...

.env.prod.example

@@ -16,5 +16,3 @@ POSTGRES_PORT=
 # MAIL
 EMAIL_HOST_USER=
 EMAIL_HOST_PASSWORD=
-# MATOMO
-MATOMO_SITE_ID

.gitea/workflows/ci.yaml

@@ -1,116 +0,0 @@
-name: CI
-
-on:
-  pull_request:
-    branches:
-      - develop
-  workflow_dispatch:
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-
-    services:
-      postgres:
-        image: postgres:16
-        env:
-          POSTGRES_USER: ${{ vars.POSTGRES_USER }}
-          POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
-          POSTGRES_DB: ${{ vars.POSTGRES_DB }}
-        ports:
-          - ${{ vars.POSTGRES_PORT}}:5432
-        options: >-
-          --health-cmd="pg_isready -U postgres"
-          --health-interval=10s
-          --health-timeout=5s
-          --health-retries=5
-
-      #redis:
-      #  image: redis:7
-      #  ports:
-      #    - 6379:6379
-      #  options: >-
-      #    --health-cmd "redis-cli ping"
-      #    --health-interval=10s
-      #    --health-timeout=5s
-      #    --health-retries=5
-
-    env:
-      RUNNER_TOOL_CACHE: /toolcache
-      EP_DATA_DIR: /opt/enviPy/
-      ALLOWED_HOSTS: 127.0.0.1,localhost
-      DEBUG: True
-      LOG_LEVEL: DEBUG
-      MODEL_BUILDING_ENABLED: True
-      APPLICABILITY_DOMAIN_ENABLED: True
-      ENVIFORMER_PRESENT: True
-      ENVIFORMER_DEVICE: cpu
-      FLAG_CELERY_PRESENT: False
-      PLUGINS_ENABLED: True
-      SERVER_URL: http://localhost:8000
-      ADMIN_APPROVAL_REQUIRED: True
-      REGISTRATION_MANDATORY: True
-      LOG_DIR: ''
-      # DB
-      POSTGRES_SERVICE_NAME: postgres
-      POSTGRES_DB: ${{ vars.POSTGRES_DB }}
-      POSTGRES_USER: ${{ vars.POSTGRES_USER }}
-      POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
-      POSTGRES_PORT: 5432
-      # SENTRY
-      SENTRY_ENABLED: False
-      # MS ENTRA
-      MS_ENTRA_ENABLED: False
-
-    steps:
-
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - name: Install system tools via apt
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y postgresql-client redis-tools openjdk-11-jre-headless
-
-      - name: Setup ssh
-        run: |
-          echo "${{ secrets.ENVIPY_CI_PRIVATE_KEY }}" > ~/.ssh/id_ed25519
-          chmod 600 ~/.ssh/id_ed25519
-          ssh-keyscan git.envipath.com >> ~/.ssh/known_hosts
-          eval $(ssh-agent -s)
-          ssh-add ~/.ssh/id_ed25519
-
-      - name: Install pnpm
-        uses: pnpm/action-setup@v4
-        with:
-          version: 10
-
-      - name: Use Node.js
-        uses: actions/setup-node@v4
-        with:
-          node-version: 20
-          cache: "pnpm"
-
-      - name: Install uv
-        uses: astral-sh/setup-uv@v6
-        with:
-          enable-cache: true
-
-      - name: Setup venv
-        run: |
-          uv sync --locked --all-extras --dev
-
-      - name: Wait for services
-        run: |
-          until pg_isready -h postgres -U postgres; do sleep 2; done
-          # until redis-cli -h redis ping; do sleep 2; done
-
-      - name: Run Django migrations
-        run: |
-          source .venv/bin/activate
-          python manage.py migrate --noinput
-
-      - name: Run Django tests
-        run: |
-          source .venv/bin/activate
-          python manage.py test tests --exclude-tag slow

.gitignore

@@ -10,8 +10,3 @@ scratches/
 data/
 
 .DS_Store
-
-node_modules/
-static/css/output.css
-
-*.code-workspace

.pre-commit-config.yaml

@@ -8,7 +8,6 @@ repos:
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-added-large-files
-        exclude: ^static/images/
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.13.3
@@ -21,15 +20,6 @@ repos:
       - id: ruff-format
         types_or: [python, pyi]
 
-  - repo: local
-    hooks:
-      - id: prettier-jinja-templates
-        name: Format Jinja templates with Prettier
-        entry: pnpm exec prettier --plugin=prettier-plugin-jinja-template --parser=jinja-template --write
-        language: system
-        types: [file]
-        files: ^templates/.*\.html$
-
   # - repo: local
   #   hooks:
   #     - id: django-check

.prettierrc.json

@@ -1,11 +0,0 @@
-{
-  "plugins": ["prettier-plugin-jinja-template", "prettier-plugin-tailwindcss"],
-  "overrides": [
-    {
-      "files": "templates/**/*.html",
-      "options": {
-        "parser": "jinja-template"
-      }
-    }
-  ]
-}

README.md

@@ -7,13 +7,11 @@ These instructions will guide you through setting up the project for local devel
 ### Prerequisites
 
 - Python 3.11 or later
-- [uv](https://github.com/astral-sh/uv) - Python package manager
-- **Docker and Docker Compose** - Required for running PostgreSQL database
+- [uv](https://github.com/astral-sh/uv) - A fast Python package installer and resolver.
+- **Docker and Docker Compose** - Required for running the PostgreSQL database.
 - Git
-- Make
-
-> **Note:** This application requires PostgreSQL (uses `ArrayField`). Docker is the easiest way to run PostgreSQL locally.
 
+> **Note:** This application requires PostgreSQL, which uses `ArrayField`. Docker is the recommended way to run PostgreSQL locally.
 
 ### 1. Install Dependencies
 
@@ -25,12 +23,7 @@ Then, sync the project dependencies. This will create a virtual environment in `
 uv sync --dev
 ```
 
-Note on RDkit installation: if you have rdkit installed on your system globally with a different version of python, the installation will try to link against that and subsequent calls fail. Only option remove global rdkit and rerun sync.
-
----
-
-The frontend requires `pnpm` to correctly display in development.
-[Install it here](https://pnpm.io/installation).
+> **Note on RDkit:** If you have a different version of rdkit installed globally, the dependency installation may fail. If this happens, please uninstall the global version and run `uv sync` again.
 
 ### 2. Set Up Environment File
 
@@ -51,7 +44,6 @@ uv run poe setup
 ```
 
 This single command will:
-
 1. Start the PostgreSQL database using Docker Compose.
 2. Run database migrations.
 3. Bootstrap initial data (anonymous user, default packages, models).
@@ -62,12 +54,9 @@ After setup, start the development server:
 uv run poe dev
 ```
 
-This will start the css-watcher as well as the django-development server,
 The application will be available at `http://localhost:8000`.
 
-**Note:** The development server automatically starts a CSS watcher (`pnpm run dev`) alongside the Django server to rebuild CSS files when changes are detected. This ensures your styles are always up-to-date during development.
-
-#### Other useful Poe commands
+#### Other useful Poe commands:
 
 You can list all available commands by running `uv run poe --help`.
 
@@ -77,7 +66,6 @@ uv run poe db-down       # Stop PostgreSQL
 uv run poe migrate       # Run migrations only
 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)
 ```
 

envipath/settings.py

@@ -52,6 +52,28 @@ INSTALLED_APPS = [
     "migration",
 ]
 
+
+# Add the TENANT providing implementations for
+# Required
+# - Package
+# - Compound (TODO)
+# - CompoundStructure (TODO)
+# Optional
+# - PackageManager (TODO)
+# - GroupManager (TODO)
+# - SettingManager (TODO)
+TENANT = os.environ.get("TENANT", "public")
+INSTALLED_APPS.append(TENANT)
+PACKAGE_IMPLEMENTATION = f"{TENANT}.Package"
+PACKAGE_MODULE_PATH = f"{TENANT}.models.Package"
+
+
+def GET_PACKAGE_MODEL():
+    from django.apps import apps
+
+    return apps.get_model(TENANT, "Package")
+
+
 AUTHENTICATION_BACKENDS = [
     "django.contrib.auth.backends.ModelBackend",
 ]
@@ -92,8 +114,6 @@ TEMPLATES = [
     },
 ]
 
-ALLOWED_HTML_TAGS = {"b", "i", "u", "br", "em", "mark", "p", "s", "strong"}
-
 WSGI_APPLICATION = "envipath.wsgi.application"
 
 # Database
@@ -245,7 +265,6 @@ LOGGING = {
 ENVIFORMER_PRESENT = os.environ.get("ENVIFORMER_PRESENT", "False") == "True"
 ENVIFORMER_DEVICE = os.environ.get("ENVIFORMER_DEVICE", "cpu")
 
-
 # If celery is not present set always eager to true which will cause delayed tasks to block until finished
 FLAG_CELERY_PRESENT = os.environ.get("FLAG_CELERY_PRESENT", "False") == "True"
 if not FLAG_CELERY_PRESENT:
@@ -346,14 +365,6 @@ LOGIN_EXEMPT_URLS = [
     "/password_reset/",
     "/reset/",
     "/microsoft/",
-    "/terms",
-    "/privacy",
-    "/cookie-policy",
-    "/about",
-    "/contact",
-    "/jobs",
-    "/cite",
-    "/legal",
 ]
 
 # MS AD/Entra
@@ -368,6 +379,3 @@ if MS_ENTRA_ENABLED:
     MS_ENTRA_AUTHORITY = f"https://login.microsoftonline.com/{MS_ENTRA_TENANT_ID}"
     MS_ENTRA_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
     MS_ENTRA_SCOPES = os.environ.get("MS_SCOPES", "").split(",")
-
-# Site ID 10 -> beta.envipath.org
-MATOMO_SITE_ID = os.environ.get("MATOMO_SITE_ID", "10")

epdb/admin.py

@@ -1,11 +1,11 @@
 from django.contrib import admin
+from django.conf import settings as s
 
 from .models import (
     User,
     UserPackagePermission,
     Group,
     GroupPackagePermission,
-    Package,
     MLRelativeReasoning,
     EnviFormer,
     Compound,
@@ -24,6 +24,9 @@ from .models import (
 )
 
 
+Package = s.GET_PACKAGE_MODEL()
+
+
 class UserAdmin(admin.ModelAdmin):
     list_display = ["username", "email", "is_active"]
 

epdb/legacy_api.py

@@ -1,5 +1,6 @@
 from typing import List, Dict, Optional, Any
 
+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
@@ -10,7 +11,6 @@ from .logic import PackageManager, UserManager, SettingManager
 from .models import (
     Compound,
     CompoundStructure,
-    Package,
     User,
     UserPackagePermission,
     Rule,
@@ -23,6 +23,9 @@ from .models import (
 )
 
 
+Package = s.GET_PACKAGE_MODEL()
+
+
 def _anonymous_or_real(request):
     if request.user.is_authenticated and not request.user.is_anonymous:
         return request.user

epdb/logic.py

@@ -4,7 +4,6 @@ import json
 from typing import Union, List, Optional, Set, Dict, Any
 from uuid import UUID
 
-import nh3
 from django.contrib.auth import get_user_model
 from django.db import transaction
 from django.conf import settings as s
@@ -12,7 +11,6 @@ from pydantic import ValidationError
 
 from epdb.models import (
     User,
-    Package,
     UserPackagePermission,
     GroupPackagePermission,
     Permission,
@@ -34,6 +32,8 @@ from utilities.misc import PackageImporter, PackageExporter
 
 logger = logging.getLogger(__name__)
 
+Package = s.GET_PACKAGE_MODEL()
+
 
 class EPDBURLParser:
     UUID_PATTERN = r"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"
@@ -186,12 +186,6 @@ class UserManager(object):
     def create_user(
         username, email, password, set_setting=True, add_to_group=True, *args, **kwargs
     ):
-        # Clean for potential XSS
-        clean_username = nh3.clean(username).strip()
-        clean_email = nh3.clean(email).strip()
-        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
 
@@ -269,9 +263,8 @@ class GroupManager(object):
     @staticmethod
     def create_group(current_user, name, description):
         g = Group()
-        # Clean for potential XSS
-        g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-        g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+        g.name = name
+        g.description = description
         g.owner = current_user
         g.save()
 
@@ -526,13 +519,8 @@ class PackageManager(object):
     @transaction.atomic
     def create_package(current_user, name: str, description: str = None):
         p = Package()
-
-        # Clean for potential XSS
-        p.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        if description is not None and description.strip() != "":
-            p.description = nh3.clean(description.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
-
+        p.name = name
+        p.description = description
         p.save()
 
         up = UserPackagePermission()
@@ -1107,29 +1095,28 @@ class SettingManager(object):
         model: EPModel = None,
         model_threshold: float = None,
     ):
-        new_s = Setting()
-        # Clean for potential XSS
-        new_s.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-        new_s.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
-        new_s.max_nodes = max_nodes
-        new_s.max_depth = max_depth
-        new_s.model = model
-        new_s.model_threshold = model_threshold
+        s = Setting()
+        s.name = name
+        s.description = description
+        s.max_nodes = max_nodes
+        s.max_depth = max_depth
+        s.model = model
+        s.model_threshold = model_threshold
 
-        new_s.save()
+        s.save()
 
         if rule_packages is not None:
             for r in rule_packages:
-                new_s.rule_packages.add(r)
-            new_s.save()
+                s.rule_packages.add(r)
+            s.save()
 
         usp = UserSettingPermission()
         usp.user = user
-        usp.setting = new_s
+        usp.setting = s
         usp.permission = Permission.ALL[0]
         usp.save()
 
-        return new_s
+        return s
 
     @staticmethod
     def get_default_setting(user: User):
@@ -1558,7 +1545,7 @@ class SPathway(object):
                         if self.prediction_setting.model.app_domain:
                             app_domain_assessment = self.prediction_setting.model.app_domain.assess(
                                 sub.smiles
-                            )
+                            )[0]
 
                             if self.persist is not None:
                                 n = self.snode_persist_lookup[sub]
@@ -1591,7 +1578,9 @@ class SPathway(object):
                                     if self.prediction_setting.model:
                                         if self.prediction_setting.model.app_domain:
                                             app_domain_assessment = (
-                                                self.prediction_setting.model.app_domain.assess(c)
+                                                self.prediction_setting.model.app_domain.assess(c)[
+                                                    0
+                                                ]
                                             )
 
                                     self.smiles_to_node[c] = SNode(

epdb/management/commands/create_ml_models.py

@@ -2,7 +2,9 @@ from django.conf import settings as s
 from django.core.management.base import BaseCommand
 from django.db import transaction
 
-from epdb.models import MLRelativeReasoning, EnviFormer, Package
+from epdb.models import EnviFormer, MLRelativeReasoning
+
+Package = s.GET_PACKAGE_MODEL()
 
 
 class Command(BaseCommand):
@@ -75,11 +77,13 @@ class Command(BaseCommand):
             return packages
 
         # Iteratively create models in options["model_names"]
-        print(f"Creating models: {options['model_names']}\n"
+        print(
+            f"Creating models: {options['model_names']}\n"
             f"Data packages: {options['data_packages']}\n"
             f"Rule Packages (only for MLRR): {options['rule_packages']}\n"
             f"Eval Packages: {options['eval_packages']}\n"
-              f"Threshold: {options['threshold']:.2f}")
+            f"Threshold: {options['threshold']:.2f}"
+        )
         data_packages = decode_packages(options["data_packages"])
         eval_packages = decode_packages(options["eval_packages"])
         rule_packages = decode_packages(options["rule_packages"])
@@ -90,7 +94,7 @@ class Command(BaseCommand):
                     pack,
                     data_packages=data_packages,
                     eval_packages=eval_packages,
-                    threshold=options['threshold'],
+                    threshold=options["threshold"],
                     name=f"EnviFormer - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
                     description=f"EnviFormer transformer trained on {options['data_packages']} "
                     f"evaluated on {options['eval_packages']}.",
@@ -101,7 +105,7 @@ class Command(BaseCommand):
                     rule_packages=rule_packages,
                     data_packages=data_packages,
                     eval_packages=eval_packages,
-                    threshold=options['threshold'],
+                    threshold=options["threshold"],
                     name=f"ECC - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
                     description=f"ML Relative Reasoning trained on {options['data_packages']} with rules from "
                     f"{options['rule_packages']} and evaluated on {options['eval_packages']}.",

epdb/management/commands/load_enviformer.py

@@ -8,7 +8,9 @@ from django.conf import settings as s
 from django.core.management.base import BaseCommand
 from django.db import transaction
 
-from epdb.models import EnviFormer, Package
+from epdb.models import EnviFormer
+
+Package = s.GET_PACKAGE_MODEL()
 
 
 class Command(BaseCommand):

epdb/management/commands/localize_urls.py

@@ -1,8 +1,8 @@
 from django.apps import apps
+from django.conf import settings as s
 from django.core.management.base import BaseCommand
-
-from django.db.models import F, Value, TextField, JSONField
-from django.db.models.functions import Replace, Cast
+from django.db.models import F, JSONField, TextField, Value
+from django.db.models.functions import Cast, Replace
 
 from epdb.models import EnviPathModel
 
@@ -23,10 +23,13 @@ class Command(BaseCommand):
         )
 
     def handle(self, *args, **options):
+        Package = s.GET_PACKAGE_MODEL()
+        print("Localizing urls for Package")
+        Package.objects.update(url=Replace(F("url"), Value(options["old"]), Value(options["new"])))
+
         MODELS = [
             "User",
             "Group",
-            "Package",
             "Compound",
             "CompoundStructure",
             "Pathway",

epdb/migrations/0010_alter_userpackagepermission_package_and_more.py

@@ -0,0 +1,190 @@
+# Generated by Django 5.2.7 on 2025-10-29 13:32
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0009_joblog"),
+        ("public", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="userpackagepermission",
+            name="package",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                to="public.package",
+                verbose_name="Permission on",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="grouppackagepermission",
+            name="package",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                to="public.package",
+                verbose_name="Permission on",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="epmodel",
+            name="package",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                to="public.package",
+                verbose_name="Package",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="rule",
+            name="package",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                to="public.package",
+                verbose_name="Package",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="compound",
+            name="package",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                to="public.package",
+                verbose_name="Package",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="scenario",
+            name="package",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                to="public.package",
+                verbose_name="Package",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="pathway",
+            name="package",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                to="public.package",
+                verbose_name="Package",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reaction",
+            name="package",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                to="public.package",
+                verbose_name="Package",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="user",
+            name="default_package",
+            field=models.ForeignKey(
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                to="public.package",
+                verbose_name="Default Package",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="enviformer",
+            name="data_packages",
+            field=models.ManyToManyField(
+                related_name="%(app_label)s_%(class)s_data_packages",
+                to="public.package",
+                verbose_name="Data Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="enviformer",
+            name="eval_packages",
+            field=models.ManyToManyField(
+                related_name="%(app_label)s_%(class)s_eval_packages",
+                to="public.package",
+                verbose_name="Evaluation Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="enviformer",
+            name="rule_packages",
+            field=models.ManyToManyField(
+                related_name="%(app_label)s_%(class)s_rule_packages",
+                to="public.package",
+                verbose_name="Rule Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="mlrelativereasoning",
+            name="data_packages",
+            field=models.ManyToManyField(
+                related_name="%(app_label)s_%(class)s_data_packages",
+                to="public.package",
+                verbose_name="Data Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="mlrelativereasoning",
+            name="eval_packages",
+            field=models.ManyToManyField(
+                related_name="%(app_label)s_%(class)s_eval_packages",
+                to="public.package",
+                verbose_name="Evaluation Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="mlrelativereasoning",
+            name="rule_packages",
+            field=models.ManyToManyField(
+                related_name="%(app_label)s_%(class)s_rule_packages",
+                to="public.package",
+                verbose_name="Rule Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="rulebasedrelativereasoning",
+            name="data_packages",
+            field=models.ManyToManyField(
+                related_name="%(app_label)s_%(class)s_data_packages",
+                to="public.package",
+                verbose_name="Data Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="rulebasedrelativereasoning",
+            name="eval_packages",
+            field=models.ManyToManyField(
+                related_name="%(app_label)s_%(class)s_eval_packages",
+                to="public.package",
+                verbose_name="Evaluation Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="rulebasedrelativereasoning",
+            name="rule_packages",
+            field=models.ManyToManyField(
+                related_name="%(app_label)s_%(class)s_rule_packages",
+                to="public.package",
+                verbose_name="Rule Packages",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="setting",
+            name="rule_packages",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="setting_rule_packages",
+                to="public.package",
+                verbose_name="Setting Rule Packages",
+            ),
+        ),
+        migrations.DeleteModel(
+            name="Package",
+        ),
+    ]

epdb/models.py

@@ -7,11 +7,10 @@ import secrets
 from abc import abstractmethod
 from collections import defaultdict
 from datetime import datetime
-from typing import Union, List, Optional, Dict, Tuple, Set, Any
+from typing import Union, List, Optional, Dict, Tuple, Set, Any, TYPE_CHECKING
 from uuid import uuid4
 import math
 import joblib
-import nh3
 import numpy as np
 from django.conf import settings as s
 from django.contrib.auth.models import AbstractUser
@@ -29,17 +28,12 @@ from sklearn.metrics import precision_score, recall_score, jaccard_score
 from sklearn.model_selection import ShuffleSplit
 
 from utilities.chem import FormatConverter, ProductSet, PredictionResult, IndigoUtils
-from utilities.ml import (
-    RuleBasedDataset,
-    ApplicabilityDomainPCA,
-    EnsembleClassifierChain,
-    RelativeReasoning,
-    EnviFormerDataset,
-    Dataset,
-)
+from utilities.ml import Dataset, ApplicabilityDomainPCA, EnsembleClassifierChain, RelativeReasoning
 
 logger = logging.getLogger(__name__)
 
+if TYPE_CHECKING:
+    Package = s.GET_PACKAGE_MODEL()
 
 ##########################
 # User/Groups/Permission #
@@ -53,7 +47,10 @@ class User(AbstractUser):
     )
     url = models.TextField(blank=False, null=True, verbose_name="URL", unique=True)
     default_package = models.ForeignKey(
-        "epdb.Package", verbose_name="Default Package", null=True, on_delete=models.SET_NULL
+        s.PACKAGE_IMPLEMENTATION,
+        verbose_name="Default Package",
+        null=True,
+        on_delete=models.SET_NULL,
     )
     default_group = models.ForeignKey(
         "Group",
@@ -243,7 +240,7 @@ class UserPackagePermission(Permission):
     )
     user = models.ForeignKey("User", verbose_name="Permission to", on_delete=models.CASCADE)
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Permission on", on_delete=models.CASCADE
     )
 
     class Meta:
@@ -259,7 +256,7 @@ class GroupPackagePermission(Permission):
     )
     group = models.ForeignKey("Group", verbose_name="Permission to", on_delete=models.CASCADE)
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Permission on", on_delete=models.CASCADE
     )
 
     class Meta:
@@ -659,7 +656,7 @@ class License(models.Model):
     image_link = models.URLField(blank=False, null=False, verbose_name="Image link")
 
 
-class Package(EnviPathModel):
+class AbstractPackage(EnviPathModel):
     reviewed = models.BooleanField(verbose_name="Reviewstatus", default=False)
     license = models.ForeignKey(
         "epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
@@ -727,10 +724,13 @@ class Package(EnviPathModel):
         rules = sorted(rules, key=lambda x: x.url)
         return rules
 
+    class Meta:
+        abstract = True
+
 
 class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     default_structure = models.ForeignKey(
         "CompoundStructure",
@@ -780,7 +780,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
     @staticmethod
     @transaction.atomic
     def create(
-        package: Package, smiles: str, name: str = None, description: str = None, *args, **kwargs
+        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
     ) -> "Compound":
         if smiles is None or smiles.strip() == "":
             raise ValueError("SMILES is required")
@@ -810,16 +810,14 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
         c = Compound()
         c.package = package
 
-        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 == "":
+        if name is None or name.strip() == "":
             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
         if description is not None and description.strip() != "":
-            c.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+            c.description = description.strip()
 
         c.save()
 
@@ -991,11 +989,11 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
             raise ValueError("Unpersisted Compound! Persist compound first!")
 
         cs = CompoundStructure()
-        # Clean for potential XSS
         if name is not None:
-            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+            cs.name = name
+
         if description is not None:
-            cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+            cs.description = description
 
         cs.smiles = smiles
         cs.compound = compound
@@ -1060,7 +1058,7 @@ class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
 
 class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
 
     # # https://github.com/django-polymorphic/django-polymorphic/issues/229
@@ -1166,7 +1164,7 @@ class SimpleAmbitRule(SimpleRule):
     @staticmethod
     @transaction.atomic
     def create(
-        package: Package,
+        package: "Package",
         name: str = None,
         description: str = None,
         smirks: str = None,
@@ -1197,29 +1195,21 @@ class SimpleAmbitRule(SimpleRule):
         r = SimpleAmbitRule()
         r.package = package
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        if name is None or name == "":
+        if name is None or name.strip() == "":
             name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
 
         r.name = name
+
         if description is not None and description.strip() != "":
-            r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+            r.description = description
 
         r.smirks = smirks
 
         if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
-            if not FormatConverter.is_valid_smarts(reactant_filter_smarts.strip()):
-                raise ValueError(f'Reactant Filter SMARTS "{reactant_filter_smarts}" is invalid!')
-            else:
-                r.reactant_filter_smarts = reactant_filter_smarts.strip()
+            r.reactant_filter_smarts = reactant_filter_smarts
 
         if product_filter_smarts is not None and product_filter_smarts.strip() != "":
-            if not FormatConverter.is_valid_smarts(product_filter_smarts.strip()):
-                raise ValueError(f'Product Filter SMARTS "{product_filter_smarts}" is invalid!')
-            else:
-                r.product_filter_smarts = product_filter_smarts.strip()
+            r.product_filter_smarts = product_filter_smarts
 
         r.save()
         return r
@@ -1240,6 +1230,7 @@ class SimpleAmbitRule(SimpleRule):
 
