[Feature] Add legacy api endpoint to mimic ReferringScenarios (#362)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#362

envipath/settings.py

@@ -92,10 +92,19 @@ if os.environ.get("REGISTRATION_MANDATORY", False) == "True":
 
 ROOT_URLCONF = "envipath.urls"
 
+TEMPLATE_DIRS = [
+    os.path.join(BASE_DIR, "templates"),
+]
+
+# If we have a non-public tenant, we might need to overwrite some templates
+# search TENANT folder first...
+if TENANT != "public":
+    TEMPLATE_DIRS.insert(0, os.path.join(BASE_DIR, TENANT, "templates"))
+
 TEMPLATES = [
     {
         "BACKEND": "django.template.backends.django.DjangoTemplates",
-        "DIRS": (os.path.join(BASE_DIR, "templates"),),
+        "DIRS": TEMPLATE_DIRS,
         "APP_DIRS": True,
         "OPTIONS": {
             "context_processors": [
@@ -399,3 +408,9 @@ if MS_ENTRA_ENABLED:
 
 # Site ID 10 -> beta.envipath.org
 MATOMO_SITE_ID = os.environ.get("MATOMO_SITE_ID", "10")
+
+# CAP
+CAP_ENABLED = os.environ.get("CAP_ENABLED", "False") == "True"
+CAP_API_BASE = os.environ.get("CAP_API_BASE", None)
+CAP_SITE_KEY = os.environ.get("CAP_SITE_KEY", None)
+CAP_SECRET_KEY = os.environ.get("CAP_SECRET_KEY", None)

epapi/tests/v1/test_scenario_creation.py

@@ -60,7 +60,7 @@ class ScenarioCreationAPITests(TestCase):
         )
 
         self.assertEqual(response.status_code, 404)
-        self.assertIn("Package not found", response.json()["detail"])
+        self.assertIn(f"Package with UUID {fake_uuid} not found", response.json()["detail"])
 
     def test_create_scenario_insufficient_permissions(self):
         """Test that unauthorized access returns 403."""

epapi/v1/dal.py

@@ -41,6 +41,24 @@ def get_package_for_read(user, package_uuid: UUID):
     return package
 
 
+def get_package_for_write(user, package_uuid: UUID):
+    """
+    Get package by UUID with permission check.
+    """
+
+    # FIXME: update package manager with custom exceptions to avoid manual checks here
+    try:
+        package = Package.objects.get(uuid=package_uuid)
+    except Package.DoesNotExist:
+        raise EPAPINotFoundError(f"Package with UUID {package_uuid} not found")
+
+    # FIXME: optimize package manager to exclusively work with UUIDs
+    if not user or user.is_anonymous or not PackageManager.writable(user, package):
+        raise EPAPIPermissionDeniedError("Insufficient permissions to access this package.")
+
+    return package
+
+
 def get_scenario_for_read(user, scenario_uuid: UUID):
     """Get scenario by UUID with read permission check."""
     try:

epapi/v1/endpoints/scenarios.py

@@ -9,7 +9,6 @@ import logging
 import json
 
 from epdb.models import Scenario
-from epdb.logic import PackageManager
 from epdb.views import _anonymous_or_real
 from ..pagination import EnhancedPageNumberPagination
 from ..schemas import (
@@ -17,7 +16,7 @@ from ..schemas import (
     ScenarioOutSchema,
     ScenarioCreateSchema,
 )
-from ..dal import get_user_entities_for_read, get_package_entities_for_read
+from ..dal import get_user_entities_for_read, get_package_entities_for_read, get_package_for_write
 from envipy_additional_information import registry
 
 logger = logging.getLogger(__name__)
@@ -58,7 +57,7 @@ def create_scenario(request, package_uuid: UUID, payload: ScenarioCreateSchema =
     user = _anonymous_or_real(request)
 
     try:
-        current_package = PackageManager.get_package_by_id(user, package_uuid)
+        current_package = get_package_for_write(user, package_uuid)
     except ValueError as e:
         error_msg = str(e)
         if "does not exist" in error_msg:

epdb/apps.py

@@ -16,6 +16,10 @@ class EPDBConfig(AppConfig):
         model_name = getattr(settings, "EPDB_PACKAGE_MODEL", "epdb.Package")
         logger.info(f"Using Package model: {model_name}")
 
+        from .autodiscovery import autodiscover
+
+        autodiscover()
+
         if settings.PLUGINS_ENABLED:
             from bridge.contracts import Property
             from utilities.plugin import discover_plugins

epdb/autodiscovery.py

@@ -0,0 +1,5 @@
+from django.utils.module_loading import autodiscover_modules
+
+
+def autodiscover():
+    autodiscover_modules("epdb_hooks")

epdb/legacy_api.py

@@ -1,3 +1,4 @@
+from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
 import nh3
@@ -11,8 +12,16 @@ from ninja.security import SessionAuth
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
 
