...

.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
+- [uv](https://github.com/astral-sh/uv) - A fast Python package installer and resolver.
-- **Docker and Docker Compose** - Required for running PostgreSQL database
+- **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.
+> **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.
-
----
-
-The frontend requires `pnpm` to correctly display in development.
-[Install it here](https://pnpm.io/installation).
 
 ### 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

@@ -87,14 +87,11 @@ TEMPLATES = [
                 "django.template.context_processors.request",
                 "django.contrib.auth.context_processors.auth",
                 "django.contrib.messages.context_processors.messages",
-                "epdb.context_processors.package_context",
             ],
         },
     },
 ]
 
-ALLOWED_HTML_TAGS = {"b", "i", "u", "br", "em", "mark", "p", "s", "strong"}
-
 WSGI_APPLICATION = "envipath.wsgi.application"
 
 # Database
@@ -246,7 +243,6 @@ 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:
@@ -347,14 +343,6 @@ LOGIN_EXEMPT_URLS = [
     "/password_reset/",
     "/reset/",
     "/microsoft/",
-    "/terms",
-    "/privacy",
-    "/cookie-policy",
-    "/about",
-    "/contact",
-    "/jobs",
-    "/cite",
-    "/legal",
 ]
 
 # MS AD/Entra
@@ -369,6 +357,3 @@ 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

@@ -21,7 +21,6 @@ from .models import (
     ExternalDatabase,
     ExternalIdentifier,
     JobLog,
-    License,
 )
 
 
@@ -63,10 +62,6 @@ class EnviFormerAdmin(EPAdmin):
     pass
 
 
-class LicenseAdmin(admin.ModelAdmin):
-    list_display = ["cc_string", "link", "image_link"]
-
-
 class CompoundAdmin(EPAdmin):
     pass
 
@@ -123,7 +118,6 @@ admin.site.register(JobLog, JobLogAdmin)
 admin.site.register(Package, PackageAdmin)
 admin.site.register(MLRelativeReasoning, MLRelativeReasoningAdmin)
 admin.site.register(EnviFormer, EnviFormerAdmin)
-admin.site.register(License, LicenseAdmin)
 admin.site.register(Compound, CompoundAdmin)
 admin.site.register(CompoundStructure, CompoundStructureAdmin)
 admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)

epdb/context_processors.py

@@ -1,32 +0,0 @@
-"""
-Context processors for enviPy application.
-
-Context processors automatically make variables available to all templates.
-"""
-
-from .logic import PackageManager
-from .models import Package
-
-
-def package_context(request):
-    """
-    Provides package data for the search modal which is included globally
-    in framework_modern.html.
-
-    Returns:
-        dict: Context dictionary with reviewed and unreviewed packages
-    """
-    current_user = request.user
-
-    reviewed_package_qs = PackageManager.get_reviewed_packages()
-
-    unreviewed_package_qs = Package.objects.none()
-
-    # Only get user-specific packages if user is authenticated
-    if current_user.is_authenticated:
-        unreviewed_package_qs = PackageManager.get_all_readable_packages(current_user)
-
-    return {
-        "reviewed_packages": reviewed_package_qs,
-        "unreviewed_packages": unreviewed_package_qs,
-    }

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
@@ -186,12 +185,6 @@ 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 +262,8 @@ class GroupManager(object):
     @staticmethod
     def create_group(current_user, name, description):
         g = Group()
-        # Clean for potential XSS
+        g.name = name
-        g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        g.description = description
-        g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
         g.owner = current_user
         g.save()
 
@@ -526,13 +518,8 @@ class PackageManager(object):
     @transaction.atomic
     def create_package(current_user, name: str, description: str = None):
         p = Package()
-
+        p.name = name
-        # Clean for potential XSS
+        p.description = description
-        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.save()
 
         up = UserPackagePermission()
@@ -1107,29 +1094,28 @@ class SettingManager(object):
         model: EPModel = None,
         model_threshold: float = None,
     ):
-        new_s = Setting()
+        s = Setting()
-        # Clean for potential XSS
+        s.name = name
-        new_s.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        s.description = description
-        new_s.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+        s.max_nodes = max_nodes
-        new_s.max_nodes = max_nodes
+        s.max_depth = max_depth
-        new_s.max_depth = max_depth
+        s.model = model
-        new_s.model = model
+        s.model_threshold = model_threshold
-        new_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)
+                s.rule_packages.add(r)
-            new_s.save()
+            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 +1544,7 @@ 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 +1577,9 @@ 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/bootstrap.py

@@ -12,16 +12,10 @@ from epdb.models import (
     Permission,
     User,
     ExternalDatabase,
-    License,
 )
 
 
 class Command(BaseCommand):
-    def add_arguments(self, parser):
-        parser.add_argument(
-            "-ol", "--only-licenses", action="store_true", help="Only create licenses."
-        )
-
     def create_users(self):
         # Anonymous User
         if not User.objects.filter(email="anon@envipath.com").exists():
@@ -89,17 +83,6 @@ class Command(BaseCommand):
 
         return anon, admin, g, user0
 
-    def create_licenses(self):
-        """Create the six default licenses supported by enviPath"""
-        cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
-        for cc_string in cc_strings:
-            if not License.objects.filter(cc_string=cc_string).exists():
-                new_license = License()
-                new_license.cc_string = cc_string
-                new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
-                new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
-                new_license.save()
-
     def import_package(self, data, owner):
         return PackageManager.import_legacy_package(
             data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
@@ -174,10 +157,6 @@ class Command(BaseCommand):
 
     @transaction.atomic
     def handle(self, *args, **options):
-        # Create licenses
-        self.create_licenses()
-        if options.get("only_licenses", False):
-            return
         # Create users
         anon, admin, g, user0 = self.create_users()
 

epdb/migrations/0010_license_cc_string.py

@@ -1,18 +0,0 @@
-# Generated by Django 5.2.7 on 2025-11-11 14:11
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0009_joblog"),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="license",
-            name="cc_string",
-            field=models.TextField(default="by-nc-sa", verbose_name="CC string"),
-            preserve_default=False,
-        ),
-    ]

epdb/migrations/0011_auto_20251111_1413.py

@@ -1,59 +0,0 @@
-# Generated by Django 5.2.7 on 2025-11-11 14:13
-
-import re
-
-from django.contrib.postgres.aggregates import ArrayAgg
-from django.db import migrations
-from django.db.models import Min
-
-
-def set_cc(apps, schema_editor):
-    License = apps.get_model("epdb", "License")
-
-    # For all existing licenses extract cc_string from link
-    for license in License.objects.all():
-        pattern = r"/licenses/([^/]+)/4\.0"
-        match = re.search(pattern, license.link)
-        if match:
-            license.cc_string = match.group(1)
-            license.save()
-        else:
-            raise ValueError(f"Could not find license for {license.link}")
-
-    # Ensure we have all licenses
-    cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
-    for cc_string in cc_strings:
-        if not License.objects.filter(cc_string=cc_string).exists():
-            new_license = License()
-            new_license.cc_string = cc_string
-            new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
-            new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
-            new_license.save()
-
-    # As we might have existing Licenses representing the same License,
-    # get min pk and all pks as a list
-    license_lookup_qs = License.objects.values("cc_string").annotate(
-        lowest_pk=Min("id"), all_pks=ArrayAgg("id", order_by=("id",))
-    )
-
-    license_lookup = {
-        row["cc_string"]: (row["lowest_pk"], row["all_pks"]) for row in license_lookup_qs
-    }
-
-    Packages = apps.get_model("epdb", "Package")
-
-    for k, v in license_lookup.items():
-        # Set min pk to all packages pointing to any of the duplicates
-        Packages.objects.filter(pk__in=v[1]).update(license_id=v[0])
-        # remove the min pk from "other" pks as we use them for deletion
-        v[1].remove(v[0])
-        # Delete redundant License objects
-        License.objects.filter(pk__in=v[1]).delete()
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0010_license_cc_string"),
-    ]
-
-    operations = [migrations.RunPython(set_cc)]

epdb/models.py

@@ -11,7 +11,6 @@ from typing import Union, List, Optional, Dict, Tuple, Set, Any
 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
@@ -29,14 +28,7 @@ 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 (
+from utilities.ml import Dataset, ApplicabilityDomainPCA, EnsembleClassifierChain, RelativeReasoning
-    RuleBasedDataset,
-    ApplicabilityDomainPCA,
-    EnsembleClassifierChain,
-    RelativeReasoning,
-    EnviFormerDataset,
-    Dataset,
-)
 
 logger = logging.getLogger(__name__)
 
@@ -655,7 +647,6 @@ class ScenarioMixin(models.Model):
 
 
 class License(models.Model):
-    cc_string = models.TextField(blank=False, null=False, verbose_name="CC string")
     link = models.URLField(blank=False, null=False, verbose_name="link")
     image_link = models.URLField(blank=False, null=False, verbose_name="Image link")
 
@@ -811,16 +802,14 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
         c = Compound()
         c.package = package
 
-        if name is not None:
+        if name is None or name.strip() == "":
-            # Clean for potential XSS
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-        if name is None or name == "":
             name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
+
         c.name = name
 
         # We have a default here only set the value if it carries some payload
         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()
 
@@ -992,11 +981,11 @@ 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
@@ -1198,29 +1187,21 @@ class SimpleAmbitRule(SimpleRule):
         r = SimpleAmbitRule()
         r.package = package
 
-        if name is not None:
+        if name is None or name.strip() == "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        if name is None or name == "":
             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()):
+            r.reactant_filter_smarts = reactant_filter_smarts
-                raise ValueError(f'Reactant Filter SMARTS "{reactant_filter_smarts}" is invalid!')
-            else:
-                r.reactant_filter_smarts = reactant_filter_smarts.strip()
 
         if product_filter_smarts is not None and product_filter_smarts.strip() != "":
-            if not FormatConverter.is_valid_smarts(product_filter_smarts.strip()):
+            r.product_filter_smarts = product_filter_smarts
-                raise ValueError(f'Product Filter SMARTS "{product_filter_smarts}" is invalid!')
-            else:
-                r.product_filter_smarts = product_filter_smarts.strip()
 
         r.save()
         return r
@@ -1421,11 +1402,12 @@ 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
 
@@ -1591,11 +1573,9 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
         while len(queue):
             current = queue.pop()
             processed.add(current)
-
             nodes.append(current.d3_json())
 
-            for e in self.edges:
+            for e in self.edges.filter(start_nodes=current).distinct():
-                if current in e.start_nodes.all():
                 for prod in e.end_nodes.all():
                     if prod not in queue and prod not in processed:
                         queue.append(prod)
@@ -1733,15 +1713,14 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     ):
         pw = Pathway()
         pw.package = package
-        if name is not None:
+
-            # Clean for potential XSS
+        if name is None or name.strip() == "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-        if name is None or name == "":
             name = f"Pathway {Pathway.objects.filter(package=package).count() + 1}"
 
         pw.name = name
+
         if description is not None and description.strip() != "":
-            pw.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+            pw.description = description
 
         pw.save()
         try:
@@ -2036,16 +2015,11 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
         for node in end_nodes:
             e.end_nodes.add(node)
 
-        # Clean for potential XSS
+        if name is None:
-        # 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 == "":
             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,
@@ -2199,7 +2173,7 @@ 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")
@@ -2208,7 +2182,7 @@ 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)
 
@@ -2249,7 +2223,7 @@ 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}!")
 
@@ -2367,39 +2341,37 @@ class PackageBasedModel(EPModel):
             eval_reactions = list(
                 Reaction.objects.filter(package__in=self.eval_packages.all()).distinct()
             )
-            ds = RuleBasedDataset.generate_dataset(
+            ds = Dataset.generate_dataset(eval_reactions, self.applicable_rules, educts_only=True)
-                eval_reactions, self.applicable_rules, educts_only=True
-            )
             if isinstance(self, RuleBasedRelativeReasoning):
-                X = ds.X(exclude_id_col=False, na_replacement=None).to_numpy()
+                X = np.array(ds.X(exclude_id_col=False, na_replacement=None))
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                y = np.array(ds.y(na_replacement=np.nan))
             else:
-                X = ds.X(na_replacement=np.nan).to_numpy()
+                X = np.array(ds.X(na_replacement=np.nan))
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                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()
+                X = np.array(ds.X(exclude_id_col=False, na_replacement=None))
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                y = np.array(ds.y(na_replacement=np.nan))
             else:
-                X = ds.X(na_replacement=np.nan).to_numpy()
+                X = np.array(ds.X(na_replacement=np.nan))
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                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)
             )
@@ -2567,15 +2539,14 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
     ):
         rbrr = RuleBasedRelativeReasoning()
         rbrr.package = package
-        if name is not None:
+
-            # Clean for potential XSS
+        if name is None or name.strip() == "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-        if name is None or name == "":
             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.")
@@ -2612,11 +2583,11 @@ 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
@@ -2626,7 +2597,7 @@ 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):
@@ -2672,15 +2643,14 @@ class MLRelativeReasoning(PackageBasedModel):
     ):
         mlrr = MLRelativeReasoning()
         mlrr.package = package
-        if name is not None:
+
-            # Clean for potential XSS
+        if name is None or name.strip() == "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-        if name is None or name == "":
             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.")
@@ -2715,11 +2685,11 @@ 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):
@@ -2742,7 +2712,7 @@ 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]
@@ -2787,9 +2757,7 @@ class ApplicabilityDomain(EnviPathModel):
 
     @cached_property
     def training_set_probs(self):
-        ds = self.model.load_dataset()
+        return joblib.load(os.path.join(s.MODEL_DIR, f"{self.model.uuid}_train_probs.pkl"))
-        col_ids = ds.block_indices("prob")
-        return ds[:, col_ids]
 
     def build(self):
         ds = self.model.load_dataset()
@@ -2797,9 +2765,9 @@ 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())
+        probs = self.model.model.predict_proba(ds.X())
-        ds.add_probs(probs)
+        f = os.path.join(s.MODEL_DIR, f"{self.model.uuid}_train_probs.pkl")
-        ds.save(os.path.join(s.MODEL_DIR, f"{self.model.uuid}_ds.pkl"))
+        joblib.dump(probs, f)
 
         ad = ApplicabilityDomainPCA(num_neighbours=self.num_neighbours)
         ad.build(ds)
@@ -2822,20 +2790,15 @@ 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 = []
+        if isinstance(structure, CompoundStructure):
-        for struct in structures:
+            smiles = structure.smiles
-            if isinstance(struct, CompoundStructure):
-                smiles.append(structures.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:
@@ -2849,61 +2812,82 @@ 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
+        probs = self.training_set_probs
-        for i, row in enumerate(assessment_ds[:, assessment_ds.triggered()].iter_rows(named=True)):
+        # preds = self.model.model.predict_proba(assessment_ds.X())
-            # 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)}
         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():
+            for rule_idx, vals in qualified_neighbours_per_rule[i].items():
-                # compute tanimoto distance for all neighbours and add to dataset
+                # 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],
+                    instance.X()[0][sf[0] : sf[1]],
-                    train_instances[:, train_instances.struct_features()].to_numpy(),
+                    [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)
+                dists_with_index = sorted(dists_with_index, key=lambda x: x[1], reverse=True)
-                train_instances = train_instances.sort("dist", descending=True)[
+                dists_with_index = dists_with_index[: self.num_neighbours]
-                    : self.num_neighbours
+
-                ]
                 # compute average distance
-                rule_reliabilities[rule_uuid] = (
+                rule_reliabilities[rule_idx] = (
-                    train_instances.select(pl.mean("dist")).fill_nan(0.0).item()
+                    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(
+                neighbour_datasets = [(d[0], ds.at(d[0])) for d in dists_with_index]
-                    rule_uuid, train_instances
+                local_compatibilities[rule_idx] = self._compute_compatibility(
+                    rule_idx, probs, neighbour_datasets
                 )
-                neighbours_per_rule[rule_uuid] = list(
+                neighbours_per_rule[rule_idx] = [
-                    CompoundStructure.objects.filter(uuid__in=train_instances["structure_id"])
+                    CompoundStructure.objects.get(uuid=ds[1].structure_id())
-                )
+                    for ds in neighbour_datasets
-                neighbor_probs_per_rule[rule_uuid] = train_instances[f"prob_{rule_uuid}"].to_list()
+                ]
+                neighbor_probs_per_rule[rule_idx] = [
+                    probs[d[0]][rule_idx] for d in dists_with_index
+                ]
 
             ad_res = {
                 "ad_params": {
@@ -2914,21 +2898,23 @@ class ApplicabilityDomain(EnviPathModel):
                     "local_compatibility_threshold": self.local_compatibilty_threshold,
                 },
                 "assessment": {
-                    "smiles": smiles[i],
+                    "smiles": smiles,
-                    "inside_app_domain": self.pca.is_applicable(assessment_ds[i])[0],
+                    "inside_app_domain": self.pca.is_applicable(instance)[0],
                 },
             }
 
             transformations = list()
-            for rule_uuid in rule_reliabilities.keys():
+            for rule_idx in rule_reliabilities.keys():
-                rule = Rule.objects.get(uuid=rule_uuid)
+                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"
@@ -2945,14 +2931,14 @@ 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],
+                    "local_compatibility": local_compatibilities[rule_idx],
-                    "probability": preds[rule_to_i[rule_uuid]].probability,
+                    "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,
@@ -2970,24 +2956,32 @@ 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(
+        for n in neighbours:
-            obs=pl.col(f"obs_{rule_idx}").cast(pl.Boolean),
+            obs = n[1].y()[0][rule_idx]
-            pred=pl.col(f"prob_{rule_idx}") >= self.model.threshold,
+            pred = preds[n[0]][rule_idx]
-        )
+            if obs and pred:
-        # Compute tp, tn, fp, fn using polars expressions
+                tp += 1
-        tp = obs_pred.filter((pl.col("obs")) & (pl.col("pred"))).height
+            elif not obs and pred:
-        tn = obs_pred.filter((~pl.col("obs")) & (~pl.col("pred"))).height
+                fp += 1
-        fp = obs_pred.filter((~pl.col("obs")) & (pl.col("pred"))).height
+            elif obs and not pred:
-        fn = obs_pred.filter((pl.col("obs")) & (~pl.col("pred"))).height
+                fn += 1
+            else:
+                tn += 1
+            # Jaccard Index
             if tp + tn > 0.0:
                 accuracy = (tp + tn) / (tp + tn + fp + fn)
+
         return accuracy
 
 
@@ -3007,15 +3001,14 @@ class EnviFormer(PackageBasedModel):
     ):
         mod = EnviFormer()
         mod.package = package
-        if name is not None:
+
-            # Clean for potential XSS
+        if name is None or name.strip() == "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-        if name is None or name == "":
             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.")
@@ -3089,24 +3082,44 @@ 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
@@ -3122,7 +3135,7 @@ 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}!")
 
@@ -3137,20 +3150,21 @@ 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:
+            for r in test_reactions:
-                reactant, true_product_set = r
+                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("."))
@@ -3185,7 +3199,7 @@ 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()
@@ -3264,35 +3278,47 @@ 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(
+            ds = []
-                Reaction.objects.filter(package__in=self.eval_packages.all()).distinct()
+            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]
+                train = [ds[i] for i in train_index]
-                test = ds[test_index]
+                test = [ds[i] for i in test_index]
                 start = datetime.now()
-                model = fine_tune(
+                model = fine_tune(train, s.MODEL_DIR, str(split_id), device=s.ENVIFORMER_DEVICE)
-                    train.X(), train.y(), 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)
@@ -3371,12 +3397,23 @@ class EnviFormer(PackageBasedModel):
                             ):
                                 overlap += 1
                                 continue
-                            train_reactions.append(reaction)
+                            educts = ".".join(
-                    train_ds = EnviFormerDataset.generate_dataset(train_reactions)
+                                [
+                                    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(
@@ -3425,44 +3462,41 @@ class Scenario(EnviPathModel):
         scenario_type: str,
         additional_information: List["EnviPyModel"],
     ):
-        new_s = Scenario()
+        s = Scenario()
-        new_s.package = package
+        s.package = package
-        if name is not None:
+
-            # Clean for potential XSS
+        if name is None or name.strip() == "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-        if name is None or name == "":
             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(info.model_dump_json())
-            ai_data = json.loads(nh3.clean(info.model_dump_json()).strip())
             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(data.model_dump_json())
-        ai_data = json.loads(nh3.clean(data.model_dump_json()).strip())
         ai_data["uuid"] = f"{uuid4()}"
 
         if cls_name not in self.additional_information:
@@ -3497,8 +3531,7 @@ 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(v.model_dump_json())
-                ai_data = json.loads(nh3.clean(v.model_dump_json()).strip())
                 if hasattr(v, "uuid"):
                     ai_data["uuid"] = str(v.uuid)
                 else:

epdb/tasks.py

@@ -1,15 +1,15 @@
 import csv
 import io
 import logging
+from datetime import datetime
 from typing import Any, Callable, List, Optional
 from uuid import uuid4
 
 from celery import shared_task
 from celery.utils.functional import LRUCache
-from django.utils import timezone
 
 from epdb.logic import SPathway
-from epdb.models import Edge, EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User
+from epdb.models import EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User, Edge
 
 logger = logging.getLogger(__name__)
 ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.
@@ -29,7 +29,7 @@ def dispatch_eager(user: "User", job: Callable, *args, **kwargs):
         log.task_id = uuid4()
         log.job_name = job.__name__
         log.status = "SUCCESS"
-        log.done_at = timezone.now()
+        log.done_at = datetime.now()
         log.task_result = str(x) if x else None
         log.save()
 
@@ -172,6 +172,7 @@ def predict(
 
     except Exception as e:
         pw.kv.update({"status": "failed"})
+        pw.kv.update(**{"error": str(e)})
         pw.save()
 
         if JobLog.objects.filter(task_id=self.request.id).exists():

epdb/urls.py

@@ -48,7 +48,6 @@ urlpatterns = [
     re_path(r"^user$", v.users, name="users"),
     re_path(r"^group$", v.groups, name="groups"),
     re_path(r"^search$", v.search, name="search"),
-    re_path(r"^predict$", v.predict_pathway, name="predict_pathway"),
     # User Detail
     re_path(rf"^user/(?P<user_uuid>{UUID})", v.user, name="user"),
     # Group Detail
@@ -142,11 +141,6 @@ urlpatterns = [
         v.package_pathway,
         name="package pathway detail",
     ),
-    re_path(
-        rf"^package/(?P<package_uuid>{UUID})/predict$",
-        v.package_predict_pathway,
-        name="package predict pathway",
-    ),
     # Pathway Nodes
     re_path(
         rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",
@@ -199,13 +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

@@ -10,7 +10,6 @@ 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
@@ -86,11 +85,7 @@ def login(request):
         from django.contrib.auth import authenticate
         from django.contrib.auth import login
 
-        username = request.POST.get("username").strip()
+        username = request.POST.get("username")
-        if username != request.POST.get("username"):
-            context["message"] = "Login failed!"
-            return render(request, "static/login.html", context)
-
         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
+        context["title"] = "enviPath"
-        next_url = request.GET.get("next", "")
+        context["next"] = request.GET.get("next", "")
-        redirect_url = reverse("login") + "#signup"
+        return render(request, "static/register.html", context)
-
-        if next_url:
-            redirect_url += f"?next={next_url}"
-
-        return redirect(redirect_url)
     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,
         },
     }
 
@@ -362,34 +350,6 @@ def index(request):
     return render(request, "index/index.html", context)
 
