fix: more defensive ketcher reference

FIx display on the login page

Reviewed-on: enviPath/enviPy#203
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>

.gitea/workflows/ci.yaml

@@ -105,7 +105,7 @@ jobs:
           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
+      - name: Run Django Migrations
         run: |
           source .venv/bin/activate
           python manage.py migrate --noinput

.gitignore

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

.pre-commit-config.yaml

@@ -8,6 +8,7 @@ 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
@@ -20,6 +21,15 @@ 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

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

README.md

@@ -7,11 +7,13 @@ 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) - A fast Python package installer and resolver.
+- [uv](https://github.com/astral-sh/uv) - Python package manager
-- **Docker and Docker Compose** - Required for running the PostgreSQL database.
+- **Docker and Docker Compose** - Required for running 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
 
@@ -23,7 +25,12 @@ Then, sync the project dependencies. This will create a virtual environment in `
 uv sync --dev
 ```
 
-> **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.
+Note on RDkit installation: if you have rdkit installed on your system globally with a different version of python, the installation will try to link against that and subsequent calls fail. Only option remove global rdkit and rerun sync.
+
+---
+
+The frontend requires `pnpm` to correctly display in development.
+[Install it here](https://pnpm.io/installation).
 
 ### 2. Set Up Environment File
 
@@ -44,6 +51,7 @@ 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).
@@ -54,9 +62,12 @@ 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`.
 
-#### Other useful Poe commands:
+**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
 
 You can list all available commands by running `uv run poe --help`.
 
@@ -66,6 +77,7 @@ 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

@@ -87,12 +87,13 @@ 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'}
+ALLOWED_HTML_TAGS = {"b", "i", "u", "br", "em", "mark", "p", "s", "strong"}
 
 WSGI_APPLICATION = "envipath.wsgi.application"
 
@@ -245,6 +246,7 @@ 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:
@@ -345,6 +347,14 @@ LOGIN_EXEMPT_URLS = [
     "/password_reset/",
     "/reset/",
     "/microsoft/",
+    "/terms",
+    "/privacy",
+    "/cookie-policy",
+    "/about",
+    "/contact",
+    "/jobs",
+    "/cite",
+    "/legal",
 ]
 
 # MS AD/Entra

epdb/admin.py

@@ -21,6 +21,7 @@ from .models import (
     ExternalDatabase,
     ExternalIdentifier,
     JobLog,
+    License,
 )
 
 
@@ -62,6 +63,10 @@ class EnviFormerAdmin(EPAdmin):
     pass
 
 
+class LicenseAdmin(admin.ModelAdmin):
+    list_display = ["cc_string", "link", "image_link"]
+
+
 class CompoundAdmin(EPAdmin):
     pass
 
@@ -118,6 +123,7 @@ 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

@@ -0,0 +1,32 @@
+"""
+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/management/commands/bootstrap.py

@@ -12,10 +12,16 @@ 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():
@@ -83,6 +89,17 @@ 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
@@ -157,6 +174,10 @@ 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

@@ -0,0 +1,18 @@
+# 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

@@ -0,0 +1,59 @@
+# 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

@@ -655,6 +655,7 @@ 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")
 

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 EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User, Edge
+from epdb.models import Edge, EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User
 
 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 = datetime.now()
+        log.done_at = timezone.now()
         log.task_result = str(x) if x else None
         log.save()
 

epdb/urls.py

@@ -48,6 +48,7 @@ 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
@@ -141,6 +142,11 @@ urlpatterns = [
         v.package_pathway,
         name="package pathway detail",
     ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/predict$",
+        v.package_predict_pathway,
+        name="package predict pathway",
+    ),
     # Pathway Nodes
     re_path(
         rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",
@@ -193,4 +199,13 @@ 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

@@ -90,6 +90,7 @@ def login(request):
         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
@@ -104,6 +105,7 @@ 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:
@@ -141,9 +143,14 @@ def register(request):
     context = get_base_context(request)
 
     if request.method == "GET":
-        context["title"] = "enviPath"
+        # Redirect to unified login page with signup tab
-        context["next"] = request.GET.get("next", "")
+        next_url = request.GET.get("next", "")
-        return render(request, "static/register.html", context)
+        redirect_url = reverse("login") + "#signup"
+
+        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"):
@@ -156,18 +163,18 @@ def register(request):
 
         if not (username and email and password):
             context["message"] = "Invalid username/email/password"
-            return render(request, "static/register.html", context)
+            return render(request, "static/login.html", context)
 
         if password != rpassword or password == "":
             context["message"] = "Registration failed, provided passwords differ!"
