[Fix] Filter Active Users (#314) (#329)

Adding users to a group or setting permissions on a package now filter for active users. Also any inactive members of group/package get marked as such.

<img width="490" alt="{3B906C71-F3AE-41E4-A61C-B8377D79F685}.png" src="attachments/09cf149a-9d7a-4560-8ce7-9f3487527ee2">

Reviewed-on: enviPath/enviPy#329
Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: Liam Brydon <lbry121@aucklanduni.ac.nz>

.gitea/actions/setup-envipy/action.yaml

@@ -48,11 +48,6 @@ runs:
       shell: bash
       run: |
         uv run python scripts/pnpm_wrapper.py install
-        cat << 'EOF' > pnpm-workspace.yaml
-        onlyBuiltDependencies:
-          - '@parcel/watcher'
-          - '@tailwindcss/oxide'
-        EOF
         uv run python scripts/pnpm_wrapper.py run build
 
     - name: Wait for Postgres

README.md

@@ -8,13 +8,12 @@ These instructions will guide you through setting up the project for local devel
 
 - Python 3.11 or later
 - [uv](https://github.com/astral-sh/uv) - Python package manager
-- **Docker and Docker Compose** - Required for running PostgreSQL database
+- **Docker and Docker Compose** - Required for running PostgreSQL database and Redis (for async Celery tasks)
 - Git
 - Make
 
 > **Note:** This application requires PostgreSQL (uses `ArrayField`). Docker is the easiest way to run PostgreSQL locally.
 
-
 ### 1. Install Dependencies
 
 This project uses `uv` to manage dependencies and `poe-the-poet` for task running. First, [install `uv` if you don't have it yet](https://docs.astral.sh/uv/guides/install-python/).
@@ -79,25 +78,48 @@ uv run poe bootstrap     # Bootstrap data only
 uv run poe shell         # Open the Django shell
 uv run poe build         # Build frontend assets and collect static files
 uv run poe clean         # Remove database volumes (WARNING: destroys all data)
+uv run poe celery        # Start Celery worker for async task processing
+uv run poe celery-dev    # Start database and Celery worker
 ```
 
+### 4. Async Celery Setup (Optional)
+
+By default, Celery tasks run synchronously (`CELERY_TASK_ALWAYS_EAGER = True`), which means prediction tasks block the HTTP request until completion. To enable asynchronous task processing with live status updates on pathway pages:
+
+1. **Set the Celery flag in your `.env` file:**
+
+   ```bash
+   FLAG_CELERY_PRESENT=True
+   ```
+
+2. **Start Redis and Celery worker:**
+
+   ```bash
+   uv run poe celery-dev
+   ```
+
+3. **Start the development server** (in another terminal):
+   ```bash
+   uv run poe dev
+   ```
+
 ### Troubleshooting
 
-*   **Docker Connection Error:** If you see an error like `open //./pipe/dockerDesktopLinuxEngine: The system cannot find the file specified` (on Windows), it likely means your Docker Desktop application is not running. Please start Docker Desktop and try the command again.
+- **Docker Connection Error:** If you see an error like `open //./pipe/dockerDesktopLinuxEngine: The system cannot find the file specified` (on Windows), it likely means your Docker Desktop application is not running. Please start Docker Desktop and try the command again.
 
-*   **SSH Keys for Git Dependencies:** Some dependencies are installed from private git repositories and require SSH authentication. Ensure your SSH keys are configured correctly for Git.
-    *   For a general guide, see [GitHub's official documentation](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent).
-    *   **Windows Users:** If `uv sync` hangs while fetching git dependencies, you may need to explicitly configure Git to use the Windows OpenSSH client and use the `ssh-agent` to manage your key's passphrase.
+- **SSH Keys for Git Dependencies:** Some dependencies are installed from private git repositories and require SSH authentication. Ensure your SSH keys are configured correctly for Git.
+  - For a general guide, see [GitHub's official documentation](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent).
+  - **Windows Users:** If `uv sync` hangs while fetching git dependencies, you may need to explicitly configure Git to use the Windows OpenSSH client and use the `ssh-agent` to manage your key's passphrase.
+    1.  **Point Git to the correct SSH executable:**
+        ```powershell
+        git config --global core.sshCommand "C:/Windows/System32/OpenSSH/ssh.exe"
+        ```
+    2.  **Enable and use the SSH agent:**
 
-        1.  **Point Git to the correct SSH executable:**
-            ```powershell
-            git config --global core.sshCommand "C:/Windows/System32/OpenSSH/ssh.exe"
-            ```
-        2.  **Enable and use the SSH agent:**
-            ```powershell
-            # Run these commands in an administrator PowerShell
-            Get-Service ssh-agent | Set-Service -StartupType Automatic -PassThru | Start-Service
+        ```powershell
+        # Run these commands in an administrator PowerShell
+        Get-Service ssh-agent | Set-Service -StartupType Automatic -PassThru | Start-Service
 
-            # Add your key to the agent. It will prompt for the passphrase once.
-            ssh-add
-            ```
+        # Add your key to the agent. It will prompt for the passphrase once.
+        ssh-add
+        ```

docker-compose.dev.yml

@@ -1,6 +1,6 @@
 services:
   db:
-    image: postgres:15
+    image: postgres:18
     container_name: envipath-postgres
     environment:
       POSTGRES_USER: postgres
@@ -9,12 +9,18 @@ services:
     ports:
       - "5432:5432"
     volumes:
-      - postgres_data:/var/lib/postgresql/data
+      - postgres_data:/var/lib/postgresql
     healthcheck:
       test: ["CMD-SHELL", "pg_isready -U postgres"]
       interval: 5s
       timeout: 5s
       retries: 5
 
+  redis:
+    image: redis:7-alpine
+    container_name: envipath-redis
+    ports:
+      - "6379:6379"
+
 volumes:
   postgres_data:

envipath/settings.py

@@ -21,7 +21,9 @@ from sklearn.tree import DecisionTreeClassifier
 # Build paths inside the project like this: BASE_DIR / 'subdir'.
 BASE_DIR = Path(__file__).resolve().parent.parent
 
-load_dotenv(BASE_DIR / ".env", override=False)
+ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env")
+print(f"Loading env from {ENV_PATH}")
+load_dotenv(ENV_PATH, override=False)
 
 # Quick-start development settings - unsuitable for production
 # See https://docs.djangoproject.com/en/4.2/howto/deployment/checklist/
@@ -50,7 +52,7 @@ INSTALLED_APPS = [
     # Custom
     "epapi",  # API endpoints (v1, etc.)
     "epdb",
-    # "migration",
+    "migration",
 ]
 
 TENANT = os.environ.get("TENANT", "public")

epapi/tests/utils/__init__.py

@@ -0,0 +1 @@
+"""Tests for epapi utility modules."""

epapi/tests/utils/test_validation_errors.py

@@ -0,0 +1,218 @@
+"""
+Tests for validation error utilities.
+
+Tests the format_validation_error() and handle_validation_error() functions
+that transform Pydantic validation errors into user-friendly messages.
+"""
+
+from django.test import TestCase, tag
+import json
+from pydantic import BaseModel, ValidationError, field_validator
+from typing import Literal
+
+from ninja.errors import HttpError
+from epapi.utils.validation_errors import format_validation_error, handle_validation_error
+
+
+@tag("api", "utils")
+class ValidationErrorUtilityTests(TestCase):
+    """Test validation error utility functions."""
+
+    def test_format_missing_field_error(self):
+        """Test formatting of missing required field error."""
+
+        # Create a model with required field
+        class TestModel(BaseModel):
+            required_field: str
+
+        # Trigger validation error
+        try:
+            TestModel()
+        except ValidationError as e:
+            errors = e.errors()
+            self.assertEqual(len(errors), 1)
+            formatted = format_validation_error(errors[0])
+            self.assertEqual(formatted, "This field is required")
+
+    def test_format_enum_error(self):
+        """Test formatting of enum validation error."""
+
+        class TestModel(BaseModel):
+            status: Literal["active", "inactive"]
+
+        try:
+            TestModel(status="invalid")
+        except ValidationError as e:
+            errors = e.errors()
+            self.assertEqual(len(errors), 1)
+            formatted = format_validation_error(errors[0])
+            # Literal errors get formatted as "Please enter ..." with the valid options
+            self.assertIn("Please enter", formatted)
+            self.assertIn("active", formatted)
+            self.assertIn("inactive", formatted)
+
+    def test_format_type_errors(self):
+        """Test formatting of type validation errors (string, int, float)."""
+        test_cases = [
+            # (field_type, invalid_value, expected_message)
+            # Note: We don't check exact error_type as Pydantic may use different types
+            # (e.g., int_type vs int_parsing) but we verify the formatted message is correct
+            (str, 123, "Please enter a valid string"),
+            (int, "not_a_number", "Please enter a valid int"),
+            (float, "not_a_float", "Please enter a valid float"),
+        ]
+
+        for field_type, invalid_value, expected_message in test_cases:
+            with self.subTest(field_type=field_type.__name__):
+
+                class TestModel(BaseModel):
+                    field: field_type
+
+                try:
+                    TestModel(field=invalid_value)
+                except ValidationError as e:
+                    errors = e.errors()
+                    self.assertEqual(len(errors), 1)
+                    formatted = format_validation_error(errors[0])
+                    self.assertEqual(formatted, expected_message)
+
+    def test_format_value_error(self):
+        """Test formatting of value error from custom validator."""
+
+        class TestModel(BaseModel):
+            age: int
+
+            @field_validator("age")
+            @classmethod
+            def validate_age(cls, v):
+                if v < 0:
+                    raise ValueError("Age must be positive")
+                return v
+
+        try:
+            TestModel(age=-5)
+        except ValidationError as e:
+            errors = e.errors()
+            self.assertEqual(len(errors), 1)
+            formatted = format_validation_error(errors[0])
+            self.assertEqual(formatted, "Age must be positive")
+
+    def test_format_unknown_error_type_fallback(self):
+        """Test that unknown error types fall back to default formatting."""
+        # Mock an error with an unknown type
+        mock_error = {
+            "type": "unknown_custom_type",
+            "msg": "Input should be a valid email address",
+            "ctx": {},
+        }
+
+        formatted = format_validation_error(mock_error)
+        # Should use the else branch which does replacements on the message
+        self.assertEqual(formatted, "Please enter a valid email address")
+
+    def test_handle_validation_error_structure(self):
+        """Test that handle_validation_error raises HttpError with correct structure."""
+
+        class TestModel(BaseModel):
+            name: str
+            count: int
+
+        try:
+            TestModel(name=123, count="invalid")
+        except ValidationError as e:
+            # handle_validation_error should raise HttpError
+            with self.assertRaises(HttpError) as context:
+                handle_validation_error(e)
+
+            http_error = context.exception
+            self.assertEqual(http_error.status_code, 400)
+
+            # Parse the JSON from the error message
+            error_data = json.loads(http_error.message)
+
+            # Check structure
+            self.assertEqual(error_data["type"], "validation_error")
+            self.assertIn("field_errors", error_data)
+            self.assertIn("message", error_data)
+            self.assertEqual(error_data["message"], "Please correct the errors below")
+
+            # Check that both fields have errors
+            self.assertIn("name", error_data["field_errors"])
+            self.assertIn("count", error_data["field_errors"])
+
+    def test_handle_validation_error_no_pydantic_internals(self):
+        """Test that handle_validation_error doesn't expose Pydantic internals."""
+
+        class TestModel(BaseModel):
+            email: str
+
+        try:
+            TestModel(email=123)
+        except ValidationError as e:
+            with self.assertRaises(HttpError) as context:
+                handle_validation_error(e)
+
+            http_error = context.exception
+            error_data = json.loads(http_error.message)
+            error_str = json.dumps(error_data)
+
+            # Ensure no Pydantic internals are exposed
+            self.assertNotIn("pydantic", error_str.lower())
+            self.assertNotIn("https://errors.pydantic.dev", error_str)
+            self.assertNotIn("loc", error_str)
+
+    def test_handle_validation_error_user_friendly_messages(self):
+        """Test that all error messages are user-friendly."""
+
+        class TestModel(BaseModel):
+            name: str
+            age: int
+            status: Literal["active", "inactive"]
+
+        try:
+            TestModel(name=123, status="invalid")  # Multiple errors
+        except ValidationError as e:
+            with self.assertRaises(HttpError) as context:
+                handle_validation_error(e)
+
+            http_error = context.exception
+            error_data = json.loads(http_error.message)
+
+            # All messages should be user-friendly (contain "Please" or "This field")
+            for field, messages in error_data["field_errors"].items():
+                for message in messages:
+                    # User-friendly messages start with "Please" or "This field"
+                    self.assertTrue(
+                        message.startswith("Please") or message.startswith("This field"),
+                        f"Message '{message}' is not user-friendly",
+                    )
+
+    def test_handle_validation_error_multiple_errors_same_field(self):
+        """Test handling multiple validation errors for the same field."""
+
+        class TestModel(BaseModel):
+            value: int
+
+            @field_validator("value")
+            @classmethod
+            def validate_range(cls, v):
+                if v < 0:
+                    raise ValueError("Must be non-negative")
+                if v > 100:
+                    raise ValueError("Must be at most 100")
+                return v
+
+        # Test with string (type error) - this will fail before the validator runs
+        try:
+            TestModel(value="invalid")
+        except ValidationError as e:
+            with self.assertRaises(HttpError) as context:
+                handle_validation_error(e)
+
+            http_error = context.exception
+            error_data = json.loads(http_error.message)
+
+            # Should have error for 'value' field
+            self.assertIn("value", error_data["field_errors"])
+            self.assertIsInstance(error_data["field_errors"]["value"], list)
+            self.assertGreater(len(error_data["field_errors"]["value"]), 0)

epapi/tests/v1/test_additional_information.py

@@ -0,0 +1,448 @@
+"""
+Tests for Additional Information API endpoints.
+
+Tests CRUD operations on scenario additional information including the new PATCH endpoint.
+"""
+
+from django.test import TestCase, tag
+import json
+from uuid import uuid4
+
+from epdb.logic import PackageManager, UserManager
+from epdb.models import Scenario
+
+
+@tag("api", "additional_information")
+class AdditionalInformationAPITests(TestCase):
+    """Test additional information API endpoints."""
+
+    @classmethod
+    def setUpTestData(cls):
+        """Set up test data: user, package, and scenario."""
+        cls.user = UserManager.create_user(
+            "ai-test-user",
+            "ai-test@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+        cls.other_user = UserManager.create_user(
+            "ai-other-user",
+            "ai-other@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+        cls.package = PackageManager.create_package(
+            cls.user, "AI Test Package", "Test package for additional information"
+        )
+        # Package owned by other_user (no access for cls.user)
+        cls.other_package = PackageManager.create_package(
+            cls.other_user, "Other Package", "Package without access"
+        )
+        # Create a scenario for testing
+        cls.scenario = Scenario.objects.create(
+            package=cls.package,
+            name="Test Scenario",
+            description="Test scenario for additional information tests",
+            scenario_type="biodegradation",
+            scenario_date="2024-01-01",
+            additional_information={},  # Initialize with empty dict
+        )
+        cls.other_scenario = Scenario.objects.create(
+            package=cls.other_package,
+            name="Other Scenario",
+            description="Scenario in package without access",
+            scenario_type="biodegradation",
+            scenario_date="2024-01-01",
+            additional_information={},
+        )
+
+    def test_list_all_schemas(self):
+        """Test GET /api/v1/information/schema/ returns all schemas."""
+        self.client.force_login(self.user)
+
+        response = self.client.get("/api/v1/information/schema/")
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertIsInstance(data, dict)
+        # Should have multiple schemas
+        self.assertGreater(len(data), 0)
+        # Each schema should have RJSF format
+        for name, schema in data.items():
+            self.assertIn("schema", schema)
+            self.assertIn("uiSchema", schema)
+            self.assertIn("formData", schema)
+            self.assertIn("groups", schema)
+
+    def test_get_specific_schema(self):
+        """Test GET /api/v1/information/schema/{model_name}/ returns specific schema."""
+        self.client.force_login(self.user)
+
+        # Assuming 'temperature' is a valid model
+        response = self.client.get("/api/v1/information/schema/temperature/")
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertIn("schema", data)
+        self.assertIn("uiSchema", data)
+
+    def test_get_nonexistent_schema_returns_404(self):
+        """Test GET for non-existent schema returns 404."""
+        self.client.force_login(self.user)
+
+        response = self.client.get("/api/v1/information/schema/nonexistent/")
+
+        self.assertEqual(response.status_code, 404)
+
+    def test_list_scenario_information_empty(self):
+        """Test GET /api/v1/scenario/{uuid}/information/ returns empty list initially."""
+        self.client.force_login(self.user)
+
+        response = self.client.get(f"/api/v1/scenario/{self.scenario.uuid}/information/")
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertIsInstance(data, list)
+        self.assertEqual(len(data), 0)
+
+    def test_create_additional_information(self):
+        """Test POST creates additional information."""
+        self.client.force_login(self.user)
+
+        # Create temperature information (assuming temperature model exists)
+        payload = {"interval": {"start": 20, "end": 25}}
+        response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertEqual(data["status"], "created")
+        self.assertIn("uuid", data)
+        self.assertIsNotNone(data["uuid"])
+
+    def test_create_with_invalid_data_returns_400(self):
+        """Test POST with invalid data returns 400 with validation errors."""
+        self.client.force_login(self.user)
+
+        # Invalid data (missing required fields or wrong types)
+        payload = {"invalid_field": "value"}
+        response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 400)
+        data = response.json()
+        # Should have validation error details in 'detail' field
+        self.assertIn("detail", data)
+
+    def test_validation_errors_are_user_friendly(self):
+        """Test that validation errors are user-friendly and field-specific."""
+        self.client.force_login(self.user)
+
+        # Invalid data - wrong type (string instead of number in interval)
+        payload = {"interval": {"start": "not_a_number", "end": 25}}
+        response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 400)
+        data = response.json()
+
+        # Parse the error response - Django Ninja wraps errors in 'detail'
+        error_str = data.get("detail") or data.get("error")
+        self.assertIsNotNone(error_str, "Response should contain error details")
+
+        # Parse the JSON error string
+        error_data = json.loads(error_str)
+
+        # Check structure
+        self.assertEqual(error_data.get("type"), "validation_error")
+        self.assertIn("field_errors", error_data)
+        self.assertIn("message", error_data)
+
+        # Ensure error messages are user-friendly (no Pydantic URLs or technical jargon)
+        error_str = json.dumps(error_data)
+        self.assertNotIn("pydantic", error_str.lower())
+        self.assertNotIn("https://errors.pydantic.dev", error_str)
+        self.assertNotIn("loc", error_str)  # No technical field like 'loc'
+
+        # Check that error message is helpful
+        self.assertIn("Please", error_data["message"])  # User-friendly language
+
+    def test_patch_additional_information(self):
+        """Test PATCH updates existing additional information."""
+        self.client.force_login(self.user)
+
+        # First create an item
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Then update it with PATCH
+        update_payload = {"interval": {"start": 30, "end": 35}}
+        patch_response = self.client.patch(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item_uuid}/",
+            data=json.dumps(update_payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(patch_response.status_code, 200)
+        data = patch_response.json()
+        self.assertEqual(data["status"], "updated")
+        self.assertEqual(data["uuid"], item_uuid)  # UUID preserved
+
+        # Verify the data was updated
+        list_response = self.client.get(f"/api/v1/scenario/{self.scenario.uuid}/information/")
+        items = list_response.json()
+        self.assertEqual(len(items), 1)
+        updated_item = items[0]
+        self.assertEqual(updated_item["uuid"], item_uuid)
+        self.assertEqual(updated_item["data"]["interval"]["start"], 30)
+        self.assertEqual(updated_item["data"]["interval"]["end"], 35)
+
+    def test_patch_nonexistent_item_returns_404(self):
+        """Test PATCH on non-existent item returns 404."""
+        self.client.force_login(self.user)
+
+        fake_uuid = str(uuid4())
+        payload = {"interval": {"start": 30, "end": 35}}
+        response = self.client.patch(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{fake_uuid}/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 404)
+
+    def test_patch_with_invalid_data_returns_400(self):
+        """Test PATCH with invalid data returns 400."""
+        self.client.force_login(self.user)
+
+        # First create an item
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Try to update with invalid data
+        invalid_payload = {"invalid_field": "value"}
+        patch_response = self.client.patch(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item_uuid}/",
+            data=json.dumps(invalid_payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(patch_response.status_code, 400)
+
+    def test_patch_validation_errors_are_user_friendly(self):
+        """Test that PATCH validation errors are user-friendly and field-specific."""
+        self.client.force_login(self.user)
+
+        # First create an item
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Update with invalid data - wrong type (string instead of number in interval)
+        invalid_payload = {"interval": {"start": "not_a_number", "end": 25}}
+        patch_response = self.client.patch(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item_uuid}/",
+            data=json.dumps(invalid_payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(patch_response.status_code, 400)
+        data = patch_response.json()
+
+        # Parse the error response - Django Ninja wraps errors in 'detail'
+        error_str = data.get("detail") or data.get("error")
+        self.assertIsNotNone(error_str, "Response should contain error details")
+
+        # Parse the JSON error string
+        error_data = json.loads(error_str)
+
+        # Check structure
+        self.assertEqual(error_data.get("type"), "validation_error")
+        self.assertIn("field_errors", error_data)
+        self.assertIn("message", error_data)
+
+        # Ensure error messages are user-friendly (no Pydantic URLs or technical jargon)
+        error_str = json.dumps(error_data)
+        self.assertNotIn("pydantic", error_str.lower())
+        self.assertNotIn("https://errors.pydantic.dev", error_str)
+        self.assertNotIn("loc", error_str)  # No technical field like 'loc'
+
+        # Check that error message is helpful
+        self.assertIn("Please", error_data["message"])  # User-friendly language
+
+    def test_delete_additional_information(self):
+        """Test DELETE removes additional information."""
+        self.client.force_login(self.user)
+
+        # Create an item
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Delete it
+        delete_response = self.client.delete(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item_uuid}/"
+        )
+
+        self.assertEqual(delete_response.status_code, 200)
+        data = delete_response.json()
+        self.assertEqual(data["status"], "deleted")
+
+        # Verify deletion
+        list_response = self.client.get(f"/api/v1/scenario/{self.scenario.uuid}/information/")
+        items = list_response.json()
+        self.assertEqual(len(items), 0)
+
+    def test_delete_nonexistent_item_returns_404(self):
+        """Test DELETE on non-existent item returns 404."""
+        self.client.force_login(self.user)
+
+        fake_uuid = str(uuid4())
+        response = self.client.delete(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{fake_uuid}/"
+        )
+
+        self.assertEqual(response.status_code, 404)
+
+    def test_multiple_items_crud(self):
+        """Test creating, updating, and deleting multiple items."""
+        self.client.force_login(self.user)
+
+        # Create first item
+        item1_payload = {"interval": {"start": 20, "end": 25}}
+        response1 = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(item1_payload),
+            content_type="application/json",
+        )
+        item1_uuid = response1.json()["uuid"]
+
+        # Create second item (different type if available, or same type)
+        item2_payload = {"interval": {"start": 30, "end": 35}}
+        response2 = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(item2_payload),
+            content_type="application/json",
+        )
+        item2_uuid = response2.json()["uuid"]
+
+        # Verify both exist
+        list_response = self.client.get(f"/api/v1/scenario/{self.scenario.uuid}/information/")
+        items = list_response.json()
+        self.assertEqual(len(items), 2)
+
+        # Update first item
+        update_payload = {"interval": {"start": 15, "end": 20}}
+        self.client.patch(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item1_uuid}/",
+            data=json.dumps(update_payload),
+            content_type="application/json",
+        )
+
+        # Delete second item
+        self.client.delete(f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item2_uuid}/")
+
+        # Verify final state: one item with updated data
+        list_response = self.client.get(f"/api/v1/scenario/{self.scenario.uuid}/information/")
+        items = list_response.json()
+        self.assertEqual(len(items), 1)
+        self.assertEqual(items[0]["uuid"], item1_uuid)
+        self.assertEqual(items[0]["data"]["interval"]["start"], 15)
+
+    def test_list_info_denied_without_permission(self):
+        """User cannot list info for scenario in package they don't have access to"""
+        self.client.force_login(self.user)
+        response = self.client.get(f"/api/v1/scenario/{self.other_scenario.uuid}/information/")
+        self.assertEqual(response.status_code, 403)
+
+    def test_add_info_denied_without_permission(self):
+        """User cannot add info to scenario in package they don't have access to"""
+        self.client.force_login(self.user)
+        payload = {"interval": {"start": 25, "end": 30}}
+        response = self.client.post(
+            f"/api/v1/scenario/{self.other_scenario.uuid}/information/temperature/",
+            json.dumps(payload),
+            content_type="application/json",
+        )
+        self.assertEqual(response.status_code, 403)
+
+    def test_update_info_denied_without_permission(self):
+        """User cannot update info in scenario they don't have access to"""
+        self.client.force_login(self.other_user)
+        # First create an item as other_user
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.other_scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Try to update as user (who doesn't have access)
+        self.client.force_login(self.user)
+        update_payload = {"interval": {"start": 30, "end": 35}}
+        response = self.client.patch(
+            f"/api/v1/scenario/{self.other_scenario.uuid}/information/item/{item_uuid}/",
+            data=json.dumps(update_payload),
+            content_type="application/json",
+        )
+        self.assertEqual(response.status_code, 403)
+
+    def test_delete_info_denied_without_permission(self):
+        """User cannot delete info from scenario they don't have access to"""
+        self.client.force_login(self.other_user)
+        # First create an item as other_user
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.other_scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Try to delete as user (who doesn't have access)
+        self.client.force_login(self.user)
+        response = self.client.delete(
+            f"/api/v1/scenario/{self.other_scenario.uuid}/information/item/{item_uuid}/"
+        )
+        self.assertEqual(response.status_code, 403)
+
+    def test_nonexistent_scenario_returns_404(self):
+        """Test operations on non-existent scenario return 404."""
+        self.client.force_login(self.user)
+
+        fake_uuid = uuid4()
+        response = self.client.get(f"/api/v1/scenario/{fake_uuid}/information/")
+
+        self.assertEqual(response.status_code, 404)

epapi/tests/v1/test_api_permissions.py

@@ -261,13 +261,6 @@ class GlobalCompoundListPermissionTest(APIPermissionTestBase):
         self.assertEqual(response.status_code, 200)
         payload = response.json()
 
-        # user2 should see compounds from:
-        # - reviewed_package (public)
-        # - unreviewed_package_read (READ permission)
-        # - unreviewed_package_write (WRITE permission)
-        # - unreviewed_package_all (ALL permission)
-        # - group_package (via group membership)
-        # Total: 5 compounds
         self.assertEqual(payload["total_items"], 5)
 
         visible_uuids = {item["uuid"] for item in payload["items"]}
@@ -303,54 +296,6 @@ class GlobalCompoundListPermissionTest(APIPermissionTestBase):
         # user1 owns all packages, so sees all compounds
         self.assertEqual(payload["total_items"], 7)
 
-    def test_read_permission_allows_viewing(self):
-        """READ permission allows viewing compounds."""
-        self.client.force_login(self.user2)
-        response = self.client.get(self.ENDPOINT)
-
-        self.assertEqual(response.status_code, 200)
-        payload = response.json()
-
-        # Check that read_compound is included
-        uuids = [item["uuid"] for item in payload["items"]]
-        self.assertIn(str(self.read_compound.uuid), uuids)
-
-    def test_write_permission_allows_viewing(self):
-        """WRITE permission also allows viewing compounds."""
-        self.client.force_login(self.user2)
-        response = self.client.get(self.ENDPOINT)
-
-        self.assertEqual(response.status_code, 200)
-        payload = response.json()
-
-        # Check that write_compound is included
-        uuids = [item["uuid"] for item in payload["items"]]
-        self.assertIn(str(self.write_compound.uuid), uuids)
-
-    def test_all_permission_allows_viewing(self):
-        """ALL permission allows viewing compounds."""
-        self.client.force_login(self.user2)
-        response = self.client.get(self.ENDPOINT)
-
-        self.assertEqual(response.status_code, 200)
-        payload = response.json()
-
-        # Check that all_compound is included
-        uuids = [item["uuid"] for item in payload["items"]]
-        self.assertIn(str(self.all_compound.uuid), uuids)
-
-    def test_group_permission_allows_viewing(self):
-        """Group membership grants access to group-permitted packages."""
-        self.client.force_login(self.user2)
-        response = self.client.get(self.ENDPOINT)
-
-        self.assertEqual(response.status_code, 200)
-        payload = response.json()
-
-        # Check that group_compound is included
-        uuids = [item["uuid"] for item in payload["items"]]
-        self.assertIn(str(self.group_compound.uuid), uuids)
-
 
 @tag("api", "end2end")
 class PackageScopedCompoundListPermissionTest(APIPermissionTestBase):

epapi/tests/v1/test_contract_get_entities.py

@@ -134,7 +134,7 @@ class BaseTestAPIGetPaginated:
                 f"({self.total_reviewed} <= {self.default_page_size})"
             )
 
-        response = self.client.get(self.global_endpoint, {"page": 2})
+        response = self.client.get(self.global_endpoint, {"page": 2, "review_status": True})
         self.assertEqual(response.status_code, 200)
 
         payload = response.json()

epapi/tests/v1/test_scenario_creation.py

@@ -0,0 +1,301 @@
+"""
+Tests for Scenario Creation Endpoint Error Handling.
+
+Tests comprehensive error handling for POST /api/v1/package/{uuid}/scenario/
+including package not found, permission denied, validation errors, and database errors.
+"""
+
+from django.test import TestCase, tag
+import json
+from uuid import uuid4
+
+from epdb.logic import PackageManager, UserManager
+from epdb.models import Scenario
+
+
+@tag("api", "scenario_creation")
+class ScenarioCreationAPITests(TestCase):
+    """Test scenario creation endpoint error handling."""
+
+    @classmethod
+    def setUpTestData(cls):
+        """Set up test data: users and packages."""
+        cls.user = UserManager.create_user(
+            "scenario-test-user",
+            "scenario-test@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+        cls.other_user = UserManager.create_user(
+            "other-user",
+            "other@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+        cls.package = PackageManager.create_package(
+            cls.user, "Test Package", "Test package for scenario creation"
+        )
+
+    def test_create_scenario_package_not_found(self):
+        """Test that non-existent package UUID returns 404."""
+        self.client.force_login(self.user)
+
+        fake_uuid = uuid4()
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{fake_uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 404)
+        self.assertIn("Package not found", response.json()["detail"])
+
+    def test_create_scenario_insufficient_permissions(self):
+        """Test that unauthorized access returns 403."""
+        self.client.force_login(self.other_user)
+
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 403)
+        self.assertIn("permission", response.json()["detail"].lower())
+
+    def test_create_scenario_invalid_ai_type(self):
+        """Test that unknown additional information type returns 400."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [
+                {"type": "invalid_type_that_does_not_exist", "data": {"some_field": "some_value"}}
+            ],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 400)
+        response_data = response.json()
+        self.assertIn("Validation errors", response_data["detail"])
+
+    def test_create_scenario_validation_error(self):
+        """Test that invalid additional information data returns 400."""
+        self.client.force_login(self.user)
+
+        # Use malformed data structure for an actual AI type
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [
+                {
+                    "type": "invalid_type_name",
+                    "data": None,  # This should cause a validation error
+                }
+            ],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        # Should return 422 for validation errors
+        self.assertEqual(response.status_code, 422)
+
+    def test_create_scenario_success(self):
+        """Test that valid scenario creation returns 200."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertEqual(data["name"], "Test Scenario")
+        self.assertEqual(data["description"], "Test description")
+
+        # Verify scenario was actually created
+        scenario = Scenario.objects.get(name="Test Scenario")
+        self.assertEqual(scenario.package, self.package)
+        self.assertEqual(scenario.scenario_type, "biodegradation")
+
+    def test_create_scenario_auto_name(self):
+        """Test that empty name triggers auto-generation."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "",  # Empty name should be auto-generated
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        # Auto-generated name should follow pattern "Scenario N"
+        self.assertTrue(data["name"].startswith("Scenario "))
+
+    def test_create_scenario_xss_protection(self):
+        """Test that XSS attempts are sanitized."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "<script>alert('xss')</script>Clean Name",
+            "description": "<img src=x onerror=alert('xss')>Description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        # XSS should be cleaned out
+        self.assertNotIn("<script>", data["name"])
+        self.assertNotIn("onerror", data["description"])
+
+    def test_create_scenario_missing_required_field(self):
+        """Test that missing required fields returns validation error."""
+        self.client.force_login(self.user)
+
+        # Missing 'name' field entirely
+        payload = {
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        # Should return 422 for schema validation errors
+        self.assertEqual(response.status_code, 422)
+
+    def test_create_scenario_type_error_in_ai(self):
+        """Test that TypeError in AI instantiation returns 400."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [
+                {
+                    "type": "invalid_type_name",
+                    "data": "string instead of dict",  # Wrong type
+                }
+            ],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        # Should return 422 for validation errors
+        self.assertEqual(response.status_code, 422)
+
+    def test_create_scenario_default_values(self):
+        """Test that default values are applied correctly."""
+        self.client.force_login(self.user)
+
+        # Minimal payload with only name
+        payload = {"name": "Minimal Scenario"}
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertEqual(data["name"], "Minimal Scenario")
+        # Check defaults are applied
+        scenario = Scenario.objects.get(name="Minimal Scenario")
+        # Default description from model is "no description"
+        self.assertIn(scenario.description.lower(), ["", "no description"])
+
+    def test_create_scenario_unicode_characters(self):
+        """Test that unicode characters are handled properly."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "Test Scenario 测试 🧪",
+            "description": "Description with émojis and spëcial çhars",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertIn("测试", data["name"])
+        self.assertIn("émojis", data["description"])

epapi/tests/v1/test_schema_generation.py

@@ -0,0 +1,114 @@
+"""
+Property-based tests for schema generation.
+
+Tests that verify schema generation works correctly for all models,
+regardless of their structure.
+"""
+
+import pytest
+from typing import Type
+from pydantic import BaseModel
+
+from envipy_additional_information import registry, EnviPyModel
+from epapi.utils.schema_transformers import build_rjsf_output
+
+
+class TestSchemaGeneration:
+    """Test that all models can generate valid RJSF schemas."""
+
+    @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
+    def test_all_models_generate_rjsf(self, model_name: str, model_cls: Type[BaseModel]):
+        """Every model in the registry should generate valid RJSF format."""
+        # Skip non-EnviPyModel classes (parsers, etc.)
+        if not issubclass(model_cls, EnviPyModel):
+            pytest.skip(f"{model_name} is not an EnviPyModel")
+
+        # Should not raise exception
+        result = build_rjsf_output(model_cls)
+
+        # Verify structure
+        assert isinstance(result, dict), f"{model_name}: Result should be a dict"
+        assert "schema" in result, f"{model_name}: Missing 'schema' key"
+        assert "uiSchema" in result, f"{model_name}: Missing 'uiSchema' key"
+        assert "formData" in result, f"{model_name}: Missing 'formData' key"
+        assert "groups" in result, f"{model_name}: Missing 'groups' key"
+
+        # Verify types
+        assert isinstance(result["schema"], dict), f"{model_name}: schema should be dict"
+        assert isinstance(result["uiSchema"], dict), f"{model_name}: uiSchema should be dict"
+        assert isinstance(result["formData"], dict), f"{model_name}: formData should be dict"
+        assert isinstance(result["groups"], list), f"{model_name}: groups should be list"
+
+        # Verify schema has properties
+        assert "properties" in result["schema"], f"{model_name}: schema should have 'properties'"
+        assert isinstance(result["schema"]["properties"], dict), (
+            f"{model_name}: properties should be dict"
+        )
+
+    @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
+    def test_ui_schema_matches_schema_fields(self, model_name: str, model_cls: Type[BaseModel]):
+        """uiSchema keys should match schema properties (or be nested for intervals)."""
+        if not issubclass(model_cls, EnviPyModel):
+            pytest.skip(f"{model_name} is not an EnviPyModel")
+
+        result = build_rjsf_output(model_cls)
+        schema_props = set(result["schema"]["properties"].keys())
+        ui_schema_keys = set(result["uiSchema"].keys())
+
+        # uiSchema should have entries for all top-level properties
+        # (intervals may have nested start/end, but the main field should be present)
+        assert ui_schema_keys.issubset(schema_props), (
+            f"{model_name}: uiSchema has keys not in schema: {ui_schema_keys - schema_props}"
+        )
+
+    @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
+    def test_groups_is_list_of_strings(self, model_name: str, model_cls: Type[BaseModel]):
+        """Groups should be a list of strings."""
+        if not issubclass(model_cls, EnviPyModel):
+            pytest.skip(f"{model_name} is not an EnviPyModel")
+
+        result = build_rjsf_output(model_cls)
+        groups = result["groups"]
+
+        assert isinstance(groups, list), f"{model_name}: groups should be list"
+        assert all(isinstance(g, str) for g in groups), (
+            f"{model_name}: all groups should be strings, got {groups}"
+        )
+        assert len(groups) > 0, f"{model_name}: should have at least one group"
+
+    @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
+    def test_form_data_matches_schema(self, model_name: str, model_cls: Type[BaseModel]):
+        """formData keys should match schema properties."""
+        if not issubclass(model_cls, EnviPyModel):
+            pytest.skip(f"{model_name} is not an EnviPyModel")
+
+        result = build_rjsf_output(model_cls)
+        schema_props = set(result["schema"]["properties"].keys())
+        form_data_keys = set(result["formData"].keys())
+
+        # formData should only contain keys that are in schema
+        assert form_data_keys.issubset(schema_props), (
+            f"{model_name}: formData has keys not in schema: {form_data_keys - schema_props}"
+        )
+
+
+class TestWidgetTypes:
+    """Test that widget types are valid."""
+
+    @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
+    def test_widget_types_are_valid(self, model_name: str, model_cls: Type[BaseModel]):
+        """All widget types in uiSchema should be valid WidgetType values."""
+        from envipy_additional_information.ui_config import WidgetType
+
+        if not issubclass(model_cls, EnviPyModel):
+            pytest.skip(f"{model_name} is not an EnviPyModel")
+
+        result = build_rjsf_output(model_cls)
+        valid_widgets = {wt.value for wt in WidgetType}
+
+        for field_name, ui_config in result["uiSchema"].items():
+            widget = ui_config.get("ui:widget")
+            if widget:
+                assert widget in valid_widgets, (
+                    f"{model_name}.{field_name}: Invalid widget '{widget}'. Valid: {valid_widgets}"
+                )

epapi/tests/v1/test_token_auth.py

@@ -0,0 +1,94 @@
+from datetime import timedelta
+
+from django.test import TestCase, tag
+from django.utils import timezone
+
+from epdb.logic import PackageManager, UserManager
+from epdb.models import APIToken
+
+
+@tag("api", "auth")
+class BearerTokenAuthTests(TestCase):
+    @classmethod
+    def setUpTestData(cls):
+        cls.user = UserManager.create_user(
+            "token-user",
+            "token-user@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+
+        default_pkg = cls.user.default_package
+        cls.user.default_package = None
+        cls.user.save()
+        if default_pkg:
+            default_pkg.delete()
+
+        cls.unreviewed_package = PackageManager.create_package(
+            cls.user, "Token Auth Package", "Package for token auth tests"
+        )
+
+    def _auth_header(self, raw_token):
+        return {"HTTP_AUTHORIZATION": f"Bearer {raw_token}"}
+
+    def test_valid_token_allows_access(self):
+        _, raw_token = APIToken.create_token(self.user, name="Valid Token", expires_days=1)
+
+        response = self.client.get("/api/v1/compounds/", **self._auth_header(raw_token))
+
+        self.assertEqual(response.status_code, 200)
+
+    def test_expired_token_rejected(self):
+        token, raw_token = APIToken.create_token(self.user, name="Expired Token", expires_days=1)
+        token.expires_at = timezone.now() - timedelta(days=1)
+        token.save(update_fields=["expires_at"])
+
+        response = self.client.get("/api/v1/compounds/", **self._auth_header(raw_token))
+
+        self.assertEqual(response.status_code, 401)
+
+    def test_inactive_token_rejected(self):
+        token, raw_token = APIToken.create_token(self.user, name="Inactive Token", expires_days=1)
+        token.is_active = False
+        token.save(update_fields=["is_active"])
+
+        response = self.client.get("/api/v1/compounds/", **self._auth_header(raw_token))
+
+        self.assertEqual(response.status_code, 401)
+
+    def test_invalid_token_rejected(self):
+        response = self.client.get("/api/v1/compounds/", HTTP_AUTHORIZATION="Bearer invalid-token")
+
+        self.assertEqual(response.status_code, 401)
+
+    def test_no_token_rejected(self):
+        self.client.logout()
+        response = self.client.get("/api/v1/compounds/")
+
+        self.assertEqual(response.status_code, 401)
+
+    def test_bearer_populates_request_user_for_packages(self):
+        response = self.client.get("/api/v1/packages/")
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+        uuids = {item["uuid"] for item in payload["items"]}
+        self.assertNotIn(str(self.unreviewed_package.uuid), uuids)
+
+        _, raw_token = APIToken.create_token(self.user, name="Package Token", expires_days=1)
+        response = self.client.get("/api/v1/packages/", **self._auth_header(raw_token))
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+        uuids = {item["uuid"] for item in payload["items"]}
+        self.assertIn(str(self.unreviewed_package.uuid), uuids)
+
+    def test_session_auth_still_works_without_bearer(self):
+        self.client.force_login(self.user)
+        response = self.client.get("/api/v1/packages/")
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+        uuids = {item["uuid"] for item in payload["items"]}
+        self.assertIn(str(self.unreviewed_package.uuid), uuids)

epapi/utils/schema_transformers.py

@@ -0,0 +1,181 @@
+"""
+Schema transformation utilities for converting Pydantic models to RJSF format.
+
+This module provides functions to extract UI configuration from Pydantic models
+and transform them into React JSON Schema Form (RJSF) compatible format.
+"""
+
+from typing import Type, Optional, Any
+
+import jsonref
+from pydantic import BaseModel
+
+from envipy_additional_information.ui_config import UIConfig
+from envipy_additional_information import registry
+
+
+def extract_groups(model_cls: Type[BaseModel]) -> list[str]:
+    """
+    Extract groups from registry-stored group information.
+
+    Args:
+        model_cls: The model class
+
+    Returns:
+        List of group names the model belongs to
+    """
+    return registry.get_groups(model_cls)
+
+
+def extract_ui_metadata(model_cls: Type[BaseModel]) -> dict[str, Any]:
+    """
+    Extract model-level UI metadata from UI class.
+
+    Returns metadata attributes that are NOT UIConfig instances.
+    Common metadata includes: unit, description, title.
+    """
+    metadata: dict[str, Any] = {}
+
+    if not hasattr(model_cls, "UI"):
+        return metadata
+
+    ui_class = getattr(model_cls, "UI")
+
+    # Iterate over all attributes in the UI class
+    for attr_name in dir(ui_class):
+        # Skip private attributes
+        if attr_name.startswith("_"):
+            continue
+
+        # Get the attribute value
+        try:
+            attr_value = getattr(ui_class, attr_name)
+        except AttributeError:
+            continue
+
+        # Skip callables but keep types/classes
+        if callable(attr_value) and not isinstance(attr_value, type):
+            continue
+
+        # Skip UIConfig instances (these are field-level configs, not metadata)
+        # This includes both UIConfig and IntervalConfig
+        if isinstance(attr_value, UIConfig):
+            continue
+
+        metadata[attr_name] = attr_value
+
+    return metadata
+
+
+def extract_ui_config_from_model(model_cls: Type[BaseModel]) -> dict[str, Any]:
+    """
+    Extract UI configuration from model's UI class.
+
+    Returns a dictionary mapping field names to their UI schema configurations.
+    Trusts the config classes to handle their own transformation logic.
+    """
+    ui_configs: dict[str, Any] = {}
+
+    if not hasattr(model_cls, "UI"):
+        return ui_configs
+
+    ui_class = getattr(model_cls, "UI")
+    schema = model_cls.model_json_schema()
+    field_names = schema.get("properties", {}).keys()
+
+    # Extract config for each field
+    for field_name in field_names:
+        # Skip if UI config doesn't exist for this field (field may be hidden from UI)
+        if not hasattr(ui_class, field_name):
+            continue
+
+        ui_config = getattr(ui_class, field_name)
+
+        if isinstance(ui_config, UIConfig):
+            ui_configs[field_name] = ui_config.to_ui_schema_field()
+
+    return ui_configs
+
+
+def build_ui_schema(model_cls: Type[BaseModel]) -> dict:
+    """Generate RJSF uiSchema from model's UI class."""
+    ui_schema = {}
+
+    # Extract field-level UI configs
+    field_configs = extract_ui_config_from_model(model_cls)
+
+    for field_name, config in field_configs.items():
+        ui_schema[field_name] = config
+
+    return ui_schema
+
+
+def build_schema(model_cls: Type[BaseModel]) -> dict[str, Any]:
+    """
+    Build JSON schema from Pydantic model, applying UI metadata.
+
+    Dereferences all $ref pointers to produce fully inlined schema.
+    This ensures the frontend receives schemas with enum values and nested
+    properties fully resolved, without needing client-side ref resolution.
+
+    Extracts model-level metadata from UI class (title, unit, etc.) and applies
+    it to the generated schema. This ensures UI metadata is the single source of truth.
+    """
+    schema = model_cls.model_json_schema()
+
+    # Dereference $ref pointers (inlines $defs) using jsonref
+    # This ensures the frontend receives schemas with enum values and nested
+    # properties fully resolved, currently necessary for client-side rendering.
+    # FIXME: This is a hack to get the schema to work with alpine schema-form.js replace once we migrate to client-side framework.
+    schema = jsonref.replace_refs(schema, proxies=False)
+
+    # Remove $defs section as all refs are now inlined
+    if "$defs" in schema:
+        del schema["$defs"]
+
+    # Extract and apply UI metadata (title, unit, description, etc.)