     @property
     def related_reactions(self):
+        Package = s.GET_PACKAGE_MODEL()
         qs = Package.objects.filter(reviewed=True)
         return self.reaction_rule.filter(package__in=qs).order_by("name")
 
@@ -1332,7 +1323,7 @@ class SequentialRuleOrdering(models.Model):
 
 class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     educts = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Educts", related_name="reaction_educts"
@@ -1354,7 +1345,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
     @staticmethod
     @transaction.atomic
     def create(
-        package: Package,
+        package: "Package",
         name: str = None,
         description: str = None,
         educts: Union[List[str], List[CompoundStructure]] = None,
@@ -1420,11 +1411,12 @@ 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()
+            r.name = name
+
         if description is not None and name.strip() != "":
-            r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+            r.description = description
 
         r.multi_step = multi_step
 
@@ -1513,7 +1505,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
 class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     setting = models.ForeignKey(
         "epdb.Setting", verbose_name="Setting", on_delete=models.CASCADE, null=True, blank=True
@@ -1732,15 +1724,14 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     ):
         pw = Pathway()
         pw.package = package
-        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 == "":
+
+        if name is None or name.strip() == "":
             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.description = description
 
         pw.save()
         try:
@@ -2035,16 +2026,11 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
         for node in end_nodes:
             e.end_nodes.add(node)
 
-        # Clean for potential XSS
-        # Cleaning technically not needed as it is also done in Reaction.create, including it here for consistency
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-        if name is None or name == "":
+        if name is None:
             name = f"Reaction {pathway.package.reactions.count() + 1}"
 
         if description is None:
             description = s.DEFAULT_VALUES["description"]
-        description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r = Reaction.create(
             pathway.package,
@@ -2075,7 +2061,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
 
 class EPModel(PolymorphicModel, EnviPathModel):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
 
     def _url(self):
@@ -2084,17 +2070,17 @@ class EPModel(PolymorphicModel, EnviPathModel):
 
 class PackageBasedModel(EPModel):
     rule_packages = models.ManyToManyField(
-        "Package",
+        s.PACKAGE_IMPLEMENTATION,
         verbose_name="Rule Packages",
         related_name="%(app_label)s_%(class)s_rule_packages",
     )
     data_packages = models.ManyToManyField(
-        "Package",
+        s.PACKAGE_IMPLEMENTATION,
         verbose_name="Data Packages",
         related_name="%(app_label)s_%(class)s_data_packages",
     )
     eval_packages = models.ManyToManyField(
-        "Package",
+        s.PACKAGE_IMPLEMENTATION,
         verbose_name="Evaluation Packages",
         related_name="%(app_label)s_%(class)s_eval_packages",
     )
@@ -2198,7 +2184,7 @@ class PackageBasedModel(EPModel):
 
         applicable_rules = self.applicable_rules
         reactions = list(self._get_reactions())
-        ds = RuleBasedDataset.generate_dataset(reactions, applicable_rules, educts_only=True)
+        ds = Dataset.generate_dataset(reactions, applicable_rules, educts_only=True)
 
         end = datetime.now()
         logger.debug(f"build_dataset took {(end - start).total_seconds()} seconds")
@@ -2207,7 +2193,7 @@ class PackageBasedModel(EPModel):
         ds.save(f)
         return ds
 
-    def load_dataset(self) -> "Dataset | RuleBasedDataset | EnviFormerDataset":
+    def load_dataset(self) -> "Dataset":
         ds_path = os.path.join(s.MODEL_DIR, f"{self.uuid}_ds.pkl")
         return Dataset.load(ds_path)
 
@@ -2248,7 +2234,7 @@ class PackageBasedModel(EPModel):
         self.model_status = self.BUILT_NOT_EVALUATED
         self.save()
 
-    def evaluate_model(self, multigen: bool, eval_packages: List["Package"] = None, **kwargs):
+    def evaluate_model(self, multigen: bool, eval_packages: List["Package"] = None):
         if self.model_status != self.BUILT_NOT_EVALUATED:
             raise ValueError(f"Can't evaluate a model in state {self.model_status}!")
 
@@ -2366,39 +2352,37 @@ class PackageBasedModel(EPModel):
             eval_reactions = list(
                 Reaction.objects.filter(package__in=self.eval_packages.all()).distinct()
             )
-            ds = RuleBasedDataset.generate_dataset(
-                eval_reactions, self.applicable_rules, educts_only=True
-            )
+            ds = Dataset.generate_dataset(eval_reactions, self.applicable_rules, educts_only=True)
             if isinstance(self, RuleBasedRelativeReasoning):
-                X = ds.X(exclude_id_col=False, na_replacement=None).to_numpy()
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                X = np.array(ds.X(exclude_id_col=False, na_replacement=None))
+                y = np.array(ds.y(na_replacement=np.nan))
             else:
-                X = ds.X(na_replacement=np.nan).to_numpy()
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                X = np.array(ds.X(na_replacement=np.nan))
+                y = np.array(ds.y(na_replacement=np.nan))
             single_gen_result = evaluate_sg(self.model, X, y, np.arange(len(X)), self.threshold)
             self.eval_results = self.compute_averages([single_gen_result])
         else:
             ds = self.load_dataset()
 
             if isinstance(self, RuleBasedRelativeReasoning):
-                X = ds.X(exclude_id_col=False, na_replacement=None).to_numpy()
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                X = np.array(ds.X(exclude_id_col=False, na_replacement=None))
+                y = np.array(ds.y(na_replacement=np.nan))
             else:
-                X = ds.X(na_replacement=np.nan).to_numpy()
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                X = np.array(ds.X(na_replacement=np.nan))
+                y = np.array(ds.y(na_replacement=np.nan))
 
-            n_splits = kwargs.get("n_splits", 20)
+            n_splits = 20
 
             shuff = ShuffleSplit(n_splits=n_splits, test_size=0.25, random_state=42)
             splits = list(shuff.split(X))
 
             from joblib import Parallel, delayed
 
-            models = Parallel(n_jobs=min(10, len(splits)))(
+            models = Parallel(n_jobs=10)(
                 delayed(train_func)(X, y, train_index, self._model_args())
                 for train_index, _ in splits
             )
-            evaluations = Parallel(n_jobs=min(10, len(splits)))(
+            evaluations = Parallel(n_jobs=10)(
                 delayed(evaluate_sg)(model, X, y, test_index, self.threshold)
                 for model, (_, test_index) in zip(models, splits)
             )
@@ -2566,15 +2550,14 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
     ):
         rbrr = RuleBasedRelativeReasoning()
         rbrr.package = package
-        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 == "":
+
+        if name is None or name.strip() == "":
             name = f"RuleBasedRelativeReasoning {RuleBasedRelativeReasoning.objects.filter(package=package).count() + 1}"
 
         rbrr.name = name
+
         if description is not None and description.strip() != "":
-            rbrr.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+            rbrr.description = description
 
         if threshold is None or (threshold <= 0 or 1 <= threshold):
             raise ValueError("Threshold must be a float between 0 and 1.")
@@ -2611,11 +2594,11 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
 
         return rbrr
 
-    def _fit_model(self, ds: RuleBasedDataset):
+    def _fit_model(self, ds: Dataset):
         X, y = ds.X(exclude_id_col=False, na_replacement=None), ds.y(na_replacement=None)
         model = RelativeReasoning(
             start_index=ds.triggered()[0],
-            end_index=ds.triggered()[-1],
+            end_index=ds.triggered()[1],
         )
         model.fit(X, y)
         return model
@@ -2625,7 +2608,7 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
         return {
             "clz": "RuleBaseRelativeReasoning",
             "start_index": ds.triggered()[0],
-            "end_index": ds.triggered()[-1],
+            "end_index": ds.triggered()[1],
         }
 
     def _save_model(self, model):
@@ -2671,15 +2654,14 @@ class MLRelativeReasoning(PackageBasedModel):
     ):
         mlrr = MLRelativeReasoning()
         mlrr.package = package
-        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 == "":
+
+        if name is None or name.strip() == "":
             name = f"MLRelativeReasoning {MLRelativeReasoning.objects.filter(package=package).count() + 1}"
 
         mlrr.name = name
+
         if description is not None and description.strip() != "":
-            mlrr.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+            mlrr.description = description
 
         if threshold is None or (threshold <= 0 or 1 <= threshold):
             raise ValueError("Threshold must be a float between 0 and 1.")
@@ -2714,11 +2696,11 @@ class MLRelativeReasoning(PackageBasedModel):
 
         return mlrr
 
-    def _fit_model(self, ds: RuleBasedDataset):
+    def _fit_model(self, ds: Dataset):
         X, y = ds.X(na_replacement=np.nan), ds.y(na_replacement=np.nan)
 
         model = EnsembleClassifierChain(**s.DEFAULT_MODEL_PARAMS)
-        model.fit(X.to_numpy(), y.to_numpy())
+        model.fit(X, y)
         return model
 
     def _model_args(self):
@@ -2741,7 +2723,7 @@ class MLRelativeReasoning(PackageBasedModel):
         start = datetime.now()
         ds = self.load_dataset()
         classify_ds, classify_prods = ds.classification_dataset([smiles], self.applicable_rules)
-        pred = self.model.predict_proba(classify_ds.X().to_numpy())
+        pred = self.model.predict_proba(classify_ds.X())
 
         res = MLRelativeReasoning.combine_products_and_probs(
             self.applicable_rules, pred[0], classify_prods[0]
@@ -2786,9 +2768,7 @@ class ApplicabilityDomain(EnviPathModel):
 
     @cached_property
     def training_set_probs(self):
-        ds = self.model.load_dataset()
-        col_ids = ds.block_indices("prob")
-        return ds[:, col_ids]
+        return joblib.load(os.path.join(s.MODEL_DIR, f"{self.model.uuid}_train_probs.pkl"))
 
     def build(self):
         ds = self.model.load_dataset()
@@ -2796,9 +2776,9 @@ class ApplicabilityDomain(EnviPathModel):
         start = datetime.now()
 
         # Get Trainingset probs and dump them as they're required when using the app domain
-        probs = self.model.model.predict_proba(ds.X().to_numpy())
-        ds.add_probs(probs)
-        ds.save(os.path.join(s.MODEL_DIR, f"{self.model.uuid}_ds.pkl"))
+        probs = self.model.model.predict_proba(ds.X())
+        f = os.path.join(s.MODEL_DIR, f"{self.model.uuid}_train_probs.pkl")
+        joblib.dump(probs, f)
 
         ad = ApplicabilityDomainPCA(num_neighbours=self.num_neighbours)
         ad.build(ds)
@@ -2821,20 +2801,15 @@ class ApplicabilityDomain(EnviPathModel):
         joblib.dump(ad, f)
 
     def assess(self, structure: Union[str, "CompoundStructure"]):
-        return self.assess_batch([structure])[0]
-
-    def assess_batch(self, structures: List["CompoundStructure | str"]):
         ds = self.model.load_dataset()
 
-        smiles = []
-        for struct in structures:
-            if isinstance(struct, CompoundStructure):
-                smiles.append(structures.smiles)
+        if isinstance(structure, CompoundStructure):
+            smiles = structure.smiles
         else:
-                smiles.append(structures)
+            smiles = structure
 
         assessment_ds, assessment_prods = ds.classification_dataset(
-            structures, self.model.applicable_rules
+            [structure], self.model.applicable_rules
         )
 
         # qualified_neighbours_per_rule is a nested dictionary structured as:
@@ -2848,61 +2823,82 @@ class ApplicabilityDomain(EnviPathModel):
         # it identifies all training structures that have the same trigger reaction activated (i.e., value 1).
         # This is used to find "qualified neighbours" — training examples that share the same triggered feature
         # with a given assessment structure under a particular rule.
-        qualified_neighbours_per_rule: Dict = {}
+        qualified_neighbours_per_rule: Dict[int, Dict[int, List[int]]] = defaultdict(
+            lambda: defaultdict(list)
+        )
 
-        import polars as pl
+        for rule_idx, feature_index in enumerate(range(*assessment_ds.triggered())):
+            feature = ds.columns[feature_index]
+            if feature.startswith("trig_"):
+                # TODO unroll loop
+                for i, cx in enumerate(assessment_ds.X(exclude_id_col=False)):
+                    if int(cx[feature_index]) == 1:
+                        for j, tx in enumerate(ds.X(exclude_id_col=False)):
+                            if int(tx[feature_index]) == 1:
+                                qualified_neighbours_per_rule[i][rule_idx].append(j)
 
-        # Select only the triggered columns
-        for i, row in enumerate(assessment_ds[:, assessment_ds.triggered()].iter_rows(named=True)):
-            # Find the rules the structure triggers. For each rule, filter the training dataset to rows that also
-            # trigger that rule.
-            train_trig = {
-                trig_uuid.split("_")[-1]: ds.filter(pl.col(trig_uuid).eq(1))
-                for trig_uuid, value in row.items()
-                if value == 1
-            }
-            qualified_neighbours_per_rule[i] = train_trig
-        rule_to_i = {str(r.uuid): i for i, r in enumerate(self.model.applicable_rules)}
+        probs = self.training_set_probs
+        # preds = self.model.model.predict_proba(assessment_ds.X())
         preds = self.model.combine_products_and_probs(
             self.model.applicable_rules,
-            self.model.model.predict_proba(assessment_ds.X().to_numpy())[0],
+            self.model.model.predict_proba(assessment_ds.X())[0],
             assessment_prods[0],
         )
 
         assessments = list()
+
         # loop through our assessment dataset
-        for i, instance in enumerate(assessment_ds[:, assessment_ds.struct_features()]):
+        for i, instance in enumerate(assessment_ds):
             rule_reliabilities = dict()
             local_compatibilities = dict()
             neighbours_per_rule = dict()
             neighbor_probs_per_rule = dict()
 
             # loop through rule indices together with the collected neighbours indices from train dataset
-            for rule_uuid, train_instances in qualified_neighbours_per_rule[i].items():
-                # compute tanimoto distance for all neighbours and add to dataset
+            for rule_idx, vals in qualified_neighbours_per_rule[i].items():
+                # collect the train dataset instances and store it along with the index (a.k.a. row number) of the
+                # train dataset
+                train_instances = []
+                for v in vals:
+                    train_instances.append((v, ds.at(v)))
+
+                # sf is a tuple with start/end index of the features
+                sf = ds.struct_features()
+
+                # compute tanimoto distance for all neighbours
+                # result ist a list of tuples with train index and computed distance
                 dists = self._compute_distances(
-                    assessment_ds[i, assessment_ds.struct_features()].to_numpy()[0],
-                    train_instances[:, train_instances.struct_features()].to_numpy(),
+                    instance.X()[0][sf[0] : sf[1]],
+                    [ti[1].X()[0][sf[0] : sf[1]] for ti in train_instances],
                 )
-                train_instances = train_instances.with_columns(dist=pl.Series(dists))
+
+                dists_with_index = list()
+                for ti, dist in zip(train_instances, dists):
+                    dists_with_index.append((ti[0], dist[1]))
 
                 #  sort them in a descending way and take at most `self.num_neighbours`
-                # TODO: Should this be descending? If we want the most similar then we want values close to zero (ascending)
-                train_instances = train_instances.sort("dist", descending=True)[
-                    : self.num_neighbours
-                ]
+                dists_with_index = sorted(dists_with_index, key=lambda x: x[1], reverse=True)
+                dists_with_index = dists_with_index[: self.num_neighbours]
+
                 # compute average distance
-                rule_reliabilities[rule_uuid] = (
-                    train_instances.select(pl.mean("dist")).fill_nan(0.0).item()
+                rule_reliabilities[rule_idx] = (
+                    sum([d[1] for d in dists_with_index]) / len(dists_with_index)
+                    if len(dists_with_index) > 0
+                    else 0.0
                 )
+
                 # for local_compatibility we'll need the datasets for the indices having the highest similarity
-                local_compatibilities[rule_uuid] = self._compute_compatibility(
-                    rule_uuid, train_instances
+                neighbour_datasets = [(d[0], ds.at(d[0])) for d in dists_with_index]
+                local_compatibilities[rule_idx] = self._compute_compatibility(
+                    rule_idx, probs, neighbour_datasets
                 )
-                neighbours_per_rule[rule_uuid] = list(
-                    CompoundStructure.objects.filter(uuid__in=train_instances["structure_id"])
-                )
-                neighbor_probs_per_rule[rule_uuid] = train_instances[f"prob_{rule_uuid}"].to_list()
+                neighbours_per_rule[rule_idx] = [
+                    CompoundStructure.objects.get(uuid=ds[1].structure_id())
+                    for ds in neighbour_datasets
+                ]
+                neighbor_probs_per_rule[rule_idx] = [
+                    probs[d[0]][rule_idx] for d in dists_with_index
+                ]
 
             ad_res = {
                 "ad_params": {
@@ -2913,21 +2909,23 @@ class ApplicabilityDomain(EnviPathModel):
                     "local_compatibility_threshold": self.local_compatibilty_threshold,
                 },
                 "assessment": {
-                    "smiles": smiles[i],
-                    "inside_app_domain": self.pca.is_applicable(assessment_ds[i])[0],
+                    "smiles": smiles,
+                    "inside_app_domain": self.pca.is_applicable(instance)[0],
                 },
             }
 
             transformations = list()
-            for rule_uuid in rule_reliabilities.keys():
-                rule = Rule.objects.get(uuid=rule_uuid)
+            for rule_idx in rule_reliabilities.keys():
+                rule = Rule.objects.get(
+                    uuid=instance.columns[instance.observed()[0] + rule_idx].replace("obs_", "")
+                )
 
                 rule_data = rule.simple_json()
                 rule_data["image"] = f"{rule.url}?image=svg"
 
                 neighbors = []
                 for n, n_prob in zip(
-                    neighbours_per_rule[rule_uuid], neighbor_probs_per_rule[rule_uuid]
+                    neighbours_per_rule[rule_idx], neighbor_probs_per_rule[rule_idx]
                 ):
                     neighbor = n.simple_json()
                     neighbor["image"] = f"{n.url}?image=svg"
@@ -2944,14 +2942,14 @@ class ApplicabilityDomain(EnviPathModel):
 
                 transformation = {
                     "rule": rule_data,
-                    "reliability": rule_reliabilities[rule_uuid],
+                    "reliability": rule_reliabilities[rule_idx],
                     # We're setting it here to False, as we don't know whether "assess" is called during pathway
                     # prediction or from Model Page. For persisted Nodes this field will be overwritten at runtime
                     "is_predicted": False,
-                    "local_compatibility": local_compatibilities[rule_uuid],
-                    "probability": preds[rule_to_i[rule_uuid]].probability,
+                    "local_compatibility": local_compatibilities[rule_idx],
+                    "probability": preds[rule_idx].probability,
                     "transformation_products": [
-                        x.product_set for x in preds[rule_to_i[rule_uuid]].product_sets
+                        x.product_set for x in preds[rule_idx].product_sets
                     ],
                     "times_triggered": ds.times_triggered(str(rule.uuid)),
                     "neighbors": neighbors,
@@ -2969,24 +2967,32 @@ class ApplicabilityDomain(EnviPathModel):
     def _compute_distances(classify_instance: List[int], train_instances: List[List[int]]):
         from utilities.ml import tanimoto_distance
 
-        distances = [tanimoto_distance(classify_instance, train) for train in train_instances]
+        distances = [
+            (i, tanimoto_distance(classify_instance, train))
+            for i, train in enumerate(train_instances)
+        ]
         return distances
 
-    def _compute_compatibility(self, rule_idx: int, neighbours: "RuleBasedDataset"):
+    @staticmethod
+    def _compute_compatibility(rule_idx: int, preds, neighbours: List[Tuple[int, "Dataset"]]):
+        tp, tn, fp, fn = 0.0, 0.0, 0.0, 0.0
         accuracy = 0.0
-        import polars as pl
 
-        obs_pred = neighbours.select(
-            obs=pl.col(f"obs_{rule_idx}").cast(pl.Boolean),
-            pred=pl.col(f"prob_{rule_idx}") >= self.model.threshold,
-        )
-        # Compute tp, tn, fp, fn using polars expressions
-        tp = obs_pred.filter((pl.col("obs")) & (pl.col("pred"))).height
-        tn = obs_pred.filter((~pl.col("obs")) & (~pl.col("pred"))).height
-        fp = obs_pred.filter((~pl.col("obs")) & (pl.col("pred"))).height
-        fn = obs_pred.filter((pl.col("obs")) & (~pl.col("pred"))).height
+        for n in neighbours:
+            obs = n[1].y()[0][rule_idx]
+            pred = preds[n[0]][rule_idx]
+            if obs and pred:
+                tp += 1
+            elif not obs and pred:
+                fp += 1
+            elif obs and not pred:
+                fn += 1
+            else:
+                tn += 1
+            # Jaccard Index
             if tp + tn > 0.0:
                 accuracy = (tp + tn) / (tp + tn + fp + fn)
+
         return accuracy
 
 
@@ -3006,15 +3012,14 @@ class EnviFormer(PackageBasedModel):
     ):
         mod = EnviFormer()
         mod.package = package
-        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 == "":
+
+        if name is None or name.strip() == "":
             name = f"EnviFormer {EnviFormer.objects.filter(package=package).count() + 1}"
 
         mod.name = name
+
         if description is not None and description.strip() != "":
-            mod.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+            mod.description = description
 
         if threshold is None or (threshold <= 0 or 1 <= threshold):
             raise ValueError("Threshold must be a float between 0 and 1.")
@@ -3088,24 +3093,44 @@ class EnviFormer(PackageBasedModel):
         self.save()
 
         start = datetime.now()
-        ds = EnviFormerDataset.generate_dataset(self._get_reactions())
+        # Standardise reactions for the training data, EnviFormer ignores stereochemistry currently
+        co2 = {"C(=O)=O", "O=C=O"}
+        ds = []
+        for reaction in self._get_reactions():
+            educts = ".".join(
+                [
+                    FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                    for smile in reaction.educts.all()
+                ]
+            )
+            products = ".".join(
+                [
+                    FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                    for smile in reaction.products.all()
+                ]
+            )
+            if products not in co2:
+                ds.append(f"{educts}>>{products}")
 
         end = datetime.now()
         logger.debug(f"build_dataset took {(end - start).total_seconds()} seconds")
         f = os.path.join(s.MODEL_DIR, f"{self.uuid}_ds.json")
-        ds.save(f)
+        with open(f, "w") as d_file:
+            json.dump(ds, d_file)
         return ds
 
-    def load_dataset(self):
+    def load_dataset(self) -> "Dataset":
         ds_path = os.path.join(s.MODEL_DIR, f"{self.uuid}_ds.json")
-        return EnviFormerDataset.load(ds_path)
+        with open(ds_path) as d_file:
+            ds = json.load(d_file)
+        return ds
 
     def _fit_model(self, ds):
         # Call to enviFormer's fine_tune function and return the model
         from enviformer.finetune import fine_tune
 
         start = datetime.now()
-        model = fine_tune(ds.X(), ds.y(), s.MODEL_DIR, str(self.uuid), device=s.ENVIFORMER_DEVICE)
+        model = fine_tune(ds, s.MODEL_DIR, str(self.uuid), device=s.ENVIFORMER_DEVICE)
         end = datetime.now()
         logger.debug(f"EnviFormer finetuning took {(end - start).total_seconds():.2f} seconds")
         return model
@@ -3121,7 +3146,7 @@ class EnviFormer(PackageBasedModel):
         args = {"clz": "EnviFormer"}
         return args
 
-    def evaluate_model(self, multigen: bool, eval_packages: List["Package"] = None, **kwargs):
+    def evaluate_model(self, multigen: bool, eval_packages: List["Package"] = None):
         if self.model_status != self.BUILT_NOT_EVALUATED:
             raise ValueError(f"Can't evaluate a model in state {self.model_status}!")
 
