethod
+    def mass(smiles):
+        return Descriptors.MolWt(FormatConverter.from_smiles(smiles))
+
+    @staticmethod
+    def charge(smiles):
+        return Chem.GetFormalCharge(FormatConverter.from_smiles(smiles))
+
+    @staticmethod
+    def formula(smiles):
+        return Chem.rdMolDescriptors.CalcMolFormula(FormatConverter.from_smiles(smiles))
+
     @staticmethod
     def from_smiles(smiles):
         return Chem.MolFromSmiles(smiles)
@@ -77,6 +91,10 @@ class FormatConverter(object):
     def InChIKey(smiles):
         return Chem.MolToInchiKey(FormatConverter.from_smiles(smiles))
 
+    @staticmethod
+    def InChI(smiles):
+        return Chem.MolToInchi(FormatConverter.from_smiles(smiles))
+
     @staticmethod
     def canonicalize(smiles: str):
         return FormatConverter.to_smiles(FormatConverter.from_smiles(smiles), canonical=True)
@@ -87,6 +105,21 @@ class FormatConverter(object):
         bitvec = MACCSkeys.GenMACCSKeys(mol)
         return bitvec.ToList()
 
+    @staticmethod
+    def get_functional_groups(smiles: str) -> List[str]:
+        res = list()
+
+        try:
+            m = Chem.MolFromSmiles(smiles)
+            fgs = ifg.identify_functional_groups(m)
+            for fg in fgs:
+                # TODO atoms or type?
+                res.append(fg.atoms)
+        except AttributeError:
+            logger.debug(f"Could not get functional groups for {smiles}")
+
+        return res
+
     @staticmethod
     def to_svg(smiles, mol_size=(200, 150), kekulize=True):
         mol = FormatConverter.from_smiles(smiles)
@@ -131,6 +164,24 @@ class FormatConverter(object):
         # TODO call to AMBIT Service
         return smiles
 
+    @staticmethod
+    def ep_standardize(smiles):
+        change = True
+        while change:
+            change = False
+            for standardizer in MATCH_STANDARDIZER:
+                tmp_smiles = standardizer.standardize(smiles)
+
+                if tmp_smiles != smiles:
+                    print(f"change {smiles} to {tmp_smiles}")
+                    change = True
+                    smiles = tmp_smiles
+
+            if change is False:
+                print(f"nothing changed")
+
+        return smiles
+
     @staticmethod
     def standardize(smiles):
         # Taken from https://bitsilla.com/blog/2021/06/standardizing-a-molecule-using-rdkit/
@@ -180,54 +231,6 @@ class FormatConverter(object):
                 atom.UpdatePropertyCache()
         return mol
 
-    # @staticmethod
-    # def apply(smiles, smirks, preprocess_smiles=True, bracketize=False, standardize=True):
-    #     logger.debug(f'Applying {smirks} on {smiles}')
-    #
-    #     if bracketize:
-    #         smirks = smirks.split('>>')[0] + ">>(" + smirks.split('>>')[1] + ")"
-    #
-    #     res = set()
-    #     try:
-    #         rxn = rdChemReactions.ReactionFromSmarts(smirks)
-    #         mol = Chem.MolFromSmiles(smiles)
-    #
-    #         # Inplace
-    #         if preprocess_smiles:
-    #             Chem.SanitizeMol(mol)
-    #             mol = Chem.AddHs(mol)
-    #
-    #         # apply!
-    #         reacts = rxn.RunReactants((mol,))
-    #         if len(reacts):
-    #             # Sanitize mols
-    #             for product_set in reacts:
-    #                 prod_set = list()
-    #                 for product in product_set:
-    #                     # Fixes
-    #                     # [2025-01-30 23:00:50] ERROR chem - Sanitizing and converting failed:
-    #                     # non-ring atom 3 marked aromatic
-    #                     # But does not improve overall performance
-    #                     #
-    #                     # for a in product.GetAtoms():
-    #                     #     if (not a.IsInRing()) and a.GetIsAromatic():
-    #                     #         a.SetIsAromatic(False)
-    #                     # for b in product.GetBonds():
-    #                     #     if (not b.IsInRing()) and b.GetIsAromatic():
-    #                     #         b.SetIsAromatic(False)
-    #
-    #                     try:
-    #                         Chem.SanitizeMol(product)
-    #                         prod_set.append(FormatConverter.standardize(Chem.MolToSmiles(product)))
-    #                     except ValueError as e:
-    #                         logger.error(f'Sanitizing and converting failed:\n{e}')
-    #                         continue
-    #                 res.add(tuple(list(set(prod_set))))
-    #     except Exception as e:
-    #         logger.error(f'Applying {smirks} on {smiles} failed:\n{e}')
-    #
-    #     return list(res)
-
     @staticmethod
     def is_valid_smirks(smirks: str) -> bool:
         try:
@@ -237,7 +240,7 @@ class FormatConverter(object):
             return False
 