-            return render(request, "static/register.html", context)
+            return render(request, "static/login.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/register.html", context)
+            return render(request, "static/login.html", context)
 
         if s.ADMIN_APPROVAL_REQUIRED:
             context["success_message"] = (
@@ -355,6 +362,34 @@ 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)
 
@@ -674,8 +709,7 @@ def search(request):
 
     if request.method == "GET":
         package_urls = request.GET.getlist("packages")
-        searchterm = request.GET.get("search").strip()
+        searchterm = request.GET.get("search", "").strip()
-
         mode = request.GET.get("mode")
 
         # add HTTP_ACCEPT check to differentiate between index and ajax call
@@ -776,6 +810,7 @@ def package_models(request, package_uuid):
 
     elif request.method == "POST":
         log_post_params(request)
+
         name = request.POST.get("model-name")
         description = request.POST.get("model-description")
 
@@ -936,6 +971,12 @@ 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()
@@ -1065,9 +1106,7 @@ def package(request, package_uuid):
         write = request.POST.get("write") == "on"
         owner = request.POST.get("owner") == "on"
 
-        license = request.POST.get("license")
+        cc_string = 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
@@ -1095,24 +1134,15 @@ 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:
+            else:  # Get the license and assign it to the package
-                if current_package.license is not None:
+                current_package.license = License.objects.get(cc_string=cc_string)
-                    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)
@@ -1167,7 +1197,7 @@ def package_compounds(request, package_uuid):
 
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
-        compound_smiles = request.POST.get("compound-smiles").strip()
+        compound_smiles = request.POST.get("compound-smiles")
         compound_description = request.POST.get("compound-description")
 
         c = Compound.create(current_package, compound_smiles, compound_name, compound_description)
@@ -1294,7 +1324,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
 
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
-        structure_smiles = request.POST.get("structure-smiles").strip()
+        structure_smiles = request.POST.get("structure-smiles")
         structure_description = request.POST.get("structure-description")
 
         try:
@@ -1476,11 +1506,11 @@ def package_rules(request, package_uuid):
 
         # Obtain parameters as required by rule type
         if rule_type == "SimpleAmbitRule":
-            params["smirks"] = request.POST.get("rule-smirks").strip()
+            params["smirks"] = request.POST.get("rule-smirks")
             params["reactant_filter_smarts"] = request.POST.get("rule-reactant-smarts")
             params["product_filter_smarts"] = request.POST.get("rule-product-smarts")
         elif rule_type == "SimpleRDKitRule":
-            params["reaction_smarts"] = request.POST.get("rule-reaction-smarts").strip()
+            params["reaction_smarts"] = request.POST.get("rule-reaction-smarts")
         elif rule_type == "ParallelRule":
             pass
         elif rule_type == "SequentialRule":
@@ -1677,8 +1707,7 @@ def package_reactions(request, package_uuid):
     elif request.method == "POST":
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
-
+        reactions_smirks = request.POST.get("reaction-smirks")
-        reactions_smirks = request.POST.get("reaction-smirks").strip()
         educts = reactions_smirks.split(">>")[0].split(".")
         products = reactions_smirks.split(">>")[1].split(".")
 
@@ -2252,6 +2281,7 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
 
     elif request.method == "POST":
         log_post_params(request)
+
         edge_name = request.POST.get("edge-name")
         edge_description = request.POST.get("edge-description")
 
@@ -2894,3 +2924,60 @@ 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

@@ -0,0 +1,25 @@
+{
+  "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

@@ -1,4 +1,740 @@
-lockfileVersion: 6.0
+lockfileVersion: '9.0'
-specifiers: {}
+
-dependencies: {}
+settings:
-packages: {}
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+        version: 5.4.3