+    ui_metadata = extract_ui_metadata(model_cls)
+
+    # Apply all metadata consistently as custom properties with x- prefix
+    # This ensures consistency and avoids conflicts with standard JSON Schema properties
+    for key, value in ui_metadata.items():
+        if value is not None:
+            schema[f"x-{key}"] = value
+
+    # Set standard title property from UI metadata for JSON Schema compliance
+    if "title" in ui_metadata:
+        schema["title"] = ui_metadata["title"]
+    elif "label" in ui_metadata:
+        schema["title"] = ui_metadata["label"]
+
+    return schema
+
+
+def build_rjsf_output(model_cls: Type[BaseModel], initial_data: Optional[dict] = None) -> dict:
+    """
+    Main function that returns complete RJSF format.
+
+    Trusts the config classes to handle their own transformation logic.
+    No special-case handling - if a config knows how to transform itself, it will.
+
+    Returns:
+        dict with keys: schema, uiSchema, formData, groups
+    """
+    # Build schema with UI metadata applied
+    schema = build_schema(model_cls)
+
+    # Build UI schema - config classes handle their own transformation
+    ui_schema = build_ui_schema(model_cls)
+
+    # Extract groups from marker interfaces
+    groups = extract_groups(model_cls)
+
+    # Use provided initial_data or empty dict
+    form_data = initial_data if initial_data is not None else {}
+
+    return {
+        "schema": schema,
+        "uiSchema": ui_schema,
+        "formData": form_data,
+        "groups": groups,
+    }

epapi/utils/validation_errors.py

@@ -0,0 +1,82 @@
+"""Shared utilities for handling Pydantic validation errors."""
+
+import json
+from pydantic import ValidationError
+from pydantic_core import ErrorDetails
+from ninja.errors import HttpError
+
+
+def format_validation_error(error: ErrorDetails) -> str:
+    """Format a Pydantic validation error into a user-friendly message.
+
+    Args:
+        error: A Pydantic error details dictionary containing 'msg', 'type', 'ctx', etc.
+
+    Returns:
+        A user-friendly error message string.
+    """
+    msg = error.get("msg") or "Invalid value"
+    error_type = error.get("type") or ""
+
+    # Handle common validation types with friendly messages
+    if error_type == "enum":
+        ctx = error.get("ctx", {})
+        expected = ctx.get("expected", "") if ctx else ""
+        return f"Please select a valid option{': ' + expected if expected else ''}"
+    elif error_type == "literal_error":
+        # Literal errors (like Literal["active", "inactive"])
+        return msg.replace("Input should be ", "Please enter ")
+    elif error_type == "missing":
+        return "This field is required"
+    elif error_type == "string_type":
+        return "Please enter a valid string"
+    elif error_type == "int_type":
+        return "Please enter a valid int"
+    elif error_type == "int_parsing":
+        return "Please enter a valid int"
+    elif error_type == "float_type":
+        return "Please enter a valid float"
+    elif error_type == "float_parsing":
+        return "Please enter a valid float"
+    elif error_type == "value_error":
+        # Strip "Value error, " prefix from custom validator messages
+        return msg.replace("Value error, ", "")
+    else:
+        # Default: use the message from Pydantic but clean it up
+        return msg.replace("Input should be ", "Please enter ").replace("Value error, ", "")
+
+
+def handle_validation_error(e: ValidationError) -> None:
+    """Convert a Pydantic ValidationError into a structured HttpError.
+
+    This function transforms Pydantic validation errors into a JSON structure
+    that the frontend expects for displaying field-level errors.
+
+    Args:
+        e: The Pydantic ValidationError to handle.
+
+    Raises:
+        HttpError: Always raises a 400 error with structured JSON containing
+                   type, field_errors, and message fields.
+    """
+    # Transform Pydantic validation errors into user-friendly format
+    field_errors: dict[str, list[str]] = {}
+    for error in e.errors():
+        # Get the field name from location tuple
+        loc = error.get("loc", ())
+        field = str(loc[-1]) if loc else "root"
+
+        # Format the error message
+        friendly_msg = format_validation_error(error)
+
+        if field not in field_errors:
+            field_errors[field] = []
+        field_errors[field].append(friendly_msg)
+
+    # Return structured error for frontend parsing
+    error_response = {
+        "type": "validation_error",
+        "field_errors": field_errors,
+        "message": "Please correct the errors below",
+    }
+    raise HttpError(400, json.dumps(error_response))

epapi/v1/auth.py

@@ -1,8 +1,34 @@
+import hashlib
+
 from ninja.security import HttpBearer
 from ninja.errors import HttpError
 
+from epdb.models import APIToken
+
 
 class BearerTokenAuth(HttpBearer):
     def authenticate(self, request, token):
-        # FIXME: placeholder; implement it in O(1) time
-        raise HttpError(401, "Invalid or expired token")
+        if token is None:
+            return None
+
+        hashed_token = hashlib.sha256(token.encode()).hexdigest()
+        user = APIToken.authenticate(hashed_token, hashed=True)
+        if not user:
+            raise HttpError(401, "Invalid or expired token")
+
+        request.user = user
+        return user
+
+
+class OptionalBearerTokenAuth:
+    """Bearer auth that allows unauthenticated access.
+
+    Validates the Bearer token if present (401 on invalid token),
+    otherwise lets the request through for anonymous/session access.
+    """
+
+    def __init__(self):
+        self._bearer = BearerTokenAuth()
+
+    def __call__(self, request):
+        return self._bearer(request) or request.user

epapi/v1/dal.py

@@ -1,12 +1,12 @@
 from django.db.models import Model
 from epdb.logic import PackageManager
-from epdb.models import CompoundStructure, User, Package, Compound
+from epdb.models import CompoundStructure, User, Package, Compound, Scenario
 from uuid import UUID
 
 from .errors import EPAPINotFoundError, EPAPIPermissionDeniedError
 
 
-def get_compound_or_error(user, compound_uuid: UUID):
+def get_compound_for_read(user, compound_uuid: UUID):
     """
     Get compound by UUID with permission check.
     """
@@ -23,7 +23,7 @@ def get_compound_or_error(user, compound_uuid: UUID):
     return compound
 
 
-def get_package_or_error(user, package_uuid: UUID):
+def get_package_for_read(user, package_uuid: UUID):
     """
     Get package by UUID with permission check.
     """
@@ -41,14 +41,40 @@ def get_package_or_error(user, package_uuid: UUID):
     return package
 
 
-def get_user_packages_qs(user: User | None):
+def get_scenario_for_read(user, scenario_uuid: UUID):
+    """Get scenario by UUID with read permission check."""
+    try:
+        scenario = Scenario.objects.select_related("package").get(uuid=scenario_uuid)
+    except Scenario.DoesNotExist:
+        raise EPAPINotFoundError(f"Scenario with UUID {scenario_uuid} not found")
+
+    if not user or user.is_anonymous or not PackageManager.readable(user, scenario.package):
+        raise EPAPIPermissionDeniedError("Insufficient permissions to access this scenario.")
+
+    return scenario
+
+
+def get_scenario_for_write(user, scenario_uuid: UUID):
+    """Get scenario by UUID with write permission check."""
+    try:
+        scenario = Scenario.objects.select_related("package").get(uuid=scenario_uuid)
+    except Scenario.DoesNotExist:
+        raise EPAPINotFoundError(f"Scenario with UUID {scenario_uuid} not found")
+
+    if not user or user.is_anonymous or not PackageManager.writable(user, scenario.package):
+        raise EPAPIPermissionDeniedError("Insufficient permissions to modify this scenario.")
+
+    return scenario
+
+
+def get_user_packages_for_read(user: User | None):
     """Get all packages readable by the user."""
     if not user or user.is_anonymous:
         return PackageManager.get_reviewed_packages()
     return PackageManager.get_all_readable_packages(user, include_reviewed=True)
 
 
-def get_user_entities_qs(model_class: Model, user: User | None):
+def get_user_entities_for_read(model_class: Model, user: User | None):
     """Build queryset for reviewed package entities."""
 
     if not user or user.is_anonymous:
@@ -60,16 +86,14 @@ def get_user_entities_qs(model_class: Model, user: User | None):
     return qs
 
 
-def get_package_scoped_entities_qs(
-    model_class: Model, package_uuid: UUID, user: User | None = None
-):
+def get_package_entities_for_read(model_class: Model, package_uuid: UUID, user: User | None = None):
     """Build queryset for specific package entities."""
-    package = get_package_or_error(user, package_uuid)
+    package = get_package_for_read(user, package_uuid)
     qs = model_class.objects.filter(package=package).select_related("package")
     return qs
 
 
-def get_user_structures_qs(user: User | None):
+def get_user_structure_for_read(user: User | None):
     """Build queryset for structures accessible to the user (via compound->package)."""
 
     if not user or user.is_anonymous:
@@ -83,13 +107,13 @@ def get_user_structures_qs(user: User | None):
     return qs
 
 
-def get_package_compound_scoped_structure_qs(
+def get_package_compound_structure_for_read(
     package_uuid: UUID, compound_uuid: UUID, user: User | None = None
 ):
     """Build queryset for specific package compound structures."""
 
-    get_package_or_error(user, package_uuid)
-    compound = get_compound_or_error(user, compound_uuid)
+    get_package_for_read(user, package_uuid)
+    compound = get_compound_for_read(user, compound_uuid)
 
     qs = CompoundStructure.objects.filter(compound=compound).select_related("compound__package")
     return qs

epapi/v1/endpoints/additional_information.py

@@ -0,0 +1,174 @@
+from ninja import Router, Body
+from ninja.errors import HttpError
+from uuid import UUID
+from pydantic import ValidationError
+from typing import Dict, Any
+import logging
+
+from envipy_additional_information import registry
+from envipy_additional_information.groups import GroupEnum
+from epapi.utils.schema_transformers import build_rjsf_output
+from epapi.utils.validation_errors import handle_validation_error
+from ..dal import get_scenario_for_read, get_scenario_for_write
+
+logger = logging.getLogger(__name__)
+
+router = Router(tags=["Additional Information"])
+
+
+@router.get("/information/schema/")
+def list_all_schemas(request):
+    """Return all schemas in RJSF format with lowercase class names as keys."""
+    result = {}
+    for name, cls in registry.list_models().items():
+        try:
+            result[name] = build_rjsf_output(cls)
+        except Exception as e:
+            logger.warning(f"Failed to generate schema for {name}: {e}")
+            continue
+    return result
+
+
+@router.get("/information/schema/{model_name}/")
+def get_model_schema(request, model_name: str):
+    """Return RJSF schema for specific model."""
+    cls = registry.get_model(model_name.lower())
+    if not cls:
+        raise HttpError(404, f"Unknown model: {model_name}")
+    return build_rjsf_output(cls)
+
+
+@router.get("/scenario/{uuid:scenario_uuid}/information/")
+def list_scenario_info(request, scenario_uuid: UUID):
+    """List all additional information for a scenario"""
+    scenario = get_scenario_for_read(request.user, scenario_uuid)
+
+    result = []
+    for ai in scenario.get_additional_information():
+        result.append(
+            {
+                "type": ai.__class__.__name__,
+                "uuid": getattr(ai, "uuid", None),
+                "data": ai.model_dump(mode="json"),
+            }
+        )
+    return result
+
+
+@router.post("/scenario/{uuid:scenario_uuid}/information/{model_name}/")
+def add_scenario_info(
+    request, scenario_uuid: UUID, model_name: str, payload: Dict[str, Any] = Body(...)
+):
+    """Add new additional information to scenario"""
+    cls = registry.get_model(model_name.lower())
+    if not cls:
+        raise HttpError(404, f"Unknown model: {model_name}")
+
+    try:
+        instance = cls(**payload)  # Pydantic validates
+    except ValidationError as e:
+        handle_validation_error(e)
+
+    scenario = get_scenario_for_write(request.user, scenario_uuid)
+
+    # Model method now returns the UUID
+    created_uuid = scenario.add_additional_information(instance)
+
+    return {"status": "created", "uuid": created_uuid}
+
+
+@router.patch("/scenario/{uuid:scenario_uuid}/information/item/{uuid:ai_uuid}/")
+def update_scenario_info(
+    request, scenario_uuid: UUID, ai_uuid: UUID, payload: Dict[str, Any] = Body(...)
+):
+    """Update existing additional information for a scenario"""
+    scenario = get_scenario_for_write(request.user, scenario_uuid)
+    ai_uuid_str = str(ai_uuid)
+
+    # Find item to determine type for validation
+    found_type = None
+    for type_name, items in scenario.additional_information.items():
+        if any(item.get("uuid") == ai_uuid_str for item in items):
+            found_type = type_name
+            break
+
+    if found_type is None:
+        raise HttpError(404, f"Additional information not found: {ai_uuid}")
+
+    # Get the model class for validation
+    cls = registry.get_model(found_type.lower())
+    if not cls:
+        raise HttpError(500, f"Unknown model type in data: {found_type}")
+
+    # Validate the payload against the model
+    try:
+        instance = cls(**payload)
+    except ValidationError as e:
+        handle_validation_error(e)
+
+    # Use model method for update
+    try:
+        scenario.update_additional_information(ai_uuid_str, instance)
+    except ValueError as e:
+        raise HttpError(404, str(e))
+
+    return {"status": "updated", "uuid": ai_uuid_str}
+
+
+@router.delete("/scenario/{uuid:scenario_uuid}/information/item/{uuid:ai_uuid}/")
+def delete_scenario_info(request, scenario_uuid: UUID, ai_uuid: UUID):
+    """Delete additional information from scenario"""
+    scenario = get_scenario_for_write(request.user, scenario_uuid)
+
+    try:
+        scenario.remove_additional_information(str(ai_uuid))
+    except ValueError as e:
+        raise HttpError(404, str(e))
+
+    return {"status": "deleted"}
+
+
+@router.get("/information/groups/")
+def list_groups(request):
+    """Return list of available group names."""
+    return {"groups": GroupEnum.values()}
+
+
+@router.get("/information/groups/{group_name}/")
+def get_group_models(request, group_name: str):
+    """
+    Return models for a specific group organized by subcategory.
+
+    Args:
+        group_name: One of "sludge", "soil", or "sediment" (string)
+
+    Returns:
+        Dictionary with subcategories (exp, spike, comp, misc, or group name)
+        as keys and lists of model info as values
+    """
+    # Convert string to enum (raises ValueError if invalid)
+    try:
+        group_enum = GroupEnum(group_name)
+    except ValueError:
+        valid = ", ".join(GroupEnum.values())
+        raise HttpError(400, f"Invalid group '{group_name}'. Valid: {valid}")
+
+    try:
+        group_data = registry.collect_group(group_enum)
+    except (ValueError, TypeError) as e:
+        raise HttpError(400, str(e))
+
+    result = {}
+    for subcategory, models in group_data.items():
+        result[subcategory] = [
+            {
+                "name": cls.__name__.lower(),
+                "class": cls.__name__,
+                "title": getattr(cls.UI, "title", cls.__name__)
+                if hasattr(cls, "UI")
+                else cls.__name__,
+            }
+            for cls in models
+        ]
+
+    return result

epapi/v1/endpoints/compounds.py

@@ -6,7 +6,7 @@ from uuid import UUID
 from epdb.models import Compound
 from ..pagination import EnhancedPageNumberPagination
 from ..schemas import CompoundOutSchema, ReviewStatusFilter
-from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
 
 router = Router()
 
@@ -21,7 +21,7 @@ def list_all_compounds(request):
     """
     List all compounds from reviewed packages.
     """
-    return get_user_entities_qs(Compound, request.user).order_by("name").all()
+    return get_user_entities_for_read(Compound, request.user).order_by("name").all()
 
 
 @router.get(
@@ -38,4 +38,4 @@ def list_package_compounds(request, package_uuid: UUID):
     List all compounds for a specific package.
     """
     user = request.user
-    return get_package_scoped_entities_qs(Compound, package_uuid, user).order_by("name").all()
+    return get_package_entities_for_read(Compound, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/models.py

@@ -6,7 +6,7 @@ from uuid import UUID
 from epdb.models import EPModel
 from ..pagination import EnhancedPageNumberPagination
 from ..schemas import ModelOutSchema, ReviewStatusFilter
-from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
 
 router = Router()
 
@@ -21,7 +21,7 @@ def list_all_models(request):
     """
     List all models from reviewed packages.
     """
-    return get_user_entities_qs(EPModel, request.user).order_by("name").all()
+    return get_user_entities_for_read(EPModel, request.user).order_by("name").all()
 
 
 @router.get(
@@ -38,4 +38,4 @@ def list_package_models(request, package_uuid: UUID):
     List all models for a specific package.
     """
     user = request.user
-    return get_package_scoped_entities_qs(EPModel, package_uuid, user).order_by("name").all()
+    return get_package_entities_for_read(EPModel, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/packages.py

@@ -3,7 +3,8 @@ from ninja import Router
 from ninja_extra.pagination import paginate
 import logging
 
-from ..dal import get_user_packages_qs
+from ..auth import OptionalBearerTokenAuth
+from ..dal import get_user_packages_for_read
 from ..pagination import EnhancedPageNumberPagination
 from ..schemas import PackageOutSchema, SelfReviewStatusFilter
 
@@ -11,7 +12,11 @@ router = Router()
 logger = logging.getLogger(__name__)
 
 
-@router.get("/packages/", response=EnhancedPageNumberPagination.Output[PackageOutSchema], auth=None)
+@router.get(
+    "/packages/",
+    response=EnhancedPageNumberPagination.Output[PackageOutSchema],
+    auth=OptionalBearerTokenAuth(),
+)
 @paginate(
     EnhancedPageNumberPagination,
     page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
@@ -23,5 +28,5 @@ def list_all_packages(request):
 
     """
     user = request.user
-    qs = get_user_packages_qs(user)
+    qs = get_user_packages_for_read(user)
     return qs.order_by("name").all()

epapi/v1/endpoints/pathways.py

@@ -6,7 +6,7 @@ from uuid import UUID
 from epdb.models import Pathway
 from ..pagination import EnhancedPageNumberPagination
 from ..schemas import PathwayOutSchema, ReviewStatusFilter
-from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
 
 router = Router()
 
@@ -22,7 +22,7 @@ def list_all_pathways(request):
     List all pathways from reviewed packages.
     """
     user = request.user
-    return get_user_entities_qs(Pathway, user).order_by("name").all()
+    return get_user_entities_for_read(Pathway, user).order_by("name").all()
 
 
 @router.get(
@@ -39,4 +39,4 @@ def list_package_pathways(request, package_uuid: UUID):
     List all pathways for a specific package.
     """
     user = request.user
-    return get_package_scoped_entities_qs(Pathway, package_uuid, user).order_by("name").all()
+    return get_package_entities_for_read(Pathway, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/reactions.py

@@ -6,7 +6,7 @@ from uuid import UUID
 from epdb.models import Reaction
 from ..pagination import EnhancedPageNumberPagination
 from ..schemas import ReactionOutSchema, ReviewStatusFilter
-from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
 
 router = Router()
 
@@ -22,7 +22,7 @@ def list_all_reactions(request):
     List all reactions from reviewed packages.
     """
     user = request.user
-    return get_user_entities_qs(Reaction, user).order_by("name").all()
+    return get_user_entities_for_read(Reaction, user).order_by("name").all()
 
 
 @router.get(
@@ -39,4 +39,4 @@ def list_package_reactions(request, package_uuid: UUID):
     List all reactions for a specific package.
     """
     user = request.user
-    return get_package_scoped_entities_qs(Reaction, package_uuid, user).order_by("name").all()
+    return get_package_entities_for_read(Reaction, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/rules.py

@@ -6,7 +6,7 @@ from uuid import UUID
 from epdb.models import Rule
 from ..pagination import EnhancedPageNumberPagination
 from ..schemas import ReviewStatusFilter, RuleOutSchema
-from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
 
 router = Router()
 
@@ -22,7 +22,7 @@ def list_all_rules(request):
     List all rules from reviewed packages.
     """
     user = request.user
-    return get_user_entities_qs(Rule, user).order_by("name").all()
+    return get_user_entities_for_read(Rule, user).order_by("name").all()
 
 
 @router.get(
@@ -39,4 +39,4 @@ def list_package_rules(request, package_uuid: UUID):
     List all rules for a specific package.
     """
     user = request.user
-    return get_package_scoped_entities_qs(Rule, package_uuid, user).order_by("name").all()
+    return get_package_entities_for_read(Rule, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/scenarios.py

@@ -1,12 +1,26 @@
 from django.conf import settings as s
-from ninja import Router
+from django.db import IntegrityError, OperationalError, DatabaseError
+from ninja import Router, Body
+from ninja.errors import HttpError
 from ninja_extra.pagination import paginate
 from uuid import UUID
+from pydantic import ValidationError
+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 ReviewStatusFilter, ScenarioOutSchema
-from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
+from ..schemas import (
+    ScenarioOutSchema,
+    ScenarioCreateSchema,
+    ScenarioReviewStatusAndRelatedFilter,
+)
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
+from envipy_additional_information import registry
+
+logger = logging.getLogger(__name__)
 
 router = Router()
 
@@ -15,11 +29,12 @@ router = Router()
 @paginate(
     EnhancedPageNumberPagination,
     page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
-    filter_schema=ReviewStatusFilter,
+    filter_schema=ScenarioReviewStatusAndRelatedFilter,
 )
 def list_all_scenarios(request):
     user = request.user
-    return get_user_entities_qs(Scenario, user).order_by("name").all()
+    items = get_user_entities_for_read(Scenario, user)
+    return items.order_by("name").all()
 
 
 @router.get(
@@ -29,8 +44,87 @@ def list_all_scenarios(request):
 @paginate(
     EnhancedPageNumberPagination,
     page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
-    filter_schema=ReviewStatusFilter,
+    filter_schema=ScenarioReviewStatusAndRelatedFilter,
 )
 def list_package_scenarios(request, package_uuid: UUID):
     user = request.user
-    return get_package_scoped_entities_qs(Scenario, package_uuid, user).order_by("name").all()
+    items = get_package_entities_for_read(Scenario, package_uuid, user)
+    return items.order_by("name").all()
+
+
+@router.post("/package/{uuid:package_uuid}/scenario/", response=ScenarioOutSchema)
+def create_scenario(request, package_uuid: UUID, payload: ScenarioCreateSchema = Body(...)):
+    """Create a new scenario with optional additional information."""
+    user = _anonymous_or_real(request)
+
+    try:
+        current_package = PackageManager.get_package_by_id(user, package_uuid)
+    except ValueError as e:
+        error_msg = str(e)
+        if "does not exist" in error_msg:
+            raise HttpError(404, f"Package not found: {package_uuid}")
+        elif "Insufficient permissions" in error_msg:
+            raise HttpError(403, "You do not have permission to access this package")
+        else:
+            logger.error(f"Unexpected ValueError from get_package_by_id: {error_msg}")
+            raise HttpError(400, "Invalid package request")
+
+    # Build additional information models from payload
+    additional_information_models = []
+    validation_errors = []
+
+    for ai_item in payload.additional_information:
+        # Get model class from registry
+        model_cls = registry.get_model(ai_item.type.lower())
+        if not model_cls:
+            validation_errors.append(f"Unknown additional information type: {ai_item.type}")
+            continue
+
+        try:
+            # Validate and create model instance
+            instance = model_cls(**ai_item.data)
+            additional_information_models.append(instance)
+        except ValidationError as e:
+            # Collect validation errors to return to user
+            error_messages = [err.get("msg", "Validation error") for err in e.errors()]
+            validation_errors.append(f"{ai_item.type}: {', '.join(error_messages)}")
+        except (TypeError, AttributeError, KeyError) as e:
+            logger.warning(f"Failed to instantiate {ai_item.type} model: {str(e)}")
+            validation_errors.append(f"{ai_item.type}: Invalid data structure - {str(e)}")
+        except Exception as e:
+            logger.error(f"Unexpected error instantiating {ai_item.type}: {str(e)}")
+            validation_errors.append(f"{ai_item.type}: Failed to process - please check your data")
+
+    # If there are validation errors, return them
+    if validation_errors:
+        raise HttpError(
+            400,
+            json.dumps(
+                {
+                    "error": "Validation errors in additional information",
+                    "details": validation_errors,
+                }
+            ),
+        )
+
+    # Create scenario using the existing Scenario.create method
+    try:
+        new_scenario = Scenario.create(
+            package=current_package,
+            name=payload.name,
+            description=payload.description,
+            scenario_date=payload.scenario_date,
+            scenario_type=payload.scenario_type,
+            additional_information=additional_information_models,
+        )
+    except IntegrityError as e:
+        logger.error(f"Database integrity error creating scenario: {str(e)}")
+        raise HttpError(400, "Scenario creation failed - data constraint violation")
+    except OperationalError as e:
+        logger.error(f"Database operational error creating scenario: {str(e)}")
+        raise HttpError(503, "Database temporarily unavailable - please try again")
+    except (DatabaseError, AttributeError) as e:
+        logger.error(f"Error creating scenario: {str(e)}")
+        raise HttpError(500, "Failed to create scenario due to database error")
+
+    return new_scenario

epapi/v1/endpoints/settings.py

@@ -0,0 +1,23 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+
+from epdb.logic import SettingManager
+
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import SettingOutSchema
+
+router = Router()
+
+
+@router.get("/settings/", response=EnhancedPageNumberPagination.Output[SettingOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+)
+def list_all_pathways(request):
+    """
+    List all pathways from reviewed packages.
+    """
+    user = request.user
+    return SettingManager.get_all_settings(user)

epapi/v1/endpoints/structure.py

@@ -6,8 +6,8 @@ from uuid import UUID
 from ..pagination import EnhancedPageNumberPagination
 from ..schemas import CompoundStructureOutSchema, StructureReviewStatusFilter
 from ..dal import (
-    get_user_structures_qs,
-    get_package_compound_scoped_structure_qs,
+    get_user_structure_for_read,
+    get_package_compound_structure_for_read,
 )
 
 router = Router()
@@ -26,7 +26,7 @@ def list_all_structures(request):
     List all structures from all packages.
     """
     user = request.user
-    return get_user_structures_qs(user).order_by("name").all()
+    return get_user_structure_for_read(user).order_by("name").all()
 
 
 @router.get(
@@ -44,7 +44,7 @@ def list_package_structures(request, package_uuid: UUID, compound_uuid: UUID):
     """
     user = request.user
     return (
-        get_package_compound_scoped_structure_qs(package_uuid, compound_uuid, user)
+        get_package_compound_structure_for_read(package_uuid, compound_uuid, user)
         .order_by("name")
         .all()
     )

epapi/v1/router.py

@@ -1,7 +1,19 @@
 from ninja import Router
 from ninja.security import SessionAuth
+
 from .auth import BearerTokenAuth
-from .endpoints import packages, scenarios, compounds, rules, reactions, pathways, models, structure
+from .endpoints import (
+    packages,
+    scenarios,
+    compounds,
+    rules,
+    reactions,
+    pathways,
+    models,
+    structure,
+    additional_information,
+    settings,
+)
 
 # Main router with authentication
 router = Router(
@@ -20,3 +32,5 @@ router.add_router("", reactions.router)
 router.add_router("", pathways.router)
 router.add_router("", models.router)
 router.add_router("", structure.router)
+router.add_router("", additional_information.router)
+router.add_router("", settings.router)

epapi/v1/schemas.py

@@ -1,5 +1,5 @@
 from ninja import FilterSchema, FilterLookup, Schema
-from typing import Annotated, Optional
+from typing import Annotated, Optional, List, Dict, Any
 from uuid import UUID
 
 
@@ -22,6 +22,12 @@ class StructureReviewStatusFilter(FilterSchema):
     review_status: Annotated[Optional[bool], FilterLookup("compound__package__reviewed")] = None
 
 
+class ScenarioReviewStatusAndRelatedFilter(ReviewStatusFilter):
+    """Filter schema for review_status and parent query parameter."""
+
+    exclude_related: Annotated[Optional[bool], FilterLookup("parent__isnull")] = None
+
+
 # Base schema for all package-scoped entities
 class PackageEntityOutSchema(Schema):
     """Base schema for entities belonging to a package."""
@@ -51,6 +57,23 @@ class ScenarioOutSchema(PackageEntityOutSchema):
     pass
 
 
+class AdditionalInformationItemSchema(Schema):
+    """Schema for additional information item in scenario creation."""
+
+    type: str
+    data: Dict[str, Any]
+
+
+class ScenarioCreateSchema(Schema):
+    """Schema for creating a new scenario."""
+
+    name: str
+    description: str = ""
+    scenario_date: str = "No date"
+    scenario_type: str = "Not specified"
+    additional_information: List[AdditionalInformationItemSchema] = []
+
+
 class CompoundOutSchema(PackageEntityOutSchema):
     pass
 
@@ -102,3 +125,10 @@ class PackageOutSchema(Schema):
     @staticmethod
     def resolve_review_status(obj):
         return "reviewed" if obj.reviewed else "unreviewed"
+
+
+class SettingOutSchema(Schema):
+    uuid: UUID
+    url: str = ""
+    name: str
+    description: str

epdb/admin.py

@@ -28,7 +28,7 @@ Package = s.GET_PACKAGE_MODEL()
 
 
 class UserAdmin(admin.ModelAdmin):
-    list_display = ["username", "email", "is_active"]
+    list_display = ["username", "email", "is_active", "is_staff", "is_superuser"]
 
 
 class UserPackagePermissionAdmin(admin.ModelAdmin):
@@ -48,7 +48,7 @@ class JobLogAdmin(admin.ModelAdmin):
 
 
 class EPAdmin(admin.ModelAdmin):
-    search_fields = ["name", "description"]
+    search_fields = ["name", "description", "url", "uuid"]
     list_display = ["name", "url", "created"]
     ordering = ["-created"]
 

epdb/api.py

@@ -2,20 +2,12 @@ from typing import List
 
 from django.contrib.auth import get_user_model
 from ninja import Router, Schema, Field
-from ninja.errors import HttpError
 from ninja.pagination import paginate
-from ninja.security import HttpBearer
+
+from epapi.v1.auth import BearerTokenAuth
 
 from .logic import PackageManager
-from .models import User, Compound, APIToken
-
-
-class BearerTokenAuth(HttpBearer):
-    def authenticate(self, request, token):
-        for token_obj in APIToken.objects.select_related("user").all():
-            if token_obj.check_token(token) and token_obj.is_valid():
-                return token_obj.user
-        raise HttpError(401, "Invalid or expired token")
+from .models import User, Compound
 
 
 def _anonymous_or_real(request):

epdb/legacy_api.py

@@ -5,27 +5,33 @@ from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.http import HttpResponse
 from django.shortcuts import redirect
-from ninja import Field, Form, Router, Schema, Query
+from ninja import Field, Form, Query, Router, Schema
 from ninja.security import SessionAuth
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
 
-from .logic import GroupManager, PackageManager, SettingManager, UserManager, SearchManager
+from .logic import GroupManager, PackageManager, SearchManager, SettingManager, UserManager
 from .models import (
     Compound,
     CompoundStructure,
     Edge,
+    EnviFormer,
     EPModel,
+    Group,
+    GroupPackagePermission,
+    MLRelativeReasoning,
     Node,
+    PackageBasedModel,
+    ParallelRule,
     Pathway,
     Reaction,
     Rule,
+    RuleBasedRelativeReasoning,
     Scenario,
     SimpleAmbitRule,
     User,
     UserPackagePermission,
-    ParallelRule,
 )
 
 Package = s.GET_PACKAGE_MODEL()
@@ -200,6 +206,82 @@ def get_user(request, user_uuid):
         }
 
 
+########
+# Group #
+########
+
+
+class GroupMember(Schema):
+    id: str
+    identifier: str
+    name: str
+
+
+class GroupWrapper(Schema):
+    group: List[SimpleGroup]
+
+
+class GroupSchema(Schema):
+    description: str
+    id: str = Field(None, alias="url")
+    identifier: str = "group"
+    members: List[GroupMember] = Field([], alias="members")
+    name: str = Field(None, alias="name")
+    ownerid: str = Field(None, alias="owner.url")
+    ownername: str = Field(None, alias="owner.get_name")
+    packages: List["SimplePackage"] = Field([], alias="packages")
+    readers: List[GroupMember] = Field([], alias="readers")
+    writers: List[GroupMember] = Field([], alias="writers")
+
+    @staticmethod
+    def resolve_members(obj: Group):
+        res = []
+        for member in obj.user_member.all():
+            res.append(GroupMember(id=member.url, identifier="usermember", name=member.get_name()))
+
+        for member in obj.group_member.all():
+            res.append(GroupMember(id=member.url, identifier="groupmember", name=member.get_name()))
+
+        return res
+
+    @staticmethod
+    def resolve_packages(obj: Group):
+        return Package.objects.filter(
+            id__in=[
+                GroupPackagePermission.objects.filter(group=obj).values_list(
+                    "package_id", flat=True
+                )
+            ]
+        )
+
+    @staticmethod
+    def resolve_readers(obj: Group):
+        return GroupSchema.resolve_members(obj)
+
+    @staticmethod
+    def resolve_writers(obj: Group):
+        return [GroupMember(id=obj.owner.url, identifier="usermember", name=obj.owner.username)]
+
+
+@router.get("/group", response={200: GroupWrapper, 403: Error})
+def get_groups(request):
+    return {"group": GroupManager.get_groups(request.user)}
+
+
+@router.get("/group/{uuid:group_uuid}", response={200: GroupSchema, 403: Error})
+def get_group(request, group_uuid):
+    try:
+        g = GroupManager.get_group_by_id(request.user, group_uuid)
+        return g
+    except ValueError:
+        return 403, {
+            "message": f"Getting Group with id {group_uuid} failed due to insufficient rights!"
+        }
+
+
+##########
+# Search #
+##########
 class Search(Schema):
     packages: List[str] = Field(alias="packages[]")
     search: str
@@ -237,11 +319,11 @@ def search(request, search: Query[Search]):
         if "Compound Structures" in search_res:
             res["structure"] = search_res["Compound Structures"]
 
-        if "Reaction" in search_res:
-            res["reaction"] = search_res["Reaction"]
+        if "Reactions" in search_res:
+            res["reaction"] = search_res["Reactions"]
 
-        if "Pathway" in search_res:
-            res["pathway"] = search_res["Pathway"]
+        if "Pathways" in search_res:
+            res["pathway"] = search_res["Pathways"]
 
         if "Rules" in search_res:
             res["rule"] = search_res["Rules"]
@@ -292,7 +374,7 @@ class PackageSchema(Schema):
             ).values_list("user", flat=True)
         ).distinct()
 
-        return [{u.id: u.name} for u in users]
+        return [{u.id: u.get_name()} for u in users]
 
     @staticmethod
     def resolve_writers(obj: Package):
@@ -302,7 +384,7 @@ class PackageSchema(Schema):
             ).values_list("user", flat=True)
         ).distinct()
 
-        return [{u.id: u.name} for u in users]
+        return [{u.id: u.get_name()} for u in users]
 
     @staticmethod
     def resolve_review_comment(obj):
@@ -884,7 +966,12 @@ def create_package_simple_rule(
             raise ValueError("Not yet implemented!")
         else:
             sr = SimpleAmbitRule.create(
-                p, r.name, r.description, r.smirks, r.reactantFilterSmarts, r.productFilterSmarts
+                p,
+                r.name,
+                r.description,
+                r.smirks,
+                r.reactantFilterSmarts,
+                r.productFilterSmarts,
             )
 
         return redirect(sr.url)
@@ -1037,7 +1124,7 @@ class ReactionSchema(Schema):
     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")
+    references: 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")
@@ -1053,8 +1140,12 @@ class ReactionSchema(Schema):
 
     @staticmethod
     def resolve_references(obj: Reaction):
-        # TODO
-        return []
+        rhea_refs = []
+        for rhea in obj.get_rhea_identifiers():
+            rhea_refs.append(f"{rhea.identifier_value}")
+
+        # TODO UniProt
+        return {"rheaReferences": rhea_refs, "uniprotCount": []}
 
     @staticmethod
     def resolve_medline_references(obj: Reaction):
@@ -1447,6 +1538,7 @@ def create_pathway(
                 setting = SettingManager.get_setting_by_url(request.user, pw.selectedSetting)
 
             new_pw.setting = setting
+            new_pw.kv.update({"status": "running"})
             new_pw.save()
 
             from .tasks import dispatch, predict
@@ -1632,7 +1724,7 @@ class EdgeSchema(Schema):
     id: str = Field(None, alias="url")
     identifier: str = "edge"
     name: str = Field(None, alias="name")
-    reactionName: str = Field(None, alias="edge_label.name")
+    reactionName: str = Field(None, alias="edge_label.get_name")
     reactionURI: str = Field(None, alias="edge_label.url")
     reviewStatus: str = Field(None, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
@@ -1681,7 +1773,7 @@ class CreateEdge(Schema):
 
 
 @router.post(
-    "/package/{uuid:package_uuid}/üathway/{uuid:pathway_uuid}/edge",
+    "/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge",
     response={200: str | Any, 403: Error},
 )
 def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
@@ -1700,10 +1792,26 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
 
         if e.edgeAsSmirks:
             for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
-                educts.append(Node.objects.get(pathway=pw, default_node_label__smiles=ed))
+                stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
+                educts.append(
+                    Node.objects.get(
+                        pathway=pw,
+                        default_node_label=CompoundStructure.objects.get(
+                            compound__package=p, smiles=stand_ed
+                        ).compound.default_structure,
+                    )
+                )
 
             for pr in e.edgeAsSmirks.split(">>")[1].split("\\."):
-                products.append(Node.objects.get(pathway=pw, default_node_label__smiles=pr))
+                stand_pr = FormatConverter.standardize(pr, remove_stereo=True)
+                products.append(
+                    Node.objects.get(
+                        pathway=pw,
+                        default_node_label=CompoundStructure.objects.get(
+                            compound__package=p, smiles=stand_pr
+                        ).compound.default_structure,
+                    )
+                )
         else:
             for ed in e.educts.split(","):
                 educts.append(Node.objects.get(pathway=pw, url=ed.strip()))
@@ -1716,7 +1824,7 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             start_nodes=educts,
             end_nodes=products,
             rule=None,
-            name=e.name,
+            name=None,
             description=e.edgeReason,
         )
 
@@ -1753,26 +1861,46 @@ class ModelWrapper(Schema):
 class ModelSchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
     description: str = Field(None, alias="description")
-    evalPackages: List["SimplePackage"] = Field([])
+    evalPackages: List["SimplePackage"] = Field([], alias="eval_packages")
     id: str = Field(None, alias="url")
     identifier: str = "relative-reasoning"
-    #   "info" : {
-    #       "Accuracy (Single-Gen)" : "0.5932962678936605" ,
-    #       "Area under PR-Curve (Single-Gen)" : "0.5654653182134282" ,
-    #       "Area under ROC-Curve (Single-Gen)" : "0.8178302405034772" ,
-    #       "Precision (Single-Gen)" : "0.6978730822873083" ,
-    #       "Probability Threshold" : "0.5" ,
-    #       "Recall/Sensitivity (Single-Gen)" : "0.4484149210261006"
-    #     } ,
+    info: dict = Field({}, alias="info")
     name: str = Field(None, alias="name")
-    pathwayPackages: List["SimplePackage"] = Field([])
+    pathwayPackages: List["SimplePackage"] = Field([], alias="pathway_packages")
     reviewStatus: str = Field(None, alias="review_status")
-    rulePackages: List["SimplePackage"] = Field([])
+    rulePackages: List["SimplePackage"] = Field([], alias="rule_packages")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
-    status: str
-    statusMessage: str
-    threshold: str
-    type: str
+    status: str = Field(None, alias="model_status")
+    statusMessage: str = Field(None, alias="status_message")
+    threshold: str = Field(None, alias="threshold")
+    type: str = Field(None, alias="model_type")
+
+    @staticmethod
+    def resolve_info(obj: EPModel):
+        return {}
+
+    @staticmethod
+    def resolve_status_message(obj: EPModel):
+        for k, v in PackageBasedModel.PROGRESS_STATUS_CHOICES.items():
+            if k == obj.model_status:
+                return v
+
+        return None
+
+    @staticmethod
+    def resolve_threshold(obj: EPModel):
+        return f"{obj.threshold:.2f}"
+
+    @staticmethod
+    def resolve_model_type(obj: EPModel):
+        if isinstance(obj, RuleBasedRelativeReasoning):
+            return "RULEBASED"
+        elif isinstance(obj, MLRelativeReasoning):
+            return "ECC"
+        elif isinstance(obj, EnviFormer):
+            return "ENVIFORMER"
+        else:
+            return None
 
 
 @router.get("/model", response={200: ModelWrapper, 403: Error})
@@ -1833,7 +1961,7 @@ def get_model(request, package_uuid, model_uuid, c: Query[Classify]):
                     if pr.rule:
                         res["id"] = pr.rule.url
                         res["identifier"] = pr.rule.get_rule_identifier()
-                        res["name"] = pr.rule.name
+                        res["name"] = pr.rule.get_name()
                         res["reviewStatus"] = (
                             "reviewed" if pr.rule.package.reviewed else "unreviewed"
                         )

epdb/logic.py

@@ -194,8 +194,6 @@ class UserManager(object):
         if clean_username != username or clean_email != email:
             # This will be caught by the try in view.py/register
             raise ValueError("Invalid username or password")
-        # avoid circular import :S
-        from .tasks import send_registration_mail
 
         extra_fields = {"is_active": not s.ADMIN_APPROVAL_REQUIRED}
 
@@ -214,10 +212,6 @@ class UserManager(object):
         u.default_package = p
         u.save()
 
-        if not u.is_active:
-            # send email for verification
-            send_registration_mail.delay(u.pk)
-
         if set_setting:
             u.default_setting = Setting.objects.get(global_default=True)
             u.save()
@@ -685,7 +679,7 @@ class PackageManager(object):
                     ai_data = json.loads(res.model_dump_json())
                     ai_data["uuid"] = f"{uuid4()}"
                     new_add_inf[res_cls_name].append(ai_data)
-                except ValidationError:
+                except (ValidationError, ValueError):
                     logger.error(f"Failed to convert {name} with {addinf_data}")
 
             scen.additional_information = new_add_inf

epdb/management/commands/bootstrap.py

@@ -8,7 +8,6 @@ from epdb.logic import UserManager, GroupManager, PackageManager, SettingManager
 from epdb.models import (
     UserSettingPermission,
     MLRelativeReasoning,
-    EnviFormer,
     Permission,
     User,
     ExternalDatabase,
@@ -231,7 +230,6 @@ class Command(BaseCommand):
             package=pack,
             rule_packages=[mapping["EAWAG-BBD"]],
             data_packages=[mapping["EAWAG-BBD"]],
-            eval_packages=[],
             threshold=0.5,
             name="ECC - BBD - T0.5",
             description="ML Relative Reasoning",
@@ -239,7 +237,3 @@ class Command(BaseCommand):
 
         ml_model.build_dataset()
         ml_model.build_model()
-
-        # If available, create EnviFormerModel
-        if s.ENVIFORMER_PRESENT:
-            EnviFormer.create(pack, "EnviFormer - T0.5", "EnviFormer Model with Threshold 0.5", 0.5)

epdb/management/commands/create_api_token.py

@@ -0,0 +1,92 @@
+from django.conf import settings as s
+from django.contrib.auth import get_user_model
+from django.core.management.base import BaseCommand, CommandError
+
+from epdb.models import APIToken
+
+
+class Command(BaseCommand):
+    help = "Create an API token for a user"
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--username",
+            required=True,
+            help="Username of the user who will own the token",
+        )
+        parser.add_argument(
+            "--name",
+            required=True,
+            help="Descriptive name for the token",
+        )
+        parser.add_argument(
+            "--expires-days",
+            type=int,
+            default=90,
+            help="Days until expiration (0 for no expiration)",
+        )
+        parser.add_argument(
+            "--inactive",
+            action="store_true",
+            help="Create the token as inactive",
+        )
+        parser.add_argument(
+            "--curl",
+            action="store_true",
+            help="Print a curl example using the token",
+        )
+        parser.add_argument(
+            "--base-url",
+            default=None,
+            help="Base URL for curl example (default SERVER_URL or http://localhost:8000)",
+        )
+        parser.add_argument(
+            "--endpoint",
+            default="/api/v1/compounds/",
+            help="Endpoint path for curl example",
+        )
+
+    def handle(self, *args, **options):
+        username = options["username"]
+        name = options["name"]
+        expires_days = options["expires_days"]
+
+        if expires_days < 0:
+            raise CommandError("--expires-days must be >= 0")
+
+        if expires_days == 0:
+            expires_days = None
+
+        user_model = get_user_model()
+        try:
+            user = user_model.objects.get(username=username)
+        except user_model.DoesNotExist as exc:
+            raise CommandError(f"User not found for username '{username}'") from exc
+
+        token, raw_token = APIToken.create_token(user, name=name, expires_days=expires_days)
+
+        if options["inactive"]:
+            token.is_active = False
+            token.save(update_fields=["is_active"])
+
+        self.stdout.write(f"User: {user.username} ({user.email})")
+        self.stdout.write(f"Token name: {token.name}")
+        self.stdout.write(f"Token id: {token.id}")
+        if token.expires_at:
+            self.stdout.write(f"Expires at: {token.expires_at.isoformat()}")
+        else:
+            self.stdout.write("Expires at: never")
+        self.stdout.write(f"Active: {token.is_active}")
+        self.stdout.write("Raw token:")
+        self.stdout.write(raw_token)
+
+        if options["curl"]:
+            base_url = (
+                options["base_url"] or getattr(s, "SERVER_URL", None) or "http://localhost:8000"
+            )
+            endpoint = options["endpoint"]
+            endpoint = endpoint if endpoint.startswith("/") else f"/{endpoint}"
+            url = f"{base_url.rstrip('/')}{endpoint}"
+            curl_cmd = f'curl -H "Authorization: Bearer {raw_token}" "{url}"'
+            self.stdout.write("Curl:")
+            self.stdout.write(curl_cmd)

epdb/management/commands/dump_enviformer.py

@@ -47,7 +47,7 @@ class Command(BaseCommand):
             "description": model.description,
             "kv": model.kv,
             "data_packages_uuids": [str(p.uuid) for p in model.data_packages.all()],
-            "eval_packages_uuids": [str(p.uuid) for p in model.data_packages.all()],
+            "eval_packages_uuids": [str(p.uuid) for p in model.eval_packages.all()],
             "threshold": model.threshold,
             "eval_results": model.eval_results,
             "multigen_eval": model.multigen_eval,

epdb/migrations/0015_user_is_reviewer.py

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

epdb/models.py

@@ -72,10 +72,14 @@ class User(AbstractUser):
         null=True,
         blank=False,
     )
+    is_reviewer = models.BooleanField(default=False)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
 
+    def get_name(self):
+        return self.username
+
     def save(self, *args, **kwargs):
         if not self.url:
             self.url = self._url()
@@ -166,17 +170,18 @@ class APIToken(TimeStampedModel):
         return token, raw_key
 
     @classmethod
-    def authenticate(cls, raw_key: str) -> Optional[User]:
+    def authenticate(cls, token: str, *, hashed: bool = False) -> Optional[User]:
         """
         Authenticate a user using an API token.