-from .logic import GroupManager, PackageManager, SearchManager, SettingManager, UserManager
+from .logic import (
+    EPDBURLParser,
+    GroupManager,
+    PackageManager,
+    SearchManager,
+    SettingManager,
+    UserManager,
+)
 from .models import (
+    AdditionalInformation,
     Compound,
     CompoundStructure,
     Edge,
@@ -94,6 +103,8 @@ class SimpleObject(Schema):
             return "reviewed" if obj.compound.package.reviewed else "unreviewed"
         elif isinstance(obj, Node) or isinstance(obj, Edge):
             return "reviewed" if obj.pathway.package.reviewed else "unreviewed"
+        elif isinstance(obj, dict) and "review_status" in obj:
+            return "reviewed" if obj.get("review_status") else "unreviewed"
         else:
             raise ValueError("Object has no package")
 
@@ -1327,7 +1338,14 @@ class ScenarioSchema(Schema):
 
     @staticmethod
     def resolve_collection(obj: Scenario):
-        return obj.additional_information
+        res = defaultdict(list)
+
+        for ai in obj.get_additional_information(direct_only=False):
+            data = ai.data
+            data["related"] = ai.content_object.simple_json() if ai.content_object else None
+            res[ai.type].append(data)
+
+        return res
 
     @staticmethod
     def resolve_review_status(obj: Rule):
@@ -1392,7 +1410,11 @@ def create_package_scenario(request, package_uuid):
         study_type = request.POST.get("type")
 
         ais = []
-        types = request.POST.getlist("adInfoTypes[]")
+        types = request.POST.get("adInfoTypes[]", [])
+
+        if types:
+            types = types.split(",")
+
         for t in types:
             ais.append(build_additional_information_from_request(request, t))
 
@@ -1434,6 +1456,49 @@ def delete_scenario(request, package_uuid, scenario_uuid):
         }
 
 
+@router.post(
+    "/package/{uuid:package_uuid}/additional-information", response={200: str | Any, 403: Error}
+)
+def create_package_additional_information(request, package_uuid):
+    from utilities.legacy import build_additional_information_from_request
+
+    try:
+        p = get_package_for_write(request.user, package_uuid)
+
+        scen = request.POST.get("scenario")
+        scenario = Scenario.objects.get(package=p, url=scen)
+
+        url_parser = EPDBURLParser(request.POST.get("attach_obj"))
+        attach_obj = url_parser.get_object()
+
+        if not hasattr(attach_obj, "additional_information"):
+            raise ValueError("Can't attach additional information to this object!")
+
+        if not attach_obj.url.startswith(p.url):
+            raise ValueError(
+                "Additional Information can only be set to objects stored in the same package!"
+            )
+
+        types = request.POST.get("adInfoTypes[]", "").split(",")
+
+        for t in types:
+            ai = build_additional_information_from_request(request, t)
+
+            AdditionalInformation.create(
+                p,
+                ai,
+                scenario=scenario,
+                content_object=attach_obj,
+            )
+
+        # TODO implement additional information endpoint ?
+        return redirect(f"{scenario.url}")
+    except ValueError:
+        return 403, {
+            "message": f"Getting Package with id {package_uuid} failed due to insufficient rights!"
+        }
+
+
 ###########
 # Pathway #
 ###########
@@ -1464,7 +1529,7 @@ class PathwayEdge(Schema):
 
 class PathwayNode(Schema):
     atomCount: int = Field(None, alias="atom_count")
-    depth: int = Field(None, alias="depth")
+    depth: float = Field(None, alias="depth")
     dt50s: List[Dict[str, str]] = Field([], alias="dt50s")
     engineeredIntermediate: bool = Field(None, alias="engineered_intermediate")
     id: str = Field(None, alias="url")
@@ -1805,7 +1870,7 @@ class EdgeSchema(Schema):
     startNodes: List["EdgeNode"] = Field([], alias="start_nodes")
 
     @staticmethod
-    def resolve_review_status(obj: Node):
+    def resolve_review_status(obj: Edge):
         return "reviewed" if obj.pathway.package.reviewed else "unreviewed"
 
 

epdb/logic.py

@@ -1,4 +1,3 @@
-import json
 import logging
 import re
 from typing import Any, Dict, List, Optional, Set, Union, Tuple
@@ -11,6 +10,7 @@ from django.db import transaction
 from pydantic import ValidationError
 
 from epdb.models import (
+    AdditionalInformation,
     Compound,
     CompoundStructure,
     Edge,
@@ -634,15 +634,30 @@ class PackageManager(object):
 