     @staticmethod
-    def apply(smiles: str, smirks: str, preprocess_smiles: bool = True, bracketize: bool = False,
+    def apply(smiles: str, smirks: str, preprocess_smiles: bool = True, bracketize: bool = True,
               standardize: bool = True, kekulize: bool = True) -> List['ProductSet']:
         logger.debug(f'Applying {smirks} on {smiles}')
 
@@ -266,8 +269,10 @@ class FormatConverter(object):
                     for product in product_set:
                         try:
                             Chem.SanitizeMol(product)
-
-                            product = FormatConverter.standardize(Chem.MolToSmiles(product))
+                            product = GetMolFrags(product, asMols=True)
+                            for p in product:
+                                p = FormatConverter.standardize(Chem.MolToSmiles(p))
+                                prods.append(p)
 
                             # if kekulize:
                             #     # from rdkit.Chem import MolStandardize
@@ -292,13 +297,12 @@ class FormatConverter(object):
                             #     #     bond.SetIsAromatic(False)
                             #     Chem.Kekulize(product)
 
-                            prods.append(product)
+
                         except ValueError as e:
                             logger.error(f'Sanitizing and converting failed:\n{e}')
                             continue
 
-                    # TODO doc!
-                    if len(prods) and len(prods) == len(product_set):
+                    if len(prods):
                         ps = ProductSet(prods)
                         pss.add(ps)
 
@@ -651,7 +655,7 @@ class IndigoUtils(object):
                         environment.add(mappedAtom.index())
 
         for k, v in functional_groups.items():
-
+            try:
                 sanitized = IndigoUtils.sanitize_functional_group(k)
 
                 query = indigo.loadSmarts(sanitized)
@@ -666,6 +670,9 @@ class IndigoUtils(object):
 
                             counts[mappedAtom.index()] = max(v, counts[mappedAtom.index()])
 
+            except IndigoException as e:
+                logger.debug(f'Colorizing failed due to {e}')
+
         for k, v in counts.items():
             if is_reaction:
                 color = "128, 0, 128"
@@ -691,6 +698,9 @@ class IndigoUtils(object):
         i.setOption("render-image-size", width, height)
         i.setOption("render-bond-line-width", 2.0)
 
+        if '~' in mol_data:
+            mol = i.loadSmarts(mol_data)
+        else:
             mol = i.loadMolecule(mol_data)
 
         if len(functional_groups.keys()) > 0:

utilities/misc.py

@@ -0,0 +1,168 @@
+import html
+import logging
+from collections import defaultdict
+from enum import Enum
+from types import NoneType
+from typing import Dict, List, Any
+
+from envipy_additional_information import Interval, EnviPyModel
+from envipy_additional_information import NAME_MAPPING
+from pydantic import BaseModel, HttpUrl
+
+logger = logging.getLogger(__name__)
+
+
+class HTMLGenerator:
+    registry = {x.__name__: x for x in NAME_MAPPING.values()}
+
+    @staticmethod
+    def generate_html(additional_information: 'EnviPyModel', prefix='') -> str:
+        from typing import get_origin, get_args, Union
+
+        if isinstance(additional_information, type):
+            clz_name = additional_information.__name__
+        else:
+            clz_name = additional_information.__class__.__name__
+
+        widget = f'<h4>{clz_name}</h4>'
+
+        if hasattr(additional_information, 'uuid'):
+            uuid = additional_information.uuid
+            widget += f'<input type="hidden" name="{clz_name}__{prefix}__uuid" value="{uuid}">'
+
+        for name, field in additional_information.model_fields.items():
+            value = getattr(additional_information, name, None)
+            full_name = f"{clz_name}__{prefix}__{name}"
+            annotation = field.annotation
+            base_type = get_origin(annotation) or annotation
+
+            # Optional[Interval[float]] alias for Union[X, None]
+            if base_type is Union:
+                for arg in get_args(annotation):
+                    if arg is not NoneType:
+                        field_type = arg
+                        break
+            else:
+                field_type = base_type
+
+            is_interval_float = (
+                    field_type == Interval[float] or
+                    str(field_type) == str(Interval[float]) or
+                    'Interval[float]' in str(field_type)
+            )
+
+            if is_interval_float:
+                widget += f"""
+                    <div class="form-group row">
+                        <div class="col-md-6">
+                            <label for="{full_name}__start">{' '.join([x.capitalize() for x in name.split('_')])} Start</label>
+                            <input type="number" class="form-control" id="{full_name}__start" name="{full_name}__start" value="{value.start if value else ''}">
+                        </div>
+                        <div class="col-md-6">
+                            <label for="{full_name}__end">{' '.join([x.capitalize() for x in name.split('_')])} End</label>
+                            <input type="number" class="form-control" id="{full_name}__end" name="{full_name}__end" value="{value.end if value else ''}">
+                        </div>
+                    </div>
+                """
+            elif issubclass(field_type, Enum):
+                options: str = ''
+                for e in field_type:
+                    options += f'<option value="{e.value}" {"selected" if e == value else ""}>{html.escape(e.name)}</option>'
+
+                widget += f"""
+                <div class="form-group">
+                    <label for="{full_name}">{' '.join([x.capitalize() for x in name.split('_')])}</label>
+                    <select class="form-control" id="{full_name}" name="{full_name}">
+                        <option value="" disabled selected>Select {' '.join([x.capitalize() for x in name.split('_')])}</option>
+                        {options}
+                    </select>
+                </div>
+                """
+            else:
+                if field_type == str or field_type == HttpUrl:
+                    input_type = 'text'
+                elif field_type == float or field_type == int:
+                    input_type = 'number'
+                elif field_type == bool:
+                    input_type = 'checkbox'
+                else:
+                    raise ValueError(f"Could not parse field type {field_type} for {name}")
+
+                value_to_use = value if value and field_type != bool else ''
+
+                widget += f"""
+                <div class="form-group">
+                    <label for="{full_name}">{' '.join([x.capitalize() for x in name.split('_')])}</label>
+                    <input type="{input_type}" class="form-control" id="{full_name}" name="{full_name}" value="{value_to_use}" {"checked" if value and field_type == bool else ""}>
+                </div>
+                """
+
+        return widget + "<hr>"
+
+    @staticmethod
+    def build_models(params) -> Dict[str, List['EnviPyModel']]:
+
+        def has_non_none(d):
+            """
+            Recursively checks if any value in a (possibly nested) dict is not None.
+            """
+            for value in d.values():
+                if isinstance(value, dict):
+                    if has_non_none(value):  # recursive check
+                        return True
+                elif value is not None:
+                    return True
+            return False
+
+        """
+        Build Pydantic model instances from flattened HTML parameters.
+
+        Args:
+            params: dict of {param_name: value}, e.g. form data
+            model_registry: mapping of class names (strings) to Pydantic model classes
+
+        Returns:
+            dict: {ClassName: [list of model instances]}
+        """
+        grouped: Dict[str, Dict[str, Dict[str, Any]]] = {}
+
+        # Step 1: group fields by ClassName and Number
+        for key, value in params.items():
+            if value == '':
+                value = None
+
+            parts = key.split("__")
+            if len(parts) < 3:
+                continue  # skip invalid keys
+
+            class_name, number, *field_parts = parts
+            grouped.setdefault(class_name, {}).setdefault(number, {})
+
+            # handle nested fields like interval__start
+            target = grouped[class_name][number]
+            current = target
+            for p in field_parts[:-1]:
+                current = current.setdefault(p, {})
+            current[field_parts[-1]] = value
+
+        # Step 2: instantiate Pydantic models
+        instances: Dict[str, List[BaseModel]] = defaultdict(list)
+        for class_name, number_dict in grouped.items():
+            model_cls = HTMLGenerator.registry.get(class_name)
+
+            if not model_cls:
+                logger.info(f"Could not find model class for {class_name}")
+                continue
+
+            for number, fields in number_dict.items():
+                if not has_non_none(fields):
+                    print(f"Skipping empty {class_name} {number} {fields}")
+                    continue
+
+                uuid = fields.pop('uuid', None)
+                instance = model_cls(**fields)
+                if uuid:
+                    instance.__dict__['uuid'] = uuid
+                instances[class_name].append(instance)
+
+        return instances