@@ -3136,20 +3161,21 @@ class EnviFormer(PackageBasedModel):
         self.model_status = self.EVALUATING
         self.save()
 
-        def evaluate_sg(test_ds, predictions, model_thresh):
+        def evaluate_sg(test_reactions, predictions, model_thresh):
             # Group the true products of reactions with the same reactant together
-            assert len(test_ds) == len(predictions)
             true_dict = {}
-            for r in test_ds:
-                reactant, true_product_set = r
+            for r in test_reactions:
+                reactant, true_product_set = r.split(">>")
                 true_product_set = {p for p in true_product_set.split(".")}
                 true_dict[reactant] = true_dict.setdefault(reactant, []) + [true_product_set]
+            assert len(test_reactions) == len(predictions)
+            assert sum(len(v) for v in true_dict.values()) == len(test_reactions)
 
             # Group the predicted products of reactions with the same reactant together
             pred_dict = {}
             for k, pred in enumerate(predictions):
                 pred_smiles, pred_proba = zip(*pred.items())
-                reactant, _ = test_ds[k, "educts"], test_ds[k, "products"]
+                reactant, true_product = test_reactions[k].split(">>")
                 pred_dict.setdefault(reactant, {"predict": [], "scores": []})
                 for smiles, proba in zip(pred_smiles, pred_proba):
                     smiles = set(smiles.split("."))
@@ -3184,7 +3210,7 @@ class EnviFormer(PackageBasedModel):
                                 break
 
             # Recall is TP (correct) / TP + FN (len(test_reactions))
-            rec = {f"{k:.2f}": v / len(test_ds) for k, v in correct.items()}
+            rec = {f"{k:.2f}": v / len(test_reactions) for k, v in correct.items()}
             # Precision is TP (correct) / TP + FP (predicted)
             prec = {
                 f"{k:.2f}": v / predicted[k] if predicted[k] > 0 else 0 for k, v in correct.items()
@@ -3263,35 +3289,47 @@ class EnviFormer(PackageBasedModel):
 
         # If there are eval packages perform single generation evaluation on them instead of random splits
         if self.eval_packages.count() > 0:
-            ds = EnviFormerDataset.generate_dataset(
-                Reaction.objects.filter(package__in=self.eval_packages.all()).distinct()
+            ds = []
+            for reaction in Reaction.objects.filter(
+                package__in=self.eval_packages.all()
+            ).distinct():
+                educts = ".".join(
+                    [
+                        FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                        for smile in reaction.educts.all()
+                    ]
                 )
-            test_result = self.model.predict_batch(ds.X())
+                products = ".".join(
+                    [
+                        FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                        for smile in reaction.products.all()
+                    ]
+                )
+                ds.append(f"{educts}>>{products}")
+            test_result = self.model.predict_batch([smirk.split(">>")[0] for smirk in ds])
             single_gen_result = evaluate_sg(ds, test_result, self.threshold)
             self.eval_results = self.compute_averages([single_gen_result])
         else:
             from enviformer.finetune import fine_tune
 
             ds = self.load_dataset()
-            n_splits = kwargs.get("n_splits", 20)
+            n_splits = 20
             shuff = ShuffleSplit(n_splits=n_splits, test_size=0.1, random_state=42)
 
             # Single gen eval is done in one loop of train then evaluate rather than storing all n_splits trained models
             # this helps reduce the memory footprint.
             single_gen_results = []
             for split_id, (train_index, test_index) in enumerate(shuff.split(ds)):
-                train = ds[train_index]
-                test = ds[test_index]
+                train = [ds[i] for i in train_index]
+                test = [ds[i] for i in test_index]
                 start = datetime.now()
-                model = fine_tune(
-                    train.X(), train.y(), s.MODEL_DIR, str(split_id), device=s.ENVIFORMER_DEVICE
-                )
+                model = fine_tune(train, s.MODEL_DIR, str(split_id), device=s.ENVIFORMER_DEVICE)
                 end = datetime.now()
                 logger.debug(
                     f"EnviFormer finetuning took {(end - start).total_seconds():.2f} seconds"
                 )
                 model.to(s.ENVIFORMER_DEVICE)
-                test_result = model.predict_batch(test.X())
+                test_result = model.predict_batch([smirk.split(">>")[0] for smirk in test])
                 single_gen_results.append(evaluate_sg(test, test_result, self.threshold))
 
             self.eval_results = self.compute_averages(single_gen_results)
@@ -3370,12 +3408,23 @@ class EnviFormer(PackageBasedModel):
                             ):
                                 overlap += 1
                                 continue
-                            train_reactions.append(reaction)
-                    train_ds = EnviFormerDataset.generate_dataset(train_reactions)
+                            educts = ".".join(
+                                [
+                                    FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                                    for smile in reaction.educts.all()
+                                ]
+                            )
+                            products = ".".join(
+                                [
+                                    FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                                    for smile in reaction.products.all()
+                                ]
+                            )
+                            train_reactions.append(f"{educts}>>{products}")
                     logging.debug(
                         f"{overlap} compounds had to be removed from multigen split due to overlap within pathways"
                     )
-                    model = fine_tune(train_ds.X(), train_ds.y(), s.MODEL_DIR, f"mg_{split_id}")
+                    model = fine_tune(train_reactions, s.MODEL_DIR, f"mg_{split_id}")
                     multi_gen_results.append(evaluate_mg(model, test_pathways, self.threshold))
 
                 self.eval_results.update(
@@ -3399,7 +3448,7 @@ class PluginModel(EPModel):
 
 class Scenario(EnviPathModel):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     scenario_date = models.CharField(max_length=256, null=False, blank=False, default="No date")
     scenario_type = models.CharField(
@@ -3424,44 +3473,41 @@ class Scenario(EnviPathModel):
         scenario_type: str,
         additional_information: List["EnviPyModel"],
     ):
-        new_s = Scenario()
-        new_s.package = package
-        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 == "":
+        s = Scenario()
+        s.package = package
+
+        if name is None or name.strip() == "":
             name = f"Scenario {Scenario.objects.filter(package=package).count() + 1}"
-        new_s.name = name
+
+        s.name = name
 
         if description is not None and description.strip() != "":
-            new_s.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+            s.description = description
 
         if scenario_date is not None and scenario_date.strip() != "":
-            new_s.scenario_date = nh3.clean(scenario_date).strip()
+            s.scenario_date = scenario_date
 
         if scenario_type is not None and scenario_type.strip() != "":
-            new_s.scenario_type = scenario_type
+            s.scenario_type = scenario_type
 
         add_inf = defaultdict(list)
 
         for info in additional_information:
             cls_name = info.__class__.__name__
-            # Clean for potential XSS hidden in the additional information fields.
-            ai_data = json.loads(nh3.clean(info.model_dump_json()).strip())
+            ai_data = json.loads(info.model_dump_json())
             ai_data["uuid"] = f"{uuid4()}"
             add_inf[cls_name].append(ai_data)
 
-        new_s.additional_information = add_inf
+        s.additional_information = add_inf
 
-        new_s.save()
+        s.save()
 
-        return new_s
+        return s
 
     @transaction.atomic
     def add_additional_information(self, data: "EnviPyModel"):
         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 = json.loads(data.model_dump_json())
         ai_data["uuid"] = f"{uuid4()}"
 
         if cls_name not in self.additional_information:
@@ -3496,8 +3542,7 @@ class Scenario(EnviPathModel):
         new_ais = defaultdict(list)
         for k, vals in data.items():
             for v in vals:
-                # Clean for potential XSS hidden in the additional information fields.
-                ai_data = json.loads(nh3.clean(v.model_dump_json()).strip())
+                ai_data = json.loads(v.model_dump_json())
                 if hasattr(v, "uuid"):
                     ai_data["uuid"] = str(v.uuid)
                 else:
@@ -3554,7 +3599,7 @@ class Setting(EnviPathModel):
     )
 
     rule_packages = models.ManyToManyField(
-        "Package",
+        s.PACKAGE_IMPLEMENTATION,
         verbose_name="Setting Rule Packages",
         related_name="setting_rule_packages",
         blank=True,

epdb/tasks.py

@@ -7,9 +7,12 @@ from uuid import uuid4
 
 from celery import shared_task
 from celery.utils.functional import LRUCache
+from django.conf import settings as s
 
 from epdb.logic import SPathway
-from epdb.models import EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User, Edge
+from epdb.models import Edge, EPModel, JobLog, Node, Pathway, Rule, Setting, User
+
+Package = s.GET_PACKAGE_MODEL()
 
 logger = logging.getLogger(__name__)
 ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.

epdb/urls.py

@@ -193,13 +193,4 @@ urlpatterns = [
     re_path(r"^jobs", v.jobs, name="jobs"),
     # OAuth Stuff
     path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
-    # Static Pages
-    re_path(r"^terms$", v.static_terms_of_use, name="terms_of_use"),
-    re_path(r"^privacy$", v.static_privacy_policy, name="privacy_policy"),
-    re_path(r"^cookie-policy$", v.static_cookie_policy, name="cookie_policy"),
-    re_path(r"^about$", v.static_about_us, name="about_us"),
-    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

@@ -1,56 +1,56 @@
 import json
 import logging
-from typing import List, Dict, Any
+from typing import Any, Dict, List
 
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
-from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, HttpResponseBadRequest
-from django.shortcuts import render, redirect
+from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed, JsonResponse
+from django.shortcuts import 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
-import nh3
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
 from utilities.misc import HTMLGenerator
+
 from .logic import (
+    EPDBURLParser,
     GroupManager,
     PackageManager,
-    UserManager,
-    SettingManager,
     SearchManager,
-    EPDBURLParser,
+    SettingManager,
+    UserManager,
 )
 from .models import (
-    Package,
-    GroupPackagePermission,
-    Group,
-    CompoundStructure,
+    APIToken,
     Compound,
+    CompoundStructure,
+    Edge,
+    EnviFormer,
+    EnzymeLink,
+    EPModel,
+    ExternalDatabase,
+    ExternalIdentifier,
+    Group,
+    GroupPackagePermission,
+    JobLog,
+    License,
+    MLRelativeReasoning,
+    Node,
+    Pathway,
+    Permission,
     Reaction,
     Rule,
-    Pathway,
-    Node,
-    EPModel,
-    EnviFormer,
-    MLRelativeReasoning,
     RuleBasedRelativeReasoning,
     Scenario,
     SimpleAmbitRule,
-    APIToken,
-    UserPackagePermission,
-    Permission,
-    License,
     User,
-    Edge,
-    ExternalDatabase,
-    ExternalIdentifier,
-    EnzymeLink,
-    JobLog,
+    UserPackagePermission,
 )
 
+Package = s.GET_PACKAGE_MODEL()
 logger = logging.getLogger(__name__)
 
 
@@ -83,14 +83,9 @@ def login(request):
         return render(request, "static/login.html", context)
 
     elif request.method == "POST":
-        from django.contrib.auth import authenticate
-        from django.contrib.auth import login
-
-        username = request.POST.get("username").strip()
-        if username != request.POST.get("username"):
-            context["message"] = "Login failed!"
-            return render(request, "static/login.html", context)
+        from django.contrib.auth import authenticate, login
 
+        username = request.POST.get("username")
         password = request.POST.get("password")
 
         # Get email for username and check if the account is active
@@ -105,7 +100,6 @@ def login(request):
         except get_user_model().DoesNotExist:
             context["message"] = "Login failed!"
             return render(request, "static/login.html", context)
-
         try:
             user = authenticate(username=email, password=password)
         except Exception:
@@ -143,14 +137,9 @@ def register(request):
     context = get_base_context(request)
 
     if request.method == "GET":
-        # Redirect to unified login page with signup tab
-        next_url = request.GET.get("next", "")
-        redirect_url = reverse("login") + "#signup"
-
-        if next_url:
-            redirect_url += f"?next={next_url}"
-
-        return redirect(redirect_url)
+        context["title"] = "enviPath"
+        context["next"] = request.GET.get("next", "")
+        return render(request, "static/register.html", context)
     elif request.method == "POST":
         context["title"] = "enviPath"
         if next := request.POST.get("next"):
@@ -163,18 +152,18 @@ def register(request):
 
         if not (username and email and password):
             context["message"] = "Invalid username/email/password"
-            return render(request, "static/login.html", context)
+            return render(request, "static/register.html", context)
 
         if password != rpassword or password == "":
             context["message"] = "Registration failed, provided passwords differ!"
-            return render(request, "static/login.html", context)
+            return render(request, "static/register.html", context)
 
         try:
             u = UserManager.create_user(username, email, password)
             logger.info(f"Created user {u.username} ({u.pk})")
         except Exception:
             context["message"] = "Registration failed! Couldn't create User Account."
-            return render(request, "static/login.html", context)
+            return render(request, "static/register.html", context)
 
         if s.ADMIN_APPROVAL_REQUIRED:
             context["success_message"] = (
@@ -248,7 +237,6 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
             "enabled_features": s.FLAGS,
             "debug": s.DEBUG,
             "external_databases": ExternalDatabase.get_databases(),
-            "site_id": s.MATOMO_SITE_ID,
         },
     }
 
@@ -681,8 +669,7 @@ def search(request):
 
     if request.method == "GET":
         package_urls = request.GET.getlist("packages")
-        searchterm = request.GET.get("search", "").strip()
-
+        searchterm = request.GET.get("search")
         mode = request.GET.get("mode")
 
         # add HTTP_ACCEPT check to differentiate between index and ajax call
@@ -783,6 +770,7 @@ def package_models(request, package_uuid):
 
     elif request.method == "POST":
         log_post_params(request)
+
         name = request.POST.get("model-name")
         description = request.POST.get("model-description")
 
@@ -844,7 +832,7 @@ def package_models(request, package_uuid):
                 request, "Invalid model type.", f'Model type "{model_type}" is not supported."'
             )
 
-        from .tasks import dispatch, build_model
+        from .tasks import build_model, dispatch
 
         dispatch(current_user, build_model, mod.pk)
 
@@ -903,7 +891,7 @@ def package_model(request, package_uuid, model_uuid):
                 return JsonResponse(res, safe=False)
 
             else:
-                app_domain_assessment = current_model.app_domain.assess(stand_smiles)
+                app_domain_assessment = current_model.app_domain.assess(stand_smiles)[0]
                 return JsonResponse(app_domain_assessment, safe=False)
 
         context = get_base_context(request)
@@ -947,14 +935,8 @@ def package_model(request, package_uuid, model_uuid):
             else:
                 return HttpResponseBadRequest()
         else:
-            # TODO: Move cleaning to property updater
-            name = request.POST.get("model-name")
-            if name is not None:
-                name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-            description = request.POST.get("model-description")
-            if description is not None:
-                description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+            name = request.POST.get("model-name", "").strip()
+            description = request.POST.get("model-description", "").strip()
 
             if any([name, description]):
                 if name:
@@ -1056,16 +1038,8 @@ def package(request, package_uuid):
             else:
                 return HttpResponseBadRequest()
 
-        # TODO: Move cleaning to property updater
         new_package_name = request.POST.get("package-name")
-        if new_package_name is not None:
-            new_package_name = nh3.clean(new_package_name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         new_package_description = request.POST.get("package-description")
-        if new_package_description is not None:
-            new_package_description = nh3.clean(
-                new_package_description, tags=s.ALLOWED_HTML_TAGS
-            ).strip()
 
         grantee_url = request.POST.get("grantee")
         read = request.POST.get("read") == "on"
@@ -1174,7 +1148,7 @@ def package_compounds(request, package_uuid):
 
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
-        compound_smiles = request.POST.get("compound-smiles").strip()
+        compound_smiles = request.POST.get("compound-smiles")
         compound_description = request.POST.get("compound-description")
 
         c = Compound.create(current_package, compound_smiles, compound_name, compound_description)
@@ -1227,16 +1201,8 @@ def package_compound(request, package_uuid, compound_uuid):
 
             return JsonResponse({"success": current_compound.url})
 
-        # TODO: Move cleaning to property updater
-        new_compound_name = request.POST.get("compound-name")
-        if new_compound_name is not None:
-            new_compound_name = nh3.clean(new_compound_name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        new_compound_description = request.POST.get("compound-description")
-        if new_compound_description is not None:
-            new_compound_description = nh3.clean(
-                new_compound_description, tags=s.ALLOWED_HTML_TAGS
-            ).strip()
+        new_compound_name = request.POST.get("compound-name", "").strip()
+        new_compound_description = request.POST.get("compound-description", "").strip()
 
         if new_compound_name:
             current_compound.name = new_compound_name
@@ -1301,7 +1267,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
 
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
-        structure_smiles = request.POST.get("structure-smiles").strip()
+        structure_smiles = request.POST.get("structure-smiles")
         structure_description = request.POST.get("structure-description")
 
         try:
@@ -1372,16 +1338,8 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
             else:
                 return HttpResponseBadRequest()
 
-        # TODO: Move cleaning to property updater
-        new_structure_name = request.POST.get("compound-structure-name")
-        if new_structure_name is not None:
-            new_structure_name = nh3.clean(new_structure_name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        new_structure_description = request.POST.get("compound-structure-description")
-        if new_structure_description is not None:
-            new_structure_description = nh3.clean(
-                new_structure_description, tags=s.ALLOWED_HTML_TAGS
-            ).strip()
+        new_structure_name = request.POST.get("compound-structure-name", "").strip()
+        new_structure_description = request.POST.get("compound-structure-description", "").strip()
 
         if new_structure_name:
             current_structure.name = new_structure_name
@@ -1483,11 +1441,11 @@ def package_rules(request, package_uuid):
 
         # Obtain parameters as required by rule type
         if rule_type == "SimpleAmbitRule":
-            params["smirks"] = request.POST.get("rule-smirks").strip()
+            params["smirks"] = request.POST.get("rule-smirks")
             params["reactant_filter_smarts"] = request.POST.get("rule-reactant-smarts")
             params["product_filter_smarts"] = request.POST.get("rule-product-smarts")
         elif rule_type == "SimpleRDKitRule":
-            params["reaction_smarts"] = request.POST.get("rule-reaction-smarts").strip()
+            params["reaction_smarts"] = request.POST.get("rule-reaction-smarts")
         elif rule_type == "ParallelRule":
             pass
         elif rule_type == "SequentialRule":
@@ -1588,14 +1546,8 @@ def package_rule(request, package_uuid, rule_uuid):
 
             return JsonResponse({"success": current_rule.url})
 
-        # TODO: Move cleaning to property updater
-        rule_name = request.POST.get("rule-name")
-        if rule_name is not None:
-            rule_name = nh3.clean(rule_name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        rule_description = request.POST.get("rule-description")
-        if rule_description is not None:
-            rule_description = nh3.clean(rule_description, tags=s.ALLOWED_HTML_TAGS).strip()
+        rule_name = request.POST.get("rule-name", "").strip()
+        rule_description = request.POST.get("rule-description", "").strip()
 
         if rule_name:
             current_rule.name = rule_name
@@ -1684,8 +1636,8 @@ def package_reactions(request, package_uuid):
     elif request.method == "POST":
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
+        reactions_smirks = request.POST.get("reaction-smirks")
 
-        reactions_smirks = request.POST.get("reaction-smirks").strip()
         educts = reactions_smirks.split(">>")[0].split(".")
         products = reactions_smirks.split(">>")[1].split(".")
 
@@ -1746,16 +1698,8 @@ def package_reaction(request, package_uuid, reaction_uuid):
 
             return JsonResponse({"success": current_reaction.url})
 
-        # TODO: Move cleaning to property updater
-        new_reaction_name = request.POST.get("reaction-name")
-        if new_reaction_name is not None:
-            new_reaction_name = nh3.clean(new_reaction_name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        new_reaction_description = request.POST.get("reaction-description")
-        if new_reaction_description is not None:
-            new_reaction_description = nh3.clean(
-                new_reaction_description, tags=s.ALLOWED_HTML_TAGS
-            ).strip()
+        new_reaction_name = request.POST.get("reaction-name", "").strip()
+        new_reaction_description = request.POST.get("reaction-description", "").strip()
 
         if new_reaction_name:
             current_reaction.name = new_reaction_name
@@ -1832,9 +1776,8 @@ def package_pathways(request, package_uuid):
 
         name = request.POST.get("name")
         description = request.POST.get("description")
-
-        smiles = request.POST.get("smiles", "").strip()
         pw_mode = request.POST.get("predict", "predict").strip()
+        smiles = request.POST.get("smiles", "").strip()
 
         if "smiles" in request.POST and smiles == "":
             return error(
@@ -1843,6 +1786,8 @@ def package_pathways(request, package_uuid):
                 "Pathway prediction failed due to missing or empty SMILES",
             )
 
+        smiles = smiles.strip()
+
         try:
             stand_smiles = FormatConverter.standardize(smiles)
         except ValueError:
@@ -2001,14 +1946,8 @@ def package_pathway(request, package_uuid, pathway_uuid):
 
             return JsonResponse({"success": current_pathway.url})
 
-        # TODO: Move cleaning to property updater
         pathway_name = request.POST.get("pathway-name")
-        if pathway_name is not None:
-            pathway_name = nh3.clean(pathway_name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         pathway_description = request.POST.get("pathway-description")
-        if pathway_description is not None:
-            pathway_description = nh3.clean(pathway_description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if any([pathway_name, pathway_description]):
             if pathway_name is not None and pathway_name.strip() != "":
@@ -2096,8 +2035,8 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
     elif request.method == "POST":
         node_name = request.POST.get("node-name")
         node_description = request.POST.get("node-description")
+        node_smiles = request.POST.get("node-smiles")
 
-        node_smiles = request.POST.get("node-smiles").strip()
         current_pathway.add_node(node_smiles, name=node_name, description=node_description)
 
         return redirect(current_pathway.url)
@@ -2259,9 +2198,9 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
 
     elif request.method == "POST":
         log_post_params(request)
+
         edge_name = request.POST.get("edge-name")
         edge_description = request.POST.get("edge-description")
-
         edge_substrates = request.POST.getlist("edge-substrates")
         edge_products = request.POST.getlist("edge-products")
 
@@ -2348,7 +2287,7 @@ 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.name, "url": s.url, "uuid": s.uuid} for s in scens]
             return JsonResponse(res, safe=False)
 
         context = get_base_context(request)
@@ -2386,9 +2325,9 @@ def package_scenarios(request, package_uuid):
         context["unreviewed_objects"] = unreviewed_scenario_qs
 
         from envipy_additional_information import (
+            SEDIMENT_ADDITIONAL_INFORMATION,
             SLUDGE_ADDITIONAL_INFORMATION,
             SOIL_ADDITIONAL_INFORMATION,
-            SEDIMENT_ADDITIONAL_INFORMATION,
         )
 
         context["scenario_types"] = {
@@ -2396,21 +2335,21 @@ def package_scenarios(request, package_uuid):
                 "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]
+                    for ai in [x for s in SOIL_ADDITIONAL_INFORMATION.values() for x in s]
                 ],
             },
             "Sludge Data": {
                 "name": "sludge",
                 "widgets": [
                     HTMLGenerator.generate_html(ai, prefix=f"sludge_{0}")
-                    for ai in [x for sv in SLUDGE_ADDITIONAL_INFORMATION.values() for x in sv]
+                    for ai in [x for s in SLUDGE_ADDITIONAL_INFORMATION.values() for x in s]
                 ],
             },
             "Water-Sediment System Data": {
                 "name": "sediment",
                 "widgets": [
                     HTMLGenerator.generate_html(ai, prefix=f"sediment_{0}")
-                    for ai in [x for sv in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in sv]
+                    for ai in [x for s in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in s]
                 ],
             },
         }
@@ -2425,7 +2364,6 @@ def package_scenarios(request, package_uuid):
 
         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")
@@ -2439,9 +2377,9 @@ def package_scenarios(request, package_uuid):
         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]
+        additional_information = [x for s in additional_information.values() for x in s]
 
-        new_scen = Scenario.create(
+        s = Scenario.create(
             current_package,
             name=scenario_name,
             description=scenario_description,
@@ -2450,7 +2388,7 @@ def package_scenarios(request, package_uuid):
             additional_information=additional_information,
         )
 
-        return redirect(new_scen.url)
+        return redirect(s.url)
     else:
         return HttpResponseNotAllowed(
             [
@@ -2750,7 +2688,6 @@ def settings(request):
 
         name = request.POST.get("prediction-setting-name")
         description = request.POST.get("prediction-setting-description")
-
         new_default = request.POST.get("prediction-setting-new-default", "off") == "on"
 
         max_nodes = min(
@@ -2901,60 +2838,3 @@ def userinfo(request):
         "email_verified": user.is_active,
     }
     return JsonResponse(res)
-
-
-# Static Pages
-def static_terms_of_use(request):
-    context = get_base_context(request)
-    context["title"] = "enviPath - Terms of Use"
-    context["public_mode"] = True
-    return render(request, "static/terms_of_use.html", context)
-
-
-def static_privacy_policy(request):
-    context = get_base_context(request)
-    context["title"] = "enviPath - Privacy Policy"
-    context["public_mode"] = True
-    return render(request, "static/privacy_policy.html", context)
-
-
-def static_cookie_policy(request):
-    context = get_base_context(request)
-    context["title"] = "enviPath - Cookie Policy"
-    context["public_mode"] = True
-    return render(request, "static/cookie_policy.html", context)
-
-
-def static_about_us(request):
-    context = get_base_context(request)
-    context["title"] = "enviPath - About Us"
-    context["public_mode"] = True
-    return render(request, "static/about_us.html", context)
-
-
-def static_contact_support(request):
-    context = get_base_context(request)
-    context["title"] = "enviPath - Contact & Support"
-    context["public_mode"] = True
-    return render(request, "static/contact.html", context)
-
-
-def static_careers(request):
-    context = get_base_context(request)
-    context["title"] = "enviPath - Careers"
-    context["public_mode"] = True
-    return render(request, "static/careers.html", context)
-
-
-def static_cite(request):
-    context = get_base_context(request)
-    context["title"] = "enviPath - How to Cite"
-    context["public_mode"] = True
-    return render(request, "static/cite.html", context)
-
-
-def static_legal(request):
-    context = get_base_context(request)
-    context["title"] = "enviPath - Legal Information"
-    context["public_mode"] = True
-    return render(request, "static/legal.html", context)

migration/views.py

@@ -1,22 +1,19 @@
-import gzip
 import json
 import logging
 import os.path
-from datetime import datetime
 
 from django.conf import settings as s
 from django.http import HttpResponseNotAllowed
 from django.shortcuts import render
-
-from epdb.logic import PackageManager
-from epdb.models import Rule, SimpleAmbitRule, Package, CompoundStructure
-from epdb.views import get_base_context, _anonymous_or_real
-from utilities.chem import FormatConverter
-
-
 from rdkit import Chem
 from rdkit.Chem.MolStandardize import rdMolStandardize
 
+from epdb.models import CompoundStructure, Rule, SimpleAmbitRule
+from epdb.views import get_base_context
+from utilities.chem import FormatConverter
+
+Package = s.GET_PACKAGE_MODEL()
+
 logger = logging.getLogger(__name__)
 