         # Stores old_id to new_id
         mapping = {}
-        # Stores new_scen_id to old_parent_scen_id
-        parent_mapping = {}
         # Mapping old scen_id to old_obj_id
         scen_mapping = defaultdict(list)
         # Enzymelink Mapping rule_id to enzymelink objects
         enzyme_mapping = defaultdict(list)
 
+        # old_parent_id to child
+        postponed_scens = defaultdict(list)
+
         # Store Scenarios
         for scenario in data["scenarios"]:
+            skip_scen = False
+            # Check if parent exists and park this Scenario to convert it later into an
+            # AdditionalInformation object
+            for ex in scenario.get("additionalInformationCollection", {}).get(
+                "additionalInformation", []
+            ):
+                if ex["name"] == "referringscenario":
+                    postponed_scens[ex["data"]].append(scenario)
+                    skip_scen = True
+                    break
+
+            if skip_scen:
+                continue
+
             scen = Scenario()
             scen.package = pack
             scen.uuid = UUID(scenario["id"].split("/")[-1]) if keep_ids else uuid4()
@@ -655,19 +670,12 @@ class PackageManager(object):
 
             mapping[scenario["id"]] = scen.uuid
 
-            new_add_inf = defaultdict(list)
-            # TODO Store AI...
             for ex in scenario.get("additionalInformationCollection", {}).get(
                 "additionalInformation", []
             ):
                 name = ex["name"]
                 addinf_data = ex["data"]
 
-                # park the parent scen id for now and link it later
-                if name == "referringscenario":
-                    parent_mapping[scen.uuid] = addinf_data
-                    continue
-
                 # Broken eP Data
                 if name == "initialmasssediment" and addinf_data == "missing data":
                     continue
@@ -675,17 +683,11 @@ class PackageManager(object):
                     continue
 
                 try:
-                    res = AdditionalInformationConverter.convert(name, addinf_data)
+                    ai = AdditionalInformationConverter.convert(name, addinf_data)
-                    res_cls_name = res.__class__.__name__
+                    AdditionalInformation.create(pack, ai, scenario=scen)
-                    ai_data = json.loads(res.model_dump_json())
-                    ai_data["uuid"] = f"{uuid4()}"
-                    new_add_inf[res_cls_name].append(ai_data)
                 except (ValidationError, ValueError):
                     logger.error(f"Failed to convert {name} with {addinf_data}")
 
-            scen.additional_information = new_add_inf
-            scen.save()
-
         print("Scenarios imported...")
 
         # Store compounds and its structures
@@ -925,14 +927,46 @@ class PackageManager(object):
 
         print("Pathways imported...")
 
-        # Linking Phase
+        for parent, children in postponed_scens.items():
-        for child, parent in parent_mapping.items():
+            for child in children:
-            child_obj = Scenario.objects.get(uuid=child)
+                for ex in child.get("additionalInformationCollection", {}).get(
-            parent_obj = Scenario.objects.get(uuid=mapping[parent])
+                    "additionalInformation", []
-            child_obj.parent = parent_obj
+                ):
-            child_obj.save()
+                    child_id = child["id"]
+                    name = ex["name"]
+                    addinf_data = ex["data"]
+
+                    if name == "referringscenario":
+                        continue
+                    # Broken eP Data
+                    if name == "initialmasssediment" and addinf_data == "missing data":
+                        continue
+                    if name == "columnheight" and addinf_data == "(2)-(2.5);(6)-(8)":
+                        continue
+
+                    ai = AdditionalInformationConverter.convert(name, addinf_data)
+
+                    if child_id not in scen_mapping:
+                        logger.info(
+                            f"{child_id} not found in scen_mapping. Seems like its not attached to any object"
+                        )
+                        print(
+                            f"{child_id} not found in scen_mapping. Seems like its not attached to any object"
+                        )
+
+                    scen = Scenario.objects.get(uuid=mapping[parent])
+                    mapping[child_id] = scen.uuid
+                    for obj in scen_mapping[child_id]:
+                        _ = AdditionalInformation.create(pack, ai, scen, content_object=obj)
 
         for scen_id, objects in scen_mapping.items():
+            new_id = mapping.get(scen_id)
+
+            if new_id is None:
+                logger.warning(f"Could not find mapping for {scen_id}")
+                print(f"Could not find mapping for {scen_id}")
+                continue
+
             scen = Scenario.objects.get(uuid=mapping[scen_id])
             for o in objects:
                 o.scenarios.add(scen)
@@ -965,6 +999,7 @@ class PackageManager(object):
                     matches = re.findall(r">(R[0-9]+)<", evidence["evidence"])
                     if not matches or len(matches) != 1:
                         logger.warning(f"Could not find reaction id in {evidence['evidence']}")
+                        print(f"Could not find reaction id in {evidence['evidence']}")
                         continue
 
                     e.add_kegg_reaction_id(matches[0])
@@ -984,7 +1019,6 @@ class PackageManager(object):
         print("Fixing Node depths...")
         total_pws = Pathway.objects.filter(package=pack).count()
         for p, pw in enumerate(Pathway.objects.filter(package=pack)):
-            print(pw.url)
             in_count = defaultdict(lambda: 0)
             out_count = defaultdict(lambda: 0)
 