utilities/ml.py

@@ -1,46 +1,29 @@
 from __future__ import annotations
 
-import dataclasses
+import logging
+from abc import ABC, abstractmethod
 from collections import defaultdict
 from datetime import datetime
-from typing import List, Optional
+from typing import List, Dict, Set, Tuple
+
 import numpy as np
 from sklearn.base import BaseEstimator, ClassifierMixin
 from sklearn.decomposition import PCA
+from sklearn.ensemble import RandomForestClassifier
 from sklearn.metrics import accuracy_score
 from sklearn.multioutput import ClassifierChain
 from sklearn.preprocessing import StandardScaler
-from sklearn.tree import DecisionTreeClassifier
-from sklearn.ensemble import RandomForestClassifier
 
-# @dataclasses.dataclass
-# class Feature:
-#     name: str
-#     value: float
-#
-#
-#
-# class Row:
-#     def __init__(self, compound_uuid: str, compound_smiles: str, descriptors: List[int]):
-#         self.data = {}
-#
-#
-#
-# class DataSet(object):
-#
-#     def __init__(self):
-#         self.rows: List[Row] = []
-#
-#     def add_row(self, row: Row):
-#         pass
+logger = logging.getLogger(__name__)
+
 
 from dataclasses import dataclass, field
 
-from utilities.chem import FormatConverter
+from utilities.chem import FormatConverter, PredictionResult
 
 
 @dataclass
-class Compound:
+class SCompound:
     smiles: str
     uuid: str = field(default=None, compare=False, hash=False)
 
@@ -53,10 +36,10 @@ class Compound:
 
 
 @dataclass
-class Reaction:
-    educts: List[Compound]
-    products: List[Compound]
-    rule_uuid: str = field(default=None, compare=False, hash=False)
+class SReaction:
+    educts: List[SCompound]
+    products: List[SCompound]
+    rule_uuid: SRule = field(default=None, compare=False, hash=False)
     reaction_uuid: str = field(default=None, compare=False, hash=False)
 
     def __hash__(self):
@@ -68,7 +51,7 @@ class Reaction:
         return self._hash
 
     def __eq__(self, other):
-        if not isinstance(other, Reaction):
+        if not isinstance(other, SReaction):
             return NotImplemented
         return (
                 sorted(self.educts, key=lambda x: x.smiles) == sorted(other.educts, key=lambda x: x.smiles) and
@@ -76,69 +59,296 @@ class Reaction:
         )
 
 
-class Dataset(object):
+@dataclass
+class SRule(ABC):
 
-    def __init__(self, headers=List['str'], data=List[List[str|int|float]]):
-        self.headers = headers
+    @abstractmethod
+    def apply(self):
+        pass
+
+
+@dataclass
+class SSimpleRule:
+    pass
+
+
+@dataclass
+class SParallelRule:
+    pass
+
+
+class Dataset:
+
+    def __init__(self, columns: List[str], num_labels: int, data: List[List[str | int | float]] = None):
+        self.columns: List[str] = columns
+        self.num_labels: int = num_labels
+
+        if data is None:
+            self.data: List[List[str | int | float]] = list()
+        else:
             self.data = data
 
+        self.num_features: int = len(columns) - self.num_labels
+        self._struct_features: Tuple[int, int] = self._block_indices('feature_')
+        self._triggered: Tuple[int, int] = self._block_indices('trig_')
+        self._observed: Tuple[int, int] = self._block_indices('obs_')
 
-    def features(self):
-        pass
+    def _block_indices(self, prefix) -> Tuple[int, int]:
+        indices: List[int] = []
+        for i, feature in enumerate(self.columns):
+            if feature.startswith(prefix):
+                indices.append(i)
 
-    def labels(self):
-        pass
+        return min(indices), max(indices)
 
-    def to_json(self):
-        pass
+    def structure_id(self):
+        return self.data[0][0]
 
-    def to_csv(self):
-        pass
+    def add_row(self, row: List[str | int | float]):
+        if len(self.columns) != len(row):
+            raise ValueError(f"Header and Data are not aligned {len(self.columns)} vs. {len(row)}")
+        self.data.append(row)
 