 
-def predict_pathway(request):
-    """Top-level predict pathway view using user's default package."""
-    if request.method != "GET":
-        return HttpResponseNotAllowed(["GET"])
-
-    context = get_base_context(request)
-    context["title"] = "enviPath - Predict Pathway"
-    context["meta"]["current_package"] = context["meta"]["user"].default_package
-
-    return render(request, "predict_pathway.html", context)
-
-
-@package_permission_required()
-def package_predict_pathway(request, package_uuid):
-    """Package-specific predict pathway view."""
-    if request.method != "GET":
-        return HttpResponseNotAllowed(["GET"])
-
-    current_user = _anonymous_or_real(request)
-    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-
-    context = get_base_context(request)
-    context["title"] = f"enviPath - {current_package.name} - Predict Pathway"
-    context["meta"]["current_package"] = current_package
-
-    return render(request, "predict_pathway.html", context)
-
-
 def packages(request):
     current_user = _anonymous_or_real(request)
 
@@ -709,7 +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
@@ -931,7 +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)
@@ -971,24 +931,12 @@ def package_model(request, package_uuid, model_uuid):
                 ]
                 dispatch(current_user, evaluate_model, current_model.pk, multigen, eval_package_ids)
 
-                return redirect(current_model.url)
-            elif hidden == "retrain":
-                from .tasks import dispatch, retrain
-
-                dispatch(current_user, retrain, current_model.pk)
-
                 return redirect(current_model.url)
             else:
                 return HttpResponseBadRequest()
         else:
-            # TODO: Move cleaning to property updater
+            name = request.POST.get("model-name", "").strip()
-            name = request.POST.get("model-name")
+            description = request.POST.get("model-description", "").strip()
-            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()
 
             if any([name, description]):
                 if name:
@@ -1090,23 +1038,17 @@ 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"
         write = request.POST.get("write") == "on"
         owner = request.POST.get("owner") == "on"
 
-        cc_string = request.POST.get("license")
+        license = request.POST.get("license")
+        license_link = request.POST.get("license-link")
+        license_image_link = request.POST.get("license-image-link")
 
         if new_package_name:
             current_package.name = new_package_name
@@ -1134,15 +1076,24 @@ def package(request, package_uuid):
 
             PackageManager.update_permissions(current_user, current_package, grantee, max_perm)
             return redirect(current_package.url)
+        elif license is not None:
+            if license == "no-license":
+                if current_package.license is not None:
+                    current_package.license.delete()
 
-        elif cc_string is not None:
-            cc_string = cc_string.strip()
-            if cc_string == "no-license":  # Reset the package's license
                 current_package.license = None
                 current_package.save()
                 return redirect(current_package.url)
-            else:  # Get the license and assign it to the package
+            else:
-                current_package.license = License.objects.get(cc_string=cc_string)
+                if current_package.license is not None:
+                    current_package.license.delete()
+
+                license = License()
+                license.link = license_link
+                license.image_link = license_image_link
+                license.save()
+
+                current_package.license = license
                 current_package.save()
 
                 return redirect(current_package.url)
@@ -1250,16 +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", "").strip()
-        new_compound_name = request.POST.get("compound-name")
+        new_compound_description = request.POST.get("compound-description", "").strip()
-        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()
 
         if new_compound_name:
             current_compound.name = new_compound_name
@@ -1395,16 +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", "").strip()
-        new_structure_name = request.POST.get("compound-structure-name")
+        new_structure_description = request.POST.get("compound-structure-description", "").strip()
-        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()
 
         if new_structure_name:
             current_structure.name = new_structure_name
@@ -1611,14 +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", "").strip()
-        rule_name = request.POST.get("rule-name")
+        rule_description = request.POST.get("rule-description", "").strip()
-        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()
 
         if rule_name:
             current_rule.name = rule_name
@@ -1708,6 +1637,7 @@ def package_reactions(request, package_uuid):
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
         reactions_smirks = request.POST.get("reaction-smirks")
+
         educts = reactions_smirks.split(">>")[0].split(".")
         products = reactions_smirks.split(">>")[1].split(".")
 
@@ -1768,16 +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", "").strip()
-        new_reaction_name = request.POST.get("reaction-name")
+        new_reaction_description = request.POST.get("reaction-description", "").strip()
-        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()
 
         if new_reaction_name:
             current_reaction.name = new_reaction_name
@@ -1854,9 +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(
@@ -1865,6 +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:
@@ -2023,14 +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() != "":
@@ -2118,8 +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)
@@ -2284,7 +2201,6 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
 
         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")
 
@@ -2371,7 +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)
@@ -2419,21 +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]
                 ],
             },
         }
@@ -2448,7 +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")
@@ -2462,9 +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,
@@ -2473,7 +2388,7 @@ def package_scenarios(request, package_uuid):
             additional_information=additional_information,
         )
 
-        return redirect(new_scen.url)
+        return redirect(s.url)
     else:
         return HttpResponseNotAllowed(
             [
@@ -2773,7 +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(
@@ -2924,60 +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)

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
-
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-
-  '@alloc/quick-lru@5.2.0':
-    resolution: {integrity: sha512-UrcABB+4bUrFABwbluTIBErXwvbsU/V7TZWfmbgJfbkwiBuziS9gxdODUyuiecfdGQ85jglMW6juS3+z5TsKLw==}
-    engines: {node: '>=10'}
-
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-
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-
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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 = """
+dev = { cmd = "python manage.py runserver", help = "Start the development server", deps = ["db-up"] }
-# 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" }
 
 # 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" }
+shell = { cmd = "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"] }

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

@@ -1,36 +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;
-  exclude: rootscrollgutter;
-}
-
-@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

@@ -0,0 +1,225 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns="http://www.w3.org/2000/svg"
+   version="1.1"
+   width="314.98749"
+   height="28.8125"
+   id="svg3004"
+   xml:space="preserve"><metadata
+     id="metadata3010"><rdf:RDF><cc:Work
+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><defs
+     id="defs3008" /><g
+     transform="matrix(1.25,0,0,-1.25,0,28.8125)"
+     id="g3012"><g
+       transform="scale(0.1,0.1)"
+       id="g3014"><path
+         d="m 957.473,175.816 0,-4.296 -18.453,0 0,-48.614 -5.04,0 0,48.614 -18.378,0 0,4.296 41.871,0"
+         id="path3016"
+         style="fill:#090c0d;fill-opacity:1;fill-rule:nonzero;stroke:none" /><path
+         d="m 969.695,175.816 0,-22.968 31.425,0 0,22.968 5.04,0 0,-52.91 -5.04,0 0,25.637 -31.425,0 0,-25.637 -5.039,0 0,52.91 5.039,0"
+         id="path3018"
+         style="fill:#090c0d;fill-opacity:1;fill-rule:nonzero;stroke:none" /><path
+         d="m 1055.58,175.816 0,-4.296 -31.49,0 0,-19.122 29.49,0 0,-4.293 -29.49,0 0,-20.898 31.87,0 0,-4.301 -36.91,0 0,52.91 36.53,0"
+         id="path3020"
+         style="fill:#090c0d;fill-opacity:1;fill-rule:nonzero;stroke:none" /><path
+         d="m 1124.58,175.816 0,-4.296 -31.5,0 0,-19.122 29.49,0 0,-4.293 -29.49,0 0,-20.898 31.87,0 0,-4.301 -36.91,0 0,52.91 36.54,0"
+         id="path3022"
+         style="fill:#090c0d;fill-opacity:1;fill-rule:nonzero;stroke:none" /><path
+         d="m 1139.76,175.816 30.83,-44.757 0.15,0 0,44.757 5.04,0 0,-52.91 -5.64,0 -30.82,44.754 -0.15,0 0,-44.754 -5.04,0 0,52.91 5.63,0"
+         id="path3024"
+         style="fill:#090c0d;fill-opacity:1;fill-rule:nonzero;stroke:none" /><path
+         d="m 1188.15,175.816 17.19,-47.355 0.15,0 17.06,47.355 5.34,0 -19.65,-52.91 -5.86,0 -19.56,52.91 5.33,0"
+         id="path3026"
+         style="fill:#090c0d;fill-opacity:1;fill-rule:nonzero;stroke:none" /><path
+         d="m 1235.15,122.906 5.043,0 0,52.9102 -5.043,0 0,-52.9102 z"
+         id="path3028"
+         style="fill:#090c0d;fill-opacity:1;fill-rule:nonzero;stroke:none" /><path
+         d="m 1277.3,150.691 c 1.54,0 2.99,0.243 4.38,0.711 1.39,0.469 2.59,1.145 3.63,2.036 1.04,0.886 1.86,1.968 2.48,3.222 0.63,1.258 0.92,2.703 0.92,4.336 0,3.262 -0.94,5.824 -2.81,7.703 -1.88,1.875 -4.74,2.821 -8.6,2.821 l -18.82,0 0,-20.829 18.82,0 z m 0.38,25.125 c 2.16,0 4.23,-0.269 6.19,-0.816 1.95,-0.543 3.65,-1.367 5.1,-2.48 1.46,-1.118 2.62,-2.54 3.49,-4.297 0.86,-1.758 1.29,-3.821 1.29,-6.192 0,-3.359 -0.86,-6.273 -2.6,-8.742 -1.72,-2.473 -4.29,-4.055 -7.69,-4.746 l 0,-0.145 c 1.73,-0.25 3.16,-0.703 4.29,-1.367 1.14,-0.668 2.06,-1.527 2.78,-2.558 0.72,-1.035 1.23,-2.239 1.56,-3.594 0.31,-1.363 0.53,-2.832 0.62,-4.41 0.05,-0.887 0.1,-1.977 0.16,-3.262 0.05,-1.285 0.15,-2.582 0.29,-3.891 0.15,-1.312 0.38,-2.543 0.71,-3.711 0.32,-1.156 0.74,-2.054 1.3,-2.699 l -5.56,0 c -0.29,0.496 -0.54,1.098 -0.7,1.809 -0.18,0.723 -0.31,1.461 -0.37,2.234 -0.08,0.762 -0.14,1.512 -0.2,2.254 -0.05,0.742 -0.1,1.387 -0.14,1.926 -0.09,1.875 -0.26,3.742 -0.49,5.598 -0.22,1.851 -0.69,3.503 -1.4,4.961 -0.72,1.46 -1.76,2.632 -3.11,3.523 -1.36,0.887 -3.23,1.281 -5.6,1.191 l -19.12,0 0,-23.496 -5.03,0 0,52.91 24.23,0"
+         id="path3030"
+         style="fill:#090c0d;fill-opacity:1;fill-rule:nonzero;stroke:none" /><path
+         d="m 1308.46,140.879 c 0.77,-2.793 1.95,-5.289 3.56,-7.484 1.61,-2.2 3.66,-3.965 6.19,-5.301 2.52,-1.336 5.54,-2.004 9.04,-2.004 3.51,0 6.51,0.668 9,2.004 2.5,1.336 4.55,3.101 6.15,5.301 1.6,2.195 2.8,4.691 3.56,7.484 0.77,2.789 1.15,5.613 1.15,8.48 0,2.914 -0.38,5.758 -1.15,8.52 -0.76,2.769 -1.96,5.25 -3.56,7.449 -1.6,2.199 -3.65,3.969 -6.15,5.297 -2.49,1.336 -5.49,2.008 -9,2.008 -3.5,0 -6.52,-0.672 -9.04,-2.008 -2.53,-1.328 -4.58,-3.098 -6.19,-5.297 -1.61,-2.199 -2.79,-4.68 -3.56,-7.449 -0.75,-2.762 -1.15,-5.606 -1.15,-8.52 0,-2.867 0.4,-5.691 1.15,-8.48 z m -4.63,18.934 c 1.04,3.308 2.6,6.23 4.67,8.777 2.08,2.547 4.68,4.57 7.82,6.078 3.14,1.504 6.79,2.254 10.93,2.254 4.15,0 7.78,-0.75 10.89,-2.254 3.11,-1.508 5.71,-3.531 7.78,-6.078 2.08,-2.547 3.64,-5.469 4.67,-8.777 1.05,-3.313 1.56,-6.797 1.56,-10.454 0,-3.656 -0.51,-7.136 -1.56,-10.449 -1.03,-3.308 -2.59,-6.226 -4.67,-8.738 -2.07,-2.52 -4.67,-4.531 -7.78,-6.043 -3.11,-1.5 -6.74,-2.266 -10.89,-2.266 -4.14,0 -7.79,0.766 -10.93,2.266 -3.14,1.512 -5.74,3.523 -7.82,6.043 -2.07,2.512 -3.63,5.43 -4.67,8.738 -1.04,3.313 -1.54,6.793 -1.54,10.449 0,3.657 0.5,7.141 1.54,10.454"
+         id="path3032"
+         style="fill:#090c0d;fill-opacity:1;fill-rule:nonzero;stroke:none" /><path
+         d="m 1367.77,175.816 30.84,-44.757 0.15,0 0,44.757 5.05,0 0,-52.91 -5.64,0 -30.83,44.754 -0.15,0 0,-44.754 -5.04,0 0,52.91 5.62,0"
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+         style="fill:#090c0d;fill-opacity:1;fill-rule:nonzero;stroke:none" /><path
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-</svg>

static/images/logo-square.svg

@@ -1,3 +0,0 @@
-<svg fill="currentColor" id="ep-logo-square" role="img" viewBox="0 0 65 65" xmlns="http://www.w3.org/2000/svg">
-    <path d="M26.538 25.283c-.532-1.519-1.274-2.861-2.24-4.037a11.163 11.163 0 0 0-3.522-2.828c-1.381-.712-2.948-1.07-4.697-1.07-1.791 0-3.379.358-4.76 1.07a11.11 11.11 0 0 0-3.522 2.828c-.966 1.176-1.737 2.533-2.308 4.07a19.839 19.839 0 0 0-1.139 4.728h23.047a15.559 15.559 0 0 0-.86-4.76zM5 38.57c.44 1.685 1.143 3.189 2.11 4.527.966 1.333 2.187 2.436 3.656 3.31 1.475.875 3.243 1.308 5.313 1.308 3.178 0 5.665-.83 7.456-2.485 1.793-1.65 3.037-3.867 3.726-6.626h4.35c-.922 4.054-2.613 7.179-5.073 9.39-2.46 2.208-5.947 3.315-10.46 3.315-2.802 0-5.233-.502-7.274-1.489-2.056-.986-3.721-2.348-5.01-4.072-1.284-1.724-2.241-3.725-2.861-6.005C.313 37.465 0 35.058 0 32.529c0-2.343.313-4.649.933-6.9.62-2.254 1.577-4.267 2.861-6.04 1.289-1.772 2.954-3.197 5.01-4.281 2.041-1.08 4.472-1.616 7.275-1.616 2.856 0 5.293.571 7.32 1.724 2.026 1.147 3.666 2.66 4.931 4.521 1.265 1.86 2.177 3.999 2.725 6.416a27.9 27.9 0 0 1 .692 7.348H4.35c0 1.567.215 3.188.65 4.868M49.301 31.456c.914 0 1.793-.07 2.638-.202.845-.136 1.586-.4 2.23-.78.641-.391 1.159-.942 1.548-1.656.387-.702.582-1.64.582-2.782 0-1.148-.195-2.08-.582-2.79-.39-.707-.907-1.26-1.547-1.65-.645-.386-1.386-.65-2.231-.78a16.554 16.554 0 0 0-2.638-.206h-6.176v10.846h6.176zm2.184-17.032c2.26 0 4.189.331 5.776.995 1.592.66 2.88 1.524 3.877 2.608a10.007 10.007 0 0 1 2.177 3.696c.46 1.393.684 2.828.684 4.313 0 1.455-.224 2.88-.684 4.28a9.955 9.955 0 0 1-2.177 3.727c-.997 1.079-2.285 1.953-3.877 2.607-1.587.664-3.516.992-5.776.992h-8.36v12.974h-7.964V14.424h16.324" class="logo-main"/>
-</svg>

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/actions/collections/compound.html

@@ -1,7 +1,6 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#new_compound_modal">
-      <span class="glyphicon glyphicon-plus"></span> New Compound</a
+            <span class="glyphicon glyphicon-plus"></span> New Compound</a>
-    >
     </li>
 {% endif %}

templates/actions/collections/compound_structure.html

@@ -1,11 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_compound_structure_modal">
-      role="button"
+            <span class="glyphicon glyphicon-plus"></span> New Compound Structure</a>
-      data-toggle="modal"
-      data-target="#new_compound_structure_modal"
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Compound Structure</a
-    >
     </li>
 {% endif %}

templates/actions/collections/edge.html

@@ -1,7 +1,6 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#new_edge_modal">
-      <span class="glyphicon glyphicon-plus"></span> New Edge</a
+            <span class="glyphicon glyphicon-plus"></span> New Edge</a>
-    >
     </li>
 {% endif %}

templates/actions/collections/group.html

@@ -1,5 +1,4 @@
 <li>
     <a role="button" data-toggle="modal" data-target="#new_group_modal">
-    <span class="glyphicon glyphicon-plus"></span> New Group</a
+        <span class="glyphicon glyphicon-plus"></span> New Group</a>
-  >
 </li>

templates/actions/collections/model.html

@@ -1,7 +1,6 @@
 {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
     <li>
         <a role="button" data-toggle="modal" data-target="#new_model_modal">
-      <span class="glyphicon glyphicon-plus"></span> New Model</a
+            <span class="glyphicon glyphicon-plus"></span> New Model</a>
-    >
     </li>
 {% endif %}

templates/actions/collections/node.html

@@ -1,7 +1,6 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#new_node_modal">
-      <span class="glyphicon glyphicon-plus"></span> New Node</a
+            <span class="glyphicon glyphicon-plus"></span> New Node</a>
-    >
     </li>
 {% endif %}

templates/actions/collections/package.html

@@ -1,20 +1,12 @@
 <li>
     <a role="button" data-toggle="modal" data-target="#new_package_modal">
-    <span class="glyphicon glyphicon-plus"></span> New Package</a
+        <span class="glyphicon glyphicon-plus"></span> New Package</a>
-  >
 </li>
 <li>
     <a role="button" data-toggle="modal" data-target="#import_package_modal">
-    <span class="glyphicon glyphicon-import"></span> Import Package from JSON</a
+        <span class="glyphicon glyphicon-import"></span> Import Package from JSON</a>
-  >
 </li>
 <li>
-  <a
+    <a role="button" data-toggle="modal" data-target="#import_legacy_package_modal">
-    role="button"
+        <span class="glyphicon glyphicon-import"></span> Import Package from legacy JSON</a>
-    data-toggle="modal"
-    data-target="#import_legacy_package_modal"
-  >
-    <span class="glyphicon glyphicon-import"></span> Import Package from legacy
-    JSON</a
-  >
 </li>

templates/actions/collections/pathway.html

@@ -1,9 +1,6 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#predict_modal">
-      href="{% if meta.current_package %}{{ meta.current_package.url }}/predict{% else %}{{ meta.server_url }}/predict{% endif %}"
+            <span class="glyphicon glyphicon-plus"></span> New Pathway</a>
-    >
-      <span class="glyphicon glyphicon-plus"></span> New Pathway</a
-    >
     </li>
 {% endif %}

templates/actions/collections/reaction.html

@@ -1,7 +1,6 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#new_reaction_modal">
-      <span class="glyphicon glyphicon-plus"></span> New Reaction</a
+            <span class="glyphicon glyphicon-plus"></span> New Reaction</a>
-    >
     </li>
 {% endif %}

templates/actions/collections/rule.html

@@ -1,7 +1,6 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#new_rule_modal">
-      <span class="glyphicon glyphicon-plus"></span> New Rule</a
+            <span class="glyphicon glyphicon-plus"></span> New Rule</a>
-    >
     </li>
 {% endif %}

templates/actions/collections/scenario.html

@@ -1,7 +1,6 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#new_scenario_modal">
-      <span class="glyphicon glyphicon-plus"></span> New Scenario</a
+            <span class="glyphicon glyphicon-plus"></span> New Scenario</a>
-    >
     </li>
 {% endif %}

templates/actions/collections/setting.html

@@ -1,7 +1,6 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#new_setting_modal">
-      <span class="glyphicon glyphicon-plus"></span>New Setting</a
+            <span class="glyphicon glyphicon-plus"></span>New Setting</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/compound.html

@@ -1,43 +1,32 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#edit_compound_modal">
-      <i class="glyphicon glyphicon-edit"></i> Edit Compound</a
+            <i class="glyphicon glyphicon-edit"></i> Edit Compound</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#add_structure_modal">
-      <i class="glyphicon glyphicon-plus"></i> Add Structure</a
+            <i class="glyphicon glyphicon-plus"></i> Add Structure</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
-      data-toggle="modal"
-      data-target="#generic_set_external_reference_modal"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set External Reference</a
-    >
     </li>
 {% endif %}
     <li>
         <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
-    <i class="glyphicon glyphicon-duplicate"></i> Copy</a
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
-  >
     </li>
 {% if meta.can_edit %}
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/compound_structure.html

@@ -1,35 +1,22 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_compound_structure_modal">
-      role="button"
+            <i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a>
-      data-toggle="modal"
-      data-target="#edit_compound_structure_modal"
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
-      data-toggle="modal"
-      data-target="#generic_set_external_reference_modal"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set External Reference</a
-    >
     </li>
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/edge.html

@@ -1,17 +1,14 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-    >
     </li>
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Edge</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Edge</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/group.html

@@ -1,12 +1,10 @@
 {% if meta.can_edit %}
     <li>
     <a role="button" data-toggle="modal" data-target="#edit_group_member_modal">
-      <i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a
+            <i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Group</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Group</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/model.html

@@ -1,22 +1,18 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#edit_model_modal">
-      <i class="glyphicon glyphicon-edit"></i> Edit Model</a
+            <i class="glyphicon glyphicon-edit"></i> Edit Model</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#evaluate_model_modal">
-      <i class="glyphicon glyphicon-ok"></i> Evaluate Model</a
+            <i class="glyphicon glyphicon-ok"></i> Evaluate Model</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#retrain_model_modal">
-      <i class="glyphicon glyphicon-repeat"></i> Retrain Model</a
+            <i class="glyphicon glyphicon-repeat"></i> Retrain Model</a>
-    >
     </li>
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Model</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Model</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/node.html

@@ -1,22 +1,18 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#edit_node_modal">
-      <i class="glyphicon glyphicon-edit"></i> Edit Node</a
+            <i class="glyphicon glyphicon-edit"></i> Edit Node</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-    >
     </li>
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Node</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Node</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/package.html

@@ -1,36 +1,26 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#edit_package_modal">
-      <i class="glyphicon glyphicon-edit"></i> Edit Package</a
+            <i class="glyphicon glyphicon-edit"></i> Edit Package</a>
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#edit_package_permissions_modal">
-      role="button"
+            <i class="glyphicon glyphicon-user"></i> Edit Permissions</a>
-      data-toggle="modal"
-      data-target="#edit_package_permissions_modal"
-    >
-      <i class="glyphicon glyphicon-user"></i> Edit Permissions</a
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#publish_package_modal">
-      <i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a
+            <i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#export_package_modal">
-      <i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a
+            <i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_license_modal">
-      <i class="glyphicon glyphicon-duplicate"></i> License</a
+            <i class="glyphicon glyphicon-duplicate"></i> License</a>
-    >
     </li>
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Package</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Package</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/pathway.html