@@ -1020,7 +1054,6 @@ class PackageManager(object):
                             if str(prod.uuid) not in seen:
                                 old_depth = prod.depth
                                 if old_depth != i + 1:
-                                    print(f"updating depth from {old_depth} to {i + 1}")
                                     prod.depth = i + 1
                                     prod.save()
 
@@ -1031,7 +1064,7 @@ class PackageManager(object):
                 if new_level:
                     levels.append(new_level)
 
-            print(f"{p + 1}/{total_pws} fixed.")
+            print(f"{p + 1}/{total_pws} fixed.", end="\r")
 
         return pack
 

epdb/management/commands/recreate_db.py

@@ -1,6 +1,7 @@
 import os
 import subprocess
 
+from django.conf import settings
 from django.core.management import call_command
 from django.core.management.base import BaseCommand
 
@@ -45,11 +46,13 @@ class Command(BaseCommand):
         if not os.path.exists(dump_file):
             raise ValueError(f"Dump file {dump_file} does not exist")
 
-        print(f"Dropping database {options['name']} y/n: ", end="")
+        db_name = options["name"]
+
+        print(f"Dropping database {db_name} y/n: ", end="")
 
         if input() in "yY":
             result = subprocess.run(
-                ["dropdb", "appdb"],
+                ["dropdb", db_name],
                 capture_output=True,
                 text=True,
             )
@@ -57,20 +60,24 @@ class Command(BaseCommand):
         else:
             raise ValueError("Aborted")
 
-        print(f"Creating database {options['name']}")
+        print(f"Creating database {db_name}")
 
         result = subprocess.run(
-            ["createdb", "appdb"],
+            ["createdb", db_name],
             capture_output=True,
             text=True,
         )
         print(result.stdout)
-        print(f"Restoring database {options['name']} from {dump_file}")
+        print(f"Restoring database {db_name} from {dump_file}")
 
         result = subprocess.run(
-            ["pg_restore", "-d", "appdb", dump_file, "--no-owner"],
+            ["pg_restore", "-d", db_name, dump_file, "--no-owner"],
             capture_output=True,
             text=True,
         )
         print(result.stdout)
-        call_command("localize_urls", "--old", options["oldurl"], "--new", options["newurl"])
+
+        if db_name == settings.DATABASES["default"]["NAME"]:
+            call_command("localize_urls", "--old", options["oldurl"], "--new", options["newurl"])
+        else:
+            print("Skipping localize_urls as database is not the default one.")

epdb/migrations/0020_alter_compoundstructure_options_and_more.py

@@ -0,0 +1,65 @@
+# Generated by Django 5.2.7 on 2026-03-09 10:41
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+def populate_polymorphic_ctype(apps, schema_editor):
+    ContentType = apps.get_model("contenttypes", "ContentType")
+    Compound = apps.get_model("epdb", "Compound")
+    CompoundStructure = apps.get_model("epdb", "CompoundStructure")
+
+    # Update Compound records
+    compound_ct = ContentType.objects.get_for_model(Compound)
+    Compound.objects.filter(polymorphic_ctype__isnull=True).update(polymorphic_ctype=compound_ct)
+
+    # Update CompoundStructure records
+    compound_structure_ct = ContentType.objects.get_for_model(CompoundStructure)
+    CompoundStructure.objects.filter(polymorphic_ctype__isnull=True).update(
+        polymorphic_ctype=compound_structure_ct
+    )
+
+
+def reverse_populate_polymorphic_ctype(apps, schema_editor):
+    Compound = apps.get_model("epdb", "Compound")
+    CompoundStructure = apps.get_model("epdb", "CompoundStructure")
+
+    Compound.objects.all().update(polymorphic_ctype=None)
+    CompoundStructure.objects.all().update(polymorphic_ctype=None)
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("contenttypes", "0002_remove_content_type_name"),
+        ("epdb", "0019_remove_scenario_additional_information_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name="compoundstructure",
+            options={"base_manager_name": "objects"},
+        ),
+        migrations.AddField(
+            model_name="compound",
+            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.AddField(
+            model_name="compoundstructure",
+            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.RunPython(populate_polymorphic_ctype, reverse_populate_polymorphic_ctype),
+    ]