 
         Args:
-            raw_key: Raw token key
+            token: Raw token key or SHA-256 hash (when hashed=True)
+            hashed: Whether the token is already hashed
 
         Returns:
             User if token is valid, None otherwise
         """
-        hashed_key = hashlib.sha256(raw_key.encode()).hexdigest()
+        hashed_key = token if hashed else hashlib.sha256(token.encode()).hexdigest()
 
         try:
             token = cls.objects.select_related("user").get(hashed_key=hashed_key)
@@ -207,7 +212,10 @@ class Group(TimeStampedModel):
     )
 
     def __str__(self):
-        return f"{self.name} (pk={self.pk})"
+        return f"{self.get_name()} (pk={self.pk})"
+
+    def get_name(self):
+        return self.name
 
     def save(self, *args, **kwargs):
         if not self.url:
@@ -595,7 +603,7 @@ class EnviPathModel(TimeStampedModel):
         res = {
             "url": self.url,
             "uuid": str(self.uuid),
-            "name": self.name,
+            "name": self.get_name(),
         }
 
         if include_description:
@@ -608,11 +616,14 @@ class EnviPathModel(TimeStampedModel):
             return self.kv.get(k, default)
         return default
 
+    def get_name(self):
+        return self.name
+
     class Meta:
         abstract = True
 
     def __str__(self):
-        return f"{self.name} (pk={self.pk})"
+        return f"{self.get_name()} (pk={self.pk})"
 
 
 class AliasMixin(models.Model):
@@ -623,7 +634,7 @@ class AliasMixin(models.Model):
     @transaction.atomic
     def add_alias(self, new_alias, set_as_default=False):
         if set_as_default:
-            self.aliases.append(self.name)
+            self.aliases.append(self.get_name())
             self.name = new_alias
 
             if new_alias in self.aliases:
@@ -764,15 +775,17 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
                 logger.debug(
                     f"#Structures: {num_structs} - #Standardized SMILES: {len(stand_smiles)}"
                 )
-                logger.debug(f"Couldn't infer normalized structure for {self.name} - {self.url}")
+                logger.debug(
+                    f"Couldn't infer normalized structure for {self.get_name()} - {self.url}"
+                )
                 raise ValueError(
-                    f"Couldn't find nor infer normalized structure for {self.name} ({self.url})"
+                    f"Couldn't find nor infer normalized structure for {self.get_name()} ({self.url})"
                 )
             else:
                 cs = CompoundStructure.create(
                     self,
                     stand_smiles.pop(),
-                    name="Normalized structure of {}".format(self.name),
+                    name="Normalized structure of {}".format(self.get_name()),
                     description="{} (in its normalized form)".format(self.description),
                     normalized_structure=True,
                 )
@@ -847,8 +860,10 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
         if name is not None:
             # Clean for potential XSS
             name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
+
         c.name = name
 
         # We have a default here only set the value if it carries some payload
@@ -977,7 +992,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
                     cs = CompoundStructure.create(
                         existing_normalized_compound,
                         structure.smiles,
-                        name=structure.name,
+                        name=structure.get_name(),
                         description=structure.description,
                         normalized_structure=structure.normalized_structure,
                     )
@@ -988,13 +1003,13 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
 
             else:
                 raise ValueError(
-                    f"Found a CompoundStructure for {default_structure_smiles} but not for {normalized_structure_smiles} in target package {target.name}"
+                    f"Found a CompoundStructure for {default_structure_smiles} but not for {normalized_structure_smiles} in target package {target.get_name()}"
                 )
         else:
             # Here we can safely use Compound.objects.create as we won't end up in a duplicate
             new_compound = Compound.objects.create(
                 package=target,
-                name=self.name,
+                name=self.get_name(),
                 description=self.description,
                 kv=self.kv.copy() if self.kv else {},
             )
@@ -1010,7 +1025,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
                         canonical_smiles=structure.canonical_smiles,
                         inchikey=structure.inchikey,
                         normalized_structure=structure.normalized_structure,
-                        name=structure.name,
+                        name=structure.get_name(),
                         description=structure.description,
                         kv=structure.kv.copy() if structure.kv else {},
                     )
@@ -1049,11 +1064,8 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
     def half_lifes(self):
         hls: Dict[Scenario, List[HalfLife]] = defaultdict(list)
 
-        for n in self.related_nodes:
-            for scen in n.scenarios.all().order_by("name"):
-                for ai in scen.get_additional_information():
-                    if isinstance(ai, HalfLife):
-                        hls[scen].append(ai)
+        for cs in self.structures:
+            hls.update(cs.half_lifes())
 
         return dict(hls)
 
@@ -1103,6 +1115,7 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
         # Clean for potential XSS
         if name is not None:
             cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
@@ -1146,6 +1159,21 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
     def is_default_structure(self):
         return self.compound.default_structure == self
 
+    @property
+    def related_nodes(self):
+        return Node.objects.filter(node_labels__in=[self], pathway__package=self.compound.package)
+
+    def half_lifes(self):
+        hls: Dict[Scenario, List[HalfLife]] = defaultdict(list)
+
+        for n in self.related_nodes:
+            for scen in n.scenarios.all().order_by("name"):
+                for ai in scen.get_additional_information():
+                    if isinstance(ai, HalfLife):
+                        hls[scen].append(ai)
+
+        return dict(hls)
+
 
 class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
     rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
@@ -1217,7 +1245,7 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
         if rule_type == SimpleAmbitRule:
             new_rule = SimpleAmbitRule.create(
                 package=target,
-                name=self.name,
+                name=self.get_name(),
                 description=self.description,
                 smirks=self.smirks,
                 reactant_filter_smarts=self.reactant_filter_smarts,
@@ -1231,7 +1259,7 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
         elif rule_type == SimpleRDKitRule:
             new_rule = SimpleRDKitRule.create(
                 package=target,
-                name=self.name,
+                name=self.get_name(),
                 description=self.description,
                 reaction_smarts=self.reaction_smarts,
             )
@@ -1249,7 +1277,7 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
             new_rule = ParallelRule.create(
                 package=target,
                 simple_rules=new_srs,
-                name=self.name,
+                name=self.get_name(),
                 description=self.description,
             )
 
@@ -1353,12 +1381,13 @@ class SimpleAmbitRule(SimpleRule):
     def get_rule_identifier(self) -> str:
         return "simple-rule"
 
-    def apply(self, smiles):
+    def apply(self, smiles, *args, **kwargs):
         return FormatConverter.apply(
             smiles,
             self.smirks,
             reactant_filter_smarts=self.reactant_filter_smarts,
             product_filter_smarts=self.product_filter_smarts,
+            **kwargs,
         )
 
     @property
@@ -1388,8 +1417,8 @@ class SimpleAmbitRule(SimpleRule):
 class SimpleRDKitRule(SimpleRule):
     reaction_smarts = models.TextField(blank=False, null=False, verbose_name="SMIRKS")
 
-    def apply(self, smiles):
-        return FormatConverter.apply(smiles, self.reaction_smarts)
+    def apply(self, smiles, *args, **kwargs):
+        return FormatConverter.apply(smiles, self.reaction_smarts, **kwargs)
 
     def _url(self):
         return "{}/simple-rdkit-rule/{}".format(self.package.url, self.uuid)
@@ -1410,10 +1439,10 @@ class ParallelRule(Rule):
     def srs(self) -> QuerySet:
         return self.simple_rules.all()
 
-    def apply(self, structure):
+    def apply(self, structure, *args, **kwargs):
         res = list()
         for simple_rule in self.srs:
-            res.extend(simple_rule.apply(structure))
+            res.extend(simple_rule.apply(structure, **kwargs))
 
         return list(set(res))
 
@@ -1518,11 +1547,11 @@ class SequentialRule(Rule):
     def srs(self):
         return self.simple_rules.all()
 
-    def apply(self, structure):
+    def apply(self, structure, *args, **kwargs):
         # TODO determine levels or see java implementation
         res = set()
         for simple_rule in self.srs:
-            res.union(set(simple_rule.apply(structure)))
+            res.union(set(simple_rule.apply(structure, **kwargs)))
         return res
 
 
@@ -1622,9 +1651,11 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
         r = Reaction()
         r.package = package
+
         # Clean for potential XSS
         if name is not None and name.strip() != "":
             r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if description is not None and name.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
@@ -1672,7 +1703,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
         new_reaction = Reaction.create(
             package=target,
-            name=self.name,
+            name=self.get_name(),
             description=self.description,
             educts=copied_reaction_educts,
             products=copied_reaction_products,
@@ -1827,8 +1858,10 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
                         queue.append(prod)
 
         # We shouldn't lose or make up nodes...
-        assert len(nodes) == len(self.nodes)
-        logger.debug(f"{self.name}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}")
+        if len(nodes) != len(self.nodes):
+            logger.debug(
+                f"{self.get_name()}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}"
+            )
 
         links = [e.d3_json() for e in self.edges]
 
@@ -1879,6 +1912,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
                         "source": pseudo_idx,
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
+                        "multi_step": link["multi_step"],
                     }
                     adjusted_links.append(new_link)
 
@@ -1895,7 +1929,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
             "isIncremental": self.kv.get("mode") == "incremental",
             "isPredicted": self.kv.get("mode") == "predicted",
             "lastModified": self.modified.strftime("%Y-%m-%d %H:%M:%S"),
-            "pathwayName": self.name,
+            "pathwayName": self.get_name(),
             "reviewStatus": "reviewed" if self.package.reviewed else "unreviewed",
             "scenarios": [],
             "upToDate": True,
@@ -1938,14 +1972,14 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
             if include_pathway_url:
                 row.append(n.pathway.url)
 
-            row += [cs.smiles, cs.name, n.depth]
+            row += [cs.smiles, cs.get_name(), n.depth]
 
             edges = self.edges.filter(end_nodes__in=[n])
             if len(edges):
                 for e in edges:
                     _row = row.copy()
                     _row.append(e.kv.get("probability"))
-                    _row.append(",".join([r.name for r in e.edge_label.rules.all()]))
+                    _row.append(",".join([r.get_name() for r in e.edge_label.rules.all()]))
                     _row.append(",".join([r.url for r in e.edge_label.rules.all()]))
                     _row.append(e.start_nodes.all()[0].default_node_label.smiles)
                     rows.append(_row)
@@ -1976,12 +2010,14 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
         if name is not None:
             # Clean for potential XSS
             name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Pathway {Pathway.objects.filter(package=package).count() + 1}"
 
         pw.name = name
         if description is not None and description.strip() != "":
             pw.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+
         pw.predicted = predicted
 
         pw.save()
@@ -2006,7 +2042,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
         # deduplicated
         new_pathway = Pathway.objects.create(
             package=target,
-            name=self.name,
+            name=self.get_name(),
             description=self.description,
             setting=self.setting,  # TODO copy settings?
             kv=self.kv.copy() if self.kv else {},
@@ -2036,7 +2072,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
                 pathway=new_pathway,
                 default_node_label=copied_structure,
                 depth=node.depth,
-                name=node.name,
+                name=node.get_name(),
                 description=node.description,
                 kv=node.kv.copy() if node.kv else {},
             )
@@ -2060,7 +2096,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
             new_edge = Edge.objects.create(
                 pathway=new_pathway,
                 edge_label=copied_reaction,
-                name=edge.name,
+                name=edge.get_name(),
                 description=edge.description,
                 kv=edge.kv.copy() if edge.kv else {},
             )
@@ -2120,6 +2156,18 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
     def _url(self):
         return "{}/node/{}".format(self.pathway.url, self.uuid)
 
+    def get_name(self):
+        non_generic_name = True
+
+        if self.name == "no name":
+            non_generic_name = False
+
+        return (
+            self.name
+            if non_generic_name
+            else f"{self.default_node_label.name} (taken from underlying structure)"
+        )
+
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
 
@@ -2132,9 +2180,9 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
             "image_svg": IndigoUtils.mol_to_svg(
                 self.default_node_label.smiles, width=40, height=40
             ),
-            "name": self.default_node_label.name,
+            "name": self.get_name(),
             "smiles": self.default_node_label.smiles,
-            "scenarios": [{"name": s.name, "url": s.url} for s in self.scenarios.all()],
+            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
                 "inside_app_domain": app_domain_data["assessment"]["inside_app_domain"]
                 if app_domain_data
@@ -2142,9 +2190,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
                 "uncovered_functional_groups": False,
             },
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
+            "timeseries": self.get_timeseries_data(),
         }
 
     @staticmethod
+    @transaction.atomic
     def create(
         pathway: "Pathway",
         smiles: str,
@@ -2178,14 +2228,24 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
     def as_svg(self):
         return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
 
+    def get_timeseries_data(self):
+        for scenario in self.scenarios.all():
+            for ai in scenario.get_additional_information():
+                if ai.__class__.__name__ == "OECD301FTimeSeries":
+                    return ai.model_dump(mode="json")
+        return None
+
     def get_app_domain_assessment_data(self):
         data = self.kv.get("app_domain_assessment", None)
 
         if data:
             rule_ids = defaultdict(list)
             for e in Edge.objects.filter(start_nodes__in=[self]):
-                for r in e.edge_label.rules.all():
-                    rule_ids[str(r.uuid)].append(e.simple_json())
+                # TODO While the Pathway is being predicted we sometimes
+                # TODO receive 'NoneType' object has no attribute 'rules'
+                if e.edge_label:
+                    for r in e.edge_label.rules.all():
+                        rule_ids[str(r.uuid)].append(e.simple_json())
 
             for t in data["assessment"]["transformations"]:
                 if t["rule"]["uuid"] in rule_ids:
@@ -2198,7 +2258,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
         res = super().simple_json()
         name = res.get("name", None)
         if name == "no name":
-            res["name"] = self.default_node_label.name
+            res["name"] = self.default_node_label.get_name()
 
         return res
 
@@ -2222,17 +2282,24 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
 
     def d3_json(self):
         edge_json = {
-            "name": self.name,
+            "name": self.get_name(),
             "id": self.url,
             "url": self.url,
             "image": self.url + "?image=svg",
-            "reaction": {"name": self.edge_label.name, "url": self.edge_label.url}
+            "reaction": {
+                "name": self.edge_label.get_name(),
+                "url": self.edge_label.url,
+                "rules": [
+                    {"name": r.get_name(), "url": r.url} for r in self.edge_label.rules.all()
+                ],
+            }
             if self.edge_label
             else None,
+            "multi_step": self.edge_label.multi_step if self.edge_label else False,
             "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.name, "url": s.url} for s in self.scenarios.all()],
+            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
         }
 
         for n in self.start_nodes.all():
@@ -2269,6 +2336,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
         return edge_json
 
     @staticmethod
+    @transaction.atomic
     def create(
         pathway,
         start_nodes: List[Node],
@@ -2320,10 +2388,22 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
         res = super().simple_json()
         name = res.get("name", None)
         if name == "no name":
-            res["name"] = self.edge_label.name
+            res["name"] = self.edge_label.get_name()
 
         return res
 
+    def get_name(self):
+        non_generic_name = True
+
+        if self.name == "no name":
+            non_generic_name = False
+
+        return (
+            self.name
+            if non_generic_name
+            else f"{self.edge_label.name} (taken from underlying reaction)"
+        )
+
 
 class EPModel(PolymorphicModel, EnviPathModel):
     package = models.ForeignKey(
@@ -2604,7 +2684,7 @@ class PackageBasedModel(EPModel):
                     root_compounds.append(pw.root_nodes[0].default_node_label)
                 else:
                     logger.info(
-                        f"Skipping MG Eval of Pathway {pw.name} ({pw.uuid}) as it has no root compounds!"
+                        f"Skipping MG Eval of Pathway {pw.get_name()} ({pw.uuid}) as it has no root compounds!"
                     )
 
             # As we need a Model Instance in our setting, get a fresh copy from db, overwrite the serialized mode and
@@ -2730,7 +2810,7 @@ class PackageBasedModel(EPModel):
                         pathways.append(pathway)
                     else:
                         logging.warning(
-                            f"No root compound in pathway {pathway.name}, excluding from multigen evaluation"
+                            f"No root compound in pathway {pathway.get_name()}, excluding from multigen evaluation"
                         )
 
                 # build lookup reaction -> {uuid1, uuid2} for overlap check
@@ -3062,7 +3142,7 @@ class ApplicabilityDomain(EnviPathModel):
         ad = ApplicabilityDomain()
         ad.model = mlrr
         # ad.uuid = mlrr.uuid
-        ad.name = f"AD for {mlrr.name}"
+        ad.name = f"AD for {mlrr.get_name()}"
         ad.num_neighbours = num_neighbours
         ad.reliability_threshold = reliability_threshold
         ad.local_compatibilty_threshold = local_compatibility_threshold
@@ -3346,7 +3426,7 @@ class EnviFormer(PackageBasedModel):
             )
             for smiles in smiles_list
         ]
-        logger.info(f"Submitting {canon_smiles} to {self.name}")
+        logger.info(f"Submitting {canon_smiles} to {self.get_name()}")
         start = datetime.now()
         products_list = self.model.predict_batch(canon_smiles)
         end = datetime.now()
@@ -3503,7 +3583,7 @@ class EnviFormer(PackageBasedModel):
                 root_node = p.root_nodes
                 if len(root_node) > 1:
                     logging.warning(
-                        f"Pathway {p.name} has more than one root compound, only {root_node[0]} will be used"
+                        f"Pathway {p.get_name()} has more than one root compound, only {root_node[0]} will be used"
                     )
                 root_node = ".".join(
                     [
@@ -3623,7 +3703,7 @@ class EnviFormer(PackageBasedModel):
                         pathways.append(pathway)
                     else:
                         logging.warning(
-                            f"No root compound in pathway {pathway.name}, excluding from multigen evaluation"
+                            f"No root compound in pathway {pathway.get_name()}, excluding from multigen evaluation"
                         )
 
                 # build lookup reaction -> {uuid1, uuid2} for overlap check
@@ -3751,11 +3831,21 @@ class Scenario(EnviPathModel):
         return new_s
 
     @transaction.atomic
-    def add_additional_information(self, data: "EnviPyModel"):
+    def add_additional_information(self, data: "EnviPyModel") -> str:
+        """
+        Add additional information to this scenario.
+
+        Args:
+            data: EnviPyModel instance to add
+
+        Returns:
+            str: UUID of the created item
+        """
         cls_name = data.__class__.__name__
         # Clean for potential XSS hidden in the additional information fields.
         ai_data = json.loads(nh3.clean(data.model_dump_json()).strip())
-        ai_data["uuid"] = f"{uuid4()}"
+        generated_uuid = str(uuid4())
+        ai_data["uuid"] = generated_uuid
 
         if cls_name not in self.additional_information:
             self.additional_information[cls_name] = []
@@ -3763,6 +3853,51 @@ class Scenario(EnviPathModel):
         self.additional_information[cls_name].append(ai_data)
         self.save()
 
+        return generated_uuid
+
+    @transaction.atomic
+    def update_additional_information(self, ai_uuid: str, data: "EnviPyModel") -> None:
+        """
+        Update existing additional information by UUID.
+
+        Args:
+            ai_uuid: UUID of the item to update
+            data: EnviPyModel instance with new data
+
+        Raises:
+            ValueError: If item with given UUID not found or type mismatch
+        """
+        found_type = None
+        found_idx = -1
+
+        # Find the item by UUID
+        for type_name, items in self.additional_information.items():
+            for idx, item_data in enumerate(items):
+                if item_data.get("uuid") == ai_uuid:
+                    found_type = type_name
+                    found_idx = idx
+                    break
+            if found_type:
+                break
+
+        if found_type is None:
+            raise ValueError(f"Additional information with UUID {ai_uuid} not found")
+
+        # Verify the model type matches (prevent type changes)
+        new_type = data.__class__.__name__
+        if new_type != found_type:
+            raise ValueError(
+                f"Cannot change type from {found_type} to {new_type}. "
+                f"Delete and create a new item instead."
+            )
+
+        # Update the item data, preserving UUID
+        ai_data = json.loads(nh3.clean(data.model_dump_json()).strip())
+        ai_data["uuid"] = ai_uuid
+
+        self.additional_information[found_type][found_idx] = ai_data
+        self.save()
+
     @transaction.atomic
     def remove_additional_information(self, ai_uuid):
         found_type = None
@@ -3777,9 +3912,9 @@ class Scenario(EnviPathModel):
 
         if found_type is not None and found_idx >= 0:
             if len(self.additional_information[found_type]) == 1:
-                del self.additional_information[k]
+                del self.additional_information[found_type]
             else:
-                self.additional_information[k].pop(found_idx)
+                self.additional_information[found_type].pop(found_idx)
             self.save()
         else:
             raise ValueError(f"Could not find additional information with uuid {ai_uuid}")
@@ -3802,7 +3937,7 @@ class Scenario(EnviPathModel):
         self.save()
 
     def get_additional_information(self):
-        from envipy_additional_information import NAME_MAPPING
+        from envipy_additional_information import registry
 
         for k, vals in self.additional_information.items():
             if k == "enzyme":
@@ -3810,14 +3945,31 @@ class Scenario(EnviPathModel):
 
             for v in vals:
                 # Per default additional fields are ignored
-                MAPPING = {c.__name__: c for c in NAME_MAPPING.values()}
-                inst = MAPPING[k](**v)
+                MAPPING = {c.__name__: c for c in registry.list_models().values()}
+                try:
+                    inst = MAPPING[k](**v)
+                except Exception as e:
+                    logger.error(f"Could not load additional information {k}: {e}")
+                    if s.SENTRY_ENABLED:
+                        from sentry_sdk import capture_exception
+
+                        capture_exception(e)
+
                 # Add uuid to uniquely identify objects for manipulation
                 if "uuid" in v:
                     inst.__dict__["uuid"] = v["uuid"]
 
                 yield inst
 
+    def related_pathways(self):
+        scens = [self]
+        if self.parent is not None:
+            scens.append(self.parent)
+
+        return Pathway.objects.filter(
+            scenarios__in=scens, package__reviewed=True, package=self.package
+        ).distinct()
+
 
 class UserSettingPermission(Permission):
     uuid = models.UUIDField(
@@ -4024,6 +4176,6 @@ class JobLog(TimeStampedModel):
         return self.task_result
 
     def is_result_downloadable(self):
-        downloadable = ["batch_predict"]
+        downloadable = ["batch_predict", "identify_missing_rules"]
 
         return self.job_name in downloadable

epdb/tasks.py

@@ -7,6 +7,7 @@ from uuid import uuid4
 from celery import shared_task
 from celery.utils.functional import LRUCache
 from django.conf import settings as s
+from django.core.mail import EmailMultiAlternatives
 from django.utils import timezone
 
 from epdb.logic import SPathway
@@ -73,7 +74,31 @@ def predict_simple(model_pk: int, smiles: str):
 
 @shared_task(queue="background")
 def send_registration_mail(user_pk: int):
-    pass
+    u = User.objects.get(id=user_pk)
+
+    tpl = """Welcome {username}!,
+
+Thank you for your interest in enviPath.
+
+The public system is intended for non-commercial use only.
+We will review your account details and usually activate your account within 24 hours.
+Once activated, you will be notified by email.
+
+If we have any questions, we will contact you at this email address.
+
+Best regards,
+
+enviPath team"""
+
+    msg = EmailMultiAlternatives(
+        "Your enviPath account",
+        tpl.format(username=u.username),
+        "admin@envipath.org",
+        [u.email],
+        bcc=["admin@envipath.org"],
+    )
+
+    msg.send(fail_silently=False)
 
 
 @shared_task(bind=True, queue="model")

epdb/urls.py

@@ -209,5 +209,4 @@ urlpatterns = [
     re_path(r"^contact$", v.static_contact_support, name="contact_support"),
     re_path(r"^careers$", v.static_careers, name="careers"),
     re_path(r"^cite$", v.static_cite, name="cite"),
-    re_path(r"^legal$", v.static_legal, name="legal"),
 ]

epdb/views.py

@@ -1,22 +1,21 @@
 import json
 import logging
-from typing import Any, Dict, List
 from datetime import datetime
+from typing import Any, Dict, List
 
 import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.core.exceptions import BadRequest, PermissionDenied
 from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed, JsonResponse
-from django.shortcuts import redirect, render
+from django.shortcuts import get_object_or_404, redirect, render
 from django.urls import reverse
 from django.views.decorators.csrf import csrf_exempt
-from envipy_additional_information import NAME_MAPPING
 from oauth2_provider.decorators import protected_resource
+from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
-from utilities.misc import HTMLGenerator
 
 from .logic import (
     EPDBURLParser,
@@ -34,6 +33,7 @@ from .models import (
     EnviFormer,
     EnzymeLink,
     EPModel,
+    ExpansionSchemeChoice,
     ExternalDatabase,
     ExternalIdentifier,
     Group,
@@ -51,7 +51,6 @@ from .models import (
     SimpleAmbitRule,
     User,
     UserPackagePermission,
-    ExpansionSchemeChoice,
 )
 
 logger = logging.getLogger(__name__)
@@ -238,6 +237,15 @@ def register(request):
         try:
             u = UserManager.create_user(username, email, password)
             logger.info(f"Created user {u.username} ({u.pk})")
+
+            try:
+                from .tasks import send_registration_mail
+
+                send_registration_mail.delay(u.pk)
+            except Exception as e:
+                logger.error(f"Failed to send registration mail to {u.email}: {e}")
+                capture_exception(e)
+
         except Exception:
             context["message"] = "Registration failed! Couldn't create User Account."
             return render(request, "static/login.html", context)
@@ -339,7 +347,7 @@ def breadcrumbs(
         {"Package": s.SERVER_URL + "/package"},
     ]
     if first_level_object is not None:
-        bread.append({first_level_object.name: first_level_object.url})
+        bread.append({first_level_object.get_name(): first_level_object.url})
 
     if second_level_namespace is not None:
         bread.append(
@@ -350,7 +358,7 @@ def breadcrumbs(
         )
 
     if second_level_object is not None:
-        bread.append({second_level_object.name: second_level_object.url})
+        bread.append({second_level_object.get_name(): second_level_object.url})
 
     if third_level_namespace is not None:
         bread.append(
@@ -361,7 +369,7 @@ def breadcrumbs(
         )
 
     if third_level_object is not None:
-        bread.append({third_level_object.name: third_level_object.url})
+        bread.append({third_level_object.get_name(): third_level_object.url})
 
     return bread
 
@@ -462,7 +470,7 @@ def package_predict_pathway(request, package_uuid):
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
 
     context = get_base_context(request)
-    context["title"] = f"enviPath - {current_package.name} - Predict Pathway"
+    context["title"] = f"enviPath - {current_package.get_name()} - Predict Pathway"
     context["meta"]["current_package"] = current_package
 
     return render(request, "predict_pathway.html", context)
@@ -475,6 +483,10 @@ def packages(request):
         context = get_base_context(request)
         context["title"] = "enviPath - Packages"
         context["meta"]["current_package"] = context["meta"]["user"].default_package
+        context["breadcrumbs"] = [
+            {"Home": s.SERVER_URL},
+            {"Package": s.SERVER_URL + "/package"},
+        ]
 
         # Context for paginated template
         context["entity_type"] = "package"
@@ -529,6 +541,10 @@ def compounds(request):
         context = get_base_context(request)
         context["title"] = "enviPath - Compounds"
         context["meta"]["current_package"] = context["meta"]["user"].default_package
+        context["breadcrumbs"] = [
+            {"Home": s.SERVER_URL},
+            {"Compound": s.SERVER_URL + "/compound"},
+        ]
 
         # Context for paginated template
         context["entity_type"] = "compound"
@@ -759,7 +775,7 @@ def package_models(request, package_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Models"
+        context["title"] = f"enviPath - {current_package.get_name()} - Models"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "model"
@@ -781,7 +797,7 @@ def package_models(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_model_qs if current_package.reviewed else unreviewed_model_qs
                         )
@@ -880,7 +896,7 @@ def package_models(request, package_uuid):
 def package_model(request, package_uuid, model_uuid):
     current_user = _anonymous_or_real(request)
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_model = EPModel.objects.get(package=current_package, uuid=model_uuid)
+    current_model = get_object_or_404(EPModel, package=current_package, uuid=model_uuid)
 
     if request.method == "GET":
         classify = request.GET.get("classify", False)
@@ -931,7 +947,7 @@ def package_model(request, package_uuid, model_uuid):
                 return JsonResponse(app_domain_assessment, safe=False)
 
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_model.name}"
+        context["title"] = f"enviPath - {current_package.get_name()} - {current_model.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "model"
@@ -1009,7 +1025,7 @@ def package(request, package_uuid):
 
     if request.method == "GET":
         if request.GET.get("export", False) == "true":
-            filename = f"{current_package.name.replace(' ', '_')}_{current_package.uuid}.json"
+            filename = f"{current_package.get_name().replace(' ', '_')}_{current_package.uuid}.json"
             pack_json = PackageManager.export_package(
                 current_package, include_models=False, include_external_identifiers=False
             )
@@ -1019,7 +1035,7 @@ def package(request, package_uuid):
             return response
 
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name}"
+        context["title"] = f"enviPath - {current_package.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "package"
@@ -1033,6 +1049,7 @@ def package(request, package_uuid):
                 "user_id", flat=True
             )
         )
+        users = users.filter(is_active=True)
 
         group_perms = GroupPackagePermission.objects.filter(package=current_package)
         groups = Group.objects.exclude(
@@ -1056,7 +1073,7 @@ def package(request, package_uuid):
                 if current_user.default_package == current_package:
                     return error(
                         request,
-                        f'Package "{current_package.name}" is the default and cannot be deleted!',
+                        f'Package "{current_package.get_name()}" is the default and cannot be deleted!',
                         "You cannot delete the default package. If you want to delete this package you have to set another default package first.",
                     )
 
@@ -1154,7 +1171,7 @@ def package_compounds(request, package_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Compounds"
+        context["title"] = f"enviPath - {current_package.get_name()} - Compounds"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "compound"
@@ -1179,7 +1196,7 @@ def package_compounds(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_compound_qs
                             if current_package.reviewed
@@ -1212,11 +1229,13 @@ def package_compounds(request, package_uuid):
 def package_compound(request, package_uuid, compound_uuid):
     current_user = _anonymous_or_real(request)
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_compound = Compound.objects.get(package=current_package, uuid=compound_uuid)
+    current_compound = get_object_or_404(Compound, package=current_package, uuid=compound_uuid)
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_compound.name}"
+        context["title"] = (
+            f"enviPath - {current_package.get_name()} - {current_compound.get_name()}"
+        )
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "compound"
@@ -1300,7 +1319,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
     if request.method == "GET":
         context = get_base_context(request)
         context["title"] = (
-            f"enviPath - {current_package.name} - {current_compound.name} - Structures"
+            f"enviPath - {current_package.get_name()} - {current_compound.get_name()} - Structures"
         )
 
         context["meta"]["current_package"] = current_package
@@ -1309,7 +1328,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
             current_package, "compound", current_compound, "structure"
         )
         context["entity_type"] = "structure"
-        context["page_title"] = f"{current_compound.name} - Structures"
+        context["page_title"] = f"{current_compound.get_name()} - Structures"
         context["api_endpoint"] = (
             f"/api/v1/package/{current_package.uuid}/compound/{current_compound.uuid}/structure/"
         )
@@ -1346,15 +1365,23 @@ def package_compound_structures(request, package_uuid, compound_uuid):
 def package_compound_structure(request, package_uuid, compound_uuid, structure_uuid):
     current_user = _anonymous_or_real(request)
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_compound = Compound.objects.get(package=current_package, uuid=compound_uuid)
-    current_structure = CompoundStructure.objects.get(
-        compound=current_compound, uuid=structure_uuid
+    current_compound = get_object_or_404(Compound, package=current_package, uuid=compound_uuid)
+    current_structure = get_object_or_404(
+        CompoundStructure, compound=current_compound, uuid=structure_uuid
     )
 
     if request.method == "GET":
+        is_image_request = request.GET.get("image")
+
+        if is_image_request:
+            if is_image_request == "svg":
+                return HttpResponse(current_structure.as_svg, content_type="image/svg+xml")
+            else:
+                return HttpResponseBadRequest("Currently only SVG as image formate supported!")
+
         context = get_base_context(request)
         context["title"] = (
-            f"enviPath - {current_package.name} - {current_compound.name} - {current_structure.name}"
+            f"enviPath - {current_package.get_name()} - {current_compound.get_name()} - {current_structure.get_name()}"
         )
 
         context["meta"]["current_package"] = current_package
@@ -1460,7 +1487,7 @@ def package_rules(request, package_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Rules"
+        context["title"] = f"enviPath - {current_package.get_name()} - Rules"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "rule"
@@ -1482,7 +1509,7 @@ def package_rules(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_rule_qs if current_package.reviewed else unreviewed_rule_qs
                         )
@@ -1534,7 +1561,7 @@ def package_rules(request, package_uuid):
 def package_rule(request, package_uuid, rule_uuid):
     current_user = _anonymous_or_real(request)
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_rule = Rule.objects.get(package=current_package, uuid=rule_uuid)
+    current_rule = get_object_or_404(Rule, package=current_package, uuid=rule_uuid)
 
     if request.method == "GET":
         context = get_base_context(request)
@@ -1572,7 +1599,7 @@ def package_rule(request, package_uuid, rule_uuid):
                 content_type="image/svg+xml",
             )
 
-        context["title"] = f"enviPath - {current_package.name} - {current_rule.name}"
+        context["title"] = f"enviPath - {current_package.get_name()} - {current_rule.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "rule"
@@ -1645,7 +1672,7 @@ def package_rule_enzymelink(request, package_uuid, rule_uuid, enzymelink_uuid):
     if request.method == "GET":
         context = get_base_context(request)
 
-        context["title"] = f"enviPath - {current_package.name} - {current_rule.name}"
+        context["title"] = f"enviPath - {current_package.get_name()} - {current_rule.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "enzyme"
@@ -1668,7 +1695,7 @@ def package_reactions(request, package_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Reactions"
+        context["title"] = f"enviPath - {current_package.get_name()} - Reactions"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "reaction"
@@ -1692,7 +1719,7 @@ def package_reactions(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_reaction_qs
                             if current_package.reviewed
@@ -1729,11 +1756,13 @@ def package_reactions(request, package_uuid):
 def package_reaction(request, package_uuid, reaction_uuid):
     current_user = _anonymous_or_real(request)
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_reaction = Reaction.objects.get(package=current_package, uuid=reaction_uuid)
+    current_reaction = get_object_or_404(Reaction, package=current_package, uuid=reaction_uuid)
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_reaction.name}"
+        context["title"] = (
+            f"enviPath - {current_package.get_name()} - {current_reaction.get_name()}"
+        )
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "reaction"
@@ -1816,7 +1845,7 @@ def package_pathways(request, package_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Pathways"
+        context["title"] = f"enviPath - {current_package.get_name()} - Pathways"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "pathway"
@@ -1838,7 +1867,7 @@ def package_pathways(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_pathway_qs
                             if current_package.reviewed
@@ -1908,6 +1937,7 @@ def package_pathways(request, package_uuid):
                 limit = 1
 
             pw.setting = prediction_setting
+            pw.kv.update({"status": "running"})
             pw.save()
 
             from .tasks import dispatch, predict
@@ -1924,7 +1954,9 @@ def package_pathways(request, package_uuid):
 def package_pathway(request, package_uuid, pathway_uuid):
     current_user: User = _anonymous_or_real(request)
     current_package: Package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_pathway: Pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
+    current_pathway: Pathway = get_object_or_404(
+        Pathway, package=current_package, uuid=pathway_uuid
+    )
 
     if request.method == "GET":
         if request.GET.get("last_modified", False):
@@ -1942,7 +1974,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
             )
 
         if request.GET.get("download", False) == "true":
-            filename = f"{current_pathway.name.replace(' ', '_')}_{current_pathway.uuid}.csv"
+            filename = f"{current_pathway.get_name().replace(' ', '_')}_{current_pathway.uuid}.csv"
             csv_pw = current_pathway.to_csv()
             response = HttpResponse(csv_pw, content_type="text/csv")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
@@ -1962,7 +1994,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
                 current_user, identify_missing_rules, [current_pathway.pk], rule_package.pk
             )
 
-            filename = f"{current_pathway.name.replace(' ', '_')}_{current_pathway.uuid}.csv"
+            filename = f"{current_pathway.get_name().replace(' ', '_')}_{current_pathway.uuid}.csv"
             response = HttpResponse(res, content_type="text/csv")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
 
@@ -1985,7 +2017,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
         ).get(uuid=pathway_uuid)
 
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_pathway.name}"
+        context["title"] = f"enviPath - {current_package.get_name()} - {current_pathway.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "pathway"
@@ -1997,9 +2029,9 @@ def package_pathway(request, package_uuid, pathway_uuid):
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Package": s.SERVER_URL + "/package"},
-            {current_package.name: current_package.url},
+            {current_package.get_name(): current_package.url},
             {"Pathway": current_package.url + "/pathway"},
-            {current_pathway.name: current_pathway.url},
+            {current_pathway.get_name(): current_pathway.url},
         ]
 
         return render(request, "objects/pathway.html", context)
@@ -2057,6 +2089,9 @@ def package_pathway(request, package_uuid, pathway_uuid):
         if node_url:
             n = current_pathway.get_node(node_url)
 
+            current_pathway.kv.update({"status": "running"})
+            current_pathway.save()
+
             from .tasks import dispatch, predict
 
             dispatch(
@@ -2079,20 +2114,22 @@ def package_pathway(request, package_uuid, pathway_uuid):
 def package_pathway_nodes(request, package_uuid, pathway_uuid):
     current_user = _anonymous_or_real(request)
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
+    current_pathway = get_object_or_404(Pathway, package=current_package, uuid=pathway_uuid)
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_pathway.name} - Nodes"
+        context["title"] = (
+            f"enviPath - {current_package.get_name()} - {current_pathway.get_name()} - Nodes"
+        )
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "node"
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Package": s.SERVER_URL + "/package"},
-            {current_package.name: current_package.url},
+            {current_package.get_name(): current_package.url},
             {"Pathway": current_package.url + "/pathway"},
-            {current_pathway.name: current_pathway.url},
+            {current_pathway.get_name(): current_pathway.url},
             {"Node": current_pathway.url + "/node"},
         ]
 
@@ -2108,7 +2145,7 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_node_qs if current_package.reviewed else unreviewed_node_qs
                         )
@@ -2138,8 +2175,8 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
 def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
     current_user = _anonymous_or_real(request)
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
-    current_node = Node.objects.get(pathway=current_pathway, uuid=node_uuid)
+    current_pathway = get_object_or_404(Pathway, package=current_package, uuid=pathway_uuid)
+    current_node = get_object_or_404(Node, pathway=current_pathway, uuid=node_uuid)
 
     if request.method == "GET":
         is_image_request = request.GET.get("image")
@@ -2182,7 +2219,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
                 return HttpResponse(svg_data, content_type="image/svg+xml")
 
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_pathway.name}"
+        context["title"] = f"enviPath - {current_package.get_name()} - {current_pathway.get_name()}"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "pathway"
@@ -2190,11 +2227,11 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Package": s.SERVER_URL + "/package"},
-            {current_package.name: current_package.url},
+            {current_package.get_name(): current_package.url},
             {"Pathway": current_package.url + "/pathway"},
-            {current_pathway.name: current_pathway.url},
+            {current_pathway.get_name(): current_pathway.url},
             {"Node": current_pathway.url + "/node"},
-            {current_node.name: current_node.url},
+            {current_node.get_name(): current_node.url},
         ]
 
         context["node"] = current_node
@@ -2243,20 +2280,22 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 def package_pathway_edges(request, package_uuid, pathway_uuid):
     current_user = _anonymous_or_real(request)
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
+    current_pathway = get_object_or_404(Pathway, package=current_package, uuid=pathway_uuid)
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_pathway.name} - Edges"
+        context["title"] = (
+            f"enviPath - {current_package.get_name()} - {current_pathway.get_name()} - Edges"
+        )
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "edge"
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Package": s.SERVER_URL + "/package"},
-            {current_package.name: current_package.url},
+            {current_package.get_name(): current_package.url},
             {"Pathway": current_package.url + "/pathway"},
-            {current_pathway.name: current_pathway.url},
+            {current_pathway.get_name(): current_pathway.url},
             {"Edge": current_pathway.url + "/edge"},
         ]
 
@@ -2272,7 +2311,7 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_edge_qs if current_package.reviewed else unreviewed_edge_qs
                         )
@@ -2312,8 +2351,8 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
 def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
     current_user = _anonymous_or_real(request)
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
-    current_edge = Edge.objects.get(pathway=current_pathway, uuid=edge_uuid)
+    current_pathway = get_object_or_404(Pathway, package=current_package, uuid=pathway_uuid)
+    current_edge = get_object_or_404(Edge, pathway=current_pathway, uuid=edge_uuid)
 
     if request.method == "GET":
         is_image_request = request.GET.get("image")
@@ -2324,7 +2363,7 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
 
         context = get_base_context(request)
         context["title"] = (
-            f"enviPath - {current_package.name} - {current_pathway.name} - {current_edge.edge_label.name}"
+            f"enviPath - {current_package.get_name()} - {current_pathway.get_name()} - {current_edge.edge_label.get_name()}"
         )
 
         context["meta"]["current_package"] = current_package
@@ -2377,11 +2416,11 @@ def package_scenarios(request, package_uuid):
             "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]
+            res = [{"name": s_.get_name(), "url": s_.url, "uuid": s_.uuid} for s_ in scens]
             return JsonResponse(res, safe=False)
 
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - Scenarios"
+        context["title"] = f"enviPath - {current_package.get_name()} - Scenarios"
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "scenario"
@@ -2405,7 +2444,7 @@ def package_scenarios(request, package_uuid):
             return JsonResponse(
                 {
                     "objects": [
-                        {"name": pw.name, "url": pw.url, "reviewed": current_package.reviewed}
+                        {"name": pw.get_name(), "url": pw.url, "reviewed": current_package.reviewed}
                         for pw in (
                             reviewed_scenario_qs
                             if current_package.reviewed
@@ -2415,72 +2454,7 @@ def package_scenarios(request, package_uuid):
                 }
             )
 
-        from envipy_additional_information import (
-            SEDIMENT_ADDITIONAL_INFORMATION,
-            SLUDGE_ADDITIONAL_INFORMATION,
-            SOIL_ADDITIONAL_INFORMATION,
-        )
-
-        context["scenario_types"] = {
-            "Soil Data": {
-                "name": "soil",
-                "widgets": [
-                    HTMLGenerator.generate_html(ai, prefix=f"soil_{0}")
-                    for ai in [x for sv in SOIL_ADDITIONAL_INFORMATION.values() for x in sv]
-                ],
-            },
-            "Sludge Data": {
-                "name": "sludge",
-                "widgets": [
-                    HTMLGenerator.generate_html(ai, prefix=f"sludge_{0}")
-                    for ai in [x for sv in SLUDGE_ADDITIONAL_INFORMATION.values() for x in sv]
-                ],
-            },
-            "Water-Sediment System Data": {
-                "name": "sediment",
-                "widgets": [
-                    HTMLGenerator.generate_html(ai, prefix=f"sediment_{0}")
-                    for ai in [x for sv in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in sv]
-                ],
-            },
-        }
-
-        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/scenarios_paginated.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 sv in additional_information.values() for x in sv]
-
-        new_scen = Scenario.create(
-            current_package,
-            name=scenario_name,
-            description=scenario_description,
-            scenario_date=scenario_date,
-            scenario_type=scenario_type,
-            additional_information=additional_information,
-        )
-
-        return redirect(new_scen.url)
     else:
         return HttpResponseNotAllowed(
             [
@@ -2493,33 +2467,25 @@ def package_scenarios(request, package_uuid):
 def package_scenario(request, package_uuid, scenario_uuid):
     current_user = _anonymous_or_real(request)
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_scenario = Scenario.objects.get(package=current_package, uuid=scenario_uuid)
+    current_scenario = get_object_or_404(Scenario, package=current_package, uuid=scenario_uuid)
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_package.name} - {current_scenario.name}"
+        context["title"] = (
+            f"enviPath - {current_package.get_name()} - {current_scenario.get_name()}"
+        )
 
         context["meta"]["current_package"] = current_package
         context["object_type"] = "scenario"
         context["breadcrumbs"] = breadcrumbs(current_package, "scenario", current_scenario)
 
         context["scenario"] = current_scenario
+        # Get scenarios that have current_scenario as a parent
+        context["children"] = current_scenario.scenario_set.order_by("name")
 
-        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())
-        ]
+        # Note: Modals now fetch schemas and data from API endpoints
+        # Keeping these for backwards compatibility if needed elsewhere
+        # They are no longer used by the main scenario template
 
         return render(request, "objects/scenario.html", context)
 
@@ -2539,30 +2505,39 @@ def package_scenario(request, package_uuid, scenario_uuid):
                 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)
+                # Legacy POST handler - no longer used, modals use API endpoints
+                return HttpResponseBadRequest(
+                    "This endpoint is deprecated. Please use the API endpoints."