@@ -1,65 +1,43 @@
 {% if meta.can_edit %}
     <li>
         <a class="button" data-toggle="modal" data-target="#add_pathway_node_modal">
-      <i class="glyphicon glyphicon-plus"></i> Add Compound</a
+            <i class="glyphicon glyphicon-plus"></i> Add Compound</a>
-    >
     </li>
     <li>
         <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">
-      <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
+            <i class="glyphicon glyphicon-plus"></i> Add Reaction</a>
-    >
     </li>
     <li role="separator" class="divider"></li>
 {% endif %}
     <li>
         <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
-    <i class="glyphicon glyphicon-duplicate"></i> Copy</a
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
-  >
     </li>
     <li>
-  <a
+        <a class="button" data-toggle="modal" data-target="#download_pathway_csv_modal">
-    class="button"
+            <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a>
-    data-toggle="modal"
-    data-target="#download_pathway_csv_modal"
-  >
-    <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a
-  >
     </li>
     <li>
-  <a
+        <a class="button" data-toggle="modal" data-target="#download_pathway_image_modal">
-    class="button"
+            <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a>
-    data-toggle="modal"
-    data-target="#download_pathway_image_modal"
-  >
-    <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a
-  >
     </li>
 {% if meta.can_edit %}
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#identify_missing_rules_modal">
-      class="button"
+            <i class="glyphicon glyphicon-question-sign"></i> Identify Missing Rules</a>
-      data-toggle="modal"
-      data-target="#identify_missing_rules_modal"
-    >
-      <i class="glyphicon glyphicon-question-sign"></i> Identify Missing
-      Rules</a
-    >
     </li>
     <li role="separator" class="divider"></li>
     <li>
         <a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
-      <i class="glyphicon glyphicon-edit"></i> Edit Pathway</a
+            <i class="glyphicon glyphicon-edit"></i> Edit Pathway</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-    >
     </li>
     {#    <li>#}
     {#        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
@@ -67,26 +45,15 @@
     {#    </li>#}
     <li role="separator" class="divider"></li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#delete_pathway_node_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
-      data-toggle="modal"
-      data-target="#delete_pathway_node_modal"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#delete_pathway_edge_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
-      data-toggle="modal"
-      data-target="#delete_pathway_edge_modal"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
-    >
     </li>
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Pathway</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Pathway</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/reaction.html

@@ -1,38 +1,28 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#edit_reaction_modal">
-      <i class="glyphicon glyphicon-edit"></i> Edit Reaction</a
+            <i class="glyphicon glyphicon-edit"></i> Edit Reaction</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
-      data-toggle="modal"
-      data-target="#generic_set_external_reference_modal"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Set External Reference</a
-    >
     </li>
 {% endif %}
     <li>
         <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
-    <i class="glyphicon glyphicon-duplicate"></i> Copy</a
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
-  >
     </li>
 {% if meta.can_edit %}
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/rule.html

@@ -1,29 +1,24 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#edit_rule_modal">
-      <i class="glyphicon glyphicon-edit"></i> Edit Rule</a
+            <i class="glyphicon glyphicon-edit"></i> Edit Rule</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
+            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
-    >
     </li>
 {% endif %}
     <li>
         <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
-    <i class="glyphicon glyphicon-duplicate"></i> Copy</a
+            <i class="glyphicon glyphicon-duplicate"></i> Copy</a>
-  >
     </li>
 {% if meta.can_edit %}
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Rule</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Rule</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/scenario.html

@@ -1,25 +1,14 @@
 {% if meta.can_edit %}
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#add_additional_information_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Add Additional Information</a>
-      data-toggle="modal"
-      data-target="#add_additional_information_modal"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Add Additional Information</a
-    >
     </li>
     <li>
-    <a
+        <a class="button" data-toggle="modal" data-target="#update_scenario_additional_information_modal">
-      class="button"
+            <i class="glyphicon glyphicon-trash"></i> Set Additional Information</a>
-      data-toggle="modal"
-      data-target="#update_scenario_additional_information_modal"
-    >
-      <i class="glyphicon glyphicon-trash"></i> Set Additional Information</a
-    >
     </li>
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Scenario</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Scenario</a>
-    >
     </li>
 {% endif %}

templates/actions/objects/user.html

@@ -1,22 +1,15 @@
 {% if meta.can_edit %}
     <li>
         <a role="button" data-toggle="modal" data-target="#edit_user_modal">
-      <i class="glyphicon glyphicon-edit"></i> Update</a
+            <i class="glyphicon glyphicon-edit"></i> Update</a>
-    >
     </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#edit_password_modal">
-      <i class="glyphicon glyphicon-lock"></i> Update Password</a
+            <i class="glyphicon glyphicon-lock"></i> Update Password</a>
-    >
     </li>
     <li>
-    <a
+        <a role="button" data-toggle="modal" data-target="#new_prediction_setting_modal">
-      role="button"
+            <i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a>
-      data-toggle="modal"
-      data-target="#new_prediction_setting_modal"
-    >
-      <i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a
-    >
     </li>
 {#    <li>#}
 {#        <a role="button" data-toggle="modal" data-target="#manage_api_token_modal">#}
@@ -24,7 +17,6 @@
 {#    </li>#}
     <li>
         <a role="button" data-toggle="modal" data-target="#generic_delete_modal">
-      <i class="glyphicon glyphicon-trash"></i> Delete Account</a
+            <i class="glyphicon glyphicon-trash"></i> Delete Account</a>
-    >
     </li>
 {% endif %}

templates/admin.html

@@ -1,17 +1,12 @@
 {% extends "framework.html" %}
 {% load static %}
 {% block content %}
-  <div id="searchContent">
+
+<div id=searchContent>
     <form id="admin-form" action="{{ SERVER_BASE }}/admin" method="post">
         <div class="form-group">
             <label for="textarea">Query</label>
-        <textarea
+            <textarea id="textarea" class="form-control" rows="10" placeholder="Paste query here" required>
-          id="textarea"
-          class="form-control"
-          rows="10"
-          placeholder="Paste query here"
-          required
-        >
 PREFIX pps: <http://localhost:8080/vocabulary#>
 SELECT ?name (count(?objId) as ?xcnt)
 WHERE {
@@ -20,29 +15,32 @@ WHERE {
     ?packageId pps:reviewStatus 'reviewed' .
     ?packageId pps:pathway ?objId .
 } GROUP BY ?name
-            </textarea
+            </textarea>
-        >
         </div>
         <button id="submit" type="button" class="btn btn-primary">Submit</button>
     </form>
     <p></p>
 </div>
-  <div id="results"></div>
+<div id="results">
+</div>
 <div id="loading"></div>
+</div>
 <script>
 $(function() {
-      $("#submit").on("click", function () {
+    $('#submit').on('click', function() {
+
         makeLoadingGif("#loading", "{% static '/images/wait.gif' %}");
 
         data = {
-          query: $("#textarea").val(),
+            "query": $("#textarea").val()
-        };
+        }
 
         $.post("{{ SERVER_BASE }}/expire", data, function(result) {
             $("#loading").empty();
             queryResultToTable("results", result);
+        })
     });
-      });
+})
-    });
 </script>
+
 {% endblock content %}

templates/collections/joblog.html

@@ -2,37 +2,30 @@
 {% load static %}
 {% load envipytags %}
 {% block content %}
+
     <div class="panel-group" id="reviewListAccordion">
         <div class="panel panel-default">
-      <div
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-        class="panel-heading"
-        id="headingPanel"
-        style="font-size:2rem;height: 46px"
-      >
                 Jobs
             </div>
             <div class="panel-body">
-        <p>Job Logs Desc</p>
+                <p>
+                    Job Logs Desc
+                </p>
+
             </div>
 
-      <div
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-        class="panel panel-default panel-heading list-group-item"
-        style="background-color:silver"
-      >
                 <h4 class="panel-title">
-          <a
+                    <a id="job-accordion-link" data-toggle="collapse" data-parent="#job-accordion" href="#jobs">
-            id="job-accordion-link"
-            data-toggle="collapse"
-            data-parent="#job-accordion"
-            href="#jobs"
-          >
                         Jobs
                     </a>
                 </h4>
             </div>
-      <div id="jobs" class="panel-collapse in collapse">
+            <div id="jobs"
+                 class="panel-collapse collapse in">
                 <div class="panel-body list-group-item" id="job-content">
-          <table class="table-bordered table-hover table">
+                    <table class="table table-bordered table-hover">
                         <tr style="background-color: rgba(0, 0, 0, 0.08);">
                             <th scope="col">ID</th>
                             <th scope="col">Name</th>
@@ -64,12 +57,10 @@
             </div>
 
             <!-- Unreviewable objects such as User / Group / Setting -->
-      <ul class="list-group">
+            <ul class='list-group'>
                 {% for obj in objects %}
                     {% if object_type == 'user' %}
-            <a class="list-group-item" href="{{ obj.url }}"
+                        <a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
-              >{{ obj.username }}</a
-            >
                     {% else %}
                         <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
                     {% endif %}

templates/collections/objects_list.html

@@ -6,22 +6,14 @@
         <div>
             <div id="load-all-error" style="display: none;">
                 <div class="alert alert-danger" role="alert">
-          <span
+                    <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
-            class="glyphicon glyphicon-exclamation-sign"
-            aria-hidden="true"
-          ></span>
                     <span class="sr-only">Error:</span>
                     Getting objects failed!
                 </div>
             </div>
 
-      <input
+            <input type="text" id="object-search" class="form-control" placeholder="Search by name"
-        type="text"
+                   style="display: none;">
-        id="object-search"
-        class="form-control"
-        placeholder="Search by name"
-        style="display: none;"
-      />
             <p></p>
         </div>
     {% endif %}
@@ -58,11 +50,7 @@
 
 <div class="panel-group" id="reviewListAccordion">
     <div class="panel panel-default">
-      <div
+        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-        class="panel-heading"
-        id="headingPanel"
-        style="font-size:2rem;height: 46px"
-      >
             {% if object_type == 'package' %}
             Packages
             {% elif object_type == 'compound' %}
@@ -90,21 +78,12 @@
             {% elif object_type == 'group' %}
             Groups
             {% endif %}
-        <div
+            <div id="actionsButton"
-          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"
+                 class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
-        >
+                                     aria-haspopup="true" aria-expanded="false"><span
-          <a
+                    class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
-            href="#"
+                    style="padding-right:1em"></span></a>
-            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 %}
                         {% if object_type == 'package' %}
@@ -139,204 +118,93 @@
         <div class="panel-body">
             <!-- Set Text above links -->
             {% if object_type == 'package' %}
-          <p>
+            <p>A package contains pathways, rules, etc. and can reflect specific experimental
-            A package contains pathways, rules, etc. and can reflect specific
+                conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
-            experimental conditions.
+                    more &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/packages"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'compound' %}
-          <p>
+            <p>A compound stores the structure of a molecule and can include meta-information.
-            A compound stores the structure of a molecule and can include
+                <a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
-            meta-information.
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/compounds"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'structure' %}
-          <p>
+            <p>The structures stored in this compound
-            The structures stored in this compound
+                <a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/compounds"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'rule' %}
-          <p>
+            <p>A rule describes a biotransformation reaction template that is defined as SMIRKS.
-            A rule describes a biotransformation reaction template that is
+                <a target="_blank" href="https://wiki.envipath.org/index.php/Rules" role="button">Learn more
-            defined as SMIRKS.
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/Rules"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'reaction' %}
-          <p>
+            <p>A reaction is a specific biotransformation from educt compounds to product compounds.
-            A reaction is a specific biotransformation from educt compounds to
+                <a target="_blank" href="https://wiki.envipath.org/index.php/reactions" role="button">Learn more
-            product compounds.
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/reactions"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'pathway' %}
-          <p>
+            <p>A pathway displays the (predicted) biodegradation of a compound as graph.
-            A pathway displays the (predicted) biodegradation of a compound as
+                <a target="_blank" href="https://wiki.envipath.org/index.php/pathways" role="button">Learn more
-            graph.
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/pathways"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'node' %}
-          <p>
+            <p>Nodes represent the (predicted) compounds in a graph.
-            Nodes represent the (predicted) compounds in a graph.
+                <a target="_blank" href="https://wiki.envipath.org/index.php/nodes" role="button">Learn more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/nodes"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'edge' %}
-          <p>
+            <p>Edges represent the links between Nodes in a graph
-            Edges represent the links between Nodes in a graph
+                <a target="_blank" href="https://wiki.envipath.org/index.php/edges" role="button">Learn more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/edges"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'scenario' %}
-          <p>
+            <p>A scenario contains meta-information that can be attached to other data (compounds, rules, ..).
-            A scenario contains meta-information that can be attached to other
+                <a target="_blank" href="https://wiki.envipath.org/index.php/scenarios" role="button">Learn more
-            data (compounds, rules, ..).
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/scenarios"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'model' %}
-          <p>
+            <p>A model applies machine learning to limit the combinatorial explosion.
-            A model applies machine learning to limit the combinatorial
+                <a target="_blank" href="https://wiki.envipath.org/index.php/relative_reasoning" role="button">Learn
-            explosion.
+                    more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/relative_reasoning"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'setting' %}
-          <p>
+            <p>A setting includes configuration parameters for pathway predictions.
-            A setting includes configuration parameters for pathway predictions.
+                <a target="_blank" href="https://wiki.envipath.org/index.php/settings" role="button">Learn more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/settings"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'user' %}
-          <p>
+            <p>Register now to create own packages and to submit and manage your data.
-            Register now to create own packages and to submit and manage your
+                <a target="_blank" href="https://wiki.envipath.org/index.php/users" role="button">Learn more
-            data.
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/users"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'group' %}
-          <p>
+            <p>Users can team up in groups to share packages.
-            Users can team up in groups to share packages.
+                <a target="_blank" href="https://wiki.envipath.org/index.php/groups" role="button">Learn more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/groups"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% endif %}
 
             <!-- If theres nothing to show extend the text above -->
             {% if reviewed_objects and unreviewed_objects %}
             {% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %}
-            <p>
+            <p>Nothing found. There are two possible reasons: <br><br>1. There is no content yet.<br>2. You have no
-              Nothing found. There are two possible reasons: <br /><br />1.
+                reading permissions.<br><br>Please be sure you have at least reading permissions.</p>
-              There is no content yet.<br />2. You have no reading
-              permissions.<br /><br />Please be sure you have at least reading
-              permissions.
-            </p>
             {% endif %}
             {% endif %}
         </div>
         {% if reviewed_objects %}
         {% if reviewed_objects|length > 0 %}
-          <div
+        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            class="panel panel-default panel-heading list-group-item"
-            style="background-color:silver"
-          >
             <h4 class="panel-title">
-              <a
+                <a id="ReviewedLink" data-toggle="collapse" data-parent="#reviewListAccordion"
-                id="ReviewedLink"
+                   href="#Reviewed">Reviewed</a>
-                data-toggle="collapse"
-                data-parent="#reviewListAccordion"
-                href="#Reviewed"
-                >Reviewed</a
-              >
             </h4>
         </div>
-          <div id="Reviewed" class="panel-collapse in collapse">
+        <div id="Reviewed" class="panel-collapse collapse in">
             <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 }}"
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}
-                    >{{ obj.name|safe }}
+                    <span class="glyphicon glyphicon-star" aria-hidden="true"
-                    <span
+                          style="float:right" data-toggle="tooltip"
-                      class="glyphicon glyphicon-star"
+                          data-placement="top" title="" data-original-title="Reviewed">
-                      aria-hidden="true"
-                      style="float:right"
-                      data-toggle="tooltip"
-                      data-placement="top"
-                      title=""
-                      data-original-title="Reviewed"
-                    >
                         </span>
                 </a>
                 {% endfor %}
                 {% else %}
                 {% for obj in reviewed_objects|slice:":50" %}
-                  <a class="list-group-item" href="{{ obj.url }}"
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}{# <i>({{ obj.package.name }})</i> #}
-                    >{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
+                    <span class="glyphicon glyphicon-star" aria-hidden="true"
-                    <span
+                          style="float:right" data-toggle="tooltip"
-                      class="glyphicon glyphicon-star"
+                          data-placement="top" title="" data-original-title="Reviewed">
-                      aria-hidden="true"
-                      style="float:right"
-                      data-toggle="tooltip"
-                      data-placement="top"
-                      title=""
-                      data-original-title="Reviewed"
-                    >
                         </span>
                 </a>
                 {% endfor %}
@@ -346,36 +214,18 @@
         {% endif %}
         {% endif %}
         {% if unreviewed_objects %}
-        <div
+        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver"><h4
-          class="panel panel-default panel-heading list-group-item"
+                class="panel-title"><a id="UnreviewedLink" data-toggle="collapse" data-parent="#unReviewListAccordion"
-          style="background-color:silver"
+                                       href="#Unreviewed">Unreviewed</a></h4></div>
-        >
+        <div id="Unreviewed" class="panel-collapse collapse {% if reviewed_objects|length == 0 or object_type == 'package' %}in{% endif %}">
-          <h4 class="panel-title">
-            <a
-              id="UnreviewedLink"
-              data-toggle="collapse"
-              data-parent="#unReviewListAccordion"
-              href="#Unreviewed"
-              >Unreviewed</a
-            >
-          </h4>
-        </div>
-        <div
-          id="Unreviewed"
-          class="panel-collapse {% if reviewed_objects|length == 0 or object_type == 'package' %}in{% endif %} collapse"
-        >
             <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 }}"
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
-                  >{{ obj.name|safe }}</a
-                >
                 {% endfor %}
                 {% else %}
                 {% for obj in unreviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}"
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
-                  >{{ obj.name|safe }}</a
-                >
                 {% endfor %}
                 {% endif %}
             </div>
@@ -383,16 +233,12 @@
         {% endif %}
         {% if objects %}
         <!-- Unreviewable objects such as User / Group / Setting -->
-        <ul class="list-group">
+        <ul class='list-group'>
             {% for obj in objects %}
             {% if object_type == 'user' %}
-              <a class="list-group-item" href="{{ obj.url }}"
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
-                >{{ obj.username|safe }}</a
-              >
             {% else %}
-              <a class="list-group-item" href="{{ obj.url }}"
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
-                >{{ obj.name|safe }}</a
-              >
             {% endif %}
             {% endfor %}
         </ul>
@@ -415,14 +261,10 @@
     </style>
 
     <div id="load-all-loading" class="spinner-widget" style="display: none">
-      <img
+        <img id="loading-gif" src="{% static '/images/wait.gif' %}" alt="Loading...">
-        id="loading-gif"
-        src="{% static '/images/wait.gif' %}"
-        alt="Loading..."
-      />
     </div>
+
 </div>
-  {# prettier-ignore-start #}
     <script>
         $(function () {
 
@@ -474,5 +316,4 @@
 
         });
     </script>
-    {# prettier-ignore-end #}
 {% endblock content %}

templates/compare.html

@@ -4,32 +4,16 @@
     <div>
         <form action="" method="post">
             {% csrf_token %}
-      <input
+            <input type="text" class="form-control" id="smiles" name="smiles" placeholder="SMILES"
-        type="text"
+                   value="{{ smiles }}"/>
-        class="form-control"
+            <input type="text" class="form-control" id="smiles" name="smirks" placeholder="SMIRKS"
-        id="smiles"
+                   value="{{ smirks }}"/>
-        name="smiles"
-        placeholder="SMILES"
-        value="{{ smiles }}"
-      />
-      <input
-        type="text"
-        class="form-control"
-        id="smiles"
-        name="smirks"
-        placeholder="SMIRKS"
-        value="{{ smirks }}"
-      />
             <button type="submit" class="btn btn-primary">Test</button>
         </form>
     </div>
     {% if result %}
-    {{ smiles }}
+        {{ smiles }}<p></p>
-    <p></p>
+        <img width='400' src='{% url 'depict' %}?smiles={{ smiles|urlencode }}'><br>
-    <img
-      width="400"
-      src="{% url 'depict' %}?smiles={{ smiles|urlencode }}"
-    /><br />
         <p></p>
         {% if rule %}
             {{ smirks }}
@@ -38,7 +22,9 @@
             <p></p>
             {{ rule.products_smarts }}
             <p></p>
-      <div>{{ rule.as_svg|safe }}</div>
+            <div>
+                {{ rule.as_svg|safe }}
+            </div>
         {% endif %}
         <h2>Diff</h2>
         {% if diff %}
@@ -52,22 +38,16 @@
             <div class="col-md-6">
                 <h2>Ambit</h2>
                 {% for p in ambit_res %}
-          {{ p }}<br />
+                    {{ p }}<br>
-          <img
+                    <img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
-            width="400"
-            src="{% url 'depict' %}?smiles={{ p|urlencode }}"
-          /><br />
                 {% endfor %}
             </div>
 
             <div class="col-md-6">
                 <h2>RDKit</h2>
                 {% for p in rdkit_res %}
-          {{ p }}<br />
+                    {{ p }}<br>
-          <img
+                    <img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
-            width="400"
-            src="{% url 'depict' %}?smiles={{ p|urlencode }}"
-          /><br />
                 {% endfor %}
             </div>
         </div>

templates/errors/400_bad_request.html

@@ -1,18 +1,15 @@
 {% extends "framework.html" %}
 {% load static %}
 {% block content %}
+
 <div class="alert alert-error" role="alert">
     <h4 class="alert-heading">Bad Request!</h4>
     <p>Lorem</p>
-    <hr />
+    <hr>
     <p class="mb-0">
-      You can find out more about permissions in our
+        You can find out more about permissions in our <a target="_blank"
-      <a
-        target="_blank"
                                                           href="https://wiki.envipath.org/index.php/packages"
-        role="button"
+                                                          role="button">Wiki &gt;&gt;</a></p>
-        >Wiki &gt;&gt;</a
-      >
-    </p>
 </div>
+
 {% endblock content %}

templates/errors/403_access_denied.html

@@ -1,18 +1,15 @@
 {% extends "framework.html" %}
 {% load static %}
 {% block content %}
+
 <div class="alert alert-error" role="alert">
     <h4 class="alert-heading">Access Denied!</h4>
     <p>Access to X denied. </p>
-    <hr />
+    <hr>
     <p class="mb-0">
-      You can find out more about permissions in our
+        You can find out more about permissions in our <a target="_blank"
-      <a
-        target="_blank"
                                                           href="https://wiki.envipath.org/index.php/packages"
-        role="button"
+                                                          role="button">Wiki &gt;&gt;</a></p>
-        >Wiki &gt;&gt;</a
-      >
-    </p>
 </div>
+
 {% endblock content %}

templates/errors/404_not_found.html

@@ -1,18 +1,15 @@
 {% extends "framework.html" %}
 {% load static %}
 {% block content %}
+
 <div class="alert alert-error" role="alert">
     <h4 class="alert-heading">Not Found!</h4>
     <p>Does not exist</p>
-    <hr />
+    <hr>
     <p class="mb-0">
-      You can find out more about permissions in our
+        You can find out more about permissions in our <a target="_blank"
-      <a
-        target="_blank"
                                                           href="https://wiki.envipath.org/index.php/packages"
-        role="button"
+                                                          role="button">Wiki &gt;&gt;</a></p>
-        >Wiki &gt;&gt;</a
-      >
-    </p>
 </div>
+
 {% endblock content %}

templates/errors/error.html

@@ -1,9 +1,13 @@
 {% extends "framework.html" %}
 {% load static %}
 {% block content %}
+
     <div class="alert alert-danger" role="alert">
         <h4 class="alert-heading">{{ error_message }}</h4>
-    <hr />
+        <hr>
-    <p class="mb-0">{{ error_detail }}</p>
+        <p class="mb-0">
+            {{ error_detail }}
+        </p>
     </div>
+
 {% endblock content %}

templates/errors/user_account_inactive.html

@@ -1,11 +1,12 @@
 {% extends "framework.html" %}
 {% load static %}
 {% block content %}
+
     <div class="alert alert-danger" role="alert">
         <h4 class="alert-heading">Your account has not been activated yet!</h4>
-    <p>
+        <p>Your account has not been activated yet. If you have questions <a href="mailto:admin@envipath.org">contact
-      Your account has not been activated yet. If you have questions
+            us.</a>
-      <a href="mailto:admin@envipath.org">contact us.</a>
         </p>
     </div>
+
 {% endblock content %}

templates/framework.html

@@ -1,52 +1,28 @@
-<!doctype html>
+<!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 #}
-    <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>
-    <script src="https://ajax.aspnetcdn.com/ajax/jquery.templates/beta1/jquery.tmpl.js"></script>
-    <link
-      href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css"
-      rel="stylesheet"
-    />
-    <link
-      rel="stylesheet"
-      href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.css"
-    />
-    <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 {
-      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>
+    <script src="https://ajax.aspnetcdn.com/ajax/jquery.templates/beta1/jquery.tmpl.js"></script>
+    <link href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
+    <link rel="stylesheet"
+          href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.css">
+    <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 -->
+    <meta name="csrf-token" content="{{ csrf_token }}">
     <script>
-      const csrftoken = document.querySelector("[name=csrf-token]").content;
+        const csrftoken = document.querySelector('[name=csrf-token]').content;
 