epdb/models.py

@@ -765,7 +765,12 @@ class Package(EnviPathModel):
 
 
 class Compound(
-    EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin, AdditionalInformationMixin
+    PolymorphicModel,
+    EnviPathModel,
+    AliasMixin,
+    ScenarioMixin,
+    ChemicalIdentifierMixin,
+    AdditionalInformationMixin,
 ):
     package = models.ForeignKey(
         s.EPDB_PACKAGE_MODEL, verbose_name="Package", on_delete=models.CASCADE, db_index=True
@@ -1095,7 +1100,12 @@ class Compound(
 
 
 class CompoundStructure(
-    EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin, AdditionalInformationMixin
+    PolymorphicModel,
+    EnviPathModel,
+    AliasMixin,
+    ScenarioMixin,
+    ChemicalIdentifierMixin,
+    AdditionalInformationMixin,
 ):
     compound = models.ForeignKey("epdb.Compound", on_delete=models.CASCADE, db_index=True)
     smiles = models.TextField(blank=False, null=False, verbose_name="SMILES")
@@ -1775,9 +1785,9 @@ class Reaction(
         edges = Edge.objects.filter(edge_label=self)
         for e in edges:
             for scen in e.scenarios.all():
-                for ai in scen.additional_information.keys():
+                for ai in scen.get_additional_information():
-                    if ai == "Enzyme":
+                    if ai.type == "Enzyme":
-                        res.extend(scen.additional_information[ai])
+                        res.append(ai.get())
         return res
 
 
@@ -2334,7 +2344,10 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "reaction_probability": self.kv.get("probability"),
             "start_node_urls": [x.url for x in self.start_nodes.all()],
             "end_node_urls": [x.url for x in self.end_nodes.all()],
-            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
+            "scenarios": [
+                {"name": s.get_name(), "url": s.url, "review_status": s.package.reviewed}
+                for s in self.scenarios.all()
+            ],
         }
 
         for n in self.start_nodes.all():
@@ -3458,9 +3471,7 @@ class EnviFormer(PackageBasedModel):
     def predict_batch(self, smiles: List[str], *args, **kwargs):
         # Standardizer removes all but one compound from a raw SMILES string, so they need to be processed separately
         canon_smiles = [
-            ".".join(
+            ".".join([FormatConverter.standardize(s, remove_stereo=True) for s in smi.split(".")])
-                [FormatConverter.standardize(s, remove_stereo=True) for s in smiles.split(".")]
-            )
             for smi in smiles
         ]
         logger.info(f"Submitting {canon_smiles} to {self.get_name()}")
@@ -4138,7 +4149,7 @@ class Scenario(EnviPathModel):
         ais = AdditionalInformation.objects.filter(scenario=self)
 
         if direct_only:
-            return ais.filter(content_object__isnull=True)
+            return ais.filter(object_id__isnull=True)
         else:
             return ais
 
@@ -4180,7 +4191,6 @@ class AdditionalInformation(models.Model):
         ai: "EnviPyModel",
         scenario=None,
         content_object=None,
-        skip_cleaning=False,
     ):
         add_inf = AdditionalInformation()
         add_inf.package = package

epdb/template_registry.py

@@ -0,0 +1,17 @@
+from collections import defaultdict
+from threading import Lock
+
+_registry = defaultdict(list)
+_lock = Lock()
+
+
+def register_template(slot: str, template_name: str, *, order: int = 100):
+    item = (order, template_name)
+    with _lock:
+        if item not in _registry[slot]:
+            _registry[slot].append(item)
+            _registry[slot].sort(key=lambda x: x[0])
+
+
+def get_templates(slot: str):
+    return [template_name for _, template_name in _registry.get(slot, [])]

epdb/templatetags/envipytags.py

@@ -2,6 +2,8 @@ from django import template
 from pydantic import AnyHttpUrl, ValidationError
 from pydantic.type_adapter import TypeAdapter
 
+from epdb.template_registry import get_templates
+
 register = template.Library()
 
 url_adapter = TypeAdapter(AnyHttpUrl)
@@ -19,3 +21,8 @@ def is_url(value):
         return True
     except ValidationError:
         return False
+
+
+@register.simple_tag
+def epdb_slot_templates(slot):
+    return get_templates(slot)

epdb/views.py

@@ -3,6 +3,7 @@ import logging
 from datetime import datetime
 from typing import Any, Dict, List, Iterable
 
+import requests
 import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
@@ -147,6 +148,11 @@ def handler500(request):
 def login(request):
     context = get_base_context(request)
 