+                )
             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)
+                # Legacy POST handler - no longer used, modals use API endpoints
+                return HttpResponseBadRequest(
+                    "This endpoint is deprecated. Please use the API endpoints."
+                )
             else:
                 return HttpResponseBadRequest()
+
+        new_scenario_name = request.POST.get("scenario-name")
+
+        if new_scenario_name is not None:
+            new_scenario_name = nh3.clean(new_scenario_name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+            if new_scenario_name:
+                current_scenario.name = new_scenario_name
+
+        new_scenario_description = request.POST.get("scenario-description")
+
+        if new_scenario_description is not None:
+            new_scenario_description = nh3.clean(
+                new_scenario_description, tags=s.ALLOWED_HTML_TAGS
+            ).strip()
+
+            if new_scenario_description:
+                current_scenario.description = new_scenario_description
+
+        if any([new_scenario_name, new_scenario_description]):
+            current_scenario.save()
+            return redirect(current_scenario.url)
         else:
             return HttpResponseBadRequest()
     else:
@@ -2628,9 +2603,11 @@ def user(request, user_uuid):
 
         if is_hidden_method and request.POST["hidden"] == "request-api-token":
             name = request.POST.get("name", "No Name")
-            valid_for = min(max(int(request.POST.get("valid-for", 90)), 1), 90)
+            expires_days = min(max(int(request.POST.get("valid-for", 90)), 1), 90)
 
-            token, raw_token = APIToken.create_token(request.user, name=name, valid_for=valid_for)
+            token, raw_token = APIToken.create_token(
+                request.user, name=name, expires_days=expires_days
+            )
 
             return JsonResponse(
                 {"raw_token": raw_token, "token": {"id": token.id, "name": token.name}}
@@ -2712,19 +2689,21 @@ def group(request, group_uuid):
 
     if request.method == "GET":
         context = get_base_context(request)
-        context["title"] = f"enviPath - {current_group.name}"
+        context["title"] = f"enviPath - {current_group.get_name()}"
 
         context["object_type"] = "group"
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
             {"Group": s.SERVER_URL + "/group"},
-            {current_group.name: current_group.url},
+            {current_group.get_name(): current_group.url},
         ]
 
         context["group"] = current_group
 
-        context["users"] = UserManager.get_users_lp().exclude(
-            id__in=current_group.user_member.all()
+        context["users"] = (
+            UserManager.get_users_lp()
+            .exclude(id__in=current_group.user_member.all())
+            .filter(is_active=True)
         )
         context["groups"] = (
             GroupManager.get_groups_lp()
@@ -2778,10 +2757,17 @@ def settings(request):
         context["object_type"] = "setting"
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
-            {"Group": s.SERVER_URL + "/setting"},
+            {"Setting": s.SERVER_URL + "/setting"},
         ]
 
-        context["objects"] = SettingManager.get_all_settings(current_user)
+        # Context for paginated template
+        context["entity_type"] = "setting"
+        context["api_endpoint"] = "/api/v1/settings/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "settings"
+        context["list_mode"] = "combined"
+
+        return render(request, "collections/settings_paginated.html", context)
 
         return render(request, "collections/objects_list.html", context)
     elif request.method == "POST":
@@ -2861,7 +2847,26 @@ def settings(request):
 
 
 def setting(request, setting_uuid):
-    pass
+    current_user = _anonymous_or_real(request)
+    current_setting = SettingManager.get_setting_by_id(current_user, setting_uuid)
+
+    if request.method == "GET":
+        context = get_base_context(request)
+        context["title"] = f"enviPath - {current_setting.get_name()}"
+
+        context["object_type"] = "setting"
+        context["breadcrumbs"] = [
+            {"Home": s.SERVER_URL},
+            {"Setting": s.SERVER_URL + "/setting"},
+            {f"{current_setting.get_name()}": current_setting.url},
+        ]
+
+        context["setting"] = current_setting
+        context["current_object"] = current_setting
+
+        return render(request, "objects/setting.html", context)
+    else:
+        return HttpResponseNotAllowed(["GET"])
 
 
 def jobs(request):
@@ -2902,8 +2907,8 @@ def jobs(request):
 
             target_package = PackageManager.create_package(
                 current_user,
-                f"Autogenerated Package for Pathway Engineering of {pathway_to_engineer.name}",
-                f"This Package was generated automatically for the engineering Task of {pathway_to_engineer.name}.",
+                f"Autogenerated Package for Pathway Engineering of {pathway_to_engineer.get_name()}",
+                f"This Package was generated automatically for the engineering Task of {pathway_to_engineer.get_name()}.",
             )
 
             from .tasks import dispatch, engineer_pathways
@@ -2957,7 +2962,7 @@ def jobs(request):
                 "This Package was generated automatically for the batch prediction task.",
             )
 
-            from .tasks import dispatch, batch_predict
+            from .tasks import batch_predict, dispatch
 
             res = dispatch(
                 current_user,
@@ -2995,6 +3000,8 @@ def job(request, job_uuid):
 
             if job.job_name == "batch_predict":
                 filename = f"{job.job_name.replace(' ', '_')}_{job.task_id}.csv"
+            elif job.job_name == "identify_missing_rules":
+                filename = f"{job.job_name.replace(' ', '_')}_{job.task_id}.csv"
             else:
                 raise BadRequest("Result is not downloadable!")
 

migration/views.py

@@ -76,9 +76,7 @@ def migration(request):
                 open(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json")
             )
         else:
-            BBD = Package.objects.get(
-                url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
-            )
+            BBD = Package.objects.get(uuid="32de3cf4-e3e6-4168-956e-32fa5ddb0ce1")
             ALL_SMILES = [
                 cs.smiles for cs in CompoundStructure.objects.filter(compound__package=BBD)
             ]
@@ -147,7 +145,7 @@ def migration_detail(request, package_uuid, rule_uuid):
     if request.method == "GET":
         context = get_base_context(request)
 
-        BBD = Package.objects.get(name="EAWAG-BBD")
+        BBD = Package.objects.get(uuid="32de3cf4-e3e6-4168-956e-32fa5ddb0ce1")
         STRUCTURES = CompoundStructure.objects.filter(compound__package=BBD)
         rule = Rule.objects.get(package=BBD, uuid=rule_uuid)
 

package.json

@@ -8,14 +8,14 @@
     "build": "tailwindcss -i static/css/input.css -o static/css/output.css --minify"
   },
   "devDependencies": {
-    "@tailwindcss/cli": "^4.1.16",
-    "@tailwindcss/postcss": "^4.1.16",
-    "daisyui": "^5.4.3",
+    "@tailwindcss/cli": "^4.1.18",
+    "@tailwindcss/postcss": "^4.1.18",
+    "daisyui": "^5.5.14",
     "postcss": "^8.5.6",
-    "prettier": "^3.6.2",
+    "prettier": "^3.7.4",
     "prettier-plugin-jinja-template": "^2.1.0",
-    "prettier-plugin-tailwindcss": "^0.7.1",
-    "tailwindcss": "^4.1.16"
+    "prettier-plugin-tailwindcss": "^0.7.2",
+    "tailwindcss": "^4.1.18"
   },
   "keywords": [
     "django",

pnpm-lock.yaml

@@ -9,29 +9,29 @@ importers:
   .:
     devDependencies:
       '@tailwindcss/cli':
-        specifier: ^4.1.16
-        version: 4.1.16
+        specifier: ^4.1.18
+        version: 4.1.18
       '@tailwindcss/postcss':
-        specifier: ^4.1.16
-        version: 4.1.16
+        specifier: ^4.1.18
+        version: 4.1.18
       daisyui:
-        specifier: ^5.4.3
-        version: 5.4.3
+        specifier: ^5.5.14
+        version: 5.5.14
       postcss:
         specifier: ^8.5.6
         version: 8.5.6
       prettier:
-        specifier: ^3.6.2
-        version: 3.6.2
+        specifier: ^3.7.4
+        version: 3.7.4
       prettier-plugin-jinja-template:
         specifier: ^2.1.0
-        version: 2.1.0(prettier@3.6.2)
+        version: 2.1.0(prettier@3.7.4)
       prettier-plugin-tailwindcss:
-        specifier: ^0.7.1
-        version: 0.7.1(prettier@3.6.2)
+        specifier: ^0.7.2
+        version: 0.7.2(prettier@3.7.4)
       tailwindcss:
-        specifier: ^4.1.16
-        version: 4.1.16
+        specifier: ^4.1.18
+        version: 4.1.18
 
 packages:
 
@@ -137,69 +137,69 @@ packages:
     resolution: {integrity: sha512-dfUnCxiN9H4ap84DvD2ubjw+3vUNpstxa0TneY/Paat8a3R4uQZDLSvWjmznAY/DoahqTHl9V46HF/Zs3F29pg==}
     engines: {node: '>= 10.0.0'}
 
-  '@tailwindcss/cli@4.1.16':
-    resolution: {integrity: sha512-dsnANPrh2ZooHyZ/8uJhc9ecpcYtufToc21NY09NS9vF16rxPCjJ8dP7TUAtPqlUJTHSmRkN2hCdoYQIlgh4fw==}
+  '@tailwindcss/cli@4.1.18':
+    resolution: {integrity: sha512-sMZ+lZbDyxwjD2E0L7oRUjJ01Ffjtme5OtjvvnC+cV4CEDcbqzbp25TCpxHj6kWLU9+DlqJOiNgSOgctC2aZmg==}
     hasBin: true
 
-  '@tailwindcss/node@4.1.16':
-    resolution: {integrity: sha512-BX5iaSsloNuvKNHRN3k2RcCuTEgASTo77mofW0vmeHkfrDWaoFAFvNHpEgtu0eqyypcyiBkDWzSMxJhp3AUVcw==}
+  '@tailwindcss/node@4.1.18':
+    resolution: {integrity: sha512-DoR7U1P7iYhw16qJ49fgXUlry1t4CpXeErJHnQ44JgTSKMaZUdf17cfn5mHchfJ4KRBZRFA/Coo+MUF5+gOaCQ==}
 
-  '@tailwindcss/oxide-android-arm64@4.1.16':
-    resolution: {integrity: sha512-8+ctzkjHgwDJ5caq9IqRSgsP70xhdhJvm+oueS/yhD5ixLhqTw9fSL1OurzMUhBwE5zK26FXLCz2f/RtkISqHA==}
+  '@tailwindcss/oxide-android-arm64@4.1.18':
+    resolution: {integrity: sha512-dJHz7+Ugr9U/diKJA0W6N/6/cjI+ZTAoxPf9Iz9BFRF2GzEX8IvXxFIi/dZBloVJX/MZGvRuFA9rqwdiIEZQ0Q==}
     engines: {node: '>= 10'}
     cpu: [arm64]
     os: [android]
 
-  '@tailwindcss/oxide-darwin-arm64@4.1.16':
-    resolution: {integrity: sha512-C3oZy5042v2FOALBZtY0JTDnGNdS6w7DxL/odvSny17ORUnaRKhyTse8xYi3yKGyfnTUOdavRCdmc8QqJYwFKA==}
+  '@tailwindcss/oxide-darwin-arm64@4.1.18':
+    resolution: {integrity: sha512-Gc2q4Qhs660bhjyBSKgq6BYvwDz4G+BuyJ5H1xfhmDR3D8HnHCmT/BSkvSL0vQLy/nkMLY20PQ2OoYMO15Jd0A==}
     engines: {node: '>= 10'}
     cpu: [arm64]
     os: [darwin]
 
-  '@tailwindcss/oxide-darwin-x64@4.1.16':
-    resolution: {integrity: sha512-vjrl/1Ub9+JwU6BP0emgipGjowzYZMjbWCDqwA2Z4vCa+HBSpP4v6U2ddejcHsolsYxwL5r4bPNoamlV0xDdLg==}
+  '@tailwindcss/oxide-darwin-x64@4.1.18':
+    resolution: {integrity: sha512-FL5oxr2xQsFrc3X9o1fjHKBYBMD1QZNyc1Xzw/h5Qu4XnEBi3dZn96HcHm41c/euGV+GRiXFfh2hUCyKi/e+yw==}
     engines: {node: '>= 10'}
     cpu: [x64]
     os: [darwin]
 
-  '@tailwindcss/oxide-freebsd-x64@4.1.16':
-    resolution: {integrity: sha512-TSMpPYpQLm+aR1wW5rKuUuEruc/oOX3C7H0BTnPDn7W/eMw8W+MRMpiypKMkXZfwH8wqPIRKppuZoedTtNj2tg==}
+  '@tailwindcss/oxide-freebsd-x64@4.1.18':
+    resolution: {integrity: sha512-Fj+RHgu5bDodmV1dM9yAxlfJwkkWvLiRjbhuO2LEtwtlYlBgiAT4x/j5wQr1tC3SANAgD+0YcmWVrj8R9trVMA==}
     engines: {node: '>= 10'}
     cpu: [x64]
     os: [freebsd]
 
-  '@tailwindcss/oxide-linux-arm-gnueabihf@4.1.16':
-    resolution: {integrity: sha512-p0GGfRg/w0sdsFKBjMYvvKIiKy/LNWLWgV/plR4lUgrsxFAoQBFrXkZ4C0w8IOXfslB9vHK/JGASWD2IefIpvw==}
+  '@tailwindcss/oxide-linux-arm-gnueabihf@4.1.18':
+    resolution: {integrity: sha512-Fp+Wzk/Ws4dZn+LV2Nqx3IilnhH51YZoRaYHQsVq3RQvEl+71VGKFpkfHrLM/Li+kt5c0DJe/bHXK1eHgDmdiA==}
     engines: {node: '>= 10'}
     cpu: [arm]
     os: [linux]
 
-  '@tailwindcss/oxide-linux-arm64-gnu@4.1.16':
-    resolution: {integrity: sha512-DoixyMmTNO19rwRPdqviTrG1rYzpxgyYJl8RgQvdAQUzxC1ToLRqtNJpU/ATURSKgIg6uerPw2feW0aS8SNr/w==}
+  '@tailwindcss/oxide-linux-arm64-gnu@4.1.18':
+    resolution: {integrity: sha512-S0n3jboLysNbh55Vrt7pk9wgpyTTPD0fdQeh7wQfMqLPM/Hrxi+dVsLsPrycQjGKEQk85Kgbx+6+QnYNiHalnw==}
     engines: {node: '>= 10'}
     cpu: [arm64]
     os: [linux]
 
-  '@tailwindcss/oxide-linux-arm64-musl@4.1.16':
-    resolution: {integrity: sha512-H81UXMa9hJhWhaAUca6bU2wm5RRFpuHImrwXBUvPbYb+3jo32I9VIwpOX6hms0fPmA6f2pGVlybO6qU8pF4fzQ==}
+  '@tailwindcss/oxide-linux-arm64-musl@4.1.18':
+    resolution: {integrity: sha512-1px92582HkPQlaaCkdRcio71p8bc8i/ap5807tPRDK/uw953cauQBT8c5tVGkOwrHMfc2Yh6UuxaH4vtTjGvHg==}
     engines: {node: '>= 10'}
     cpu: [arm64]
     os: [linux]
 
-  '@tailwindcss/oxide-linux-x64-gnu@4.1.16':
-    resolution: {integrity: sha512-ZGHQxDtFC2/ruo7t99Qo2TTIvOERULPl5l0K1g0oK6b5PGqjYMga+FcY1wIUnrUxY56h28FxybtDEla+ICOyew==}
+  '@tailwindcss/oxide-linux-x64-gnu@4.1.18':
+    resolution: {integrity: sha512-v3gyT0ivkfBLoZGF9LyHmts0Isc8jHZyVcbzio6Wpzifg/+5ZJpDiRiUhDLkcr7f/r38SWNe7ucxmGW3j3Kb/g==}
     engines: {node: '>= 10'}
     cpu: [x64]
     os: [linux]
 
-  '@tailwindcss/oxide-linux-x64-musl@4.1.16':
-    resolution: {integrity: sha512-Oi1tAaa0rcKf1Og9MzKeINZzMLPbhxvm7rno5/zuP1WYmpiG0bEHq4AcRUiG2165/WUzvxkW4XDYCscZWbTLZw==}
+  '@tailwindcss/oxide-linux-x64-musl@4.1.18':
+    resolution: {integrity: sha512-bhJ2y2OQNlcRwwgOAGMY0xTFStt4/wyU6pvI6LSuZpRgKQwxTec0/3Scu91O8ir7qCR3AuepQKLU/kX99FouqQ==}
     engines: {node: '>= 10'}
     cpu: [x64]
     os: [linux]
 
-  '@tailwindcss/oxide-wasm32-wasi@4.1.16':
-    resolution: {integrity: sha512-B01u/b8LteGRwucIBmCQ07FVXLzImWESAIMcUU6nvFt/tYsQ6IHz8DmZ5KtvmwxD+iTYBtM1xwoGXswnlu9v0Q==}
+  '@tailwindcss/oxide-wasm32-wasi@4.1.18':
+    resolution: {integrity: sha512-LffYTvPjODiP6PT16oNeUQJzNVyJl1cjIebq/rWWBF+3eDst5JGEFSc5cWxyRCJ0Mxl+KyIkqRxk1XPEs9x8TA==}
     engines: {node: '>=14.0.0'}
     cpu: [wasm32]
     bundledDependencies:
@@ -210,31 +210,31 @@ packages:
       - '@emnapi/wasi-threads'
       - tslib
 
-  '@tailwindcss/oxide-win32-arm64-msvc@4.1.16':
-    resolution: {integrity: sha512-zX+Q8sSkGj6HKRTMJXuPvOcP8XfYON24zJBRPlszcH1Np7xuHXhWn8qfFjIujVzvH3BHU+16jBXwgpl20i+v9A==}
+  '@tailwindcss/oxide-win32-arm64-msvc@4.1.18':
+    resolution: {integrity: sha512-HjSA7mr9HmC8fu6bdsZvZ+dhjyGCLdotjVOgLA2vEqxEBZaQo9YTX4kwgEvPCpRh8o4uWc4J/wEoFzhEmjvPbA==}
     engines: {node: '>= 10'}
     cpu: [arm64]
     os: [win32]
 
-  '@tailwindcss/oxide-win32-x64-msvc@4.1.16':
-    resolution: {integrity: sha512-m5dDFJUEejbFqP+UXVstd4W/wnxA4F61q8SoL+mqTypId2T2ZpuxosNSgowiCnLp2+Z+rivdU0AqpfgiD7yCBg==}
+  '@tailwindcss/oxide-win32-x64-msvc@4.1.18':
+    resolution: {integrity: sha512-bJWbyYpUlqamC8dpR7pfjA0I7vdF6t5VpUGMWRkXVE3AXgIZjYUYAK7II1GNaxR8J1SSrSrppRar8G++JekE3Q==}
     engines: {node: '>= 10'}
     cpu: [x64]
     os: [win32]
 
-  '@tailwindcss/oxide@4.1.16':
-    resolution: {integrity: sha512-2OSv52FRuhdlgyOQqgtQHuCgXnS8nFSYRp2tJ+4WZXKgTxqPy7SMSls8c3mPT5pkZ17SBToGM5LHEJBO7miEdg==}
+  '@tailwindcss/oxide@4.1.18':
+    resolution: {integrity: sha512-EgCR5tTS5bUSKQgzeMClT6iCY3ToqE1y+ZB0AKldj809QXk1Y+3jB0upOYZrn9aGIzPtUsP7sX4QQ4XtjBB95A==}
     engines: {node: '>= 10'}
 
-  '@tailwindcss/postcss@4.1.16':
-    resolution: {integrity: sha512-Qn3SFGPXYQMKR/UtqS+dqvPrzEeBZHrFA92maT4zijCVggdsXnDBMsPFJo1eArX3J+O+Gi+8pV4PkqjLCNBk3A==}
+  '@tailwindcss/postcss@4.1.18':
+    resolution: {integrity: sha512-Ce0GFnzAOuPyfV5SxjXGn0CubwGcuDB0zcdaPuCSzAa/2vII24JTkH+I6jcbXLb1ctjZMZZI6OjDaLPJQL1S0g==}
 
   braces@3.0.3:
     resolution: {integrity: sha512-yQbXgO/OSZVD2IsiLlro+7Hf6Q18EJrKSEsdoMzKePKXct3gvD8oLcOQdIzGupr5Fj+EDe8gO/lxc1BzfMpxvA==}
     engines: {node: '>=8'}
 
-  daisyui@5.4.3:
-    resolution: {integrity: sha512-dfDCJnN4utErGoWfElgdEE252FtfHV9Mxj5Dq1+JzUq3nVkluWdF3JYykP0Xy/y/yArnPXYztO1tLNCow3kjmg==}
+  daisyui@5.5.14:
+    resolution: {integrity: sha512-L47rvw7I7hK68TA97VB8Ee0woHew+/ohR6Lx6Ah/krfISOqcG4My7poNpX5Mo5/ytMxiR40fEaz6njzDi7cuSg==}
 
   detect-libc@1.0.3:
     resolution: {integrity: sha512-pGjwhsmsp4kL2RTz08wcOlGN83otlqHeD/Z5T8GXZB+/YcpQ/dgo+lbU8ZsGxV0HIvqqxo9l7mqYwyYMD9bKDg==}
@@ -245,8 +245,8 @@ packages:
     resolution: {integrity: sha512-Btj2BOOO83o3WyH59e8MgXsxEQVcarkUOpEYrubB0urwnN10yQ364rsiByU11nZlqWYZm05i/of7io4mzihBtQ==}
     engines: {node: '>=8'}
 
-  enhanced-resolve@5.18.3:
-    resolution: {integrity: sha512-d4lC8xfavMeBjzGr2vECC3fsGXziXZQyJxD868h2M/mBI3PwAuODxAkLkq5HYuvrPYcUtiLzsTo8U3PgX3Ocww==}
+  enhanced-resolve@5.18.4:
+    resolution: {integrity: sha512-LgQMM4WXU3QI+SYgEc2liRgznaD5ojbmY3sb8LxyguVkIg5FxdpTkvk72te2R38/TGKxH634oLxXRGY6d7AP+Q==}
     engines: {node: '>=10.13.0'}
 
   fill-range@7.1.1:
@@ -377,8 +377,8 @@ packages:
     peerDependencies:
       prettier: ^3.0.0
 
-  prettier-plugin-tailwindcss@0.7.1:
-    resolution: {integrity: sha512-Bzv1LZcuiR1Sk02iJTS1QzlFNp/o5l2p3xkopwOrbPmtMeh3fK9rVW5M3neBQzHq+kGKj/4LGQMTNcTH4NGPtQ==}
+  prettier-plugin-tailwindcss@0.7.2:
+    resolution: {integrity: sha512-LkphyK3Fw+q2HdMOoiEHWf93fNtYJwfamoKPl7UwtjFQdei/iIBoX11G6j706FzN3ymX9mPVi97qIY8328vdnA==}
     engines: {node: '>=20.19'}
     peerDependencies:
       '@ianvs/prettier-plugin-sort-imports': '*'
@@ -432,8 +432,8 @@ packages:
       prettier-plugin-svelte:
         optional: true
 
-  prettier@3.6.2:
-    resolution: {integrity: sha512-I7AIg5boAr5R0FFtJ6rCfD+LFsWHp81dolrFD8S79U9tb8Az2nGrJncnMSnys+bpQJfRUzqs9hnA81OAA3hCuQ==}
+  prettier@3.7.4:
+    resolution: {integrity: sha512-v6UNi1+3hSlVvv8fSaoUbggEM5VErKmmpGA7Pl3HF8V6uKY7rvClBOJlH6yNwQtfTueNkGVpOv/mtWL9L4bgRA==}
     engines: {node: '>=14'}
     hasBin: true
 
@@ -441,8 +441,8 @@ packages:
     resolution: {integrity: sha512-UXWMKhLOwVKb728IUtQPXxfYU+usdybtUrK/8uGE8CQMvrhOpwvzDBwj0QhSL7MQc7vIsISBG8VQ8+IDQxpfQA==}
     engines: {node: '>=0.10.0'}
 
-  tailwindcss@4.1.16:
-    resolution: {integrity: sha512-pONL5awpaQX4LN5eiv7moSiSPd/DLDzKVRJz8Q9PgzmAdd1R4307GQS2ZpfiN7ZmekdQrfhZZiSE5jkLR4WNaA==}
+  tailwindcss@4.1.18:
+    resolution: {integrity: sha512-4+Z+0yiYyEtUVCScyfHCxOYP06L5Ne+JiHhY2IjR2KWMIWhJOYZKLSGZaP5HkZ8+bY0cxfzwDE5uOmzFXyIwxw==}
 
   tapable@2.3.0:
     resolution: {integrity: sha512-g9ljZiwki/LfxmQADO3dEY1CbpmXT5Hm2fJ+QaGKwSXUylMybePR7/67YW7jOrrvjEgL1Fmz5kzyAjWVWLlucg==}
@@ -535,96 +535,96 @@ snapshots:
       '@parcel/watcher-win32-ia32': 2.5.1
       '@parcel/watcher-win32-x64': 2.5.1
 
-  '@tailwindcss/cli@4.1.16':
+  '@tailwindcss/cli@4.1.18':
     dependencies:
       '@parcel/watcher': 2.5.1
-      '@tailwindcss/node': 4.1.16
-      '@tailwindcss/oxide': 4.1.16
-      enhanced-resolve: 5.18.3
+      '@tailwindcss/node': 4.1.18
+      '@tailwindcss/oxide': 4.1.18
+      enhanced-resolve: 5.18.4
       mri: 1.2.0
       picocolors: 1.1.1
-      tailwindcss: 4.1.16
+      tailwindcss: 4.1.18
 
-  '@tailwindcss/node@4.1.16':
+  '@tailwindcss/node@4.1.18':
     dependencies:
       '@jridgewell/remapping': 2.3.5
-      enhanced-resolve: 5.18.3
+      enhanced-resolve: 5.18.4
       jiti: 2.6.1
       lightningcss: 1.30.2
       magic-string: 0.30.21
       source-map-js: 1.2.1
-      tailwindcss: 4.1.16
+      tailwindcss: 4.1.18
 
-  '@tailwindcss/oxide-android-arm64@4.1.16':
+  '@tailwindcss/oxide-android-arm64@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-darwin-arm64@4.1.16':
+  '@tailwindcss/oxide-darwin-arm64@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-darwin-x64@4.1.16':
+  '@tailwindcss/oxide-darwin-x64@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-freebsd-x64@4.1.16':
+  '@tailwindcss/oxide-freebsd-x64@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-linux-arm-gnueabihf@4.1.16':
+  '@tailwindcss/oxide-linux-arm-gnueabihf@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-linux-arm64-gnu@4.1.16':
+  '@tailwindcss/oxide-linux-arm64-gnu@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-linux-arm64-musl@4.1.16':
+  '@tailwindcss/oxide-linux-arm64-musl@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-linux-x64-gnu@4.1.16':
+  '@tailwindcss/oxide-linux-x64-gnu@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-linux-x64-musl@4.1.16':
+  '@tailwindcss/oxide-linux-x64-musl@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-wasm32-wasi@4.1.16':
+  '@tailwindcss/oxide-wasm32-wasi@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-win32-arm64-msvc@4.1.16':
+  '@tailwindcss/oxide-win32-arm64-msvc@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide-win32-x64-msvc@4.1.16':
+  '@tailwindcss/oxide-win32-x64-msvc@4.1.18':
     optional: true
 
-  '@tailwindcss/oxide@4.1.16':
+  '@tailwindcss/oxide@4.1.18':
     optionalDependencies:
-      '@tailwindcss/oxide-android-arm64': 4.1.16
-      '@tailwindcss/oxide-darwin-arm64': 4.1.16
-      '@tailwindcss/oxide-darwin-x64': 4.1.16
-      '@tailwindcss/oxide-freebsd-x64': 4.1.16
-      '@tailwindcss/oxide-linux-arm-gnueabihf': 4.1.16
-      '@tailwindcss/oxide-linux-arm64-gnu': 4.1.16
-      '@tailwindcss/oxide-linux-arm64-musl': 4.1.16
-      '@tailwindcss/oxide-linux-x64-gnu': 4.1.16
-      '@tailwindcss/oxide-linux-x64-musl': 4.1.16
-      '@tailwindcss/oxide-wasm32-wasi': 4.1.16
-      '@tailwindcss/oxide-win32-arm64-msvc': 4.1.16
-      '@tailwindcss/oxide-win32-x64-msvc': 4.1.16
+      '@tailwindcss/oxide-android-arm64': 4.1.18
+      '@tailwindcss/oxide-darwin-arm64': 4.1.18
+      '@tailwindcss/oxide-darwin-x64': 4.1.18
+      '@tailwindcss/oxide-freebsd-x64': 4.1.18
+      '@tailwindcss/oxide-linux-arm-gnueabihf': 4.1.18
+      '@tailwindcss/oxide-linux-arm64-gnu': 4.1.18
+      '@tailwindcss/oxide-linux-arm64-musl': 4.1.18
+      '@tailwindcss/oxide-linux-x64-gnu': 4.1.18
+      '@tailwindcss/oxide-linux-x64-musl': 4.1.18
+      '@tailwindcss/oxide-wasm32-wasi': 4.1.18
+      '@tailwindcss/oxide-win32-arm64-msvc': 4.1.18
+      '@tailwindcss/oxide-win32-x64-msvc': 4.1.18
 
-  '@tailwindcss/postcss@4.1.16':
+  '@tailwindcss/postcss@4.1.18':
     dependencies:
       '@alloc/quick-lru': 5.2.0
-      '@tailwindcss/node': 4.1.16
-      '@tailwindcss/oxide': 4.1.16
+      '@tailwindcss/node': 4.1.18
+      '@tailwindcss/oxide': 4.1.18
       postcss: 8.5.6
-      tailwindcss: 4.1.16
+      tailwindcss: 4.1.18
 
   braces@3.0.3:
     dependencies:
       fill-range: 7.1.1
 
-  daisyui@5.4.3: {}
+  daisyui@5.5.14: {}
 
   detect-libc@1.0.3: {}
 
   detect-libc@2.1.2: {}
 
-  enhanced-resolve@5.18.3:
+  enhanced-resolve@5.18.4:
     dependencies:
       graceful-fs: 4.2.11
       tapable: 2.3.0
@@ -719,19 +719,19 @@ snapshots:
       picocolors: 1.1.1
       source-map-js: 1.2.1
 
-  prettier-plugin-jinja-template@2.1.0(prettier@3.6.2):
+  prettier-plugin-jinja-template@2.1.0(prettier@3.7.4):
     dependencies:
-      prettier: 3.6.2
+      prettier: 3.7.4
 
-  prettier-plugin-tailwindcss@0.7.1(prettier@3.6.2):
+  prettier-plugin-tailwindcss@0.7.2(prettier@3.7.4):
     dependencies:
-      prettier: 3.6.2
+      prettier: 3.7.4
 
-  prettier@3.6.2: {}
+  prettier@3.7.4: {}
 
   source-map-js@1.2.1: {}
 
-  tailwindcss@4.1.16: {}
+  tailwindcss@4.1.18: {}
 
   tapable@2.3.0: {}
 

pnpm-workspace.yaml

@@ -0,0 +1,3 @@
+onlyBuiltDependencies:
+  - '@parcel/watcher'
+  - '@tailwindcss/oxide'

pyproject.toml

@@ -19,6 +19,7 @@ dependencies = [
     "envipy-plugins",
     "epam-indigo>=1.30.1",
     "gunicorn>=23.0.0",
+    "jsonref>=1.1.0",
     "networkx>=3.4.2",
     "psycopg2-binary>=2.9.10",
     "python-dotenv>=1.1.0",
@@ -35,7 +36,7 @@ dependencies = [
 [tool.uv.sources]
 enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.4" }
 envipy-plugins = { git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git", rev = "v0.1.0" }
-envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.7" }
+envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.4.2" }
 envipy-ambit = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" }
 
 [project.optional-dependencies]
@@ -85,8 +86,15 @@ build = { sequence = [
 ], help = "Build frontend assets and collect static files" }
 
 # Database tasks
-db-up = { cmd = "docker compose -f docker-compose.dev.yml up -d", help = "Start PostgreSQL database using Docker Compose" }
-db-down = { cmd = "docker compose -f docker-compose.dev.yml down", help = "Stop PostgreSQL database" }
+db-up = { cmd = "docker compose -p envipath -f docker-compose.dev.yml up -d", help = "Start PostgreSQL database using Docker Compose" }
+db-down = { cmd = "docker compose -p envipath -f docker-compose.dev.yml down", help = "Stop PostgreSQL database" }
+
+# Celery tasks
+celery = { cmd = "celery -A envipath worker -l INFO -Q predict,model,background", help = "Start Celery worker for async task processing" }
+celery-dev = { sequence = [
+    "db-up",
+    "celery",
+], help = "Start database and Celery worker" }
 
 # Frontend tasks
 js-deps = { cmd = "uv run python scripts/pnpm_wrapper.py install", help = "Install frontend dependencies" }

scripts/dev_server.py

@@ -11,6 +11,8 @@ import signal
 import subprocess
 import sys
 import time
+import os
+import dotenv
 
 
 def find_pnpm():
@@ -65,6 +67,7 @@ class DevServerManager:
                     bufsize=1,
                 )
             self.processes.append((process, description))
+            print(" ".join(command))
             print(f"✓ Started {description} (PID: {process.pid})")
             return process
         except Exception as e:
@@ -146,6 +149,7 @@ class DevServerManager:
 
 def main():
     """Main entry point."""
+    dotenv.load_dotenv()
     manager = DevServerManager()
     manager.register_cleanup()
 
@@ -174,9 +178,10 @@ def main():
     time.sleep(1)
 
     # Start Django dev server
+    port = os.environ.get("DJANGO_PORT", "8000")
     django_process = manager.start_process(
-        ["uv", "run", "python", "manage.py", "runserver"],
-        "Django server",
+        ["uv", "run", "python", "manage.py", "runserver", f"0:{port}"],
+        f"Django server on port {port}",
         shell=False,
     )
 

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

@@ -0,0 +1,378 @@
+/**
+ * Alpine.js Schema Renderer Component
+ *
+ * Renders forms dynamically from JSON Schema with RJSF format support.
+ * Supports uiSchema for widget hints, labels, help text, and field ordering.
+ *
+ * Usage:
+ * <div x-data="schemaRenderer({
+ *     rjsf: { schema: {...}, uiSchema: {...}, formData: {...}, groups: [...] },
+ *     data: { interval: { start: 20, end: 25 } },
+ *     mode: 'view', // 'view' | 'edit'
+ *     endpoint: '/api/v1/scenario/{uuid}/information/temperature/'
+ * })">
+ */
+document.addEventListener("alpine:init", () => {
+  // Global validation error store with context scoping
+  Alpine.store('validationErrors', {
+    errors: {},
+
+    // Set errors for a specific context (UUID) or globally (no context)
+    setErrors(errors, context = null) {
+      if (context) {
+        // Namespace all field names with context prefix
+        const namespacedErrors = {};
+        Object.entries(errors).forEach(([field, messages]) => {
+          const key = `${context}.${field}`;
+          namespacedErrors[key] = messages;
+        });
+        // Merge into existing errors (preserves other contexts)
+        this.errors = { ...this.errors, ...namespacedErrors };
+      } else {
+        // No context - merge as-is for backward compatibility
+        this.errors = { ...this.errors, ...errors };
+      }
+    },
+
+    // Clear errors for a specific context or all errors
+    clearErrors(context = null) {
+      if (context) {
+        // Clear only errors for this context
+        const newErrors = {};
+        const prefix = `${context}.`;
+        Object.keys(this.errors).forEach(key => {
+          if (!key.startsWith(prefix)) {
+            newErrors[key] = this.errors[key];
+          }
+        });
+        this.errors = newErrors;
+      } else {
+        // Clear all errors
+        this.errors = {};
+      }
+    },
+
+    // Clear a specific field, optionally within a context
+    clearField(fieldName, context = null) {
+      const key = context ? `${context}.${fieldName}` : fieldName;
+      if (this.errors[key]) {
+        delete this.errors[key];
+        // Trigger reactivity by creating new object
+        this.errors = { ...this.errors };
+      }
+    },
+
+    // Check if a field has errors, optionally within a context
+    hasError(fieldName, context = null) {
+      const key = context ? `${context}.${fieldName}` : fieldName;
+      return Array.isArray(this.errors[key]) && this.errors[key].length > 0;
+    },
+
+    // Get errors for a field, optionally within a context
+    getErrors(fieldName, context = null) {
+      const key = context ? `${context}.${fieldName}` : fieldName;
+      return this.errors[key] || [];
+    }
+  });
+
+  Alpine.data("schemaRenderer", (options = {}) => ({
+    schema: null,
+    uiSchema: {},
+    data: {},
+    mode: options.mode || "view", // 'view' | 'edit'
+    endpoint: options.endpoint || "",
+    loading: false,
+    error: null,
+    context: options.context || null, // UUID for items, null for single forms
+    debugErrors:
+      options.debugErrors ??
+      (typeof window !== "undefined" &&
+        window.location?.search?.includes("debugErrors=1")),
+
+    async init() {
+      if (options.schemaUrl) {
+        try {
+          this.loading = true;
+          const res = await fetch(options.schemaUrl);
+          if (!res.ok) {
+            throw new Error(`Failed to load schema: ${res.statusText}`);
+          }
+          const rjsf = await res.json();
+
+          // RJSF format: {schema, uiSchema, formData, groups}
+          if (!rjsf.schema) {
+            throw new Error("Invalid RJSF format: missing schema property");
+          }
+
+          this.schema = rjsf.schema;
+          this.uiSchema = rjsf.uiSchema || {};
+          this.data = options.data
+            ? JSON.parse(JSON.stringify(options.data))
+            : rjsf.formData || {};
+        } catch (err) {
+          this.error = err.message;
+          console.error("Error loading schema:", err);
+        } finally {
+          this.loading = false;
+        }
+      } else if (options.rjsf) {
+        // Direct RJSF object passed
+        if (!options.rjsf.schema) {
+          throw new Error("Invalid RJSF format: missing schema property");
+        }
+
+        this.schema = options.rjsf.schema;
+        this.uiSchema = options.rjsf.uiSchema || {};
+        this.data = options.data
+          ? JSON.parse(JSON.stringify(options.data))
+          : options.rjsf.formData || {};
+      }
+
+      // Initialize data from formData or options
+      if (!this.data || Object.keys(this.data).length === 0) {
+        this.data = {};
+      }
+
+      // Ensure all schema fields are properly initialized
+      if (this.schema && this.schema.properties) {
+        for (const [key, propSchema] of Object.entries(
+          this.schema.properties,
+        )) {
+          const widget = this.getWidget(key, propSchema);
+
+          if (widget === "interval") {
+            // Ensure interval fields are objects with start/end
+            if (!this.data[key] || typeof this.data[key] !== "object") {
+              this.data[key] = { start: null, end: null };
+            } else {
+              // Ensure start and end exist
+              if (this.data[key].start === undefined)
+                this.data[key].start = null;
+              if (this.data[key].end === undefined) this.data[key].end = null;
+            }
+          } else if (widget === "timeseries-table") {
+            // Ensure timeseries fields are arrays
+            if (!this.data[key] || !Array.isArray(this.data[key])) {
+              this.data[key] = [];
+            }
+          } else if (this.data[key] === undefined) {
+            // ONLY initialize if truly undefined, not just falsy
+            // This preserves empty strings, null, 0, false as valid values
+            if (propSchema.type === "boolean") {
+              this.data[key] = false;
+            } else if (
+              propSchema.type === "number" ||
+              propSchema.type === "integer"
+            ) {
+              this.data[key] = null;
+            } else if (propSchema.enum) {
+              // For select fields, use null to show placeholder
+              this.data[key] = null;
+            } else {
+              this.data[key] = "";
+            }
+          }
+          // If data[key] exists (even if empty string or null), don't overwrite
+        }
+      }
+
+      // UX: Clear field errors when fields change (with context)
+      if (this.mode === "edit" && this.schema?.properties) {
+        Object.keys(this.schema.properties).forEach((key) => {
+          this.$watch(
+            `data.${key}`,
+            () => {
+              Alpine.store('validationErrors').clearField(key, this.context);
+            },
+            { deep: true },
+          );
+        });
+      }
+    },
+
+    getWidget(fieldName, fieldSchema) {
+      // Defensive check: ensure fieldSchema is provided
+      if (!fieldSchema) return "text";
+
+      try {
+        // Check uiSchema first (RJSF format)
+        if (
+          this.uiSchema &&
+          this.uiSchema[fieldName] &&
+          this.uiSchema[fieldName]["ui:widget"]
+        ) {
+          return this.uiSchema[fieldName]["ui:widget"];
+        }
+
+        // Check for interval type (object with start/end properties)
+        if (
+          fieldSchema.type === "object" &&
+          fieldSchema.properties &&
+          fieldSchema.properties.start &&
+          fieldSchema.properties.end
+        ) {
+          return "interval";
+        }
+
+        // Check for measurements array type (timeseries-table widget)
+        if (
+          fieldSchema.type === "array" &&
+          fieldSchema.items?.properties?.timestamp &&
+          fieldSchema.items?.properties?.value
+        ) {
+          return "timeseries-table";
+        }
+
+        // Infer from JSON Schema type
+        if (fieldSchema.enum) return "select";
+        if (fieldSchema.type === "number" || fieldSchema.type === "integer")
+          return "number";
+        if (fieldSchema.type === "boolean") return "checkbox";
+        return "text";
+      } catch (e) {
+        // Fallback to text widget if anything fails
+        console.warn("Error in getWidget:", e);
+        return "text";
+      }
+    },
+
+    getLabel(fieldName, fieldSchema) {
+      // Check uiSchema (RJSF format)
+      if (this.uiSchema[fieldName] && this.uiSchema[fieldName]["ui:label"]) {
+        return this.uiSchema[fieldName]["ui:label"];
+      }
+
+      // Default: format field name
+      return fieldName
+        .replace(/_/g, " ")
+        .replace(/\b\w/g, (c) => c.toUpperCase());
+    },
+
+    getFieldOrder() {
+      try {
+        // Get ordered list of field names based on ui:order
+        if (!this.schema || !this.schema.properties) return [];
+
+        // Only include fields that have UI configs
+        const fields = Object.keys(this.schema.properties).filter(
+          (fieldName) => this.uiSchema && this.uiSchema[fieldName],
+        );
+
+        // Sort by ui:order if available
+        return fields.sort((a, b) => {
+          const orderA = this.uiSchema[a]?.["ui:order"] || "999";
+          const orderB = this.uiSchema[b]?.["ui:order"] || "999";
+          return parseInt(orderA) - parseInt(orderB);
+        });
+      } catch (e) {
+        // Return empty array if anything fails to prevent errors
+        console.warn("Error in getFieldOrder:", e);
+        return [];
+      }
+    },
+
+    hasTimeseriesField() {
+      try {
+        // Check if any field in the schema is a timeseries-table widget
+        if (!this.schema || !this.schema.properties) {
+          return false;
+        }
+
+        return Object.keys(this.schema.properties).some((fieldName) => {
+          const fieldSchema = this.schema.properties[fieldName];
+          if (!fieldSchema) return false;
+          return this.getWidget(fieldName, fieldSchema) === "timeseries-table";
+        });
+      } catch (e) {
+        // Return false if anything fails to prevent errors
+        console.warn("Error in hasTimeseriesField:", e);
+        return false;
+      }
+    },
+
+    async submit() {
+      if (!this.endpoint) {
+        console.error("No endpoint specified for submission");
+        return;
+      }
+
+      this.loading = true;
+      this.error = null;
+
+      try {
+        const csrftoken =
+          document.querySelector("[name=csrf-token]")?.content || "";
+        const res = await fetch(this.endpoint, {
+          method: "POST",
+          headers: {
+            "Content-Type": "application/json",
+            "X-CSRFToken": csrftoken,
+          },
+          body: JSON.stringify(this.data),
+        });
+
+        if (!res.ok) {
+          let errorData;
+          try {
+            errorData = await res.json();
+          } catch {
+            errorData = { error: res.statusText };
+          }
+
+          // Handle validation errors (field-level)
+          Alpine.store('validationErrors').clearErrors();
+
+          // Try to parse structured error response
+          let parsedError = errorData;
+
+          // If error is a JSON string, parse it
+          if (
+            typeof errorData.error === "string" &&
+            errorData.error.startsWith("{")
+          ) {
+            parsedError = JSON.parse(errorData.error);
+          }
+
+          if (parsedError.detail && Array.isArray(parsedError.detail)) {
+            // Pydantic validation errors format: [{loc: ['field'], msg: '...', type: '...'}]
+            const fieldErrors = {};
+            for (const err of parsedError.detail) {
+              const field =
+                err.loc && err.loc.length > 0
+                  ? err.loc[err.loc.length - 1]
+                  : "root";
+              if (!fieldErrors[field]) {
+                fieldErrors[field] = [];
+              }
+              fieldErrors[field].push(
+                err.msg || err.message || "Validation error",
+              );
+            }
+            Alpine.store('validationErrors').setErrors(fieldErrors);
+            throw new Error(
+              "Validation failed. Please check the fields below.",
+            );
+          } else {
+            // General error
+            throw new Error(
+              parsedError.error ||
+                parsedError.detail ||
+                `Request failed: ${res.statusText}`,
+            );
+          }
+        }
+
+        // Clear errors on success
+        Alpine.store('validationErrors').clearErrors();
+
+        const result = await res.json();
+        return result;
+      } catch (err) {
+        this.error = err.message;
+        throw err;
+      } finally {
+        this.loading = false;
+      }
+    },
+  }));
+});

static/js/alpine/components/widgets.js

@@ -0,0 +1,462 @@
+/**
+ * Alpine.js Widget Components for Schema Forms
+ *
+ * Centralized widget component definitions for dynamic form rendering.
+ * Each widget receives explicit parameters instead of context object for better traceability.