         // Setup CSRF header for all jQuery AJAX requests
         $.ajaxSetup({
@@ -54,15 +30,17 @@
                 if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
                     xhr.setRequestHeader("X-CSRFToken", csrftoken);
                 }
-        },
+            }
         });
     </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 #}-->
     <!--    <link id="css-pps_white_general" href="{% static 'css/epp.css' %}" rel="stylesheet" type="text/css"/>-->
 
+
     {# General EP JS #}
     <script src="{% static 'js/pps.js' %}"></script>
     {# Modal Steps for Stepwise Modal Wizards #}
@@ -71,33 +49,26 @@
     {% if not debug %}
         <!-- Matomo -->
         <script>
-        var _paq = (window._paq = window._paq || []);
+            var _paq = window._paq = window._paq || [];
             /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
-        _paq.push(["trackPageView"]);
+            _paq.push(['trackPageView']);
-        _paq.push(["enableLinkTracking"]);
+            _paq.push(['enableLinkTracking']);
             (function () {
                 var u = "//matomo.envipath.com/";
-          _paq.push(["setTrackerUrl", u + "matomo.php"]);
+                _paq.push(['setTrackerUrl', u + 'matomo.php']);
-          _paq.push(["setSiteId", "{{ meta.site_id }}"]);
+                _paq.push(['setSiteId', '10']);
-          var d = document,
+                var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
-            g = d.createElement("script"),
-            s = d.getElementsByTagName("script")[0];
                 g.async = true;
-          g.src = u + "matomo.js";
+                g.src = u + 'matomo.js';
                 s.parentNode.insertBefore(g, s);
             })();
         </script>
         <!-- End Matomo Code -->
     {% endif %}
+
 </head>
 <body>
-    <!-- Legacy Bootstrap navbar - isolated from Tailwind -->
+<nav class="navbar navbar-default navbar-inverse" style="border-radius:0px;" role="navigation">
-    <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 -->
         <div class="navbar-header navbar-header-framework">
@@ -108,28 +79,19 @@
             <!--                <span class="icon-bar"></span>-->
             <!--                <span class="icon-bar"></span>-->
             <!--            </button>-->
-            <a
+            <a id="pictureLink" href="{{ meta.server_url }}" class="navbar-brand">
-              id="pictureLink"
+                <img id="image-logo-short-white.svg" src='{% static "/images/logo-short-white.svg" %}' width="100"
-              href="{{ meta.server_url }}"
+                     alt="enviPath">
-              class="navbar-brand"
-            >
-              <img
-                id="image-logo-short-white.svg"
-                src="{% static "/images/logo-short-white.svg" %}"
-                width="100"
-                alt="enviPath"
-              />
             </a>
         </div>
 
         <!-- Collect the nav links, forms, and other content for toggling -->
-          <div
+        <div class="collapse navbar-collapse collapse-framework navbar-collapse-framework" id="navbarCollapse">
-            class="navbar-collapse collapse-framework navbar-collapse-framework collapse"
-            id="navbarCollapse"
-          >
             <ul class="nav navbar-nav navbar-nav-framework">
                 <li>
-                <a href="{{ meta.server_url }}/predict"> Predict Pathway </a>
+                    <a href="#" data-toggle="modal" data-target="#predict_modal">
+                        Predict Pathway
+                    </a>
                 </li>
 {#                <li class="dropdown">#}
 {#                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
@@ -146,148 +108,67 @@
 {#                        </li>#}
 {#                    </ul>#}
 {#                </li>#}
-              <li>
+                <li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li>
-                <a href="{{ meta.server_url }}/package" id="packageLink"
+                <li><a href="{{ meta.server_url }}/search" id="searchLink">Search</a></li>
-                  >Package</a
+                <li><a href="{{ meta.server_url }}/model" id="modelLink">Modelling</a></li>
-                >
-              </li>
-              <li>
-                <a href="{{ meta.server_url }}/search" id="searchLink"
-                  >Search</a
-                >
-              </li>
-              <li>
-                <a href="{{ meta.server_url }}/model" id="modelLink"
-                  >Modelling</a
-                >
-              </li>
                 <li class="dropdown">
-                <a data-toggle="dropdown" class="dropdown-toggle" href="#"
+                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Browse Data<b class="caret"></b></a>
-                  >Browse Data<b class="caret"></b
-                ></a>
                     <ul role="menu" class="dropdown-menu">
-                  <li>
+                        <li><a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a></li>
-                    <a href="{{ meta.server_url }}/pathway" id="pathwayLink"
+                        <li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
-                      >Pathway</a
+                        <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>
+                        <li><a href="{{ meta.server_url }}/model" id="relative-reasoningLink">Model</a></li>
-                  <li>
+                        <li><a href="{{ meta.server_url }}/scenario" id="scenarioLink">Scenario</a></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>
                         {#                        <li><a href="{{ meta.server_url }}/setting" id="settingLink">Setting</a></li>#}
                         {#                        <li><a href="{{ meta.server_url }}/user" id="userLink">User</a></li>#}
                         {#                        <li><a href="{{ meta.server_url }}/group" id="groupLink">Group</a></li>#}
                     </ul>
                 </li>
+
             </ul>
 
-            <ul
+            <ul class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework">
-              class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework"
+                <li><a href="https://community.envipath.org/" id="communityLink">Community</a></li>
-            >
-              <li>
-                <a href="https://community.envipath.org/" id="communityLink"
-                  >Community</a
-                >
-              </li>
                 <li class="dropdown">
-                <a data-toggle="dropdown" class="dropdown-toggle" href="#"
+                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Info <b class="caret"></b></a>
-                  >Info <b class="caret"></b
-                ></a>
                     <ul role="menu" class="dropdown-menu">
                         <!--<li><a href="{{ meta.server_url }}/funding" id="fundingLink">Funding</a></li>-->
-                  <li>
+                        <li><a href="https://community.envipath.org/t/envipath-license/109" id="licenceLink">Licences</a></li>
-                    <a
-                      href="https://community.envipath.org/t/envipath-license/109"
-                      id="licenceLink"
-                      >Licences</a
-                    >
-                  </li>
                         <li class="divider"></li>
-                  <li>
+                        <li><a target="_blank" href="https://wiki.envipath.org/" id="wikiLink">Documentation Wiki</a>
-                    <a
-                      target="_blank"
-                      href="https://wiki.envipath.org/"
-                      id="wikiLink"
-                      >Documentation Wiki</a
-                    >
-                  </li>
-                  <li>
-                    <a
-                      href="#"
-                      id="citeButton"
-                      data-toggle="modal"
-                      data-target="#citemodal"
-                      >How to cite enviPath</a
-                    >
                         </li>
+                        <li><a href="#" id="citeButton" data-toggle="modal" data-target="#citemodal">How to cite
+                            enviPath</a></li>
                         <li class="divider"></li>
                         <li><a>Version: {{ meta.version }}</a></li>
                     </ul>
                 </li>
                 {% if meta.user.username == 'anonymous' %}
                     <li>
-                  <a
+                        <a href="#signup" id="loginButton" data-toggle="modal" data-target="#signupmodal"
-                    href="{% url 'login' %}"
+                           style="margin-right:10px">Login</a>
-                    id="loginButton"
-                    style="margin-right:10px"
-                    >Login</a
-                  >
                     </li>
                 {% else %}
                     <li class="dropdown">
-                  <a
+                        <a data-toggle="dropdown" id="loggedInButton" class="dropdown-toggle" id="logedInButton"
-                    data-toggle="dropdown"
+                           href="#">
-                    id="loggedInButton"
-                    class="dropdown-toggle"
-                    id="logedInButton"
-                    href="#"
-                  >
                             <div id="username">
                                 {{ user.username }}<b class="caret"></b>
                             </div>
                         </a>
                         <ul role="menu" class="dropdown-menu">
                             <li>
-                      <a href="{{ meta.user.url }}" id="accountbutton"
+                                <a href="{{ meta.user.url }}" id="accountbutton">My Account</a>
-                        >My Account</a
-                      >
                             </li>
                             <li class="divider"></li>
-                    <form
+                            <form class="navbar-form navbar-left navbar-left-framework" role="logout"
-                      class="navbar-form navbar-left navbar-left-framework"
+                                  action="{% url 'logout' %}" method="post">
-                      role="logout"
-                      action="{% url 'logout' %}"
-                      method="post"
-                    >
                                 {% csrf_token %}
                                 <div class="form-group">
-                        <input type="hidden" name="logout" value="true" />
+                                    <input type="hidden" name="logout" value="true">
                                 </div>
-                      <button type="submit" class="btn btn-default">
+                                <button type="submit" class="btn btn-default">Logout</button>
-                        Logout
-                      </button>
                             </form>
                         </ul>
                     </li>
@@ -296,9 +177,6 @@
         </div>
     </div>
 </nav>
-    </div>
-    <!-- End legacy Bootstrap navbar -->
-
 <div id="docContent" class="content container">
     {% if breadcrumbs %}
         <div id="bread">
@@ -318,30 +196,24 @@
         </div>
     {% endif %}
     {% if message %}
-        <div id="message">{{ message }}</div>
+        <div id="message">
+            {{ message }}
+        </div>
     {% endif %}
     {% block content %}
     {% endblock content %}
     {% if meta.url_contains_package and meta.current_package.license %}
         <p></p>
         <div class="panel-group" id="license_accordion">
-          <div
+            <div class="panel panel-default list-group-item" style="background-color:#f5f5f5">
-            class="panel panel-default list-group-item"
-            style="background-color:#f5f5f5"
-          >
                 <div class="panel-title">
-              <a
+                    <a data-toggle="collapse" data-parent="#licence_accordion" href="#license">License</a>
-                data-toggle="collapse"
-                data-parent="#licence_accordion"
-                href="#license"
-                >License</a
-              >
                 </div>
             </div>
-          <div id="license" class="panel-collapse in collapse">
+            <div id="license" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     <a target="_blank" href="{{ meta.current_package.license.link }}">
-                <img src="{{ meta.current_package.license.image_link }}" />
+                        <img src="{{ meta.current_package.license.image_link }}">
                     </a>
                 </div>
             </div>
@@ -349,8 +221,7 @@
     {% endif %}
 </div>
 
-    <!-- FOOTER - Legacy Bootstrap -->
+<!-- FOOTER -->
-    <div class="legacy-bootstrap">
 <div class="container text-center">
     <hr/>
     <div class="row">
@@ -358,32 +229,19 @@
             <ul class="nav nav-pills nav-justified">
                 <li>
                     <a href="http://ml.auckland.ac.nz" target="_blank">
-                  <img
+                        <img id="image-uoalogo" height="60" src='{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}'
-                    id="image-uoalogo"
+                             alt="The Univserity of Auckland"/>
-                    height="60"
-                    src="{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}"
-                    alt="The Univserity of Auckland"
-                  />
                     </a>
                 </li>
                 <li>
                     <a href="https://eawag.ch" target="_blank">
-                  <img
+                        <img id="image-ealogo" height="60" src='{% static "/images/ealogo.gif" %}' alt="Eawag"/>
-                    id="image-ealogo"
-                    height="60"
-                    src="{% static "/images/ealogo.gif" %}"
-                    alt="Eawag"
-                  />
                     </a>
                 </li>
                 <li>
                     <a href="https://www.uzh.ch/" target="_blank">
-                  <img
+                        <img id="image-ufzlogo" height="60" src='{% static "/images/uzh-logo.svg" %}'
-                    id="image-ufzlogo"
+                             alt="University of Zurich"/>
-                    height="60"
-                    src="{% static "/images/uzh-logo.svg" %}"
-                    alt="University of Zurich"
-                  />
                     </a>
                 </li>
             </ul>
@@ -394,27 +252,23 @@
     <div class="col-lg-12">
         <ul class="nav nav-pills nav-justified">
             <!--            <li><a href="https://envipath.com/imprint/" target="_blank">Impressum/Imprint</a></li>-->
-            <li>
+            <li><a href="mailto:admin@envipath.org" target="_blank">Contact</a></li>
-              <a href="mailto:admin@envipath.org" target="_blank">Contact</a>
-            </li>
             <!--            <li><a href="http://envipath.com" target="_blank"> enviPath UG (haftungsbeschr&auml;nkt) &amp; Co. KG &copy;-->
             <!--                {{ YEAR }}</a></li>-->
         </ul>
     </div>
 </div>
-    </div>
-    <!-- End legacy Bootstrap footer -->
-
 <script>
     $(function () {
         // Hide actionsbutton if theres no action defined
-        if ($("#actionsButton ul").children().length > 0) {
+        if ($('#actionsButton ul').children().length > 0) {
-          $("#actionsButton").show();
+            $('#actionsButton').show();
         }
     });
 </script>
 {% block modals %}
     {% include "modals/cite_modal.html" %}
+    {% include "modals/signup_modal.html" %}
     {% include "modals/predict_modal.html" %}
     {% include "modals/batch_predict_modal.html" %}
 {% endblock %}

templates/framework_modern.html

@@ -1,223 +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="bg-base-300 min-h-screen">
-    {% 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="mx-auto max-w-7xl px-4 py-4">
-            <div class="breadcrumbs text-sm">
-              <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="bg-base-100 mx-auto md:my-8 md:max-w-6xl md:rounded-lg md:shadow-xl"
-        >
-          {# 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-arrow bg-base-200 collapse p-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 top-1/2 right-0 z-50 -translate-y-1/2">
-        <a
-          href="https://community.envipath.org/"
-          target="_blank"
-          class="btn btn-secondary hover:btn-secondary-focus text-secondary-content flex items-center justify-center text-sm shadow-lg transition-all duration-300 hover:-translate-x-1 hover:scale-105"
-          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 %}
-
-    {% block modals %}
-      {% include "modals/search_modal.html" %}
-    {% endblock %}
-
-    <script>
-      $(function () {
-        // Hide actionsbutton if there's no action defined
-        if ($("#actionsButton ul").children().length > 0) {
-          $("#actionsButton").show();
-        }
-      });
-
-      // Open search modal function
-      function openSearchModal() {
-        const searchModal = document.getElementById("search_modal");
-        if (searchModal) {
-          searchModal.showModal();
-        }
-      }
-
-      // Click handler for search badge
-      const searchTrigger = document.getElementById("search-trigger");
-      if (searchTrigger) {
-        searchTrigger.addEventListener("click", function (event) {
-          event.preventDefault();
-          openSearchModal();
-        });
-      }
-
-      // 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();
-          openSearchModal();
-        }
-      });
-    </script>
-  </body>
-</html>

templates/includes/footer.html

@@ -1,94 +0,0 @@
-{% load static %}
-<div class="bg-base-300 text-base-content mx-auto mt-10 lg:max-w-5xl">
-  <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">Predict</a>
-        <a class="link link-hover" href="/package">Packages</a>
-        {% if user.is_authenticated %}
-          <a class="link link-hover" href="/model">Your Collections</a>
-        {% endif %}
-        <a
-          href="https://wiki.envipath.org/"
-          target="_blank"
-          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-t-2 border-neutral-300 px-10 py-4">
-    <div class="flex w-full flex-row items-start justify-between">
-      <aside class="grid-flow-col items-center">
-        <svg
-          class="fill-neutral-content m-2 h-14 flex-shrink-0"
-          viewbox="0 0 65 65"
-        >
-          <use
-            href="{% static "/images/logo-square.svg" %}#ep-logo-square"
-          ></use>
-        </svg>
-
-        enviPath Ltd.
-        <br />
-        Biodegredation prediction since 2015.
-      </aside>
-      <aside class="text-base-200 mt-2 text-sm">
-        <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="h-6 w-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="h-6 w-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="h-6 w-6"
-          />
-        </a>
-      </div>
-    </nav>
-  </footer>
-</div>

templates/includes/navbar.html

@@ -1,150 +0,0 @@
-{% load static %}
-{# Modern DaisyUI Navbar #}
-<div class="navbar x-50 bg-neutral-50 text-neutral-950 shadow-lg">
-  <div class="navbar-start">
-    <a href="{{ meta.server_url }}" class="btn btn-ghost text-xl normal-case">
-      <svg class="fill-base-content h-8" 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="{{ meta.server_url }}/predict"
-        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 }}/package" id="packageLink">Package</a>
-          </li>
-          <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 id="search-trigger" role="button" class="cursor-pointer">
-        <div
-          class="badge badge-dash bg-base-200 text-base-content/50 m-1 flex items-center space-x-1 p-2"
-        >
-          <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 btn-circle m-1"
-          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

@@ -1,453 +1,186 @@
-{% extends "framework_modern.html" %}
+{% extends "framework.html" %}
 {% load static %}
-{% block main_content %}
+{% block content %}
-  <!-- Hero Section with Logo and Search -->
+    <!-- TODO rename ids as well as remove pathways if modal is closed!-->
-  <section class="hero relative mx-auto h-fit w-full max-w-5xl shadow-none">
+    <div class="modal fade" tabindex="-1" id="foundMatching" role="dialog" aria-labelledby="foundModal"
-    <div
+         aria-hidden="true">
-      class="hero from-primary-800 to-primary-600 min-h-[calc(100vh*0.4)] bg-gradient-to-br"
+        <div class="modal-dialog">
-      style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
+            <div class="modal-content">
-    >
+                <div class="modal-header">
-      <div class="hero-overlay"></div>
+                    <button type="button" class="close" data-dismiss="modal">
-      <!-- Predict Pathway text over the image -->
+                        <span aria-hidden="true">&times;</span>
-      <div class="absolute bottom-40 left-1/8 z-10 -translate-x-8">
+                        <span class="sr-only">Close</span>
-        <h2 class="text-base-100 text-left text-3xl text-shadow-lg">
-          Predict Your Pathway
-        </h2>
-      </div>
-    </div>
-  </section>
-
-  <div class="bg-base-200 mx-auto max-w-5xl shadow-md">
-    <!-- Predict Pathway Section -->
-    <div
-      class="relative z-20 mx-auto -mt-32 mb-10 w-full flex-col lg:flex-row-reverse"
-    >
-      <div
-        class="card bg-base-100 mx-auto w-3/4 shrink-0 shadow-xl transition-all duration-300 ease-in-out"
-      >
-        <div class="card-body">
-          <div class="my-4 ml-8 flex h-fit flex-row items-center justify-start">
-            <div class="flex items-center gap-1">
-              <label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
-                <input type="checkbox" />
-                <span class="swap-on flex items-center gap-1">
-                  <div
-                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
-                  >
-                    <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>
-                  </div>
-                  <span class="ext-xs">SMILES</span>
-                </span>
-                <span class="swap-off flex items-center gap-1">
-                  <div
-                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
-                  >
-                    <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>
-                  </div>
-                  <span class="text-base/50 text-xs">Draw</span>
-                </span>
-              </label>
-            </div>
-          </div>
-
-          <fieldset
-            class="fieldset overflow-hidden transition-all duration-300 ease-in-out"
-          >
-            <form
-              id="index-form"
-              action="{{ meta.current_package.url }}/pathway"
-              method="POST"
-            >
-              {% csrf_token %}
-              <div
-                id="text-input-container"
-                class="scale-100 transform opacity-100 transition-all duration-300 ease-in-out"
-              >
-                <div class="join mx-auto w-full">
-                  <input
-                    type="text"
-                    id="index-form-text-input"
-                    placeholder="canonical SMILES string"
-                    class="input input-md join-item grow"
-                  />
-                  <button class="btn btn-neutral join-item">Predict!</button>
-                </div>
-                <div class="label relative mt-1 w-full">
-                  <div class="flex gap-2">
-                    <a
-                      href="#"
-                      class="example-link hover:text-primary cursor-pointer"
-                      data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
-                      title="load example"
-                      >Caffeine</a
-                    >
-                    <a
-                      href="#"
-                      class="example-link hover:text-primary cursor-pointer"
-                      data-smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
-                      title="load example"
-                      >Ibuprofen</a
-                    >
-                  </div>
-                  <a class="absolute top-0 left-[calc(100%-5.4rem)]" href="#"
-                    >Advanced</a
-                  >
-                </div>
-              </div>
-              <div
-                id="ketcher-container"
-                class="hidden w-full scale-95 transform opacity-0 transition-all duration-300 ease-in-out"
-              >
-                <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 mt-2 w-full"
-                >
-                  Predict!
                     </button>
-                <div class="mt-1 flex w-full justify-end">
+                    <h4 class="modal-title" id="newPackMod">Found Pathway in Database</h4>
-                  <a class="label justify-end" href="/predict">Advanced</a>
                 </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>
-              <input
+                <div class="modal-footer">
-                type="hidden"
+                    <a id="modal-predict" class="btn btn-primary" href="#">Predict</a>
-                id="index-form-smiles"
+                    <button type="button" id="cancel-predict" class="btn btn-default" data-dismiss="modal">Cancel
-                name="smiles"
+                    </button>
-                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="bg-base-200 z-10 mx-8 py-16">
-      <div class="mx-auto max-w-7xl px-4">
-        <h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>
-
-        <div id="community-news-container" class="flex justify-center gap-4">
-          <!-- News cards will be populated here -->
-          <div id="loading" class="flex w-full justify-center">
-            <span class="loading loading-spinner loading-lg"></span>
     </div>
-        </div>
+    <div class="row">
-
+        <div class="col-xs-8">
-        <div class="mt-6 text-right">
+            <div class="jumbotron">
-          <a
+                <h1>
-            href="https://community.envipath.org/c/announcements/10"
+                    <img id="image-logo-long" class="img-responsive" alt="enviPath" width="1000ex"
-            target="_blank"
+                         src='{% static "/images/logo-long.svg" %}'/>
-            class="btn btn-ghost btn-sm"
+                </h1>
-          >
+                <p>enviPath is a database and prediction system for the microbial
-            Read More Announcements
-          </a>
-        </div>
-
-        <!-- Discourse API integration -->
-        <script src="{% static 'js/discourse-api.js' %}"></script>
-      </div>
-    </section>
-
-    <!-- Mission Statement Section -->
-    <section class="from-base-200 to-base-100 bg-gradient-to-b py-16">
-      <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="h-full w-full object-contain"
-            />
-          </div>
-          <div class="mr-8 w-2/3 space-y-4 text-left">
-            <h2 class="h2 mb-8 font-bold">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.
+                    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 class="">
+                <p>
-              The pathway prediction system provides different relative
+                    <a class="btn" style="background-color:#222222;color:#9d9d9d" role="button" target="_blank"
-              reasoning models to predict likely biotransformation pathways and
+                       href="https://wiki.envipath.org/index.php/Main_Page">Learn more &gt;&gt;</a>
-              products. Explore our tools and contribute to advancing
-              environmental biotransformation research.
                 </p>
-            <div class="float-right flex flex-row gap-4">
-              <a href="/about" class="btn btn-ghost-neutral">Read More</a>
-              <a href="/about" class="btn btn-neutral">Publications</a>
-            </div>
-          </div>
-        </div>
-      </div>
-    </section>
-
-    <!-- Partners Section -->
-    <section class="bg-base-100 py-14 sm:py-12">
-      <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>
 