+    if s.CAP_ENABLED:
+        context["CAP_ENABLED"] = s.CAP_ENABLED
+        context["CAP_API_BASE"] = s.CAP_API_BASE
+        context["CAP_SITE_KEY"] = s.CAP_SITE_KEY
+
     if request.method == "GET":
         context["title"] = "enviPath"
         context["next"] = request.GET.get("next", "")
@@ -224,6 +230,11 @@ def logout(request):
 def register(request):
     context = get_base_context(request)
 
+    if s.CAP_ENABLED:
+        context["CAP_ENABLED"] = s.CAP_ENABLED
+        context["CAP_API_BASE"] = s.CAP_API_BASE
+        context["CAP_SITE_KEY"] = s.CAP_SITE_KEY
+
     if request.method == "GET":
         # Redirect to unified login page with signup tab
         next_url = request.GET.get("next", "")
@@ -238,6 +249,33 @@ def register(request):
         if next := request.POST.get("next"):
             context["next"] = next
 
+        # Catpcha
+        if s.CAP_ENABLED:
+            cap_token = request.POST.get("cap-token")
+
+            if not cap_token:
+                context["message"] = "Missing CAP Token."
+                return render(request, "static/login.html", context)
+
+            verify_url = f"{s.CAP_API_BASE}/{s.CAP_SITE_KEY}/siteverify"
+            payload = {
+                "secret": s.CAP_SECRET_KEY,
+                "response": cap_token,
+            }
+
+            try:
+                resp = requests.post(verify_url, json=payload, timeout=10)
+                resp.raise_for_status()
+                verify_data = resp.json()
+            except requests.RequestException:
+                context["message"] = "Captcha verification failed."
+                return render(request, "static/login.html", context)
+
+            if not verify_data.get("success"):
+                context["message"] = "Captcha check failed. Please try again."
+                return render(request, "static/login.html", context)
+        # End Captcha
+
         username = request.POST.get("username", "").strip()
         email = request.POST.get("email", "").strip()
         password = request.POST.get("password", "").strip()
@@ -917,7 +955,7 @@ def package_models(request, package_uuid):
             params["threshold"] = threshold
 
             mod = EnviFormer.create(**params)
-        elif model_type == "mlrr":
+        elif model_type == "ml-relative-reasoning":
             # ML Specific
             threshold = float(request.POST.get("model-threshold", 0.5))
             # TODO handle additional fingerprinter
@@ -941,7 +979,7 @@ def package_models(request, package_uuid):
             params["app_domain_local_compatibility_threshold"] = local_compatibility_threshold
 
             mod = MLRelativeReasoning.create(**params)
-        elif model_type == "rbrr":
+        elif model_type == "rule-based-relative-reasoning":
             params["rule_packages"] = [
                 PackageManager.get_package_by_url(current_user, p) for p in rule_packages
             ]

pepper/__init__.py

@@ -79,9 +79,9 @@ class PepperPrediction(PredictedProperty):
         dist = stats.lognorm(s=sigma_ln, scale=np.exp(mu_ln))
 
         # Exact probabilities
-        p_green = dist.cdf(p)  # P(X < a)
+        p_green = dist.cdf(p)  # P(X < p) prob not persistent
-        p_yellow = dist.cdf(vp) - p_green  # P(a <= X <= b)
+        p_yellow = 1.0 - dist.cdf(p)  # P (X > p) prob persistent
-        p_red = 1.0 - dist.cdf(vp)  # P(X > b)
+        p_red = 1.0 - dist.cdf(vp)  # P(X > vp) prob very persistent
 
         # Plotting range
         q_low, q_high = dist.ppf(quantiles)

static/js/alpine/components/schema-form.js

@@ -88,6 +88,7 @@ document.addEventListener("alpine:init", () => {
       options.debugErrors ??
       (typeof window !== "undefined" &&
         window.location?.search?.includes("debugErrors=1")),
+    attach_object: options.attach_object || null,
 
     async init() {
       if (options.schemaUrl) {

templates/collections/compounds_paginated.html

@@ -1,21 +1,34 @@
 {% extends "collections/paginated_base.html" %}
+{% load envipytags %}
 
 {% block page_title %}Compounds{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  <div class="flex items-center gap-2">
-    <button
+    {% if meta.can_edit %}
-      type="button"
+      <button
-      class="btn btn-primary btn-sm"
+        type="button"
-      onclick="document.getElementById('new_compound_modal').showModal(); return false;"
+        class="btn btn-primary btn-sm"
-    >
+        onclick="document.getElementById('new_compound_modal').showModal(); return false;"
-      New Compound
+      >
-    </button>
+        New Compound
-  {% endif %}
+      </button>
+    {% endif %}
+    {% epdb_slot_templates "epdb.actions.collections.compound" as action_button_templates %}
+
+    {% for tpl in action_button_templates %}
+      {% include tpl %}
+    {% endfor %}
+  </div>
 {% endblock action_button %}
 
