[Feature] Legacy API Layer (#80)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#80

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

@@ -308,11 +308,22 @@ 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

envipath/urls.py

@@ -17,11 +17,12 @@ 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),
 ]

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}")
 
@@ -426,11 +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()
 

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

@@ -2,7 +2,6 @@ from django.conf import settings
 from django.shortcuts import redirect
 from django.urls import reverse
 
-
 class LoginRequiredMiddleware:
     def __init__(self, get_response):
         self.get_response = get_response
@@ -11,6 +10,7 @@ class LoginRequiredMiddleware:
                                reverse('logout'),
                                reverse('admin:login'),
                                reverse('admin:index'),
+                               '/api/legacy/'
                            ] + getattr(settings, 'LOGIN_EXEMPT_URLS', [])
 
     def __call__(self, 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/models.py

@@ -20,6 +20,7 @@ from django.db import models, transaction
 from django.db.models import JSONField, Count, Q, QuerySet
 from django.utils import timezone
 from django.utils.functional import cached_property
+from envipy_additional_information import EnviPyModel
 from model_utils.models import TimeStampedModel
 from polymorphic.models import PolymorphicModel
 from sklearn.metrics import precision_score, recall_score, jaccard_score
@@ -37,9 +38,8 @@ logger = logging.getLogger(__name__)
 
 class User(AbstractUser):
     email = models.EmailField(unique=True)
-
-    uuid = models.UUIDField(null=False, blank=False, verbose_name='UUID of this object', unique=True,
-                            default=uuid4)
+    uuid = models.UUIDField(null=False, blank=False, verbose_name='UUID of this object', unique=True, default=uuid4)
+    url = models.TextField(blank=False, null=True, verbose_name='URL', unique=True)
     default_package = models.ForeignKey('epdb.Package', verbose_name='Default Package', null=True,
                                         on_delete=models.SET_NULL)
     default_group = models.ForeignKey('Group', verbose_name='Default Group', null=True, blank=False,
@@ -50,8 +50,13 @@ class User(AbstractUser):
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ['username']
 
-    @property
-    def url(self):
+    def save(self, *args, **kwargs):
+        if not self.url:
+            self.url = self._url()
+
+        super().save(*args, **kwargs)
+
+    def _url(self):
         return '{}/user/{}'.format(s.SERVER_URL, self.uuid)
 
     def prediction_settings(self):
@@ -169,6 +174,7 @@ class APIToken(TimeStampedModel):
 
 class Group(TimeStampedModel):
     uuid = models.UUIDField(null=False, blank=False, verbose_name='UUID of this object', unique=True, default=uuid4)
+    url = models.TextField(blank=False, null=True, verbose_name='URL', unique=True)
     name = models.TextField(blank=False, null=False, verbose_name='Group name')
     owner = models.ForeignKey("User", verbose_name='Group Owner', on_delete=models.CASCADE)
     public = models.BooleanField(verbose_name='Public Group', default=False)
@@ -179,8 +185,13 @@ class Group(TimeStampedModel):
     def __str__(self):
         return f"{self.name} (pk={self.pk})"
 
-    @property
-    def url(self):
+    def save(self, *args, **kwargs):
+        if not self.url:
+            self.url = self._url()
+
+        super().save(*args, **kwargs)
+
+    def _url(self):
         return '{}/group/{}'.format(s.SERVER_URL, self.uuid)
 
 
@@ -476,11 +487,18 @@ class EnviPathModel(TimeStampedModel):
     name = models.TextField(blank=False, null=False, verbose_name='Name', default='no name')
     description = models.TextField(blank=False, null=False, verbose_name='Descriptions', default='no description')
 
+    url = models.TextField(blank=False, null=True, verbose_name='URL', unique=True)
+
     kv = JSONField(null=True, blank=True, default=dict)
 