+      postcss:
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+        version: 8.5.6
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+        version: 3.6.2
+      prettier-plugin-jinja-template:
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+        version: 2.1.0(prettier@3.6.2)
+      prettier-plugin-tailwindcss:
+        specifier: ^0.7.1
+        version: 0.7.1(prettier@3.6.2)
+      tailwindcss:
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+        version: 4.1.16
+
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+    resolution: {integrity: sha512-Cfd46gdmj1vQ+lR6VRTTadNHu6ALuw2pKR9lYq4FnhvgBc4zWY1EtZcAc6EffShbb1MFrIPfLDXD6Xprbnni4w==}
+    engines: {node: '>= 12.0.0'}
+    cpu: [x64]
+    os: [linux]
+
+  lightningcss-linux-x64-musl@1.30.2:
+    resolution: {integrity: sha512-XJaLUUFXb6/QG2lGIW6aIk6jKdtjtcffUT0NKvIqhSBY3hh9Ch+1LCeH80dR9q9LBjG3ewbDjnumefsLsP6aiA==}
+    engines: {node: '>= 12.0.0'}
+    cpu: [x64]
+    os: [linux]
+
+  lightningcss-win32-arm64-msvc@1.30.2:
+    resolution: {integrity: sha512-FZn+vaj7zLv//D/192WFFVA0RgHawIcHqLX9xuWiQt7P0PtdFEVaxgF9rjM/IRYHQXNnk61/H/gb2Ei+kUQ4xQ==}
+    engines: {node: '>= 12.0.0'}
+    cpu: [arm64]
+    os: [win32]
+
+  lightningcss-win32-x64-msvc@1.30.2:
+    resolution: {integrity: sha512-5g1yc73p+iAkid5phb4oVFMB45417DkRevRbt/El/gKXJk4jid+vPFF/AXbxn05Aky8PapwzZrdJShv5C0avjw==}
+    engines: {node: '>= 12.0.0'}
+    cpu: [x64]
+    os: [win32]
+
+  lightningcss@1.30.2:
+    resolution: {integrity: sha512-utfs7Pr5uJyyvDETitgsaqSyjCb2qNRAtuqUeWIAKztsOYdcACf2KtARYXg2pSvhkt+9NfoaNY7fxjl6nuMjIQ==}
+    engines: {node: '>= 12.0.0'}
+
+  magic-string@0.30.21:
+    resolution: {integrity: sha512-vd2F4YUyEXKGcLHoq+TEyCjxueSeHnFxyyjNp80yg0XV4vUhnDer/lvvlqM/arB5bXQN5K2/3oinyCRyx8T2CQ==}
+
+  micromatch@4.0.8:
+    resolution: {integrity: sha512-PXwfBhYu0hBCPw8Dn0E+WDYb7af3dSLVWKi3HGv84IdF4TyFoC0ysxFd0Goxw7nSv4T/PzEJQxsYsEiFCKo2BA==}
+    engines: {node: '>=8.6'}
+
+  mri@1.2.0:
+    resolution: {integrity: sha512-tzzskb3bG8LvYGFF/mDTpq3jpI6Q9wc3LEmBaghu+DdCssd1FakN7Bc0hVNmEyGq1bq3RgfkCb3cmQLpNPOroA==}
+    engines: {node: '>=4'}
+
+  nanoid@3.3.11:
+    resolution: {integrity: sha512-N8SpfPUnUp1bK+PMYW8qSWdl9U+wwNWI4QKxOYDy9JAro3WMX7p2OeVRF9v+347pnakNevPmiHhNmZ2HbFA76w==}
+    engines: {node: ^10 || ^12 || ^13.7 || ^14 || >=15.0.1}
+    hasBin: true
+
+  node-addon-api@7.1.1:
+    resolution: {integrity: sha512-5m3bsyrjFWE1xf7nz7YXdN4udnVtXK6/Yfgn5qnahL6bCkf2yKt4k3nuTKAtT4r3IG8JNR2ncsIMdZuAzJjHQQ==}
+
+  picocolors@1.1.1:
+    resolution: {integrity: sha512-xceH2snhtb5M9liqDsmEw56le376mTZkEX/jEb/RxNFyegNul7eNslCXP9FDj/Lcu0X8KEyMceP2ntpaHrDEVA==}
+
+  picomatch@2.3.1:
+    resolution: {integrity: sha512-JU3teHTNjmE2VCGFzuY8EXzCDVwEqB2a8fsIvwaStHhAWJEeVd1o1QD80CU6+ZdEXXSLbSsuLwJjkCBWqRQUVA==}
+    engines: {node: '>=8.6'}
+
+  postcss@8.5.6:
+    resolution: {integrity: sha512-3Ybi1tAuwAP9s0r1UQ2J4n5Y0G05bJkpUIO0/bI9MhwmD70S5aTWbXGBwxHrelT+XM1k6dM0pk+SwNkpTRN7Pg==}
+    engines: {node: ^10 || ^12 || >=14}
+
+  prettier-plugin-jinja-template@2.1.0:
+    resolution: {integrity: sha512-mzoCp2Oy9BDSug80fw3B3J4n4KQj1hRvoQOL1akqcDKBb5nvYxrik9zUEDs4AEJ6nK7QDTGoH0y9rx7AlnQ78Q==}
+    peerDependencies:
+      prettier: ^3.0.0
+
+  prettier-plugin-tailwindcss@0.7.1:
+    resolution: {integrity: sha512-Bzv1LZcuiR1Sk02iJTS1QzlFNp/o5l2p3xkopwOrbPmtMeh3fK9rVW5M3neBQzHq+kGKj/4LGQMTNcTH4NGPtQ==}
+    engines: {node: '>=20.19'}
+    peerDependencies:
+      '@ianvs/prettier-plugin-sort-imports': '*'
+      '@prettier/plugin-hermes': '*'
+      '@prettier/plugin-oxc': '*'
+      '@prettier/plugin-pug': '*'
+      '@shopify/prettier-plugin-liquid': '*'
+      '@trivago/prettier-plugin-sort-imports': '*'
+      '@zackad/prettier-plugin-twig': '*'
+      prettier: ^3.0
+      prettier-plugin-astro: '*'
+      prettier-plugin-css-order: '*'
+      prettier-plugin-jsdoc: '*'
+      prettier-plugin-marko: '*'
+      prettier-plugin-multiline-arrays: '*'
+      prettier-plugin-organize-attributes: '*'
+      prettier-plugin-organize-imports: '*'
+      prettier-plugin-sort-imports: '*'
+      prettier-plugin-svelte: '*'
+    peerDependenciesMeta:
+      '@ianvs/prettier-plugin-sort-imports':
+        optional: true
+      '@prettier/plugin-hermes':
+        optional: true
+      '@prettier/plugin-oxc':
+        optional: true