 
@@ -59,9 +56,7 @@ def run_both_engines(SMILES, SMIRKS):
         set(
             [
                 normalize_smiles(str(x))
-                for x in FormatConverter.sanitize_smiles(
-                    [str(s) for s in all_rdkit_prods]
-                )[0]
+                for x in FormatConverter.sanitize_smiles([str(s) for s in all_rdkit_prods])[0]
             ]
         )
     )
@@ -85,8 +80,7 @@ def migration(request):
                 url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
             )
             ALL_SMILES = [
-                cs.smiles
-                for cs in CompoundStructure.objects.filter(compound__package=BBD)
+                cs.smiles for cs in CompoundStructure.objects.filter(compound__package=BBD)
             ]
             RULES = SimpleAmbitRule.objects.filter(package=BBD)
 
@@ -142,9 +136,7 @@ def migration(request):
             )
 
         for r in migration_status["results"]:
-            r["detail_url"] = r["detail_url"].replace(
-                "http://localhost:8000", s.SERVER_URL
-            )
+            r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
 
         context.update(**migration_status)
 
@@ -152,8 +144,6 @@ def migration(request):
 
 
 def migration_detail(request, package_uuid, rule_uuid):
-    current_user = _anonymous_or_real(request)
-
     if request.method == "GET":
         context = get_base_context(request)
 
@@ -235,9 +225,7 @@ def compare(request):
         context["smirks"] = (
             "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O"
         )
-        context["smiles"] = (
-            "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
-        )
+        context["smiles"] = "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
         return render(request, "compare.html", context)
 
     elif request.method == "POST":

package.json

@@ -1,25 +0,0 @@
-{
-  "name": "envipy",
-  "version": "1.0.0",
-  "private": true,
-  "description": "enviPath UI - Tailwind CSS + DaisyUI",
-  "scripts": {
-    "dev": "tailwindcss -i static/css/input.css -o static/css/output.css --watch=always",
-    "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",
-    "postcss": "^8.5.6",
-    "prettier": "^3.6.2",
-    "prettier-plugin-jinja-template": "^2.1.0",
-    "prettier-plugin-tailwindcss": "^0.7.1",
-    "tailwindcss": "^4.1.16"
-  },
-  "keywords": [
-    "django",
-    "tailwindcss",
-    "daisyui"
-  ]
-}

pnpm-lock.yaml

@@ -1,740 +0,0 @@
-lockfileVersion: '9.0'
-
-settings:
-  autoInstallPeers: true
-  excludeLinksFromLockfile: false
-
-importers:
-
-  .:
-    devDependencies:
-      '@tailwindcss/cli':
-        specifier: ^4.1.16
-        version: 4.1.16
-      '@tailwindcss/postcss':
-        specifier: ^4.1.16
-        version: 4.1.16
-      daisyui:
-        specifier: ^5.4.3
-        version: 5.4.3
-      postcss:
-        specifier: ^8.5.6
-        version: 8.5.6
-      prettier:
-        specifier: ^3.6.2
-        version: 3.6.2
-      prettier-plugin-jinja-template:
-        specifier: ^2.1.0
-        version: 2.1.0(prettier@3.6.2)
-      prettier-plugin-tailwindcss:
-        specifier: ^0.7.1
-        version: 0.7.1(prettier@3.6.2)
-      tailwindcss:
-        specifier: ^4.1.16
-        version: 4.1.16
-
-packages:
-
-  '@alloc/quick-lru@5.2.0':
-    resolution: {integrity: sha512-UrcABB+4bUrFABwbluTIBErXwvbsU/V7TZWfmbgJfbkwiBuziS9gxdODUyuiecfdGQ85jglMW6juS3+z5TsKLw==}
-    engines: {node: '>=10'}
-
-  '@jridgewell/gen-mapping@0.3.13':
-    resolution: {integrity: sha512-2kkt/7niJ6MgEPxF0bYdQ6etZaA+fQvDcLKckhy1yIQOzaoKjBBjSj63/aLVjYE3qhRt5dvM+uUyfCg6UKCBbA==}
-
-  '@jridgewell/remapping@2.3.5':
-    resolution: {integrity: sha512-LI9u/+laYG4Ds1TDKSJW2YPrIlcVYOwi2fUC6xB43lueCjgxV4lffOCZCtYFiH6TNOX+tQKXx97T4IKHbhyHEQ==}
-
-  '@jridgewell/resolve-uri@3.1.2':
-    resolution: {integrity: sha512-bRISgCIjP20/tbWSPWMEi54QVPRZExkuD9lJL+UIxUKtwVJA8wW1Trb1jMs1RFXo1CBTNZ/5hpC9QvmKWdopKw==}
-    engines: {node: '>=6.0.0'}
-
-  '@jridgewell/sourcemap-codec@1.5.5':
-    resolution: {integrity: sha512-cYQ9310grqxueWbl+WuIUIaiUaDcj7WOq5fVhEljNVgRfOUhY9fy2zTvfoqWsnebh8Sl70VScFbICvJnLKB0Og==}
-
-  '@jridgewell/trace-mapping@0.3.31':
-    resolution: {integrity: sha512-zzNR+SdQSDJzc8joaeP8QQoCQr8NuYx2dIIytl1QeBEZHJ9uW6hebsrYgbz8hJwUQao3TWCMtmfV8Nu1twOLAw==}
-
-  '@parcel/watcher-android-arm64@2.5.1':
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-      '@prettier/plugin-hermes': '*'
-      '@prettier/plugin-oxc': '*'
-      '@prettier/plugin-pug': '*'
-      '@shopify/prettier-plugin-liquid': '*'
-      '@trivago/prettier-plugin-sort-imports': '*'
-      '@zackad/prettier-plugin-twig': '*'
-      prettier: ^3.0
-      prettier-plugin-astro: '*'
-      prettier-plugin-css-order: '*'
-      prettier-plugin-jsdoc: '*'
-      prettier-plugin-marko: '*'
-      prettier-plugin-multiline-arrays: '*'
-      prettier-plugin-organize-attributes: '*'
-      prettier-plugin-organize-imports: '*'
-      prettier-plugin-sort-imports: '*'
-      prettier-plugin-svelte: '*'
-    peerDependenciesMeta:
-      '@ianvs/prettier-plugin-sort-imports':
-        optional: true
-      '@prettier/plugin-hermes':
-        optional: true
-      '@prettier/plugin-oxc':
-        optional: true
-      '@prettier/plugin-pug':
-        optional: true
-      '@shopify/prettier-plugin-liquid':
-        optional: true
-      '@trivago/prettier-plugin-sort-imports':
-        optional: true
-      '@zackad/prettier-plugin-twig':
-        optional: true
-      prettier-plugin-astro:
-        optional: true
-      prettier-plugin-css-order:
-        optional: true
-      prettier-plugin-jsdoc:
-        optional: true
-      prettier-plugin-marko:
-        optional: true
-      prettier-plugin-multiline-arrays:
-        optional: true
-      prettier-plugin-organize-attributes:
-        optional: true
-      prettier-plugin-organize-imports:
-        optional: true
-      prettier-plugin-sort-imports:
-        optional: true
-      prettier-plugin-svelte:
-        optional: true
-
-  prettier@3.6.2:
-    resolution: {integrity: sha512-I7AIg5boAr5R0FFtJ6rCfD+LFsWHp81dolrFD8S79U9tb8Az2nGrJncnMSnys+bpQJfRUzqs9hnA81OAA3hCuQ==}
-    engines: {node: '>=14'}
-    hasBin: true
-
-  source-map-js@1.2.1:
-    resolution: {integrity: sha512-UXWMKhLOwVKb728IUtQPXxfYU+usdybtUrK/8uGE8CQMvrhOpwvzDBwj0QhSL7MQc7vIsISBG8VQ8+IDQxpfQA==}
-    engines: {node: '>=0.10.0'}
-
-  tailwindcss@4.1.16:
-    resolution: {integrity: sha512-pONL5awpaQX4LN5eiv7moSiSPd/DLDzKVRJz8Q9PgzmAdd1R4307GQS2ZpfiN7ZmekdQrfhZZiSE5jkLR4WNaA==}
-
-  tapable@2.3.0:
-    resolution: {integrity: sha512-g9ljZiwki/LfxmQADO3dEY1CbpmXT5Hm2fJ+QaGKwSXUylMybePR7/67YW7jOrrvjEgL1Fmz5kzyAjWVWLlucg==}
-    engines: {node: '>=6'}
-
-  to-regex-range@5.0.1:
-    resolution: {integrity: sha512-65P7iz6X5yEr1cwcgvQxbbIw7Uk3gOy5dIdtZ4rDveLqhrdJP+Li/Hx6tyK0NEb+2GCyneCMJiGqrADCSNk8sQ==}
-    engines: {node: '>=8.0'}
-
-snapshots:
-
-  '@alloc/quick-lru@5.2.0': {}
-
-  '@jridgewell/gen-mapping@0.3.13':
-    dependencies:
-      '@jridgewell/sourcemap-codec': 1.5.5
-      '@jridgewell/trace-mapping': 0.3.31
-
-  '@jridgewell/remapping@2.3.5':
-    dependencies:
-      '@jridgewell/gen-mapping': 0.3.13
-      '@jridgewell/trace-mapping': 0.3.31
-
-  '@jridgewell/resolve-uri@3.1.2': {}
-
-  '@jridgewell/sourcemap-codec@1.5.5': {}
-
-  '@jridgewell/trace-mapping@0.3.31':
-    dependencies:
-      '@jridgewell/resolve-uri': 3.1.2
-      '@jridgewell/sourcemap-codec': 1.5.5
-
-  '@parcel/watcher-android-arm64@2.5.1':
-    optional: true
-
-  '@parcel/watcher-darwin-arm64@2.5.1':
-    optional: true
-
-  '@parcel/watcher-darwin-x64@2.5.1':
-    optional: true
-
-  '@parcel/watcher-freebsd-x64@2.5.1':
-    optional: true
-
-  '@parcel/watcher-linux-arm-glibc@2.5.1':
-    optional: true
-
-  '@parcel/watcher-linux-arm-musl@2.5.1':
-    optional: true
-
-  '@parcel/watcher-linux-arm64-glibc@2.5.1':
-    optional: true
-
-  '@parcel/watcher-linux-arm64-musl@2.5.1':
-    optional: true
-
-  '@parcel/watcher-linux-x64-glibc@2.5.1':
-    optional: true
-
-  '@parcel/watcher-linux-x64-musl@2.5.1':
-    optional: true
-
-  '@parcel/watcher-win32-arm64@2.5.1':
-    optional: true
-
-  '@parcel/watcher-win32-ia32@2.5.1':
-    optional: true
-
-  '@parcel/watcher-win32-x64@2.5.1':
-    optional: true
-
-  '@parcel/watcher@2.5.1':
-    dependencies:
-      detect-libc: 1.0.3
-      is-glob: 4.0.3
-      micromatch: 4.0.8
-      node-addon-api: 7.1.1
-    optionalDependencies:
-      '@parcel/watcher-android-arm64': 2.5.1
-      '@parcel/watcher-darwin-arm64': 2.5.1
-      '@parcel/watcher-darwin-x64': 2.5.1
-      '@parcel/watcher-freebsd-x64': 2.5.1
-      '@parcel/watcher-linux-arm-glibc': 2.5.1
-      '@parcel/watcher-linux-arm-musl': 2.5.1
-      '@parcel/watcher-linux-arm64-glibc': 2.5.1
-      '@parcel/watcher-linux-arm64-musl': 2.5.1
-      '@parcel/watcher-linux-x64-glibc': 2.5.1
-      '@parcel/watcher-linux-x64-musl': 2.5.1
-      '@parcel/watcher-win32-arm64': 2.5.1
-      '@parcel/watcher-win32-ia32': 2.5.1
-      '@parcel/watcher-win32-x64': 2.5.1
-
-  '@tailwindcss/cli@4.1.16':
-    dependencies:
-      '@parcel/watcher': 2.5.1
-      '@tailwindcss/node': 4.1.16
-      '@tailwindcss/oxide': 4.1.16
-      enhanced-resolve: 5.18.3
-      mri: 1.2.0
-      picocolors: 1.1.1
-      tailwindcss: 4.1.16
-
-  '@tailwindcss/node@4.1.16':
-    dependencies:
-      '@jridgewell/remapping': 2.3.5
-      enhanced-resolve: 5.18.3
-      jiti: 2.6.1
-      lightningcss: 1.30.2
-      magic-string: 0.30.21
-      source-map-js: 1.2.1
-      tailwindcss: 4.1.16
-
-  '@tailwindcss/oxide-android-arm64@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-darwin-arm64@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-darwin-x64@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-freebsd-x64@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-linux-arm-gnueabihf@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-linux-arm64-gnu@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-linux-arm64-musl@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-linux-x64-gnu@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-linux-x64-musl@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-wasm32-wasi@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-win32-arm64-msvc@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide-win32-x64-msvc@4.1.16':
-    optional: true
-
-  '@tailwindcss/oxide@4.1.16':
-    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/postcss@4.1.16':
-    dependencies:
-      '@alloc/quick-lru': 5.2.0
-      '@tailwindcss/node': 4.1.16
-      '@tailwindcss/oxide': 4.1.16
-      postcss: 8.5.6
-      tailwindcss: 4.1.16
-
-  braces@3.0.3:
-    dependencies:
-      fill-range: 7.1.1
-
-  daisyui@5.4.3: {}
-
-  detect-libc@1.0.3: {}
-
-  detect-libc@2.1.2: {}
-
-  enhanced-resolve@5.18.3:
-    dependencies:
-      graceful-fs: 4.2.11
-      tapable: 2.3.0
-
-  fill-range@7.1.1:
-    dependencies:
-      to-regex-range: 5.0.1
-
-  graceful-fs@4.2.11: {}
-
-  is-extglob@2.1.1: {}
-
-  is-glob@4.0.3:
-    dependencies:
-      is-extglob: 2.1.1
-
-  is-number@7.0.0: {}
-
-  jiti@2.6.1: {}
-
-  lightningcss-android-arm64@1.30.2:
-    optional: true
-
-  lightningcss-darwin-arm64@1.30.2:
-    optional: true
-
-  lightningcss-darwin-x64@1.30.2:
-    optional: true
-
-  lightningcss-freebsd-x64@1.30.2:
-    optional: true
-
-  lightningcss-linux-arm-gnueabihf@1.30.2:
-    optional: true
-
-  lightningcss-linux-arm64-gnu@1.30.2:
-    optional: true
-
-  lightningcss-linux-arm64-musl@1.30.2:
-    optional: true
-
-  lightningcss-linux-x64-gnu@1.30.2:
-    optional: true
-
-  lightningcss-linux-x64-musl@1.30.2:
-    optional: true
-
-  lightningcss-win32-arm64-msvc@1.30.2:
-    optional: true
-
-  lightningcss-win32-x64-msvc@1.30.2:
-    optional: true
-
-  lightningcss@1.30.2:
-    dependencies:
-      detect-libc: 2.1.2
-    optionalDependencies:
-      lightningcss-android-arm64: 1.30.2
-      lightningcss-darwin-arm64: 1.30.2
-      lightningcss-darwin-x64: 1.30.2
-      lightningcss-freebsd-x64: 1.30.2
-      lightningcss-linux-arm-gnueabihf: 1.30.2
-      lightningcss-linux-arm64-gnu: 1.30.2
-      lightningcss-linux-arm64-musl: 1.30.2
-      lightningcss-linux-x64-gnu: 1.30.2
-      lightningcss-linux-x64-musl: 1.30.2
-      lightningcss-win32-arm64-msvc: 1.30.2
-      lightningcss-win32-x64-msvc: 1.30.2
-
-  magic-string@0.30.21:
-    dependencies:
-      '@jridgewell/sourcemap-codec': 1.5.5
-
-  micromatch@4.0.8:
-    dependencies:
-      braces: 3.0.3
-      picomatch: 2.3.1
-
-  mri@1.2.0: {}
-
-  nanoid@3.3.11: {}
-
-  node-addon-api@7.1.1: {}
-
-  picocolors@1.1.1: {}
-
-  picomatch@2.3.1: {}
-
-  postcss@8.5.6:
-    dependencies:
-      nanoid: 3.3.11
-      picocolors: 1.1.1
-      source-map-js: 1.2.1
-
-  prettier-plugin-jinja-template@2.1.0(prettier@3.6.2):
-    dependencies:
-      prettier: 3.6.2
-
-  prettier-plugin-tailwindcss@0.7.1(prettier@3.6.2):
-    dependencies:
-      prettier: 3.6.2
-
-  prettier@3.6.2: {}
-
-  source-map-js@1.2.1: {}
-
-  tailwindcss@4.1.16: {}
-
-  tapable@2.3.0: {}
-
-  to-regex-range@5.0.1:
-    dependencies:
-      is-number: 7.0.0

public/admin.py

@@ -0,0 +1 @@
+# Register your models here.

public/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class PublicConfig(AppConfig):
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "public"

public/migrations/0001_initial.py

@@ -0,0 +1,56 @@
+# Generated by Django 5.2.7 on 2025-10-29 13:32
+
+import django.utils.timezone
+import model_utils.fields
+import uuid
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    initial = True
+
+    dependencies = []
+
+    operations = [
+        migrations.CreateModel(
+            name="Package",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                (
+                    "created",
+                    model_utils.fields.AutoCreatedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="created"
+                    ),
+                ),
+                (
+                    "modified",
+                    model_utils.fields.AutoLastModifiedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="modified"
+                    ),
+                ),
+                (
+                    "uuid",
+                    models.UUIDField(
+                        default=uuid.uuid4, unique=True, verbose_name="UUID of this object"
+                    ),
+                ),
+                ("name", models.TextField(default="no name", verbose_name="Name")),
+                (
+                    "description",
+                    models.TextField(default="no description", verbose_name="Descriptions"),
+                ),
+                ("url", models.TextField(null=True, unique=True, verbose_name="URL")),
+                ("kv", models.JSONField(blank=True, default=dict, null=True)),
+                ("reviewed", models.BooleanField(default=False, verbose_name="Reviewstatus")),
+            ],
+            options={
+                "db_table": "epdb_package",
+                "managed": False,
+            },
+        ),
+    ]

public/migrations/0002_alter_package_options.py

@@ -0,0 +1,16 @@
+# Generated by Django 5.2.7 on 2025-10-29 18:39
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("public", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name="package",
+            options={},
+        ),
+    ]

public/migrations/0003_package_license.py

@@ -0,0 +1,25 @@
+# Generated by Django 5.2.7 on 2025-10-29 18:40
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0010_alter_userpackagepermission_package_and_more"),
+        ("public", "0002_alter_package_options"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="package",
+            name="license",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                to="epdb.license",
+                verbose_name="License",
+            ),
+        ),
+    ]

public/models.py

@@ -0,0 +1,6 @@
+from epdb.models import AbstractPackage
+
+
+class Package(AbstractPackage):
+    class Meta:
+        db_table = "epdb_package"

public/tests.py

@@ -0,0 +1 @@
+# Create your tests here.

public/views.py

@@ -0,0 +1 @@
+# Create your views here.

pyproject.toml

@@ -27,12 +27,10 @@ dependencies = [
     "scikit-learn>=1.6.1",
     "sentry-sdk[django]>=2.32.0",
     "setuptools>=80.8.0",
-    "nh3==0.3.2",
-    "polars==1.35.1",
 ]
 
 [tool.uv.sources]
-enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.4" }
+enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.2" }
 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-ambit = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" }
@@ -67,54 +65,22 @@ docstring-code-format = true
 [tool.poe.tasks]
 # Main tasks
 setup = { sequence = ["db-up", "migrate", "bootstrap"], help = "Complete setup: start database, run migrations, and bootstrap data" }
-dev = { shell = """
-# Start pnpm CSS watcher in background
-pnpm run dev &
-PNPM_PID=$!
-echo "Started CSS watcher (PID: $PNPM_PID)"
-
-# Cleanup function
-cleanup() {
-    echo "\nShutting down..."
-    if kill -0 $PNPM_PID 2>/dev/null; then
-        kill $PNPM_PID
-        echo "✓ CSS watcher stopped"
-    fi
-    if [ ! -z "${DJ_PID:-}" ] && kill -0 $DJ_PID 2>/dev/null; then
-        kill $DJ_PID
-        echo "✓ Django server stopped"
-    fi
-}
-
-# Set trap for cleanup
-trap cleanup EXIT INT TERM
-
-# Start Django dev server in background
-uv run python manage.py runserver &
-DJ_PID=$!
-
-# Wait for Django to finish
-wait $DJ_PID
-""", help = "Start the development server with CSS watcher", deps = ["db-up", "js-deps"] }
-build = { sequence = ["build-frontend", "collectstatic"], help = "Build frontend assets and collect static files" }
+dev = { cmd = "python manage.py runserver", help = "Start the development server", deps = ["db-up"] }
 
 # 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" }
 
-# Frontend tasks
-js-deps = { cmd = "pnpm install", help = "Install frontend dependencies" }
-
 # Full cleanup tasks
 clean = { sequence = ["clean-db"], help = "Remove model files and database volumes (WARNING: destroys all data!)" }
 clean-db = { cmd = "docker compose -f docker-compose.dev.yml down -v", help = "Removes the database container and volume." }
 
 # Django tasks
-migrate = { cmd = "uv run python manage.py migrate", help = "Run database migrations" }
+migrate = { cmd = "python manage.py migrate", help = "Run database migrations" }
 bootstrap = { shell = """
 echo "Bootstrapping initial data..."
 echo "This will take a bit ⏱️. Get yourself some coffee..."
-uv run python manage.py bootstrap
+python manage.py bootstrap
 echo "✓ Bootstrap complete"
 echo ""
 echo "Default admin credentials:"
@@ -122,8 +88,4 @@ echo "  Username: admin"
 echo "  Email: admin@envipath.com"
 echo "  Password: SuperSafe"
 """, help = "Bootstrap initial data (anonymous user, packages, models)"  }
-shell = { cmd = "uv run python manage.py shell", help = "Open Django shell" }
-
-# Build tasks
-build-frontend = { cmd = "pnpm run build", help = "Build frontend assets using pnpm", deps = ["js-deps"] }
-collectstatic = { cmd = "uv run python manage.py collectstatic --noinput", help = "Collect static files for production", deps = ["build-frontend"] }
+shell = { cmd = "python manage.py shell", help = "Open Django shell" }

static/css/daisyui-theme.css

@@ -1,84 +0,0 @@
-/**
- * DaisyUI Themes - Generated by Style Dictionary
- * Theme mappings defined in tokens/daisyui-themes.json
- */
-
-/* Light theme (default) */
-@plugin "daisyui/theme" {
-  name: "envipath";
-  default: true;
-  color-scheme: light;
-
-  --color-base-100: var(--color-neutral-50);
-  --color-base-200: var(--color-neutral-100);
-  --color-base-300: var(--color-neutral-200);
-  --color-base-content: var(--color-neutral-900);
-  --color-primary: var(--color-primary-500);
-  --color-primary-content: var(--color-primary-50);
-  --color-secondary: var(--color-secondary-500);
-  --color-secondary-content: var(--color-secondary-50);
-  --color-accent: var(--color-accent-500);
-  --color-accent-content: var(--color-accent-50);
-  --color-neutral: var(--color-neutral-950);
-  --color-neutral-content: var(--color-neutral-100);
-  --color-info: var(--color-info-500);
-  --color-info-content: var(--color-info-950);
-  --color-success: var(--color-success-500);
-  --color-success-content: var(--color-success-950);
-  --color-warning: var(--color-warning-500);
-  --color-warning-content: var(--color-warning-950);
-  --color-error: var(--color-error-500);
-  --color-error-content: var(--color-error-950);
-
-  /* border radius */
-  --radius-selector: 1rem;
-  --radius-field: 0.25rem;
-  --radius-box: 0.5rem;
-
-  /* base sizes */
-  --size-selector: 0.25rem;
-  --size-field: 0.25rem;
-
-  /* border size */
-  --border: 1px;
-
-  /* effects */
-  --depth: 1;
-  --noise: 0;
-}
-
-/* Dark theme (prefers-color-scheme: dark) */
-@plugin "daisyui/theme" {
-  name: "envipath-dark";
-  prefersdark: true;
-  color-scheme: dark;
-
-  --color-primary: var(--color-primary-400);
-  --color-primary-content: var(--color-neutral-950);
-  --color-secondary: var(--color-secondary-400);
-  --color-secondary-content: var(--color-neutral-950);
-  --color-accent: var(--color-primary-500);
-  --color-accent-content: var(--color-neutral-950);
-  --color-neutral: var(--color-neutral-300);
-  --color-neutral-content: var(--color-neutral-900);
-  --color-base-100: var(--color-neutral-900);
-  --color-base-200: var(--color-neutral-800);
-  --color-base-300: var(--color-neutral-700);
-  --color-base-content: var(--color-neutral-50);
-  --color-info: var(--color-primary-400);
-  --color-info-content: var(--color-neutral-950);
-  --color-success: var(--color-success-400);
-  --color-success-content: var(--color-neutral-950);
-  --color-warning: var(--color-warning-400);
-  --color-warning-content: var(--color-neutral-950);
-  --color-error: var(--color-error-400);
-  --color-error-content: var(--color-neutral-950);
-  --radius-selector: 1rem;
-  --radius-field: 0.25rem;
-  --radius-box: 0.5rem;
-  --size-selector: 0.25rem;
-  --size-field: 0.25rem;
-  --border: 1px;
-  --depth: 1;
-  --noise: 0;
-}