+ */
+document.addEventListener("alpine:init", () => {
+  // Base widget factory with common functionality
+  const baseWidget = (
+    fieldName,
+    data,
+    schema,
+    uiSchema,
+    mode,
+    debugErrors,
+    context = null  // NEW: context for error namespacing
+  ) => ({
+    fieldName,
+    data,
+    schema,
+    uiSchema,
+    mode,
+    debugErrors,
+    context,  // Store context for use in templates
+
+    // Field schema access
+    get fieldSchema() {
+      return this.schema?.properties?.[this.fieldName] || {};
+    },
+
+    // Common metadata
+    get label() {
+      // Check uiSchema first (RJSF format)
+      if (this.uiSchema?.[this.fieldName]?.["ui:label"]) {
+        return this.uiSchema[this.fieldName]["ui:label"];
+      }
+      // Fall back to schema title
+      if (this.fieldSchema.title) {
+        return this.fieldSchema.title;
+      }
+      // Default: format field name
+      return this.fieldName
+        .replace(/_/g, " ")
+        .replace(/\b\w/g, (c) => c.toUpperCase());
+    },
+    get helpText() {
+      return this.fieldSchema.description || "";
+    },
+
+    // Field-level unit extraction from uiSchema (RJSF format)
+    get unit() {
+      return this.uiSchema?.[this.fieldName]?.["ui:unit"] || null;
+    },
+
+    // Mode checks
+    get isViewMode() {
+      return this.mode === "view";
+    },
+    get isEditMode() {
+      return this.mode === "edit";
+    },
+  });
+
+  // Text widget
+  Alpine.data(
+    "textWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get value() {
+        return this.data[this.fieldName] || "";
+      },
+      set value(v) {
+        this.data[this.fieldName] = v;
+      },
+    }),
+  );
+
+  // Textarea widget
+  Alpine.data(
+    "textareaWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get value() {
+        return this.data[this.fieldName] || "";
+      },
+      set value(v) {
+        this.data[this.fieldName] = v;
+      },
+    }),
+  );
+
+  // Number widget with unit support
+  Alpine.data(
+    "numberWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get value() {
+        return this.data[this.fieldName];
+      },
+      set value(v) {
+        this.data[this.fieldName] =
+          v === "" || v === null ? null : parseFloat(v);
+      },
+      get hasValue() {
+        return (
+          this.value !== null && this.value !== undefined && this.value !== ""
+        );
+      },
+      // Format value with unit for view mode
+      get displayValue() {
+        if (!this.hasValue) return "—";
+        return this.unit ? `${this.value} ${this.unit}` : String(this.value);
+      },
+    }),
+  );
+
+  // Select widget
+  Alpine.data(
+    "selectWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get value() {
+        return this.data[this.fieldName] || "";
+      },
+      set value(v) {
+        this.data[this.fieldName] = v;
+      },
+      get options() {
+        return this.fieldSchema.enum || [];
+      },
+    }),
+  );
+
+  // Checkbox widget
+  Alpine.data(
+    "checkboxWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get checked() {
+        return !!this.data[this.fieldName];
+      },
+      set checked(v) {
+        this.data[this.fieldName] = v;
+      },
+    }),
+  );
+
+  // Interval widget with unit support
+  Alpine.data(
+    "intervalWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get start() {
+        return this.data[this.fieldName]?.start ?? null;
+      },
+      set start(v) {
+        if (!this.data[this.fieldName]) this.data[this.fieldName] = {};
+        this.data[this.fieldName].start =
+          v === "" || v === null ? null : parseFloat(v);
+      },
+      get end() {
+        return this.data[this.fieldName]?.end ?? null;
+      },
+      set end(v) {
+        if (!this.data[this.fieldName]) this.data[this.fieldName] = {};
+        this.data[this.fieldName].end =
+          v === "" || v === null ? null : parseFloat(v);
+      },
+      // Format interval with unit for view mode
+      get displayValue() {
+        const s = this.start,
+          e = this.end;
+        const unitStr = this.unit ? ` ${this.unit}` : "";
+
+        if (s !== null && e !== null) return `${s} – ${e}${unitStr}`;
+        if (s !== null) return `≥ ${s}${unitStr}`;
+        if (e !== null) return `≤ ${e}${unitStr}`;
+        return "—";
+      },
+
+      get isSameValue() {
+        return this.start !== null && this.start === this.end;
+      },
+
+      // Validation: start must be <= end (client-side)
+      get hasValidationError() {
+        if (this.isViewMode) return false;
+        const s = this.start;
+        const e = this.end;
+        // Only validate if both values are provided
+        if (
+          s !== null &&
+          e !== null &&
+          typeof s === "number" &&
+          typeof e === "number"
+        ) {
+          return s > e;
+        }
+        return false;
+      },
+    }),
+  );
+
+  // PubMed link widget
+  Alpine.data(
+    "pubmedWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get value() {
+        return this.data[this.fieldName] || "";
+      },
+      set value(v) {
+        this.data[this.fieldName] = v;
+      },
+      get pubmedUrl() {
+        return this.value
+          ? `https://pubmed.ncbi.nlm.nih.gov/${this.value}`
+          : null;
+      },
+    }),
+  );
+
+  // Compound link widget
+  Alpine.data(
+    "compoundWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get value() {
+        return this.data[this.fieldName] || "";
+      },
+      set value(v) {
+        this.data[this.fieldName] = v;
+      },
+    }),
+  );
+
+  // TimeSeries table widget
+  Alpine.data(
+    "timeseriesTableWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      chartInstance: null,
+
+      // Getter/setter for measurements array
+      get measurements() {
+        return this.data[this.fieldName] || [];
+      },
+      set measurements(v) {
+        this.data[this.fieldName] = v;
+      },
+
+      // Get description from sibling field
+      get description() {
+        return this.data?.description || "";
+      },
+
+      // Get method from sibling field
+      get method() {
+        return this.data?.method || "";
+      },
+
+      // Computed property for chart options
+      get chartOptions() {
+        return {
+          measurements: this.measurements,
+          xAxisLabel: this.data?.x_axis_label || "Time",
+          yAxisLabel: this.data?.y_axis_label || "Value",
+          xAxisUnit: this.data?.x_axis_unit || "",
+          yAxisUnit: this.data?.y_axis_unit || "",
+        };
+      },
+
+      // Add new measurement
+      addMeasurement() {
+        if (!this.data[this.fieldName]) {
+          this.data[this.fieldName] = [];
+        }
+        this.data[this.fieldName].push({
+          timestamp: null,
+          value: null,
+          error: null,
+          note: "",
+        });
+      },
+
+      // Remove measurement by index
+      removeMeasurement(index) {
+        if (
+          this.data[this.fieldName] &&
+          Array.isArray(this.data[this.fieldName])
+        ) {
+          this.data[this.fieldName].splice(index, 1);
+        }
+      },
+
+      // Update specific measurement field
+      updateMeasurement(index, field, value) {
+        if (this.data[this.fieldName] && this.data[this.fieldName][index]) {
+          if (field === "timestamp" || field === "value" || field === "error") {
+            // Parse all numeric fields (timestamp is days as float)
+            this.data[this.fieldName][index][field] =
+              value === "" || value === null ? null : parseFloat(value);
+          } else {
+            // Store other fields as-is
+            this.data[this.fieldName][index][field] = value;
+          }
+        }
+      },
+
+      // Format timestamp for display (timestamp is numeric days as float)
+      formatTimestamp(timestamp) {
+        return timestamp ?? "";
+      },
+
+      // Sort by timestamp (numeric days)
+      sortByTimestamp() {
+        if (
+          this.data[this.fieldName] &&
+          Array.isArray(this.data[this.fieldName])
+        ) {
+          this.data[this.fieldName].sort((a, b) => {
+            const tsA = a.timestamp ?? Infinity;
+            const tsB = b.timestamp ?? Infinity;
+            return tsA - tsB;
+          });
+        }
+      },
+
+      // Chart lifecycle methods (delegates to TimeSeriesChart utility)
+      initChart() {
+        if (!this.isViewMode || !window.Chart || !window.TimeSeriesChart)
+          return;
+
+        const canvas = this.$refs?.chartCanvas;
+        if (!canvas) return;
+
+        this.destroyChart();
+
+        if (this.measurements.length === 0) return;
+
+        this.chartInstance = window.TimeSeriesChart.create(
+          canvas,
+          this.chartOptions,
+        );
+      },
+
+      updateChart() {
+        if (!this.chartInstance || !this.isViewMode) return;
+        window.TimeSeriesChart.update(
+          this.chartInstance,
+          this.measurements,
+          this.chartOptions,
+        );
+      },
+
+      destroyChart() {
+        if (this.chartInstance) {
+          window.TimeSeriesChart.destroy(this.chartInstance);
+          this.chartInstance = null;
+        }
+      },
+
+      // Alpine lifecycle hooks
+      init() {
+        if (this.isViewMode && window.Chart) {
+          // Use $nextTick to ensure DOM is ready
+          this.$nextTick(() => {
+            this.initChart();
+          });
+
+          // Watch measurements array for changes and update chart
+          this.$watch("data." + this.fieldName, () => {
+            if (this.chartInstance) {
+              this.updateChart();
+            }
+          });
+        }
+      },
+    }),
+  );
+});

static/js/alpine/pathway.js

@@ -21,6 +21,7 @@ document.addEventListener('alpine:init', () => {
   Alpine.data('pathwayViewer', (config) => ({
     status: config.status,
     modified: config.modified,
+    modifiedDate: null,
     statusUrl: config.statusUrl,
     emptyDueToThreshold: config.emptyDueToThreshold === "True",
     showUpdateNotice: false,
@@ -39,6 +40,8 @@ document.addEventListener('alpine:init', () => {
     },
 
     init() {
+      this.modifiedDate = this.parseDate(this.modified);
+
       if (this.status === 'running') {
         this.startPolling();
       }
@@ -66,26 +69,39 @@ document.addEventListener('alpine:init', () => {
           this.showEmptyDueToThresholdNotice = true;
         }
 
-        if (data.modified > this.modified) {
-          if (!this.emptyDueToThreshold) {
-            this.showUpdateNotice = true;
-            this.updateMessage = this.getUpdateMessage(data.status);
-          }
+        const nextModifiedDate = this.parseDate(data.modified);
+        const modifiedChanged = this.hasNewerTimestamp(nextModifiedDate, this.modifiedDate);
+        const statusChanged = data.status !== this.status;
+
+        if ((modifiedChanged || statusChanged) && !this.emptyDueToThreshold) {
+          this.showUpdateNotice = true;
+          this.updateMessage = this.getUpdateMessage(data.status, modifiedChanged, statusChanged);
         }
 
-        if (data.status !== 'running') {
-          this.status = data.status;
-          if (this.pollInterval) {
-            clearInterval(this.pollInterval);
-            this.pollInterval = null;
-          }
+        this.modified = data.modified;
+        this.modifiedDate = nextModifiedDate;
+        this.status = data.status;
+
+        if (data.status !== 'running' && this.pollInterval) {
+          clearInterval(this.pollInterval);
+          this.pollInterval = null;
         }
       } catch (err) {
         console.error('Polling error:', err);
       }
     },
 
-    getUpdateMessage(status) {
+    getUpdateMessage(status, modifiedChanged, statusChanged) {
+      // Prefer explicit status change messaging, otherwise fall back to modified change copy
+      if (statusChanged) {
+        if (status === 'completed') {
+          return 'Prediction completed. Reload the page to see the updated Pathway.';
+        }
+        if (status === 'failed') {
+          return 'Prediction failed. Reload the page to see the latest status.';
+        }
+      }
+
       let msg = 'Prediction ';
 
       if (status === 'running') {
@@ -99,6 +115,18 @@ document.addEventListener('alpine:init', () => {
       return msg;
     },
 
+    parseDate(dateString) {
+      // Normalize "YYYY-MM-DD HH:mm:ss" into an ISO-compatible string to avoid locale issues
+      if (!dateString) return null;
+      return new Date(dateString.replace(' ', 'T'));
+    },
+
+    hasNewerTimestamp(nextDate, currentDate) {
+      if (!nextDate) return false;
+      if (!currentDate) return true;
+      return nextDate.getTime() > currentDate.getTime();
+    },
+
     reloadPage() {
       location.reload();
     }

static/js/api/additional-information.js

@@ -0,0 +1,419 @@
+/**
+ * Unified API client for Additional Information endpoints
+ * Provides consistent error handling, logging, and CRUD operations
+ */
+window.AdditionalInformationApi = {
+  // Configuration
+  _debug: false,
+
+  /**
+   * Enable or disable debug logging
+   * @param {boolean} enabled - Whether to enable debug mode
+   */
+  setDebug(enabled) {
+    this._debug = enabled;
+  },
+
+  /**
+   * Internal logging helper
+   * @private
+   */
+  _log(action, data) {
+    if (this._debug) {
+      console.log(`[AdditionalInformationApi] ${action}:`, data);
+    }
+  },
+  //FIXME: this has the side effect of users not being able to explicitly set an empty string for a field.
+  /**
+   * Remove empty strings from payload recursively
+   * @param {any} value
+   * @returns {any}
+   */
+  sanitizePayload(value) {
+    if (Array.isArray(value)) {
+      return value
+        .map((item) => this.sanitizePayload(item))
+        .filter((item) => item !== "");
+    }
+
+    if (value && typeof value === "object") {
+      const cleaned = {};
+      for (const [key, item] of Object.entries(value)) {
+        if (item === "") continue;
+        cleaned[key] = this.sanitizePayload(item);
+      }
+      return cleaned;
+    }
+
+    return value;
+  },
+
+  /**
+   * Get CSRF token from meta tag
+   * @returns {string} CSRF token
+   */
+  getCsrfToken() {
+    return document.querySelector("[name=csrf-token]")?.content || "";
+  },
+
+  /**
+   * Build headers for API requests
+   * @private
+   */
+  _buildHeaders(includeContentType = true) {
+    const headers = {
+      "X-CSRFToken": this.getCsrfToken(),
+    };
+    if (includeContentType) {
+      headers["Content-Type"] = "application/json";
+    }
+    return headers;
+  },
+
+  /**
+   * Handle API response with consistent error handling
+   * @private
+   */
+  async _handleResponse(response, action) {
+    if (!response.ok) {
+      let errorData;
+      try {
+        errorData = await response.json();
+      } catch {
+        errorData = { error: response.statusText };
+      }
+
+      // Try to parse the error if it's a JSON string
+      let parsedError = errorData;
+      const errorStr = errorData.detail || errorData.error;
+      if (typeof errorStr === "string" && errorStr.startsWith("{")) {
+        try {
+          parsedError = JSON.parse(errorStr);
+        } catch {
+          // Not JSON, use as-is
+        }
+      }
+
+      // If it's a structured validation error, throw with field errors
+      if (parsedError.type === "validation_error" && parsedError.field_errors) {
+        this._log(`${action} VALIDATION ERROR`, parsedError);
+        const error = new Error(parsedError.message || "Validation failed");
+        error.fieldErrors = parsedError.field_errors;
+        error.isValidationError = true;
+        throw error;
+      }
+
+      // General error
+      const errorMsg =
+        parsedError.message ||
+        parsedError.error ||
+        parsedError.detail ||
+        `${action} failed: ${response.statusText}`;
+      this._log(`${action} ERROR`, {
+        status: response.status,
+        error: errorMsg,
+      });
+      throw new Error(errorMsg);
+    }
+
+    const data = await response.json();
+    this._log(`${action} SUCCESS`, data);
+    return data;
+  },
+
+  /**
+   * Load all available schemas
+   * @returns {Promise<Object>} Object with schema definitions
+   */
+  async loadSchemas() {
+    this._log("loadSchemas", "Starting...");
+    const response = await fetch("/api/v1/information/schema/");
+    return this._handleResponse(response, "loadSchemas");
+  },
+
+  /**
+   * Load additional information items for a scenario
+   * @param {string} scenarioUuid - UUID of the scenario
+   * @returns {Promise<Array>} Array of additional information items
+   */
+  async loadItems(scenarioUuid) {
+    this._log("loadItems", { scenarioUuid });
+    const response = await fetch(
+      `/api/v1/scenario/${scenarioUuid}/information/`,
+    );
+    return this._handleResponse(response, "loadItems");
+  },
+
+  /**
+   * Load both schemas and items in parallel
+   * @param {string} scenarioUuid - UUID of the scenario
+   * @returns {Promise<{schemas: Object, items: Array}>}
+   */
+  async loadSchemasAndItems(scenarioUuid) {
+    this._log("loadSchemasAndItems", { scenarioUuid });
+
+    const [schemas, items] = await Promise.all([
+      this.loadSchemas(),
+      this.loadItems(scenarioUuid),
+    ]);
+
+    return { schemas, items };
+  },
+
+  /**
+   * Create new additional information for a scenario
+   * @param {string} scenarioUuid - UUID of the scenario
+   * @param {string} modelName - Name/type of the additional information model
+   * @param {Object} data - Data for the new item
+   * @returns {Promise<{status: string, uuid: string}>}
+   */
+  async createItem(scenarioUuid, modelName, data) {
+    const sanitizedData = this.sanitizePayload(data);
+    this._log("createItem", { scenarioUuid, modelName, data: sanitizedData });
+
+    // Normalize model name to lowercase
+    const normalizedName = modelName.toLowerCase();
+
+    const response = await fetch(
+      `/api/v1/scenario/${scenarioUuid}/information/${normalizedName}/`,
+      {
+        method: "POST",
+        headers: this._buildHeaders(),
+        body: JSON.stringify(sanitizedData),
+      },
+    );
+
+    return this._handleResponse(response, "createItem");
+  },
+
+  /**
+   * Delete additional information from a scenario
+   * @param {string} scenarioUuid - UUID of the scenario
+   * @param {string} itemUuid - UUID of the item to delete
+   * @returns {Promise<{status: string}>}
+   */
+  async deleteItem(scenarioUuid, itemUuid) {
+    this._log("deleteItem", { scenarioUuid, itemUuid });
+
+    const response = await fetch(
+      `/api/v1/scenario/${scenarioUuid}/information/item/${itemUuid}/`,
+      {
+        method: "DELETE",
+        headers: this._buildHeaders(false),
+      },
+    );
+
+    return this._handleResponse(response, "deleteItem");
+  },
+
+  /**
+   * Update existing additional information
+   * Tries PATCH first, falls back to delete+recreate if not supported
+   * @param {string} scenarioUuid - UUID of the scenario
+   * @param {Object} item - Item object with uuid, type, and data properties
+   * @returns {Promise<{status: string, uuid: string}>}
+   */
+  async updateItem(scenarioUuid, item) {
+    const sanitizedData = this.sanitizePayload(item.data);
+    this._log("updateItem", {
+      scenarioUuid,
+      item: { ...item, data: sanitizedData },
+    });
+
+    const { uuid, type } = item;
+
+    // Try PATCH first (preferred method - preserves UUID)
+    const response = await fetch(
+      `/api/v1/scenario/${scenarioUuid}/information/item/${uuid}/`,
+      {
+        method: "PATCH",
+        headers: this._buildHeaders(),
+        body: JSON.stringify(sanitizedData),
+      },
+    );
+
+    if (response.status === 405) {
+      // PATCH not supported, fall back to delete+recreate
+      this._log(
+        "updateItem",
+        "PATCH not supported, falling back to delete+recreate",
+      );
+      await this.deleteItem(scenarioUuid, uuid);
+      return await this.createItem(scenarioUuid, type, sanitizedData);
+    }
+
+    return this._handleResponse(response, "updateItem");
+  },
+
+  /**
+   * Update multiple items sequentially to avoid race conditions
+   * @param {string} scenarioUuid - UUID of the scenario
+   * @param {Array<Object>} items - Array of items to update
+   * @returns {Promise<Array>} Array of results with success status
+   */
+  async updateItems(scenarioUuid, items) {
+    this._log("updateItems", { scenarioUuid, itemCount: items.length });
+
+    const results = [];
+    for (const item of items) {
+      try {
+        const result = await this.updateItem(scenarioUuid, item);
+        results.push({
+          success: true,
+          oldUuid: item.uuid,
+          newUuid: result.uuid,
+        });
+      } catch (error) {
+        results.push({
+          success: false,
+          oldUuid: item.uuid,
+          error: error.message,
+          fieldErrors: error.fieldErrors,
+          isValidationError: error.isValidationError,
+        });
+      }
+    }
+
+    const failed = results.filter((r) => !r.success);
+    if (failed.length > 0) {
+      // If all failures are validation errors, return all validation errors for display
+      const validationErrors = failed.filter((f) => f.isValidationError);
+      if (validationErrors.length === failed.length) {
+        // All failures are validation errors - return all field errors by item UUID
+        const allFieldErrors = {};
+        validationErrors.forEach((ve) => {
+          allFieldErrors[ve.oldUuid] = ve.fieldErrors || {};
+        });
+        const error = new Error(
+          `${failed.length} item(s) have validation errors. Please correct them.`,
+        );
+        error.fieldErrors = allFieldErrors; // Map of UUID -> field errors
+        error.isValidationError = true;
+        error.isMultipleErrors = true; // Flag indicating multiple items have errors
+        throw error;
+      }
+      // Multiple failures or mixed errors - show count
+      throw new Error(
+        `Failed to update ${failed.length} item(s). Please check the form for errors.`,
+      );
+    }
+
+    return results;
+  },
+
+  /**
+   * Create a new scenario with optional additional information
+   * @param {string} packageUuid - UUID of the package
+   * @param {Object} payload - Scenario data matching ScenarioCreateSchema
+   * @param {string} payload.name - Scenario name (required)
+   * @param {string} payload.description - Scenario description (optional, default: "")
+   * @param {string} payload.scenario_date - Scenario date (optional, default: "No date")
+   * @param {string} payload.scenario_type - Scenario type (optional, default: "Not specified")
+   * @param {Array} payload.additional_information - Array of additional information (optional, default: [])
+   * @returns {Promise<{uuid, url, name, description, review_status, package}>}
+   */
+  async createScenario(packageUuid, payload) {
+    this._log("createScenario", { packageUuid, payload });
+    const response = await fetch(`/api/v1/package/${packageUuid}/scenario/`, {
+      method: "POST",
+      headers: this._buildHeaders(),
+      body: JSON.stringify(payload),
+    });
+    return this._handleResponse(response, "createScenario");
+  },
+
+  /**
+   * Load all available group names
+   * @returns {Promise<{groups: string[]}>}
+   */
+  async loadGroups() {
+    this._log("loadGroups", "Starting...");
+    const response = await fetch("/api/v1/information/groups/");
+    return this._handleResponse(response, "loadGroups");
+  },
+
+  /**
+   * Load model definitions for a specific group
+   * @param {string} groupName - One of 'soil', 'sludge', 'sediment'
+   * @returns {Promise<Object>} Object with subcategories as keys and arrays of model info
+   */
+  async loadGroupModels(groupName) {
+    this._log("loadGroupModels", { groupName });
+    const response = await fetch(`/api/v1/information/groups/${groupName}/`);
+    return this._handleResponse(response, `loadGroupModels-${groupName}`);
+  },
+
+  /**
+   * Load model information for multiple groups in parallel
+   * @param {Array<string>} groupNames - Defaults to ['soil', 'sludge', 'sediment']
+   * @returns {Promise<Object>} Object with group names as keys
+   */
+  async loadGroupsWithModels(groupNames = ["soil", "sludge", "sediment"]) {
+    this._log("loadGroupsWithModels", { groupNames });
+
+    const results = {};
+    const promises = groupNames.map(async (groupName) => {
+      try {
+        results[groupName] = await this.loadGroupModels(groupName);
+      } catch (err) {
+        this._log(`loadGroupsWithModels-${groupName} ERROR`, err);
+        results[groupName] = {};
+      }
+    });
+
+    await Promise.all(promises);
+    return results;
+  },
+
+  /**
+   * Helper to organize schemas by group based on group model information
+   * @param {Object} schemas - Full schema map from loadSchemas()
+   * @param {Object} groupModelsData - Group models data from loadGroupsWithModels()
+   * @returns {Object} Object with group names as keys and filtered schemas as values
+   */
+  organizeSchemasByGroup(schemas, groupModelsData) {
+    this._log("organizeSchemasByGroup", {
+      schemaCount: Object.keys(schemas).length,
+      groupCount: Object.keys(groupModelsData).length,
+    });
+
+    const organized = {};
+
+    for (const groupName in groupModelsData) {
+      organized[groupName] = {};
+      const groupData = groupModelsData[groupName];
+
+      // Iterate through subcategories in the group
+      for (const subcategory in groupData) {
+        for (const model of groupData[subcategory]) {
+          // Look up schema by lowercase model name
+          if (schemas[model.name]) {
+            organized[groupName][model.name] = schemas[model.name];
+          }
+        }
+      }
+    }
+
+    return organized;
+  },
+
+  /**
+   * Convenience method that loads schemas and organizes them by group in one call
+   * @param {Array<string>} groupNames - Defaults to ['soil', 'sludge', 'sediment']
+   * @returns {Promise<{schemas, groupSchemas, groupModels}>}
+   */
+  async loadSchemasWithGroups(groupNames = ["soil", "sludge", "sediment"]) {
+    this._log("loadSchemasWithGroups", { groupNames });
+
+    // Load schemas and all groups in parallel
+    const [schemas, groupModels] = await Promise.all([
+      this.loadSchemas(),
+      this.loadGroupsWithModels(groupNames),
+    ]);
+
+    // Organize schemas by group
+    const groupSchemas = this.organizeSchemasByGroup(schemas, groupModels);
+
+    return { schemas, groupSchemas, groupModels };
+  },
+};

static/js/pw.js

@@ -361,6 +361,83 @@ function draw(pathway, elem) {
 
     function node_popup(n) {
         popupContent = "";
+
+        if (timeseriesViewEnabled && n.timeseries && n.timeseries.measurements) {
+            for (var s of n.scenarios) {
+                popupContent += "<a href='" + s.url + "'>" + s.name + "</a><br>";
+            }
+
+            popupContent += '<div style="width:100%;height:120px"><canvas id="ts-popover-canvas"></canvas></div>';
+            const tsMeasurements = n.timeseries.measurements;
+            setTimeout(() => {
+                const canvas = document.getElementById('ts-popover-canvas');
+                if (canvas && window.Chart) {
+                    const valid = tsMeasurements
+                        .filter(m => m.timestamp != null && m.value != null)
+                        .map(m => ({ ...m, timestamp: typeof m.timestamp === 'number' ? m.timestamp : new Date(m.timestamp).getTime() }))
+                        .sort((a, b) => a.timestamp - b.timestamp);
+
+                    const datasets = [];
+
+                    // Error band (lower + upper with fill between)
+                    const withErrors = valid.filter(m => m.error != null && m.error > 0);
+                    if (withErrors.length > 0) {
+                        datasets.push({
+                            data: withErrors.map(m => ({ x: m.timestamp, y: m.value - m.error })),
+                            borderColor: 'rgba(59,130,246,0.3)',
+                            backgroundColor: 'rgba(59,130,246,0.15)',
+                            pointRadius: 0,
+                            fill: false,
+                            tension: 0.1,
+                        });
+                        datasets.push({
+                            data: withErrors.map(m => ({ x: m.timestamp, y: m.value + m.error })),
+                            borderColor: 'rgba(59,130,246,0.3)',
+                            backgroundColor: 'rgba(59,130,246,0.15)',
+                            pointRadius: 0,
+                            fill: '-1',
+                            tension: 0.1,
+                        });
+                    }
+
+                    // Main value line
+                    datasets.push({
+                        data: valid.map(m => ({ x: m.timestamp, y: m.value })),
+                        borderColor: 'rgb(59,130,246)',
+                        pointRadius: 0,
+                        tension: 0.1,
+                        fill: false,
+                    });
+
+                    new Chart(canvas.getContext('2d'), {
+                        type: 'line',
+                        data: { datasets },
+                        options: {
+                            responsive: true,
+                            maintainAspectRatio: false,
+                            plugins: {
+                                legend: { display: false },
+                                tooltip: { enabled: false },
+                            },
+                            scales: {
+                                x: {
+                                    type: 'linear',
+                                    ticks: { font: { size: 10 } },
+                                    title: { display: false },
+                                },
+                                y: {
+                                    ticks: { font: { size: 10 } },
+                                    title: { display: false },
+                                },
+                            },
+                        },
+                    });
+                }
+            }, 0);
+
+            return popupContent;
+        }
+
         if (n.stereo_removed) {
             popupContent += "<span class='alert alert-warning alert-soft'>Removed stereochemistry for prediction</span>";
         }
@@ -393,7 +470,14 @@ function draw(pathway, elem) {
     }
 
     function edge_popup(e) {
-        popupContent = "<a href='" + e.url + "'>" + e.name + "</a><br>";
+        popupContent = "<a href='" + e.url + "'>" + e.name + "</a><br><br>";
+
+        if (e.reaction.rules) {
+            console.log(e.reaction.rules);
+            for (var rule of e.reaction.rules) {
+                popupContent += "Rule <a href='" + rule.url + "'>" + rule.name + "</a><br>";
+            }
+        }
 
         if (e.app_domain) {
             adcontent = "<p>";
@@ -498,7 +582,8 @@ function draw(pathway, elem) {
         .enter().append("line")
         // Check if target is pseudo and draw marker only if not pseudo
         .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-        .attr("marker-end", d => d.target.pseudo ? '' : 'url(#arrow)')
+        .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
+
 
     // add element to links array
     link.each(function (d) {

static/js/utils/timeseries-chart.js

@@ -0,0 +1,351 @@
+/**
+ * TimeSeriesChart Utility
+ *
+ * Provides chart rendering capabilities for time series data with error bounds.
+ * Uses Chart.js to create interactive and static visualizations.
+ *
+ * Usage:
+ *   const chart = window.TimeSeriesChart.create(canvas, {
+ *     measurements: [...],
+ *     xAxisLabel: "Time",
+ *     yAxisLabel: "Concentration",
+ *     xAxisUnit: "days",
+ *     yAxisUnit: "mg/L"
+ *   });
+ *
+ *   window.TimeSeriesChart.update(chart, newMeasurements, options);
+ *   window.TimeSeriesChart.destroy(chart);
+ */
+window.TimeSeriesChart = {
+  // === PUBLIC API ===
+
+  /**
+   * Create an interactive time series chart
+   *
+   * @param {HTMLCanvasElement} canvas - Canvas element to render chart on
+   * @param {Object} options - Chart configuration options
+   * @param {Array} options.measurements - Array of measurement objects with timestamp, value, error, note
+   * @param {string} options.xAxisLabel - Label for x-axis (default: "Time")
+   * @param {string} options.yAxisLabel - Label for y-axis (default: "Value")
+   * @param {string} options.xAxisUnit - Unit for x-axis (default: "")
+   * @param {string} options.yAxisUnit - Unit for y-axis (default: "")
+   * @returns {Chart|null} Chart.js instance or null if creation failed
+   */
+  create(canvas, options = {}) {
+    if (!this._validateCanvas(canvas)) return null;
+    if (!window.Chart) {
+      console.warn("Chart.js is not loaded");
+      return null;
+    }
+
+    const ctx = canvas.getContext("2d");
+    if (!ctx) return null;
+
+    const chartData = this._transformData(options.measurements || [], options);
+
+    if (chartData.datasets.length === 0) {
+      return null; // No data to display
+    }
+
+    const config = this._buildConfig(chartData, options);
+
+    return new Chart(ctx, config);
+  },
+
+  /**
+   * Update an existing chart with new data
+   *
+   * @param {Chart} chartInstance - Chart.js instance to update
+   * @param {Array} measurements - New measurements array
+   * @param {Object} options - Chart configuration options
+   */
+  update(chartInstance, measurements, options = {}) {
+    if (!chartInstance) return;
+
+    const chartData = this._transformData(measurements || [], options);
+
+    chartInstance.data.datasets = chartData.datasets;
+    chartInstance.options.scales.x.title.text = chartData.xAxisLabel;
+    chartInstance.options.scales.y.title.text = chartData.yAxisLabel;
+    chartInstance.update("none");
+  },
+
+  /**
+   * Destroy chart instance and cleanup
+   *
+   * @param {Chart} chartInstance - Chart.js instance to destroy
+   */
+  destroy(chartInstance) {
+    if (chartInstance && typeof chartInstance.destroy === "function") {
+      chartInstance.destroy();
+    }
+  },
+
+  // === PRIVATE HELPERS ===
+
+  /**
+   * Transform measurements into Chart.js datasets
+   * @private
+   */
+  _transformData(measurements, options) {
+    const preparedData = this._prepareData(measurements);
+
+    if (preparedData.length === 0) {
+      return { datasets: [], xAxisLabel: "Time", yAxisLabel: "Value" };
+    }
+
+    const xAxisLabel = options.xAxisLabel || "Time";
+    const yAxisLabel = options.yAxisLabel || "Value";
+    const xAxisUnit = options.xAxisUnit || "";
+    const yAxisUnit = options.yAxisUnit || "";
+
+    const datasets = [];
+
+    // Error bounds datasets FIRST (if errors exist) - renders as background
+    const errorDatasets = this._buildErrorDatasets(preparedData);
+    if (errorDatasets.length > 0) {
+      datasets.push(...errorDatasets);
+    }
+
+    // Main line dataset LAST - renders on top
+    datasets.push(this._buildMainDataset(preparedData, yAxisLabel));
+
+    return {
+      datasets: datasets,
+      xAxisLabel: this._formatAxisLabel(xAxisLabel, xAxisUnit),
+      yAxisLabel: this._formatAxisLabel(yAxisLabel, yAxisUnit),
+    };
+  },
+
+  /**
+   * Prepare and validate measurements data
+   * @private
+   */
+  _prepareData(measurements) {
+    return measurements
+      .filter(
+        (m) => m.timestamp != null && m.value != null,
+      )
+      .map((m) => {
+        // Normalize timestamp - handle both numeric and date strings
+        let timestamp;
+        if (typeof m.timestamp === "number") {
+          timestamp = m.timestamp;
+        } else {
+          timestamp = new Date(m.timestamp).getTime();
+        }
+        return {
+          ...m,
+          timestamp: timestamp,
+        };
+      })
+      .sort((a, b) => a.timestamp - b.timestamp);
+  },
+
+  /**
+   * Build main line dataset
+   * @private
+   */
+  _buildMainDataset(validMeasurements, yAxisLabel) {
+    return {
+      label: yAxisLabel,
+      data: validMeasurements.map((m) => ({
+        x: m.timestamp,
+        y: m.value,
+        error: m.error || null,
+      })),
+      borderColor: "rgb(59, 130, 246)",
+      backgroundColor: "rgba(59, 130, 246, 0.1)",
+      tension: 0.1,
+      pointRadius: 0, // Hide individual points
+      pointHoverRadius: 6,
+      fill: false,
+    };
+  },
+
+  /**
+   * Build error bound datasets (upper and lower)
+   * @private
+   */
+  _buildErrorDatasets(validMeasurements) {
+    const hasErrors = validMeasurements.some(
+      (m) => m.error !== null && m.error !== undefined && m.error > 0,
+    );
+
+    if (!hasErrors) return [];
+
+    const measurementsWithErrors = validMeasurements.filter(
+      (m) => m.error !== null && m.error !== undefined && m.error > 0,
+    );
+
+    return [
+      // Lower error bound - FIRST (bottom layer)
+      {
+        label: "Error (lower)",
+        data: measurementsWithErrors.map((m) => ({
+          x: m.timestamp,
+          y: m.value - m.error,
+        })),
+        borderColor: "rgba(59, 130, 246, 0.3)",
+        backgroundColor: "rgba(59, 130, 246, 0.15)",
+        pointRadius: 0,
+        fill: false,
+        tension: 0.1,
+      },
+      // Upper error bound - SECOND (fill back to lower)
+      {
+        label: "Error (upper)",
+        data: measurementsWithErrors.map((m) => ({
+          x: m.timestamp,
+          y: m.value + m.error,
+        })),
+        borderColor: "rgba(59, 130, 246, 0.3)",
+        backgroundColor: "rgba(59, 130, 246, 0.15)",
+        pointRadius: 0,
+        fill: "-1", // Fill back to previous dataset (lower bound)
+        tension: 0.1,
+      },
+    ];
+  },
+
+  /**
+   * Build complete Chart.js configuration
+   * @private
+   */
+  _buildConfig(chartData, options) {
+    return {
+      type: "line",
+      data: { datasets: chartData.datasets },
+      options: {
+        responsive: true,
+        maintainAspectRatio: false,
+        interaction: {
+          intersect: false,
+          mode: "index",
+        },
+        plugins: {
+          legend: {
+            display: false,
+          },
+          tooltip: this._buildTooltipConfig(
+            options.xAxisUnit || "",
+            options.yAxisUnit || "",
+          ),
+        },
+        scales: this._buildScalesConfig(
+          chartData.xAxisLabel,
+          chartData.yAxisLabel,
+        ),
+      },
+    };
+  },
+
+  /**
+   * Build tooltip configuration with custom callbacks
+   * @private
+   */
+  _buildTooltipConfig(xAxisUnit, yAxisUnit) {
+    return {
+      enabled: true,
+      callbacks: {
+        title: (contexts) => {
+          // Show timestamp
+          const context = contexts[0];
+          if (!context) return "Measurement";
+          const timestamp = context.parsed.x;
+          return xAxisUnit
+            ? `Time: ${timestamp} ${xAxisUnit}`
+            : `Time: ${timestamp}`;
+        },
+        label: (context) => {
+          // Show value with unit
+          try {
+            const value = context.parsed.y;
+            if (value === null || value === undefined) {
+              return `${context.dataset.label || "Value"}: N/A`;
+            }
+
+            const valueStr = yAxisUnit
+              ? `${value} ${yAxisUnit}`
+              : String(value);
+            return `${context.dataset.label || "Value"}: ${valueStr}`;
+          } catch (e) {
+            console.error("Tooltip label error:", e);
+            return `${context.dataset.label || "Value"}: ${context.parsed.y ?? "N/A"}`;
+          }
+        },
+        afterLabel: (context) => {
+          // Show error information
+          try {
+            const point = context.raw;
+            // Main line is now the last dataset (after error bounds if they exist)
+            const isMainDataset = context.dataset.label &&
+                                 !context.dataset.label.startsWith("Error");
+            if (!point || !isMainDataset) return null;
+
+            const lines = [];
+
+            // Show error if available
+            if (
+              point.error !== null &&
+              point.error !== undefined &&
+              point.error > 0
+            ) {
+              const errorStr = yAxisUnit
+                ? `±${point.error.toFixed(4)} ${yAxisUnit}`
+                : `±${point.error.toFixed(4)}`;
+              lines.push(`Error: ${errorStr}`);
+            }
+
+            return lines.length > 0 ? lines : null;
+          } catch (e) {
+            console.error("Tooltip afterLabel error:", e);
+            return null;
+          }
+        },
+      },
+    };
+  },
+
+  /**
+   * Build scales configuration
+   * @private
+   */
+  _buildScalesConfig(xAxisLabel, yAxisLabel) {
+    return {
+      x: {
+        type: "linear",
+        title: {
+          display: true,
+          text: xAxisLabel || "Time",
+        },
+      },
+      y: {
+        title: {
+          display: true,
+          text: yAxisLabel || "Value",
+        },
+      },
+    };
+  },
+
+  /**
+   * Format axis label with unit
+   * @private
+   */
+  _formatAxisLabel(label, unit) {
+    return unit ? `${label} (${unit})` : label;
+  },
+
+  /**
+   * Validate canvas element
+   * @private
+   */
+  _validateCanvas(canvas) {
+    if (!canvas || !(canvas instanceof HTMLCanvasElement)) {
+      console.warn("Invalid canvas element provided to TimeSeriesChart");
+      return false;
+    }
+    return true;
+  },
+};

templates/actions/objects/scenario.html

@@ -1,4 +1,12 @@
 {% if meta.can_edit %}
+  <li>
+    <a
+      class="button"
+      onclick="document.getElementById('edit_scenario_modal').showModal(); return false;"
+    >
+      <i class="glyphicon glyphicon-trash"></i> Edit Scenario</a
+    >
+  </li>
   <li>
     <a
       class="button"

templates/collections/paginated_base.html

@@ -98,7 +98,7 @@
           class="mt-6"
           x-show="activeTab === 'reviewed' && !isEmpty"
           x-data="remotePaginatedList({
-              endpoint: '{{ api_endpoint }}?review_status=true',
+              endpoint: '{{ api_endpoint }}?review_status=true{% if entity_type == 'scenario' %}&exclude_related=true{% endif %}',
               instanceId: '{{ entity_type }}_reviewed',
               isReviewed: true,
               perPage: {{ per_page|default:50 }}
@@ -113,7 +113,7 @@
           class="mt-6"
           x-show="activeTab === 'unreviewed' && !isEmpty"
           x-data="remotePaginatedList({
-              endpoint: '{{ api_endpoint }}?review_status=false',
+              endpoint: '{{ api_endpoint }}?review_status=false{% if entity_type == 'scenario' %}&exclude_related=true{% endif %}',
               instanceId: '{{ entity_type }}_unreviewed',
               isReviewed: false,
               perPage: {{ per_page|default:50 }}

templates/collections/scenarios_paginated.html

@@ -1,7 +1,15 @@
 {% extends "collections/paginated_base.html" %}
+{% load static %}
 
 {% block page_title %}Scenarios{% endblock %}
 
+{% block action_modals %}
+  {# Load required scripts before modal #}
+  <script src="{% static 'js/alpine/components/widgets.js' %}"></script>
+  <script src="{% static 'js/api/additional-information.js' %}"></script>
+  {% include "modals/collections/new_scenario_modal.html" %}
+{% endblock action_modals %}
+
 {% block action_button %}
   {% if meta.can_edit %}
     <button
@@ -14,10 +22,6 @@
   {% endif %}
 {% endblock action_button %}
 
-{% block action_modals %}
-  {% include "modals/collections/new_scenario_modal.html" %}
-{% endblock action_modals %}
-
 {% block description %}
   <p>
     A scenario contains meta-information that can be attached to other data

templates/collections/settings_paginated.html

@@ -0,0 +1,20 @@
+{% extends "collections/paginated_base.html" %}
+
+{% block page_title %}Settings{% endblock %}
+
+{% block action_button %}
+{% endblock action_button %}
+
+{% block action_modals %}
+{% endblock action_modals %}
+
+{% block description %}
+  <p>A setting includes configuration parameters for pathway predictions.</p>
+  <a
+    target="_blank"
+    href="https://wiki.envipath.org/index.php/Setting"
+    class="link link-primary"
+  >
+    Learn more &gt;&gt;
+  </a>
+{% endblock description %}

templates/components/footer.html

@@ -5,10 +5,8 @@
       <nav>
         <h6 class="footer-title">Services</h6>
         <a class="link link-hover" href="/predict">Predict</a>
+        <a class="link link-hover" href="/batch-predict">Batch Predict</a>
         <a class="link link-hover" href="/package">Packages</a>
-        {#        {% if user.is_authenticated %}#}
-        {#          <a class="link link-hover" href="/model">Your Collections</a>#}
-        {#        {% endif %}#}
         <a
           href="https://wiki.envipath.org/"
           target="_blank"
@@ -19,10 +17,7 @@
     {% endif %}
     <nav>
       <h6 class="footer-title">Company</h6>
-      <a class="link link-hover" href="/about">About us</a>
-      <a class="link link-hover" href="/contact">Contact us</a>
-      <a class="link link-hover" href="/careers">Careers</a>
-      <a class="link link-hover" href="/legal">Legal</a>
+      <a class="link link-hover" href="/about" target="_blank">About us</a>
     </nav>
     <nav>
       <h6 class="footer-title">Legal</h6>

templates/components/loading-spinner.html

@@ -9,6 +9,11 @@
   }
   .spinner-slow svg {
     animation: spin-slow 3s linear infinite;
+    width: 100%;
+    height: 100%;
+    transform-origin: center;
+    transform-box: fill-box;
+    display: block;
   }
 </style>
 <div class="spinner-slow flex h-full w-full items-center justify-center">

templates/components/modals/error_state.html

@@ -0,0 +1,5 @@
+<template x-if="{{ error_var }}">
+  <div class="alert alert-error mb-4">
+    <span x-text="{{ error_var }}"></span>
+  </div>
+</template>

templates/components/modals/loading_state.html

@@ -0,0 +1,5 @@
+<template x-if="{{ loading_var }}">
+  <div class="flex justify-center items-center p-4">
+    <span class="loading loading-spinner loading-md"></span>
+  </div>
+</template>

templates/components/schema_form.html

@@ -0,0 +1,146 @@
+{% load static %}
+
+<div>
+  <!-- Loading state -->
+  <template x-if="loading">
+    <div class="flex items-center justify-center p-4">
+      <span class="loading loading-spinner loading-md"></span>
+    </div>
+  </template>
+
+  <!-- Error state -->
+  <template x-if="error">
+    <div class="alert alert-error mb-4">
+      <span x-text="error"></span>
+    </div>
+  </template>
+
+  <!-- Schema form -->
+  <template x-if="schema && !loading">
+    <div class="space-y-4">
+      <!-- Title from schema -->
+      <template x-if="schema['x-title'] || schema.title">
+        <h4
+          class="text-lg font-semibold"
+          x-text="data.name || schema['x-title'] || schema.title"
+        ></h4>
+      </template>
+
+      <!-- Render each field (ordered by ui:order) -->
+      <template x-for="fieldName in getFieldOrder()" :key="fieldName">
+        <div>
+          <!-- Text widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'text'"
+          >
+            <div
+              x-data="textWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/text_widget.html" %}
+            </div>
+          </template>
+
+          <!-- Textarea widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'textarea'"
+          >
+            <div
+              x-data="textareaWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/textarea_widget.html" %}
+            </div>
+          </template>
+
+          <!-- Number widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'number'"
+          >
+            <div
+              x-data="numberWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/number_widget.html" %}
+            </div>
+          </template>
+
+          <!-- Select widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'select'"
+          >
+            <div
+              x-data="selectWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/select_widget.html" %}
+            </div>
+          </template>
+
+          <!-- Checkbox widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'checkbox'"
+          >
+            <div
+              x-data="checkboxWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/checkbox_widget.html" %}
+            </div>
+          </template>
+
+          <!-- Interval widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'interval'"
+          >
+            <div
+              x-data="intervalWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/interval_widget.html" %}
+            </div>
+          </template>
+
+          <!-- PubMed link widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'pubmed-link'"
+          >
+            <div
+              x-data="pubmedWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/pubmed_link_widget.html" %}
+            </div>
+          </template>
+
+          <!-- Compound link widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'compound-link'"
+          >
+            <div
+              x-data="compoundWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/compound_link_widget.html" %}
+            </div>
+          </template>
+
+          <!-- TimeSeries table widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'timeseries-table'"
+          >
+            <div
+              x-data="timeseriesTableWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/timeseries_table_widget.html" %}
+            </div>
+          </template>
+        </div>
+      </template>
+
+      <!-- Submit button (only in edit mode with endpoint) -->
+      <template x-if="mode === 'edit' && endpoint">
+        <div class="form-control mt-4">
+          <button class="btn btn-primary" @click="submit()" :disabled="loading">
+            <template x-if="loading">
+              <span class="loading loading-spinner loading-sm"></span>
+            </template>
+            <span x-text="loading ? 'Submitting...' : 'Submit'"></span>
+          </button>
+        </div>
+      </template>
+    </div>
+  </template>
+</div>

templates/components/widgets/checkbox_widget.html

@@ -0,0 +1,53 @@
+{# Checkbox widget - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <span class="text-base" x-text="checked ? 'Yes' : 'No'"></span>
+        </div>
+      </template>
+
+      <!-- Edit mode -->
+      <template x-if="isEditMode">
+        <input type="checkbox" class="checkbox" x-model="checked" />
+      </template>
+
+      <!-- Errors -->
+      <template x-if="$store.validationErrors.hasError(fieldName, context)">
+        <div class="label">
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

templates/components/widgets/compound_link_widget.html

@@ -0,0 +1,69 @@
+{# Compound link widget - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode: display as link -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <template x-if="value">
+            <a
+              :href="value"
+              class="link link-primary break-all"
+              target="_blank"
+              x-text="value"
+            ></a>
+          </template>
+          <template x-if="!value">
+            <span class="text-base-content/50">—</span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Edit mode -->
+      <template x-if="isEditMode">
+        <input
+          type="url"
+          class="input input-bordered w-full"
+          :class="{ 'input-error': $store.validationErrors.hasError(fieldName, context) }"
+          placeholder="Compound URL"
+          x-model="value"
+        />
+      </template>
+
+      <!-- Errors -->
+      <template x-if="$store.validationErrors.hasError(fieldName, context)">
+        <div class="label">
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

templates/components/widgets/interval_widget.html

@@ -0,0 +1,89 @@
+{# Interval widget for range inputs - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': hasValidationError || $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode: formatted range with unit -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <span class="text-base" x-text="start"></span>
+          <span class="text-base-content/60 text-xs" x-show="!isSameValue"
+            >to</span
+          >
+          <span class="text-base" x-text="end" x-show="!isSameValue"></span>
+          <template x-if="start && end && unit">
+            <span class="text-xs" x-text="unit"></span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Edit mode: two inputs with shared unit badge -->
+      <template x-if="isEditMode">
+        <div class="flex items-center gap-2">
+          <input
+            type="number"
+            class="input input-bordered flex-1"
+            :class="{ 'input-error': hasValidationError || $store.validationErrors.hasError(fieldName, context) }"
+            placeholder="Min"
+            x-model="start"
+          />
+          <span class="text-base-content/60">to</span>
+          <input
+            type="number"
+            class="input input-bordered flex-1"
+            :class="{ 'input-error': hasValidationError || $store.validationErrors.hasError(fieldName, context) }"
+            placeholder="Max"
+            x-model="end"
+          />
+          <template x-if="unit">
+            <span class="badge badge-ghost badge-lg" x-text="unit"></span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Errors -->
+      <template
+        x-if="hasValidationError || $store.validationErrors.hasError(fieldName, context)"
+      >
+        <div class="label">
+          <!-- Client-side validation error -->
+          <template x-if="hasValidationError">
+            <span class="label-text-alt text-error">
+              Start value must be less than or equal to end value
+            </span>
+          </template>
+
+          <!-- Server-side validation errors from store -->
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

templates/components/widgets/number_widget.html

@@ -0,0 +1,69 @@
+{# Number input widget - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode: show value with unit -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <span class="text-base" x-text="value"></span>
+          <template x-if="value && unit">
+            <span class="text-xs" x-text="unit"></span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Edit mode: input with unit suffix -->
+      <template x-if="isEditMode">
+        <div :class="unit ? 'join w-full' : ''">
+          <input
+            type="number"
+            :class="unit ? 'input input-bordered join-item flex-1' : 'input input-bordered w-full'"
+            class:input-error="$store.validationErrors.hasError(fieldName, context)"
+            x-model="value"
+          />
+          <template x-if="unit">
+            <span
+              class="btn btn-ghost join-item no-animation pointer-events-none"
+              x-text="unit"
+            ></span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Errors -->
+      <template x-if="$store.validationErrors.hasError(fieldName, context)">
+        <div class="label">
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

templates/components/widgets/pubmed_link_widget.html

@@ -0,0 +1,69 @@
+{# PubMed link widget - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode: display as link -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <template x-if="value && pubmedUrl">
+            <a
+              :href="pubmedUrl"
+              class="link link-primary"
+              target="_blank"
+              x-text="value"
+            ></a>
+          </template>
+          <template x-if="!value">
+            <span class="text-base-content/50">—</span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Edit mode -->
+      <template x-if="isEditMode">
+        <input
+          type="text"
+          class="input input-bordered w-full"
+          :class="{ 'input-error': $store.validationErrors.hasError(fieldName, context) }"
+          placeholder="PubMed ID"
+          x-model="value"
+        />
+      </template>
+
+      <!-- Errors -->
+      <template x-if="$store.validationErrors.hasError(fieldName, context)">
+        <div class="label">
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

templates/components/widgets/select_widget.html

@@ -0,0 +1,71 @@
+{# Select dropdown widget - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <template x-if="value">
+            <span class="text-base" x-text="value"></span>
+          </template>
+          <template x-if="!value">
+            <span class="text-base-content/50">—</span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Edit mode -->
+      <template x-if="isEditMode">
+        <select
+          class="select select-bordered w-full"
+          :class="{ 'select-error': $store.validationErrors.hasError(fieldName, context) }"
+          x-model="value"
+        >
+          <option value="" :selected="!value">Select...</option>
+          <template x-for="opt in options" :key="opt">
+            <option
+              :value="opt"
+              :selected="value === opt"
+              x-text="opt"
+            ></option>
+          </template>
+        </select>
+      </template>
+
+      <!-- Errors -->
+      <template x-if="$store.validationErrors.hasError(fieldName, context)">
+        <div class="label">
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

templates/components/widgets/text_widget.html

@@ -0,0 +1,63 @@
+{# Text input widget - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <template x-if="value">
+            <span class="text-base" x-text="value"></span>
+          </template>
+          <template x-if="!value">
+            <span class="text-base-content/50">—</span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Edit mode -->
+      <template x-if="isEditMode">
+        <input
+          type="text"
+          class="input input-bordered w-full"
+          :class="{ 'input-error': $store.validationErrors.hasError(fieldName, context) }"
+          x-model="value"
+        />
+      </template>
+
+      <!-- Errors -->
+      <template x-if="$store.validationErrors.hasError(fieldName, context)">
+        <div class="label">
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

templates/components/widgets/textarea_widget.html

@@ -0,0 +1,62 @@
+{# Textarea widget - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <template x-if="value">
+            <p class="text-base whitespace-pre-wrap" x-text="value"></p>
+          </template>
+          <template x-if="!value">
+            <span class="text-base-content/50">—</span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Edit mode -->
+      <template x-if="isEditMode">
+        <textarea
+          class="textarea textarea-bordered w-full"
+          :class="{ 'textarea-error': $store.validationErrors.hasError(fieldName, context) }"
+          x-model="value"
+        ></textarea>
+      </template>
+
+      <!-- Errors -->
+      <template x-if="$store.validationErrors.hasError(fieldName, context)">
+        <div class="label">
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

templates/components/widgets/timeseries_table_widget.html

@@ -0,0 +1,234 @@
+{# TimeSeries table widget for measurement data #}
+<div class="form-control">
+  <div class="flex flex-col gap-2">
+    <!-- Label -->
+    <label class="label">
+      <span
+        class="label-text"
+        :class="{
+          'text-error': $store.validationErrors.hasError(fieldName, context),
+          'text-sm text-base-content/60': isViewMode
+        }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Help text -->
+    <template x-if="helpText">
+      <div class="label">
+        <span
+          class="label-text-alt text-base-content/60"
+          x-text="helpText"
+        ></span>
+      </div>
+    </template>
+
+    <!-- Form-level validation errors (root errors) for timeseries -->
+    <template x-if="$store.validationErrors.hasError('root', context)">
+      <div class="text-error">
+        <template
+          x-for="errMsg in $store.validationErrors.getErrors('root', context)"
+          :key="errMsg"
+        >
+          <span x-text="errMsg"></span>
+        </template>
+      </div>
+    </template>
+
+    <!-- View mode: display measurements as chart -->
+    <template x-if="isViewMode">
+      <div class="space-y-4">
+        <!-- Chart container -->
+        <template x-if="measurements.length > 0">
+          <div class="w-full">
+            <div class="h-64 w-full">
+              <canvas x-ref="chartCanvas"></canvas>
+            </div>
+          </div>
+        </template>
+        <template x-if="measurements.length === 0">
+          <div class="text-base-content/60 text-sm italic">No measurements</div>
+        </template>
+
+        <!-- Description and Method metadata -->
+        <template x-if="description || method">
+          <div class="space-y-2 text-sm">
+            <template x-if="description">
+              <div>
+                <span class="text-base-content/80 font-semibold"
+                  >Description:</span
+                >
+                <p
+                  class="text-base-content/70 mt-1 whitespace-pre-wrap"
+                  x-text="description"
+                ></p>
+              </div>
+            </template>
+            <template x-if="method">
+              <div>
+                <span class="text-base-content/80 font-semibold">Method:</span>
+                <span class="text-base-content/70 ml-2" x-text="method"></span>
+              </div>
+            </template>
+          </div>
+        </template>
+      </div>
+    </template>
+
+    <!-- Edit mode: editable table with add/remove controls -->
+    <template x-if="isEditMode">
+      <div class="space-y-2">
+        <!-- Measurements table -->
+        <div class="overflow-x-auto">
+          <template x-if="measurements.length > 0">
+            <table class="table-zebra table-sm table">
+              <thead>
+                <tr>
+                  <th>Timestamp</th>
+                  <th>Value</th>
+                  <th>Error</th>
+                  <th>Note</th>
+                  <th class="w-12"></th>
+                </tr>
+              </thead>
+              <tbody>
+                <template
+                  x-for="(measurement, index) in measurements"
+                  :key="index"
+                >
+                  <tr>
+                    <td>
+                      <input
+                        type="number"
+                        class="input input-bordered input-sm w-full"
+                        :class="{ 'input-error': $store.validationErrors.hasError(fieldName, context) }"
+                        :value="formatTimestamp(measurement.timestamp)"
+                        @input="updateMeasurement(index, 'timestamp', $event.target.value)"
+                      />
+                    </td>
+                    <td>
+                      <input
+                        type="number"
+                        class="input input-bordered input-sm w-full"
+                        :class="{ 'input-error': $store.validationErrors.hasError(fieldName, context) }"
+                        placeholder="Value"
+                        :value="measurement.value"
+                        @input="updateMeasurement(index, 'value', $event.target.value)"
+                      />
+                    </td>
+                    <td>
+                      <input
+                        type="number"
+                        class="input input-bordered input-sm w-full"
+                        placeholder="±"
+                        :value="measurement.error"
+                        @input="updateMeasurement(index, 'error', $event.target.value)"
+                      />
+                    </td>
+                    <td>
+                      <input
+                        type="text"
+                        class="input input-bordered input-sm w-full"
+                        placeholder="Note"
+                        :value="measurement.note"
+                        @input="updateMeasurement(index, 'note', $event.target.value)"
+                      />
+                    </td>
+                    <td>
+                      <button
+                        type="button"
+                        class="btn btn-ghost btn-sm btn-circle"
+                        @click="removeMeasurement(index)"
+                        title="Remove measurement"
+                      >
+                        <svg
+                          xmlns="http://www.w3.org/2000/svg"
+                          class="h-4 w-4"
+                          fill="none"
+                          viewBox="0 0 24 24"
+                          stroke="currentColor"
+                        >
+                          <path
+                            stroke-linecap="round"
+                            stroke-linejoin="round"
+                            stroke-width="2"
+                            d="M6 18L18 6M6 6l12 12"
+                          />
+                        </svg>
+                      </button>
+                    </td>
+                  </tr>
+                </template>
+              </tbody>
+            </table>
+          </template>
+          <template x-if="measurements.length === 0">
+            <div class="text-base-content/60 py-2 text-sm italic">
+              No measurements yet. Click "Add Measurement" to start.