-    @property
+    def save(self, *args, **kwargs):
+        if not self.url:
+            self.url = self._url()
+
+        super().save(*args, **kwargs)
+
     @abc.abstractmethod
-    def url(self):
+    def _url(self):
         pass
 
     def simple_json(self, include_description=False):
@@ -516,15 +534,16 @@ class AliasMixin(models.Model):
     @transaction.atomic
     def add_alias(self, new_alias, set_as_default=False):
         if set_as_default:
-            self.aliases.add(self.name)
+            self.aliases.append(self.name)
             self.name = new_alias
 
             if new_alias in self.aliases:
                 self.aliases.remove(new_alias)
         else:
             if new_alias not in self.aliases:
-                self.aliases.add(new_alias)
+                self.aliases.append(new_alias)
 
+        self.aliases = sorted(list(set(self.aliases)), key=lambda x: x.lower())
         self.save()
 
     class Meta:
@@ -585,8 +604,7 @@ class Package(EnviPathModel):
     def models(self):
         return EPModel.objects.filter(package=self)
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/package/{}'.format(s.SERVER_URL, self.uuid)
 
     def get_applicable_rules(self):
@@ -632,8 +650,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
     def normalized_structure(self):
         return CompoundStructure.objects.get(compound=self, normalized_structure=True)
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/compound/{}'.format(self.package.url, self.uuid)
 
     @transaction.atomic
@@ -747,6 +764,64 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
 
         return cs
 
+    @transaction.atomic
+    def copy(self, target: 'Package', mapping: Dict):
+        if self in mapping:
+            return mapping[self]
+
+        new_compound = Compound.objects.create(
+            package=target,
+            name=self.name,
+            description=self.description,
+            kv=self.kv.copy() if self.kv else {}
+        )
+        mapping[self] = new_compound
+
+        # Copy compound structures
+        for structure in self.structures.all():
+            if structure not in mapping:
+                new_structure = CompoundStructure.objects.create(
+                    compound=new_compound,
+                    smiles=structure.smiles,
+                    canonical_smiles=structure.canonical_smiles,
+                    inchikey=structure.inchikey,
+                    normalized_structure=structure.normalized_structure,
+                    name=structure.name,
+                    description=structure.description,
+                    kv=structure.kv.copy() if structure.kv else {}
+                )
+                mapping[structure] = new_structure
+
+                # Copy external identifiers for structure
+                for ext_id in structure.external_identifiers.all():
+                    ExternalIdentifier.objects.create(
+                        content_object=new_structure,
+                        database=ext_id.database,
+                        identifier_value=ext_id.identifier_value,
+                        url=ext_id.url,
+                        is_primary=ext_id.is_primary
+                    )
+
+        if self.default_structure:
+            new_compound.default_structure = mapping.get(self.default_structure)
+            new_compound.save()
+
+        for a in self.aliases:
+            new_compound.add_alias(a)
+            new_compound.save()
+
+        # Copy external identifiers for compound
+        for ext_id in self.external_identifiers.all():
+            ExternalIdentifier.objects.create(
+                content_object=new_compound,
+                database=ext_id.database,
+                identifier_value=ext_id.identifier_value,
+                url=ext_id.url,
+                is_primary=ext_id.is_primary
+            )
+
+        return new_compound
+
     class Meta:
         unique_together = [('uuid', 'package')]
 
@@ -773,8 +848,7 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
 
         super().save(*args, **kwargs)
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/structure/{}'.format(self.compound.url, self.uuid)
 
     @staticmethod
@@ -803,10 +877,35 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
 
         return cs
 
+    @transaction.atomic
+    def copy(self, target: 'Package', mapping: Dict):
+        if self in mapping:
+            return mapping[self]
+
+        self.compound.copy(target, mapping)
+        return mapping[self]
+
     @property
     def as_svg(self, width: int = 800, height: int = 400):
         return IndigoUtils.mol_to_svg(self.smiles, width=width, height=height)
 
+    @property
+    def related_pathways(self):
+        pathways = Node.objects.filter(node_labels__in=[self]).values_list('pathway', flat=True)
+        return Pathway.objects.filter(package=self.compound.package, id__in=set(pathways)).order_by('name')
+
+    @property
+    def related_reactions(self):
+        return (
+                Reaction.objects.filter(package=self.compound.package, educts__in=[self])
+                |
+                Reaction.objects.filter(package=self.compound.package, products__in=[self])
+        ).order_by('name')
+
+    @property
+    def is_default_structure(self):
+        return self.compound.default_structure == self
+
 
 class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey('epdb.Package', verbose_name='Package', on_delete=models.CASCADE, db_index=True)
@@ -842,22 +941,54 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
         return cls.create(*args, **kwargs)
 