 {% block action_modals %}
   {% include "modals/collections/new_compound_modal.html" %}
+  {% epdb_slot_templates "modals.collections.compound" as action_modals_templates %}
+
+  {% for tpl in action_modals_templates %}
+    {% include tpl %}
+  {% endfor %}
 {% endblock action_modals %}
 
 {% block description %}

templates/components/schema_form.html

@@ -18,8 +18,25 @@
   <!-- Schema form -->
   <template x-if="schema && !loading">
     <div class="space-y-4">
+      <template x-if="attach_object">
+        <div>
+          <h4>
+            <span
+              class="text-lg font-semibold"
+              x-text="schema['x-title'] + ' attached to'"
+            ></span>
+            <a
+              class="text-lg font-semibold underline text-blue-600 hover:text-blue-800"
+              :href="attach_object.url"
+              x-text="attach_object.name"
+              target="_blank"
+            ></a>
+          </h4>
+        </div>
+      </template>
+
       <!-- Title from schema -->
-      <template x-if="schema['x-title'] || schema.title">
+      <template x-if="(schema['x-title'] || schema.title) && !attach_object">
         <h4
           class="text-lg font-semibold"
           x-text="data.name || schema['x-title'] || schema.title"

templates/modals/objects/edit_package_permissions_modal.html

@@ -71,24 +71,129 @@
             <label class="label">
               <span class="label-text">User or Group</span>
             </label>
-            <select
+            <div
-              id="select_grantee"
+              class="relative"
-              name="grantee"
+              x-data="{
-              class="select select-bordered w-full select-sm"
+      searchQuery: '',
-              required
+      selectedItem: null,
+      showResults: false,
+      filteredResults: [],
+      allItems: [
+        {% for u in users %}
+                { type: 'user', name: '{{ u.username }}', url: '{{ u.url }}',
+                display: '{{ u.username }}' },
+              {% endfor %}
+        {% for g in groups %}
+                { type: 'group', name: '{{ g.name|safe }}', url: '{{ g.url }}',
+                display: '{{ g.name|safe }}' },
+              {% endfor %}
+      ],
+      init() {
+        this.filteredResults = this.allItems;
+      },
+      search() {
+        if (this.searchQuery.length === 0) {
+          this.filteredResults = this.allItems;
+        } else {
+          this.filteredResults = this.allItems.filter(item =>
+            item.name.toLowerCase().includes(this.searchQuery.toLowerCase())
+          );
+        }
+        this.showResults = true;
+      },
+      selectItem(item) {
+        this.selectedItem = item;
+        this.searchQuery = item.display;
+        this.showResults = false;
+      },
+      clearSelection() {
+        this.selectedItem = null;
+        this.searchQuery = '';
+        this.showResults = false;
+      }
+    }"
+              @click.away="showResults = false"
             >
-              <optgroup label="Users">
+              <input
-                {% for u in users %}
+                type="text"
-                  <option value="{{ u.url }}">{{ u.username }}</option>
+                x-model="searchQuery"
-                {% endfor %}
+                @input="search()"
-              </optgroup>
+                @focus="showResults = true; search()"
-              <optgroup label="Groups">
+                @keydown.escape="showResults = false"
-                {% for g in groups %}
+                @keydown.arrow-down.prevent="$refs.resultsList?.children[0]?.focus()"
-                  <option value="{{ g.url }}">{{ g.name|safe }}</option>
+                class="input input-bordered w-full input-sm"
-                {% endfor %}
+                placeholder="Search users or groups..."
-              </optgroup>
+                autocomplete="off"
-            </select>
+                required
+              />
+
+              <!-- Clear button -->
+              <button
+                type="button"
+                x-show="searchQuery.length > 0"
+                @click="clearSelection()"
+                class="absolute right-2 top-1/2 transform -translate-y-1/2 text-gray-400 hover:text-gray-600"
+              >
+                ✕
+              </button>
+
+              <!-- Hidden input for form submission -->
+              <input
+                type="hidden"
+                name="grantee"
+                x-bind:value="selectedItem?.url || ''"
+                required
+              />
+
+              <!-- Search results dropdown -->
+              <div
+                x-show="showResults && filteredResults.length > 0"
+                x-transition
+                class="absolute z-50 w-full mt-1 bg-base-100 border border-base-300 rounded-lg shadow-lg max-h-60 overflow-y-auto"
+              >
+                <ul x-ref="resultsList" id="resultsList" class="py-1">
+                  <template
+                    x-for="(item, index) in filteredResults"
+                    :key="item.url"
+                  >
+                    <li>
+                      <button
+                        type="button"
+                        @click="selectItem(item)"
+                        @keydown.enter="selectItem(item)"
+                        @keydown.escape="showResults = false"
+                        @keydown.arrow-up.prevent="index > 0 ? $event.target.parentElement.previousElementSibling?.children[0]?.focus() : null"
+                        @keydown.arrow-down.prevent="index < filteredResults.length - 1 ? $event.target.parentElement.nextElementSibling?.children[0]?.focus() : null"
+                        class="w-full px-4 py-2 text-left hover:bg-base-200 focus:bg-base-200 focus:outline-none flex items-center space-x-2"
+                      >
+                        <span
+                          x-text="item.type === 'user' ? '👤' : '👥'"
+                          class="text-sm opacity-60"
+                        ></span>
+                        <span x-text="item.display"></span>
+                        <span
+                          x-text="item.type === 'user' ? '(User)' : '(Group)'"
+                          class="text-xs opacity-50 ml-auto"
+                        ></span>
+                      </button>
+                    </li>
+                  </template>
+                </ul>
+              </div>
+
+              <!-- No results message -->
+              <div
+                x-show="showResults && filteredResults.length === 0 && searchQuery.length > 0"
+                x-transition
+                class="absolute z-50 w-full mt-1 bg-base-100 border border-base-300 rounded-lg shadow-lg"
+              >
+                <div class="px-4 py-2 text-gray-500 text-sm">
+                  No users or groups found
+                </div>
+              </div>
+            </div>
           </div>
+
           <div class="col-span-2 text-center">
             <label class="label justify-center">
               <span class="label-text">Read</span>