-    def to_arff(self):
-        pass
+    def times_triggered(self, rule_uuid) -> int:
+        idx = self.columns.index(f'trig_{rule_uuid}')
+
+        times_triggered = 0
+        for row in self.data:
+            if row[idx] == 1:
+                times_triggered += 1
+
+        return times_triggered
+
+    def struct_features(self) -> Tuple[int, int]:
+        return self._struct_features
+
+    def triggered(self) -> Tuple[int, int]:
+        return self._triggered
+
+    def observed(self) -> Tuple[int, int]:
+        return self._observed
+
+    def at(self, position: int) -> Dataset:
+        return Dataset(self.columns, self.num_labels, [self.data[position]])
+
+    def limit(self, limit: int) -> Dataset:
+        return Dataset(self.columns, self.num_labels, self.data[:limit])
+
+    def __iter__(self):
+        return (self.at(i) for i, _ in enumerate(self.data))
 
 
+    def classification_dataset(self, structures: List[str | 'CompoundStructure'], applicable_rules: List['Rule']) -> Tuple[Dataset, List[List[PredictionResult]]]:
+        classify_data = []
+        classify_products = []
+        for struct in structures:
 
-class DatasetGenerator(object):
+            if isinstance(struct, str):
+                struct_id = None
+                struct_smiles = struct
+            else:
+                struct_id = str(struct.uuid)
+                struct_smiles = struct.smiles
+
+            features = FormatConverter.maccs(struct_smiles)
+
+            trig = []
+            prods = []
+            for rule in applicable_rules:
+                products = rule.apply(struct_smiles)
+
+                if len(products):
+                    trig.append(1)
+                    prods.append(products)
+                else:
+                    trig.append(0)
+                    prods.append([])
+
+            classify_data.append([struct_id] + features + trig + ([-1] * len(trig)))
+            classify_products.append(prods)
+
+        return Dataset(columns=self.columns, num_labels=self.num_labels, data=classify_data), classify_products
 
     @staticmethod
-    def generate_dataset(compounds: List[Compound], reactions: List[Reaction], applicable_rules: 'Rule',
-                         compounds_to_exclude: Optional[Compound] = None, educts_only: bool = False) -> Dataset:
+    def generate_dataset(reactions: List['Reaction'], applicable_rules: List['Rule'], educts_only: bool = True) -> Dataset:
+        _structures = set()
 
-        rows = []
-
-        if educts_only:
-            compounds = set()
         for r in reactions:
-                for e in r.educts:
-                    compounds.add(e)
-            compounds = list(compounds)
+            for e in r.educts.all():
+                _structures.add(e)
 
-        total = len(compounds)
-        for i, c in enumerate(compounds):
-            row = []
-            print(f"{i + 1}/{total} - {c.smiles}")
-            for r in applicable_rules:
-                product_sets = r.rule.apply(c.smiles)
+            if not educts_only:
+                for e in r.products:
+                    _structures.add(e)
+
+        compounds = sorted(_structures, key=lambda x: x.url)
+
+        triggered: Dict[str, Set[str]] = defaultdict(set)
+        observed: Set[str] = set()
+
+        # Apply rules on collected compounds and store tps
+        for i, comp in enumerate(compounds):
+            logger.debug(f"{i + 1}/{len(compounds)}...")
+
+            for rule in applicable_rules:
+                product_sets = rule.apply(comp.smiles)
 
                 if len(product_sets) == 0:
-                    row.append([])
                     continue
 
-                #triggered.add(f"{r.uuid} + {c.uuid}")
-                reacts = set()
-                for ps in product_sets:
-                    products = []
-                    for p in ps:
-                        products.append(Compound(FormatConverter.standardize(p)))
+                key = f"{rule.uuid} + {comp.uuid}"
 
-                    reacts.add(Reaction([c], products, r))
-                row.append(list(reacts))
+                if key in triggered:
+                    logger.info(f"{key} already present. Duplicate reaction?")
 