 
-#
-#     @property
-#     def related_pathways(self):
-#         reaction_ids = self.related_reactions.values_list('id', flat=True)
-#         pathways = Edge.objects.filter(edge_label__in=reaction_ids).values_list('pathway', flat=True)
-#         return Pathway.objects.filter(package=self.package, id__in=set(pathways)).order_by('name')
-#
-#     @property
-#     def related_reactions(self):
-#         return (
-#                 Reaction.objects.filter(package=self.package, rules__in=[self])
-#                 |
-#                 Reaction.objects.filter(package=self.package, rules__in=[self])
-#         ).order_by('name')
-#
-#
+    @transaction.atomic
+    def copy(self, target: 'Package', mapping: Dict):
+        """Copy a rule to the target package."""
+        if self in mapping:
+            return mapping[self]
+
+        # Get the specific rule type and copy accordingly
+        rule_type = type(self)
+
+        if rule_type == SimpleAmbitRule:
+            new_rule = SimpleAmbitRule.objects.create(
+                package=target,
+                name=self.name,
+                description=self.description,
+                smirks=self.smirks,
+                reactant_filter_smarts=self.reactant_filter_smarts,
+                product_filter_smarts=self.product_filter_smarts,
+                kv=self.kv.copy() if self.kv else {}
+            )
+        elif rule_type == SimpleRDKitRule:
+            new_rule = SimpleRDKitRule.objects.create(
+                package=target,
+                name=self.name,
+                description=self.description,
+                reaction_smarts=self.reaction_smarts,
+                kv=self.kv.copy() if self.kv else {}
+            )
+        elif rule_type == ParallelRule:
+            new_rule = ParallelRule.objects.create(
+                package=target,
+                name=self.name,
+                description=self.description,
+                kv=self.kv.copy() if self.kv else {}
+            )
+            # Copy simple rules relationships
+            for simple_rule in self.simple_rules.all():
+                copied_simple_rule = simple_rule.copy(target, mapping)
+                new_rule.simple_rules.add(copied_simple_rule)
+        elif rule_type == SequentialRule:
+            raise ValueError("SequentialRule copy not implemented!")
+        else:
+            raise ValueError(f"Unknown rule type: {rule_type}")
+
+        mapping[self] = new_rule
+
+        return new_rule
+
+
 class SimpleRule(Rule):
     pass
 
@@ -917,8 +1048,7 @@ class SimpleAmbitRule(SimpleRule):
         r.save()
         return r
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/simple-ambit-rule/{}'.format(self.package.url, self.uuid)
 
     def apply(self, smiles):
@@ -953,8 +1083,7 @@ class SimpleRDKitRule(SimpleRule):
     def apply(self, smiles):
         return FormatConverter.apply(smiles, self.reaction_smarts)
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/simple-rdkit-rule/{}'.format(self.package.url, self.uuid)
 
 
@@ -963,8 +1092,7 @@ class SimpleRDKitRule(SimpleRule):
 class ParallelRule(Rule):
     simple_rules = models.ManyToManyField('epdb.SimpleRule', verbose_name='Simple rules')
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/parallel-rule/{}'.format(self.package.url, self.uuid)
 
     @property
@@ -1003,8 +1131,7 @@ class SequentialRule(Rule):
     simple_rules = models.ManyToManyField('epdb.SimpleRule', verbose_name='Simple rules',
                                           through='SequentialRuleOrdering')
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/sequential-rule/{}'.format(self.compound.url, self.uuid)
 
     @property
@@ -1039,8 +1166,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
     external_identifiers = GenericRelation('ExternalIdentifier')
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/reaction/{}'.format(self.package.url, self.uuid)
 
     @staticmethod
@@ -1132,6 +1258,50 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
         r.save()
         return r
 