+        </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 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>
+                <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>
+            </div>
+            <input type="hidden" id="index-form-smiles" name="smiles" value="smiles">
+            <input type="hidden" id="index-form-predict" name="predict" value="predict">
+        </form>
+    </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
+            var action = $('#action-button').text().trim();
-    function renderDiscourseTopics(topics) {
-      const container = document.getElementById("community-news-container");
-      if (!container) return;
 
-      // Clear container
+            var textSmiles = $('#index-form-text-input').val().trim();
-      container.innerHTML = "";
 
-      // Create cards for each topic
+            if (textSmiles === '') {
-      topics.forEach((topic) => {
+                $(this).prop("disabled", false);
-        const card = createDiscourseCard(topic);
+                return;
-        container.insertAdjacentHTML("beforeend", card);
-      });
             }
 
-    // Function to create HTML card for a topic
+            var ketcherSmiles = getKetcher('index-form-ketcher').getSmiles().trim();
-    function createDiscourseCard(topic) {
-      const date = new Date(topic.created_at).toLocaleDateString();
 
-      return `
+            if (action !== 'Search' && ketcherSmiles !== '' && textSmiles !== ketcherSmiles) {
-                <div class="card bg-white shadow-xs hover:shadow-lg transition-shadow duration-300 h-64 w-75 flex-shrink-0">
+                console.log("Ketcher and TextInput differ!");
-                    <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>
-            `;
             }
 
-    // Make render function globally available
+            if (action === 'Search') {
-    window.renderDiscourseTopics = renderDiscourseTopics;
+                var par = {};
-
+                par['search'] = textSmiles;
-    // Toggle functionality with smooth animations
+                par['mode'] = 'text';
-    function toggleInputMode() {
+                var queryString = $.param(par, true);
-      const toggle = $('input[type="checkbox"]');
+                window.location.href = "/search?" + queryString;
-      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);
             } else {
-        // SMILES mode - show text input, hide Ketcher
+                $('#index-form-smiles').val(textSmiles);
-        ketcherContainer.addClass("opacity-0 transform scale-95");
+                $('#index-form').submit();
-        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);
-          }
-        }
             }
         }
 
-    // Ketcher integration
+        function actionDropdownClicked() {
-    function indexKetcherToTextInput() {
+            var suffix = ' <span class="caret"></span>';
-      $("#index-form-smiles").val(this.ketcher.getSmiles());
+            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
+            $('#index-form').on("keydown", function (e) {
-      $('input[type="checkbox"]').on("change", toggleInputMode);
+                if (e.key === "Enter") {
+                    e.preventDefault();
+                    goButtonClicked();
+                }
+            });
 
-      // Ketcher iframe load handler
+            // Code that should be executed once DOM is ready goes here
-      $("#index-ketcher").on("load", function () {
+            $('#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) {
+                    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,
+                            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

@@ -3,11 +3,7 @@
 {% block content %}
 <div class="panel-group" id="migration-detail">
     <div class="panel panel-default">
-      <div
+        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-        class="panel-heading"
-        id="headingPanel"
-        style="font-size:2rem;height: 46px"
-      >
             Migration Status BT Rules
         </div>
         <div class="panel-body">
@@ -16,56 +12,33 @@
         </div>
 
         {% for obj in results %}
-        <div
+        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-          class="panel panel-default panel-heading list-group-item"
-          style="background-color:silver"
-        >
             {% if obj.status %}
-            <span
+            <span class="glyphicon glyphicon-ok" aria-hidden="true"
-              class="glyphicon glyphicon-ok"
+                  style="float:right" data-toggle="tooltip"
-              aria-hidden="true"
+                  data-placement="top" title="" data-original-title="Reviewed">
-              style="float:right"
-              data-toggle="tooltip"
-              data-placement="top"
-              title=""
-              data-original-title="Reviewed"
-            >
             </span>
             {% else %}
-            <span
+            <span class="glyphicon glyphicon-remove" aria-hidden="true"
-              class="glyphicon glyphicon-remove"
+                  style="float:right" data-toggle="tooltip"
-              aria-hidden="true"
+                  data-placement="top" title="" data-original-title="Reviewed">
-              style="float:right"
-              data-toggle="tooltip"
-              data-placement="top"
-              title=""
-              data-original-title="Reviewed"
-            >
             </span>
             {% endif %}
             <h4 class="panel-title">
-            <a
+                <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-              id="{{ obj.id }}-link"
+                   href="#{{ obj.id }}">{{ obj.name }}</a>
-              data-toggle="collapse"
-              data-parent="#migration-detail"
-              href="#{{ obj.id }}"
-              >{{ obj.name|safe }}</a
-            >
             </h4>
         </div>
-        <div
+        <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
-          id="{{ obj.id }}"
-          class="panel-collapse {% if not obj.status %}in{% endif %} collapse"
-        >
             <div class="panel-body list-group-item">
-            <a class="list-group-item" href="{{ obj.detail_url }}"
+                <a class="list-group-item" href="{{ obj.detail_url }}">{{ obj.name }} Migration Detail Page</a>
-              >{{ obj.name|safe }} Migration Detail Page</a
-            >
             </div>
         </div>
         {% endfor %}
     </div>
 </div>
 
-  <script></script>
+<script>
+
+</script>
 {% endblock content %}

templates/migration_detail.html

@@ -3,68 +3,34 @@
 {% block content %}
     <div class="panel-group" id="migration-detail">
         <div class="panel panel-default">
-      <div
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-        class="panel-heading"
-        id="headingPanel"
-        style="font-size:2rem;height: 46px"
-      >
                 Migration Status for {{ bt_rule_name }}
             </div>
             <div class="panel-body">
-        <p>
+                <p>A package contains pathways, rules, etc. and can reflect specific experimental
-          A package contains pathways, rules, etc. and can reflect specific
+                    conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
-          experimental conditions.
+                        more &gt;&gt;</a></p>
-          <a
-            target="_blank"
-            href="https://wiki.envipath.org/index.php/packages"
-            role="button"
-            >Learn more &gt;&gt;</a
-          >
-        </p>
             </div>
 
             {% for obj in results %}
-        <div
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-          class="panel panel-default panel-heading list-group-item"
-          style="background-color:silver"
-        >
                     {% if obj.status %}
-            <span
+                        <span class="glyphicon glyphicon-ok" aria-hidden="true"
-              class="glyphicon glyphicon-ok"
+                              style="float:right" data-toggle="tooltip"
-              aria-hidden="true"
+                              data-placement="top" title="" data-original-title="Reviewed">
-              style="float:right"
-              data-toggle="tooltip"
-              data-placement="top"
-              title=""
-              data-original-title="Reviewed"
-            >
                         </span>
                     {% else %}
-            <span
+                        <span class="glyphicon glyphicon-remove" aria-hidden="true"
-              class="glyphicon glyphicon-remove"
+                              style="float:right" data-toggle="tooltip"
-              aria-hidden="true"
+                              data-placement="top" title="" data-original-title="Reviewed">
-              style="float:right"
-              data-toggle="tooltip"
-              data-placement="top"
-              title=""
-              data-original-title="Reviewed"
-            >
                         </span>
                     {% endif %}
                     <h4 class="panel-title">
-            <a
+                        <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-              id="{{ obj.id }}-link"
+                           href="#{{ obj.id }}">{{ obj.name }}</a>
-              data-toggle="collapse"
-              data-parent="#migration-detail"
-              href="#{{ obj.id }}"
-              >{{ obj.name|safe }}</a
-            >
                     </h4>
                 </div>
-        <div
+                <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
-          id="{{ obj.id }}"
-          class="panel-collapse {% if not obj.status %}in{% endif %} collapse"
-        >
                     <div class="panel-body list-group-item">
                         <pre>{{ obj.detail }}</pre>
                     </div>
@@ -73,5 +39,7 @@
         </div>
     </div>
 
-  <script></script>
+    <script>
+
+    </script>
 {% endblock content %}

templates/modals/cite_modal.html

@@ -1,11 +1,5 @@
-<div
+<div class="modal fade bs-modal-lg" id="citemodal" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel"
-  class="modal fade bs-modal-lg"
+     aria-hidden="true">
-  id="citemodal"
-  tabindex="-1"
-  role="dialog"
-  aria-labelledby="myLargeModalLabel"
-  aria-hidden="true"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
@@ -15,33 +9,22 @@
                 <ol class="list-group list-group-numbered">
                     <li class="list-group-item">
                         Hafner, J., Lorsbach, T., Schmidt, S. <em>et al.</em>
-            <cite
+                        <cite>Advancements in biotransformation pathway prediction: enhancements, datasets, and novel
-              >Advancements in biotransformation pathway prediction:
+                            functionalities in enviPath.</cite>
-              enhancements, datasets, and novel functionalities in
+                        <a href="https://doi.org/10.1186/s13321-024-00881-6" target="_blank">J Cheminform 16, 93
-              enviPath.</cite
+                            (2024)</a>
-            >
-            <a href="https://doi.org/10.1186/s13321-024-00881-6" target="_blank"
-              >J Cheminform 16, 93 (2024)</a
-            >
                     </li>
                     <li class="list-group-item">
-            Wicker, J., Lorsbach, T., Gütlein, M., Schmid, E., Latino, D.,
+                        Wicker, J., Lorsbach, T., Gütlein, M., Schmid, E., Latino, D., Kramer, S., Fenner, K.
-            Kramer, S., Fenner, K.
+                        <cite>enviPath - The environmental contaminant biotransformation pathway resource</cite>
-            <cite
-              >enviPath - The environmental contaminant biotransformation
-              pathway resource</cite
-            >
                         <a href="https://doi.org/10.1093/nar/gkv1229" target="_blank">
-              Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages
+                            Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D502-D508
-              D502-D508
                         </a>
                     </li>
                 </ol>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-default" data-dismiss="modal">
+                <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
-          Close
-        </button>
             </div>
         </div>
     </div>

templates/modals/collections/import_legacy_package_modal.html

@@ -1,11 +1,5 @@
-<div
+<div class="modal fade" tabindex="-1" id="import_legacy_package_modal" role="dialog"
-  class="modal fade"
+     aria-labelledby="import_legacy_package_modal" aria-hidden="true">
-  tabindex="-1"
-  id="import_legacy_package_modal"
-  role="dialog"
-  aria-labelledby="import_legacy_package_modal"
-  aria-hidden="true"
->
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
@@ -17,54 +11,32 @@
             </div>
             <div class="modal-body">
                 <p>Create a Package based on the JSON Export of the legacy system.</p>
-        <form
+                <form id="import-legacy-package-modal-form" accept-charset="UTF-8" data-remote="true" method="post"
-          id="import-legacy-package-modal-form"
+                      enctype="multipart/form-data">
-          accept-charset="UTF-8"
-          data-remote="true"
-          method="post"
-          enctype="multipart/form-data"
-        >
                     {% csrf_token %}
                     <p>
                         <label class="btn btn-primary" for="legacyJsonFile">
-              <input
+                            <input id="legacyJsonFile" name="file" type="file" style="display:none;"
-                id="legacyJsonFile"
+                                   onchange="$('#upload-legacy-file-info').html(this.files[0].name)">
-                name="file"
-                type="file"
-                style="display:none;"
-                onchange="$('#upload-legacy-file-info').html(this.files[0].name)"
-              />
                             Choose JSON File
                         </label>
                         <span class="label label-info" id="upload-legacy-file-info"></span>
-            <input
+                        <input type="hidden" value="import-legacy-package-json" name="hidden" readonly="">
-              type="hidden"
-              value="import-legacy-package-json"
-              name="hidden"
-              readonly=""
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <a
+                <a id="import-legacy-package-modal-form-submit" class="btn btn-primary" href="#">Submit</a>
-          id="import-legacy-package-modal-form-submit"
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-          class="btn btn-primary"
-          href="#"
-          >Submit</a
-        >
-        <button type="button" class="btn btn-default" data-dismiss="modal">
-          Cancel
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
     $(function () {
-    $("#import-legacy-package-modal-form-submit").on("click", function (e) {
+        $('#import-legacy-package-modal-form-submit').on('click', function (e) {
             e.preventDefault();
-      $("#import-legacy-package-modal-form").submit();
+            $('#import-legacy-package-modal-form').submit();
         });
     });
 </script>

templates/modals/collections/import_package_modal.html

@@ -1,11 +1,5 @@
-<div
+<div class="modal fade" tabindex="-1" id="import_package_modal" role="dialog"
-  class="modal fade"
+     aria-labelledby="import_package_modal" aria-hidden="true">
-  tabindex="-1"
-  id="import_package_modal"
-  role="dialog"
-  aria-labelledby="import_package_modal"
-  aria-hidden="true"
->
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
@@ -17,54 +11,32 @@
             </div>
             <div class="modal-body">
                 <p>Create a Package based on a JSON Export.</p>
-        <form
+                <form id="import-package-modal-form" accept-charset="UTF-8" data-remote="true" method="post"
-          id="import-package-modal-form"
+                      enctype="multipart/form-data">
-          accept-charset="UTF-8"
-          data-remote="true"
-          method="post"
-          enctype="multipart/form-data"
-        >
                     {% csrf_token %}
                     <p>
                         <label class="btn btn-primary" for="jsonFile">
-              <input
+                            <input id="jsonFile" name="file" type="file" style="display:none;"
-                id="jsonFile"
+                                   onchange="$('#upload-file-info').html(this.files[0].name)">
-                name="file"
-                type="file"
-                style="display:none;"
-                onchange="$('#upload-file-info').html(this.files[0].name)"
-              />
                             Choose JSON File
                         </label>
                         <span class="label label-info" id="upload-file-info"></span>
-            <input
+                        <input type="hidden" value="import-package-json" name="hidden" readonly="">
-              type="hidden"
-              value="import-package-json"
-              name="hidden"
-              readonly=""
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <a
+                <a id="import-package-modal-form-submit" class="btn btn-primary" href="#">Submit</a>
-          id="import-package-modal-form-submit"
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-          class="btn btn-primary"
-          href="#"
-          >Submit</a
-        >
-        <button type="button" class="btn btn-default" data-dismiss="modal">
-          Cancel
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
     $(function () {
-    $("#import-package-modal-form-submit").on("click", function (e) {
+        $('#import-package-modal-form-submit').on('click', function (e) {
             e.preventDefault();
-      $("#import-package-modal-form").submit();
+            $('#import-package-modal-form').submit();
         });
     });
 </script>

templates/modals/collections/new_compound_modal.html

@@ -1,102 +1,57 @@
 {% load static %}
-<div
+<div class="modal fade bs-modal-lg" id="new_compound_modal" tabindex="-1" aria-labelledby="new_compound_modal" aria-modal="true"
-  class="modal fade bs-modal-lg"
+     role="dialog">
-  id="new_compound_modal"
-  tabindex="-1"
-  aria-labelledby="new_compound_modal"
-  aria-modal="true"
-  role="dialog"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">×</span>
                 </button>
                 <h4 class="modal-title">Create a new Compound</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="new_compound_modal_form" accept-charset="UTF-8" action="{% url 'package compound list' meta.current_package.uuid %}" data-remote="true" method="post">
-          id="new_compound_modal_form"
-          accept-charset="UTF-8"
-          action="{% url 'package compound list' meta.current_package.uuid %}"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <label for="compound-name">Name</label>
-          <input
+                    <input id="compound-name" class="form-control" name="compound-name" placeholder="Name"/>
-            id="compound-name"
-            class="form-control"
-            name="compound-name"
-            placeholder="Name"
-          />
                     <label for="compound-description">Description</label>
-          <input
+                    <input id="compound-description" class="form-control" name="compound-description" placeholder="Description"/>
-            id="compound-description"
-            class="form-control"
-            name="compound-description"
-            placeholder="Description"
-          />
                     <label for="compound-smiles">SMILES</label>
-          <input
+                    <input type="text" class="form-control" name="compound-smiles" placeholder="SMILES" id="compound-smiles">
-            type="text"
-            class="form-control"
-            name="compound-smiles"
-            placeholder="SMILES"
-            id="compound-smiles"
-          />
                     <p></p>
                     <div>
-            <iframe
+                        <iframe id="new_compound_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-              id="new_compound_ketcher"
+                                height="510"></iframe>
-              src="{% static '/js/ketcher2/ketcher.html' %}"
-              width="100%"
-              height="510"
-            ></iframe>
                     </div>
                     <p></p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-          type="button"
-          class="btn btn-secondary pull-left"
-          data-dismiss="modal"
-        >
-          Close
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="new_compound_modal_form_submit"
-        >
-          Submit
                 </button>
+                <button type="button" class="btn btn-primary" id="new_compound_modal_form_submit">Submit</button>
             </div>
         </div>
     </div>
+
 </div>
 <script>
+
 function newCompoundModalketcherToNewCompoundModalTextInput() {
-    $("#compound-smiles").val(this.ketcher.getSmiles());
+    $('#compound-smiles').val(this.ketcher.getSmiles());
 }
 
 $(function() {
-    $("#new_compound_ketcher").on("load", function () {
+
+    $('#new_compound_ketcher').on('load', function() {
         const checkKetcherReady = () => {
-        win = this.contentWindow;
+            win = this.contentWindow
-        if (win.ketcher && "editor" in win.ketcher) {
+            if (win.ketcher && 'editor' in win.ketcher) {
                 win.ketcher.editor.event.change.handlers.push({
                     once: false,
                     priority: 0,
                     f: newCompoundModalketcherToNewCompoundModalTextInput,
-            ketcher: win.ketcher,
+                    ketcher: win.ketcher
                 });
             } else {
                 setTimeout(checkKetcherReady, 100);
@@ -104,16 +59,20 @@
         };
 
         checkKetcherReady();
-    });
+    })
 
     $(function() {
-      $("#new_compound_modal_form_submit").on("click", function (e) {
+        $('#new_compound_modal_form_submit').on('click', function(e) {
             e.preventDefault();
             $(this).prop("disabled",true);
 
+
+
             // submit form
-        $("#new_compound_modal_form").submit();
+            $('#new_compound_modal_form').submit();
         });
     });
+
 });
+
 </script>

templates/modals/collections/new_group_modal.html

@@ -1,11 +1,5 @@
-<div
+<div class="modal fade" tabindex="-1" id="new_group_modal" role="dialog" aria-labelledby="new_group_modal"
-  class="modal fade"
+     aria-hidden="true">
-  tabindex="-1"
-  id="new_group_modal"
-  role="dialog"
-  aria-labelledby="new_group_modal"
-  aria-hidden="true"
->
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
@@ -16,44 +10,25 @@
                 <h4 class="modal-title">New Group</h4>
             </div>
             <div class="modal-body">
-        <p>
+                <p>Create new Group. You can assign users to the group once
-          Create new Group. You can assign users to the group once it is
+                    it is created. Description can be changed after creation.</p>
-          created. Description can be changed after creation.
+                <form id="new_group_modal_form" accept-charset="UTF-8" action="{{ SERVER_BASE }}/group"
-        </p>
-        <form
-          id="new_group_modal_form"
-          accept-charset="UTF-8"
-          action="{{ SERVER_BASE }}/group"
                       data-remote="true"
-          method="post"
+                      method="post">
-        >
                     {% csrf_token %}
                     <p>
                         <label for="name">Name</label>
-            <input
+                        <input id="name" type="text" name="group-name" class="form-control" placeholder="Name"/>
-              id="name"
-              type="text"
-              name="group-name"
-              class="form-control"
-              placeholder="Name"
-            />
                     </p>
                     <p>
                         <label for="description">Description</label>
-            <input
+                        <input id="description" type="text" class="form-control" placeholder="Description..."
-              id="description"
+                               name="group-description"/>
-              type="text"
-              class="form-control"
-              placeholder="Description..."
-              name="group-description"
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <a id="new_group_modal_form_submit" class="btn btn-primary" href="#"
+                <a id="new_group_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-          >Submit</a
-        >
                 <button type="button" class="btn btn-default" data-dismiss="modal">
                     Cancel
                 </button>
@@ -63,8 +38,8 @@
 </div>
 <script>
 $(function() {
-    $("#new_group_modal_form_submit").on("click", function () {
+    $('#new_group_modal_form_submit').on('click', function() {
-      $("#new_group_modal_form").submit();
+        $('#new_group_modal_form').submit();
     });
 });
 </script>

templates/modals/collections/new_model_modal.html

@@ -1,11 +1,5 @@
-<div
+<div class="modal fade" tabindex="-1" id="new_model_modal" role="dialog" aria-labelledby="new_model_modal"
-  class="modal fade"
+     aria-hidden="true">
-  tabindex="-1"
-  id="new_model_modal"
-  role="dialog"
-  aria-labelledby="new_model_modal"
-  aria-hidden="true"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
@@ -16,52 +10,29 @@
                 <h4 class="modal-title">New Model</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="new_model_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/model"
-          id="new_model_form"
+                      data-remote="true" method="post">
-          accept-charset="UTF-8"
-          action="{{ meta.current_package.url }}/model"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <div class="jumbotron">
+                    <div class="jumbotron">Create a new Model to
-            Create a new Model to limit the number of degradation products in
+                        limit the number of degradation products in the
-            the prediction. You just need to set a name and the packages you
+                        prediction. You just need to set a name and the packages
-            want the object to be based on. There are multiple types of models
+                        you want the object to be based on. There are multiple types of models available.
-            available. For additional information have a look at our
+                        For additional information have a look at our
-            <a
+                        <a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki
-              target="_blank"
+                            &gt;&gt;</a>
-              href="https://wiki.envipath.org/index.php/relative-reasoning"
-              role="button"
-              >wiki &gt;&gt;</a
-            >
                     </div>
                     <!-- Name -->
                     <label for="model-name">Name</label>
-          <input
+                    <input id="model-name" name="model-name" class="form-control" placeholder="Name"/>
-            id="model-name"
-            name="model-name"
-            class="form-control"
-            placeholder="Name"
-          />
 
                     <!-- Description -->
                     <label for="model-description">Description</label>
-          <input
+                    <input id="model-description" name="model-description" class="form-control"
-            id="model-description"
+                           placeholder="Description"/>
-            name="model-description"
-            class="form-control"
-            placeholder="Description"
-          />
 