+      '@prettier/plugin-pug':
+        optional: true
+      '@shopify/prettier-plugin-liquid':
+        optional: true
+      '@trivago/prettier-plugin-sort-imports':
+        optional: true
+      '@zackad/prettier-plugin-twig':
+        optional: true
+      prettier-plugin-astro:
+        optional: true
+      prettier-plugin-css-order:
+        optional: true
+      prettier-plugin-jsdoc:
+        optional: true
+      prettier-plugin-marko:
+        optional: true
+      prettier-plugin-multiline-arrays:
+        optional: true
+      prettier-plugin-organize-attributes:
+        optional: true
+      prettier-plugin-organize-imports:
+        optional: true
+      prettier-plugin-sort-imports:
+        optional: true
+      prettier-plugin-svelte:
+        optional: true
+
+  prettier@3.6.2:
+    resolution: {integrity: sha512-I7AIg5boAr5R0FFtJ6rCfD+LFsWHp81dolrFD8S79U9tb8Az2nGrJncnMSnys+bpQJfRUzqs9hnA81OAA3hCuQ==}
+    engines: {node: '>=14'}
+    hasBin: true
+
+  source-map-js@1.2.1:
+    resolution: {integrity: sha512-UXWMKhLOwVKb728IUtQPXxfYU+usdybtUrK/8uGE8CQMvrhOpwvzDBwj0QhSL7MQc7vIsISBG8VQ8+IDQxpfQA==}
+    engines: {node: '>=0.10.0'}
+
+  tailwindcss@4.1.16:
+    resolution: {integrity: sha512-pONL5awpaQX4LN5eiv7moSiSPd/DLDzKVRJz8Q9PgzmAdd1R4307GQS2ZpfiN7ZmekdQrfhZZiSE5jkLR4WNaA==}
+
+  tapable@2.3.0:
+    resolution: {integrity: sha512-g9ljZiwki/LfxmQADO3dEY1CbpmXT5Hm2fJ+QaGKwSXUylMybePR7/67YW7jOrrvjEgL1Fmz5kzyAjWVWLlucg==}
+    engines: {node: '>=6'}
+
+  to-regex-range@5.0.1:
+    resolution: {integrity: sha512-65P7iz6X5yEr1cwcgvQxbbIw7Uk3gOy5dIdtZ4rDveLqhrdJP+Li/Hx6tyK0NEb+2GCyneCMJiGqrADCSNk8sQ==}
+    engines: {node: '>=8.0'}
+
+snapshots:
+
+  '@alloc/quick-lru@5.2.0': {}
+
+  '@jridgewell/gen-mapping@0.3.13':
+    dependencies:
+      '@jridgewell/sourcemap-codec': 1.5.5
+      '@jridgewell/trace-mapping': 0.3.31
+
+  '@jridgewell/remapping@2.3.5':
+    dependencies:
+      '@jridgewell/gen-mapping': 0.3.13
+      '@jridgewell/trace-mapping': 0.3.31
+
+  '@jridgewell/resolve-uri@3.1.2': {}
+
+  '@jridgewell/sourcemap-codec@1.5.5': {}
+
+  '@jridgewell/trace-mapping@0.3.31':
+    dependencies:
+      '@jridgewell/resolve-uri': 3.1.2
+      '@jridgewell/sourcemap-codec': 1.5.5
+
+  '@parcel/watcher-android-arm64@2.5.1':
+    optional: true
+
+  '@parcel/watcher-darwin-arm64@2.5.1':
+    optional: true
+
+  '@parcel/watcher-darwin-x64@2.5.1':
+    optional: true
+
+  '@parcel/watcher-freebsd-x64@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-arm-glibc@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-arm-musl@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-arm64-glibc@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-arm64-musl@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-x64-glibc@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-x64-musl@2.5.1':
+    optional: true
+
+  '@parcel/watcher-win32-arm64@2.5.1':
+    optional: true
+
+  '@parcel/watcher-win32-ia32@2.5.1':
+    optional: true
+
+  '@parcel/watcher-win32-x64@2.5.1':
+    optional: true
+
+  '@parcel/watcher@2.5.1':
+    dependencies:
+      detect-libc: 1.0.3
+      is-glob: 4.0.3
+      micromatch: 4.0.8
+      node-addon-api: 7.1.1
+    optionalDependencies:
+      '@parcel/watcher-android-arm64': 2.5.1
+      '@parcel/watcher-darwin-arm64': 2.5.1
+      '@parcel/watcher-darwin-x64': 2.5.1
+      '@parcel/watcher-freebsd-x64': 2.5.1
+      '@parcel/watcher-linux-arm-glibc': 2.5.1
+      '@parcel/watcher-linux-arm-musl': 2.5.1
+      '@parcel/watcher-linux-arm64-glibc': 2.5.1
+      '@parcel/watcher-linux-arm64-musl': 2.5.1
+      '@parcel/watcher-linux-x64-glibc': 2.5.1
+      '@parcel/watcher-linux-x64-musl': 2.5.1
+      '@parcel/watcher-win32-arm64': 2.5.1
+      '@parcel/watcher-win32-ia32': 2.5.1
+      '@parcel/watcher-win32-x64': 2.5.1
+
+  '@tailwindcss/cli@4.1.16':
+    dependencies:
+      '@parcel/watcher': 2.5.1
+      '@tailwindcss/node': 4.1.16
+      '@tailwindcss/oxide': 4.1.16
+      enhanced-resolve: 5.18.3
+      mri: 1.2.0
+      picocolors: 1.1.1
+      tailwindcss: 4.1.16
+
+  '@tailwindcss/node@4.1.16':
+    dependencies:
+      '@jridgewell/remapping': 2.3.5
+      enhanced-resolve: 5.18.3
+      jiti: 2.6.1
+      lightningcss: 1.30.2
+      magic-string: 0.30.21
+      source-map-js: 1.2.1
+      tailwindcss: 4.1.16
+