+    @transaction.atomic
+    def copy(self, target: 'Package', mapping: Dict ) -> 'Reaction':
+        """Copy a reaction to the target package."""
+        if self in mapping:
+            return mapping[self]
+
+        # Create new reaction
+        new_reaction = Reaction.objects.create(
+            package=target,
+            name=self.name,
+            description=self.description,
+            multi_step=self.multi_step,
+            medline_references=self.medline_references,
+            kv=self.kv.copy() if self.kv else {}
+        )
+        mapping[self] = new_reaction
+
+        # Copy educts (reactant compounds)
+        for educt in self.educts.all():
+            copied_educt = educt.copy(target, mapping)
+            new_reaction.educts.add(copied_educt)
+
+        # Copy products
+        for product in self.products.all():
+            copied_product = product.copy(target, mapping)
+            new_reaction.products.add(copied_product)
+
+        # Copy rules
+        for rule in self.rules.all():
+            copied_rule = rule.copy(target, mapping)
+            new_reaction.rules.add(copied_rule)
+
+        # Copy external identifiers
+        for ext_id in self.external_identifiers.all():
+            ExternalIdentifier.objects.create(
+                content_object=new_reaction,
+                database=ext_id.database,
+                identifier_value=ext_id.identifier_value,
+                url=ext_id.url,
+                is_primary=ext_id.is_primary
+            )
+
+        return new_reaction
+
     def smirks(self):
         return f"{'.'.join([cs.smiles for cs in self.educts.all()])}>>{'.'.join([cs.smiles for cs in self.products.all()])}"
 
@@ -1167,8 +1337,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     def edges(self):
         return Edge.objects.filter(pathway=self)
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/pathway/{}'.format(self.package.url, self.uuid)
 
     # Mode
@@ -1367,6 +1536,87 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
 
         return pw
 
+    @transaction.atomic
+    def copy(self, target: 'Package', mapping: Dict) -> 'Pathway':
+
+        if self in mapping:
+            return mapping[self]
+
+        # Start copying the pathway
+        new_pathway = Pathway.objects.create(
+            package=target,
+            name=self.name,
+            description=self.description,
+            setting=self.setting, # TODO copy settings?
+            kv=self.kv.copy() if self.kv else {}
+        )
+
+        # # Copy aliases if they exist
+        # if hasattr(self, 'aliases'):
+        #     new_pathway.aliases.set(self.aliases.all())
+        #
+        # # Copy scenarios if they exist
+        # if hasattr(self, 'scenarios'):
+        #     new_pathway.scenarios.set(self.scenarios.all())
+
+        # Copy all nodes first
+        for node in self.nodes.all():
+            # Copy the compound structure for the node label
+            copied_structure = None
+            if node.default_node_label:
+                copied_compound = node.default_node_label.compound.copy(target, mapping)
+                # Find the corresponding structure in the copied compound
+                for structure in copied_compound.structures.all():
+                    if structure.smiles == node.default_node_label.smiles:
+                        copied_structure = structure
+                        break
+
+            new_node = Node.objects.create(
+                pathway=new_pathway,
+                default_node_label=copied_structure,
+                depth=node.depth,
+                name=node.name,
+                description=node.description,
+                kv=node.kv.copy() if node.kv else {}
+            )
+            mapping[node] = new_node
+
+            # Copy node labels (many-to-many relationship)
+            for label in node.node_labels.all():
+                copied_label_compound = label.compound.copy(target, mapping)
+                for structure in copied_label_compound.structures.all():
+                    if structure.smiles == label.smiles:
+                        new_node.node_labels.add(structure)
+                        break
+
+        # Copy all edges
+        for edge in self.edges.all():
+            # Copy the reaction for edge label if it exists
+            copied_reaction = None
+            if edge.edge_label:
+                copied_reaction = edge.edge_label.copy(target, mapping)
+
+            new_edge = Edge.objects.create(
+                pathway=new_pathway,
+                edge_label=copied_reaction,
+                name=edge.name,
+                description=edge.description,
+                kv=edge.kv.copy() if edge.kv else {}
+            )
+
+            # Copy start and end nodes relationships
+            for start_node in edge.start_nodes.all():
+                if start_node in mapping:
+                    new_edge.start_nodes.add(mapping[start_node])
+
+            for end_node in edge.end_nodes.all():
+                if end_node in mapping:
+                    new_edge.end_nodes.add(mapping[end_node])
+
+        mapping[self] = new_pathway
+
+        return new_pathway
+
     @transaction.atomic
     def add_node(self, smiles: str, name: Optional[str] = None, description: Optional[str] = None):
         return Node.create(self, smiles, 0)
@@ -1386,8 +1636,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
     out_edges = models.ManyToManyField('epdb.Edge', verbose_name='Outgoing Edges')
     depth = models.IntegerField(verbose_name='Node depth', null=False, blank=False)
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/node/{}'.format(self.pathway.url, self.uuid)
 