templates/objects/scenario.html

@@ -189,7 +189,8 @@
                         x-data="schemaRenderer({
                              rjsf: schemas[item.type.toLowerCase()],
                              data: item.data,
-                             mode: 'view'
+                             mode: 'view',
+                             attach_object: item.attach_object
                            })"
                         x-init="init()"
                       >

templates/static/login.html

@@ -218,6 +218,12 @@
 
       <input type="hidden" name="next" value="{{ next }}" />
 
+      {% if CAP_ENABLED %}
+        <cap-widget
+          data-cap-api-endpoint="{{ CAP_API_BASE }}/{{ CAP_SITE_KEY }}/"
+        ></cap-widget>
+      {% endif %}
+
       <!-- ToS and Academic Use Notice -->
       <div class="text-xs text-base-content/70 mt-2">
         <p>
@@ -233,7 +239,6 @@
           enviPath is free for academic and non-commercial use only.
         </p>
       </div>
-
       <button type="submit" name="confirmsignup" class="btn btn-success w-full">
         Sign Up
       </button>

templates/static/login_base.html

@@ -19,7 +19,16 @@
       type="text/css"
     />
 
-    {% block extra_styles %}{% endblock %}
+    {% if CAP_ENABLED %}
+      <script src="https://cdn.jsdelivr.net/npm/@cap.js/widget@0.1.41/cap.min.js"></script>
+      <link
+        rel="stylesheet"
+        href="https://cdn.jsdelivr.net/npm/@cap.js/widget@0.1.41/src/cap.min.css"
+      />
+    {% endif %}
+
+    {% block extra_styles %}
+    {% endblock %}
   </head>
   <body class="bg-base-100">
     <div class="flex h-screen">

tests/frontend/test_packagepage.py

@@ -20,7 +20,16 @@ class TestPackagePage(EnviPyStaticLiveServerTestCase):
         page.get_by_role("button", name="Actions").click()
         page.get_by_role("button", name="Edit Permissions").click()
         # Add read and write permission to enviPath Users group
-        page.locator("#select_grantee").select_option(label="enviPath Users")
+        search_input = page.locator('input[placeholder="Search users or groups..."]')
+        search_input.fill("enviPath")
+
+        # Wait for the results list to appear and be populated
+        page.wait_for_selector("#resultsList", state="visible")
+
+        # Click the first button in the results list
+        first_button = page.locator("#resultsList button").first
+        first_button.click()
+
         page.locator("#read_new").check()
         page.locator("#write_new").check()
         page.get_by_role("button", name="+", exact=True).click()

uv.lock

@@ -841,7 +841,7 @@ provides-extras = ["ms-login", "dev", "pepper-plugin"]
 [[package]]
 name = "envipy-additional-information"
 version = "0.4.2"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#40459366648a03b01432998b32fdabd5556a1bae" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#04f6a01b8c5cd1342464e004e0cfaec9abc13ac5" }
 dependencies = [
     { name = "pydantic" },
 ]