+  '@tailwindcss/oxide-android-arm64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-darwin-arm64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-darwin-x64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-freebsd-x64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-arm-gnueabihf@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-arm64-gnu@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-arm64-musl@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-x64-gnu@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-x64-musl@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-wasm32-wasi@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-win32-arm64-msvc@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-win32-x64-msvc@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide@4.1.16':
+    optionalDependencies:
+      '@tailwindcss/oxide-android-arm64': 4.1.16
+      '@tailwindcss/oxide-darwin-arm64': 4.1.16
+      '@tailwindcss/oxide-darwin-x64': 4.1.16
+      '@tailwindcss/oxide-freebsd-x64': 4.1.16
+      '@tailwindcss/oxide-linux-arm-gnueabihf': 4.1.16
+      '@tailwindcss/oxide-linux-arm64-gnu': 4.1.16
+      '@tailwindcss/oxide-linux-arm64-musl': 4.1.16
+      '@tailwindcss/oxide-linux-x64-gnu': 4.1.16
+      '@tailwindcss/oxide-linux-x64-musl': 4.1.16
+      '@tailwindcss/oxide-wasm32-wasi': 4.1.16
+      '@tailwindcss/oxide-win32-arm64-msvc': 4.1.16
+      '@tailwindcss/oxide-win32-x64-msvc': 4.1.16
+
+  '@tailwindcss/postcss@4.1.16':
+    dependencies:
+      '@alloc/quick-lru': 5.2.0
+      '@tailwindcss/node': 4.1.16
+      '@tailwindcss/oxide': 4.1.16
+      postcss: 8.5.6
+      tailwindcss: 4.1.16
+
+  braces@3.0.3:
+    dependencies:
+      fill-range: 7.1.1
+
+  daisyui@5.4.3: {}
+
+  detect-libc@1.0.3: {}
+
+  detect-libc@2.1.2: {}
+
+  enhanced-resolve@5.18.3:
+    dependencies:
+      graceful-fs: 4.2.11
+      tapable: 2.3.0
+
+  fill-range@7.1.1:
+    dependencies:
+      to-regex-range: 5.0.1
+
+  graceful-fs@4.2.11: {}
+
+  is-extglob@2.1.1: {}
+
+  is-glob@4.0.3:
+    dependencies:
+      is-extglob: 2.1.1
+
+  is-number@7.0.0: {}
+
+  jiti@2.6.1: {}
+
+  lightningcss-android-arm64@1.30.2:
+    optional: true
+
+  lightningcss-darwin-arm64@1.30.2:
+    optional: true
+
+  lightningcss-darwin-x64@1.30.2:
+    optional: true
+
+  lightningcss-freebsd-x64@1.30.2:
+    optional: true
+
+  lightningcss-linux-arm-gnueabihf@1.30.2:
+    optional: true
+
+  lightningcss-linux-arm64-gnu@1.30.2:
+    optional: true
+
+  lightningcss-linux-arm64-musl@1.30.2:
+    optional: true
+
+  lightningcss-linux-x64-gnu@1.30.2:
+    optional: true
+
+  lightningcss-linux-x64-musl@1.30.2:
+    optional: true
+
+  lightningcss-win32-arm64-msvc@1.30.2:
+    optional: true
+
+  lightningcss-win32-x64-msvc@1.30.2:
+    optional: true
+
+  lightningcss@1.30.2:
+    dependencies:
+      detect-libc: 2.1.2
+    optionalDependencies:
+      lightningcss-android-arm64: 1.30.2
+      lightningcss-darwin-arm64: 1.30.2
+      lightningcss-darwin-x64: 1.30.2
+      lightningcss-freebsd-x64: 1.30.2
+      lightningcss-linux-arm-gnueabihf: 1.30.2
+      lightningcss-linux-arm64-gnu: 1.30.2
+      lightningcss-linux-arm64-musl: 1.30.2
+      lightningcss-linux-x64-gnu: 1.30.2
+      lightningcss-linux-x64-musl: 1.30.2
+      lightningcss-win32-arm64-msvc: 1.30.2
+      lightningcss-win32-x64-msvc: 1.30.2
+
+  magic-string@0.30.21:
+    dependencies:
+      '@jridgewell/sourcemap-codec': 1.5.5
+
+  micromatch@4.0.8:
+    dependencies:
+      braces: 3.0.3
+      picomatch: 2.3.1
+
+  mri@1.2.0: {}
+
+  nanoid@3.3.11: {}
+
+  node-addon-api@7.1.1: {}
+
+  picocolors@1.1.1: {}
+
+  picomatch@2.3.1: {}
+
+  postcss@8.5.6:
+    dependencies:
+      nanoid: 3.3.11
+      picocolors: 1.1.1
+      source-map-js: 1.2.1
+
+  prettier-plugin-jinja-template@2.1.0(prettier@3.6.2):
+    dependencies:
+      prettier: 3.6.2
+
+  prettier-plugin-tailwindcss@0.7.1(prettier@3.6.2):
+    dependencies:
+      prettier: 3.6.2
+
+  prettier@3.6.2: {}
+
+  source-map-js@1.2.1: {}
+
+  tailwindcss@4.1.16: {}
+
+  tapable@2.3.0: {}
+
+  to-regex-range@5.0.1:
+    dependencies:
+      is-number: 7.0.0

pyproject.toml

@@ -67,22 +67,54 @@ 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 = { cmd = "python manage.py runserver", help = "Start the development server", deps = ["db-up"] }
+dev = { shell = """
+# Start pnpm CSS watcher in background
+pnpm run dev &
+PNPM_PID=$!