+            </div>
+          </template>
+        </div>
+
+        <!-- Action buttons -->
+        <div class="flex gap-2">
+          <button
+            type="button"
+            class="btn btn-sm btn-primary"
+            @click="addMeasurement()"
+          >
+            <svg
+              xmlns="http://www.w3.org/2000/svg"
+              class="h-4 w-4"
+              fill="none"
+              viewBox="0 0 24 24"
+              stroke="currentColor"
+            >
+              <path
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                stroke-width="2"
+                d="M12 4v16m8-8H4"
+              />
+            </svg>
+            Add Measurement
+          </button>
+          <template x-if="measurements.length > 1">
+            <button
+              type="button"
+              class="btn btn-sm btn-ghost"
+              @click="sortByTimestamp()"
+            >
+              <svg
+                xmlns="http://www.w3.org/2000/svg"
+                class="h-4 w-4"
+                fill="none"
+                viewBox="0 0 24 24"
+                stroke="currentColor"
+              >
+                <path
+                  stroke-linecap="round"
+                  stroke-linejoin="round"
+                  stroke-width="2"
+                  d="M7 16V4m0 0L3 8m4-4l4 4m6 0v12m0 0l4-4m-4 4l-4-4"
+                />
+              </svg>
+              Sort by Timestamp
+            </button>
+          </template>
+        </div>
+      </div>
+    </template>
+
+    <!-- Errors -->
+    <template x-if="$store.validationErrors.hasError(fieldName, context)">
+      <div class="label">
+        <template
+          x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+          :key="errMsg"
+        >
+          <span class="label-text-alt text-error" x-text="errMsg"></span>
+        </template>
+      </div>
+    </template>
+  </div>
+</div>

templates/framework_modern.html

@@ -21,6 +21,10 @@
       type="text/css"
     />
 
+    {# Chart.js - For timeseries charts #}
+    <script src="https://cdn.jsdelivr.net/npm/chart.js@4.4.0/dist/chart.umd.min.js"></script>
+    <script src="{% static 'js/utils/timeseries-chart.js' %}"></script>
+
     {# Alpine.js - For reactive components #}
     <script
       defer
@@ -30,6 +34,8 @@
     <script src="{% static 'js/alpine/search.js' %}"></script>
     <script src="{% static 'js/alpine/pagination.js' %}"></script>
     <script src="{% static 'js/alpine/pathway.js' %}"></script>
+    <script src="{% static 'js/alpine/components/schema-form.js' %}"></script>
+    <script src="{% static 'js/alpine/components/widgets.js' %}"></script>
 
     {# Font Awesome #}
     <link

templates/index/index.html

@@ -176,8 +176,8 @@
                       href="#"
                       class="example-link hover:text-primary cursor-pointer"
                       title="load example"
-                      @click.prevent="loadExample('CC(C)CC1=CC=C(C=C1)C(C)C(=O)O', $el)"
-                      >Ibuprofen</a
+                      @click.prevent="loadExample('COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@H](CC(=O)O)N', $el)"
+                      >Aspartame</a
                     >
                   </div>
                   <a
@@ -287,7 +287,7 @@
             </p>
             <div class="float-right flex flex-row gap-4">
               <a href="/about" class="btn btn-ghost-neutral">Read More</a>
-              <a href="/about" class="btn btn-neutral">Publications</a>
+              <a href="/cite" class="btn btn-neutral">Publications</a>
             </div>
           </div>
         </div>

templates/modals/collections/new_scenario_modal.html

@@ -4,17 +4,152 @@
   id="new_scenario_modal"
   class="modal"
   x-data="{
-    ...modalForm(),
+    isSubmitting: false,
+    error: null,
     scenarioType: 'empty',
+    schemas: {},
+    groupSchemas: {},
+    loadingSchemas: false,
+    formData: {
+      name: '',
+      description: '',
+      dateYear: '',
+      dateMonth: '',
+      dateDay: '',
+      scenarioType: 'empty',
+      additionalInformation: {}
+    },
+    // Track form data from each schema renderer
+    schemaFormData: {},
+
     validateYear(el) {
       if (el.value && el.value.length < 4) {
         el.value = new Date().getFullYear();
       }
+    },
+
+    async init() {
+      try {
+        this.loadingSchemas = true;
+        // Ensure API client is available
+        if (!window.AdditionalInformationApi) {
+          throw new Error('Additional Information API client not loaded. Please refresh the page.');
+        }
+
+        // Use single API call to load schemas organized by groups
+        const { schemas, groupSchemas } =
+          await window.AdditionalInformationApi.loadSchemasWithGroups(['soil', 'sludge', 'sediment']);
+
+        this.schemas = schemas;
+        this.groupSchemas = groupSchemas;
+      } catch (err) {
+        this.error = err.message;
+        console.error('Error loading schemas:', err);
+      } finally {
+        this.loadingSchemas = false;
+      }
+    },
+
+    reset() {
+      this.isSubmitting = false;
+      this.error = null;
+      this.scenarioType = 'empty';
+      this.formData = {
+        name: '',
+        description: '',
+        dateYear: '',
+        dateMonth: '',
+        dateDay: '',
+        scenarioType: 'empty',
+        additionalInformation: {}
+      };
+      this.schemaFormData = {};
+    },
+
+    setSchemaFormData(schemaName, data) {
+      this.schemaFormData[schemaName] = data;
+    },
+
+    async submit() {
+      if (!this.formData.name || this.formData.name.trim() === '') {
+        this.error = 'Please enter a scenario name';
+        return;
+      }
+
+      this.isSubmitting = true;
+      this.error = null;
+
+      try {
+        // Build scenario date
+        let scenarioDate = this.formData.dateYear || '';
+        if (this.formData.dateMonth && this.formData.dateMonth.trim() !== '') {
+          scenarioDate += `-${parseInt(this.formData.dateMonth).toString().padStart(2, '0')}`;
+          if (this.formData.dateDay && this.formData.dateDay.trim() !== '') {
+            scenarioDate += `-${parseInt(this.formData.dateDay).toString().padStart(2, '0')}`;
+          }
+        }
+
+        if (!scenarioDate || scenarioDate.trim() === '') {
+          scenarioDate = 'No date';
+        }
+
+        // Collect additional information from schema forms
+        const additionalInformation = [];
+        const currentGroupSchemas = this.groupSchemas[this.scenarioType] || {};
+
+        for (const schemaName in this.schemaFormData) {
+          const data = this.schemaFormData[schemaName];
+          // Only include if schema belongs to current group and has data
+          if (currentGroupSchemas[schemaName] && data && Object.keys(data).length > 0) {
+            // Check if data has any non-null/non-empty values
+            const hasData = Object.values(data).some(val => {
+              if (val === null || val === undefined || val === '') return false;
+              if (typeof val === 'object' && val !== null) {
+                // For interval objects, check if start or end has value
+                if (val.start !== null && val.start !== undefined && val.start !== '') return true;
+                if (val.end !== null && val.end !== undefined && val.end !== '') return true;
+                return false;
+              }
+              return true;
+            });
+
+            if (hasData) {
+              additionalInformation.push({
+                type: schemaName,
+                data: data
+              });
+            }
+          }
+        }
+
+        // Build payload
+        const payload = {
+          name: this.formData.name.trim(),
+          description: this.formData.description ? this.formData.description.trim() : '',
+          scenario_date: scenarioDate,
+          scenario_type: this.scenarioType === 'empty' ? 'Not specified' : this.scenarioType,
+          additional_information: additionalInformation
+        };
+
+        const packageUuid = '{{ meta.current_package.uuid }}';
+
+        // Use API client for scenario creation
+        const result = await window.AdditionalInformationApi.createScenario(packageUuid, payload);
+
+        // Close modal and redirect to new scenario
+        document.getElementById('new_scenario_modal').close();
+        window.location.href = result.url || `{{ meta.current_package.url }}/scenario/${result.uuid}`;
+      } catch (err) {
+        this.error = err.message;
+      } finally {
+        this.isSubmitting = false;
+      }
     }
   }"
   @close="reset()"
+  @schema-form-data-changed.window="setSchemaFormData($event.detail.schemaName, $event.detail.data)"
 >
-  <div class="modal-box max-w-3xl">
+  <div class="modal-box max-w-3xl max-h-[90vh] overflow-y-auto">
     <!-- Header -->
     <h3 class="text-lg font-bold">New Scenario</h3>
 
@@ -30,135 +165,212 @@
 
     <!-- Body -->
     <div class="py-4">
-      <form
-        id="new-scenario-modal-form"
-        accept-charset="UTF-8"
-        action="{{ meta.current_package.url }}/scenario"
-        method="post"
-      >
-        {% csrf_token %}
+      <div class="alert alert-info mb-4">
+        <span>
+          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"
+            class="link"
+            >wiki &gt;&gt;</a
+          >
+        </span>
+      </div>
 
-        <div class="alert alert-info mb-4">
-          <span>
-            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"
-              class="link"
-              >wiki &gt;&gt;</a
-            >
-          </span>
+      <!-- Error state -->
+      <template x-if="error">
+        <div class="alert alert-error mb-4">
+          <span x-text="error"></span>
         </div>
+      </template>
 
-        <div class="form-control mb-3">
-          <label class="label" for="scenario-name">
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="scenario-name"
-            name="scenario-name"
-            class="input input-bordered w-full"
-            placeholder="Name"
-            required
-          />
+      <!-- Loading state -->
+      <template x-if="loadingSchemas">
+        <div class="flex items-center justify-center p-4">
+          <span class="loading loading-spinner loading-md"></span>
         </div>
+      </template>
 
-        <div class="form-control mb-3">
-          <label class="label" for="scenario-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="scenario-description"
-            name="scenario-description"
-            class="input input-bordered w-full"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label">
-            <span class="label-text">Date</span>
-          </label>
-          <div class="flex gap-2">
+      <!-- Form fields -->
+      <template x-if="!loadingSchemas">
+        <div>
+          <div class="form-control mb-3">
+            <label class="label" for="scenario-name">
+              <span class="label-text">Name</span>
+            </label>
             <input
-              type="number"
-              id="dateYear"
-              name="scenario-date-year"
-              class="input input-bordered w-24"
-              placeholder="YYYY"
-              max="{% now 'Y' %}"
-              @blur="validateYear($el)"
-            />
-            <input
-              type="number"
-              id="dateMonth"
-              name="scenario-date-month"
-              min="1"
-              max="12"
-              class="input input-bordered w-20"
-              placeholder="MM"
-            />
-            <input
-              type="number"
-              id="dateDay"
-              name="scenario-date-day"
-              min="1"
-              max="31"
-              class="input input-bordered w-20"
-              placeholder="DD"
+              id="scenario-name"
+              type="text"
+              class="input input-bordered w-full"
+              placeholder="Name"
+              x-model="formData.name"
+              required
             />
           </div>
-        </div>
 
-        <div class="form-control mb-3">
-          <label class="label">
-            <span class="label-text">Scenario Type</span>
-          </label>
-          <div role="tablist" class="tabs tabs-border">
-            <button
-              type="button"
-              role="tab"
-              class="tab"
-              :class="{ 'tab-active': scenarioType === 'empty' }"
-              @click="scenarioType = 'empty'"
-            >
-              Empty Scenario
-            </button>
-            {% for k, v in scenario_types.items %}
+          <div class="form-control mb-3">
+            <label class="label" for="scenario-description">
+              <span class="label-text">Description</span>
+            </label>
+            <input
+              id="scenario-description"
+              type="text"
+              class="input input-bordered w-full"
+              placeholder="Description"
+              x-model="formData.description"
+            />
+          </div>
+
+          <div class="form-control mb-3">
+            <label class="label">
+              <span class="label-text">Date</span>
+            </label>
+            <div class="flex gap-2">
+              <input
+                type="number"
+                class="input input-bordered w-24"
+                placeholder="YYYY"
+                max="{% now 'Y' %}"
+                x-model="formData.dateYear"
+                @blur="validateYear($el)"
+              />
+              <input
+                type="number"
+                min="1"
+                max="12"
+                class="input input-bordered w-20"
+                placeholder="MM"
+                x-model="formData.dateMonth"
+              />
+              <input
+                type="number"
+                min="1"
+                max="31"
+                class="input input-bordered w-20"
+                placeholder="DD"
+                x-model="formData.dateDay"
+              />
+            </div>
+          </div>
+
+          <div class="form-control mb-3">
+            <label class="label">
+              <span class="label-text">Scenario Type</span>
+            </label>
+            <div role="tablist" class="tabs tabs-border">
               <button
                 type="button"
                 role="tab"
                 class="tab"
-                :class="{ 'tab-active': scenarioType === '{{ v.name }}' }"
-                @click="scenarioType = '{{ v.name }}'"
+                :class="{ 'tab-active': scenarioType === 'empty' }"
+                @click="scenarioType = 'empty'"
               >
-                {{ k }}
+                Empty Scenario
               </button>
-            {% endfor %}
+              <button
+                type="button"
+                role="tab"
+                class="tab"
+                :class="{ 'tab-active': scenarioType === 'soil' }"
+                @click="scenarioType = 'soil'"
+              >
+                Soil Data
+              </button>
+              <button
+                type="button"
+                role="tab"
+                class="tab"
+                :class="{ 'tab-active': scenarioType === 'sludge' }"
+                @click="scenarioType = 'sludge'"
+              >
+                Sludge Data
+              </button>
+              <button
+                type="button"
+                role="tab"
+                class="tab"
+                :class="{ 'tab-active': scenarioType === 'sediment' }"
+                @click="scenarioType = 'sediment'"
+              >
+                Water-Sediment System Data
+              </button>
+            </div>
           </div>
-          <input
-            type="hidden"
-            id="scenario-type"
-            name="scenario-type"
-            x-model="scenarioType"
-          />
-        </div>
 
-        {% for type in scenario_types.values %}
-          <div
-            id="{{ type.name }}-specific-inputs"
-            x-show="scenarioType === '{{ type.name }}'"
-            x-cloak
-          >
-            {% for widget in type.widgets %}
-              {{ widget|safe }}
-            {% endfor %}
-          </div>
-        {% endfor %}
-      </form>
+          <!-- Schema forms for each scenario type -->
+          <template x-if="scenarioType === 'soil'">
+            <div class="space-y-4 mt-4">
+              <template
+                x-for="(rjsf, schemaName) in groupSchemas.soil"
+                :key="schemaName"
+              >
+                <div
+                  x-data="schemaRenderer({
+                    rjsf: rjsf,
+                    mode: 'edit'
+                  })"
+                  x-init="await init();
+                  const currentSchemaName = schemaName;
+                  $watch('data', (value) => {
+                    $dispatch('schema-form-data-changed', { schemaName: currentSchemaName, data: value });
+                  }, { deep: true })"
+                >
+                  {% include "components/schema_form.html" %}
+                </div>
+              </template>
+            </div>
+          </template>
+
+          <template x-if="scenarioType === 'sludge'">
+            <div class="space-y-4 mt-4">
+              <template
+                x-for="(rjsf, schemaName) in groupSchemas.sludge"
+                :key="schemaName"
+              >
+                <div
+                  x-data="schemaRenderer({
+                    rjsf: rjsf,
+                    mode: 'edit'
+                  })"
+                  x-init="await init();
+                  const currentSchemaName = schemaName;
+                  $watch('data', (value) => {
+                    $dispatch('schema-form-data-changed', { schemaName: currentSchemaName, data: value });
+                  }, { deep: true })"
+                >
+                  {% include "components/schema_form.html" %}
+                </div>
+              </template>
+            </div>
+          </template>
+
+          <template x-if="scenarioType === 'sediment'">
+            <div class="space-y-4 mt-4">
+              <template
+                x-for="(rjsf, schemaName) in groupSchemas.sediment"
+                :key="schemaName"
+              >
+                <div
+                  x-data="schemaRenderer({
+                    rjsf: rjsf,
+                    mode: 'edit'
+                  })"
+                  x-init="await init();
+                  const currentSchemaName = schemaName;
+                  $watch('data', (value) => {
+                    $dispatch('schema-form-data-changed', { schemaName: currentSchemaName, data: value });
+                  }, { deep: true })"
+                >
+                  {% include "components/schema_form.html" %}
+                </div>
+              </template>
+            </div>
+          </template>
+        </div>
+      </template>
     </div>
 
     <!-- Footer -->
@@ -174,8 +386,8 @@
       <button
         type="button"
         class="btn btn-primary"
-        @click="submit('new-scenario-modal-form')"
-        :disabled="isSubmitting"
+        @click="submit()"
+        :disabled="isSubmitting || loadingSchemas"
       >
         <span x-show="!isSubmitting">Submit</span>
         <span

templates/modals/objects/add_additional_information_modal.html

@@ -6,27 +6,117 @@
   x-data="{
     isSubmitting: false,
     selectedType: '',
+    schemas: {},
+    loadingSchemas: false,
+    error: null,
+    formData: null,  // Store reference to form data
+    formRenderKey: 0,  // Counter to force form re-render
+    existingTypes: [],  // Track existing additional information types
+
+    // Get sorted unique schema names for dropdown, excluding already-added types
+    get sortedSchemaNames() {
+      const names = Object.keys(this.schemas);
+      // Remove duplicates, exclude existing types, and sort alphabetically by display title
+      const unique = [...new Set(names)];
+      const available = unique.filter(name =>
+        !this.existingTypes.includes(name) || this.schemas[name]?.schema?.['x-repeatable']
+      );
+      return available.sort((a, b) => {
+        const titleA = (this.schemas[a]?.schema?.['x-title'] || a).toLowerCase();
+        const titleB = (this.schemas[b]?.schema?.['x-title'] || b).toLowerCase();
+        return titleA.localeCompare(titleB);
+      });
+    },
+
+    async init() {
+      // Watch for selectedType changes
+      this.$watch('selectedType', (value) => {
+        // Reset formData when type changes and increment key to force re-render
+        this.formData = null;
+        this.formRenderKey++;
+        // Clear previous errors
+        this.error = null;
+        Alpine.store('validationErrors').clearErrors(); // No context - clears all
+      });
+
+      // Load schemas and existing items
+      try {
+        this.loadingSchemas = true;
+        const scenarioUuid = '{{ scenario.uuid }}';
+        const [schemasRes, itemsRes] = await Promise.all([
+          fetch('/api/v1/information/schema/'),
+          fetch(`/api/v1/scenario/${scenarioUuid}/information/`)
+        ]);
+
+        if (!schemasRes.ok) throw new Error('Failed to load schemas');
+        if (!itemsRes.ok) throw new Error('Failed to load existing items');
+
+        this.schemas = await schemasRes.json();
+        const items = await itemsRes.json();
+
+        // Get unique existing types (normalize to lowercase)
+        this.existingTypes = [...new Set(items.map(item => item.type.toLowerCase()))];
+      } catch (err) {
+        this.error = err.message;
+      } finally {
+        this.loadingSchemas = false;
+      }
+    },
 
     reset() {
       this.isSubmitting = false;
       this.selectedType = '';
+      this.error = null;
+      this.formData = null;
+      Alpine.store('validationErrors').clearErrors(); // No context - clears all
     },
 
-    submit() {
+    setFormData(data) {
+      this.formData = data;
+    },
+
+    async submit() {
       if (!this.selectedType) return;
 
-      const form = document.getElementById('add_' + this.selectedType + '_add-additional-information-modal-form');
-      if (form && form.checkValidity()) {
-        this.isSubmitting = true;
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
+      const payload = window.AdditionalInformationApi.sanitizePayload(this.formData);
+
+      // Validate that form has data
+      if (!payload || Object.keys(payload).length === 0) {
+        this.error = 'Please fill in at least one field';
+        return;
+      }
+
+      this.isSubmitting = true;
+      this.error = null;
+
+      try {
+        const scenarioUuid = '{{ scenario.uuid }}';
+        await window.AdditionalInformationApi.createItem(
+          scenarioUuid,
+          this.selectedType,
+          payload
+        );
+
+        // Close modal and reload page to show new item
+        document.getElementById('add_additional_information_modal').close();
+        window.location.reload();
+      } catch (err) {
+        if (err.isValidationError && err.fieldErrors) {
+          // No context for add modal - simple flat errors
+          Alpine.store('validationErrors').setErrors(err.fieldErrors);
+          this.error = err.message || 'Please correct the errors in the form';
+        } else {
+          this.error = err.message || 'An error occurred. Please try again.';
+        }
+      } finally {
+        this.isSubmitting = false;
       }
     }
   }"
   @close="reset()"
+  @form-data-ready="formData = $event.detail"
 >
-  <div class="modal-box">
+  <div class="modal-box max-w-2xl">
     <!-- Header -->
     <h3 class="text-lg font-bold">Add Additional Information</h3>
 
@@ -42,46 +132,60 @@
 
     <!-- Body -->
     <div class="py-4">
-      <div class="form-control">
-        <label class="label" for="select-additional-information-type">
-          <span class="label-text">Select the type to add</span>
-        </label>
-        <select
-          id="select-additional-information-type"
-          class="select select-bordered w-full"
-          x-model="selectedType"
-        >
-          <option value="" 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>
-      </div>
-
-      {% for add_inf in available_additional_information %}
-        <div
-          class="mt-4"
-          x-show="selectedType === '{{ add_inf.name }}'"
-          x-cloak
-        >
-          <form
-            id="add_{{ add_inf.name }}_add-additional-information-modal-form"
-            accept-charset="UTF-8"
-            action=""
-            method="post"
-          >
-            {% csrf_token %}
-            {{ add_inf.widget|safe }}
-            <input
-              type="hidden"
-              name="hidden"
-              value="add-additional-information"
-            />
-          </form>
+      <!-- Loading state -->
+      <template x-if="loadingSchemas">
+        <div class="flex items-center justify-center p-4">
+          <span class="loading loading-spinner loading-md"></span>
         </div>
-      {% endfor %}
+      </template>
+
+      <!-- Error state -->
+      <template x-if="error">
+        <div class="alert alert-error mb-4">
+          <span x-text="error"></span>
+        </div>
+      </template>
+
+      <!-- Schema selection -->
+      <template x-if="!loadingSchemas">
+        <div>
+          <div class="form-control mb-4">
+            <label class="label" for="select-additional-information-type">
+              <span class="label-text">Select the type to add</span>
+            </label>
+            <select
+              id="select-additional-information-type"
+              class="select select-bordered w-full"
+              x-model="selectedType"
+            >
+              <option value="" selected disabled>Select the type to add</option>
+              <template x-for="name in sortedSchemaNames" :key="name">
+                <option
+                  :value="name"
+                  x-text="(schemas[name].schema && (schemas[name].schema['x-title'] || schemas[name].schema.title)) || name"
+                ></option>
+              </template>
+            </select>
+          </div>
+
+          <!-- Form renderer for selected type -->
+          <!-- Use unique key per type to force re-render -->
+          <template x-for="renderKey in [formRenderKey]" :key="renderKey">
+            <div x-show="selectedType && schemas[selectedType]">
+              <div
+                x-data="schemaRenderer({
+                  rjsf: schemas[selectedType],
+                  mode: 'edit'
+                  // No context - single form, backward compatible
+                })"
+                x-init="await init(); $dispatch('form-data-ready', data)"
+              >
+                {% include "components/schema_form.html" %}
+              </div>
+            </div>
+          </template>
+        </div>
+      </template>
     </div>
 
     <!-- Footer -->
@@ -98,7 +202,7 @@
         type="button"
         class="btn btn-primary"
         @click="submit()"
-        :disabled="isSubmitting || !selectedType"
+        :disabled="isSubmitting || !selectedType || loadingSchemas"
       >
         <span x-show="!isSubmitting">Add</span>
         <span

templates/modals/objects/edit_group_member_modal.html

@@ -93,7 +93,10 @@
             >
               {% csrf_token %}
               <div class="flex items-center gap-2">
-                <span class="flex-1">{{ u.username }}</span>
+                <span class="flex-1"
+                  >{{ u.username }}
+                  {% if not u.is_active %}<i>(inactive)</i>{% endif %}</span
+                >
                 <input type="hidden" name="member" value="{{ u.url }}" />
                 <input type="hidden" name="action" value="remove" />
                 <button type="submit" class="btn btn-error btn-sm">

templates/modals/objects/edit_package_permissions_modal.html

@@ -146,6 +146,7 @@
               <div class="grid grid-cols-12 gap-2 items-center">
                 <div class="col-span-5 truncate">
                   {{ up.user.username }}
+                  {% if not up.user.is_active %}<i>(inactive)</i>{% endif %}
                   <input
                     type="hidden"
                     name="grantee"

templates/modals/objects/edit_scenario_modal.html

@@ -0,0 +1,91 @@
+{% load static %}
+
+<dialog
+  id="edit_scenario_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- Header -->
+    <h3 class="font-bold text-lg">Edit Scenario</h3>
+
+    <!-- Close button (X) -->
+    <form method="dialog">
+      <button
+        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
+        :disabled="isSubmitting"
+      >
+        ✕
+      </button>
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <form
+        id="edit-scenario-modal-form"
+        accept-charset="UTF-8"
+        action=""
+        method="post"
+      >
+        {% csrf_token %}
+
+        <div class="form-control mb-3">
+          <label class="label" for="scenario-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="scenario-name"
+            class="input input-bordered w-full"
+            name="scenario-name"
+            value="{{ scenario.name|safe }}"
+            required
+          />
+        </div>
+
+        <div class="form-control mb-3">
+          <label class="label" for="scenario-description">
+            <span class="label-text">Description</span>
+          </label>
+          <input
+            id="scenario-description"
+            type="text"
+            class="input input-bordered w-full"
+            value="{{ scenario.description|safe }}"
+            name="scenario-description"
+          />
+        </div>
+      </form>
+    </div>
+
+    <!-- Footer -->
+    <div class="modal-action">
+      <button
+        type="button"
+        class="btn"
+        onclick="this.closest('dialog').close()"
+        :disabled="isSubmitting"
+      >
+        Close
+      </button>
+      <button
+        type="button"
+        class="btn btn-primary"
+        @click="submit('edit-scenario-modal-form')"
+        :disabled="isSubmitting"
+      >
+        <span x-show="!isSubmitting">Update</span>
+        <span
+          x-show="isSubmitting"
+          class="loading loading-spinner loading-sm"
+        ></span>
+        <span x-show="isSubmitting">Updating...</span>
+      </button>
+    </div>
+  </div>
+
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/modals/objects/update_scenario_additional_information_modal.html

@@ -3,10 +3,97 @@
 <dialog
   id="update_scenario_additional_information_modal"
   class="modal"
-  x-data="modalForm()"
+  x-data="{
+    isSubmitting: false,
+    items: [],
+    schemas: {},
+    loading: false,
+    error: null,
+    originalItems: [],  // Store original data to detect changes
+    modifiedUuids: new Set(),  // Track which items were modified
+
+    async init() {
+      try {
+        this.loading = true;
+        const scenarioUuid = '{{ scenario.uuid }}';
+        const { items, schemas } =
+          await window.AdditionalInformationApi.loadSchemasAndItems(scenarioUuid);
+        this.schemas = schemas;
+        // Store deep copy of original items for comparison
+        this.originalItems = JSON.parse(JSON.stringify(items));
+        this.items = items;
+      } catch (err) {
+        this.error = err.message;
+      } finally {
+        this.loading = false;
+      }
+    },
+
+    reset() {
+      this.isSubmitting = false;
+      this.error = null;
+      this.modifiedUuids.clear();
+      Alpine.store('validationErrors').clearErrors(); // Clear all contexts
+    },
+
+    updateItemData(uuid, data) {
+      // Update the item's data in the items array
+      const item = this.items.find(i => i.uuid === uuid);
+      if (item) {
+        item.data = data;
+        // Mark this item as modified
+        this.modifiedUuids.add(uuid);
+      }
+    },
+
+    async submit() {
+      if (this.items.length === 0) {
+        this.error = 'No data to update';
+        return;
+      }
+
+      // Filter to only items that were actually modified
+      const modifiedItems = this.items.filter(item => this.modifiedUuids.has(item.uuid));
+
+      if (modifiedItems.length === 0) {
+        this.error = 'No changes to save';
+        return;
+      }
+
+      this.isSubmitting = true;
+      this.error = null;
+
+      try {
+        const scenarioUuid = '{{ scenario.uuid }}';
+
+        // Use the unified API client for sequential, safe updates - only modified items
+        await window.AdditionalInformationApi.updateItems(scenarioUuid, modifiedItems);
+
+        // Close modal and reload page
+        document.getElementById('update_scenario_additional_information_modal').close();
+        window.location.reload();
+      } catch (err) {
+        // Handle validation errors with field-level details
+        if (err.isValidationError && err.fieldErrors) {
+          this.error = err.message || 'Please correct the errors in the form';
+
+          // Backend returns errors keyed by UUID, each with field-level error arrays
+          // Set errors for each item with its UUID as context
+          Object.entries(err.fieldErrors).forEach(([uuid, fieldErrors]) => {
+            Alpine.store('validationErrors').setErrors(fieldErrors, uuid);
+          });
+        } else {
+          this.error = err.message || 'An error occurred. Please try again.';
+        }
+      } finally {
+        this.isSubmitting = false;
+      }
+    }
+  }"
   @close="reset()"
+  @update-item-data.window="updateItemData($event.detail.uuid, $event.detail.data)"
 >
-  <div class="modal-box">
+  <div class="modal-box max-h-[90vh] max-w-4xl overflow-y-auto">
     <!-- Header -->
     <h3 class="text-lg font-bold">Update Additional Information</h3>
 
@@ -22,18 +109,40 @@
 
     <!-- Body -->
     <div class="py-4">
-      <form
-        id="edit-scenario-additional-information-modal-form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
-        {% csrf_token %}
-        {% for widget in update_widgets %}
-          {{ widget|safe }}
-        {% endfor %}
-        <input type="hidden" name="hidden" value="set-additional-information" />
-      </form>
+      <!-- Loading state -->
+      {% include "components/modals/loading_state.html" with loading_var="loading" %}
+
+      <!-- Error state -->
+      {% include "components/modals/error_state.html" with error_var="error" %}
+
+      <!-- Items list -->
+      <template x-if="!loading">
+        <div class="space-y-4">
+          <template x-if="items.length === 0">
+            <p class="text-base-content/60">
+              No additional information to update.
+            </p>
+          </template>
+
+          <template x-for="(item, index) in items" :key="item.uuid">
+            <div class="card bg-base-200 shadow-sm">
+              <div class="card-body p-4">
+                <div
+                  x-data="schemaRenderer({
+                    rjsf: schemas[item.type.toLowerCase()],
+                    data: item.data,
+                    mode: 'edit',
+                    context: item.uuid  // Pass item UUID as context for error scoping
+                  })"
+                  x-init="await init(); $watch('data', (value) => { $dispatch('update-item-data', { uuid: item.uuid, data: value }) }, { deep: true })"
+                >
+                  {% include "components/schema_form.html" %}
+                </div>
+              </div>
+            </div>
+          </template>
+        </div>
+      </template>
     </div>
 
     <!-- Footer -->
@@ -49,10 +158,17 @@
       <button
         type="button"
         class="btn btn-primary"
-        @click="submit('edit-scenario-additional-information-modal-form')"
-        :disabled="isSubmitting"
+        @click="submit()"
+        :disabled="isSubmitting || loading || items.length === 0 || modifiedUuids.size === 0"
       >
-        <span x-show="!isSubmitting">Update</span>
+        <span x-show="!isSubmitting">
+          <template x-if="modifiedUuids.size > 0">
+            <span x-text="`Update (${modifiedUuids.size})`"></span>
+          </template>
+          <template x-if="modifiedUuids.size === 0">
+            <span>No Changes</span>
+          </template>
+        </span>
         <span
           x-show="isSubmitting"
           class="loading loading-spinner loading-sm"

templates/objects/compound_structure.html

@@ -85,6 +85,55 @@
       </div>
     {% endif %}
 
+    {% if compound_structure.half_lifes %}
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" />
+        <div class="collapse-title text-xl font-medium">Half-lives</div>
+        <div class="collapse-content">
+          <div class="overflow-x-auto">
+            <table class="table-zebra table">
+              <thead>
+                <tr>
+                  <th>Scenario</th>
+                  <th>Values</th>
+                </tr>
+              </thead>
+              <tbody>
+                {% for scenario, half_lifes in compound_structure.half_lifes.items %}
+                  <tr>
+                    <td>
+                      <a href="{{ scenario.url }}" class="hover:bg-base-200"
+                        >{{ scenario.name }}
+                        <i>({{ scenario.package.name }})</i></a
+                      >
+                    </td>
+                    <td>
+                      <table class="table-zebra table">
+                        <tbody>
+                          <tr>
+                            <td>Scenario Type</td>
+                            <td>{{ scenario.scenario_type }}</td>
+                          </tr>
+                          <tr>
+                            <td>Half-life (days)</td>
+                            <td>{{ half_lifes.0.dt50 }}</td>
+                          </tr>
+                          <tr>
+                            <td>Model</td>
+                            <td>{{ half_lifes.0.model }}</td>
+                          </tr>
+                        </tbody>
+                      </table>
+                    </td>
+                  </tr>
+                {% endfor %}
+              </tbody>
+            </table>
+          </div>
+        </div>
+      </div>
+    {% endif %}
+
     {% if compound_structure.scenarios.all %}
       <!-- Scenarios -->
       <div class="collapse-arrow bg-base-200 collapse">

templates/objects/edge.html

@@ -14,7 +14,7 @@
     <div class="card bg-base-100">
       <div class="card-body">
         <div class="flex items-center justify-between">
-          <h2 class="card-title text-2xl">{{ edge.edge_label.name }}</h2>
+          <h2 class="card-title text-2xl">{{ edge.get_name }}</h2>
           <div id="actionsButton" class="dropdown dropdown-end hidden">
             <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
               <svg
@@ -45,6 +45,11 @@
             </ul>
           </div>
         </div>
+        <p class="mt-2">
+          The underlying reaction can be found
+          <a href="{{ edge.edge_label.url }}" class="link link-primary">here</a
+          >.