     def d3_json(self):
@@ -1463,8 +1712,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
     start_nodes = models.ManyToManyField('epdb.Node', verbose_name='Start Nodes', related_name='edge_educts')
     end_nodes = models.ManyToManyField('epdb.Node', verbose_name='End Nodes', related_name='edge_products')
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/edge/{}'.format(self.pathway.url, self.uuid)
 
     def d3_json(self):
@@ -1556,8 +1804,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
 class EPModel(PolymorphicModel, EnviPathModel):
     package = models.ForeignKey('epdb.Package', verbose_name='Package', on_delete=models.CASCADE, db_index=True)
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/model/{}'.format(self.package.url, self.uuid)
 
 
@@ -2063,7 +2310,8 @@ class ApplicabilityDomain(EnviPathModel):
                 transformation = {
                     'rule': rule_data,
                     'reliability': rule_reliabilities[rule_idx],
-                    # TODO
+                    # We're setting it here to False, as we don't know whether "assess" is called during pathway
+                    # prediction or from Model Page. For persisted Nodes this field will be overwritten at runtime
                     'is_predicted': False,
                     'local_compatibility': local_compatibilities[rule_idx],
                     'probability': preds[rule_idx].probability,
@@ -2173,33 +2421,93 @@ class Scenario(EnviPathModel):
 
     additional_information = models.JSONField(verbose_name='Additional Information')
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/scenario/{}'.format(self.package.url, self.uuid)
 
     @staticmethod
     @transaction.atomic
-    def create(package, name, description, date, type, additional_information):
+    def create(package: 'Package', name:str, description:str, scenario_date:str, scenario_type:str, additional_information: List['EnviPyModel']):
         s = Scenario()
         s.package = package
+
+        if name is None or name.strip() == '':
+            name = f"Scenario {Scenario.objects.filter(package=package).count() + 1}"
+
         s.name = name
-        s.description = description
-        s.date = date
-        s.type = type
-        s.additional_information = additional_information
+
+        if description is not None and description.strip() != '':
+            s.description = description
+
+        if scenario_date is not None and scenario_date.strip() != '':
+            s.scenario_date = scenario_date
+
+        if scenario_type is not None and scenario_type.strip() != '':
+            s.scenario_type = scenario_type
+
+        add_inf = defaultdict(list)
+
+        for info in additional_information:
+            cls_name = info.__class__.__name__
+            ai_data = json.loads(info.model_dump_json())
+            ai_data['uuid'] = f"{uuid4()}"
+            add_inf[cls_name].append(ai_data)
+
+
+        s.additional_information = add_inf
 
         s.save()
 
         return s
 
-    def add_additional_information(self, data):
-        pass
+    @transaction.atomic
+    def add_additional_information(self, data: 'EnviPyModel'):
+        cls_name = data.__class__.__name__
+        ai_data = json.loads(data.model_dump_json())
+        ai_data['uuid'] = f"{uuid4()}"
 
-    def remove_additional_information(self, data):
-        pass
+        if cls_name not in self.additional_information:
+            self.additional_information[cls_name] = []
 