                     <!-- Model Type -->
                     <label for="model-type">Model Type</label>
-          <select
+                    <select id="model-type" name="model-type" class="form-control" data-width='100%'>
-            id="model-type"
-            name="model-type"
-            class="form-control"
-            data-width="100%"
-          >
                         <option disabled selected>Select Model Type</option>
                         {% for k, v in model_types.items %}
                             <option value="{{ v }}">{{ k }}</option>
@@ -71,25 +42,19 @@
                     <!-- Rule Packages -->
                     <div id="rule-packages" class="ep-model-param mlrr rbrr">
                         <label for="model-rule-packages">Rule Packages</label>
-            <select
+                        <select id="model-rule-packages" name="model-rule-packages" data-actions-box='true'
-              id="model-rule-packages"
+                                class="form-control" multiple data-width='100%'>
-              name="model-rule-packages"
-              data-actions-box="true"
-              class="form-control"
-              multiple
-              data-width="100%"
-            >
                             <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>
@@ -98,25 +63,19 @@
                     <!-- Data Packages -->
                     <div id="data-packages" class="ep-model-param mlrr rbrr enviformer">
                         <label for="model-data-packages">Data Packages</label>
-            <select
+                        <select id="model-data-packages" name="model-data-packages" data-actions-box='true'
-              id="model-data-packages"
+                                class="form-control" multiple data-width='100%'>
-              name="model-data-packages"
-              data-actions-box="true"
-              class="form-control"
-              multiple
-              data-width="100%"
-            >
                             <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>
@@ -125,19 +84,11 @@
                     <!-- Fingerprinter -->
                     <div id="fingerprinter" class="ep-model-param mlrr">
                         <label for="model-fingerprinter">Fingerprinter</label>
-            <select
+                        <select id="model-fingerprinter" name="model-fingerprinter" data-actions-box='true'
-              id="model-fingerprinter"
+                                class="form-control" multiple data-width='100%'>
-              name="model-fingerprinter"
-              data-actions-box="true"
-              class="form-control"
-              multiple
-              data-width="100%"
-            >
                             <option value="MACCS" selected>MACCS Fingerprinter</option>
                             {% if meta.enabled_features.PLUGINS and additional_descriptors %}
-                <option disabled selected>
+                                <option disabled selected>Select Additional Fingerprinter / Descriptor</option>
-                  Select Additional Fingerprinter / Descriptor
-                </option>
                                 {% for k, v in additional_descriptors.items %}
                                     <option value="{{ v }}">{{ k }}</option>
                                 {% endfor %}
@@ -148,16 +99,8 @@
                     <!-- Threshold -->
                     <div id="threshold" class="ep-model-param mlrr enviformer">
                         <label for="model-threshold">Threshold</label>
-            <input
+                        <input type="number" min="0" max="1" step="0.05" value="0.5" id="model-threshold"
-              type="number"
+                               name="model-threshold" class="form-control">
-              min="0"
-              max="1"
-              step="0.05"
-              value="0.5"
-              id="model-threshold"
-              name="model-threshold"
-              class="form-control"
-            />
                     </div>
 
                     <div id="appdomain" class="ep-model-param mlrr">
@@ -165,64 +108,33 @@
                             <!-- Build AD? -->
                             <div class="checkbox">
                                 <label>
-                  <input
+                                    <input type="checkbox" id="build-app-domain" name="build-app-domain">Also build an
-                    type="checkbox"
+                                    Applicability Domain?
-                    id="build-app-domain"
-                    name="build-app-domain"
-                  />Also build an Applicability Domain?
                                 </label>
                             </div>
                             <div id="ad-params" style="display:none">
                                 <!-- Num Neighbors -->
                                 <label for="num-neighbors">Number of Neighbors</label>
-                <input
+                                <input id="num-neighbors" name="num-neighbors" type="number" class="form-control"
-                  id="num-neighbors"
-                  name="num-neighbors"
-                  type="number"
-                  class="form-control"
                                        value="5"
-                  step="1"
+                                       step="1" min="0" max="10">
-                  min="0"
-                  max="10"
-                />
                                 <!-- Local Compatibility -->
-                <label for="local-compatibility-threshold"
+                                <label for="local-compatibility-threshold">Local Compatibility Threshold</label>
-                  >Local Compatibility Threshold</label
+                                <input id="local-compatibility-threshold" name="local-compatibility-threshold"
-                >
-                <input
-                  id="local-compatibility-threshold"
-                  name="local-compatibility-threshold"
                                        type="number"
-                  class="form-control"
+                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
-                  value="0.5"
-                  step="0.01"
-                  min="0"
-                  max="1"
-                />
                                 <!-- Reliability -->
                                 <label for="reliability-threshold">Reliability Threshold</label>
-                <input
+                                <input id="reliability-threshold" name="reliability-threshold" type="number"
-                  id="reliability-threshold"
+                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
-                  name="reliability-threshold"
-                  type="number"
-                  class="form-control"
-                  value="0.5"
-                  step="0.01"
-                  min="0"
-                  max="1"
-                />
                             </div>
                         {% endif %}
                     </div>
                 </form>
             </div>
             <div class="modal-footer">
-        <a id="new_model_modal_form_submit" class="btn btn-primary" href="#"
+                <a id="new_model_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-          >Submit</a
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-        >
-        <button type="button" class="btn btn-default" data-dismiss="modal">
-          Cancel
-        </button>
             </div>
         </div>
     </div>
@@ -231,40 +143,45 @@
 <script>
     $(function () {
         // Built in Model Types
-    var nativeModelTypes = ["mlrr", "rbrr", "enviformer"];
+        var nativeModelTypes = [
+            "mlrr",
+            "rbrr",
+            "enviformer",
+        ]
 
         // Initially hide all "specific" forms
         $(".ep-model-param").each(function () {
             $(this).hide();
         });
 
-    $("#model-type").selectpicker();
+        $('#model-type').selectpicker();
         $("#model-fingerprinter").selectpicker();
         $("#model-rule-packages").selectpicker();
         $("#model-data-packages").selectpicker();
 
         $("#build-app-domain").change(function () {
             if ($(this).is(":checked")) {
-        $("#ad-params").show();
+                $('#ad-params').show();
             } else {
-        $("#ad-params").hide();
+                $('#ad-params').hide();
             }
         });
 
         // On change hide all and show only selected
         $("#model-type").change(function () {
-      $(".ep-model-param").hide();
+            $('.ep-model-param').hide();
-      var modelType = $("#model-type").val();
+            var modelType = $('#model-type').val();
             if (nativeModelTypes.indexOf(modelType) !== -1) {
-        $("." + modelType).show();
+                $('.' + modelType).show();
             } else {
                 // do nothing
             }
         });
 
-    $("#new_model_modal_form_submit").on("click", function (e) {
+        $('#new_model_modal_form_submit').on('click', function (e) {
             e.preventDefault();
-      $("#new_model_form").submit();
+            $('#new_model_form').submit();
         });
+
     });
 </script>

templates/modals/collections/new_package_modal.html

@@ -1,15 +1,15 @@
-<div
+<div class="modal fade"
-  class="modal fade"
      tabindex="-1"
      id="new_package_modal"
      role="dialog"
      aria-labelledby="new_package_modal"
-  aria-hidden="true"
+     aria-hidden="true">
->
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-        <button type="button" class="close" data-dismiss="modal">
+                <button type="button"
+                        class="close"
+                        data-dismiss="modal">
                     <span aria-hidden="true">&times;</span>
                     <span class="sr-only">Close</span>
                 </button>
@@ -17,42 +17,36 @@
             </div>
             <div class="modal-body">
                 <p>Create new package. Description can be changed later.</p>
-        <form
+                <form id="new_package_modal_form"
-          id="new_package_modal_form"
                       accept-charset="UTF-8"
                       action=""
                       data-remote="true"
-          method="post"
+                      method="post">
-        >
                     {% csrf_token %}
                     <p>
                         <label for="name">Name</label>
-            <input
+                        <input id="name" class="form-control"
-              id="name"
-              class="form-control"
                                name="package-name"
-              placeholder="Name"
+                               placeholder="Name"/>
-            />
                     </p>
                     <p>
                         <label for="description">Description</label>
-            <input
+                        <input id="description"
-              id="description"
                                type="text"
                                rows="3"
                                class="form-control"
                                placeholder="Description..."
-              name="package-description"
+                               name="package-description"/>
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <a id="new_package_modal_form_submit" class="btn btn-primary" href="#"
+                <a id="new_package_modal_form_submit"
-          >Submit</a
+                   class="btn btn-primary"
-        >
+                   href="#">Submit</a>
-        <button type="button" class="btn btn-default" data-dismiss="modal">
+                <button type="button"
-          Cancel
+                        class="btn btn-default"
+                        data-dismiss="modal">Cancel
                 </button>
             </div>
         </div>
@@ -60,9 +54,9 @@
 </div>
 <script>
 $(function() {
-    $("#new_package_modal_form_submit").on("click", function (e) {
+    $('#new_package_modal_form_submit').on('click', function (e) {
         e.preventDefault();
-      $("#new_package_modal_form").submit();
+        $('#new_package_modal_form').submit();
     });
 });
 </script>

templates/modals/collections/new_pathway_modal.html

@@ -1,57 +1,39 @@
 {% load static %}
-<div
+<div class="modal fade" tabindex="-1" id="new_pathway_modal" role="dialog" aria-labelledby="new_pathway_modal"
-  class="modal fade"
+     aria-hidden="true" style="overflow-y: auto;">
-  tabindex="-1"
-  id="new_pathway_modal"
-  role="dialog"
-  aria-labelledby="new_pathway_modal"
-  aria-hidden="true"
-  style="overflow-y: auto;"
->
     <!-- FIXME: make width dynamic-->
     <div class="modal-dialog" id="new_pathway_modal_dialog" style="width:900px">
         <div class="modal-content">
             <div class="modal-header">
                 <button type="button" class="close" data-dismiss="modal">
-          <span aria-hidden="true">&times;</span>
+                    <span aria-hidden="true">&times;</span> <span class="sr-only">Close</span>
-          <span class="sr-only">Close</span>
                 </button>
                 <h4 class="js-title-step"></h4>
             </div>
             <div class="modal-body hide" data-step="1" data-title="New Pathway">
-        <div class="jumbotron">
+                <div class="jumbotron">Create a new pathway by entering
-          Create a new pathway by entering the root compound and a name. Then
+                    the root compound and a name. Then select if you want to
-          select if you want to use the prediction engine to generate a
+                    use the prediction engine to generate a predicted pathway or
-          predicted pathway or create an empty pathway that you fill in by
+                    create an empty pathway that you fill in by yourself. If
-          yourself. If you choose to predict a pathway, you can modify the
+                    you choose to predict a pathway, you can modify the
-          settings for the prediction, or use the default settings and just
+                    settings for the prediction, or use the default settings
-          click Submit.
+                    and just click Submit.
                 </div>
                 <div class="modal-body">
                     {% if current_user.name == 'anonymous' %}
                     <div class="alert alert-warning">
-              You are currently logged in as Anonymous. Please note: Pathways
+                        You are currently logged in as Anonymous. Please note:
-              entered or predicted as anonymous user will be deleted after 30
+                        Pathways entered or predicted as anonymous user will be deleted after 30 days.
-              days. Please log in to save your results.
+                        Please log in to save your results.
                     </div>
                     {% endif %}
                 </div>
                 <div class="row">
                     <div class="col-md-6">
                         <label for="name">Name</label>
-            <input
+                        <input id="name" class="form-control" name="name" placeholder="Name"/>
-              id="name"
-              class="form-control"
-              name="name"
-              placeholder="Name"
-            />
                         <label for="description">Description</label>
-            <input
+                        <input id="description" class="form-control" name="description" placeholder="no description"/>
-              id="description"
-              class="form-control"
-              name="description"
-              placeholder="no description"
-            />
                     </div>
 
                     <div class="col-md-6">
@@ -59,33 +41,17 @@
                         <div class="radio" id="predict">
                             <p>
                                 <label>
-                  <input
+                                    <input type="radio" name="predict" id="radioPredict" value="predict" checked/>Predict pathway
-                    type="radio"
-                    name="predict"
-                    id="radioPredict"
-                    value="predict"
-                    checked
-                  />Predict pathway
                                 </label>
                             </p>
                             <p>
                                 <label>
-                  <input
+                                    <input type="radio" name="predict" id="radioIncremental"value="incremental"/>Incremental prediction
-                    type="radio"
-                    name="predict"
-                    id="radioIncremental"
-                    value="incremental"
-                  />Incremental prediction
                                 </label>
                             </p>
                             <p>
                                 <label>
-                  <input
+                                    <input type="radio" name="predict" id="radioBuild" value="build"/>Build pathway
-                    type="radio"
-                    name="predict"
-                    id="radioBuild"
-                    value="build"
-                  />Build pathway
                                 </label>
                             </p>
                         </div>
@@ -94,18 +60,13 @@
                 <label for="smilesinput">SMILES</label>
                 <table style="width: 100%">
                     <colgroup>
-            <col span="1" style="width: 90%;" />
+                        <col span="1" style="width: 90%;">
-            <col span="1" style="width: 10%;" />
+                        <col span="1" style="width: 10%;">
                     </colgroup>
                     <tr>
                         <td>
-              <input
+                            <input id="smilesinput" class="form-control" name="smilesinput" placeholder="C1CCCCC1"
-                id="smilesinput"
+                                   autocapitalize="none"/>
-                class="form-control"
-                name="smilesinput"
-                placeholder="C1CCCCC1"
-                autocapitalize="none"
-              />
                         </td>
                         <td>
                             <button type="button" class="btn btn-default" id="render-button">
@@ -116,57 +77,33 @@
                 </table>
                 <p id="ketcher_container"></p>
                 <div>
-          <iframe
+                    <iframe id="ifKetcher" src="{% static '/js/ketcher/ketcher.html' %}" width="850"
-            id="ifKetcher"
+                            height="510"></iframe>
-            src="{% static '/js/ketcher/ketcher.html' %}"
-            width="850"
-            height="510"
-          ></iframe>
                 </div>
             </div>
-      <div
+            <div class="modal-body hide" data-step="2" data-title="New Pathway - Advanced Settings">
-        class="modal-body hide"
+                <div class="jumbotron">Choose if you want to use an existing
-        data-step="2"
+                    setting, or create a new one for this pathway
-        data-title="New Pathway - Advanced Settings"
+                    prediction. Then click Submit to use the specified setting,
-      >
+                    or click next to set the parameters.
-        <div class="jumbotron">
-          Choose if you want to use an existing setting, or create a new one for
-          this pathway prediction. Then click Submit to use the specified
-          setting, or click next to set the parameters.
                 </div>
                 <div id="settings">
                     <div class="radio" id="settingRadio">
                         <p>
                             <label>
-                <input
+                                <input type="radio" name="existing" id="radioDefault" value="exisiting" checked/>
-                  type="radio"
-                  name="existing"
-                  id="radioDefault"
-                  value="exisiting"
-                  checked
-                />
                                 Use Default
                             </label>
                         </p>
                         <p>
                             <label>
-                <input
+                                <input type="radio" name="existing" id="radioExists" value="exisiting"/>
-                  type="radio"
-                  name="existing"
-                  id="radioExists"
-                  value="exisiting"
-                />
                                 Select Existing
                             </label>
                         </p>
                         <p>
                             <label>
-                <input
+                                <input type="radio" name="existing" id="radioNew" value="temporary"/>
-                  type="radio"
-                  name="existing"
-                  id="radioNew"
-                  value="temporary"
-                />
                                 Create New
                             </label>
                         </p>
@@ -174,7 +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>
@@ -184,25 +121,12 @@
             {% include "templates/modals/collections/new_setting_modal_body.html" %}
             {% endwith %}
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-default js-btn-step pull-left" data-orientation="cancel"
-          type="button"
+                        onclick="reset()" data-dismiss="modal"></button>
-          class="btn btn-default js-btn-step pull-left"
+                <button type="button" class="btn btn-default js-btn-step" data-orientation="previous"
-          data-orientation="cancel"
+                        id="backbutton"></button>
-          onclick="reset()"
+                <button type="button" class="btn btn-default js-btn-step" data-orientation="next"
-          data-dismiss="modal"
+                        id="nextbutton"></button>
-        ></button>
-        <button
-          type="button"
-          class="btn btn-default js-btn-step"
-          data-orientation="previous"
-          id="backbutton"
-        ></button>
-        <button
-          type="button"
-          class="btn btn-default js-btn-step"
-          data-orientation="next"
-          id="nextbutton"
-        ></button>
                 <a id="modal-form-submit" class="btn btn-primary" href="#">Submit</a>
             </div>
         </div>
@@ -211,86 +135,86 @@
 
 <script>
 s = new Setting(
-    "settingName",
+    'settingName',
-    "package_multi_select",
+    'package_multi_select',
-    "modelSelect",
+    'modelSelect',
-    "cutoff",
+    'cutoff',
-    "evalType",
+    'evalType',
-    "availableTS",
+    'availableTS',
-    "forms",
+    'forms',
-    "truncatorTable",
+    'truncatorTable',
-    "summaryTable",
+    'summaryTable',
 );
 
 $(function() {
     // hide all forms
-    $("#forms").children().hide();
+    $('#forms').children().hide()
 
     $("#render-button").on("click", function() {
-      syncKetcherAndTextInput("text", "ifKetcher", "smilesinput");
+        syncKetcherAndTextInput('text', "ifKetcher", "smilesinput");
     });
 
     // If theres a change in the in '#smilesinput' sync the value to ketcher
-    $("#smilesinput").on("input", function () {
+    $('#smilesinput').on('input', function() {
-      syncKetcherAndTextInput("text", "ifKetcher", "smilesinput");
+        syncKetcherAndTextInput('text', 'ifKetcher', 'smilesinput');
     });
 
     // If theres an update in ketcher sync it to textinput
     setInterval(function() {
-      syncKetcherAndTextInput("ketcher", "ifKetcher", "smilesinput");
+        syncKetcherAndTextInput('ketcher', 'ifKetcher', 'smilesinput');
     }, 250);
 
     $("#smilesinput").on("blur", function() {
-      syncKetcherAndTextInput("text", "ifKetcher", "smilesinput");
+        syncKetcherAndTextInput('text', 'ifKetcher', 'smilesinput');
     });
 
     $("#smilesinput").on("keypress", function(event) {
         if (event.keyCode == 13) {
-        syncKetcherAndTextInput("text", "ifKetcher", "smilesinput");
+            syncKetcherAndTextInput('text', 'ifKetcher', 'smilesinput');
         }
     });
 
     // Show forms depending on the selected TS
-    $("#availableTS").on("change", function (e) {
+    $('#availableTS').on('change', function(e) {
         e.preventDefault();
 
         var type = $(this).val();
         // hide current content
-      $("#forms").children().hide();
+        $('#forms').children().hide()
 
-      if (type === "") {
+        if(type === '') {
             return;
         }
 
-      $("#" + type + "_form").show();
+        $('#' + type + '_form').show()
     });
 
     $("#modelSelect").on("change", function() {
         setCutoff = function (thresh) {
             $("#cutoff").val(thresh);
-      };
+        }
 
         var modelUri = $("#modelSelect :selected").val();
         fillPRCurve(modelUri, setCutoff);
     });
 
     // Add a TS to the setting
-    $("#add-ts-button").on("click", function (e) {
+    $('#add-ts-button').on('click', function(e) {
         e.preventDefault();
         s.addTruncator();
     });
 
-    $("input[type=radio][name=predict]").change(function () {
+    $('input[type=radio][name=predict]').change(function() {
-      if (this.id == "radioBuild") {
+        if (this.id == 'radioBuild') {
           $("#nextbutton").prop("disabled", true);
         } else {
           $("#nextbutton").prop("disabled", false);
         }
     });
 
-    $("input[type=radio][name=existing]").change(function () {
+    $('input[type=radio][name=existing]').change(function() {
-      if (this.id == "radioDefault" || this.id == "radioExists") {
+        if (this.id == 'radioDefault' || this.id == 'radioExists') {
-        if (this.id == "radioDefault") {
+          if(this.id == 'radioDefault') {
             $("#settingSelect").prop("disabled", true);
           } else {
             $("#settingSelect").prop("disabled", false);
@@ -306,71 +230,72 @@
     var pwStep1 = function() {
         console.log("pw step 1");
         // Make "Next" to "Advanced"
-      $("#nextbutton").val("Advanced");
+        $('#nextbutton').val("Advanced");
-    };
+    }
 
     var pwStep2 = function() {
         console.log("pw step 2");
         // Make "Advanced" to "Next"
-      $("#nextbutton").val("Next");
+        $('#nextbutton').val("Next");
         // As "Use default is preselected" disable "Next" button
         $("#nextbutton").prop("disabled",true);
         // Disable setting dropdown as long as the correspndonding radio isnt checked
         $("#settingSelect").prop("disabled",true);
         // Show submit button
         $("#modal-form-submit").show();
-    };
+    }
 
     var settingStep1 = function (){
         // First step sets name and packages
         s.extractName();
         s.extractSelectedPackages();
-    };
+    }
 
     var settingStep2 = function (){
         // Seconds step gathers relative reasoning params
         s.extractRelativeReasoning();
         s.extractCutoff();
         s.extractEvaluationType();
-    };
+    }
 
     var settingStep3 = function() {
         s.updateTable();
         s.updateSummaryTable();
         // hide duplicate submit...
         $("#nextbutton").hide();
-    };
+    }
 
     var postPathway = function(){
         console.log("Complete!");
         console.log(s.tsParams);
         console.log("Getting SMILES");
-    };
+    }
 
     function dummy() {
         console.log("dummy");
     }
 
-    $("#new_pathway_modal").modalSteps({
+    $('#new_pathway_modal').modalSteps({
-      btnCancelHtml: "Cancel",
+      btnCancelHtml: 'Cancel',
-      btnPreviousHtml: "Back",
+      btnPreviousHtml: 'Back',
-      btnNextHtml: "Next",
+      btnNextHtml: 'Next',
-      btnLastStepHtml: "Submit",
+      btnLastStepHtml: 'Submit',
       disableNextButton: false,
       completeCallback: postPathway,
       callbacks: {
-        1: pwStep1,
+        '1': pwStep1,
-        2: pwStep2,
+        '2' : pwStep2,
-        3: dummy,
+        '3' : dummy,
-        4: settingStep1,
+        '4' : settingStep1,
-        5: settingStep2,
+        '5' : settingStep2,
-        6: settingStep3,
+        '6' : settingStep3,
-      },
+      }
     });
 
-    $("#modal-form-submit").on("click", function () {
+   $('#modal-form-submit').on('click', function() {
       e.preventDefault();
       postPathway();
    });
 });
+
 </script>

templates/modals/collections/new_prediction_setting_modal.html

@@ -5,157 +5,80 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Create a Prediction Setting</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-        <p>
+                <p>To create a Prediction Setting fill the form below and click "Create"</p>
-          To create a Prediction Setting fill the form below and click "Create"
+                <form id="new-prediction-setting-modal-form" accept-charset="UTF-8" action="" data-remote="true"
-        </p>
+                      method="post">
-        <form
-          id="new-prediction-setting-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
 
                     <label for="prediction-setting-name">Name</label>
-          <input
+                    <input id="prediction-setting-name" name="prediction-setting-name" class="form-control" placeholder="Name"/>
-            id="prediction-setting-name"
-            name="prediction-setting-name"
-            class="form-control"
-            placeholder="Name"
-          />
                     <label for="prediction-setting-description">Description</label>
-          <input
+                    <input id="prediction-setting-description" name="prediction-setting-description" class="form-control"
-            id="prediction-setting-description"
+                           placeholder="Description"/>
-            name="prediction-setting-description"
-            class="form-control"
-            placeholder="Description"
-          />
 