+echo "Started CSS watcher (PID: $PNPM_PID)"
+
+# Cleanup function
+cleanup() {
+    echo "\nShutting down..."
+    if kill -0 $PNPM_PID 2>/dev/null; then
+        kill $PNPM_PID
+        echo "✓ CSS watcher stopped"
+    fi
+    if [ ! -z "${DJ_PID:-}" ] && kill -0 $DJ_PID 2>/dev/null; then
+        kill $DJ_PID
+        echo "✓ Django server stopped"
+    fi
+}
+
+# Set trap for cleanup
+trap cleanup EXIT INT TERM
+
+# Start Django dev server in background
+uv run python manage.py runserver &
+DJ_PID=$!
+
+# Wait for Django to finish
+wait $DJ_PID
+""", help = "Start the development server with CSS watcher", deps = ["db-up", "js-deps"] }
+build = { sequence = ["build-frontend", "collectstatic"], help = "Build frontend assets and collect static files" }
 
 # 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 = "python manage.py migrate", help = "Run database migrations" }
+migrate = { cmd = "uv run python manage.py migrate", help = "Run database migrations" }
 bootstrap = { shell = """
 echo "Bootstrapping initial data..."
 echo "This will take a bit ⏱️. Get yourself some coffee..."
-python manage.py bootstrap
+uv run python manage.py bootstrap
 echo "✓ Bootstrap complete"
 echo ""
 echo "Default admin credentials:"
@@ -90,4 +122,8 @@ echo "  Username: admin"
 echo "  Email: admin@envipath.com"
 echo "  Password: SuperSafe"
 """, help = "Bootstrap initial data (anonymous user, packages, models)"  }
-shell = { cmd = "python manage.py shell", help = "Open Django shell" }
+shell = { cmd = "uv run python manage.py shell", help = "Open Django shell" }
+
+# Build tasks
+build-frontend = { cmd = "pnpm run build", help = "Build frontend assets using pnpm", deps = ["js-deps"] }
+collectstatic = { cmd = "uv run python manage.py collectstatic --noinput", help = "Collect static files for production", deps = ["build-frontend"] }

static/css/daisyui-theme.css

@@ -0,0 +1,84 @@
+/**
+ * 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

@@ -0,0 +1,36 @@
+@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

@@ -0,0 +1,111 @@
+/**
+ * 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;
+}

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static/images/logo-name.svg

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+</svg>

static/images/logo-square.svg

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+<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"/>
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static/js/discourse-api.js

@@ -0,0 +1,170 @@
+/**
+ * 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

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

templates/actions/collections/compound_structure.html

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

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

templates/actions/collections/group.html

@@ -1,4 +1,5 @@
 <li>
-    <a role="button" data-toggle="modal" data-target="#new_group_modal">
+  <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

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

templates/actions/collections/node.html

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

templates/actions/collections/package.html

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

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

templates/actions/collections/reaction.html

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

templates/actions/collections/rule.html

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

templates/actions/collections/scenario.html

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

templates/actions/collections/setting.html

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

templates/actions/objects/compound.html

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

templates/actions/objects/compound_structure.html

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

templates/actions/objects/edge.html

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

templates/actions/objects/group.html

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

templates/actions/objects/model.html

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

templates/actions/objects/node.html

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

templates/actions/objects/package.html

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

templates/actions/objects/pathway.html

@@ -1,59 +1,92 @@
 {% if meta.can_edit %}
-    <li>
+  <li>
-        <a class="button" data-toggle="modal" data-target="#add_pathway_node_modal">
+    <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>
+  </li>
-        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">
+  <li>
-            <i class="glyphicon glyphicon-plus"></i> Add Reaction</a>
+    <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">
-    </li>
+      <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
-    <li role="separator" class="divider"></li>
+    >
+  </li>
+  <li role="separator" class="divider"></li>
 {% endif %}
-    <li>
+<li>
-        <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
+  <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>
+</li>
-        <a class="button" data-toggle="modal" data-target="#download_pathway_csv_modal">
+<li>
-            <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a>
+  <a
-    </li>
+    class="button"
-    <li>
+    data-toggle="modal"
-        <a class="button" data-toggle="modal" data-target="#download_pathway_image_modal">
+    data-target="#download_pathway_csv_modal"
-            <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a>
+  >
-    </li>
+    <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a
+  >
+</li>
+<li>
+  <a