-            rows.append(row)
+                for prod_set in product_sets:
+                    for smi in prod_set:
 
-        return rows
+                        try:
+                            smi = FormatConverter.standardize(smi)
+                        except Exception:
+                            # :shrug:
+                            logger.debug(f'Standardizing SMILES failed for {smi}')
+                            pass
+
+                        triggered[key].add(smi)
+
+        for i, r in enumerate(reactions):
+            logger.debug(f"{i + 1}/{len(reactions)}...")
+
+            if len(r.educts.all()) != 1:
+                logger.debug(f"Skipping {r.url} as it has {len(r.educts.all())} substrates!")
+                continue
+
+            for comp in r.educts.all():
+                for rule in applicable_rules:
+                    key = f"{rule.uuid} + {comp.uuid}"
+
+                    if key not in triggered:
+                        continue
+
+                    # standardize products from reactions for comparison
+                    standardized_products = []
+                    for cs in r.products.all():
+                        smi = cs.smiles
+
+                        try:
+                            smi = FormatConverter.standardize(smi)
+                        except Exception as e:
+                            # :shrug:
+                            logger.debug(f'Standardizing SMILES failed for {smi}')
+                            pass
+
+                        standardized_products.append(smi)
+
+                    if len(set(standardized_products).difference(triggered[key])) == 0:
+                        observed.add(key)
+                    else:
+                        pass
+
+        ds = None
+
+        for i, comp in enumerate(compounds):
+            # Features
+            feat = FormatConverter.maccs(comp.smiles)
+            trig = []
+            obs = []
+
+            for rule in applicable_rules:
+                key = f"{rule.uuid} + {comp.uuid}"
+
+                # Check triggered
+                if key in triggered:
+                    trig.append(1)
+                else:
+                    trig.append(0)
+
+                # Check obs
+                if key in observed:
+                    obs.append(1)
+                elif key not in triggered:
+                    obs.append(None)
+                else:
+                    obs.append(0)
+
+            if ds is None:
+                header = ['structure_id'] + \
+                         [f'feature_{i}' for i, _ in enumerate(feat)] \
+                         + [f'trig_{r.uuid}' for r in applicable_rules] \
+                         + [f'obs_{r.uuid}' for r in applicable_rules]
+                ds = Dataset(header, len(applicable_rules))
+
+            ds.add_row([str(comp.uuid)] + feat + trig + obs)
+
+        return ds
+
+
+    def X(self, exclude_id_col=True, na_replacement=0):
+        res =  self.__getitem__((slice(None), slice(1 if exclude_id_col else 0, len(self.columns) - self.num_labels)))
+        if na_replacement is not None:
+            res = [[x if x is not None else na_replacement for x in row] for row in res]
+        return res
+
+
+    def y(self, na_replacement=0):
+        res = self.__getitem__((slice(None), slice(len(self.columns) - self.num_labels, None)))
+        if na_replacement is not None:
+            res = [[x if x is not None else na_replacement for x in row] for row in res]
+        return res
+
+
+    def __getitem__(self, key):
+        if not isinstance(key, tuple):
+            raise TypeError("Dataset must be indexed with dataset[rows, columns]")
+
+        row_key, col_key = key
+
+        # Normalize rows
+        if isinstance(row_key, int):
+            rows = [self.data[row_key]]
+        else:
+            rows = self.data[row_key]
+
+        # Normalize columns
+        if isinstance(col_key, int):
+            res = [row[col_key] for row in rows]
+        else:
+            res = [[row[i] for i in range(*col_key.indices(len(row)))] if isinstance(col_key, slice)
+                    else [row[i] for i in col_key] for row in rows]
+
+        return res
+
+    def save(self, path: 'Path'):
+        import pickle
+        with open(path, "wb") as fh:
+            pickle.dump(self, fh)
+
+    @staticmethod
+    def load(path: 'Path'):
+        import pickle
+        return pickle.load(open(path, "rb"))
+
+    def to_arff(self, path: 'Path'):
+        arff = f"@relation 'enviPy-dataset: -C {self.num_labels}'\n"
+        arff += "\n"
+        for c in self.columns[-self.num_labels:] + self.columns[:self.num_features]:
+            if c == 'structure_id':
+                arff += f"@attribute {c} string\n"
+            else:
+                arff += f"@attribute {c} {{0,1}}\n"
+
+        arff += f"\n@data\n"
+        for d in self.data:
+            ys = ','.join([str(v if v is not None else '?') for v in d[-self.num_labels:]])
+            xs = ','.join([str(v if v is not None else '?') for v in d[:self.num_features]])
+            arff += f'{ys},{xs}\n'
+
+        with open(path, "w") as fh:
+            fh.write(arff)
+            fh.flush()
+
+    def __repr__(self):
+        return f"<Dataset #rows={len(self.data)} #cols={len(self.columns)} #labels={self.num_labels}>"
 