static/css/input.css

@@ -1,35 +0,0 @@
-@import "tailwindcss";
-
-/* fira-code-latin-wght-normal */
-@font-face {
-  font-family: 'Fira Code Variable';
-  font-style: normal;
-  font-display: swap;
-  font-weight: 300 700;
-  src: url(https://cdn.jsdelivr.net/fontsource/fonts/fira-code:vf@latest/latin-wght-normal.woff2) format('woff2-variations');
-  unicode-range: U+0000-00FF,U+0131,U+0152-0153,U+02BB-02BC,U+02C6,U+02DA,U+02DC,U+0304,U+0308,U+0329,U+2000-206F,U+20AC,U+2122,U+2191,U+2193,U+2212,U+2215,U+FEFF,U+FFFD;
-}
-
-/* inter-latin-wght-normal */
-@font-face {
-  font-family: 'Inter Variable';
-  font-style: normal;
-  font-display: swap;
-  font-weight: 100 900;
-  src: url(https://cdn.jsdelivr.net/fontsource/fonts/inter:vf@latest/latin-wght-normal.woff2) format('woff2-variations');
-  unicode-range: U+0000-00FF,U+0131,U+0152-0153,U+02BB-02BC,U+02C6,U+02DA,U+02DC,U+0304,U+0308,U+0329,U+2000-206F,U+20AC,U+2122,U+2191,U+2193,U+2212,U+2215,U+FEFF,U+FFFD;
-}
-
-
-/* Tell Tailwind where to find Django templates and Python files */
-@source "../../templates";
-
-/* Custom theme configuration - must come before plugins */
-@import "./theme.css";
-
-/* Import DaisyUI plugin */
-@plugin "daisyui" {
-  logs: true;
-}
-
-@import "./daisyui-theme.css";

static/css/theme.css

@@ -1,111 +0,0 @@
-/**
- * Tailwind v4 Theme - Generated by Style Dictionary
- * This creates Tailwind utility classes from design tokens
- */
-
-@theme {
-  /* Colors */
-  --color-primary-50: oklch(0.98 0.02 201);
-  --color-primary-100: oklch(0.96 0.04 203);
-  --color-primary-200: oklch(0.92 0.08 205);
-  --color-primary-300: oklch(0.87 0.12 207);
-  --color-primary-400: oklch(0.80 0.13 212);
-  --color-primary-500: oklch(0.71 0.13 215);
-  --color-primary-600: oklch(0.61 0.11 222);
-  --color-primary-700: oklch(0.52 0.09 223);
-  --color-primary-800: oklch(0.45 0.08 224);
-  --color-primary-900: oklch(0.40 0.07 227);
-  --color-primary-950: oklch(0.30 0.05 230);
-  --color-secondary-50: oklch(0.98 0.02 166);
-  --color-secondary-100: oklch(0.95 0.05 163);
-  --color-secondary-200: oklch(0.90 0.09 164);
-  --color-secondary-300: oklch(0.85 0.13 165);
-  --color-secondary-400: oklch(0.77 0.15 163);
-  --color-secondary-500: oklch(0.70 0.15 162);
-  --color-secondary-600: oklch(0.60 0.13 163);
-  --color-secondary-700: oklch(0.51 0.10 166);
-  --color-secondary-800: oklch(0.43 0.09 167);
-  --color-secondary-900: oklch(0.38 0.07 169);
-  --color-secondary-950: oklch(0.26 0.05 173);
-  --color-success-50: oklch(0.98 0.02 156);
-  --color-success-100: oklch(0.96 0.04 157);
-  --color-success-200: oklch(0.93 0.08 156);
-  --color-success-300: oklch(0.87 0.14 154);
-  --color-success-400: oklch(0.80 0.18 152);
-  --color-success-500: oklch(0.72 0.19 150);
-  --color-success-600: oklch(0.63 0.17 149);
-  --color-success-700: oklch(0.53 0.14 150);
-  --color-success-800: oklch(0.45 0.11 151);
-  --color-success-900: oklch(0.39 0.09 153);
-  --color-success-950: oklch(0.27 0.06 153);
-  --color-warning-50: oklch(0.99 0.03 102);
-  --color-warning-100: oklch(0.97 0.07 103);
-  --color-warning-200: oklch(0.95 0.12 102);
-  --color-warning-300: oklch(0.91 0.17 98);
-  --color-warning-400: oklch(0.86 0.17 92);
-  --color-warning-500: oklch(0.80 0.16 86);
-  --color-warning-600: oklch(0.68 0.14 76);
-  --color-warning-700: oklch(0.55 0.12 66);
-  --color-warning-800: oklch(0.48 0.10 62);
-  --color-warning-900: oklch(0.42 0.09 58);
-  --color-warning-950: oklch(0.29 0.06 54);
-  --color-error-50: oklch(0.97 0.01 17);
-  --color-error-100: oklch(0.94 0.03 18);
-  --color-error-200: oklch(0.88 0.06 18);
-  --color-error-300: oklch(0.81 0.10 20);
-  --color-error-400: oklch(0.71 0.17 22);
-  --color-error-500: oklch(0.64 0.21 25);
-  --color-error-600: oklch(0.58 0.22 27);
-  --color-error-700: oklch(0.51 0.19 28);
-  --color-error-800: oklch(0.44 0.16 27);
-  --color-error-900: oklch(0.40 0.13 26);
-  --color-error-950: oklch(0.26 0.09 26);
-  --color-neutral-50: oklch(0.98 0.00 248);
-  --color-neutral-100: oklch(0.97 0.01 248);
-  --color-neutral-200: oklch(0.93 0.01 256);
-  --color-neutral-300: oklch(0.87 0.02 253);
-  --color-neutral-400: oklch(0.71 0.04 257);
-  --color-neutral-500: oklch(0.55 0.04 257);
-  --color-neutral-600: oklch(0.45 0.04 257);
-  --color-neutral-700: oklch(0.37 0.04 257);
-  --color-neutral-800: oklch(0.28 0.04 260);
-  --color-neutral-900: oklch(0.28 0.04 260);
-  --color-neutral-950: oklch(0.28 0.04 260);
-
-  /* Spacing */
-  --spacing-0: 0;
-  --spacing-1: 0.25rem;
-  --spacing-2: 0.5rem;
-  --spacing-3: 0.75rem;
-  --spacing-4: 1rem;
-  --spacing-5: 1.25rem;
-  --spacing-6: 1.5rem;
-  --spacing-7: 1.75rem;
-  --spacing-8: 2rem;
-  --spacing-10: 2.5rem;
-  --spacing-12: 3rem;
-  --spacing-16: 4rem;
-  --spacing-20: 5rem;
-  --spacing-24: 6rem;
-  --spacing-32: 8rem;
-  --spacing-40: 10rem;
-  --spacing-48: 12rem;
-  --spacing-56: 14rem;
-  --spacing-64: 16rem;
-
-  /* Typography */
-  --font-family-sans: 'Inter Variable', system-ui, -apple-system, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
-  --font-family-mono: 'Fira Code Variable', 'Cascadia Code', 'Source Code Pro', Menlo, Consolas, monospace;
-  --font-family-base: 'Inter Variable', system-ui, -apple-system, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
-  --font-size-xs: 0.75rem;
-  --font-size-sm: 0.875rem;
-  --font-size-base: 1rem;
-  --font-size-lg: 1.125rem;
-  --font-size-xl: 1.25rem;
-  --font-size-2xl: 1.5rem;
-  --font-size-3xl: 1.875rem;
-  --font-size-4xl: 2.25rem;
-  --font-size-5xl: 3rem;
-  --font-size-6xl: 3.75rem;
-  --font-size-7xl: 4.5rem;
-}

static/images/logo-long.svg

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+
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+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
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static/images/logo-name.svg

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static/images/logo-square.svg

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static/js/discourse-api.js

@@ -1,170 +0,0 @@
-/**
- * Discourse API Integration for enviPath Community
- * Handles fetching topics from the Discourse forum API
- */
-
-class DiscourseAPI {
-    constructor() {
-        this.baseUrl = 'https://community.envipath.org';
-        this.categoryId = 10; // Announcements category
-        this.limit = 3; // Number of topics to fetch
-    }
-
-    /**
-     * Fetch topics from Discourse API
-     * @param {number} limit - Number of topics to fetch
-     * @returns {Promise<Array>} Array of topic objects
-     */
-    async fetchTopics(limit = this.limit) {
-        try {
-            const url = `${this.baseUrl}/c/announcements/${this.categoryId}.json`;
-            const response = await fetch(url);
-
-            if (!response.ok) {
-                throw new Error(`HTTP error! status: ${response.status}`);
-            }
-
-            const data = await response.json();
-            return this.processTopics(data.topic_list.topics, limit);
-        } catch (error) {
-            console.error('Error fetching Discourse topics:', error);
-            return this.getFallbackTopics();
-        }
-    }
-
-    /**
-     * Process raw Discourse topics into standardized format
-     * @param {Array} topics - Raw topics from Discourse API
-     * @param {number} limit - Number of topics to return
-     * @returns {Array} Processed topics
-     */
-    processTopics(topics, limit) {
-        return topics
-            .slice(0, limit)
-            .map(topic => ({
-                id: topic.id,
-                title: topic.title,
-                excerpt: this.extractExcerpt(topic.excerpt),
-                url: `${this.baseUrl}/t/${topic.slug}/${topic.id}`,
-                replies: topic.reply_count,
-                views: topic.views,
-                created_at: topic.created_at,
-                category: 'Announcements',
-                category_id: this.categoryId,
-                author: topic.last_poster_username,
-                author_avatar: this.getAvatarUrl(topic.last_poster_username)
-            }))
-            .sort((a, b) => new Date(b.created_at) - new Date(a.created_at)); // Latest first
-    }
-
-    /**
-     * Extract excerpt from topic content
-     * @param {string} excerpt - Raw excerpt from Discourse
-     * @returns {string} Cleaned excerpt
-     */
-    extractExcerpt(excerpt) {
-        if (!excerpt) return 'Click to read more';
-
-        // Remove HTML tags and clean up; collapse whitespace; do not add manual ellipsis
-        return excerpt
-            .replace(/<[^>]*>/g, '') // Remove HTML tags
-            .replace(/&nbsp;/g, ' ') // Replace &nbsp; with spaces
-            .replace(/&amp;/g, '&') // Replace &amp; with &
-            .replace(/&lt;/g, '<') // Replace &lt; with <
-            .replace(/&gt;/g, '>') // Replace &gt; with >
-            .replace(/\s+/g, ' ') // Collapse all whitespace/newlines
-            .trim()
-    }
-
-    /**
-     * Get avatar URL for user
-     * @param {string} username - Username
-     * @returns {string} Avatar URL
-     */
-    getAvatarUrl(username) {
-        if (!username) return `${this.baseUrl}/letter_avatar_proxy/v4/letter/u/1.png`;
-        return `${this.baseUrl}/user_avatar/${this.baseUrl.replace('https://', '')}/${username}/40/1_1.png`;
-    }
-
-    /**
-     * Get fallback topics when API fails
-     * @returns {Array} Fallback topics
-     */
-    getFallbackTopics() {
-        return [
-            {
-                id: 110,
-                title: "enviPath Beta Update: Major Improvements to Prediction, Analysis & Collaboration!",
-                excerpt: "We're excited to announce major updates to the enviPath beta platform! This release includes significant improvements to our prediction algorithms, enhanced analysis tools, and new collaboration features that will make environmental biotransformation research more accessible and efficient.",
-                url: "https://community.envipath.org/t/envipath-beta-update-major-improvements-to-prediction-analysis-collaboration/110",
-                replies: 0,
-                views: 16,
-                created_at: "2025-09-23T00:00:00Z",
-                category: "Announcements",
-                category_id: 10,
-                author: "wicker",
-                author_avatar: "https://community.envipath.org/user_avatar/community.envipath.org/wicker/40/1_1.png"
-            }
-        ];
-    }
-
-    /**
-     * Format date for display
-     * @param {string} dateString - ISO date string
-     * @returns {string} Formatted date
-     */
-    formatDate(dateString) {
-        const date = new Date(dateString);
-        return date.toLocaleDateString();
-    }
-
-
-    /**
-     * Load topics and call render function
-     * @param {string} containerId - ID of container element
-     * @param {Function} renderCallback - Function to render topics
-     */
-    async loadTopics(containerId = 'community-news-container', renderCallback = null) {
-        const container = document.getElementById(containerId);
-        if (!container) {
-            console.error(`Container with ID '${containerId}' not found`);
-            return;
-        }
-
-        // Hide loading spinner
-        const loading = document.getElementById('loading');
-        if (loading) {
-            loading.style.display = 'none';
-        }
-
-        try {
-            const topics = await this.fetchTopics();
-
-            if (renderCallback && typeof renderCallback === 'function') {
-                renderCallback(topics);
-            } else {
-                // Default rendering - just log topics
-                console.log('Topics loaded:', topics);
-            }
-        } catch (error) {
-            console.error('Error loading topics:', error);
-            container.innerHTML = '<p class="text-neutral">No updates found. Head over to the <a href="https://community.envipath.org" target="_blank" class="link link-primary">community</a> to see the latest discussions.</p>';
-        }
-    }
-}
-
-// Export for use in other scripts
-window.DiscourseAPI = DiscourseAPI;
-
-// Auto-initialize if container exists
-document.addEventListener('DOMContentLoaded', function() {
-    if (document.getElementById('community-news-container')) {
-        const discourseAPI = new DiscourseAPI();
-        discourseAPI.loadTopics('community-news-container', function(topics) {
-            // This will be handled by the template's render function
-            if (window.renderDiscourseTopics) {
-                window.renderDiscourseTopics(topics);
-            }
-        });
-    }
-});

templates/collections/joblog.html

@@ -1,5 +1,6 @@
 {% extends "framework.html" %}
 {% load static %}
+{% load envipytags %}
 {% block content %}
 
     <div class="panel-group" id="reviewListAccordion">

templates/collections/objects_list.html

@@ -192,7 +192,7 @@
             <div class="panel-body list-group-item" id="ReviewedContent">
                 {% if object_type == 'package' %}
                 {% for obj in reviewed_objects %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}
                     <span class="glyphicon glyphicon-star" aria-hidden="true"
                           style="float:right" data-toggle="tooltip"
                           data-placement="top" title="" data-original-title="Reviewed">
@@ -201,7 +201,7 @@
                 {% endfor %}
                 {% else %}
                 {% for obj in reviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}{# <i>({{ obj.package.name }})</i> #}
                     <span class="glyphicon glyphicon-star" aria-hidden="true"
                           style="float:right" data-toggle="tooltip"
                           data-placement="top" title="" data-original-title="Reviewed">
@@ -221,11 +221,11 @@
             <div class="panel-body list-group-item" id="UnreviewedContent">
                 {% if object_type == 'package' %}
                 {% for obj in unreviewed_objects %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
                 {% endfor %}
                 {% else %}
                 {% for obj in unreviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
                 {% endfor %}
                 {% endif %}
             </div>
@@ -236,9 +236,9 @@
         <ul class='list-group'>
             {% for obj in objects %}
             {% if object_type == 'user' %}
-            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username|safe }}</a>
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
             {% else %}
-            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
             {% endif %}
             {% endfor %}
         </ul>

templates/framework.html

@@ -1,17 +1,15 @@
 <!DOCTYPE html>
-<html data-theme="envipath">
+<html>
 {% load static %}
 <head>
     <title>{{ title }}</title>
-    <meta name="csrf-token" content="{{ csrf_token }}">
-    {# Favicon #}
-    <link rel="shortcut icon" type="image/png" href="{% static 'images/favicon.ico' %}"/>
-
-    {# Tailwind CSS disabled for legacy Bootstrap framework #}
-    {# Pages using this framework will be migrated to framework_modern.html incrementally #}
-    {# <link href="{% static 'css/output.css' %}" rel="stylesheet" type="text/css"/> #}
-
-    {# Legacy Bootstrap 3.3.7 - scoped to .legacy-bootstrap #}
+    <style>
+        html, body {
+            height: 100%; /* ensure body fills viewport */
+            overflow-x: hidden; /* prevent horizontal scroll */
+        }
+    </style>
+    {# TODO use bundles from bootstrap 3.3.7 #}
     <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
     <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
     <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
@@ -22,16 +20,7 @@
     <script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/js/bootstrap-select.min.js"></script>
     <script src="https://community.envipath.org/javascripts/embed-topics.js"></script>
     <!-- CDN END -->
-
-    {# Bootstrap compatibility styles #}
-    <style>
-        /* Ensure proper viewport behavior */
-        html, body {
-            height: 100%; /* ensure body fills viewport */
-            overflow-x: hidden; /* prevent horizontal scroll */
-        }
-    </style>
-
+    <meta name="csrf-token" content="{{ csrf_token }}">
     <script>
         const csrftoken = document.querySelector('[name=csrf-token]').content;
 
@@ -44,7 +33,8 @@
             }
         });
     </script>
-
+    {# Favicon #}
+    <link rel="shortcut icon" type="image/png" href="{% static 'images/favicon.ico' %}"/>
     <!--    {# C3 CSS #}-->
     <!--    <link id="css-c3" href="{% static 'css/c3.css' %}" rel="stylesheet" type="text/css"/>-->
     <!--    {# EP CSS #}-->
@@ -66,7 +56,7 @@
             (function () {
                 var u = "//matomo.envipath.com/";
                 _paq.push(['setTrackerUrl', u + 'matomo.php']);
-                _paq.push(['setSiteId', '{{ meta.site_id }}']);
+                _paq.push(['setSiteId', '10']);
                 var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
                 g.async = true;
                 g.src = u + 'matomo.js';
@@ -78,8 +68,6 @@
 
 </head>
 <body>
-<!-- Legacy Bootstrap navbar - isolated from Tailwind -->
-<div class="legacy-bootstrap">
 <nav class="navbar navbar-default navbar-inverse" style="border-radius:0px;" role="navigation">
     <div class="container-fluid">
         <!-- Brand and toggle get grouped for better mobile display -->
@@ -158,7 +146,8 @@
                 </li>
                 {% if meta.user.username == 'anonymous' %}
                     <li>
-                        <a href="{% url 'login' %}" id="loginButton" style="margin-right:10px">Login</a>
+                        <a href="#signup" id="loginButton" data-toggle="modal" data-target="#signupmodal"
+                           style="margin-right:10px">Login</a>
                     </li>
                 {% else %}
                     <li class="dropdown">
@@ -188,9 +177,6 @@
         </div>
     </div>
 </nav>
-</div>
-<!-- End legacy Bootstrap navbar -->
-
 <div id="docContent" class="content container">
     {% if breadcrumbs %}
         <div id="bread">
@@ -235,8 +221,7 @@
     {% endif %}
 </div>
 
-<!-- FOOTER - Legacy Bootstrap -->
-<div class="legacy-bootstrap">
+<!-- FOOTER -->
 <div class="container text-center">
     <hr/>
     <div class="row">
@@ -273,9 +258,6 @@
         </ul>
     </div>
 </div>
-</div>
-<!-- End legacy Bootstrap footer -->
-
 <script>
     $(function () {
         // Hide actionsbutton if theres no action defined

templates/framework_modern.html

@@ -1,176 +0,0 @@
-<!DOCTYPE html>
-<html data-theme="envipath" lang="en">
-{% load static %}
-<head>
-    <title>{{ title }}</title>
-    <meta charset="UTF-8">
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <meta name="csrf-token" content="{{ csrf_token }}">
-
-    {# Favicon #}
-    <link rel="shortcut icon" type="image/png" href="{% static 'images/favicon.ico' %}"/>
-
-    {# Tailwind CSS + DaisyUI Output #}
-    <link href="{% static 'css/output.css' %}" rel="stylesheet" type="text/css"/>
-
-    {# jQuery - Keep for compatibility with existing JS #}
-    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
-
-    {# Font Awesome #}
-    <link href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
-
-    {# Discourse embed for community #}
-    <script src="https://community.envipath.org/javascripts/embed-topics.js"></script>
-
-    <script>
-        const csrftoken = document.querySelector('[name=csrf-token]').content;
-
-        // Setup CSRF header for all jQuery AJAX requests
-        $.ajaxSetup({
-            beforeSend: function(xhr, settings) {
-                if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
-                    xhr.setRequestHeader("X-CSRFToken", csrftoken);
-                }
-            }
-        });
-    </script>
-
-    {# General EP JS #}
-    <script src="{% static 'js/pps.js' %}"></script>
-    {# Modal Steps for Stepwise Modal Wizards #}
-    <script src="{% static 'js/jquery-bootstrap-modal-steps.js' %}"></script>
-
-    {% if not debug %}
-        <!-- Matomo -->
-        <script>
-            var _paq = window._paq = window._paq || [];
-            _paq.push(['trackPageView']);
-            _paq.push(['enableLinkTracking']);
-            (function () {
-                var u = "//matomo.envipath.com/";
-                _paq.push(['setTrackerUrl', u + 'matomo.php']);
-                _paq.push(['setSiteId', '{{ meta.site_id }}']);
-                var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
-                g.async = true;
-                g.src = u + 'matomo.js';
-                s.parentNode.insertBefore(g, s);
-            })();
-        </script>
-        <!-- End Matomo Code -->
-    {% endif %}
-</head>
-<body class="min-h-screen bg-base-300">
-    {% include "includes/navbar.html" %}
-
-    {# Main Content Area #}
-    <main class="w-full">
-        {% block main_content %}
-            {# Breadcrumbs - outside main content, optional #}
-            {% if breadcrumbs %}
-                <div id="bread" class="max-w-7xl mx-auto px-4 py-4">
-                    <div class="text-sm breadcrumbs">
-                        <ul>
-                            {% for elem in breadcrumbs %}
-                                {% for name, url in elem.items %}
-                                    {% if forloop.parentloop.last %}
-                                        <li>{{ name }}</li>
-                                    {% else %}
-                                        <li><a href="{{ url }}">{{ name }}</a></li>
-                                    {% endif %}
-                                {% endfor %}
-                            {% endfor %}
-                        </ul>
-                    </div>
-                </div>
-            {% endif %}
-
-            {# Main content container - paper effect on medium+ screens #}
-            <div id="docContent" class="w-full xl:w-xl md:mx-auto md:my-8 bg-base-100 md:shadow-2xl md:rounded-lg border-2">
-                {# Messages - inside paper #}
-                {% if message %}
-                    <div id="message" class="alert alert-info m-4">
-                        {{ message }}
-                    </div>
-                {% endif %}
-
-                {# Page content - no enforced styles #}
-                {% block content %}
-                {% endblock content %}
-
-                {# License - inside paper if present #}
-                {% if meta.url_contains_package and meta.current_package.license %}
-                    <div class="collapse collapse-arrow bg-base-200 m-8">
-                        <input type="checkbox" checked />
-                        <div class="collapse-title text-xl font-medium">
-                            License
-                        </div>
-                        <div class="collapse-content">
-                            <a target="_blank" href="{{ meta.current_package.license.link }}">
-                                <img src="{{ meta.current_package.license.image_link }}" alt="License">
-                            </a>
-                        </div>
-                    </div>
-                {% endif %}
-            </div>
-        {% endblock main_content %}
-    </main>
-
-    {% include "includes/footer.html" %}
-
-    {# Floating Help Tab #}
-    {% if not public_mode %}
-    <div class="fixed right-0 top-1/2 -translate-y-1/2 z-50">
-        <a href="https://community.envipath.org/" target="_blank"
-           class="flex items-center justify-center btn btn-secondary hover:btn-secondary-focus text-secondary-content text-sm shadow-lg transition-all duration-300 hover:scale-105 hover:-translate-x-1"
-           title="Get Help from the Community">
-            <svg xmlns="http://www.w3.org/2000/svg" width="24" height="24" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round" class="lucide lucide-message-circle-question-mark-icon lucide-message-circle-question-mark"><path d="M2.992 16.342a2 2 0 0 1 .094 1.167l-1.065 3.29a1 1 0 0 0 1.236 1.168l3.413-.998a2 2 0 0 1 1.099.092 10 10 0 1 0-4.777-4.719"/><path d="M9.09 9a3 3 0 0 1 5.83 1c0 2-3 3-3 3"/>
-                <path d="M12 17h.01"/>
-            </svg>
-        </a>
-    </div>
-    {% endif %}
-
-    {# Modals - TODO: Convert these to DaisyUI modals #}
-    {% block modals %}
-        {# Note: These modals still use Bootstrap markup and will need conversion #}
-        {% include "modals/cite_modal.html" %}
-        {% include "modals/signup_modal.html" %}
-        {% include "modals/predict_modal.html" %}
-        {% include "modals/batch_predict_modal.html" %}
-    {% endblock %}
-
-    <script>
-        $(function () {
-            // Hide actionsbutton if there's no action defined
-            if ($('#actionsButton ul').children().length > 0) {
-                $('#actionsButton').show();
-            }
-
-        });
-
-        // Global keyboard shortcut for search (Cmd+K on Mac, Ctrl+K on Windows/Linux)
-        document.addEventListener('keydown', function(event) {
-            // Check if user is typing in an input field
-            const activeElement = document.activeElement;
-            const isInputField = activeElement && (
-                activeElement.tagName === 'INPUT' ||
-                activeElement.tagName === 'TEXTAREA' ||
-                activeElement.contentEditable === 'true'
-            );
-
-            if (isInputField) {
-                return; // Don't trigger shortcut when typing in input fields
-            }
-
-            // Check for Cmd+K (Mac) or Ctrl+K (Windows/Linux)
-            const isMac = /Mac/.test(navigator.platform);
-            const isCorrectModifier = isMac ? event.metaKey : event.ctrlKey;
-
-            if (isCorrectModifier && event.key === 'k') {
-                event.preventDefault();
-                window.location.href = '/search';
-            }
-        });
-    </script>
-</body>
-</html>