+    class="button"
+    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>
+  <li>
-        <a class="button" data-toggle="modal" data-target="#identify_missing_rules_modal">
+    <a
-            <i class="glyphicon glyphicon-question-sign"></i> Identify Missing Rules</a>
+      class="button"
-    </li>
+      data-toggle="modal"
-    <li role="separator" class="divider"></li>
+      data-target="#identify_missing_rules_modal"
-    <li>
+    >
-        <a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
+      <i class="glyphicon glyphicon-question-sign"></i> Identify Missing
-            <i class="glyphicon glyphicon-edit"></i> Edit Pathway</a>
+      Rules</a
-    </li>
+    >
-    <li>
+  </li>
-        <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
+  <li role="separator" class="divider"></li>
-            <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
+  <li>
-    </li>
+    <a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
-    <li>
+      <i class="glyphicon glyphicon-edit"></i> Edit Pathway</a
-        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+    >
-            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+  </li>
-    </li>
+  <li>
-    {#    <li>#}
+    <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
-    {#        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
+      <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
-    {#            <i class="glyphicon glyphicon-plus"></i> Calculate Compound Properties</a>#}
+    >
-    {#    </li>#}
+  </li>
-    <li role="separator" class="divider"></li>
+  <li>
-    <li>
+    <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
-        <a class="button" data-toggle="modal" data-target="#delete_pathway_node_modal">
+      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
-            <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
+    >
-    </li>
+  </li>
-    <li>
+  {#    <li>#}
-        <a class="button" data-toggle="modal" data-target="#delete_pathway_edge_modal">
+  {#        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
-            <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
+  {#            <i class="glyphicon glyphicon-plus"></i> Calculate Compound Properties</a>#}
-    </li>
+  {#    </li>#}
-    <li>
+  <li role="separator" class="divider"></li>
-        <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
+  <li>
-            <i class="glyphicon glyphicon-trash"></i> Delete Pathway</a>
+    <a
-    </li>
+      class="button"
+      data-toggle="modal"
+      data-target="#delete_pathway_node_modal"
+    >
+      <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
+    >
+  </li>
+  <li>
+    <a
+      class="button"
+      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
+    >
+  </li>
 {% endif %}

templates/actions/objects/reaction.html

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

templates/actions/objects/rule.html

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

templates/actions/objects/scenario.html

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

templates/actions/objects/user.html

@@ -1,22 +1,30 @@
 {% if meta.can_edit %}
-    <li>
+  <li>
-        <a role="button" data-toggle="modal" data-target="#edit_user_modal">
+    <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>
+  </li>
-        <a role="button" data-toggle="modal" data-target="#edit_password_modal">
+  <li>
-            <i class="glyphicon glyphicon-lock"></i> Update Password</a>
+    <a role="button" data-toggle="modal" data-target="#edit_password_modal">
-    </li>
+      <i class="glyphicon glyphicon-lock"></i> Update Password</a
-    <li>
+    >
-        <a role="button" data-toggle="modal" data-target="#new_prediction_setting_modal">
+  </li>
-            <i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a>
+  <li>
-    </li>
+    <a
-{#    <li>#}
+      role="button"
-{#        <a role="button" data-toggle="modal" data-target="#manage_api_token_modal">#}
+      data-toggle="modal"
-{#            <i class="glyphicon glyphicon-console"></i> Manage API Token</a>#}
+      data-target="#new_prediction_setting_modal"
-{#    </li>#}
+    >
-    <li>
+      <i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a
-        <a role="button" data-toggle="modal" data-target="#generic_delete_modal">
+    >
-            <i class="glyphicon glyphicon-trash"></i> Delete Account</a>
+  </li>
-    </li>
+  {#    <li>#}
+  {#        <a role="button" data-toggle="modal" data-target="#manage_api_token_modal">#}
+  {#            <i class="glyphicon glyphicon-console"></i> Manage API Token</a>#}
+  {#    </li>#}
+  <li>
+    <a role="button" data-toggle="modal" data-target="#generic_delete_modal">
+      <i class="glyphicon glyphicon-trash"></i> Delete Account</a
+    >
+  </li>
 {% endif %}

templates/admin.html

@@ -1,12 +1,17 @@
 {% 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">
+      <div class="form-group">
-            <label for="textarea">Query</label>
+        <label for="textarea">Query</label>
-            <textarea id="textarea" class="form-control" rows="10" placeholder="Paste query here" required>
+        <textarea
+          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 {
@@ -15,32 +20,29 @@ 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>
+      </div>
+      <button id="submit" type="button" class="btn btn-primary">Submit</button>
     </form>
     <p></p>
-</div>
+  </div>
-<div id="results">
+  <div id="results"></div>
-</div>
+  <div id="loading"></div>
-<div id="loading"></div>
+  <script>
-</div>
+    $(function () {
-<script>
+      $("#submit").on("click", function () {
-$(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) {