-    def set_additional_information(self, data):
-        pass
+        self.additional_information[cls_name].append(ai_data)
+        self.save()
+
+
+    @transaction.atomic
+    def remove_additional_information(self, ai_uuid):
+        found_type = None
+        found_idx = -1
+
+        for k, vals in self.additional_information.items():
+            for i, v in enumerate(vals):
+                if v['uuid'] == ai_uuid:
+                    found_type = k
+                    found_idx = i
+                    break
+
+        if found_type is not None and found_idx >= 0:
+            if len(self.additional_information[found_type]) == 1:
+                del self.additional_information[k]
+            else:
+                self.additional_information[k].pop(found_idx)
+            self.save()
+        else:
+            raise ValueError(f"Could not find additional information with uuid {ai_uuid}")
+
+    @transaction.atomic
+    def set_additional_information(self, data: Dict[str, 'EnviPyModel']):
+        new_ais = defaultdict(list)
+        for k, vals in data.items():
+            for v in vals:
+                ai_data = json.loads(v.model_dump_json())
+                if hasattr(v, 'uuid'):
+                    ai_data['uuid'] = str(v.uuid)
+                else:
+                    ai_data['uuid'] = str(uuid4())
+
+                new_ais[k].append(ai_data)
+
+        self.additional_information = new_ais
+        self.save()
 
     def get_additional_information(self):
         from envipy_additional_information import NAME_MAPPING
@@ -2209,7 +2517,14 @@ class Scenario(EnviPathModel):
                 continue
 
             for v in vals:
-                yield NAME_MAPPING[k](**json.loads(v))
+                # Per default additional fields are ignored
+                MAPPING = {c.__name__: c for c in NAME_MAPPING.values()}
+                inst = MAPPING[k](**v)
+                # Add uuid to uniquely identify objects for manipulation
+                if 'uuid' in v:
+                    inst.__dict__['uuid'] = v['uuid']
+
+                yield inst
 
 
 class UserSettingPermission(Permission):
@@ -2238,8 +2553,7 @@ class Setting(EnviPathModel):
                               blank=True)
     model_threshold = models.FloatField(null=True, blank=True, verbose_name='Setting Model Threshold', default=0.25)
 
-    @property
-    def url(self):
+    def _url(self):
         return '{}/setting/{}'.format(s.SERVER_URL, self.uuid)
 
     @cached_property

epdb/views.py

@@ -4,16 +4,15 @@ from typing import List, Dict, Any
 
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
-from django.db.models import F, Value
-from django.db.models.fields import CharField
-from django.db.models.functions import Concat
 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 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
@@ -150,6 +149,12 @@ 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
 
@@ -160,6 +165,7 @@ 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),
@@ -211,6 +217,32 @@ def set_scenarios(current_user, attach_object, scenario_urls: List[str]):
 
     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'
@@ -439,16 +471,7 @@ def scenarios(request):
         if request.GET.get('all'):
             return JsonResponse({
                 "objects": [
-                    {"name": s.name, "url": s.full_url, "reviewed": True}
-                    for s in reviewed_scenario_qs.annotate(
-                        full_url=Concat(
-                            Value(s.SERVER_URL + '/package/'),
-                            F("package__uuid"),
-                            Value("/scenario/"),
-                            F("uuid"),
-                            output_field=CharField(),
-                        )
-                    )
+                    {"name": s.name, "url": s.url, "reviewed": True} for s in reviewed_scenario_qs
                 ]
             })
 
@@ -773,6 +796,14 @@ def package(request, package_uuid):
                 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()
 
@@ -1694,7 +1725,7 @@ def package_scenarios(request, package_uuid):
 
     if request.method == 'GET':
 
-        if 'application/json' in request.META.get('HTTP_ACCEPT'): #request.headers.get('Accept') == 'application/json':
+        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)
@@ -1704,7 +1735,7 @@ def package_scenarios(request, package_uuid):
 
         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()
@@ -1725,8 +1756,57 @@ 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', ])
 
@@ -1747,10 +1827,63 @@ 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 HttpResponseBadRequest()
+        else:
+            return HttpResponseBadRequest()
     else:
-        return HttpResponseNotAllowed(['GET', ])
+        return HttpResponseNotAllowed(['GET', 'POST'])
 
 
 ##############

pyproject.toml

@@ -29,4 +29,4 @@ 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"}

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

@@ -11,6 +11,12 @@
         <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>

templates/actions/objects/pathway.html

@@ -8,10 +8,16 @@
             <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">

templates/actions/objects/reaction.html

@@ -7,6 +7,12 @@
         <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>

templates/actions/objects/rule.html

@@ -7,6 +7,12 @@
         <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>