                     <label for="prediction-setting-max-nodes">Max #Nodes</label>
-          <input
+                    <input id="prediction-setting-max-nodes" type="number" class="form-control" name="prediction-setting-max-nodes" value="30" min="1" max="50" step="1">
-            id="prediction-setting-max-nodes"
-            type="number"
-            class="form-control"
-            name="prediction-setting-max-nodes"
-            value="30"
-            min="1"
-            max="50"
-            step="1"
-          />
                     <label for="prediction-setting-max-depth">Max Depth</label>
-          <input
+                    <input id="prediction-setting-max-depth" type="number" class="form-control" name="prediction-setting-max-depth" value="5" min="1" max="8" step="1">
-            id="prediction-setting-max-depth"
-            type="number"
-            class="form-control"
-            name="prediction-setting-max-depth"
-            value="5"
-            min="1"
-            max="8"
-            step="1"
-          />
 
                     <label for="tp-generation-method">TP Generation Method</label>
-          <select
+                    <select id="tp-generation-method" name="tp-generation-method" class="form-control" data-width='100%'>
-            id="tp-generation-method"
-            name="tp-generation-method"
-            class="form-control"
-            data-width="100%"
-          >
                         <option disabled selected>Select how TPs are generated</option>
                         <option value="rule-based-prediction-setting">Rule Based</option>
                         <option value="model-based-prediction-setting">Model Based</option>
                     </select>
                     <div id="rule-based-prediction-setting-specific-form">
                         <!-- Rule Packages -->
-            <label>Rule Packages</label><br />
+                        <label>Rule Packages</label><br>
-            <select
+                        <select id="rule-based-prediction-setting-packages" name="rule-based-prediction-setting-packages"
-              id="rule-based-prediction-setting-packages"
+                                data-actions-box='true' class="form-control" multiple data-width='100%'>
-              name="rule-based-prediction-setting-packages"
-              data-actions-box="true"
-              class="form-control"
-              multiple
-              data-width="100%"
-            >
                             <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>
                     </div>
                     <div id="model-based-prediction-setting-specific-form">
-            <label>Select Model</label><br />
+                        <label>Select Model</label><br>
-            <select
+                        <select id="model-based-prediction-setting-model" name="model-based-prediction-setting-model" class="form-control" data-width='100%'>
-              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"
+                        <label for="model-based-prediction-setting-threshold">Threshold</label>
-              >Threshold</label
+                        <input id="model-based-prediction-setting-threshold" name="model-based-prediction-setting-threshold" class="form-control" placeholder="0.25" type="number"/>
-            >
-            <input
-              id="model-based-prediction-setting-threshold"
-              name="model-based-prediction-setting-threshold"
-              class="form-control"
-              placeholder="0.25"
-              type="number"
-            />
                     </div>
 
-          <input
+                    <input class="form-check-input" type="checkbox" value="on" id="prediction-setting-new-default" name="prediction-setting-new-default">
-            class="form-check-input"
+                    <label class="form-check-label" for="prediction-setting-new-default">Set this setting as new default</label>
-            type="checkbox"
+
-            value="on"
-            id="prediction-setting-new-default"
-            name="prediction-setting-new-default"
-          />
-          <label class="form-check-label" for="prediction-setting-new-default"
-            >Set this setting as new default</label
-          >
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="new-prediction-setting-modal-submit">Create</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="new-prediction-setting-modal-submit"
-        >
-          Create
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
     $(function() {
+
         // Initially hide all "specific" forms
         $("div[id$='-specific-form']").each( function() {
             $(this).hide();
@@ -168,18 +91,18 @@
             $("div[id$='-specific-form']").each( function() {
                 $(this).hide();
             });
-      val = $("option:selected", this).val();
+            val = $('option:selected', this).val();
             $("#" + val + "-specific-form").show();
         });
 
-    $("#new-prediction-setting-modal-submit").click(function (e) {
+        $('#new-prediction-setting-modal-submit').click(function(e){
             e.preventDefault();
             // $('#new-prediction-setting-modal-form').submit();
 
-      const formData = $("#new-prediction-setting-modal-form").serialize();
+            const formData = $('#new-prediction-setting-modal-form').serialize();
-      $.post("/setting", formData, function (response) {
+            $.post('/setting', formData, function(response) {
                 location.reload();
             });
         });
-  });
+    })
 </script>

templates/modals/collections/new_reaction_modal.html

@@ -1,91 +1,50 @@
 {% load static %}
-<div
+<div class="modal fade bs-modal-lg" id="new_reaction_modal" tabindex="-1" aria-labelledby="new_reaction_modal" aria-modal="true"
-  class="modal fade bs-modal-lg"
+     role="dialog">
-  id="new_reaction_modal"
-  tabindex="-1"
-  aria-labelledby="new_reaction_modal"
-  aria-modal="true"
-  role="dialog"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">×</span>
                 </button>
                 <h4 class="modal-title">Create a new Reaction</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="new_reaction_modal_form" accept-charset="UTF-8" action="{% url 'package reaction list' meta.current_package.uuid %}" data-remote="true" method="post">
-          id="new_reaction_modal_form"
-          accept-charset="UTF-8"
-          action="{% url 'package reaction list' meta.current_package.uuid %}"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <label for="reaction-name">Name</label>
-          <input
+                    <input id="reaction-name" class="form-control" name="reaction-name" placeholder="Name"/>
-            id="reaction-name"
-            class="form-control"
-            name="reaction-name"
-            placeholder="Name"
-          />
                     <label for="reaction-description">Description</label>
-          <input
+                    <input id="reaction-description" class="form-control" name="reaction-description" placeholder="Description"/>
-            id="reaction-description"
-            class="form-control"
-            name="reaction-description"
-            placeholder="Description"
-          />
                     <p></p>
                     <div>
-            <iframe
+                        <iframe id="new_reaction_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-              id="new_reaction_ketcher"
+                                height="510"></iframe>
-              src="{% static '/js/ketcher2/ketcher.html' %}"
-              width="100%"
-              height="510"
-            ></iframe>
                     </div>
-          <input type="hidden" name="reaction-smirks" id="reaction-smirks" />
+                    <input type="hidden" name="reaction-smirks" id="reaction-smirks">
                     <p></p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-          type="button"
-          class="btn btn-secondary pull-left"
-          data-dismiss="modal"
-        >
-          Close
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="new_reaction_modal_form_submit"
-        >
-          Submit
                 </button>
+                <button type="button" class="btn btn-primary" id="new_reaction_modal_form_submit">Submit</button>
             </div>
         </div>
     </div>
+
 </div>
 <script>
 $(function() {
-    $("#new_reaction_modal_form_submit").on("click", function (e) {
+    $('#new_reaction_modal_form_submit').on('click', function(e) {
         e.preventDefault();
         $(this).prop("disabled",true);
 
-      k = getKetcher("new_reaction_ketcher");
+        k = getKetcher('new_reaction_ketcher');
-      $("#reaction-smirks").val(k.getSmiles());
+        $('#reaction-smirks').val(k.getSmiles());
 
         // submit form
-      $("#new_reaction_modal_form").submit();
+        $('#new_reaction_modal_form').submit();
     });
 });
 </script>

templates/modals/collections/new_rule_modal.html

@@ -1,102 +1,54 @@
 {% load static %}
-<div
+<div class="modal fade bs-modal-lg" id="new_rule_modal" tabindex="-1" aria-labelledby="new_rule_modal" aria-modal="true"
-  class="modal fade bs-modal-lg"
+     role="dialog">
-  id="new_rule_modal"
-  tabindex="-1"
-  aria-labelledby="new_rule_modal"
-  aria-modal="true"
-  role="dialog"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">×</span>
                 </button>
                 <h4 class="modal-title">Create a new Rule</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="new_rule_modal_form" accept-charset="UTF-8" action="{% url 'package rule list' meta.current_package.uuid %}" data-remote="true" method="post">
-          id="new_rule_modal_form"
-          accept-charset="UTF-8"
-          action="{% url 'package rule list' meta.current_package.uuid %}"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <label for="rule-name">Name</label>
-          <input
+                    <input id="rule-name" class="form-control" name="rule-name" placeholder="Name"/>
-            id="rule-name"
-            class="form-control"
-            name="rule-name"
-            placeholder="Name"
-          />
                     <label for="rule-description">Description</label>
-          <input
+                    <input id="rule-description" class="form-control" name="rule-description" placeholder="Description"/>
-            id="rule-description"
-            class="form-control"
-            name="rule-description"
-            placeholder="Description"
-          />
                     <label for="rule-smirks">SMIRKS</label>
-          <input
+                    <input id="rule-smirks" class="form-control" name="rule-smirks" placeholder="SMIRKS"/>
-            id="rule-smirks"
-            class="form-control"
-            name="rule-smirks"
-            placeholder="SMIRKS"
-          />
                     <p></p>
                     <div id="rule-smirks-viz"></div>
-          <input
+                    <input type="hidden" name="rule-type" id="rule-type" value="SimpleAmbitRule">
-            type="hidden"
-            name="rule-type"
-            id="rule-type"
-            value="SimpleAmbitRule"
-          />
                     <p></p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-          type="button"
-          class="btn btn-secondary pull-left"
-          data-dismiss="modal"
-        >
-          Close
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="new_rule_modal_form_submit"
-        >
-          Submit
                 </button>
+                <button type="button" class="btn btn-primary" id="new_rule_modal_form_submit">Submit</button>
             </div>
         </div>
     </div>
+
 </div>
 <script>
 $(function() {
-    $("#rule-smirks").on("input", function (e) {
-      $("#rule-smirks-viz").empty();
 
-      smirks = $("#rule-smirks").val();
+    $('#rule-smirks').on('input', function(e) {
+        $('#rule-smirks-viz').empty()
+
+        smirks = $('#rule-smirks').val()
 
         const img = new Image();
-      img.src =
+        img.src = "{% url 'depict' %}?is_query_smirks=true&smirks=" + encodeURIComponent(smirks);
-        "{% url 'depict' %}?is_query_smirks=true&smirks=" +
+        img.style.width = '100%';
-        encodeURIComponent(smirks);
+        img.style.height = '100%';
-      img.style.width = "100%";
+        img.style.objectFit = 'cover';
-      img.style.height = "100%";
-      img.style.objectFit = "cover";
 
         img.onload = function () {
-        $("#rule-smirks-viz").append(img);
+            $('#rule-smirks-viz').append(img);
         };
 
         img.onerror = function () {
@@ -105,16 +57,16 @@
                     <h4 class="alert-heading">Could not render SMIRKS!</h4>
                     <p>Could not render SMIRKS - Have you entered a valid SMIRKS?</a>
                     </p>
-                </div>`;
+                </div>`
-        $("#rule-smirks-viz").append(error_tpl);
+            $('#rule-smirks-viz').append(error_tpl);
         };
     });
 
-    $("#new_rule_modal_form_submit").on("click", function (e) {
+    $('#new_rule_modal_form_submit').on('click', function(e) {
         e.preventDefault();
         $(this).prop("disabled",true);
         // submit form
-      $("#new_rule_modal_form").submit();
+        $('#new_rule_modal_form').submit();
     });
 });
 </script>

templates/modals/collections/new_scenario_modal.html

@@ -1,11 +1,5 @@
-<div
+<div class="modal fade" tabindex="-1" id="new_scenario_modal" role="dialog" aria-labelledby="new_scenario_modal"
-  class="modal fade"
+     aria-hidden="true">
-  tabindex="-1"
-  id="new_scenario_modal"
-  role="dialog"
-  aria-labelledby="new_scenario_modal"
-  aria-hidden="true"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
@@ -16,84 +10,39 @@
                 <h4 class="modal-title">New Scenario</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="new_scenario_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/scenario"
-          id="new_scenario_form"
+                      data-remote="true" method="post">
-          accept-charset="UTF-8"
-          action="{{ meta.current_package.url }}/scenario"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <div class="jumbotron">
+                    <div class="jumbotron">Please enter name, description, and date of scenario. Date should be
-            Please enter name, description, and date of scenario. Date should be
+                        associated to the data, not the current date. For example, this could reflect the publishing
-            associated to the data, not the current date. For example, this
+                        date of a study. You can leave all fields but the name empty and fill them in later.
-            could reflect the publishing date of a study. You can leave all
+                        <a target="_blank" href="https://wiki.envipath.org/index.php/scenario" role="button">wiki
-            fields but the name empty and fill them in later.
+                            &gt;&gt;</a>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/scenario"
-              role="button"
-              >wiki &gt;&gt;</a
-            >
                     </div>
                     <label for="scenario-name">Name</label>
-          <input
+                    <input id="scenario-name" name="scenario-name" class="form-control" placeholder="Name"/>
-            id="scenario-name"
-            name="scenario-name"
-            class="form-control"
-            placeholder="Name"
-          />
                     <label for="scenario-description">Description</label>
-          <input
+                    <input id="scenario-description" name="scenario-description" class="form-control"
-            id="scenario-description"
+                           placeholder="Description"/>
-            name="scenario-description"
-            class="form-control"
-            placeholder="Description"
-          />
                     <label id="dateField" for="dateYear">Date</label>
                     <table>
                         <tr>
                             <th>
-                <input
+                                <input type="number" id="dateYear" name="scenario-date-year" class="form-control"
-                  type="number"
+                                       placeholder="YYYY" max="{% now "Y" %}">
-                  id="dateYear"
-                  name="scenario-date-year"
-                  class="form-control"
-                  placeholder="YYYY"
-                  max="{% now "Y" %}"
-                />
                             </th>
                             <th>
-                <input
+                                <input type="number" id="dateMonth" name="scenario-date-month" min="1" max="12"
-                  type="number"
+                                       class="form-control" placeholder="MM" >
-                  id="dateMonth"
-                  name="scenario-date-month"
-                  min="1"
-                  max="12"
-                  class="form-control"
-                  placeholder="MM"
-                />
                             </th>
                             <th>
-                <input
+                                <input type="number" id="dateDay" name="scenario-date-day" min="1" max="31" class="form-control"
-                  type="number"
+                                       placeholder="DD">
-                  id="dateDay"
-                  name="scenario-date-day"
-                  min="1"
-                  max="31"
-                  class="form-control"
-                  placeholder="DD"
-                />
                             </th>
                         </tr>
                     </table>
                     <label for="scenario-type">Scenario Type</label>
-          <select
+                    <select id="scenario-type" name="scenario-type" class="form-control" data-width='100%'>
-            id="scenario-type"
-            name="scenario-type"
-            class="form-control"
-            data-width="100%"
-          >
                         <option value="empty" selected>Empty Scenario</option>
                         {% for k, v in scenario_types.items %}
                             <option value="{{ v.name }}">{{ k }}</option>
@@ -107,15 +56,12 @@
                             {% endfor %}
                         </div>
                     {% endfor %}
+
                 </form>
             </div>
             <div class="modal-footer">
-        <a id="new_scenario_modal_form_submit" class="btn btn-primary" href="#"
+                <a id="new_scenario_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-          >Submit</a
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-        >
-        <button type="button" class="btn btn-default" data-dismiss="modal">
-          Cancel
-        </button>
             </div>
         </div>
     </div>
@@ -133,21 +79,24 @@
             $("div[id$='-specific-inputs']").each(function () {
                 $(this).hide();
             });
-      val = $("option:selected", this).val();
+            val = $('option:selected', this).val();
             $("#" + val + "-specific-inputs").show();
         });
 
-    $("#new_scenario_modal_form_submit").on("click", function (e) {
+        $('#new_scenario_modal_form_submit').on('click', function (e) {
             e.preventDefault();
-      $("#new_scenario_form").submit();
+            $('#new_scenario_form').submit();
         });
 
         var dateYear = document.getElementById("dateYear");
         dateYear.addEventListener("change", () => {
             console.log("Final value after editing:", dateYear.value);
             if (dateYear.value.length < 4) {
-        dateYear.value = new Date().getFullYear();
+                dateYear.value = {% now "Y" %};
             }
         });
+
     });
+
 </script>
+

templates/modals/objects/add_additional_information_modal.html

@@ -4,60 +4,32 @@
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
                 <h3 class="modal-title">Add Additional Information</h3>
             </div>
             <div class="modal-body">
-        <select
+                <select id="select-additional-information-type" data-actions-box='true' class="form-control" data-width='100%'>
-          id="select-additional-information-type"
-          data-actions-box="true"
-          class="form-control"
-          data-width="100%"
-        >
                     <option selected disabled>Select the type to add</option>
                     {% for add_inf in available_additional_information %}
-            <option value="{{ add_inf.name }}">
+                        <option value="{{ add_inf.name }}">{{ add_inf.display_name }}</option>
-              {{ add_inf.display_name }}
-            </option>
                     {% endfor %}
                 </select>
                 {% for add_inf in available_additional_information %}
                     <div class="aiform {{ add_inf.name }}" style="display: none;">
-            <form
+                        <form id="add_{{ add_inf.name }}_add-additional-information-modal-form" accept-charset="UTF-8"
-              id="add_{{ add_inf.name }}_add-additional-information-modal-form"
+                              action="" data-remote="true" method="post">
-              accept-charset="UTF-8"
-              action=""
-              data-remote="true"
-              method="post"
-            >
                             {% csrf_token %}
                             {{ add_inf.widget|safe }}
-              <input
+                            <input type="hidden" name="hidden" value="add-additional-information">
-                type="hidden"
-                name="hidden"
-                value="add-additional-information"
-              />
                         </form>
                     </div>
                 {% endfor %}
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="add-additional-information-modal-submit">Add
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="add-additional-information-modal-submit"
-        >
-          Add
                 </button>
             </div>
         </div>
@@ -65,28 +37,25 @@
 </div>
 <script>
 $(function() {
-    $("#select-additional-information-type").change(function (e) {
-      var selectedType = $(
-        "#select-additional-information-type :selected",
-      ).val();
-      $(".aiform").hide();
-      $("." + selectedType).show();
-    });
 
-    $("#add-additional-information-modal-submit").click(function (e) {
+    $('#select-additional-information-type').change(function(e){
+        var selectedType = $("#select-additional-information-type :selected").val();
+        $('.aiform').hide();
+        $('.' + selectedType).show();
+    })
+
+    $('#add-additional-information-modal-submit').click(function(e){
         e.preventDefault();
 
-      var selectedType = $(
+        var selectedType = $("#select-additional-information-type :selected").val();
-        "#select-additional-information-type :selected",
-      ).val();
         console.log(selectedType);
-      if (
+        if (selectedType !== null && selectedType !== undefined && selectedType !== '') {
-        selectedType !== null &&
+            $('.' + selectedType + ' >form').submit();
-        selectedType !== undefined &&
-        selectedType !== ""
-      ) {
-        $("." + selectedType + " >form").submit();
         }
+
     });
+
 });
+
+
 </script>

templates/modals/objects/add_pathway_edge_modal.html

@@ -1,150 +1,94 @@
 {% load static %}
-<div
+<div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_modal"
-  class="modal fade bs-modal-lg"
-  id="add_pathway_edge_modal"
-  tabindex="-1"
-  aria-labelledby="add_pathway_edge_modal"
      aria-modal="true"
-  role="dialog"
+     role="dialog">
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
                 <h4 class="modal-title">Add a Reaction</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="add_pathway_edge_modal_form" accept-charset="UTF-8"
-          id="add_pathway_edge_modal_form"
-          accept-charset="UTF-8"
                       action="{% url 'package pathway edge list' meta.current_package.uuid pathway.uuid %}"
-          data-remote="true"
+                      data-remote="true" method="post">
-          method="post"
-        >
                     {% csrf_token %}
                     <label for="edge-name">Name</label>
-          <input
+                    <input id="edge-name" class="form-control" name="edge-name" placeholder="Name"/>
-            id="edge-name"
-            class="form-control"
-            name="edge-name"
-            placeholder="Name"
-          />
                     <label for="edge-description">Description</label>
-          <input
+                    <input id="edge-description" class="form-control" name="edge-description" placeholder="Description"/>
-            id="edge-description"
-            class="form-control"
-            name="edge-description"
-            placeholder="Description"
-          />
                     <p></p>
                     <div class="row">
                         <div class="col-xs-5">
                             <legend>Substrate(s)</legend>
                         </div>
-            <div class="col-xs-2"></div>
+                        <div class="col-xs-2">
+
+                        </div>
                         <div class="col-xs-5">
                             <legend>Product(s)</legend>
                         </div>
                     </div>
                     <div class="row">
                         <div class="col-xs-5">
-              <select
+                            <select id="add_pathway_edge_substrates" name="edge-substrates"
-                id="add_pathway_edge_substrates"
+                                    data-actions-box='true' class="form-control" multiple data-width='100%'>
-                name="edge-substrates"
-                data-actions-box="true"
-                class="form-control"
-                multiple
-                data-width="100%"
-              >
                                 {% for n in pathway.nodes %}
-                  <option
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
-                    data-smiles="{{ n.default_node_label.smiles }}"
-                    value="{{ n.url }}"
-                  >
-                    {{ n.default_node_label.name|safe }}
-                  </option>
                                 {% endfor %}
                             </select>
                         </div>
-            <div
+                        <div class="col-xs-2" style="display: flex; justify-content: center; align-items: center;">
-              class="col-xs-2"
-              style="display: flex; justify-content: center; align-items: center;"
-            >
                             <i class="glyphicon glyphicon-arrow-right"></i>
                         </div>
                         <div class="col-xs-5">
-              <select
+                            <select id="add_pathway_edge_products" name="edge-products"
-                id="add_pathway_edge_products"
+                                    data-actions-box='true' class="form-control" multiple data-width='100%'>
-                name="edge-products"
-                data-actions-box="true"
-                class="form-control"
-                multiple
-                data-width="100%"
-              >
                                 {% for n in pathway.nodes %}
-                  <option
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
-                    data-smiles="{{ n.default_node_label.smiles }}"
-                    value="{{ n.url }}"
-                  >
-                    {{ n.default_node_label.name|safe }}
-                  </option>
                                 {% endfor %}
                             </select>
                         </div>
                     </div>
                     <div class="row">
                         <p></p>
-            <div class="col-xs-12" id="reaction_image"></div>
+                        <div class="col-xs-12" id="reaction_image">
+
+                        </div>
                     </div>
                 </form>
             </div>
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-          type="button"
-          class="btn btn-secondary pull-left"
-          data-dismiss="modal"
-        >
-          Close
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="add_pathway_edge_modal_form_submit"
-        >
-          Submit
                 </button>
+                <button type="button" class="btn btn-primary" id="add_pathway_edge_modal_form_submit">Submit</button>
             </div>
         </div>
     </div>
+
 </div>
 <script>
+
     function reactionImage() {
         var substrates = [];
-    $("#add_pathway_edge_substrates option:selected").each(function () {
+        $('#add_pathway_edge_substrates option:selected').each(function () {
-      var smiles = $(this).data("smiles"); // read data-smiles attribute
+          var smiles = $(this).data('smiles'); // read data-smiles attribute
           substrates.push(smiles);
         });
 
-    var products = [];
+        var products = []
-    $("#add_pathway_edge_products option:selected").each(function () {
+        $('#add_pathway_edge_products option:selected').each(function () {
-      var smiles = $(this).data("smiles"); // read data-smiles attribute
+          var smiles = $(this).data('smiles'); // read data-smiles attribute
           products.push(smiles);
         });
 
         if (substrates.length > 0 && products.length > 0) {
-      reaction = substrates.join(".") + ">>" + products.join(".");
+            reaction = substrates.join('.') + ">>" + products.join('.');
-      $("#reaction_image").empty();
+            $('#reaction_image').empty();
-      $("#reaction_image").append(
+            $('#reaction_image').append(
-        "<img width='100%' src='{% url 'depict' %}?smirks=" +
+                "<img width='100%' src='{% url 'depict' %}?smirks=" + encodeURIComponent(reaction) +"'>"
-          encodeURIComponent(reaction) +
-          "'>",
             );
         }
     }
@@ -153,22 +97,30 @@
         $("#add_pathway_edge_substrates").selectpicker();
         $("#add_pathway_edge_products").selectpicker();
 