 
 class SparseLabelECC(BaseEstimator, ClassifierMixin):
@@ -166,8 +376,7 @@ class SparseLabelECC(BaseEstimator, ClassifierMixin):
                 self.keep_columns_.append(col)
 
         y_reduced = y[:, self.keep_columns_]
-        self.chains_ = [ClassifierChain(self.base_clf, order='random', random_state=i)
-                        for i in range(self.num_chains)]
+        self.chains_ = [ClassifierChain(self.base_clf) for i in range(self.num_chains)]
 
         for i, chain in enumerate(self.chains_):
             print(f"{datetime.now()} fitting {i + 1}/{self.num_chains}")
@@ -208,26 +417,169 @@ class SparseLabelECC(BaseEstimator, ClassifierMixin):
         return accuracy_score(y_true, y_pred, sample_weight=sample_weight)
 
 
-class ApplicabilityDomain(PCA):
 
-    def __init__(self, n_components=5):
-        super().__init__(n_components=n_components)
+import copy
+
+import numpy as np
+from sklearn.dummy import DummyClassifier
+from sklearn.tree import DecisionTreeClassifier
+
+
+class BinaryRelevance:
+    def __init__(self, baseline_clf):
+        self.clf = baseline_clf
+        self.classifiers = None
+
+    def fit(self, X, Y):
+        if self.classifiers is None:
+            self.classifiers = []
+
+        for l in range(len(Y[0])):
+            X_l = X[~np.isnan(Y[:, l])]
+            Y_l = (Y[~np.isnan(Y[:, l]), l])
+            if len(X_l) == 0:  # all labels are nan -> predict 0
+                clf = DummyClassifier(strategy='constant', constant=0)
+                clf.fit([X[0]], [0])
+                self.classifiers.append(clf)
+                continue
+            elif len(np.unique(Y_l)) == 1:  # only one class -> predict that class
+                clf = DummyClassifier(strategy='most_frequent')
+            else:
+                clf = copy.deepcopy(self.clf)
+            clf.fit(X_l, Y_l)
+            self.classifiers.append(clf)
+
+    def predict(self, X):
+        labels = []
+        for clf in self.classifiers:
+            labels.append(clf.predict(X))
+        return np.column_stack(labels)
+
+    def predict_proba(self, X):
+        labels = np.empty((len(X), 0))
+        for clf in self.classifiers:
+            pred = clf.predict_proba(X)
+            if pred.shape[1] > 1:
+                pred = pred[:, 1]
+            else:
+                pred = pred * clf.predict([X[0]])[0]
+            labels = np.column_stack((labels, pred))
+        return labels
+
+
+class MissingValuesClassifierChain:
+    def __init__(self, base_clf):
+        self.base_clf = base_clf
+        self.permutation = None
+        self.classifiers = None
+
+    def fit(self, X, Y):
+        X = np.array(X)
+        Y = np.array(Y)
+        if self.permutation is None:
+            self.permutation = np.random.permutation(len(Y[0]))
+
+        Y = Y[:, self.permutation]
+
+        if self.classifiers is None:
+            self.classifiers = []
+
+        for p in range(len(self.permutation)):
+            X_p = X[~np.isnan(Y[:, p])]
+            Y_p = Y[~np.isnan(Y[:, p]), p]
+            if len(X_p) == 0:  # all labels are nan -> predict 0
+                clf = DummyClassifier(strategy='constant', constant=0)
+                self.classifiers.append(clf.fit([X[0]], [0]))
+            elif len(np.unique(Y_p)) == 1:  # only one class -> predict that class
+                clf = DummyClassifier(strategy='most_frequent')
+                self.classifiers.append(clf.fit(X_p, Y_p))
+            else:
+                clf = copy.deepcopy(self.base_clf)
+                self.classifiers.append(clf.fit(X_p, Y_p))
+            newcol = Y[:, p]
+            pred = clf.predict(X)
+            newcol[np.isnan(newcol)] = pred[np.isnan(newcol)]  # fill in missing values with clf predictions
+            X = np.column_stack((X, newcol))
+
+    def predict(self, X):
+        labels = np.empty((len(X), 0))
+        for clf in self.classifiers:
+            pred = clf.predict(np.column_stack((X, labels)))
+            labels = np.column_stack((labels, pred))
+        return labels[:, np.argsort(self.permutation)]
+
+    def predict_proba(self, X):
+        labels = np.empty((len(X), 0))
+        for clf in self.classifiers:
+            pred = clf.predict_proba(np.column_stack((X, np.round(labels))))
+            if pred.shape[1] > 1:
+                pred = pred[:, 1]
+            else:
+                pred = pred * clf.predict(np.column_stack(([X[0]], np.round([labels[0]]))))[0]
+            labels = np.column_stack((labels, pred))
+        return labels[:, np.argsort(self.permutation)]
+
+
+class EnsembleClassifierChain:
+    def __init__(self, base_clf, num_chains=10):
+        self.base_clf = base_clf
+        self.num_chains = num_chains
+        self.num_labels = None
+        self.classifiers = None
+
+    def fit(self, X, Y):
+        if self.classifiers is None:
+            self.classifiers = []
+
+        if self.num_labels is None:
+            self.num_labels = len(Y[0])
+
+        for p in range(self.num_chains):
+            print(f"{datetime.now()} fitting {p + 1}/{self.num_chains}")
+            clf = MissingValuesClassifierChain(self.base_clf)
+            clf.fit(X, Y)
+            self.classifiers.append(clf)
+
+    def predict(self, X):
+        labels = np.zeros((len(X), self.num_labels))
+        for clf in self.classifiers:
+            labels += clf.predict(X)
+        return np.round(labels / self.num_chains)
+
+    def predict_proba(self, X):
+        labels = np.zeros((len(X), self.num_labels))
+        for clf in self.classifiers:
+            labels += clf.predict_proba(X)
+        return labels / self.num_chains
+
+
+
+
+class ApplicabilityDomainPCA(PCA):
+
+    def __init__(self, num_neighbours: int = 5):
+        super().__init__(n_components=num_neighbours)
         self.scaler = StandardScaler()
+        self.num_neighbours = num_neighbours
         self.min_vals = None
         self.max_vals = None
 