+        </p>
       </div>
     </div>
 

templates/objects/group.html

@@ -57,7 +57,8 @@
           {% for um in group.user_member.all %}
             <li>
               <a href="{{ um.url }}" class="hover:bg-base-300"
-                >{{ um.username }}</a
+                >{{ um.username }}
+                {% if not um.is_active %}<i>(inactive)</i>{% endif %}</a
               >
             </li>
           {% endfor %}

templates/objects/joblog.html

@@ -103,7 +103,7 @@
                 </ul>
               </div>
             </div>
-          {% elif job.job_name == 'batch_predict' %}
+          {% elif job.job_name == 'batch_predict' or job.job_name == 'identify_missing_rules' %}
             <div
               id="table-container"
               class="overflow-x-auto overflow-y-auto max-h-96 border rounded-lg"

templates/objects/node.html

@@ -14,7 +14,7 @@
     <div class="card bg-base-100">
       <div class="card-body">
         <div class="flex items-center justify-between">
-          <h2 class="card-title text-2xl">{{ node.name }}</h2>
+          <h2 class="card-title text-2xl">{{ node.get_name }}</h2>
           <div id="actionsButton" class="dropdown dropdown-end hidden">
             <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
               <svg
@@ -54,28 +54,6 @@
       </div>
     </div>
 
-    <!-- Description -->
-    <div class="collapse-arrow bg-base-200 collapse">
-      <input type="checkbox" checked />
-      <div class="collapse-title text-xl font-medium">Description</div>
-      <div class="collapse-content">{{ node.description }}</div>
-    </div>
-
-    {% if node.aliases %}
-      <!-- Aliases -->
-      <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
-        <div class="collapse-title text-xl font-medium">Aliases</div>
-        <div class="collapse-content">
-          <ul class="menu bg-base-100 rounded-box">
-            {% for alias in node.aliases %}
-              <li><a class="hover:bg-base-200">{{ alias }}</a></li>
-            {% endfor %}
-          </ul>
-        </div>
-      </div>
-    {% endif %}
-
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />
@@ -96,6 +74,70 @@
       <div class="collapse-content">{{ node.default_node_label.smiles }}</div>
     </div>
 
+    {% if node.default_node_label.aliases %}
+      <!-- Aliases -->
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" checked />
+        <div class="collapse-title text-xl font-medium">Aliases</div>
+        <div class="collapse-content">
+          <ul class="menu bg-base-100 rounded-box">
+            {% for alias in node.default_node_label.aliases %}
+              <li><a class="hover:bg-base-200">{{ alias }}</a></li>
+            {% endfor %}
+          </ul>
+        </div>
+      </div>
+    {% endif %}
+
+    {% if node.default_node_label.half_lifes %}
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" />
+        <div class="collapse-title text-xl font-medium">Half-lives</div>
+        <div class="collapse-content">
+          <div class="overflow-x-auto">
+            <table class="table-zebra table">
+              <thead>
+                <tr>
+                  <th>Scenario</th>
+                  <th>Values</th>
+                </tr>
+              </thead>
+              <tbody>
+                {% for scenario, half_lifes in node.default_node_label.half_lifes.items %}
+                  <tr>
+                    <td>
+                      <a href="{{ scenario.url }}" class="hover:bg-base-200"
+                        >{{ scenario.name }}
+                        <i>({{ scenario.package.name }})</i></a
+                      >
+                    </td>
+                    <td>
+                      <table class="table-zebra table">
+                        <tbody>
+                          <tr>
+                            <td>Scenario Type</td>
+                            <td>{{ scenario.scenario_type }}</td>
+                          </tr>
+                          <tr>
+                            <td>Half-life (days)</td>
+                            <td>{{ half_lifes.0.dt50 }}</td>
+                          </tr>
+                          <tr>
+                            <td>Model</td>
+                            <td>{{ half_lifes.0.model }}</td>
+                          </tr>
+                        </tbody>
+                      </table>
+                    </td>
+                  </tr>
+                {% endfor %}
+              </tbody>
+            </table>
+          </div>
+        </div>
+      </div>
+    {% endif %}
+
     {% if node.scenarios.all %}
       <!-- Scenarios -->
       <div class="collapse-arrow bg-base-200 collapse">

templates/objects/pathway.html

@@ -61,6 +61,11 @@
       stroke-opacity: 0.6;
     }
 
+    .has_timeseries {
+      stroke: #3b82f6;
+      stroke-width: 3px;
+    }
+
     .highlighted {
       stroke: red;
       stroke-width: 3px;
@@ -134,30 +139,30 @@
                   {% include "actions/objects/pathway.html" %}
                 </ul>
               </div>
-              {% if pathway.setting.model.app_domain %}
-                <div class="dropdown">
-                  <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
-                    <svg
-                      xmlns="http://www.w3.org/2000/svg"
-                      width="16"
-                      height="16"
-                      viewBox="0 0 24 24"
-                      fill="none"
-                      stroke="currentColor"
-                      stroke-width="2"
-                      stroke-linecap="round"
-                      stroke-linejoin="round"
-                      class="lucide lucide-eye"
-                    >
-                      <path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z" />
-                      <circle cx="12" cy="12" r="3" />
-                    </svg>
-                    View
-                  </div>
-                  <ul
-                    tabindex="0"
-                    class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+              <div class="dropdown">
+                <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
+                  <svg
+                    xmlns="http://www.w3.org/2000/svg"
+                    width="16"
+                    height="16"
+                    viewBox="0 0 24 24"
+                    fill="none"
+                    stroke="currentColor"
+                    stroke-width="2"
+                    stroke-linecap="round"
+                    stroke-linejoin="round"
+                    class="lucide lucide-eye"
                   >
+                    <path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z" />
+                    <circle cx="12" cy="12" r="3" />
+                  </svg>
+                  View
+                </div>
+                <ul
+                  tabindex="0"
+                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+                >
+                  {% if pathway.setting.model.app_domain %}
                     <li>
                       <a id="app-domain-toggle-button" class="cursor-pointer">
                         <svg
@@ -181,9 +186,28 @@
                         App Domain View
                       </a>
                     </li>
-                  </ul>
-                </div>
-              {% endif %}
+                  {% endif %}
+                  <li>
+                    <a id="timeseries-toggle-button" class="cursor-pointer">
+                      <svg
+                        id="timeseries-icon"
+                        xmlns="http://www.w3.org/2000/svg"
+                        width="16"
+                        height="16"
+                        viewBox="0 0 24 24"
+                        fill="none"
+                        stroke="currentColor"
+                        stroke-width="2"
+                        stroke-linecap="round"
+                        stroke-linejoin="round"
+                      >
+                        <polyline points="22 12 18 12 15 21 9 3 6 12 2 12" />
+                      </svg>
+                      OECD 301F View
+                    </a>
+                  </li>
+                </ul>
+              </div>
             </div>
             <div class="flex-none gap-2">
               <button
@@ -276,7 +300,7 @@
           <div
             x-show="showUpdateNotice"
             x-cloak
-            class="alert alert-info absolute right-4 bottom-4 left-4 z-10"
+            class="alert alert-info absolute top-4 right-4 left-4 z-10"
           >
             <span x-html="updateMessage"></span>
             <button @click="reloadPage()" class="btn btn-primary btn-sm mt-2">
@@ -306,6 +330,21 @@
               >
                 <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
               </marker>
+              <marker
+                id="doublearrow"
+                viewBox="0 0 20 30"
+                refX="53"
+                refY="5"
+                markerWidth="18"
+                markerHeight="18"
+                orient="auto-start-reverse"
+                markerUnits="userSpaceOnUse"
+              >
+                <!-- first triangle -->
+                <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
+                <!-- second triangle -->
+                <path d="M 10 0 L 20 5 L 10 10 Z" fill="#999" />
+              </marker>
               <marker
                 id="arrow_passes_app_domain"
                 viewBox="0 0 10 10"
@@ -400,6 +439,8 @@
   <script>
     // Global switch for app domain view
     var appDomainViewEnabled = false;
+    // Global switch for timeseries view
+    var timeseriesViewEnabled = false;
 
     function goFullscreen(id) {
       var element = document.getElementById(id);
@@ -493,6 +534,35 @@
         });
       }
 
+      // Timeseries toggle
+      const timeseriesBtn = document.getElementById("timeseries-toggle-button");
+      if (timeseriesBtn) {
+        timeseriesBtn.addEventListener("click", function () {
+          timeseriesViewEnabled = !timeseriesViewEnabled;
+          const icon = document.getElementById("timeseries-icon");
+
+          if (timeseriesViewEnabled) {
+            icon.innerHTML =
+              '<polyline points="22 12 18 12 15 21 9 3 6 12 2 12" style="stroke:#3b82f6"/>';
+
+            nodes.forEach((x) => {
+              if (x.timeseries) {
+                d3.select(x.el)
+                  .select("circle")
+                  .classed("has_timeseries", true);
+              }
+            });
+          } else {
+            icon.innerHTML =
+              '<polyline points="22 12 18 12 15 21 9 3 6 12 2 12"/>';
+
+            nodes.forEach((x) => {
+              d3.select(x.el).select("circle").classed("has_timeseries", false);
+            });
+          }
+        });
+      }
+
       // Show actions button if there are actions
       const actionsButton = document.getElementById("actionsButton");
       const actionsList = actionsButton?.querySelector("ul");

templates/objects/scenario.html

@@ -1,8 +1,12 @@
 {% extends "framework_modern.html" %}
+{% load static %}
 
 {% block content %}
+  <script src="{% static 'js/alpine/components/widgets.js' %}"></script>
+  <script src="{% static 'js/api/additional-information.js' %}"></script>
 
   {% block action_modals %}
+    {% include "modals/objects/edit_scenario_modal.html" %}
     {% include "modals/objects/add_additional_information_modal.html" %}
     {% include "modals/objects/update_scenario_additional_information_modal.html" %}
     {% include "modals/objects/generic_delete_modal.html" %}
@@ -57,46 +61,88 @@
       </div>
     </div>
 
-    <!-- Additional Information Table -->
+    <!-- Additional Information -->
     <div class="card bg-base-100">
       <div class="card-body">
         <h3 class="card-title mb-4 text-lg">Additional Information</h3>
-        <div class="overflow-x-auto">
-          <table class="table-zebra table">
-            <thead>
-              <tr>
-                <th>Property</th>
-                <th>Value</th>
-                <th>Unit</th>
-                {% if meta.can_edit %}
-                  <th>Remove</th>
-                {% endif %}
-              </tr>
-            </thead>
-            <tbody>
-              {% for ai in scenario.get_additional_information %}
-                <tr>
-                  <td>{{ ai.property_name|safe }}</td>
-                  <td>{{ ai.property_data|safe }}</td>
-                  <td>{{ ai.property_unit|safe }}</td>
-                  {% if meta.can_edit %}
-                    <td>
-                      <form
-                        action="{% url 'package scenario detail' scenario.package.uuid scenario.uuid %}"
-                        method="post"
+        <div
+          x-data="{
+            items: [],
+            schemas: {},
+            loading: true,
+            error: null,
+            async init() {
+              try {
+                // Use the unified API client for loading data
+                const { items, schemas } = await window.AdditionalInformationApi.loadSchemasAndItems('{{ scenario.uuid }}');
+                this.items = items;
+                this.schemas = schemas;
+              } catch (err) {
+                this.error = err.message;
+                console.error('Error loading additional information:', err);
+              } finally {
+                this.loading = false;
+              }
+            },
+            async deleteItem(uuid) {
+              if (!confirm('Are you sure you want to delete this item?')) return;
+
+              try {
+                // Use the unified API client for delete operations
+                await window.AdditionalInformationApi.deleteItem('{{ scenario.uuid }}', uuid);
+
+                // Remove from items array
+                this.items = this.items.filter(item => item.uuid !== uuid);
+              } catch (err) {
+                alert('Error deleting item: ' + err.message);
+                console.error('Error deleting item:', err);
+              }
+            }
+          }"
+        >
+          <!-- Loading state -->
+          <template x-if="loading">
+            <div class="flex items-center justify-center p-4">
+              <span class="loading loading-spinner loading-md"></span>
+            </div>
+          </template>
+
+          <!-- Error state -->
+          <template x-if="error">
+            <div class="alert alert-error mb-4">
+              <span x-text="error"></span>
+            </div>
+          </template>
+
+          <!-- Items list -->
+          <template x-if="!loading && !error">
+            <div class="space-y-4">
+              <template x-if="items.length === 0">
+                <p class="text-base-content/60">
+                  No additional information available.
+                </p>
+              </template>
+
+              <template x-for="item in items" :key="item.uuid">
+                <div class="card bg-base-200 shadow-sm">
+                  <div class="card-body p-4">
+                    <div class="flex items-start justify-between">
+                      <div
+                        class="flex-1"
+                        x-data="schemaRenderer({
+                             rjsf: schemas[item.type.toLowerCase()],
+                             data: item.data,
+                             mode: 'view'
+                           })"
+                        x-init="init()"
                       >
-                        {% csrf_token %}
-                        <input
-                          type="hidden"
-                          name="uuid"
-                          value="{{ ai.uuid }}"
-                        />
-                        <input
-                          type="hidden"
-                          name="hidden"
-                          value="delete-additional-information"
-                        />
-                        <button type="submit" class="btn btn-sm btn-ghost">
+                        {% include "components/schema_form.html" %}
+                      </div>
+                      {% if meta.can_edit %}
+                        <button
+                          class="btn btn-sm btn-ghost ml-2"
+                          @click="deleteItem(item.uuid)"
+                        >
                           <svg
                             xmlns="http://www.w3.org/2000/svg"
                             width="16"
@@ -107,59 +153,155 @@
                             stroke-width="2"
                             stroke-linecap="round"
                             stroke-linejoin="round"
-                            class="lucide lucide-minus"
+                            class="lucide lucide-trash"
                           >
-                            <path d="M5 12h14" />
+                            <path d="M3 6h18" />
+                            <path d="M19 6v14c0 1-1 2-2 2H7c-1 0-2-1-2-2V6" />
+                            <path d="M8 6V4c0-1 1-2 2-2h4c1 0 2 1 2 2v2" />
                           </svg>
                         </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 btn-sm btn-ghost">
-                        <svg
-                          xmlns="http://www.w3.org/2000/svg"
-                          width="16"
-                          height="16"
-                          viewBox="0 0 24 24"
-                          fill="none"
-                          stroke="currentColor"
-                          stroke-width="2"
-                          stroke-linecap="round"
-                          stroke-linejoin="round"
-                          class="lucide lucide-trash"
-                        >
-                          <path d="M3 6h18" />
-                          <path d="M19 6v14c0 1-1 2-2 2H7c-1 0-2-1-2-2V6" />
-                          <path d="M8 6V4c0-1 1-2 2-2h4c1 0 2 1 2 2v2" />
-                        </svg>
-                      </button>
-                    </form>
-                  </td>
-                </tr>
-              {% endif %}
-            </tbody>
-          </table>
+                      {% endif %}
+                    </div>
+                  </div>
+                </div>
+              </template>
+            </div>
+          </template>
         </div>
       </div>
     </div>
+
+    {% if scenario.parent %}
+      <div class="card bg-base-100">
+        <div class="card-body">
+          <h3 class="card-title mb-4 text-lg">
+            Parent Scenario Additional Information
+          </h3>
+          <div
+            x-data="{
+            items: [],
+            schemas: {},
+            loading: true,
+            error: null,
+            async init() {
+              try {
+                // Use the unified API client for loading data
+                const { items, schemas } = await window.AdditionalInformationApi.loadSchemasAndItems('{{ scenario.parent.uuid }}');
+                this.items = items;
+                this.schemas = schemas;
+              } catch (err) {
+                this.error = err.message;
+                console.error('Error loading additional information:', err);
+              } finally {
+                this.loading = false;
+              }
+            },
+          }"
+          >
+            <!-- Loading state -->
+            <template x-if="loading">
+              <div class="flex items-center justify-center p-4">
+                <span class="loading loading-spinner loading-md"></span>
+              </div>
+            </template>
+
+            <!-- Error state -->
+            <template x-if="error">
+              <div class="alert alert-error mb-4">
+                <span x-text="error"></span>
+              </div>
+            </template>
+
+            <!-- Items list -->
+            <template x-if="!loading && !error">
+              <div class="space-y-4">
+                <template x-if="items.length === 0">
+                  <p class="text-base-content/60">
+                    No additional information available.
+                  </p>
+                </template>
+
+                <template x-for="item in items" :key="item.uuid">
+                  <div class="card bg-base-200 shadow-sm">
+                    <div class="card-body p-4">
+                      <div class="flex items-start justify-between">
+                        <div
+                          class="flex-1"
+                          x-data="schemaRenderer({
+                             rjsf: schemas[item.type.toLowerCase()],
+                             data: item.data,
+                             mode: 'view'
+                           })"
+                          x-init="init()"
+                        >
+                          {% include "components/schema_form.html" %}
+                        </div>
+                      </div>
+                    </div>
+                  </div>
+                </template>
+              </div>
+            </template>
+          </div>
+        </div>
+      </div>
+    {% endif %}
+
+    <!-- Pathways -->
+    {% if scenario.related_pathways %}
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" checked />
+        <div class="collapse-title text-xl font-medium">Pathways</div>
+        <div class="collapse-content">
+          <ul class="menu bg-base-100 rounded-box">
+            {% for p in scenario.related_pathways %}
+              <li>
+                <a href="{{ p.url }}" class="hover:bg-base-200"
+                  >{{ p.name }} <i>({{ p.package.name }})</i></a
+                >
+              </li>
+            {% endfor %}
+          </ul>
+        </div>
+      </div>
+    {% endif %}
+
+    <!-- Related Scenarios -->
+    {% if children.exists %}
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" />
+        <div class="collapse-title text-xl font-medium">Related Scenarios</div>
+        <div class="collapse-content">
+          <ul class="menu bg-base-100 rounded-box">
+            {% for s in children %}
+              <li>
+                <a href="{{ s.url }}" class="hover:bg-base-200"
+                  >{{ s.name }} <i>({{ s.package.name }})</i></a
+                >
+              </li>
+            {% endfor %}
+          </ul>
+        </div>
+      </div>
+    {% endif %}
+
+    <!-- Parent Scenarios -->
+    {% if scenario.parent %}
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" />
+        <div class="collapse-title text-xl font-medium">Parent Scenario</div>
+        <div class="collapse-content">
+          <ul class="menu bg-base-100 rounded-box">
+            <li>
+              <a href="{{ scenario.parent.url }}" class="hover:bg-base-200"
+                >{{ scenario.parent.name }}
+                <i>({{ scenario.parent.package.name }})</i></a
+              >
+            </li>
+          </ul>
+        </div>
+      </div>
+    {% endif %}
   </div>
 
   <script>

templates/objects/setting.html

@@ -0,0 +1,67 @@
+{% extends "framework_modern.html" %}
+
+{% block content %}
+
+  {% block action_modals %}
+  {% endblock action_modals %}
+
+  <div class="space-y-2 p-4">
+    <!-- Header Section -->
+    <div class="card bg-base-100">
+      <div class="card-body">
+        <div class="flex items-center justify-between">
+          <h2 class="card-title text-2xl">{{ setting.name }}</h2>
+          <div id="actionsButton" class="dropdown dropdown-end hidden">
+            <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
+              <svg
+                xmlns="http://www.w3.org/2000/svg"
+                width="16"
+                height="16"
+                viewBox="0 0 24 24"
+                fill="none"
+                stroke="currentColor"
+                stroke-width="2"
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                class="lucide lucide-wrench"
+              >
+                <path
+                  d="M14.7 6.3a1 1 0 0 0 0 1.4l1.6 1.6a1 1 0 0 0 1.4 0l3.77-3.77a6 6 0 0 1-7.94 7.94l-6.91 6.91a2.12 2.12 0 0 1-3-3l6.91-6.91a6 6 0 0 1 7.94-7.94l-3.76 3.76z"
+                />
+              </svg>
+              Actions
+            </div>
+            <ul
+              tabindex="-1"
+              class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+            >
+              {% block actions %}
+              {% endblock %}
+            </ul>
+          </div>
+        </div>
+      </div>
+    </div>
+
+    <!-- The actual setting -->
+    <div class="collapse-arrow bg-base-200 collapse">
+      <input type="checkbox" checked />
+      <div class="collapse-content">
+        {% with setting_to_render=setting can_be_default=False %}
+          {% include "objects/setting_template.html" %}
+        {% endwith %}
+      </div>
+    </div>
+  </div>
+
+  <script>
+    // Show actions button if there are actions
+    document.addEventListener("DOMContentLoaded", function () {
+      const actionsButton = document.getElementById("actionsButton");
+      const actionsList = actionsButton?.querySelector("ul");
+      if (actionsList && actionsList.children.length > 0) {
+        actionsButton?.classList.remove("hidden");
+      }
+    });
+  </script>
+{% endblock content %}

templates/predict_pathway.html

@@ -122,17 +122,27 @@
         </select>
       </label>
 
-      <div class="flex justify-end gap-2">
-        <a href="{{ meta.current_package.url }}/pathway" class="btn btn-outline"
-          >Cancel</a
+      <div class="flex h-fit w-full justify-between">
+        <a
+          href="/batch-predict"
+          class="link-hover text-neutral/50 self-end text-sm"
+          >More than one compound?</a
         >
-        <button
-          type="submit"
-          id="predict-submit-button"
-          class="btn btn-primary"
-        >
-          Predict
-        </button>
+
+        <div class="flex justify-end gap-2">
+          <a
+            href="{{ meta.current_package.url }}/pathway"
+            class="btn btn-outline"
+            >Cancel</a
+          >
+          <button
+            type="submit"
+            id="predict-submit-button"
+            class="btn btn-primary"
+          >
+            Predict
+          </button>
+        </div>
       </div>
     </form>
   </div>

templates/static/about_us.html

@@ -33,23 +33,15 @@
           biodegradation pathways.
         </p>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">Our Mission</h2>
-        <p class="mb-4">
-          Our mission is to advance environmental science through innovative
-          computational tools that predict and analyze the biotransformation of
-          chemical compounds. We strive to provide researchers, regulators, and
-          industry professionals with accurate, accessible tools for
-          understanding environmental fate and behavior.
-        </p>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">What We Offer</h2>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">Services</h2>
         <div class="mb-6 grid gap-6 md:grid-cols-2">
           <div class="card bg-base-200 shadow-md">
             <div class="card-body">
               <h3 class="card-title text-primary">Pathway Database</h3>
               <p>
                 Access experimentally observed biotransformation pathways and
-                reactions from curated scientific literature.
+                reactions from curated scientific literature and assessment
+                reports.
               </p>
             </div>
           </div>
@@ -57,8 +49,8 @@
             <div class="card-body">
               <h3 class="card-title text-primary">Prediction System</h3>
               <p>
-                Use our relative reasoning models to predict likely
-                biotransformation pathways and products for new compounds.
+                Use our models to predict likely biotransformation pathways and
+                products for new compounds.
               </p>
             </div>
           </div>
@@ -66,8 +58,8 @@
             <div class="card-body">
               <h3 class="card-title text-primary">Machine Learning Models</h3>
               <p>
-                Leverage advanced ML algorithms trained on extensive
-                biodegradation data for accurate predictions.
+                Leverage advanced Machine Learning algorithms trained on
+                extensive biodegradation data for accurate predictions.
               </p>
             </div>
           </div>
@@ -75,37 +67,14 @@
             <div class="card-body">
               <h3 class="card-title text-primary">Community Platform</h3>
               <p>
-                Join our active community of researchers to share knowledge,
-                discuss findings, and collaborate.
+                Join our active community of researchers to access
+                documentation, get help, share knowledge, discuss findings, and
+                collaborate.
               </p>
             </div>
           </div>
         </div>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">Our Technology</h2>
-        <p class="mb-4">
-          enviPath employs a unique combination of rule-based and machine
-          learning approaches to predict biotransformation pathways:
-        </p>
-        <ul class="mb-4 list-inside list-disc space-y-2">
-          <li>
-            <strong>Relative Reasoning:</strong> Uses structural similarity to
-            known biotransformations
-          </li>
-          <li>
-            <strong>Rule-Based Systems:</strong> Applies expert-curated
-            transformation rules
-          </li>
-          <li>
-            <strong>Machine Learning:</strong> Leverages neural networks for
-            pattern recognition
-          </li>
-          <li>
-            <strong>Hybrid Models:</strong> Combines multiple approaches for
-            optimal accuracy
-          </li>
-        </ul>
-
         <h2 class="mt-8 mb-4 text-2xl font-semibold">Our Partners</h2>
         <p class="mb-4">
           enviPath is backed by leading research institutions and collaborators:
@@ -128,66 +97,41 @@
           />
         </div>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">Our Team</h2>
-        <p class="mb-4">
-          enviPath is developed and maintained by a dedicated team of
-          computational chemists, environmental scientists, and software
-          engineers. Our interdisciplinary approach ensures that the platform
-          meets the needs of the scientific community while remaining accessible
-          and user-friendly.
-        </p>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">Research Impact</h2>
-        <p class="mb-4">
-          Since its inception, enviPath has contributed to numerous scientific
-          publications and environmental assessments. Our tools are used by:
-        </p>
-        <ul class="mb-4 list-inside list-disc space-y-2">
-          <li>
-            Academic researchers in environmental chemistry and toxicology
-          </li>
-          <li>Regulatory agencies for chemical risk assessment</li>
-          <li>
-            Chemical manufacturers for product development and safety evaluation
-          </li>
-          <li>Environmental consultants for contamination studies</li>
-        </ul>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          Open Science Commitment
-        </h2>
-        <p class="mb-4">
-          We are committed to open science principles. enviPath provides free
-          access to our database and prediction tools for academic research. We
-          actively contribute to the scientific community through publications,
-          open-source software, and collaboration.
-        </p>
-
-        <div class="card bg-primary text-primary-content mt-8">
-          <div class="card-body">
-            <h3 class="card-title">Get Involved</h3>
-            <p>
-              Join our community, contribute data, or collaborate on research
-              projects.
-            </p>
-            <div class="card-actions mt-4 justify-end">
-              <a
-                href="https://community.envipath.org/"
-                target="_blank"
-                class="btn btn-secondary"
-                >Visit Community</a
-              >
-              <a href="/contact" class="btn btn-ghost">Contact Us</a>
+        <div class="mb-6 grid gap-6 md:grid-cols-2">
+          <div class="card bg-primary text-primary-content mt-8">
+            <div class="card-body">
+              <h3 class="card-title">Get Involved</h3>
+              <p>
+                Join our community, contribute data, or collaborate on research
+                projects.
+              </p>
+              <div class="card-actions mt-4 justify-end">
+                <a
+                  href="https://community.envipath.org/"
+                  target="_blank"
+                  class="btn btn-secondary"
+                  >Visit Community</a
+                >
+                <a href="/contact" class="btn btn-ghost">Contact Us</a>
+              </div>
+            </div>
+          </div>
+          <div class="card bg-primary text-primary-content mt-8">
+            <div class="card-body">
+              <h3 class="card-title">Cite Us</h3>
+              <p>
+                To learn more about the science behind enviPath, please visit
+                our publications page for key publications and how to cite our
+                work.
+              </p>
+              <div class="card-actions mt-4 justify-end">
+                <a href="/cite" target="_blank" class="btn btn-secondary"
+                  >Publications</a
+                >
+              </div>
             </div>
           </div>
         </div>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">Publications</h2>
-        <p class="mb-4">
-          To learn more about the science behind enviPath, please visit our
-          <a href="/cite" class="link link-primary">citations page</a> for key
-          publications and how to cite our work.
-        </p>
       </div>
     </div>
   </div>

templates/static/cite.html

@@ -73,20 +73,65 @@
               <input type="checkbox" />
               <div class="collapse-title text-sm font-medium">Show BibTeX</div>
               <div class="collapse-content">
-                <pre class="overflow-x-auto text-xs"><code>@ARTICLE{Hafner2024,
-title     = "Advancements in biotransformation pathway prediction:
-                enhancements, datasets, and novel functionalities in enviPath",
-author    = "Hafner, Jasmin and Lorsbach, Tim and Schmidt, Sebastian and
-                Brydon, Liam and Dost, Katharina and Zhang, Kunyang and Fenner,
-                Kathrin and Wicker, J{\"o}rg",
-journal   = "J. Cheminform.",
-publisher = "Springer Science and Business Media LLC",
-volume    =  16,
-number    =  1,
-pages     = "93",
-month     =  aug,
-year      =  2024,
-doi       = "10.1186/s13321-024-00881-6"
+                <pre
+                  class="overflow-x-auto text-xs"
+                ><code>@ARTICLE{Hafner2024enviPath,
+    title     = "Advancements in biotransformation pathway prediction:
+                    enhancements, datasets, and novel functionalities in enviPath",
+    author    = "Hafner, Jasmin and Lorsbach, Tim and Schmidt, Sebastian and
+                    Brydon, Liam and Dost, Katharina and Zhang, Kunyang and Fenner,
+                    Kathrin and Wicker, J{\"o}rg",
+    journal   = "J. Cheminform.",
+    publisher = "Springer Science and Business Media LLC",
+    volume    =  16,
+    number    =  1,
+    pages     = "93",
+    month     =  aug,
+    year      =  2024,
+    doi       = "10.1186/s13321-024-00881-6"
+}</code></pre>
+              </div>
+            </div>
+          </div>
+        </div>
+
+        <div class="card bg-base-200 mb-6">
+          <div class="card-body">
+            <h3 class="mb-2 font-semibold">
+              enviPath – The environmental contaminant biotransformation pathway
+              resource
+            </h3>
+            <p class="mb-4 text-sm">
+              <strong>Authors:</strong> Wicker, J., Lorsbach, T., Gütlein, M.,
+              Schmid, E., Latino, D., Kramer, S., Fenner, K.<br />
+              <strong>Journal:</strong> Nucleic Acids Research, 44(D1),
+              D502-D508<br />
+              <strong>Year:</strong> 2016<br />
+              <strong>DOI:</strong>
+              <a
+                href="https://doi.org/10.1093/nar/gkv1229"
+                target="_blank"
+                class="link link-primary"
+                >10.1093/nar/gkv1229</a
+              >
+            </p>
+            <div class="collapse-arrow bg-base-300 collapse">
+              <input type="checkbox" />
+              <div class="collapse-title text-sm font-medium">Show BibTeX</div>
+              <div class="collapse-content">
+                <pre
+                  class="overflow-x-auto text-xs"
+                ><code>@ARTICLE{Wicker2016enviPath,
+    title = "enviPath – The environmental contaminant biotransformation pathway resource",
+    author = "Wicker, J{\"o}rg and Lorsbach, Tim and Gütlein, Martin and Schmid,
+                  Emanuel and Latino, Diogo and Kramer, Stefan and Fenner, Kathrin",
+    journal = "Nucleic Acids Research",
+    volume = 44,
+    number = "D1",
+    pages = "D502-D508",
+    year = 2016,
+    month = jan,
+    doi = "10.1093/nar/gkv1229"
 }</code></pre>
               </div>
             </div>
@@ -103,57 +148,47 @@ doi       = "10.1186/s13321-024-00881-6"
         <div class="card bg-base-200 mb-6">
           <div class="card-body">
             <h3 class="mb-2 font-semibold">
-              Predicting Biodegradation Pathways Using a Hybrid Relative
-              Reasoning Model
+              A Hybrid Machine Learning and Knowledge Based Approach to Limit
+              Combinatorial Explosion in Biodegradation Prediction
             </h3>
             <p class="mb-4 text-sm">
-              <strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L.,
-              Kramer, S.<br />
-              <strong>Journal:</strong> Biotechnology and Bioengineering,
-              110(3), 837-846<br />
-              <strong>Year:</strong> 2013<br />
+              <strong>Authors:</strong> Wicker, J., Fenner, K., Kramer, S.<br />
+              <strong>Book:</strong> Computational Sustainability, 75-97<br />
+              <strong>Year:</strong> 2016<br />
               <strong>DOI:</strong>
               <a
-                href="https://doi.org/10.1002/bit.24744"
+                href="https://doi.org/10.1007/978-3-319-31858-5_5"
                 target="_blank"
                 class="link link-primary"
-                >10.1002/bit.24744</a
+                >10.1007/978-3-319-31858-5_5</a
               >
             </p>
             <div class="collapse-arrow bg-base-300 collapse">
               <input type="checkbox" />
               <div class="collapse-title text-sm font-medium">Show BibTeX</div>
               <div class="collapse-content">
-                <pre
-                  class="overflow-x-auto text-xs"
-                ><code>@article{wicker2013predicting,
-  title={Predicting biodegradation pathways using a hybrid relative reasoning model},
-  author={Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Kramer, Stefan},
-  journal={Biotechnology and Bioengineering},
-  volume={110},
-  number={3},
-  pages={837--846},
-  year={2013},
-  publisher={Wiley Online Library},
-  doi={10.1002/bit.24744}
+                <pre class="overflow-x-auto text-xs"><code>@INBOOK{Wicker2016ML,
+    title="A Hybrid Machine Learning and Knowledge Based Approach to
+                      Limit Combinatorial Explosion in Biodegradation Prediction",
+    author="Wicker, J{\"o}rg and Fenner, Kathrin and Kramer, Stefan",
+    editor="L{\"a}ssig, J{\"o}rg and Kersting, Kristian and Morik, Katharina",
+    bookTitle="Computational Sustainability",
+    year=2016,
+    publisher="Springer International Publishing",
+    pages="75--97",
+    doi="10.1007/978-3-319-31858-5_5"
 }</code></pre>
               </div>
             </div>
           </div>
         </div>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          Machine Learning Models
-        </h2>
-
-        <h3 class="mt-6 mb-3 text-xl font-semibold">
-          enviPath-Transformer (Latest ML Model)
-        </h3>
         <div class="card bg-base-200 mb-6">
           <div class="card-body">
-            <p class="mb-2 text-sm">
-              If you use the Transformer-based prediction model, please cite:
-            </p>
+            <h3 class="mb-2 font-semibold">
+              Predictive modeling of biodegradation pathways using transformer
+              architectures
+            </h3>
             <p class="mb-4 text-sm">
               <strong>Authors:</strong> Brydon, L., Zhang, K., Dobbie, G.,
               Taškova, K., and Wicker, J.<br />
@@ -167,31 +202,118 @@ doi       = "10.1186/s13321-024-00881-6"
                 >10.1186/s13321-025-00969-7</a
               >
             </p>
+            <div class="collapse-arrow bg-base-300 collapse">
+              <input type="checkbox" />
+              <div class="collapse-title text-sm font-medium">Show BibTeX</div>
+              <div class="collapse-content">
+                <pre
+                  class="overflow-x-auto text-xs"
+                ><code>@article{Brydon2025Transformer,
+    title = "Predictive modeling of biodegradation pathways using transformer architectures",
+    author = "Brydon, Liam and Zhang, Kunyang and Dobbie, Gillian and
+                  Ta\v{s}kova, Katerina and Wicker, J{\"o}rg Simon",
+    journal = "Journal of Cheminformatics",
+    volume = 17,
+    number = 1,
+    pages = "1--16",
+    year = 2025,
+    month = feb,
+    doi = "10.1186/s13321-025-00969-7",
+}</code></pre>
+              </div>
+            </div>
           </div>
         </div>
 
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          Machine Learning Models
+        </h2>
+
         <h3 class="mt-6 mb-3 text-xl font-semibold">
           Relative Reasoning Models
         </h3>
+        <p class="mb-4">
+          For relative reasoning and machine learning approaches, please cite:
+        </p>
         <div class="card bg-base-200 mb-6">
           <div class="card-body">
-            <p class="mb-2 text-sm">
-              For relative reasoning and machine learning approaches:
-            </p>
+            <h3 class="mb-2 font-semibold">
+              Predicting biodegradation products and pathways: a hybrid
+              knowledge- and machine learning-based approach
+            </h3>
             <p class="mb-4 text-sm">
-              <strong>Authors:</strong> Fenner, K., Gao, J., Kramer, S., Ellis,
-              L., Wackett, L.<br />
-              <strong>Journal:</strong> Environmental Science & Technology,
-              42(15), 5761-5767<br />
+              <strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L.,
+              Wackett, L., Kramer, S.<br />
+              <strong>Journal:</strong> Bioinformatics, 26(6), 814-821<br />
+              <strong>Year:</strong> 2010<br />
+              <strong>DOI:</strong>
+              <a
+                href="https://doi.org/10.1093/bioinformatics/btq024"
+                target="_blank"
+                class="link link-primary"
+                >10.1093/bioinformatics/btq024</a
+              >
+            </p>
+            <div class="collapse-arrow bg-base-300 collapse">
+              <input type="checkbox" />
+              <div class="collapse-title text-sm font-medium">Show BibTeX</div>
+              <div class="collapse-content">
+                <pre class="overflow-x-auto text-xs"><code>@ARTICLE{Wicker2010,
+    title = "Predicting biodegradation products and pathways:
+                  a hybrid knowledge- and machine learning-based approach",
+    author = "Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Wackett, Larry and Kramer, Stefan",
+    journal = "Bioinformatics",
+    volume = 26,
+    number = 6,
+    pages = "814-821",
+    year = 2010,
+    month = jan,
+    doi = "10.1093/bioinformatics/btq024"
+}</code></pre>
+              </div>
+            </div>
+          </div>
+        </div>
+
+        <div class="card bg-base-200 mb-6">
+          <div class="card-body">
+            <h3 class="mb-2 font-semibold">
+              Data-driven extraction of relative reasoning rules to limit
+              combinatorial explosion in biodegradation pathway prediction
+            </h3>
+            <p class="mb-4 text-sm">
+              <strong>Authors:</strong> Fenner, K., Junfeng, G., Kramer, S.,
+              Ellis, L., Wackett, L.<br />
+              <strong>Journal:</strong> Bioinformatics, 26(18), 2079-2085<br />
               <strong>Year:</strong> 2008<br />
               <strong>DOI:</strong>
               <a
-                href="https://doi.org/10.1021/es800408g"
+                href="https://doi.org/10.1093/bioinformatics/btn378"
                 target="_blank"
                 class="link link-primary"
-                >10.1021/es800408g</a
+                >10.1093/bioinformatics/btn378</a
               >
             </p>
+            <div class="collapse-arrow bg-base-300 collapse">
+              <input type="checkbox" />
+              <div class="collapse-title text-sm font-medium">Show BibTeX</div>
+              <div class="collapse-content">
+                <pre
+                  class="overflow-x-auto text-xs"
+                ><code>@ARTICLE{Fenner2008Reason,
+    title = "Data-driven extraction of relative reasoning rules to
+                  limit combinatorial explosion in biodegradation pathway prediction",
+    author = "Fenner, Kathrin and Gao, Junfeng and Kramer, Stefan and Ellis, Lynda and Wackett, Larry",
+    journal = "Bioinformatics",
+    volume = 24,
+    number = 18,
+    pages = "2079-2085",
+    year = 2008,
+    month = 07,
+    doi = "10.1093/bioinformatics/btn378"
+}</code></pre>
+              </div>
+            </div>
           </div>
         </div>
 
@@ -234,22 +356,13 @@ doi       = "10.1186/s13321-024-00881-6"
         <ul class="mb-6 list-inside list-disc space-y-2">
           <li>
             <a
-              href="https://community.envipath.org/"
+              href="https://community.envipath.org/t/envipath-publications/"
               target="_blank"
               class="link link-primary"
             >
               enviPath Community - Publications Section
             </a>
           </li>
-          <li>
-            <a
-              href="https://wiki.envipath.org/"
-              target="_blank"
-              class="link link-primary"
-            >
-              enviPath Documentation - References
-            </a>
-          </li>
         </ul>
 
         <div class="alert alert-success mt-8">

templates/static/contact.html

@@ -79,7 +79,7 @@
               <p>Browse our comprehensive documentation and tutorials.</p>
               <div class="card-actions justify-end">
                 <a
-                  href="https://wiki.envipath.org/"
+                  href="https://community.envipath.org/c/documentation"
                   target="_blank"
                   class="btn btn-neutral"
                   >Read Docs</a
@@ -139,6 +139,18 @@
             <h3 class="card-title">enviPath Ltd.</h3>
             <p>Biodegradation prediction since 2015</p>
             <div class="mt-4 flex gap-4">
+              <a
+                href="https://envipath.com/"
+                target="_blank"
+                class="btn btn-outline btn-sm"
+              >
+                <img
+                  src="{% static '/images/logo-square.svg' %}"
+                  width="24"
+                  height="24"
+                />
+                enviPath.com
+              </a>
               <a
                 href="https://www.linkedin.com/company/envipath/"
                 target="_blank"
@@ -208,7 +220,7 @@
                 Simply visit our homepage and try the prediction tool! For full
                 access to all features, create a free account. Check out our
                 <a
-                  href="https://wiki.envipath.org/"
+                  href="https://community.envipath.org/c/documentation"
                   target="_blank"
                   class="link link-primary"
                   >documentation</a

templates/static/cookie_policy.html

@@ -39,20 +39,35 @@
           </li>
           <li>
             <strong>Analytics Cookies:</strong> Help us understand how visitors
-            interact with our platform
+            interact with our platform (where enabled)
           </li>
           <li>
             <strong>Functional Cookies:</strong> Enable enhanced functionality
             and personalization
           </li>
           <li>
-            <strong>Security Cookies:</strong> Authenticate users and prevent
-            fraudulent use
+            <strong>Security Cookies:</strong> Authenticate users and help
+            prevent fraudulent use
           </li>
         </ul>
 
         <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          3. Types of Cookies We Use
+          3. Legal Basis and Consent
+        </h2>
+        <p class="mb-4">
+          Essential cookies are used because they are necessary for the Platform
+          to operate securely and reliably.
+        </p>
+        <p class="mb-4">
+          Where required by applicable law,
+          <strong>non-essential cookies</strong> are only set after you provide
+          your consent. You can withdraw or change your consent at any time
+          using any cookie management tools provided on the Platform (if
+          available) and/or through your browser settings.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          4. Types of Cookies We Use
         </h2>
 
         <div class="mb-6 overflow-x-auto">
@@ -77,25 +92,30 @@
               </tr>
               <tr>
                 <td><strong>Matomo Analytics</strong></td>
-                <td>Track usage patterns and improve our services</td>
-                <td>13 months</td>
+                <td>Measure usage patterns and improve our services</td>
               </tr>
               <tr>
                 <td><strong>OAuth Tokens</strong></td>
                 <td>Authentication and authorization for API access</td>
-                <td>Varies</td>
+                <td>Varies (typically session-based or time-limited)</td>
               </tr>
             </tbody>
           </table>
         </div>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">4. Matomo Analytics</h2>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">5. Matomo Analytics</h2>
         <p class="mb-4">
-          We use Matomo, an open-source web analytics platform, to collect
-          information about how visitors use enviPath. Matomo uses cookies to
-          collect standard internet log information and visitor behavior
-          patterns. The information generated by cookies about your use of the
-          platform is transmitted to our servers.
+          We use Matomo, an open-source web analytics platform, to help us
+          understand how visitors use enviPath. Where enabled, Matomo may use
+          cookies and similar technologies to collect standard internet log
+          information and information about visitor behavior patterns.
+        </p>
+        <p class="mb-4">
+          Where required by law, Matomo analytics cookies are only activated
+          after user consent. We configure Matomo to minimise data collection
+          and, where applicable, to anonymise IP addresses. Analytics data is
+          used solely for internal analytics, platform improvement, and system
+          monitoring.
         </p>
         <p class="mb-4">We analyze this information to:</p>
         <ul class="mb-4 list-inside list-disc space-y-2">
@@ -105,10 +125,14 @@
           <li>Generate reports on platform usage</li>
         </ul>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">5. Third-Party Cookies</h2>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">6. Third-Party Cookies</h2>
         <p class="mb-4">
-          In addition to our own cookies, we may use various third-party cookies
-          to report usage statistics and provide integrated services:
+          Some features of the Platform may integrate third-party services.
+          These third parties may set their own cookies and process information
+          independently in accordance with their own privacy and cookie
+          policies. We do not control the operation of third-party cookies and
+          recommend reviewing the relevant third-party policies for further
+          information.
         </p>
         <ul class="mb-4 list-inside list-disc space-y-2">
           <li>
@@ -116,12 +140,12 @@
             community.envipath.org
           </li>
           <li>
-            <strong>External CDNs:</strong> For loading libraries like jQuery
-            and Font Awesome
+            <strong>External CDNs:</strong> For loading libraries and assets
+            (for example, jQuery and Font Awesome)
           </li>
         </ul>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">6. Managing Cookies</h2>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">7. Managing Cookies</h2>
         <p class="mb-4">
           Most web browsers allow you to control cookies through their settings.
           However, if you limit the ability of websites to set cookies, you may
@@ -144,7 +168,7 @@
             />
           </svg>
           <span
-            ><strong>Note:</strong> Disabling essential cookies will prevent you
+            ><strong>Note:</strong> Disabling essential cookies may prevent you
             from using certain features of enviPath.</span
           >
         </div>
@@ -171,15 +195,15 @@
         </ul>
 
         <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          7. Updates to This Policy
+          8. Updates to This Policy
         </h2>
         <p class="mb-4">
           We may update this Cookie Policy from time to time to reflect changes
           in technology, legislation, or our operations. Please check this page
-          regularly for updates.
+          regularly for updates. Changes take effect when posted.