templates/includes/footer.html

@@ -1,69 +0,0 @@
-{% load static %}
-<div class="lg:max-w-5xl mt-10 mx-auto bg-base-300 text-base-content">
-
-    <footer class="footer sm:footer-horizontal p-10">
-        {% if not public_mode %}
-        <nav>
-            <h6 class="footer-title">Services</h6>
-            <a class="link link-hover" href="/">Predict</a>
-            <a class="link link-hover" href="/search">Search</a>
-            <a class="link link-hover" href="/package">Browse</a>
-            {% if user.is_authenticated %}
-            <a class="link link-hover" href="/model">Your Collections</a>
-            {% endif %}
-            <a href="https://wiki.envipath.org/" target="_blank" class="link link-hover">Documentation</a>
-    </nav>
-        {% 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>
-    </nav>
-    <nav>
-      <h6 class="footer-title">Legal</h6>
-      <a class="link link-hover" href="/terms">Terms of use</a>
-      <a class="link link-hover" href="/privacy">Privacy policy</a>
-      <a class="link link-hover" href="/cookie-policy">Cookie policy</a>
-      <a class="link link-hover" href="/cite">Cite enviPath</a>
-    </nav>
-  </footer>
-  <footer class="footer border-neutral-300 border-t-2 px-10 py-4">
-    <div class="flex flex-row justify-between w-full items-start">
-      <aside class="grid-flow-col items-center">
-          <svg class="fill-neutral-content flex-shrink-0 h-14 m-2" viewbox="0 0 65 65" >
-              <use
-                href="{% static "/images/logo-square.svg" %}#ep-logo-square"
-              >
-              </use>
-            </svg>
-
-          enviPath Ltd.
-          <br />
-          Biodegredation prediction since 2015.
-        </p>
-      </aside>
-      <aside class="text-sm text-base-200 mt-2"><span class="text-xs tracking-tight">Version</span> <span class="text-base font-bold">{{ meta.version }}</span></aside>
-    </div>
-    <nav class="md:place-self-center md:justify-self-end">
-      <div class="grid grid-flow-col gap-4">
-        <a href="https://www.youtube.com/@envipath7231" target="_blank">
-            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
-                <title>YouTube</title>
-                <path d="M23.498 6.186a3.016 3.016 0 0 0-2.122-2.136C19.505 3.545 12 3.545 12 3.545s-7.505 0-9.377.505A3.017 3.017 0 0 0 .502 6.186C0 8.07 0 12 0 12s0 3.93.502 5.814a3.016 3.016 0 0 0 2.122 2.136c1.871.505 9.376.505 9.376.505s7.505 0 9.377-.505a3.015 3.015 0 0 0 2.122-2.136C24 15.93 24 12 24 12s0-3.93-.502-5.814zM9.545 15.568V8.432L15.818 12l-6.273 3.568z"/>
-            </svg>
-        </a>
-        <a href="https://community.envipath.org/" target="_blank">
-            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
-                <title>Discourse</title>
-                <path d="M12.103 0C18.666 0 24 5.485 24 11.997c0 6.51-5.33 11.99-11.9 11.99L0 24V11.79C0 5.28 5.532 0 12.103 0zm.116 4.563c-2.593-.003-4.996 1.352-6.337 3.57-1.33 2.208-1.387 4.957-.148 7.22L4.4 19.61l4.794-1.074c2.745 1.225 5.965.676 8.136-1.39 2.17-2.054 2.86-5.228 1.737-7.997-1.135-2.778-3.84-4.59-6.84-4.585h-.008z"/>
-            </svg>
-        </a>
-        <a href="https://www.linkedin.com/company/envipath/" target="_blank">
-            <img src="{% static "/images/linkedin.png" %}" alt="LinkedIn" class="w-6 h-6">
-        </a>
-      </div>
-    </nav>
-  </footer>
-</div>

templates/includes/navbar.html

@@ -1,71 +0,0 @@
-{% load static %}
-{# Modern DaisyUI Navbar #}
-<div class="navbar bg-neutral-50 text-neutral-950 shadow-lg x-50">
-    <div class="navbar-start">
-        <a href="{{ meta.server_url }}" class="btn btn-ghost normal-case text-xl">
-            <svg class="h-8 fill-base-content" viewBox="0 0 104 26"  role="img">
-                <use href='{% static "/images/logo-name.svg" %}#ep-logo-name' />
-            </svg>
-        </a>
-    </div>
-
-    {% if not public_mode %}
-    <div class="navbar-center hidden lg:flex">
-        <a href="#" role="button" class="btn btn-ghost" id="predictLink">Predict</a>
-        <!-- <li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li> -->
-        <!--<li><a href="{{ meta.server_url }}/browse" id="browseLink">Browse</a></li>-->
-        <div class="dropdown dropdown-center">
-            <div tabindex="0" role="button" class="btn btn-ghost">Browse</div>
-            <ul tabindex="-1" class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm">
-                <li><a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a></li>
-                <li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
-                <li><a href="{{ meta.server_url }}/compound" id="compoundLink">Compound</a></li>
-                <li><a href="{{ meta.server_url }}/reaction" id="reactionLink">Reaction</a></li>
-                <li><a href="{{ meta.server_url }}/model" id="relative-reasoningLink">Model</a></li>
-                <li><a href="{{ meta.server_url }}/scenario" id="scenarioLink">Scenario</a></li>
-            </ul>
-        </div>
-    </div>
-    {% endif %}
-
-    <div class="navbar-end">
-        {% if not public_mode %}
-        <a href="/search" role="button" >
-            <div class="flex items-center badge badge-dash space-x-1 bg-base-200 text-base-content/50 p-2 m-1">
-                <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-search-icon lucide-search"><path d="m21 21-4.34-4.34"/><circle cx="11" cy="11" r="8"/></svg>
-                <span id="search-shortcut">⌘K</span>
-            </div>
-        </a>
-        {% endif %}
-            {% if meta.user.username == 'anonymous' or public_mode %}
-            <a href="{% url 'login' %}" id="loginButton" class="p-2">Login</a>
-        {% else %}
-            <div class="dropdown dropdown-end">
-                <div tabindex="0" role="button" class="btn btn-ghost m-1 btn-circle" id="loggedInButton">
-                    <svg xmlns="http://www.w3.org/2000/svg" width="24" height="24" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round" class="lucide lucide-circle-user-icon lucide-circle-user"><circle cx="12" cy="12" r="10"/><circle cx="12" cy="10" r="3"/><path d="M7 20.662V19a2 2 0 0 1 2-2h6a2 2 0 0 1 2 2v1.662"/></svg>
-                </div>
-                <ul tabindex="-1" class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2 shadow-sm">
-                    <li><a href="{{ meta.user.url }}" id="accountbutton">Settings</a></li>
-                    <li>
-                        <form id="logoutForm" action="{% url 'logout' %}" method="post" style="display: none;">
-                            {% csrf_token %}
-                            <input type="hidden" name="logout" value="true">
-                        </form>
-                        <a href="#" id="logoutButton" onclick="event.preventDefault(); document.getElementById('logoutForm').submit();">Logout</a>
-                    </li>
-                </ul>
-            </div>
-        {% endif %}
-    </div>
-</div>
-
-<script>
-    // OS-aware search shortcut display
-    (function() {
-        const isMac = /Mac/.test(navigator.platform);
-        const shortcutElement = document.getElementById('search-shortcut');
-        if (shortcutElement) {
-            shortcutElement.textContent = isMac ? '⌘K' : 'Ctrl+K';
-        }
-    })();
-</script>

templates/index/index.html

@@ -1,360 +1,186 @@
-{% extends "framework_modern.html" %}
+{% extends "framework.html" %}
 {% load static %}
-{% block main_content %}
-
-    <!-- Hero Section with Logo and Search -->
-<section class="hero h-fit max-w-5xl w-full shadow-none mx-auto relative">
-
-        <div class="hero min-h-[calc(100vh*0.4)] bg-gradient-to-br from-primary-800 to-primary-600"
-            style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
-            >
-            <div class="hero-overlay"></div>
-            <!-- Predict Pathway text over the image -->
-            <div class="absolute bottom-40 left-1/8 -translate-x-8 z-10">
-                <h2 class="text-3xl text-base-100 text-shadow-lg text-left">Predict Your Pathway</h2>
+{% block content %}
+    <!-- TODO rename ids as well as remove pathways if modal is closed!-->
+    <div class="modal fade" tabindex="-1" id="foundMatching" role="dialog" aria-labelledby="foundModal"
+         aria-hidden="true">
+        <div class="modal-dialog">
+            <div class="modal-content">
+                <div class="modal-header">
+                    <button type="button" class="close" data-dismiss="modal">
+                        <span aria-hidden="true">&times;</span>
+                        <span class="sr-only">Close</span>
+                    </button>
+                    <h4 class="modal-title" id="newPackMod">Found Pathway in Database</h4>
+                </div>
+                <div class="modal-body">
+                    <p>We found at least one pathway in the database with the given root
+                        compound. Do you want to open any of the existing pathways or
+                        predict a new one? To open an existing pathway, simply click
+                        on the pathway, to predict a new one, click Predict. The predicted
+                        pathway might differ from the ones in the database due to the
+                        settings used in the prediction.</p>
+                    <div id="foundPathways"></div>
+                </div>
+                <div class="modal-footer">
+                    <a id="modal-predict" class="btn btn-primary" href="#">Predict</a>
+                    <button type="button" id="cancel-predict" class="btn btn-default" data-dismiss="modal">Cancel
+                    </button>
                 </div>
             </div>
-</section>
-
-<div class="shadow-md max-w-5xl mx-auto bg-base-200">
-
-    <!-- Predict Pathway Section -->
-    <div class="flex-col lg:flex-row-reverse w-full mx-auto -mt-32 relative z-20 mb-10 ">
-        <div class="card bg-base-100 shrink-0 shadow-xl w-3/4 mx-auto transition-all duration-300 ease-in-out">
-            <div class="card-body">
-                <!-- Input Mode Toggle - Fixed position outside fieldset -->
-                <div class="flex flex-row justify-start items-center h-fit ml-8 my-4">
-                    <div class="flex items-center gap-2">
-                        <!-- <span class="text-sm text-neutral-500">Input Mode:</span> -->
-                        <label class="toggle text-base-content toggle-md">
-                            <input type="checkbox" />
-                            <svg aria-label="smiles mode" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 20 20" class="size-5">
-                                <g
-                                stroke-linejoin="round"
-                                stroke-linecap="round"
-                                stroke-width="2"
-                                fill="currentColor"
-                                stroke="none"
-                                >
-                                    <path fill-rule="evenodd" d="M8 2.75A.75.75 0 0 1 8.75 2h7.5a.75.75 0 0 1 0 1.5h-3.215l-4.483 13h2.698a.75.75 0 0 1 0 1.5h-7.5a.75.75 0 0 1 0-1.5h3.215l4.483-13H8.75A.75.75 0 0 1 8 2.75Z" clip-rule="evenodd" />
-                                </g>
-                            </svg>
-                            <svg
-                                aria-label="draw mode"
-                                xmlns="http://www.w3.org/2000/svg"
-                                viewBox="0 0 20 20"
-                                fill="currentColor"
-                                stroke="none"
-                                class="size-5"
-                            >
-                                <path d="m2.695 14.762-1.262 3.155a.5.5 0 0 0 .65.65l3.155-1.262a4 4 0 0 0 1.343-.886L17.5 5.501a2.121 2.121 0 0 0-3-3L3.58 13.419a4 4 0 0 0-.885 1.343Z" />
-
-                            </svg>
-                        </label>
         </div>
     </div>
+    <div class="row">
+        <div class="col-xs-8">
+            <div class="jumbotron">
+                <h1>
+                    <img id="image-logo-long" class="img-responsive" alt="enviPath" width="1000ex"
+                         src='{% static "/images/logo-long.svg" %}'/>
+                </h1>
+                <p>enviPath is a database and prediction system for the microbial
+                    biotransformation of organic environmental contaminants. The
+                    database provides the possibility to store and view experimentally
+                    observed biotransformation pathways. The pathway prediction system
+                    provides different relative reasoning models to predict likely biotransformation
+                    pathways and products. You can try it out below.
+                </p>
+                <p>
+                    <a class="btn" style="background-color:#222222;color:#9d9d9d" role="button" target="_blank"
+                       href="https://wiki.envipath.org/index.php/Main_Page">Learn more &gt;&gt;</a>
+                </p>
+            </div>
 
-                <fieldset class="fieldset transition-all duration-300 ease-in-out overflow-hidden">
+        </div>
+        <div id="loading"></div>
+        <div class="col-xs-4">
+            <d-topics-list discourse-url="https://community.envipath.org" per-page="10" category="10"
+                           template="complete"></d-topics-list>
+        </div>
+    </div>
+    <div class="row">
         <form id="index-form" action="{{ meta.current_package.url }}/pathway" method="POST">
             {% csrf_token %}
-                            <div id="text-input-container" class="transition-all duration-300 ease-in-out opacity-100 transform scale-100">
-                                <div class="join w-full mx-auto">
-                                    <input type="text" id="index-form-text-input" placeholder="canonical SMILES string" class="input grow input-md join-item" />
-                                    <button class="btn btn-neutral join-item">Predict!</button>
+            <div class="input-group" id="index-form-bar">
+                <div class="input-group-btn">
+                    <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
+                            aria-expanded="false">
+                        <span class="caret"></span>
+                    </button>
+                    <ul class="dropdown-menu" role="menu">
+                        <li>
+                            <iframe id="index-form-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
+                                    height="510"></iframe>
+                        </li>
+                    </ul>
                 </div>
-                                <div class="label relative w-full mt-1" >
-                                    <div class="flex gap-2">
-                                        <a href="#" class="example-link cursor-pointer hover:text-primary"
-                                           data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
-                                           title="load example">Caffeine</a>
-                                        <a href="#" class="example-link cursor-pointer hover:text-primary"
-                                           data-smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
-                                           title="load example">Ibuprofen</a>
+                <input type="text" class="form-control" id='index-form-text-input'
+                       placeholder="Enter a SMILES to predict a Pathway or type something to search">
+                <div class="input-group-btn">
+                    <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
+                            aria-haspopup="true"
+                            aria-expanded="false" id="action-button">Predict <span class="caret"></span></button>
+                    <ul class="dropdown-menu">
+                        <li><a id="dropdown-predict">Predict</a></li>
+                        <li><a id="dropdown-search">Search</a></li>
+                    </ul>
+                    <button class="btn" style="background-color:#222222;color:#9d9d9d" type="button" id="run-button">Go!
+                    </button>
                 </div>
-                                    <a class="absolute top-0 left-[calc(100%-5.4rem)]" href="#">Advanced</a>
-                                </div>
-                            </div>
-                             <div id="ketcher-container" class="hidden w-full transition-all duration-300 ease-in-out opacity-0 transform scale-95">
-                                 <iframe id="index-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}"
-                                 width="100%" height="400" class="rounded-lg"></iframe>
-                                 <button class="btn btn-lg bg-primary-950 text-primary-50 join-item w-full mt-2">Predict!</button>
-                                 <a class="label mx-auto w-full mt-1" href="#">Advanced</a>
             </div>
             <input type="hidden" id="index-form-smiles" name="smiles" value="smiles">
             <input type="hidden" id="index-form-predict" name="predict" value="predict">
-                        <input type="hidden" id="current-action" value="predict">
         </form>
-                </fieldset>
     </div>
-        </div>
-    </div>
-
-
-    <!-- Community News Section -->
-    <section class="py-16 bg-base-200 z-10 mx-8">
-        <div class="max-w-7xl mx-auto px-4">
-            <h2 class="h2 font-bold text-left mb-8">Community Updates</h2>
-
-            <div id="community-news-container" class="flex gap-4 justify-center">
-                <!-- News cards will be populated here -->
-                <div id="loading" class="flex justify-center w-full">
-                    <span class="loading loading-spinner loading-lg"></span>
-                </div>
-            </div>
-
-            <div class="text-right mt-6">
-                <a href="https://community.envipath.org/c/announcements/10" target="_blank" class="btn btn-ghost btn-sm">
-                    Read More Announcements
-                </a>
-            </div>
-
-            <!-- Discourse API integration -->
-            <script src="{% static 'js/discourse-api.js' %}"></script>
-        </div>
-    </section>
-
-    <!-- Mission Statement Section -->
-    <section class="py-16 from-base-200 to-base-100 bg-gradient-to-b">
-        <div class="mx-auto px-8 md:px-12">
-            <div class="flex flex-row gap-4">
-                <div class="w-1/3">
-                    <img src="{% static "/images/ep-rule-artwork.png" %}" alt="rule-based iterative tree greneration" class="w-full h-full object-contain" />
-                </div>
-                <div class="space-y-4 text-left w-2/3 mr-8">
-                    <h2 class="h2 font-bold mb-8">About enviPath</h2>
-                    <p class="">
-                        enviPath is a database and prediction system for the microbial
-                        biotransformation of organic environmental contaminants. The
-                        database provides the possibility to store and view experimentally
-                        observed biotransformation pathways.
-                    </p>
-                    <p class="">
-                        The pathway prediction system provides different relative reasoning models
-                        to predict likely biotransformation pathways and products. Explore our tools
-                        and contribute to advancing environmental biotransformation research.
-                    </p>
-                    <div class="flex flex-row gap-4 float-right">
-                        <a href="/about" class="btn btn-ghost-neutral">Read More</a>
-                        <a href="/about" class="btn btn-neutral">Publications</a>
-                    </div>
-                </div>
-            </div>
-
-        </div>
-    </section>
-
-    <!-- Partners Section -->
-    <section class="py-14 sm:py-12 bg-base-100">
-        <div class="mx-auto px-6 lg:px-8">
-            <div class="divider"><h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2></div>
-            <div class="mx-auto mt-10 grid max-w-lg grid-cols-4 items-center gap-x-8 gap-y-10 sm:max-w-xl sm:grid-cols-6 sm:gap-x-10 lg:mx-0 lg:max-w-none lg:grid-cols-3">
-                <img src="{% static "/images/uoa-logo-small.png" %}" alt="The University of Auckland" class=" max-h-20 w-full object-contain lg:col-span-1" />
-                <img src="{% static "/images/logo-eawag.svg" %}" alt="Eawag" class=" max-h-12 w-full object-contain lg:col-span-1" />
-                <img src="{% static "/images/uzh-logo.svg" %}" alt="University of Zurich" class="2 max-h-16 w-full object-contain lg:col-span-1" />
-            </div>
-        </div>
-    </section>
-
-
-
-
-</div>
-
+    <p></p>
     <script language="javascript">
         var currentPackage = "{{ meta.current_package.url }}";
 
-        // Discourse API integration is now handled by discourse-api.js
+        function goButtonClicked() {
+            $(this).prop("disabled", true);
 
-        // Function to render Discourse topics into cards
-        function renderDiscourseTopics(topics) {
-            const container = document.getElementById('community-news-container');
-            if (!container) return;
+            var action = $('#action-button').text().trim();
 
-            // Clear container
-            container.innerHTML = '';
+            var textSmiles = $('#index-form-text-input').val().trim();
 
-            // Create cards for each topic
-            topics.forEach(topic => {
-                const card = createDiscourseCard(topic);
-                container.insertAdjacentHTML('beforeend', card);
-            });
+            if (textSmiles === '') {
+                $(this).prop("disabled", false);
+                return;
             }
 
-        // Function to create HTML card for a topic
-        function createDiscourseCard(topic) {
-            const date = new Date(topic.created_at).toLocaleDateString();
+            var ketcherSmiles = getKetcher('index-form-ketcher').getSmiles().trim();
 
-            return `
-                <div class="card bg-white shadow-xs hover:shadow-lg transition-shadow duration-300 h-64 w-75 flex-shrink-0">
-                    <div class="card-body flex flex-col h-full">
-                        <h3 class="card-title leading-tight font-normal tracking-tight h-12 mb-2 line-clamp-2 text-ellipsis wrap-break-word overflow-hidden">
-                            <a href="${topic.url}" target="_blank" class="hover:text-primary">
-                                ${topic.title}
-                            </a>
-                        </h3>
-                        <div class="text-sm line-clamp-4 break-words" >
-                            ${topic.excerpt}
-                        </div>
-
-                        <div class="flex flex-row items-center justify-between">
-                            <div class="flex items-center gap-2">
-                                <div class="avatar tooltip tooltip-right" data-tip="${topic.author}">
-                                    <div class="w-8 rounded-full">
-                                        <img src="${topic.author_avatar}" alt="${topic.author}" />
-                                    </div>
-                                </div>
-                                <span class="text-xs text-gray-500">${date}</span>
-                            </div>
-                            <a href="${topic.url}" target="_blank" class="btn btn-ghost text-neutral-500 rounded-full p-2">
-                                <svg xmlns="http://www.w3.org/2000/svg" class="h-5 w-5" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
-                                    <path d="M12 7v14"/>
-                                    <path d="M3 18a1 1 0 0 1-1-1V4a1 1 0 0 1 1-1h5a4 4 0 0 1 4 4 4 4 0 0 1 4-4h5a1 1 0 0 1 1 1v13a1 1 0 0 1-1 1h-6a3 3 0 0 0-3 3 3 3 0 0 0-3-3z"/>
-                                </svg>
-                            </a>
-                        </div>
-                    </div>
-                </div>
-            `;
+            if (action !== 'Search' && ketcherSmiles !== '' && textSmiles !== ketcherSmiles) {
+                console.log("Ketcher and TextInput differ!");
             }
 
-        // Make render function globally available
-        window.renderDiscourseTopics = renderDiscourseTopics;
-
-        // Toggle functionality with smooth animations
-        function toggleInputMode() {
-            const toggle = $('input[type="checkbox"]');
-            const textContainer = $('#text-input-container');
-            const ketcherContainer = $('#ketcher-container');
-            const formCard = $('.card');
-            const fieldset = $('.fieldset');
-
-            if (toggle.is(':checked')) {
-                // Draw mode - show Ketcher, hide text input
-                textContainer.addClass('opacity-0 transform scale-95');
-                textContainer.removeClass('opacity-100 transform scale-100');
-
-                // Adjust fieldset padding for Ketcher mode - reduce padding and make more compact
-                fieldset.removeClass('p-8');
-                fieldset.addClass('p-4');
-
-                // Wait for fade out to complete, then hide and show new content
-                setTimeout(() => {
-                    textContainer.addClass('hidden');
-                    ketcherContainer.removeClass('hidden opacity-0 transform scale-95');
-                    ketcherContainer.addClass('opacity-100 transform scale-100');
-
-                    // Force re-evaluation of iframe size
-                    const iframe = document.getElementById('index-ketcher');
-                    if (iframe) {
-                        iframe.style.height = '400px';
-                    }
-                }, 300);
+            if (action === 'Search') {
+                var par = {};
+                par['search'] = textSmiles;
+                par['mode'] = 'text';
+                var queryString = $.param(par, true);
+                window.location.href = "/search?" + queryString;
             } else {
-                // SMILES mode - show text input, hide Ketcher
-                ketcherContainer.addClass('opacity-0 transform scale-95');
-                ketcherContainer.removeClass('opacity-100 transform scale-100');
-
-                // Restore fieldset padding for text input mode
-                fieldset.removeClass('p-4');
-                fieldset.addClass('p-8');
-
-                // Wait for fade out to complete, then hide and show new content
-                setTimeout(() => {
-                    ketcherContainer.addClass('hidden');
-                    textContainer.removeClass('hidden opacity-0 transform scale-95');
-                    textContainer.addClass('opacity-100 transform scale-100');
-                }, 300);
-
-                // Transfer SMILES from Ketcher to text input if available
-                if (window.indexKetcher && window.indexKetcher.getSmiles) {
-                    const smiles = window.indexKetcher.getSmiles();
-                    if (smiles && smiles.trim() !== '') {
-                        $('#index-form-text-input').val(smiles);
-                    }
-                }
+                $('#index-form-smiles').val(textSmiles);
+                $('#index-form').submit();
             }
         }
 
-        // Ketcher integration
-        function indexKetcherToTextInput() {
-            $('#index-form-smiles').val(this.ketcher.getSmiles());
+        function actionDropdownClicked() {
+            var suffix = ' <span class="caret"></span>';
+            var dropdownVal = $(this).text();
+
+            if (dropdownVal === 'Search') {
+                $("#index-form").attr("action", '/search');
+                $("#index-form").attr("method", 'GET');
+            } else {
+                $("#index-form").attr("action", currentPackage + "/pathway");
+            }
+
+            $('#action-button').html(dropdownVal + suffix);
+        }
+
+        function ketcherToTextInput() {
+            $('#index-form-text-input').val(this.ketcher.getSmiles());
         }
 
         $(function () {
-            // Initialize fieldset with proper padding
-            $('.fieldset').addClass('p-8');
 
-            // Toggle event listener
-            $('input[type="checkbox"]').on('change', toggleInputMode);
+            $('#index-form').on("keydown", function (e) {
+                if (e.key === "Enter") {
+                    e.preventDefault();
+                    goButtonClicked();
+                }
+            });
 
-            // Ketcher iframe load handler
-            $('#index-ketcher').on('load', function() {
+            // Code that should be executed once DOM is ready goes here
+            $('#dropdown-predict').on('click', actionDropdownClicked);
+            $('#dropdown-search').on('click', actionDropdownClicked);
+
+            $('#run-button').on('click', goButtonClicked);
+
+            // Update Ketcher Width
+            var fullWidth = $('#index-form-bar').width();
+            $('#index-form-ketcher').width(fullWidth);
+
+            // add a listener that gets triggered whenever the structure in ketcher has changed
+            $('#index-form-ketcher').on('load', function () {
                 const checkKetcherReady = () => {
-                    const win = this.contentWindow;
+                    win = this.contentWindow
                     if (win.ketcher && 'editor' in win.ketcher) {
-                        window.indexKetcher = win.ketcher;
                         win.ketcher.editor.event.change.handlers.push({
                             once: false,
                             priority: 0,
-                            f: indexKetcherToTextInput,
+                            f: ketcherToTextInput,
                             ketcher: win.ketcher
                         });
                     } else {
                         setTimeout(checkKetcherReady, 100);
                     }
                 };
+
                 checkKetcherReady();
             });
 