-    def build(self, X):
+    def build(self, train_dataset: 'Dataset'):
         # transform
-        X_scaled = self.scaler.fit_transform(X)
+        X_scaled = self.scaler.fit_transform(train_dataset.X())
         # fit pca
         X_pca = self.fit_transform(X_scaled)
 
         self.max_vals = np.max(X_pca, axis=0)
         self.min_vals = np.min(X_pca, axis=0)
 
-    def is_applicable(self, instances):
+    def __transform(self, instances):
         instances_scaled = self.scaler.transform(instances)
         instances_pca = self.transform(instances_scaled)
+        return instances_pca
+
+    def is_applicable(self, classify_instances: 'Dataset'):
+        instances_pca = self.__transform(classify_instances.X())
 
         is_applicable = []
         for i, instance in enumerate(instances_pca):
@@ -237,3 +589,17 @@ class ApplicabilityDomain(PCA):
                     is_applicable[i] = False
 
         return is_applicable
+
+
+def tanimoto_distance(a: List[int], b: List[int]):
+    if len(a) != len(b):
+        raise ValueError(f"Lists must be the same length {len(a)} != {len(b)}")
+
+    sum_a = sum(a)
+    sum_b = sum(b)
+    sum_c = sum(v1 and v2 for v1, v2 in zip(a, b))
+
+    if sum_a + sum_b - sum_c == 0:
+        return 0.0
+
+    return 1 - (sum_c / (sum_a + sum_b - sum_c))

uv.lock

@@ -200,6 +200,63 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/4a/7e/3db2bd1b1f9e95f7cddca6d6e75e2f2bd9f51b1246e546d88addca0106bd/certifi-2025.4.26-py3-none-any.whl", hash = "sha256:30350364dfe371162649852c63336a15c70c6510c2ad5015b21c2345311805f3", size = 159618 },
 ]
 
+[[package]]
+name = "cffi"
+version = "1.17.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pycparser" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/fc/97/c783634659c2920c3fc70419e3af40972dbaf758daa229a7d6ea6135c90d/cffi-1.17.1.tar.gz", hash = "sha256:1c39c6016c32bc48dd54561950ebd6836e1670f2ae46128f67cf49e789c52824", size = 516621 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/90/07/f44ca684db4e4f08a3fdc6eeb9a0d15dc6883efc7b8c90357fdbf74e186c/cffi-1.17.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:df8b1c11f177bc2313ec4b2d46baec87a5f3e71fc8b45dab2ee7cae86d9aba14", size = 182191 },
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