-    $("#add_pathway_edge_substrates").on("change", function (e) {
+        $("#add_pathway_edge_substrates").on('change', function (e) {
             reactionImage();
-    });
+        })
 
-    $("#add_pathway_edge_products").on("change", function (e) {
+        $("#add_pathway_edge_products").on('change', function (e) {
             reactionImage();
-    });
+        })
 
         $(function () {
-      $("#add_pathway_edge_modal_form_submit").on("click", function (e) {
+            $('#add_pathway_edge_modal_form_submit').on('click', function (e) {
                 e.preventDefault();
                 $(this).prop("disabled", true);
 
+
                 // submit form
-        $("#add_pathway_edge_modal_form").submit();
+                $('#add_pathway_edge_modal_form').submit();
             });
         });
+
     });
+
 </script>
+
+
+
+
+

templates/modals/objects/add_pathway_node_modal.html

@@ -1,102 +1,57 @@
 {% load static %}
-<div
+<div class="modal fade bs-modal-lg" id="add_pathway_node_modal" tabindex="-1" aria-labelledby="add_pathway_node_modal" aria-modal="true"
-  class="modal fade bs-modal-lg"
+     role="dialog">
-  id="add_pathway_node_modal"
-  tabindex="-1"
-  aria-labelledby="add_pathway_node_modal"
-  aria-modal="true"
-  role="dialog"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
                 <h4 class="modal-title">Add a Node</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="add_pathway_node_modal_form" accept-charset="UTF-8" action="{% url 'package pathway node list' meta.current_package.uuid pathway.uuid %}" data-remote="true" method="post">
-          id="add_pathway_node_modal_form"
-          accept-charset="UTF-8"
-          action="{% url 'package pathway node list' meta.current_package.uuid pathway.uuid %}"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <label for="node-name">Name</label>
-          <input
+                    <input id="node-name" class="form-control" name="node-name" placeholder="Name"/>
-            id="node-name"
-            class="form-control"
-            name="node-name"
-            placeholder="Name"
-          />
                     <label for="node-description">Description</label>
-          <input
+                    <input id="node-description" class="form-control" name="node-description" placeholder="Description"/>
-            id="node-description"
-            class="form-control"
-            name="node-description"
-            placeholder="Description"
-          />
                     <label for="node-smiles">SMILES</label>
-          <input
+                    <input type="text" class="form-control" name="node-smiles" placeholder="SMILES" id="node-smiles">
-            type="text"
-            class="form-control"
-            name="node-smiles"
-            placeholder="SMILES"
-            id="node-smiles"
-          />
                     <p></p>
                     <div>
-            <iframe
+                        <iframe id="add_node_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-              id="add_node_ketcher"
+                                height="510"></iframe>
-              src="{% static '/js/ketcher2/ketcher.html' %}"
-              width="100%"
-              height="510"
-            ></iframe>
                     </div>
                     <p></p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-          type="button"
-          class="btn btn-secondary pull-left"
-          data-dismiss="modal"
-        >
-          Close
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="add_pathway_node_modal_form_submit"
-        >
-          Submit
                 </button>
+                <button type="button" class="btn btn-primary" id="add_pathway_node_modal_form_submit">Submit</button>
             </div>
         </div>
     </div>
+
 </div>
 <script>
+
 function newStructureModalketcherToNewStructureModalTextInput() {
-    $("#node-smiles").val(this.ketcher.getSmiles());
+    $('#node-smiles').val(this.ketcher.getSmiles());
 }
 
 $(function() {
-    $("#add_node_ketcher").on("load", function () {
+
+    $('#add_node_ketcher').on('load', function() {
         const checkKetcherReady = () => {
-        win = this.contentWindow;
+            win = this.contentWindow
-        if (win.ketcher && "editor" in win.ketcher) {
+            if (win.ketcher && 'editor' in win.ketcher) {
                 win.ketcher.editor.event.change.handlers.push({
                     once: false,
                     priority: 0,
                     f: newStructureModalketcherToNewStructureModalTextInput,
-            ketcher: win.ketcher,
+                    ketcher: win.ketcher
                 });
             } else {
                 setTimeout(checkKetcherReady, 100);
@@ -104,16 +59,20 @@
         };
 
         checkKetcherReady();
-    });
+    })
 
     $(function() {
-      $("#add_pathway_node_modal_form_submit").on("click", function (e) {
+        $('#add_pathway_node_modal_form_submit').on('click', function(e) {
             e.preventDefault();
             $(this).prop("disabled",true);
 
+
+
             // submit form
-        $("#add_pathway_node_modal_form").submit();
+            $('#add_pathway_node_modal_form').submit();
         });
     });
+
 });
+
 </script>

templates/modals/objects/add_structure_modal.html

@@ -1,102 +1,57 @@
 {% load static %}
-<div
+<div class="modal fade bs-modal-lg" id="add_structure_modal" tabindex="-1" aria-labelledby="add_structure_modal" aria-modal="true"
-  class="modal fade bs-modal-lg"
+     role="dialog">
-  id="add_structure_modal"
-  tabindex="-1"
-  aria-labelledby="add_structure_modal"
-  aria-modal="true"
-  role="dialog"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">×</span>
                 </button>
                 <h4 class="modal-title">Create a new Structure</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="add_structure_modal_form" accept-charset="UTF-8" action="{% url 'package compound structure list' meta.current_package.uuid compound.uuid %}" data-remote="true" method="post">
-          id="add_structure_modal_form"
-          accept-charset="UTF-8"
-          action="{% url 'package compound structure list' meta.current_package.uuid compound.uuid %}"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <label for="structure-name">Name</label>
-          <input
+                    <input id="structure-name" class="form-control" name="structure-name" placeholder="Name"/>
-            id="structure-name"
-            class="form-control"
-            name="structure-name"
-            placeholder="Name"
-          />
                     <label for="structure-description">Description</label>
-          <input
+                    <input id="structure-description" class="form-control" name="structure-description" placeholder="Description"/>
-            id="structure-description"
-            class="form-control"
-            name="structure-description"
-            placeholder="Description"
-          />
                     <label for="structure-smiles">SMILES</label>
-          <input
+                    <input type="text" class="form-control" name="structure-smiles" placeholder="SMILES" id="structure-smiles">
-            type="text"
-            class="form-control"
-            name="structure-smiles"
-            placeholder="SMILES"
-            id="structure-smiles"
-          />
                     <p></p>
                     <div>
-            <iframe
+                        <iframe id="add_structure_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-              id="add_structure_ketcher"
+                                height="510"></iframe>
-              src="{% static '/js/ketcher2/ketcher.html' %}"
-              width="100%"
-              height="510"
-            ></iframe>
                     </div>
                     <p></p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-          type="button"
-          class="btn btn-secondary pull-left"
-          data-dismiss="modal"
-        >
-          Close
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="add_structure_modal_form_submit"
-        >
-          Submit
                 </button>
+                <button type="button" class="btn btn-primary" id="add_structure_modal_form_submit">Submit</button>
             </div>
         </div>
     </div>
+
 </div>
 <script>
+
 function newStructureModalketcherToNewStructureModalTextInput() {
-    $("#structure-smiles").val(this.ketcher.getSmiles());
+    $('#structure-smiles').val(this.ketcher.getSmiles());
 }
 
 $(function() {
-    $("#add_structure_ketcher").on("load", function () {
+
+    $('#add_structure_ketcher').on('load', function() {
         const checkKetcherReady = () => {
-        win = this.contentWindow;
+            win = this.contentWindow
-        if (win.ketcher && "editor" in win.ketcher) {
+            if (win.ketcher && 'editor' in win.ketcher) {
                 win.ketcher.editor.event.change.handlers.push({
                     once: false,
                     priority: 0,
                     f: newStructureModalketcherToNewStructureModalTextInput,
-            ketcher: win.ketcher,
+                    ketcher: win.ketcher
                 });
             } else {
                 setTimeout(checkKetcherReady, 100);
@@ -104,16 +59,20 @@
         };
 
         checkKetcherReady();
-    });
+    })
 
     $(function() {
-      $("#add_structure_modal_form_submit").on("click", function (e) {
+        $('#add_structure_modal_form_submit').on('click', function(e) {
             e.preventDefault();
             $(this).prop("disabled",true);
 
+
+
             // submit form
-        $("#add_structure_modal_form").submit();
+            $('#add_structure_modal_form').submit();
         });
     });
+
 });
+
 </script>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -5,38 +5,21 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h3 class="modal-title">Delete Edge</h3>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 Deletes the Edge. Nodes referenced by this edge will remain.
                 <p></p>
-        <form
+                <form id="delete-pathway-edge-modal-form" accept-charset="UTF-8" action="" data-remote="true"
-          id="delete-pathway-edge-modal-form"
+                      method="post">
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <select
+                    <select id="delete_pathway_edge_edges" name="edge-url"
-            id="delete_pathway_edge_edges"
+                            data-actions-box='true' class="form-control" data-width='100%'>
-            name="edge-url"
+                        <option value="" disabled selected>Select Reaction to delete</option>
-            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"/>
@@ -45,16 +28,8 @@
                 <div id="delete_pathway_edge_image"></div>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="delete-pathway-edge-modal-submit">Delete</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="delete-pathway-edge-modal-submit"
-        >
-          Delete
-        </button>
             </div>
         </div>
     </div>
@@ -63,27 +38,28 @@
     $(function () {
         $("#delete_pathway_edge_edges").selectpicker();
 
-    $("#delete_pathway_edge_edges").on("change", function (e) {
+        $("#delete_pathway_edge_edges").on('change', function (e) {
-      edge_url = $("#delete_pathway_edge_edges option:selected").val();
+            edge_url = $('#delete_pathway_edge_edges option:selected').val()
 
             if (edge_url !== "") {
-        $("#delete_pathway_edge_image").empty();
+                $('#delete_pathway_edge_image').empty();
-        $("#delete_pathway_edge_image").append(
+                $('#delete_pathway_edge_image').append(
-          "<img width='100%' src='" + edge_url + "?image=svg'>",
+                    "<img width='100%' src='" + edge_url + "?image=svg'>"
                 );
             }
-    });
+        })
 
-    $("#delete-pathway-edge-modal-submit").click(function (e) {
+        $('#delete-pathway-edge-modal-submit').click(function (e) {
             e.preventDefault();
-      edge_url = $("#delete_pathway_edge_edges option:selected").val();
+            edge_url = $('#delete_pathway_edge_edges option:selected').val()
 
             if (edge_url === "") {
                 return;
             }
 
-      $("#delete-pathway-edge-modal-form").attr("action", edge_url);
+            $('#delete-pathway-edge-modal-form').attr('action', edge_url)
-      $("#delete-pathway-edge-modal-form").submit();
+            $('#delete-pathway-edge-modal-form').submit();
-    });
         });
+
+    })
 </script>

templates/modals/objects/delete_pathway_node_modal.html

@@ -1,46 +1,25 @@
 {% load static %}
-
 <!-- Delete Node -->
 <div id="delete_pathway_node_modal" class="modal" tabindex="-1">
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
                 <h3 class="modal-title">Delete Node</h3>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-        Deletes the Node. Edges having this Node as Substrate or Product will be
+                Deletes the Node. Edges having this Node as Substrate or Product will be removed as well.
-        removed as well.
                 <p></p>
-        <form
+                <form id="delete-pathway-node-modal-form" accept-charset="UTF-8" action="" data-remote="true"
-          id="delete-pathway-node-modal-form"
+                      method="post">
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <select
+                    <select id="delete_pathway_node_nodes" name="node-url"
-            id="delete_pathway_node_nodes"
+                            data-actions-box='true' class="form-control" data-width='100%'>
-            name="node-url"
+                        <option value="" disabled selected>Select Compound to delete</option>
-            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 }}">
+                            <option value="{{ n.url }}">{{ n.default_node_label.name }}</option>
-                {{ n.default_node_label.name|safe }}
-              </option>
                         {% endfor %}
                     </select>
                     <input type="hidden" id="hidden" name="hidden" value="delete"/>
@@ -49,16 +28,8 @@
                 <div id="delete_pathway_node_image"></div>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="delete-pathway-node-modal-submit">Delete</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="delete-pathway-node-modal-submit"
-        >
-          Delete
-        </button>
             </div>
         </div>
     </div>
@@ -67,27 +38,28 @@
     $(function () {
         $("#delete_pathway_node_nodes").selectpicker();
 
-    $("#delete_pathway_node_nodes").on("change", function (e) {
+        $("#delete_pathway_node_nodes").on('change', function (e) {
-      node_url = $("#delete_pathway_node_nodes option:selected").val();
+            node_url = $('#delete_pathway_node_nodes option:selected').val()
 
             if (node_url !== "") {
-        $("#delete_pathway_node_image").empty();
+                $('#delete_pathway_node_image').empty();
-        $("#delete_pathway_node_image").append(
+                $('#delete_pathway_node_image').append(
-          "<img width='100%' src='" + node_url + "?image=svg'>",
+                    "<img width='100%' src='" + node_url + "?image=svg'>"
                 );
             }
-    });
+        })
 
-    $("#delete-pathway-node-modal-submit").click(function (e) {
+        $('#delete-pathway-node-modal-submit').click(function (e) {
             e.preventDefault();
-      node_url = $("#delete_pathway_node_nodes option:selected").val();
+            node_url = $('#delete_pathway_node_nodes option:selected').val()
 
             if (node_url === "") {
                 return;
             }
 
-      $("#delete-pathway-node-modal-form").attr("action", node_url);
+            $('#delete-pathway-node-modal-form').attr('action', node_url)
-      $("#delete-pathway-node-modal-form").submit();
+            $('#delete-pathway-node-modal-form').submit();
-    });
         });
+
+    })
 </script>

templates/modals/objects/download_pathway_csv_modal.html

@@ -5,49 +5,32 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h3 class="modal-title">Download Pathway as CSV</h3>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-        By clicking on Download the Pathway will be converted into a CSV and
+                By clicking on Download the Pathway will be converted into a CSV and directly downloaded.
-        directly downloaded.
+                <form id="download-pathway-csv-modal-form" accept-charset="UTF-8" action="{{ pathway.url }}"
-        <form
+                      data-remote="true" method="GET">
-          id="download-pathway-csv-modal-form"
-          accept-charset="UTF-8"
-          action="{{ pathway.url }}"
-          data-remote="true"
-          method="GET"
-        >
                     <input type="hidden" name="download" value="true"/>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="download-pathway-csv-modal-submit">Download</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="download-pathway-csv-modal-submit"
-        >
-          Download
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
     $(function () {
-    $("#download-pathway-csv-modal-submit").click(function (e) {
+
+        $('#download-pathway-csv-modal-submit').click(function (e) {
             e.preventDefault();
-      $("#download-pathway-csv-modal-form").submit();
+            $('#download-pathway-csv-modal-form').submit();
-      $("#download_pathway_csv_modal").modal("hide");
+            $('#download_pathway_csv_modal').modal('hide');
-    });
         });
+
+    })
 </script>

templates/modals/objects/download_pathway_image_modal.html

@@ -5,12 +5,7 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h3 class="modal-title">Download Pathway as Image</h3>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
@@ -18,26 +13,20 @@
                 By clicking on Download the Pathway will be saved as SVG.
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="download-pathway-image-modal-submit">Download</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="download-pathway-image-modal-submit"
-        >
-          Download
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
     $(function () {
-    $("#download-pathway-image-modal-submit").click(function (e) {
+
+        $('#download-pathway-image-modal-submit').click(function (e) {
             e.preventDefault();
-      downloadSVG($("#pwsvg")[0], '{{ pathway.name.split|join:"_" }}.svg');
+            downloadSVG($('#pwsvg')[0], '{{ pathway.name.split|join:"_" }}.svg')
-      $("#download_pathway_image_modal").modal("hide");
+            $('#download_pathway_image_modal').modal('hide');
-    });
         });
+
+    })
 </script>

templates/modals/objects/edit_compound_modal.html

@@ -5,66 +5,42 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Edit Compound</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>Edit Compound.</p>
-        <form
+                <form id="edit-compound-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-compound-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="compound-name">Name</label>
-            <input
+                        <input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name}}">
-              id="compound-name"
-              class="form-control"
-              name="compound-name"
-              value="{{ compound.name|safe }}"
-            />
                     </p>
                     <p>
                         <label for="compound-description">Description</label>
-            <input
+                        <input id="compound-description" type="text" class="form-control"
-              id="compound-description"
+                               value="{{ compound.description }}"
-              type="text"
+                               name="compound-description">
-              class="form-control"
-              value="{{ compound.description|safe }}"
-              name="compound-description"
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-compound-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-compound-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
 $(function() {
-    $("#edit-compound-modal-submit").click(function (e) {
+
+    $('#edit-compound-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-compound-modal-form").submit();
+        $('#edit-compound-modal-form').submit();
     });
+
 });
+
+
 </script>

templates/modals/objects/edit_compound_structure_modal.html

@@ -5,66 +5,41 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Create a Compound</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>Edit a Compound Structure.</p>
-        <form
+                <form id="edit-compound-structure-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-compound-structure-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="compound-structure-name">Name</label>
-            <input
+                        <input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name }}">
-              id="compound-structure-name"
-              class="form-control"
-              name="compound-structure-name"
-              value="{{ compound_structure.name|safe }}"
-            />
                     </p>
                     <p>
                         <label for="compound-structure-description">Description</label>
-            <input
+                        <input id="compound-structure-description" type="text" class="form-control"
-              id="compound-structure-description"
+                               value="{{ compound_structure.description }}" name="compound-structure-description">
-              type="text"
-              class="form-control"
-              value="{{ compound_structure.description|safe }}"
-              name="compound-structure-description"
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-compound-structure-modal-submit">Create</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-compound-structure-modal-submit"
-        >
-          Create
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
 $(function() {
-    $("#edit-compound-structure-modal-submit").click(function (e) {
+
+    $('#edit-compound-structure-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-compound-structure-modal-form").submit();
+        $('#edit-compound-structure-modal-form').submit();
     });
+
 });
+
+
 </script>

templates/modals/objects/edit_group_member_modal.html

@@ -5,20 +5,15 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Add or Remove Group Member</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>
-          To add member (either User or entire Groups) to this group select the
+                    To add member (either User or entire Groups) to this group select the entity you want to add below
-          entity you want to add below and click the check mark.
+                    and click the check mark.
-          <br />
+                    <br>
                     To remove member simply click the <code>X</code> next to the member.
                 </p>
 
@@ -32,36 +27,25 @@
 				</div>
 
                 <div class="row">
-          <form
+                    <form id="modal-form-group-member" class="form-inline" role="form" accept-charset="UTF-8" action=""
-            id="modal-form-group-member"
+                          data-remote="true" method="post">
-            class="form-inline"
-            role="form"
-            accept-charset="UTF-8"
-            action=""
-            data-remote="true"
-            method="post"
-          >
                         {% csrf_token %}
                         <div class="col-xs-8">
-              <select
+                            <select id="select_member" name="member" data-actions-box='true'
-                id="select_member"
+                                    class="selPackages" data-width='100%'>
-                name="member"
-                data-actions-box="true"
-                class="selPackages"
-                data-width="100%"
-              >
                                 <option disabled selected>User</option>
                                 {% for u in users %}
                                 <option value="{{ u.url }}">{{ u.username }}</option>
                                 {% 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" />
+                            <input type="hidden" name="action" value="add">
+                        </div>
+                        <div class="col-xs-2">
                         </div>
-            <div class="col-xs-2"></div>
                         <div class="col-xs-2">
                             <button type="submit" style="width:60%;" class="btn col-xs-2">
                                 <span class="glyphicon glyphicon-ok"></span>
@@ -72,22 +56,16 @@
                 <p></p>
                 {% for u in group.user_member.all %}
                 <div class="row">
-            <form
+                    <form id="modal-form-group-member_{{ u.uuid }}" class="form-inline" role="form"
-              id="modal-form-group-member_{{ u.uuid }}"
+                          accept-charset="UTF-8" action="" data-remote="true" method="post">
-              class="form-inline"
-              role="form"
-              accept-charset="UTF-8"
-              action=""
-              data-remote="true"
-              method="post"
-            >
                         {% csrf_token %}
                         <div class="col-xs-8">
                             {{ u.username }}
                             <input type="hidden" name="member" value="{{ u.url }}"/>
-                <input type="hidden" name="action" value="remove" />
+                            <input type="hidden" name="action" value="remove">
+                        </div>
+                        <div class="col-xs-2">
                         </div>
-              <div class="col-xs-2"></div>
                         <div class="col-xs-2">
                             <button type="submit" style="width:60%;" class="btn col-xs-2">
                                 <span class="glyphicon glyphicon-trash"></span>
@@ -99,22 +77,16 @@
                 <p></p>
                 {% for g in group.group_member.all %}
                 <div class="row">
-            <form
+                    <form id="modal-form-group-member_{{ g.uuid }}" class="form-inline" role="form"
-              id="modal-form-group-member_{{ g.uuid }}"
+                          accept-charset="UTF-8" action="" data-remote="true" method="post">
-              class="form-inline"
-              role="form"
-              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" />
+                            <input type="hidden" name="action" value="remove">
+                        </div>
+                        <div class="col-xs-2">
                         </div>
-              <div class="col-xs-2"></div>
                         <div class="col-xs-2">
                             <button type="submit" style="width:60%;" class="btn col-xs-2">
                                 <span class="glyphicon glyphicon-trash"></span>
@@ -123,29 +95,26 @@
                     </form>
                 </div>
                 {% endfor %}
+
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-package-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
+
+
 $(function() {
-    $("#edit-package-modal-submit").click(function (e) {
+
+    $('#edit-package-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-package-modal-form").submit();
+        $('#edit-package-modal-form').submit();
     });
 
     $("#select_member").selectpicker();
-  });
+
+})
 </script>

templates/modals/objects/edit_model_modal.html

@@ -4,68 +4,41 @@
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
                 <h3 class="modal-title">Update Model</h3>
             </div>
             <div class="modal-body">
                 <p>Alter Name and Description of the Model.</p>
-        <form
+                <form id="edit-model-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-model-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="model-name">Name</label>
-            <input
+                        <input id="model-name" type="text" class="form-control" name="model-name"
-              id="model-name"
+                               value="{{ model.name }}">
-              type="text"
-              class="form-control"
-              name="model-name"
-              value="{{ model.name|safe }}"
-            />
                     </p>
                     <p>
                         <label for="model-description">Description</label>
-            <input
+                        <input id="model-description" type="text" class="form-control" name="model-description"
-              id="model-description"
+                               value="{{ model.description }}">
-              type="text"
-              class="form-control"
-              name="model-description"
-              value="{{ model.description|safe }}"
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-model-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-model-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
     $(function () {
-    $("#edit-model-modal-submit").click(function (e) {
+
+        $('#edit-model-modal-submit').click(function (e) {
             e.preventDefault();
-      $("#edit-model-modal-form").submit();
+            $('#edit-model-modal-form').submit();
-    });
         });
+
+    })
 </script>