-            // Handle example link clicks
-            $('.example-link').on('click', function(e) {
-                e.preventDefault();
-                const smiles = $(this).data('smiles');
-                const title = $(this).attr('title');
-
-                // Check if we're in Ketcher mode or text input mode
-                if ($('input[type="checkbox"]').is(':checked')) {
-                    // In Ketcher mode - set the SMILES in Ketcher
-                    if (window.indexKetcher && window.indexKetcher.setMolecule) {
-                        window.indexKetcher.setMolecule(smiles);
-                    }
-                } else {
-                    // In text input mode - set the SMILES in the text input
-                    $('#index-form-text-input').val(smiles);
-                }
-
-                // Show a brief feedback
-                const originalText = $(this).text();
-                $(this).text(`loaded!`);
-                setTimeout(() => {
-                    $(this).text(originalText);
-                }, 1000);
-            });
-
-            // Handle form submission on Enter
-            $('#index-form').on("submit", function (e) {
-                e.preventDefault();
-
-                var textSmiles = '';
-
-                // Check if we're in Ketcher mode and extract SMILES
-                if ($('input[type="checkbox"]').is(':checked') && window.indexKetcher) {
-                    textSmiles = window.indexKetcher.getSmiles().trim();
-                } else {
-                    textSmiles = $('#index-form-text-input').val().trim();
-                }
-
-                if (textSmiles === '') {
-                    return;
-                }
-
-                $('#index-form-smiles').val(textSmiles);
-                $("#index-form").attr("action", currentPackage + "/pathway");
-                $("#index-form").attr("method", 'POST');
-                this.submit();
-            });
-
-            // Discourse topics are now loaded automatically by discourse-api.js
         });
     </script>
-{% endblock main_content %}
+{% endblock content %}

templates/migration.html

@@ -26,12 +26,12 @@
             {% endif %}
             <h4 class="panel-title">
                 <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-                   href="#{{ obj.id }}">{{ obj.name|safe }}</a>
+                   href="#{{ obj.id }}">{{ obj.name }}</a>
             </h4>
         </div>
         <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
             <div class="panel-body list-group-item">
-                <a class="list-group-item" href="{{ obj.detail_url }}">{{ obj.name|safe }} Migration Detail Page</a>
+                <a class="list-group-item" href="{{ obj.detail_url }}">{{ obj.name }} Migration Detail Page</a>
             </div>
         </div>
         {% endfor %}

templates/migration_detail.html

@@ -27,7 +27,7 @@
                     {% endif %}
                     <h4 class="panel-title">
                         <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-                           href="#{{ obj.id }}">{{ obj.name|safe }}</a>
+                           href="#{{ obj.id }}">{{ obj.name }}</a>
                     </h4>
                 </div>
                 <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">

templates/modals/collections/new_model_modal.html

@@ -1,4 +1,3 @@
-
 <div class="modal fade" tabindex="-1" id="new_model_modal" role="dialog" aria-labelledby="new_model_modal"
      aria-hidden="true">
     <div class="modal-dialog modal-lg">
@@ -48,14 +47,14 @@
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if obj.reviewed %}
-                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
                                 {% endif %}
                             {% endfor %}
 
                             <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if not obj.reviewed %}
-                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
                                 {% endif %}
                             {% endfor %}
                         </select>
@@ -69,14 +68,14 @@
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if obj.reviewed %}
-                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
                                 {% endif %}
                             {% endfor %}
 
                             <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if not obj.reviewed %}
-                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
                                 {% endif %}
                             {% endfor %}
                         </select>

templates/modals/collections/new_pathway_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <div class="modal fade" tabindex="-1" id="new_pathway_modal" role="dialog" aria-labelledby="new_pathway_modal"
      aria-hidden="true" style="overflow-y: auto;">
@@ -112,7 +111,7 @@
 
                     <select id="settingSelect" name="settingSelect" class="form-control">
                         {% for setting in available_settings %}
-                        <option value="{{ setting.id }}">{{ setting.name|safe }}</option>
+                        <option value="{{ setting.id }}">{{ setting.name }}</option>
                         {% endfor %}
                     </select>
                     <p></p>

templates/modals/collections/new_prediction_setting_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 
 <div id="new_prediction_setting_modal" class="modal" tabindex="-1">
@@ -41,14 +40,14 @@
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                             {% if obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                            <option value="{{ obj.url }}">{{ obj.name }}</option>
                             {% endif %}
                             {% endfor %}
 
                             <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                             {% if not obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                            <option value="{{ obj.url }}">{{ obj.name }}</option>
                             {% endif %}
                             {% endfor %}
                         </select>
@@ -58,7 +57,7 @@
                         <select id="model-based-prediction-setting-model" name="model-based-prediction-setting-model" class="form-control" data-width='100%'>
                         <option disabled selected>Select the model</option>
                         {% for m in models %}
-                        <option value="{{ m.url }}">{{ m.name|safe }}</option>
+                        <option value="{{ m.url }}">{{ m.name }}</option>
                         {% endfor %}
                         </select>
                         <label for="model-based-prediction-setting-threshold">Threshold</label>

templates/modals/objects/add_pathway_edge_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_modal"
      aria-modal="true"
@@ -37,7 +36,7 @@
                             <select id="add_pathway_edge_substrates" name="edge-substrates"
                                     data-actions-box='true' class="form-control" multiple data-width='100%'>
                                 {% for n in pathway.nodes %}
-                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
                                 {% endfor %}
                             </select>
                         </div>
@@ -48,7 +47,7 @@
                             <select id="add_pathway_edge_products" name="edge-products"
                                     data-actions-box='true' class="form-control" multiple data-width='100%'>
                                 {% for n in pathway.nodes %}
-                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
                                 {% endfor %}
                             </select>
                         </div>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Delete Edge -->
 <div id="delete_pathway_edge_modal" class="modal" tabindex="-1">
@@ -20,7 +19,7 @@
                             data-actions-box='true' class="form-control" data-width='100%'>
                         <option value="" disabled selected>Select Reaction to delete</option>
                         {% for e in pathway.edges %}
-                            <option value="{{ e.url }}">{{ e.edge_label.name|safe }}</option>
+                            <option value="{{ e.url }}">{{ e.edge_label.name }}</option>
                         {% endfor %}
                     </select>
                     <input type="hidden" id="hidden" name="hidden" value="delete"/>

templates/modals/objects/delete_pathway_node_modal.html

@@ -1,5 +1,4 @@
 {% load static %}
-
 <!-- Delete Node -->
 <div id="delete_pathway_node_modal" class="modal" tabindex="-1">
     <div class="modal-dialog">
@@ -20,7 +19,7 @@
                             data-actions-box='true' class="form-control" data-width='100%'>
                         <option value="" disabled selected>Select Compound to delete</option>
                         {% for n in pathway.nodes %}
-                            <option value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
+                            <option value="{{ n.url }}">{{ n.default_node_label.name }}</option>
                         {% endfor %}
                     </select>
                     <input type="hidden" id="hidden" name="hidden" value="delete"/>

templates/modals/objects/edit_compound_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit Compound -->
 <div id="edit_compound_modal" class="modal" tabindex="-1">
@@ -16,12 +15,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="compound-name">Name</label>
-                        <input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name|safe}}">
+                        <input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name}}">
                     </p>
                     <p>
                         <label for="compound-description">Description</label>
                         <input id="compound-description" type="text" class="form-control"
-                               value="{{ compound.description|safe }}"
+                               value="{{ compound.description }}"
                                name="compound-description">
                     </p>
                 </form>

templates/modals/objects/edit_compound_structure_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit Compound -->
 <div id="edit_compound_structure_modal" class="modal" tabindex="-1">
@@ -16,12 +15,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="compound-structure-name">Name</label>
-                        <input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name|safe }}">
+                        <input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name }}">
                     </p>
                     <p>
                         <label for="compound-structure-description">Description</label>
                         <input id="compound-structure-description" type="text" class="form-control"
-                               value="{{ compound_structure.description|safe }}" name="compound-structure-description">
+                               value="{{ compound_structure.description }}" name="compound-structure-description">
                     </p>
                 </form>
             </div>

templates/modals/objects/edit_group_member_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit Package Permission -->
 <div id="edit_group_member_modal" class="modal" tabindex="-1">
@@ -40,7 +39,7 @@
                                 {% endfor %}
                                 <option disabled>Groups</option>
                                 {% for g in groups %}
-                                <option value="{{ g.url }}">{{ g.name|safe }}</option>
+                                <option value="{{ g.url }}">{{ g.name }}</option>
                                 {% endfor %}
                             </select>
                             <input type="hidden" name="action" value="add">
@@ -82,7 +81,7 @@
                           accept-charset="UTF-8" action="" data-remote="true" method="post">
                         {% csrf_token %}
                         <div class="col-xs-8">
-                            {{ g.name|safe }}
+                            {{ g.name }}
                             <input type="hidden" name="member" value="{{ g.url }}"/>
                             <input type="hidden" name="action" value="remove">
                         </div>

templates/modals/objects/edit_model_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit Model -->
 <div id="edit_model_modal" class="modal" tabindex="-1">
@@ -17,12 +16,12 @@
                     <p>
                         <label for="model-name">Name</label>
                         <input id="model-name" type="text" class="form-control" name="model-name"
-                               value="{{ model.name|safe }}">
+                               value="{{ model.name }}">
                     </p>
                     <p>
                         <label for="model-description">Description</label>
                         <input id="model-description" type="text" class="form-control" name="model-description"
-                               value="{{ model.description|safe }}">
+                               value="{{ model.description }}">
                     </p>
                 </form>
             </div>

templates/modals/objects/edit_node_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit Node -->
 <div id="edit_node_modal" class="modal" tabindex="-1">
@@ -16,12 +15,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="node-name">Name</label>
-                        <input id="node-name" class="form-control" name="node-name" value="{{ node.name|safe}}">
+                        <input id="node-name" class="form-control" name="node-name" value="{{ node.name}}">
                     </p>
                     <p>
                         <label for="node-description">Description</label>
                         <input id="node-description" type="text" class="form-control"
-                               value="{{ node.description|safe }}"
+                               value="{{ node.description }}"
                                name="node-description">
                     </p>
                 </form>

templates/modals/objects/edit_package_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit Package -->
 <div id="edit_package_modal" class="modal" tabindex="-1">
@@ -16,12 +15,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="package-name">Name</label>
-                        <input id="package-name" class="form-control" name="package-name" value="{{ package.name|safe}}">
+                        <input id="package-name" class="form-control" name="package-name" value="{{ package.name}}">
                     </p>
                     <p>
                         <label for="package-description">Description</label>
                         <input id="package-description" type="text" class="form-control"
-                               value="{{ package.description|safe }}"
+                               value="{{ package.description }}"
                                name="package-description">
                     </p>
                 </form>

templates/modals/objects/edit_package_permissions_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit Package Permission -->
 <div id="edit_package_permissions_modal" class="modal" tabindex="-1">
@@ -47,7 +46,7 @@
                                 {% endfor %}
                                 <option disabled>Groups</option>
                                 {% for g in groups %}
-                                <option value="{{ g.url }}">{{ g.name|safe }}</option>
+                                <option value="{{ g.url }}">{{ g.name }}</option>
                                 {% endfor %}
                             </select>
                         </div>
@@ -101,7 +100,7 @@
                           accept-charset="UTF-8" action="" data-remote="true" method="post">
                         {% csrf_token %}
                         <div class="col-xs-4">
-                            {{ gp.group.name|safe }}
+                            {{ gp.group.name }}
                             <input type="hidden" name="grantee" value="{{ gp.group.url }}"/>
                         </div>
                         <div class="col-xs-2">

templates/modals/objects/edit_pathway_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit Pathway -->
 <div id="edit_pathway_modal" class="modal" tabindex="-1">
@@ -16,12 +15,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="pathway-name">Name</label>
-                        <input id="pathway-name" class="form-control" name="pathway-name" value="{{ pathway.name|safe }}">
+                        <input id="pathway-name" class="form-control" name="pathway-name" value="{{ pathway.name }}">
                     </p>
                     <p>
                         <label for="pathway-description">Description</label>
                         <textarea id="pathway-description" type="text" class="form-control" name="pathway-description"
-                                  rows="10">{{ pathway.description|safe }}</textarea>
+                                  rows="10">{{ pathway.description }}</textarea>
                     </p>
                 </form>
             </div>

templates/modals/objects/edit_prediction_setting_modal.html

@@ -32,7 +32,7 @@
                                                 <td colspan="2">
                                                     <select id="model" name="model" class="form-control" data-width='100%'>
                                                     {% for m in models %}
-                                                    <option value="{{ m.id }}" {% if user.prediction_settings.model.url == m.url %}selected{% endif %}>{{ m.name|safe }}</option>
+                                                    <option value="{{ m.id }}" {% if user.prediction_settings.model.url == m.url %}selected{% endif %}>{{ m.name }}</option>
                                                     {% endfor %}
                                                     </select>
                                                 </td>

templates/modals/objects/edit_reaction_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit Reaction -->
 <div id="edit_reaction_modal" class="modal" tabindex="-1">
@@ -15,12 +14,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="reaction-name">Name</label>
-                        <input id="reaction-name" class="form-control" name="reaction-name" value="{{ reaction.name|safe }}">
+                        <input id="reaction-name" class="form-control" name="reaction-name" value="{{ reaction.name }}">
                     </p>
                     <p>
                         <label for="reaction-description">Description</label>
                         <input id="reaction-description" type="text" class="form-control"
-                               value="{{ reaction.description|safe }}" name="reaction-description">
+                               value="{{ reaction.description }}" name="reaction-description">
                     </p>
                 </form>
             </div>

templates/modals/objects/edit_rule_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit Rule -->
 <div id="edit_rule_modal" class="modal" tabindex="-1">
@@ -15,12 +14,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="rule-name">Name</label>
-                        <input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name|safe }}">
+                        <input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name }}">
                     </p>
                     <p>
                         <label for="rule-description">Description</label>
                         <input id="rule-description" type="text" class="form-control"
-                               value="{{ rule.description|safe }}" name="rule-description">
+                               value="{{ rule.description }}" name="rule-description">
                     </p>
                 </form>
             </div>

templates/modals/objects/edit_user_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Edit User -->
 <div id="edit_user_modal" class="modal" tabindex="-1">
@@ -19,7 +18,7 @@
                         <select id="default-package" name="default-package" class="form-control" data-width='100%'>
                             <option disabled>Select a Package</option>
                             {% for p in meta.writeable_packages %}
-                            <option value="{{ p.url }}" {% if p.id == meta.user.default_package.id %}selected{% endif %}>{{ p.name|safe }}</option>
+                            <option value="{{ p.url }}" {% if p.id == meta.user.default_package.id %}selected{% endif %}>{{ p.name }}</option>
                             {% endfor %}
                         </select>
                     </p>
@@ -28,7 +27,7 @@
                         <select id="default-group" name="default-group" class="form-control" data-width='100%'>
                             <option disabled>Select a Group</option>
                             {% for g in meta.available_groups %}
-                            <option value="{{ g.url }}" {% if g.id == meta.user.default_group.id %}selected{% endif %}>{{ g.name|safe }}</option>
+                            <option value="{{ g.url }}" {% if g.id == meta.user.default_group.id %}selected{% endif %}>{{ g.name }}</option>
                             {% endfor %}
                         </select>
                     </p>
@@ -37,7 +36,7 @@
                         <select id="default-prediction-setting" name="default-prediction-setting" class="form-control" data-width='100%'>
                             <option disabled>Select a Setting</option>
                             {% for s in meta.available_settings %}
-                            <option value="{{ s.url }}" {% if s.id == meta.user.default_setting.id %}selected{% endif %}>{{ s.name|safe }}</option>
+                            <option value="{{ s.url }}" {% if s.id == meta.user.default_setting.id %}selected{% endif %}>{{ s.name }}</option>
                             {% endfor %}
                         </select>
                     </p>

templates/modals/objects/evaluate_model_modal.html

@@ -1,4 +1,3 @@
-
 <div class="modal fade" tabindex="-1" id="evaluate_model_modal" role="dialog" aria-labelledby="evaluate_model_modal"
      aria-hidden="true">
     <div class="modal-dialog modal-lg">
@@ -25,14 +24,14 @@
                         <option disabled>Reviewed Packages</option>
                         {% for obj in meta.readable_packages %}
                             {% if obj.reviewed %}
-                                <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                                <option value="{{ obj.url }}">{{ obj.name }}</option>
                             {% endif %}
                         {% endfor %}
 
                         <option disabled>Unreviewed Packages</option>
                         {% for obj in meta.readable_packages %}
                             {% if not obj.reviewed %}
-                                <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                                <option value="{{ obj.url }}">{{ obj.name }}</option>
                             {% endif %}
                         {% endfor %}
                     </select>

templates/modals/objects/generic_copy_object_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Copy Object -->
 <div id="generic_copy_object_modal" class="modal" tabindex="-1">
@@ -19,7 +18,7 @@
                             data-width='100%'>
                         <option disabled selected>Select Target Package</option>
                         {% for p in meta.writeable_packages %}
-                            <option value="{{ p.url }}">{{ p.name|safe }}</option>`
+                            <option value="{{ p.url }}">{{ p.name }}</option>`
                         {% endfor %}
                     </select>
                     <input type="hidden" name="hidden" value="copy">

templates/modals/objects/generic_set_aliases_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 
 <style>
@@ -56,7 +55,7 @@
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close">
                     <span aria-hidden="true">×</span>
                 </button>
-                <h4 class="modal-title">Set Aliases for {{ current_object.name|safe }}</h4>
+                <h4 class="modal-title">Set Aliases for {{ current_object.name }}</h4>
             </div>
             <div class="modal-body">
                 <form id="set_aliases_modal_form" accept-charset="UTF-8" action="{{ current_object.url }}"

templates/modals/objects/generic_set_external_reference_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <!-- Delete Object -->
 <div id="generic_set_external_reference_modal" class="modal" tabindex="-1">
@@ -24,7 +23,7 @@
                             {% if entity == object_type %}
                                 {% for db in databases %}
                                     <option id="db-select-{{ db.database.pk }}" data-input-placeholder="{{ db.placeholder }}"
-                                            value="{{ db.database.id }}">{{ db.database.name|safe }}</option>`
+                                            value="{{ db.database.id }}">{{ db.database.name }}</option>`
                                 {% endfor %}
                             {% endif %}
                         {% endfor %}

templates/modals/objects/generic_set_scenario_modal.html

@@ -1,4 +1,3 @@
-
 {% load static %}
 <div class="modal fade bs-modal-lg" id="set_scenario_modal" tabindex="-1" aria-labelledby="set_scenario_modal"
      aria-modal="true" role="dialog">
@@ -8,7 +7,7 @@
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close">
                     <span aria-hidden="true">×</span>
                 </button>
-                <h4 class="modal-title">Set Scenarios for {{ current_object.name|safe }}</h4>
+                <h4 class="modal-title">Set Scenarios for {{ current_object.name }}</h4>
             </div>
             <div class="modal-body">
                 <div id="loading_scenario_div" class="text-center"></div>

templates/modals/objects/manage_api_token_modal.html

@@ -1,4 +1,3 @@
-
 <div class="modal fade"
      tabindex="-1"
      id="manage_api_token_modal"
@@ -42,7 +41,7 @@
                         <div class="input-group">
                             <input type="hidden" name="hidden" value="delete">
                             <input type="hidden" name="token-id" value="{{ t.pk }}">
-                            <input type="text" class="form-control" value="{{ t.name|safe }}" disabled>
+                            <input type="text" class="form-control" value="{{ t.name }}" disabled>
                             <span class="input-group-btn">
                                 <button type="submit" class="btn btn-danger">Delete</button>
                             </span>

templates/modals/predict_modal.html

@@ -56,7 +56,7 @@
                         <option disabled>Select a Setting</option>
                         {% for s in meta.available_settings %}
                             <option value="{{ s.url }}"{% if s.id == meta.user.default_setting.id %}selected{% endif %}>
-                                {{ s.name|safe }}{% if s.id == meta.user.default_setting.id %} <i>(User default)</i>{% endif %}
+                                {{ s.name }}{% if s.id == meta.user.default_setting.id %} <i>(User default)</i>{% endif %}
                             </option>
                         {% endfor %}
                     </select>

templates/objects/composite_rule.html

@@ -13,7 +13,7 @@
 <div class="panel-group" id="rule-detail">
     <div class="panel panel-default">
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-            {{ rule.name|safe }}
+            {{ rule.name }}
             <div id="actionsButton"
                  style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -60,7 +60,7 @@
         <div id="rule-reaction-patterns" class="panel-collapse collapse in">
             <div class="panel-body list-group-item">
                 {% for r in rule.srs %}
-                <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
+                <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
                 <div align="center">
                     <p>
                         {{r.as_svg|safe}}
@@ -81,7 +81,7 @@
             <div id="rule-scenario" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     {% for s in rule.scenarios.all %}
-                        <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
+                        <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
                     {% endfor %}
                 </div>
             </div>

templates/objects/compound.html

@@ -15,7 +15,7 @@
     <div class="panel-group" id="compound-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ compound.name|safe }}
+                {{ compound.name }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -64,7 +64,7 @@
             </div>
             <div id="compound-desc" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
-                    {{ compound.description|safe }}
+                    {{ compound.description }}
                 </div>
             </div>
 
@@ -133,7 +133,7 @@
                 <div id="compound-reaction" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for r in compound.related_reactions %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }} <i>({{ r.package.name|safe }})</i></a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
                         {% endfor %}
                     </div>
                 </div>
@@ -150,7 +150,7 @@
                 <div id="compound-pathway" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for r in compound.related_pathways %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }} <i>({{ r.package.name|safe }})</i></a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
                         {% endfor %}
                     </div>
                 </div>
@@ -167,7 +167,7 @@
                 <div id="compound-scenario" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for s in compound.scenarios.all %}
-                            <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
                         {% endfor %}
                     </div>
                 </div>

templates/objects/compound_structure.html

@@ -13,7 +13,7 @@
 <div class="panel-group" id="compound-structure-detail">
     <div class="panel panel-default">
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-            {{ compound_structure.name|safe }}
+            {{ compound_structure.name }}
             <div id="actionsButton"
                  style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -28,7 +28,7 @@
             </div>
         </div>
         <div class="panel-body">
-            <p> {{ compound_structure.description|safe }} </p>
+            <p> {{ compound_structure.description }} </p>
         </div>
 
         <!-- Image -->
@@ -86,7 +86,7 @@
             <div id="compound-structure-scenario" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     {% for s in compound_structure.scenarios.all %}
-                        <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
+                        <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
                     {% endfor %}
                 </div>
             </div>

templates/objects/edge.html

@@ -12,7 +12,7 @@
     <div class="panel-group" id="edge-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ edge.edge_label.name|safe }}
+                {{ edge.edge_label.name }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -36,7 +36,7 @@
             </div>
             <div id="edge-desc" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
-                    {{ edge.description|safe }}
+                    {{ edge.description }}
                 </div>
             </div>
 
@@ -82,12 +82,12 @@
             <div id="edge-description-smiles" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     {% for educt in edge.start_nodes.all %}
-                        <a class="btn btn-default" href="{{ educt.url }}">{{ educt.name|safe }}</a>
+                        <a class="btn btn-default" href="{{ educt.url }}">{{ educt.name }}</a>
                     {% endfor %}
                     <span class="glyphicon glyphicon-arrow-right" style="margin-left:5em;margin-right:5em;"
                           aria-hidden="true"></span>
                     {% for product in edge.end_nodes.all %}
-                        <a class="btn btn-default" href="{{ product.url }}">{{ product.name|safe }}</a>
+                        <a class="btn btn-default" href="{{ product.url }}">{{ product.name }}</a>
                     {% endfor %}
                 </div>
             </div>
@@ -116,7 +116,7 @@
                 <div id="edge-rules" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for r in edge.edge_label.rules.all %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -132,7 +132,7 @@
             <div id="edge-scenario" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     {% for s in edge.scenarios.all %}
-                        <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
+                        <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
                     {% endfor %}
                 </div>
             </div>

templates/objects/group.html

@@ -11,7 +11,7 @@
 <div class="panel-group" id="package-detail">
     <div class="panel panel-default">
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-            {{ group.name|safe }}
+            {{ group.name }}
             <div id="actionsButton"
                  style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -26,7 +26,7 @@
             </div>
         </div>
         <div class="panel-body">
-            <p> {{ group.description|safe }} </p>
+            <p> {{ group.description }} </p>
         </div>
     </div>
 