         </p>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">8. Contact Us</h2>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">9. Contact Us</h2>
         <p class="mb-4">
           If you have questions about our use of cookies, please
           <a href="/contact" class="link link-primary">contact us</a>.
@@ -199,7 +223,7 @@
               d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"
             ></path>
           </svg>
-          <span>Last updated: 2025</span>
+          <span>version: 1, Last updated: January 2026</span>
         </div>
       </div>
     </div>

templates/static/legal.html

@@ -1,215 +0,0 @@
-{% extends "framework_modern.html" %}
-{% load static %}
-
-{% block main_content %}
-  <div class="mx-auto max-w-4xl px-4 py-8">
-    <!-- Breadcrumbs -->
-    <div class="breadcrumbs mb-4 text-sm">
-      <ul>
-        <li><a href="/">Home</a></li>
-        <li>Legal</li>
-      </ul>
-    </div>
-
-    <!-- Main Content -->
-    <div class="bg-base-100 rounded-lg p-8 shadow-xl">
-      <h1 class="mb-6 text-4xl font-bold">Legal Information</h1>
-
-      <div class="prose max-w-none">
-        <p class="mb-6 text-lg">
-          Welcome to enviPath's legal information center. Here you can find all
-          our legal documents, policies, and terms that govern the use of our
-          platform.
-        </p>
-
-        <!-- Legal Documents Grid -->
-        <div class="mb-8 grid gap-6 md:grid-cols-2">
-          <!-- Terms of Use -->
-          <div class="card bg-base-200 shadow-md">
-            <div class="card-body">
-              <h3 class="card-title text-primary">
-                <svg
-                  xmlns="http://www.w3.org/2000/svg"
-                  class="h-6 w-6"
-                  fill="none"
-                  viewBox="0 0 24 24"
-                  stroke="currentColor"
-                >
-                  <path
-                    stroke-linecap="round"
-                    stroke-linejoin="round"
-                    stroke-width="2"
-                    d="M9 12h6m-6 4h6m2 5H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z"
-                  />
-                </svg>
-                Terms of Use
-              </h3>
-              <p class="mb-4 text-sm">
-                Our terms and conditions that govern the use of enviPath
-                services, including licensing, user responsibilities, and
-                platform usage guidelines.
-              </p>
-              <div class="card-actions justify-end">
-                <a href="/terms" class="btn btn-primary btn-sm">Read Terms</a>
-              </div>
-            </div>
-          </div>
-
-          <!-- Privacy Policy -->
-          <div class="card bg-base-200 shadow-md">
-            <div class="card-body">
-              <h3 class="card-title text-primary">
-                <svg
-                  xmlns="http://www.w3.org/2000/svg"
-                  class="h-6 w-6"
-                  fill="none"
-                  viewBox="0 0 24 24"
-                  stroke="currentColor"
-                >
-                  <path
-                    stroke-linecap="round"
-                    stroke-linejoin="round"
-                    stroke-width="2"
-                    d="M12 15v2m-6 4h12a2 2 0 002-2v-6a2 2 0 00-2-2H6a2 2 0 00-2 2v6a2 2 0 002 2zm10-10V7a4 4 0 00-8 0v4h8z"
-                  />
-                </svg>
-                Privacy Policy
-              </h3>
-              <p class="mb-4 text-sm">
-                How we collect, use, and protect your personal information when
-                you use enviPath, including data handling practices and your
-                privacy rights.
-              </p>
-              <div class="card-actions justify-end">
-                <a href="/privacy" class="btn btn-primary btn-sm"
-                  >Read Policy</a
-                >
-              </div>
-            </div>
-          </div>
-
-          <!-- Cookie Policy -->
-          <div class="card bg-base-200 shadow-md">
-            <div class="card-body">
-              <h3 class="card-title text-primary">
-                <svg
-                  xmlns="http://www.w3.org/2000/svg"
-                  class="h-6 w-6"
-                  fill="none"
-                  viewBox="0 0 24 24"
-                  stroke="currentColor"
-                >
-                  <path
-                    stroke-linecap="round"
-                    stroke-linejoin="round"
-                    stroke-width="2"
-                    d="M9 19v-6a2 2 0 00-2-2H5a2 2 0 00-2 2v6a2 2 0 002 2h2a2 2 0 002-2zm0 0V9a2 2 0 012-2h2a2 2 0 012 2v10m-6 0a2 2 0 002 2h2a2 2 0 002-2m0 0V5a2 2 0 012-2h2a2 2 0 012 2v14a2 2 0 01-2 2h-2a2 2 0 01-2-2z"
-                  />
-                </svg>
-                Cookie Policy
-              </h3>
-              <p class="mb-4 text-sm">
-                Information about the cookies and tracking technologies we use
-                on enviPath, including analytics and essential functionality
-                cookies.
-              </p>
-              <div class="card-actions justify-end">
-                <a href="/cookie-policy" class="btn btn-primary btn-sm"
-                  >Read Policy</a
-                >
-              </div>
-            </div>
-          </div>
-
-          <!-- Citation Guidelines -->
-          <div class="card bg-base-200 shadow-md">
-            <div class="card-body">
-              <h3 class="card-title text-primary">
-                <svg
-                  xmlns="http://www.w3.org/2000/svg"
-                  class="h-6 w-6"
-                  fill="none"
-                  viewBox="0 0 24 24"
-                  stroke="currentColor"
-                >
-                  <path
-                    stroke-linecap="round"
-                    stroke-linejoin="round"
-                    stroke-width="2"
-                    d="M9 12h6m-6 4h6m2 5H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z"
-                  />
-                </svg>
-                Citation Guidelines
-              </h3>
-              <p class="mb-4 text-sm">
-                How to properly cite enviPath in your research publications and
-                academic work, including recommended citation formats and
-                acknowledgments.
-              </p>
-              <div class="card-actions justify-end">
-                <a href="/cite" class="btn btn-primary btn-sm"
-                  >View Guidelines</a
-                >
-              </div>
-            </div>
-          </div>
-        </div>
-
-        <!-- Quick Access Section -->
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">Quick Access</h2>
-        <div class="mb-6 grid gap-4 md:grid-cols-3">
-          <a href="/terms" class="btn btn-outline btn-sm w-full"
-            >Terms of Use</a
-          >
-          <a href="/privacy" class="btn btn-outline btn-sm w-full"
-            >Privacy Policy</a
-          >
-          <a href="/cookie-policy" class="btn btn-outline btn-sm w-full"
-            >Cookie Policy</a
-          >
-        </div>
-
-        <!-- Important Information -->
-        <div class="alert alert-info mt-8">
-          <svg
-            xmlns="http://www.w3.org/2000/svg"
-            fill="none"
-            viewBox="0 0 24 24"
-            class="h-6 w-6 shrink-0 stroke-current"
-          >
-            <path
-              stroke-linecap="round"
-              stroke-linejoin="round"
-              stroke-width="2"
-              d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"
-            ></path>
-          </svg>
-          <div>
-            <h3 class="font-bold">Important Notice</h3>
-            <p class="text-sm">
-              By using enviPath, you agree to be bound by our Terms of Use and
-              Privacy Policy. We recommend reviewing these documents regularly
-              as they may be updated from time to time. For questions about our
-              legal policies, please
-              <a href="/contact" class="link link-primary">contact us</a>.
-            </p>
-          </div>
-        </div>
-
-        <!-- Contact Information -->
-        <div class="card bg-primary text-primary-content mt-8">
-          <div class="card-body">
-            <h3 class="card-title">Questions About Our Legal Policies?</h3>
-            <p>
-              If you have any questions or concerns about our legal documents,
-              please don't hesitate to reach out to us.
-            </p>
-            <div class="card-actions mt-4 justify-end">
-              <a href="/contact" class="btn btn-secondary">Contact Us</a>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-{% endblock main_content %}

templates/static/login.html

@@ -31,6 +31,32 @@
 {% endblock %}
 
 {% block content %}
+  <div class="card bg-base-200 mb-6 ">
+    <div class="card-body">
+      <h3 class="card-title">Welcome to the new enviPath!</h3>
+      <p class="mb-4 text-sm">
+        Rebuilt from the ground up for faster predictions, greater stability,
+        and powerful scalability. Explore a decade of research on a modern,
+        reliable platform.<br />
+        The old system is still accessible but will be shut down at a later
+        date. If you want to back up your data, download it from the
+        <a
+          href="https://legacy.envipath.org"
+          class="link link-primary"
+          target="_blank"
+          >old system</a
+        >
+        or contact us via the
+        <a
+          href="https://community.envipath.org/"
+          class="link link-primary"
+          target="_blank"
+          >community forum</a
+        >
+        for assistance.
+      </p>
+    </div>
+  </div>
   <!-- Tab Navigation -->
   <div class="border-base-300 mb-6 border-b">
     <div class="flex justify-start">
@@ -190,6 +216,22 @@
 
       <input type="hidden" name="next" value="{{ next }}" />
 
+      <!-- ToS and Academic Use Notice -->
+      <div class="text-xs text-base-content/70 mt-2">
+        <p>
+          By clicking Sign Up, you agree to our
+          <a
+            href="{% url 'terms_of_use' %}"
+            target="_blank"
+            class="link link-primary"
+            >Terms of Use</a
+          >.
+        </p>
+        <p class="mt-1 font-semibold">
+          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/privacy_policy.html

@@ -18,153 +18,304 @@
       <div class="prose max-w-none">
         <p class="mb-6 text-lg">
           enviPath is committed to protecting your privacy. This Privacy Policy
-          explains how we collect, use, disclose, and safeguard your information
-          when you use our platform.
+          explains how we collect, use, disclose, and safeguard personal
+          information when you use the enviPath platform and related services
+          (together, the "Platform").
         </p>
 
         <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          1. Information We Collect
+          1. Who We Are (Data Controller)
+        </h2>
+        <p class="mb-4">
+          enviPath is operated by enviPath Limited, a legal entity established
+          in New Zealand, with its principal place of business in Auckland, New
+          Zealand ("enviPath", "we", "us", or "our").
+        </p>
+        <p class="mb-4">
+          For the purposes of applicable data protection laws, enviPath Limited
+          is the data controller responsible for personal information processed
+          through the Platform.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          2. Information We Collect
         </h2>
 
-        <h3 class="mt-6 mb-3 text-xl font-semibold">Personal Information</h3>
+        <h3 class="mt-6 mb-3 text-xl font-semibold">
+          2.1 Personal Information You Provide
+        </h3>
         <p class="mb-4">
           We may collect personal information that you voluntarily provide when
           you:
         </p>
         <ul class="mb-4 list-inside list-disc space-y-2">
           <li>Register for an account</li>
-          <li>Use our prediction services</li>
-          <li>Submit data or pathways</li>
           <li>Contact our support team</li>
-          <li>Participate in our community forums</li>
+          <li>
+            Participate in community forums or other community features (where
+            available)
+          </li>
         </ul>
         <p class="mb-4">
-          This information may include: name, email address, institution
-          affiliation, and research interests.
+          This may include your name, email address, institution affiliation,
+          and research interests (if provided).
         </p>
 
-        <h3 class="mt-6 mb-3 text-xl font-semibold">Usage Data</h3>
+        <h3 class="mt-6 mb-3 text-xl font-semibold">
+          2.2 Usage and Technical Data
+        </h3>
         <p class="mb-4">
           We automatically collect certain information when you visit, use, or
-          navigate the platform. This includes:
-        </p>
-        <ul class="mb-4 list-inside list-disc space-y-2">
-          <li>IP address and browser type</li>
-          <li>Pages visited and time spent</li>
-          <li>Referring/exit pages</li>
-          <li>Prediction queries and results</li>
-          <li>Operating system and device information</li>
-        </ul>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          2. How We Use Your Information
-        </h2>
-        <p class="mb-4">We use the information we collect to:</p>
-        <ul class="mb-4 list-inside list-disc space-y-2">
-          <li>Provide, operate, and maintain our services</li>
-          <li>Improve and personalize user experience</li>
-          <li>Understand and analyze usage patterns</li>
-          <li>Develop new features and services</li>
-          <li>Communicate with you about updates and support</li>
-          <li>Prevent fraudulent activities and ensure security</li>
-          <li>Conduct research and analysis for scientific advancement</li>
-        </ul>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          3. Data Sharing and Disclosure
-        </h2>
-        <p class="mb-4">
-          We do not sell your personal information. We may share your
-          information in the following situations:
+          navigate the Platform. This may include:
         </p>
         <ul class="mb-4 list-inside list-disc space-y-2">
           <li>
-            <strong>Academic Research:</strong> Anonymized usage data may be
-            used for research purposes
+            IP address, browser type, and device/operating system information
+          </li>
+          <li>Pages or endpoints accessed and time spent</li>
+          <li>Referring/exit pages or URLs (where available)</li>
+          <li>
+            Prediction queries, submitted data, and generated results, including
+            associated metadata, for the purposes of platform functionality,
+            performance monitoring, and research analysis
           </li>
           <li>
-            <strong>Legal Requirements:</strong> When required by law or to
-            protect our rights
-          </li>
-          <li>
-            <strong>Service Providers:</strong> With trusted third parties who
-            assist in operating our platform
-          </li>
-          <li>
-            <strong>Public Data:</strong> Data you explicitly mark as public
-            will be accessible to other users
+            Log and diagnostic information (such as timestamps and error logs)
           </li>
         </ul>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">4. Data Retention</h2>
+        <h3 class="mt-6 mb-3 text-xl font-semibold">
+          2.3 Cookies and Similar Technologies
+        </h3>
         <p class="mb-4">
-          We retain your personal information for as long as necessary to
-          provide our services and fulfill the purposes outlined in this policy.
-          You may request deletion of your account and associated data at any
-          time.
-        </p>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          5. Analytics and Cookies
-        </h2>
-        <p class="mb-4">
-          We use Matomo analytics to understand how users interact with our
-          platform. This helps us improve our services. For more details, see
-          our
+          We use cookies and similar technologies for essential functionality
+          and, where applicable, analytics. For more details, see our
           <a href="/cookie-policy" class="link link-primary">Cookie Policy</a>.
         </p>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">6. Data Security</h2>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          3. How We Use Your Information
+        </h2>
         <p class="mb-4">
-          We implement appropriate technical and organizational security
-          measures to protect your personal information. However, no electronic
-          transmission or storage is 100% secure, and we cannot guarantee
-          absolute security.
-        </p>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">7. Your Rights</h2>
-        <p class="mb-4">
-          Depending on your location, you may have the following rights:
+          We collect and use personal information only where necessary for
+          legitimate and lawful purposes connected with operation and
+          improvement of the Platform. These purposes include:
         </p>
         <ul class="mb-4 list-inside list-disc space-y-2">
-          <li>Access to your personal data</li>
-          <li>Correction of inaccurate data</li>
-          <li>Deletion of your data</li>
-          <li>Restriction of processing</li>
-          <li>Data portability</li>
-          <li>Objection to processing</li>
+          <li>Providing, operating, and maintaining the Platform</li>
+          <li>
+            Creating and administering user accounts, authentication, and access
+            control
+          </li>
+          <li>Responding to enquiries and providing support</li>
+          <li>
+            Monitoring usage patterns and improving Platform functionality,
+            performance, and usability
+          </li>
+          <li>
+            Ensuring Platform security, preventing misuse, and investigating
+            suspected breaches
+          </li>
+          <li>
+            Conducting scientific research and statistical analysis using
+            <strong>anonymised or aggregated data only</strong>, such that
+            individuals are not identifiable in published outputs
+          </li>
+          <li>
+            Complying with legal obligations and responding to lawful requests
+          </li>
         </ul>
 
         <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          8. Third-Party Services
+          4. Legal Bases for Processing (EEA, UK, and Swiss Users)
         </h2>
         <p class="mb-4">
-          Our platform may contain links to third-party websites or integrate
-          with external services (e.g., Discourse community forums). We are not
-          responsible for the privacy practices of these third parties.
+          Where the GDPR (or similar laws) applies, we process personal data on
+          the following legal bases:
         </p>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">9. Children's Privacy</h2>
+        <ul class="mb-4 list-inside list-disc space-y-2">
+          <li>
+            <strong>Performance of a contract</strong> (to provide access to the
+            Platform and its services)
+          </li>
+          <li>
+            <strong>Legitimate interests</strong> (such as operating the
+            Platform, improving functionality, conducting anonymised research,
+            ensuring security, and maintaining service reliability)
+          </li>
+          <li>
+            <strong>Compliance with legal obligations</strong> (where
+            applicable)
+          </li>
+          <li>
+            <strong>Consent</strong> (where required, for example for
+            non-essential cookies)
+          </li>
+        </ul>
         <p class="mb-4">
-          enviPath is not intended for users under the age of 16. We do not
-          knowingly collect personal information from children. If you believe
-          we have collected information from a child, please contact us.
+          Where processing is based on consent, you may withdraw your consent at
+          any time. Withdrawal does not affect the lawfulness of processing
+          before withdrawal.
         </p>
 
         <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          10. Changes to This Policy
+          5. Data Sharing and Disclosure
         </h2>
         <p class="mb-4">
-          We may update this Privacy Policy from time to time. We will notify
-          you of any changes by posting the new policy on this page and updating
-          the "Last updated" date.
+          We do not sell personal information. We only share personal
+          information in the following limited circumstances:
+        </p>
+        <ul class="mb-4 list-inside list-disc space-y-2">
+          <li>
+            <strong>Service Providers:</strong> With trusted third-party
+            providers who process data on our behalf for hosting,
+            authentication, analytics, or technical support, subject to
+            confidentiality and data protection obligations
+          </li>
+          <li>
+            <strong>Academic and Scientific Research:</strong> Using
+            <strong>anonymised or aggregated</strong> data only, such that
+            individuals cannot be identified
+          </li>
+          <li>
+            <strong>Legal and Regulatory Requirements:</strong> Where disclosure
+            is required by law, or necessary to protect our legal rights or the
+            rights and safety of others
+          </li>
+          <li>
+            <strong>Public Contributions:</strong> Content or data that you
+            explicitly designate as public may be accessible to other users and
+            the public (depending on Platform functionality)
+          </li>
+        </ul>
+        <p class="mb-4">
+          We do not authorise third parties to use personal information for
+          their own independent purposes.
         </p>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">11. Contact Us</h2>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          6. International Data Transfers
+        </h2>
         <p class="mb-4">
-          If you have questions or concerns about this Privacy Policy, please
-          <a href="/contact" class="link link-primary">contact us</a>.
+          The Platform is operated from New Zealand. Personal information may be
+          processed or stored in New Zealand and other jurisdictions where we or
+          our service providers operate.
         </p>
+        <p class="mb-4">
+          New Zealand is recognised by the European Commission as providing an
+          adequate level of protection for personal data. Where personal
+          information is transferred to jurisdictions outside the European
+          Economic Area, we take reasonable steps to ensure appropriate
+          safeguards are in place.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">7. Data Retention</h2>
+        <p class="mb-4">
+          We retain personal information only for as long as reasonably
+          necessary to fulfil the purposes described in this Privacy Policy,
+          unless a longer retention period is required or permitted by law.
+        </p>
+        <ul class="mb-4 list-inside list-disc space-y-2">
+          <li>
+            <strong>Account information:</strong> retained for the duration of
+            the user account
+          </li>
+          <li>
+            <strong>Usage and log data:</strong> retained for up to
+            <strong>[X] months</strong>
+          </li>
+          <li>
+            <strong>Backup data:</strong> retained for up to
+            <strong>[Y] months</strong>
+          </li>
+        </ul>
+        <p class="mb-4">
+          You may request deletion of your account and associated personal
+          information at any time, subject to legal or technical retention
+          requirements (for example, security logs and backups retained for
+          limited periods).
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">8. Data Security</h2>
+        <p class="mb-4">
+          We implement appropriate technical and organisational measures
+          designed to protect personal information from loss, unauthorised
+          access, misuse, alteration, or disclosure. However, no electronic
+          transmission or storage method is 100% secure, and we cannot guarantee
+          absolute security.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          9. Your Rights and Choices
+        </h2>
+        <p class="mb-4">
+          Depending on your location, you may have rights relating to your
+          personal information, including:
+        </p>
+        <ul class="mb-4 list-inside list-disc space-y-2">
+          <li>Request access to personal information we hold about you</li>
+          <li>Request correction of inaccurate or incomplete information</li>
+          <li>Request deletion of personal information (where applicable)</li>
+          <li>Object to or restrict certain processing (where applicable)</li>
+          <li>Request data portability (where applicable)</li>
+        </ul>
+        <p class="mb-4">
+          <strong>New Zealand users</strong> have rights under the Privacy Act
+          2020 to request access to, and correction of, personal information.
+        </p>
+        <p class="mb-4">
+          To exercise your rights, please contact us using the details in the
+          "Contact Us" section below. We may need to verify your identity before
+          responding.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          10. Third-Party Services
+        </h2>
+        <p class="mb-4">
+          The Platform may integrate or link to third-party services (for
+          example, community forums such as Discourse). Third-party services
+          operate independently and have their own privacy practices. We
+          encourage you to review their policies.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">11. Children’s Privacy</h2>
+        <p class="mb-4">
+          The Platform is not intended for users under the age of 16. We do not
+          knowingly collect personal information from children. If you believe
+          that we have collected personal information from a child, please
+          contact us so we can take appropriate steps.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          12. Changes to This Policy
+        </h2>
+        <p class="mb-4">
+          We may update this Privacy Policy from time to time. We will post the
+          updated policy on this page and update the "Last updated" date.
+          Changes take effect when posted.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">13. Contact Us</h2>
+        <p class="mb-4">
+          For questions, requests, or concerns about this Privacy Policy or our
+          handling of personal information, please contact us:
+        </p>
+        <ul class="mb-4 list-inside list-disc space-y-2">
+          <li>
+            <strong>Email:</strong>
+            <a href="mailto:privacy@envipath.org" class="link link-primary"
+              >privacy@envipath.org</a
+            >
+          </li>
+          <li>
+            <strong>Contact:</strong>
+            <a href="/contact" class="link link-primary">/contact</a>
+          </li>
+          <li>
+            <strong>Operator:</strong> enviPath Limited, Auckland, New Zealand
+          </li>
+        </ul>
 
         <div class="alert alert-info mt-8">
           <svg
@@ -180,7 +331,7 @@
               d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"
             ></path>
           </svg>
-          <span>Last updated: 2025</span>
+          <span>version: 1, Last updated: January 2026</span>
         </div>
       </div>
     </div>

templates/static/terms_of_use.html

@@ -17,65 +17,363 @@
 
       <div class="prose max-w-none">
         <p class="mb-6 text-lg">
-          Welcome to enviPath. By accessing and using this platform, you agree
-          to be bound by these terms of use.
-        </p>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">1. Acceptance of Terms</h2>
-        <p class="mb-4">
-          By accessing and using enviPath, you accept and agree to be bound by
-          the terms and provision of this agreement. If you do not agree to
-          these terms, please do not use our services.
-        </p>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">2. Use License</h2>
-        <p class="mb-4">
-          Permission is granted to temporarily access the materials (information
-          or software) on enviPath for personal, non-commercial research and
-          educational use only. This is the grant of a license, not a transfer
-          of title.
-        </p>
-        <p class="mb-4">Under this license you may not:</p>
-        <ul class="mb-4 list-inside list-disc space-y-2">
-          <li>Modify or copy the materials</li>
-          <li>Use the materials for any commercial purpose</li>
-          <li>
-            Attempt to decompile or reverse engineer any software contained on
-            enviPath
-          </li>
-          <li>
-            Remove any copyright or other proprietary notations from the
-            materials
-          </li>
-        </ul>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">3. Data and Content</h2>
-        <p class="mb-4">
-          Users may submit, upload, or otherwise make available data and content
-          to enviPath. By doing so, you grant enviPath a license to use, modify,
-          publicly perform, publicly display, reproduce, and distribute such
-          content.
-        </p>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">4. Disclaimer</h2>
-        <p class="mb-4">
-          The materials on enviPath are provided on an 'as is' basis. enviPath
-          makes no warranties, expressed or implied, and hereby disclaims and
-          negates all other warranties including, without limitation, implied
-          warranties or conditions of merchantability, fitness for a particular
-          purpose, or non-infringement of intellectual property.
-        </p>
-
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">5. Limitations</h2>
-        <p class="mb-4">
-          In no event shall enviPath or its suppliers be liable for any damages
-          (including, without limitation, damages for loss of data or profit, or
-          due to business interruption) arising out of the use or inability to
-          use the materials on enviPath.
+          Welcome to enviPath. enviPath is an online scientific platform
+          providing (a) database content about chemical and biotransformation
+          pathways and (b) prediction outputs derived from models and
+          algorithms. Outputs may be incomplete and probabilistic and are
+          intended for research use only.
         </p>
 
         <h2 class="mt-8 mb-4 text-2xl font-semibold">
-          6. Academic Use and Citations
+          1. Acceptance and Agreement
+        </h2>
+        <p class="mb-4">
+          These Terms of Use (the <strong>&ldquo;Terms&rdquo;</strong>) govern
+          your access to and use of enviPath. By creating an account, obtaining
+          or using an API key, clicking &ldquo;I agree&rdquo; (or equivalent),
+          or otherwise accessing or using enviPath, you agree to be bound by
+          these Terms and any policies referenced in them.
+        </p>
+        <p class="mb-4">
+          If you do not agree, you must not access or use enviPath.
+        </p>
+        <p class="mb-4">
+          If you are using enviPath on behalf of an organisation, you represent
+          that you have authority to bind that organisation, and
+          &ldquo;you&rdquo; includes that organisation.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">2. Definitions</h2>
+        <p class="mb-4">In these Terms:</p>
+        <ul class="mb-4 list-inside list-disc space-y-2">
+          <li>
+            <strong>&ldquo;Operator&rdquo;</strong> means the entity operating
+            enviPath.
+          </li>
+          <li>
+            <strong>&ldquo;enviPath&rdquo;</strong> means the enviPath platform,
+            including its databases, software, prediction systems, APIs,
+            documentation, and related services.
+          </li>
+          <li>
+            <strong>&ldquo;Academic Research&rdquo;</strong> means research
+            conducted primarily to generate scholarly knowledge, where:
+            <ul class="mt-2 ml-6 list-disc space-y-1">
+              <li>
+                the results are intended for publication in a scholarly outlet
+                (journal, thesis, dissertation, preprint, or equivalent);
+              </li>
+              <li>
+                the research outputs, methods, and conclusions are made publicly
+                accessible as part of that publication (subject to lawful
+                confidentiality limits); and
+              </li>
+              <li>
+                the research is not conducted for commercial advantage, private
+                financial gain, or the development of proprietary products or
+                services.
+              </li>
+            </ul>
+          </li>
+          <li>
+            <strong>&ldquo;Commercial Use&rdquo;</strong> means any use of
+            enviPath that is not Academic Research, including (without
+            limitation):
+            <ul class="mt-2 ml-6 list-disc space-y-1">
+              <li>
+                use in connection with commercial products, services, or
+                consulting activities;
+              </li>
+              <li>
+                internal research and development within a for-profit
+                organisation;
+              </li>
+              <li>
+                regulatory submissions or compliance activities conducted on
+                behalf of a commercial entity;
+              </li>
+              <li>
+                use to support fee-based services, contract research,
+                commissioned research, or proprietary decision-making; or
+              </li>
+              <li>
+                use where outputs are not made publicly available as part of a
+                scholarly work (except where prevented by law or ethics).
+              </li>
+            </ul>
+          </li>
+          <li>
+            <strong>&ldquo;Mixed-Use&rdquo;</strong> means a use case that
+            includes both academic and commercial elements (for example,
+            industry-sponsored academic research, research conducted under
+            contract, or research whose results are used for internal or
+            commercial decision-making).
+          </li>
+          <li>
+            <strong>&ldquo;User Content&rdquo;</strong> means any data or
+            content you submit, upload, or otherwise make available to enviPath.
+          </li>
+        </ul>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          3. Eligibility, Declarations, and Account Security
+        </h2>
+        <p class="mb-4">
+          You must provide accurate and complete information when creating an
+          account or requesting API access, and keep it up to date.
+        </p>
+        <p class="mb-4">
+          <strong>Academic-use declaration.</strong> Where required by the
+          Operator during signup, API key issuance, or access renewal, you must
+          confirm that your intended use qualifies as Academic Research and is
+          not Commercial Use.
+        </p>
+        <p class="mb-4">
+          You are responsible for maintaining the confidentiality of your
+          credentials and API keys, and for all activity performed under your
+          account or using your API keys. You must promptly notify us of any
+          unauthorised use or suspected compromise.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          4. Permitted Use and Licence
+        </h2>
+        <p class="mb-4">
+          Subject to these Terms, the Operator grants you a limited,
+          non-exclusive, non-transferable, revocable licence to access and use
+          enviPath solely for Academic Research.
+        </p>
+        <p class="mb-4">
+          <strong>Commercial Use prohibited.</strong> All Commercial Use
+          (including Mixed-Use) is prohibited unless you have entered into a
+          separate written commercial licence agreement with the Operator.
+        </p>
+        <p class="mb-4">
+          <strong>Mixed-Use presumption.</strong> Where a use involves Mixed-Use
+          elements, or where results are used for internal decision-making,
+          regulatory purposes, or on behalf of a third party, that use is
+          presumed to be Commercial Use unless the Operator agrees otherwise in
+          writing.
+        </p>
+        <p class="mb-4">
+          If you are unsure whether your intended use is Academic Research, you
+          must contact us before using enviPath. We may request additional
+          information to assess your use case, and we may determine (acting
+          reasonably) whether a particular use is permitted.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">5. Acceptable Use</h2>
+        <p class="mb-4">
+          You must use enviPath only for lawful purposes and in accordance with
+          these Terms and all applicable laws.
+        </p>
+        <p class="mb-4">You must not, directly or indirectly:</p>
+        <ul class="mb-4 list-inside list-disc space-y-2">
+          <li>
+            Use enviPath in a manner that is unlawful, harmful, misleading, or
+            infringes any third-party rights;
+          </li>
+          <li>
+            Attempt to circumvent, probe, or test security, access controls, or
+            technical limitations;
+          </li>
+          <li>
+            Use automated systems (including bots, scrapers, crawlers, or
+            scripts) to access enviPath in a way that degrades performance,
+            bypasses controls, or exceeds reasonable usage limits or published
+            quotas;
+          </li>
+          <li>
+            Systematically extract, cache, reproduce, mirror, republish, or
+            redistribute substantial portions of the database or outputs,
+            whether manually or through automated means, even if individual
+            queries are permitted;
+          </li>
+          <li>
+            Reverse engineer, decompile, disassemble, or otherwise attempt to
+            derive source code, underlying models, parameters, algorithms, or
+            proprietary data (except to the extent expressly permitted by
+            non-excludable law);
+          </li>
+          <li>
+            Use enviPath to develop, train, validate, benchmark, or improve
+            competing databases, models, or commercial products without prior
+            written permission;
+          </li>
+          <li>
+            Interfere with, disrupt, or impose an unreasonable load on enviPath,
+            including through high-volume or abusive query patterns;
+          </li>
+          <li>
+            Use outputs in contexts where incorrect, incomplete, or
+            probabilistic results could reasonably lead to harm without
+            appropriate validation and domain expertise.
+          </li>
+        </ul>
+        <p class="mb-4">
+          We may publish technical documentation, rate limits, quotas, or usage
+          rules. Those rules form part of these Terms.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          6. Monitoring, Logging, and Privacy
+        </h2>
+        <p class="mb-4">
+          We may monitor, log, and analyse usage of enviPath (including API
+          calls, request metadata, and account activity) to operate the service,
+          ensure security, prevent abuse, enforce these Terms, comply with legal
+          obligations, and improve performance and reliability.
+        </p>
+        <p class="mb-4">
+          Our collection, use, storage, and disclosure of personal information
+          is governed by our Privacy Policy, which forms part of these Terms.
+          Please review our
+          <a href="/privacy" class="link link-primary">Privacy Policy</a>.
+        </p>
+        <p class="mb-4">
+          If you provide personal information about others in User Content, you
+          must ensure you have the right to do so and that those individuals
+          have been informed as required by applicable privacy laws.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          7. User-Submitted Content
+        </h2>
+        <p class="mb-4">
+          Users may submit, upload, or otherwise make available User Content to
+          enviPath. You retain ownership of your User Content.
+        </p>
+        <p class="mb-4">
+          By submitting User Content, you grant the Operator a non-exclusive,
+          worldwide, royalty-free licence to use, host, store, reproduce,
+          process, adapt (including to normalise formats), and analyse that User
+          Content solely to operate, maintain, secure, support, improve, and
+          validate enviPath and its scientific outputs (including model
+          validation and quality assurance).
+        </p>
+        <p class="mb-4">
+          For the avoidance of doubt, any enhancements, modifications, or
+          improvements to enviPath (including its models, algorithms, and
+          scientific outputs) that result from or are informed by User Content
+          may be implemented and made available across all licence types and
+          access tiers offered by the Operator for enviPath, including
+          commercial licences, provided that such use remains within and forms
+          part of enviPath.
+        </p>
+
+        <p class="mb-4">
+          The Operator does not sell, licence, or otherwise disclose User
+          Content itself to other users or licensees. Access by commercial or
+          other licensees is limited to enviPath and any improvements thereto,
+          and does not include access to the underlying User Content.
+        </p>
+
+        <p class="mb-4">
+          You represent and warrant that: (a) you have all necessary rights and
+          consents to submit the User Content; and (b) submitting and using the
+          User Content as contemplated by these Terms does not infringe any
+          third-party rights or breach any obligation of confidence.
+        </p>
+
+        <p class="mb-4">
+          You must not submit User Content that is unlawful, harmful,
+          misleading, or infringes any third-party rights.
+        </p>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          8. Intellectual Property
+        </h2>
+        <p class="mb-4">
+          enviPath and all associated intellectual property rights (including
+          software, databases, compilations, documentation, models, algorithms,
+          and trademarks) are owned by or licenced to the Operator and its
+          licensors.
+        </p>
+        <p class="mb-4">
+          Except for the limited licence granted in these Terms, no rights are
+          granted to you. You must not remove or alter any proprietary notices.
+        </p>
+        <p class="mb-4">
+          Where third-party datasets, publications, or open-source components
+          are used, additional licence terms may apply. To the extent there is a
+          conflict, those third-party terms prevail for the relevant component.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          9. Scientific Nature of Outputs
+        </h2>
+        <p class="mb-4">
+          enviPath provides data-driven predictions, transformations, and
+          scientific information that may be incomplete, probabilistic, or
+          subject to error. Outputs are provided for research and informational
+          purposes only and must be independently verified by suitably qualified
+          users before being relied upon.
+        </p>
+        <p class="mb-4">
+          You acknowledge enviPath is not a substitute for experimental
+          validation, regulatory assessment, or professional judgment.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">10. Disclaimer</h2>
+        <p class="mb-4">
+          To the maximum extent permitted by law, enviPath is provided on an
+          &ldquo;as is&rdquo; and &ldquo;as available&rdquo; basis. The Operator
+          disclaims all warranties, representations, and conditions (express or
+          implied), including implied warranties or conditions of
+          merchantability, fitness for a particular purpose, accuracy,
+          availability, and non-infringement.
+        </p>
+        <p class="mb-4">
+          We do not warrant that enviPath will be uninterrupted, timely, secure,
+          or error-free, or that defects will be corrected.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          11. Limitation of Liability
+        </h2>
+        <p class="mb-4">
+          To the maximum extent permitted by law, the Operator (and its
+          contributors, suppliers, partners, and licensors) excludes all
+          liability for any loss or damage arising out of or in connection with
+          enviPath, whether in contract, tort (including negligence), equity,
+          breach of statutory duty, or otherwise.
+        </p>
+        <p class="mb-4">
+          To the maximum extent permitted by law, the Operator will not be
+          liable for any indirect, consequential, special, incidental, or
+          exemplary damages (including loss of profits, loss of revenue, loss of
+          data, loss of goodwill, or business interruption), even if we have
+          been advised of the possibility of such loss.
+        </p>
+        <p class="mb-4">
+          Where liability cannot be excluded, the Operator’s total aggregate
+          liability to you for all claims arising out of or in connection with
+          these Terms or enviPath is limited to the greater of: (a) NZD 100; and
+          (b) any fees paid by you to the Operator for enviPath in the 12 months
+          immediately preceding the event giving rise to the claim.
+        </p>
+        <p class="mb-4">
+          Nothing in these Terms limits any liability that cannot lawfully be
+          excluded.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          12. New Zealand Consumer Law
+        </h2>
+        <p class="mb-4">
+          Nothing in these Terms limits any rights you may have under the
+          Consumer Guarantees Act 1993 (the <strong>&ldquo;CGA&rdquo;</strong>)
+          where those rights cannot lawfully be excluded.
+        </p>
+        <p class="mb-4">
+          If you acquire or use enviPath <strong>in trade</strong> (as defined
+          in the CGA), you warrant that the services are acquired for business
+          purposes. You agree that, to the extent permitted by law, the CGA does
+          not apply, and the parties agree it is fair and reasonable to contract
+          out of the CGA for that supply.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          13. Academic Use and Citations
         </h2>
         <p class="mb-4">
           If you use enviPath in your research, we request that you cite our
@@ -84,29 +382,79 @@
           details.
         </p>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">7. License Information</h2>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          14. Enforcement, Suspension, and Termination
+        </h2>
         <p class="mb-4">
-          For detailed license information about enviPath data and software,
+          We may suspend, restrict, throttle, or terminate your access to
+          enviPath (including disabling API keys) where we reasonably believe
+          you have violated these Terms, exceeded usage limits, engaged in
+          abusive or high-volume access, attempted scraping or model extraction,
+          or otherwise used enviPath inconsistently with its intended purpose.
+        </p>
+        <p class="mb-4">
+          Where practicable, we will provide notice and an opportunity to remedy
+          before taking action. However, we may take immediate action without
+          notice where we reasonably consider it necessary to protect enviPath,
+          other users, data integrity, security, service availability, or our
+          legal interests.
+        </p>
+        <p class="mb-4">
+          Termination does not affect any rights or obligations that by their
+          nature should survive termination, including intellectual property,
+          disclaimers, limitations of liability, and governing law.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          15. Licence Information and Third-Party Terms
+        </h2>
+        <p class="mb-4">
+          For detailed licence information about enviPath data and software,
           please refer to the
           <a
             href="https://community.envipath.org/t/envipath-license/109"
             target="_blank"
+            rel="noopener noreferrer"
             class="link link-primary"
           >
-            enviPath License documentation </a
-          >.
+            enviPath licence documentation </a
+          >. Where third-party licences apply, you agree to comply with them.
         </p>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">8. Modifications</h2>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          16. Changes to These Terms
+        </h2>
         <p class="mb-4">
-          enviPath may revise these terms of use at any time without notice. By
-          using this platform, you are agreeing to be bound by the then current
-          version of these terms of use.
+          We may update these Terms from time to time. The updated Terms will be
+          posted on this page with a revised &ldquo;Last updated&rdquo; date.
+          Material changes may be notified through the platform (for example, at
+          login or via the API dashboard). Your continued use after the
+          effective date of an update constitutes acceptance of the updated
+          Terms.
+        </p>
+        <p class="mb-4">
+          For certain changes, we may require you to actively re-accept the
+          Terms (for example, when obtaining or renewing API keys).
         </p>
 
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">9. Contact Information</h2>
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">
+          17. Governing Law and Jurisdiction
+        </h2>
         <p class="mb-4">
-          If you have any questions about these Terms of Use, please
+          These Terms are governed by and construed in accordance with the laws
+          of New Zealand. To the extent permitted by law, you submit to the
+          exclusive jurisdiction of the courts of New Zealand for any dispute
+          arising out of or in connection with these Terms or enviPath.
+        </p>
+        <p class="mb-4">
+          Mandatory consumer protection laws in your jurisdiction may still
+          apply where they cannot be excluded.
+        </p>
+
+        <h2 class="mt-8 mb-4 text-2xl font-semibold">18. Contact</h2>
+        <p class="mb-4">
+          If you have questions about these Terms, or wish to request a
+          commercial licence, please
           <a href="/contact" class="link link-primary">contact us</a>.
         </p>
 
@@ -124,7 +472,7 @@
               d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"
             ></path>
           </svg>
-          <span>Last updated: 2025</span>
+          <span>version: 1, Last updated: January 2026</span>
         </div>
       </div>
     </div>

tests/test_ruleapplication.py

@@ -37,7 +37,7 @@ class RuleApplicationTest(TestCase):
 
     def tearDown(self):
         super().tearDown()
-        print(f"\nTotal errors {self.total_errors}")
+        # print(f"\nTotal errors {self.total_errors}")
 
     @staticmethod
     def normalize_smiles(smiles):

utilities/chem.py

@@ -2,14 +2,12 @@ import logging
 import re
 from abc import ABC
 from collections import defaultdict
-from typing import List, Optional, Dict, TYPE_CHECKING, Union
+from typing import TYPE_CHECKING, Dict, List, Optional, Union
 
 from indigo import Indigo, IndigoException, IndigoObject
 from indigo.renderer import IndigoRenderer
 from rdkit import Chem, rdBase
-from rdkit.Chem import MACCSkeys, Descriptors, rdFingerprintGenerator
-from rdkit.Chem import rdchem
-from rdkit.Chem import rdChemReactions
+from rdkit.Chem import Descriptors, MACCSkeys, rdchem, rdChemReactions, rdFingerprintGenerator
 from rdkit.Chem.Draw import rdMolDraw2D
 from rdkit.Chem.MolStandardize import rdMolStandardize
 from rdkit.Chem.rdmolops import GetMolFrags
@@ -335,9 +333,14 @@ class FormatConverter(object):
 
             # Inplace
             if preprocess_smiles:
+                # from rdkit.Chem.rdmolops import AROMATICITY_RDKIT
+                # Chem.SetAromaticity(mol, AROMATICITY_RDKIT)
                 Chem.SanitizeMol(mol)
                 mol = Chem.AddHs(mol)
 
+                # for std in BASIC:
+                #     mol = std.standardize(mol)
+
             # Check if reactant_filter_smarts matches and we shouldn't apply the rule
             if reactant_filter_smarts and FormatConverter.smarts_matches(
                 mol, reactant_filter_smarts
@@ -376,29 +379,6 @@ class FormatConverter(object):
 
                                 prods.append(p)
 
-                            # if kekulize:
-                            #     # from rdkit.Chem import MolStandardize
-                            #     #
-                            #     # # Attempt re-sanitization via standardizer
-                            #     # cleaner = MolStandardize.rdMolStandardize.Cleanup()
-                            #     # mol = cleaner.cleanup(product)
-                            #     # # Fixes
-                            #     # # [2025-01-30 23:00:50] ERROR chem - Sanitizing and converting failed:
-                            #     # # non-ring atom 3 marked aromatic
-                            #     # # But does not improve overall performance
-                            #     # # for a in product.GetAtoms():
-                            #     # #     if (not a.IsInRing()) and a.GetIsAromatic():
-                            #     # #         a.SetIsAromatic(False)
-                            #     # #
-                            #     # # for b in product.GetBonds():
-                            #     # #     if (not b.IsInRing()) and b.GetIsAromatic():
-                            #     # #         b.SetIsAromatic(False)
-                            #     # for atom in product.GetAtoms():
-                            #     #     atom.SetIsAromatic(False)
-                            #     # for bond in product.GetBonds():
-                            #     #     bond.SetIsAromatic(False)
-                            #     Chem.Kekulize(product)
-
                         except ValueError as e:
                             logger.error(f"Sanitizing and converting failed:\n{e}")
                             continue
@@ -524,8 +504,8 @@ class Standardizer(ABC):
     def __init__(self, name):
         self.name = name
 
-    def standardize(self, smiles: str) -> str:
-        return FormatConverter.normalize(smiles)
+    def standardize(self, mol: rdchem.Mol) -> rdchem.Mol:
+        return mol
 
 
 class RuleStandardizer(Standardizer):
@@ -533,18 +513,20 @@ class RuleStandardizer(Standardizer):
         super().__init__(name)
         self.smirks = smirks
 
-    def standardize(self, smiles: str) -> str:
-        standardized_smiles = list(set(FormatConverter.apply(smiles, self.smirks)))
+    def standardize(self, mol: rdchem.Mol) -> rdchem.Mol:
+        rxn = rdChemReactions.ReactionFromSmarts(self.smirks)
+        sites = rxn.RunReactants((mol,))
 
-        if len(standardized_smiles) > 1:
-            logger.warning(f"{self.smirks} generated more than 1 compound {standardized_smiles}")
-            print(f"{self.smirks} generated more than 1 compound {standardized_smiles}")
-            standardized_smiles = standardized_smiles[:1]
+        if len(sites) == 1:
+            sites = sites[0]
 
-        if standardized_smiles:
-            smiles = standardized_smiles[0]
+            if len(sites) > 1:
+                logger.warning(f"{self.smirks} generated more than 1 compound {sites}")
+                print(f"{self.smirks} generated more than 1 compound {sites}")
 
-        return super().standardize(smiles)
+            mol = sites[0]
+
+        return mol
 
 
 class RegExStandardizer(Standardizer):
@@ -552,19 +534,20 @@ class RegExStandardizer(Standardizer):
         super().__init__(name)
         self.replacements = replacements
 
-    def standardize(self, smiles: str) -> str:
-        smi = smiles
-        mod_smi = smiles
-
-        for k, v in self.replacements.items():
-            mod_smi = smi.replace(k, v)
-
-        while mod_smi != smi:
-            mod_smi = smi
-            for k, v in self.replacements.items():
-                smi = smi.replace(k, v)
-
-        return super().standardize(smi)
+    def standardize(self, mol: rdchem.Mol) -> rdchem.Mol:
+        # smi = smiles
+        # mod_smi = smiles
+        #
+        # for k, v in self.replacements.items():
+        #     mod_smi = smi.replace(k, v)
+        #
+        # while mod_smi != smi:
+        #     mod_smi = smi
+        #     for k, v in self.replacements.items():
+        #         smi = smi.replace(k, v)
+        #
+        # return super().standardize(smi)
+        raise ValueError("Not implemented yet!")
 
 
 FLATTEN = [RegExStandardizer("Remove Stereo", {"@": ""})]