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/collections/objects_list.html

@@ -2,27 +2,21 @@
 {% 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 id="load-all-error" style="display: none;">
-        <div class="alert alert-danger" role="alert">
-          <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
-          <span class="sr-only">Error:</span>
-          Getting objects failed!
-        </div>
-    </div>
+    {% if object_type != 'package' %}
+        <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>
+                    <span class="sr-only">Error:</span>
+                    Getting objects failed!
+                </div>
+            </div>
 
-    <input type="text" id="object-search" class="form-control" placeholder="Search by name" style="display: none;">
-    <p></p>
-</div>
-{% endif %}
-{% endif %}
+            <input type="text" id="object-search" class="form-control" placeholder="Search by name"
+                   style="display: none;">
+            <p></p>
+        </div>
+    {% 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">
@@ -124,7 +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">
@@ -197,22 +202,22 @@
     {% endif %}
     {% block content %}
     {% endblock content %}
-    {%  if 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>
+    {% 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>
-        <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>
 

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>
-                </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>
-            </form>
+                    <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>
+                    {% 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>
 
+<script>
+    $(function () {
+        // 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();
+        });
 
-<p></p>
-<div id="scenariocontent"></div>
+        $('#new_scenario_modal_form_submit').on('click', function (e) {
+            e.preventDefault();
+            $('#new_scenario_form').submit();
+        });
 
-<!--Template index -->
-<script language="javascript">
-$(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,
     });
-});
+
+
 </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/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/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/objects/composite_rule.html

@@ -5,6 +5,7 @@
 {% 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 %}
 

templates/objects/compound.html

@@ -6,6 +6,7 @@
         {% include "modals/objects/edit_compound_modal.html" %}
         {% include "modals/objects/add_structure_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 %}
 

templates/objects/pathway.html

@@ -82,6 +82,7 @@
         {% 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" %}

templates/objects/reaction.html

@@ -5,6 +5,7 @@
     {% block action_modals %}
         {% include "modals/objects/edit_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 %}
 

templates/objects/scenario.html

@@ -3,6 +3,8 @@
 {% 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">
@@ -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>
@@ -31,18 +45,42 @@
                 <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 %}
                 <tr>
-                    <td>{{ ai.property_name|safe }} </td>
+                    <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

@@ -5,6 +5,7 @@
     {% 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 %}
 

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)
+

utilities/chem.py

@@ -8,7 +8,7 @@ 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
@@ -67,6 +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)
@@ -79,6 +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)
@@ -682,7 +698,10 @@ class IndigoUtils(object):
         i.setOption("render-image-size", width, height)
         i.setOption("render-bond-line-width", 2.0)
 
-        mol = i.loadMolecule(mol_data)
+        if '~' in mol_data:
+            mol = i.loadSmarts(mol_data)
+        else:
+            mol = i.loadMolecule(mol_data)
 
         if len(functional_groups.keys()) > 0:
             IndigoUtils._colorize(i, mol, functional_groups, False)

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

uv.lock

@@ -426,7 +426,7 @@ requires-dist = [
     { name = "django-ninja", specifier = ">=1.4.1" },
     { name = "django-polymorphic", specifier = ">=4.1.0" },
     { name = "enviformer", git = "ssh://git@git.envipath.com/enviPath/enviformer.git?rev=v0.1.0" },
-    { name = "envipy-additional-information", git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git" },
+    { name = "envipy-additional-information", git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?rev=v0.1.4" },
     { name = "envipy-plugins", git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git?rev=v0.1.0" },
     { name = "epam-indigo", specifier = ">=1.30.1" },
     { name = "gunicorn", specifier = ">=23.0.0" },
@@ -443,7 +443,7 @@ requires-dist = [
 [[package]]
 name = "envipy-additional-information"
 version = "0.1.0"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git#4804b24b3479bed6108a49e4401bff8947c03cbd" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?rev=v0.1.4#4da604090bf7cf1f3f552d69485472dbc623030a" }
 dependencies = [
     { name = "pydantic" },
 ]