@@ -39,10 +39,10 @@
         </div>
         <ul class="list-group">
             {% for um in group.user_member.all %}
-            <a class="list-group-item" href="{{ um.url }}">{{ um.username|safe }}</a>
+            <a class="list-group-item" href="{{ um.url }}">{{ um.username }}</a>
             {% endfor %}
             {% for gm in group.group_member.all %}
-            <a class="list-group-item" href="{{ gm.url }}">{{ gm.name|safe }}</a>
+            <a class="list-group-item" href="{{ gm.url }}">{{ gm.name }}</a>
             {% endfor %}
         </ul>
     </div>
@@ -56,7 +56,7 @@
         </div>
         <ul class="list-group">
             {% for p in packages %}
-            <a class="list-group-item" href="{{ p.url }}">{{ p.name|safe }}</a>
+            <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
             {% endfor %}
         </ul>
     </div>

templates/objects/model.html

@@ -13,34 +13,18 @@
     <!-- Include required libs -->
     <script src="https://d3js.org/d3.v5.min.js"></script>
     <script src="https://cdn.jsdelivr.net/npm/c3@0.7.20/c3.min.js"></script>
-  <link
-    href="https://cdn.jsdelivr.net/npm/c3@0.7.20/c3.min.css"
-    rel="stylesheet"
-  />
+    <link href="https://cdn.jsdelivr.net/npm/c3@0.7.20/c3.min.css" rel="stylesheet">
 
     <div class="panel-group" id="model-detail">
         <div class="panel panel-default">
-      <div
-        class="panel-heading"
-        id="headingPanel"
-        style="font-size:2rem;height: 46px"
-      >
-        {{ model.name|safe }}
-        <div
-          id="actionsButton"
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+                {{ model.name }}
+                <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
-          class="dropdown"
-        >
-          <a
-            href="#"
-            class="dropdown-toggle"
-            data-toggle="dropdown"
-            role="button"
-            aria-haspopup="true"
-            aria-expanded="false"
-            ><span class="glyphicon glyphicon-wrench"></span> Actions
-            <span class="caret"></span><span style="padding-right:1em"></span
-          ></a>
+                     class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
+                                         aria-haspopup="true" aria-expanded="false"><span
+                        class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
+                        style="padding-right:1em"></span></a>
                     <ul id="actionsList" class="dropdown-menu">
                         {% block actions %}
                             {% include "actions/objects/model.html" %}
@@ -49,135 +33,81 @@
                 </div>
             </div>
             <div class="panel-body">
-        <p>{{ model.description|safe }}</p>
+                <p> {{ model.description }} </p>
             </div>
-      {% if model|classname == 'MLRelativeReasoning' or model|classname == 'RuleBasedRelativeReasoning' %}
+            {% if model|classname == 'MLRelativeReasoning' or model|classname == 'RuleBasedRelativeReasoning'%}
                 <!-- Rule Packages -->
-        <div
-          class="panel panel-default panel-heading list-group-item"
-          style="background-color:silver"
-        >
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">
-            <a
-              id="rule-package-link"
-              data-toggle="collapse"
-              data-parent="#model-detail"
-              href="#rule-package"
-              >Rule Packages</a
-            >
+                        <a id="rule-package-link" data-toggle="collapse" data-parent="#model-detail"
+                           href="#rule-package">Rule Packages</a>
                     </h4>
                 </div>
                 <div id="rule-package" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for p in model.rule_packages.all %}
-              <a class="list-group-item" href="{{ p.url }}"
-                >{{ p.name|safe }}</a
-              >
+                            <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
                         {% endfor %}
                     </div>
                 </div>
                 <!-- Reaction Packages -->
-        <div
-          class="panel panel-default panel-heading list-group-item"
-          style="background-color:silver"
-        >
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">
-            <a
-              id="reaction-package-link"
-              data-toggle="collapse"
-              data-parent="#model-detail"
-              href="#reaction-package"
-              >Rule Packages</a
-            >
+                        <a id="reaction-package-link" data-toggle="collapse" data-parent="#model-detail"
+                           href="#reaction-package">Rule Packages</a>
                     </h4>
                 </div>
                 <div id="reaction-package" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for p in model.data_packages.all %}
-              <a class="list-group-item" href="{{ p.url }}"
-                >{{ p.name|safe }}</a
-              >
+                            <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
                         {% endfor %}
                     </div>
                 </div>
                 {% if model.eval_packages.all|length > 0 %}
                     <!-- Eval Packages -->
-          <div
-            class="panel panel-default panel-heading list-group-item"
-            style="background-color:silver"
-          >
+                    <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                         <h4 class="panel-title">
-              <a
-                id="eval-package-link"
-                data-toggle="collapse"
-                data-parent="#model-detail"
-                href="#eval-package"
-                >Rule Packages</a
-              >
+                            <a id="eval-package-link" data-toggle="collapse" data-parent="#model-detail"
+                               href="#eval-package">Rule Packages</a>
                         </h4>
                     </div>
                     <div id="eval-package" class="panel-collapse collapse in">
                         <div class="panel-body list-group-item">
                             {% for p in model.eval_packages.all %}
-                <a class="list-group-item" href="{{ p.url }}"
-                  >{{ p.name|safe }}</a
-                >
+                                <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
                             {% endfor %}
                         </div>
                     </div>
                 {% endif %}
                 <!-- Model Status -->
-        <div
-          class="panel panel-default panel-heading list-group-item"
-          style="background-color:silver"
-        >
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">
-            <a
-              id="model-status-link"
-              data-toggle="collapse"
-              data-parent="#model-detail"
-              href="#model-status"
-              >Model Status</a
-            >
+                        <a id="model-status-link" data-toggle="collapse" data-parent="#model-detail"
+                           href="#model-status">Model Status</a>
                     </h4>
                 </div>
                 <div id="model-status" class="panel-collapse collapse in">
-          <div class="panel-body list-group-item">{{ model.status }}</div>
+                    <div class="panel-body list-group-item">
+                        {{ model.status }}
+                    </div>
                 </div>
             {% endif %}
             {% if model.ready_for_prediction %}
                 <!-- Predict Panel -->
-        <div
-          class="panel panel-default panel-heading list-group-item"
-          style="background-color:silver"
-        >
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">
-            <a
-              id="predict-smiles-link"
-              data-toggle="collapse"
-              data-parent="#model-detail"
-              href="#predict-smiles"
-              >Predict</a
-            >
+                        <a id="predict-smiles-link" data-toggle="collapse" data-parent="#model-detail"
+                           href="#predict-smiles">Predict</a>
                     </h4>
                 </div>
                 <div id="predict-smiles" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         <div class="input-group">
-              <input
-                id="smiles-to-predict"
-                type="text"
-                class="form-control"
-                placeholder="CCN(CC)C(=O)C1=CC(=CC=C1)C"
-              />
+                            <input id="smiles-to-predict" type="text" class="form-control"
+                                   placeholder="CCN(CC)C(=O)C1=CC(=CC=C1)C">
                             <span class="input-group-btn">
-                <button
-                  class="btn btn-default"
-                  type="submit"
-                  id="predict-button"
-                >
-                  Predict!
-                </button>
+                        <button class="btn btn-default" type="submit" id="predict-button">Predict!</button>
                     </span>
                         </div>
                         <div id="predictLoading"></div>
@@ -189,37 +119,18 @@
 
             {% if model.ready_for_prediction and model.app_domain %}
                 <!-- App Domain -->
-        <div
-          class="panel panel-default panel-heading list-group-item"
-          style="background-color:silver"
-        >
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">
-            <a
-              id="app-domain-assessment-link"
-              data-toggle="collapse"
-              data-parent="#model-detail"
-              href="#app-domain-assessment"
-              >Applicability Domain Assessment</a
-            >
+                        <a id="app-domain-assessment-link" data-toggle="collapse" data-parent="#model-detail"
+                           href="#app-domain-assessment">Applicability Domain Assessment</a>
                     </h4>
                 </div>
                 <div id="app-domain-assessment" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         <div class="input-group">
-              <input
-                id="smiles-to-assess"
-                type="text"
-                class="form-control"
-                placeholder="CCN(CC)C(=O)C1=CC(=CC=C1)C"
-              />
+                            <input id="smiles-to-assess" type="text" class="form-control" placeholder="CCN(CC)C(=O)C1=CC(=CC=C1)C">
                             <span class="input-group-btn">
-                <button
-                  class="btn btn-default"
-                  type="submit"
-                  id="assess-button"
-                >
-                  Assess!
-                </button>
+                        <button class="btn btn-default" type="submit" id="assess-button">Assess!</button>
                     </span>
                         </div>
                         <div id="appDomainLoading"></div>
@@ -231,34 +142,23 @@
 
             {% if model.model_status == 'FINISHED' %}
                 <!-- Single Gen Curve Panel -->
-        <div
-          class="panel panel-default panel-heading list-group-item"
-          style="background-color:silver"
-        >
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">
-            <a
-              id="sg-curve-link"
-              data-toggle="collapse"
-              data-parent="#model-detail"
-              href="#sg-curve"
-              >Precision Recall Curve</a
-            >
+                        <a id="sg-curve-link" data-toggle="collapse" data-parent="#model-detail"
+                           href="#sg-curve">Precision Recall Curve</a>
                     </h4>
                 </div>
                 <div id="sg-curve" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         <!-- Center container contents -->
-            <div
-              class="container"
-              style="display: flex;justify-content: center;"
-            >
+                        <div class="container" style="display: flex;justify-content: center;">
                             <div id="sg-curve-plotdiv" class="chart">
                                 <div id="sg-chart"></div>
                             </div>
                         </div>
+
                     </div>
                 </div>
-        {# prettier-ignore-start #}
                 <script>
                     $(function () {
                         if (!($('#sg-chart').length > 0)) {
@@ -365,61 +265,44 @@
                         });
                     });
                 </script>
-                {# prettier-ignore-end #}
                 <!-- End Single Gen Curve Panel       -->
             {% endif %}
         </div>
     </div>
 
     <script>
-    function handlePredictionResponse(data) {
-      res = "<table class='table table-striped'>";
-      res += "<thead>";
-      res += "<th scope='col'>#</th>";
 
-      columns = ["products", "image", "probability", "btrule"];
+        function handlePredictionResponse(data) {
+            res = "<table class='table table-striped'>"
+            res += "<thead>"
+            res += "<th scope='col'>#</th>"
+
+            columns = ['products', 'image', 'probability', 'btrule']
 
             for (col in columns) {
-        res += "<th scope='col'>" + columns[col] + "</th>";
+                res += "<th scope='col'>" + columns[col] + "</th>"
             }
 
-      res += "</thead>";
-      res += "<tbody>";
+            res += "</thead>"
+            res += "<tbody>"
             var cnt = 1;
             for (transformation in data) {
-        res += "<tr>";
-        res += "<th scope='row'>" + cnt + "</th>";
-        res +=
-          "<th scope='row'>" +
-          data[transformation]["products"][0].join(", ") +
-          "</th>";
-        res +=
-          "<th scope='row'>" +
-          "<img width='400' src='{% url 'depict' %}?smiles=" +
-          encodeURIComponent(data[transformation]["products"][0].join(".")) +
-          "'></th>";
-        res +=
-          "<th scope='row'>" +
-          data[transformation]["probability"].toFixed(3) +
-          "</th>";
-        if (data[transformation]["btrule"] != null) {
-          res +=
-            "<th scope='row'>" +
-            "<a href='" +
-            data[transformation]["btrule"]["url"] +
-            "'>" +
-            data[transformation]["btrule"]["name"] +
-            "</a>" +
-            "</th>";
+                res += "<tr>"
+                res += "<th scope='row'>" + cnt + "</th>"
+                res += "<th scope='row'>" + data[transformation]['products'][0].join(', ') + "</th>"
+                res += "<th scope='row'>" + "<img width='400' src='{% url 'depict' %}?smiles=" + encodeURIComponent(data[transformation]['products'][0].join('.')) + "'></th>"
+                res += "<th scope='row'>" + data[transformation]['probability'].toFixed(3) + "</th>"
+                if (data[transformation]['btrule'] != null) {
+                    res += "<th scope='row'>" + "<a href='" + data[transformation]['btrule']['url'] + "'>" + data[transformation]['btrule']['name'] + "</a>" + "</th>"
                 } else {
-          res += "<th scope='row'>N/A</th>";
+                    res += "<th scope='row'>N/A</th>"
                 }
-        res += "</tr>";
+                res += "</tr>"
                 cnt += 1;
             }
 
-      res += "</tbody>";
-      res += "</table>";
+            res += "</tbody>"
+            res += "</table>"
             $("#predictResultTable").append(res);
         }
 
@@ -428,40 +311,37 @@
             $("#" + divid).empty();
         }
 
-    if ($("#predict-button").length > 0) {
+        if ($('#predict-button').length > 0) {
             $("#predict-button").on("click", function (e) {
                 e.preventDefault();
 
                 clear("predictResultTable");
 
                 data = {
-          smiles: $("#smiles-to-predict").val(),
-          classify: "ILikeCats!",
-        };
+                    "smiles": $("#smiles-to-predict").val(),
+                    "classify": "ILikeCats!"
+                }
 
                 if (data["smiles"].trim() === "") {
                     $("#predictResultTable").addClass("alert alert-danger");
-          $("#predictResultTable").append(
-            "Please enter a SMILES string to predict!",
-          );
+                    $("#predictResultTable").append("Please enter a SMILES string to predict!");
                     return;
                 }
 
                 makeLoadingGif("#predictLoading", "{% static '/images/wait.gif' %}");
                 $.ajax({
-          type: "get",
+                    type: 'get',
                     data: data,
-          url: "",
+                    url: '',
                     success: function (data, textStatus) {
                         try {
                             $("#predictLoading").empty();
                             handlePredictionResponse(data);
                         } catch (error) {
+
                             $("#predictLoading").empty();
                             $("#predictResultTable").addClass("alert alert-danger");
-              $("#predictResultTable").append(
-                "Error while processing response :/",
-              );
+                            $("#predictResultTable").append("Error while processing response :/");
                         }
                     },
                     error: function (jqXHR, textStatus, errorThrown, x) {
@@ -473,30 +353,30 @@
             });
         }
 
-    if ($("#assess-button").length > 0) {
+        if ($('#assess-button').length > 0) {
             $("#assess-button").on("click", function (e) {
                 e.preventDefault();
 
                 clear("appDomainAssessmentResultTable");
 
                 data = {
-          smiles: $("#smiles-to-assess").val(),
-          "app-domain-assessment": "ILikeCats!",
-        };
+                    "smiles": $("#smiles-to-assess").val(),
+                    "app-domain-assessment": "ILikeCats!"
+                }
 
                 if (data["smiles"].trim() === "") {
                     $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
-          $("#appDomainAssessmentResultTable").append(
-            "Please enter a SMILES string to predict!",
-          );
+                    $("#appDomainAssessmentResultTable").append("Please enter a SMILES string to predict!");
                     return;
                 }
 
+
+
                 makeLoadingGif("#appDomainLoading", "{% static '/images/wait.gif' %}");
                 $.ajax({
-          type: "get",
+                    type: 'get',
                     data: data,
-          url: "",
+                    url: '',
                     success: function (data, textStatus) {
                         try {
                             $("#appDomainLoading").empty();
@@ -504,23 +384,19 @@
                             console.log(data);
                         } catch (error) {
                             $("#appDomainLoading").empty();
-              $("#appDomainAssessmentResultTable").addClass(
-                "alert alert-danger",
-              );
-              $("#appDomainAssessmentResultTable").append(
-                "Error while processing response :/",
-              );
+                            $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
+                            $("#appDomainAssessmentResultTable").append("Error while processing response :/");
                         }
                     },
                     error: function (jqXHR, textStatus, errorThrown) {
                         $("#appDomainLoading").empty();
                         $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
-            $("#appDomainAssessmentResultTable").append(
-              jqXHR.responseJSON.error,
-            );
-          },
+                        $("#appDomainAssessmentResultTable").append(jqXHR.responseJSON.error);
+                    }
                 });
             });
         }
+
     </script>
+
 {% endblock content %}

templates/objects/node.html

@@ -12,7 +12,7 @@
     <div class="panel-group" id="node-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ node.name|safe }}
+                {{ node.name }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -39,7 +39,7 @@
             </div>
             <div id="node-desc" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
-                    {{ node.description|safe }}
+                    {{ node.description }}
                 </div>
             </div>
 
@@ -98,7 +98,7 @@
                 <div id="node-scenario" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for s in node.scenarios.all %}
-                            <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
                         {% endfor %}
                     </div>
                 </div>

templates/objects/package.html

@@ -14,7 +14,7 @@
 <div class="panel-group" id="package-detail">
     <div class="panel panel-default">
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-            {{ package.name|safe }}
+            {{ package.name }}
             <div id="actionsButton"
                  style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"

templates/objects/pathway.html

@@ -98,7 +98,7 @@
         <div class="panel-group" id="pwAccordion">
             <div class="panel panel-default">
                 <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                    {{ pathway.name|safe }}
+                    {{ pathway.name }}
                 </div>
             </div>
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
@@ -236,7 +236,7 @@
                 <div id="pathway-scenario" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for s in pathway.scenarios.all %}
-                            <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
                         {% endfor %}
                     </div>
                 </div>
@@ -266,7 +266,7 @@
                                                 <td colspan="2">
                                                     <li class="list-group-item">
                                                         <a href="{{ pathway.setting.model.url }}">
-                                                            {{ pathway.setting.model.name|safe }}
+                                                            {{ pathway.setting.model.name }}
                                                         </a>
                                                     </li>
                                                 </td>
@@ -299,7 +299,7 @@
                                                     {% for p in pathway.setting.rule_packages.all %}
                                                         <li class="list-group-item">
                                                             <a href="{{ p.url }}">
-                                                                {{ p.name|safe }}
+                                                                {{ p.name }}
                                                             </a>
                                                         </li>
                                                     {% endfor %}

templates/objects/reaction.html

@@ -14,7 +14,7 @@
     <div class="panel-group" id="reaction-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ reaction.name|safe }}
+                {{ reaction.name }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -38,7 +38,7 @@
             </div>
             <div id="reaction-desc" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
-                    {{ reaction.description|safe }}
+                    {{ reaction.description }}
                 </div>
             </div>
 
@@ -84,12 +84,12 @@
             <div id="reaction-description-smiles" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     {% for educt in reaction.educts.all %}
-                        <a class="btn btn-default" href="{{ educt.url }}">{{ educt.name|safe }}</a>
+                        <a class="btn btn-default" href="{{ educt.url }}">{{ educt.name }}</a>
                     {% endfor %}
                     <span class="glyphicon glyphicon-arrow-right" style="margin-left:5em;margin-right:5em;"
                           aria-hidden="true"></span>
                     {% for product in reaction.products.all %}
-                        <a class="btn btn-default" href="{{ product.url }}">{{ product.name|safe }}</a>
+                        <a class="btn btn-default" href="{{ product.url }}">{{ product.name }}</a>
                     {% endfor %}
                 </div>
             </div>
@@ -118,7 +118,7 @@
                 <div id="reaction-rules" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for r in reaction.rules.all %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -152,7 +152,7 @@
                 <div id="reaction-pathway" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for r in reaction.related_pathways %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -168,7 +168,7 @@
                 <div id="reaction-scenario" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for s in reaction.scenarios.all %}
-                            <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
                         {% endfor %}
                     </div>
                 </div>

templates/objects/scenario.html

@@ -10,7 +10,7 @@
     <div class="panel-group" id="scenario-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ scenario.name|safe }}
+                {{ scenario.name }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -30,7 +30,7 @@
     <div class="panel panel-default">
         <div class="panel-heading">Description</div>
         <div class="panel-body">
-            {{ scenario.description|safe }}
+            {{ scenario.description }}
             <br>
             {{ scenario.scenario_type }}
             <br>

templates/objects/simple_rule.html

@@ -13,7 +13,7 @@
     <div class="panel-group" id="rule-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ rule.name|safe }}
+                {{ rule.name }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -29,7 +29,7 @@
             </div>
             <div class="panel-body">
                 <p>
-                    {{ rule.description|safe }}
+                    {{ rule.description }}
                 </p>
             </div>
 
@@ -145,7 +145,7 @@
                 <div id="rule-composite-rule" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for cr in rule.parallelrule_set.all %}
-                            <a class="list-group-item" href="{{ cr.url }}">{{ cr.name|safe }}</a>
+                            <a class="list-group-item" href="{{ cr.url }}">{{ cr.name }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -162,7 +162,7 @@
                 <div id="rule-scenario" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for s in rule.scenarios.all %}
-                            <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }}</a>
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -179,7 +179,7 @@
                 <div id="rule-reaction" class="panel-collapse collapse">
                     <div class="panel-body list-group-item">
                         {% for r in rule.related_reactions %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -196,7 +196,7 @@
                 <div id="rule-pathway" class="panel-collapse collapse">
                     <div class="panel-body list-group-item">
                         {% for r in rule.related_pathways %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
                         {% endfor %}
                     </div>
                 </div>

templates/objects/user.html

@@ -41,7 +41,7 @@
     <div id="default-package" class="panel-collapse collapse in">
         <div class="panel-body list-group-item">
             <li class="list-group-item">
-                <a href="{{ user.default_package.url }}"> {{ user.default_package.name|safe }}</a>
+                <a href="{{ user.default_package.url }}"> {{ user.default_package.name }}</a>
             </li>
         </div>
     </div>
@@ -58,7 +58,7 @@
         <div class="panel-body list-group-item">
             {% for g in meta.available_groups %}
             <li class="list-group-item">
-                <a href="{{ g.url }}"> {{ g.name|safe }}</a>
+                <a href="{{ g.url }}"> {{ g.name }}</a>
             </li>
             {% endfor %}
         </div>
@@ -90,7 +90,7 @@
                                 <td colspan="2">
                                     <li class="list-group-item">
                                         <a href="{{user.default_setting.model.url}}">
-                                            {{ user.default_setting.model.name|safe }}
+                                            {{ user.default_setting.model.name }}
                                         </a>
                                     </li>
                                 </td>
@@ -123,7 +123,7 @@
                                     {% for p in user.default_setting.rule_packages.all %}
                                     <li class="list-group-item">
                                         <a href="{{p.url}}">
-                                            {{ p.name|safe }}
+                                            {{ p.name }}
                                         </a>
                                     </li>
                                     {% endfor %}

templates/pathway_playground2.html

@@ -18,7 +18,7 @@
 </head>
 <body>
 <p></p>
-{{ pathway.name|safe }}
+{{ pathway.name }}
 <div id="viz">
     <svg width="2000" height="2000"> <!-- Sehr großes SVG für Zoom -->
         <defs>

templates/search.html

@@ -11,13 +11,13 @@
                     <option disabled>Reviewed Packages</option>
                 {% endif %}
                 {% for obj in reviewed_objects %}
-                    <option value="{{ obj.url }}" selected>{{ obj.name|safe }}</option>
+                    <option value="{{ obj.url }}" selected>{{ obj.name }}</option>
                 {% endfor %}
                 {% if unreviewed_objects %}
                     <option disabled>Unreviewed Packages</option>
                 {% endif %}
                 {% for obj in unreviewed_objects %}
-                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                    <option value="{{ obj.url }}">{{ obj.name }}</option>
                 {% endfor %}
             </select>
         </div>

templates/static/about_us.html

@@ -1,132 +0,0 @@
-{% extends "framework_modern.html" %}
-{% load static %}
-
-{% block main_content %}
-<div class="max-w-4xl mx-auto px-4 py-8">
-    <!-- Breadcrumbs -->
-    <div class="text-sm breadcrumbs mb-4">
-        <ul>
-            <li><a href="/">Home</a></li>
-            <li>About Us</li>
-        </ul>
-    </div>
-
-    <!-- Main Content -->
-    <div class="bg-base-100 shadow-xl rounded-lg p-8">
-        <h1 class="text-4xl font-bold mb-6">About enviPath</h1>
-
-        <div class="prose max-w-none">
-            <!-- Hero Image/Graphic -->
-            <div class="mb-8">
-                <img src="{% static '/images/ep-rule-artwork.png' %}" alt="enviPath System" class="w-full max-w-2xl mx-auto rounded-lg shadow-md" />
-            </div>
-
-            <p class="text-lg mb-6">
-                enviPath is a comprehensive database and prediction system for the microbial biotransformation of
-                organic environmental contaminants. Since 2015, we have been at the forefront of computational
-                environmental chemistry, helping researchers understand and predict biodegradation pathways.
-            </p>
-
-            <h2 class="text-2xl font-semibold mt-8 mb-4">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="text-2xl font-semibold mt-8 mb-4">What We Offer</h2>
-            <div class="grid md:grid-cols-2 gap-6 mb-6">
-                <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.</p>
-                    </div>
-                </div>
-                <div class="card bg-base-200 shadow-md">
-                    <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.</p>
-                    </div>
-                </div>
-                <div class="card bg-base-200 shadow-md">
-                    <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.</p>
-                    </div>
-                </div>
-                <div class="card bg-base-200 shadow-md">
-                    <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.</p>
-                    </div>
-                </div>
-            </div>
-
-            <h2 class="text-2xl font-semibold mt-8 mb-4">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="list-disc list-inside mb-4 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="text-2xl font-semibold mt-8 mb-4">Our Partners</h2>
-            <p class="mb-4">
-                enviPath is backed by leading research institutions and collaborators:
-            </p>
-            <div class="flex flex-wrap justify-center items-center gap-8 my-8">
-                <img src="{% static '/images/uoa-logo-small.png' %}" alt="The University of Auckland" class="h-20 object-contain" />
-                <img src="{% static '/images/logo-eawag.svg' %}" alt="Eawag" class="h-16 object-contain" />
-                <img src="{% static '/images/uzh-logo.svg' %}" alt="University of Zurich" class="h-20 object-contain" />
-            </div>
-
-            <h2 class="text-2xl font-semibold mt-8 mb-4">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="text-2xl font-semibold mt-8 mb-4">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="list-disc list-inside mb-4 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="text-2xl font-semibold mt-8 mb-4">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 justify-end mt-4">
-                        <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>
-
-            <h2 class="text-2xl font-semibold mt-8 mb-4">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>
-{% endblock main_content %}