+        $.post("{{ SERVER_BASE }}/expire", data, function (result) {
-            $("#loading").empty();
+          $("#loading").empty();
-            queryResultToTable("results", result);
+          queryResultToTable("results", result);
-        })
+        });
+      });
     });
-})
+  </script>
-</script>
-
 {% endblock content %}

templates/collections/joblog.html

@@ -1,70 +1,80 @@
 {% extends "framework.html" %}
 {% load static %}
+{% load envipytags %}
 {% block content %}
+  <div class="panel-group" id="reviewListAccordion">
+    <div class="panel panel-default">
+      <div
+        class="panel-heading"
+        id="headingPanel"
+        style="font-size:2rem;height: 46px"
+      >
+        Jobs
+      </div>
+      <div class="panel-body">
+        <p>Job Logs Desc</p>
+      </div>
 
-    <div class="panel-group" id="reviewListAccordion">
+      <div
-        <div class="panel panel-default">
+        class="panel panel-default panel-heading list-group-item"
-            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+        style="background-color:silver"
-                Jobs
+      >
-            </div>
+        <h4 class="panel-title">
-            <div class="panel-body">
+          <a
-                <p>
+            id="job-accordion-link"
-                    Job Logs Desc
+            data-toggle="collapse"
-                </p>
+            data-parent="#job-accordion"
-
+            href="#jobs"
-            </div>
+          >
-
+            Jobs
-            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+          </a>
-                <h4 class="panel-title">
+        </h4>
-                    <a id="job-accordion-link" data-toggle="collapse" data-parent="#job-accordion" href="#jobs">
+      </div>
-                        Jobs
+      <div id="jobs" class="panel-collapse in collapse">
-                    </a>
+        <div class="panel-body list-group-item" id="job-content">
-                </h4>
+          <table class="table-bordered table-hover table">
-            </div>
+            <tr style="background-color: rgba(0, 0, 0, 0.08);">
-            <div id="jobs"
+              <th scope="col">ID</th>
-                 class="panel-collapse collapse in">
+              <th scope="col">Name</th>
-                <div class="panel-body list-group-item" id="job-content">
+              <th scope="col">Status</th>
-                    <table class="table table-bordered table-hover">
+              <th scope="col">Queued</th>
-                        <tr style="background-color: rgba(0, 0, 0, 0.08);">
+              <th scope="col">Done</th>
-                            <th scope="col">ID</th>
+              <th scope="col">Result</th>
-                            <th scope="col">Name</th>
+            </tr>
-                            <th scope="col">Status</th>
+            <tbody>
-                            <th scope="col">Queued</th>
+              {% for job in jobs %}
-                            <th scope="col">Done</th>
+                <tr>
-                            <th scope="col">Result</th>
+                  <td>{{ job.task_id }}</td>
-                        </tr>
+                  <td>{{ job.job_name }}</td>
-                        <tbody>
+                  <td>{{ job.status }}</td>
-                        {% for job in jobs %}
+                  <td>{{ job.created }}</td>
-                            <tr>
+                  <td>{{ job.done_at }}</td>
-                                <td>{{ job.task_id }}</td>
+                  {% if job.task_result and job.task_result|is_url == True %}
-                                <td>{{ job.job_name }}</td>
+                    <td><a href="{{ job.task_result }}">Result</a></td>
-                                <td>{{ job.status }}</td>
+                  {% elif job.task_result %}
-                                <td>{{ job.created }}</td>
+                    <td>{{ job.task_result|slice:"40" }}...</td>
-                                <td>{{ job.done_at }}</td>
+                  {% else %}
-                                {% if job.task_result and job.task_result|is_url == True %}
+                    <td>Empty</td>
-                                    <td><a href="{{ job.task_result }}">Result</a></td>
+                  {% endif %}
-                                {% elif job.task_result %}
+                </tr>
-                                    <td>{{ job.task_result|slice:"40" }}...</td>
+              {% endfor %}
-                                {% else %}
+            </tbody>
-                                    <td>Empty</td>
+          </table>
-                                {% endif %}
-                            </tr>
-                        {% endfor %}
-                        </tbody>
-                    </table>
-                </div>
-            </div>
-
-            <!-- Unreviewable objects such as User / Group / Setting -->
-            <ul class='list-group'>
-                {% for obj in objects %}
-                    {% if object_type == 'user' %}
-                        <a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
-                    {% else %}
-                        <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
-                    {% endif %}
-                {% endfor %}
-            </ul>
         </div>
+      </div>
+
+      <!-- Unreviewable objects such as User / Group / Setting -->
+      <ul class="list-group">
+        {% for obj in objects %}
+          {% if object_type == 'user' %}
+            <a class="list-group-item" href="{{ obj.url }}"
+              >{{ obj.username }}</a
+            >
+          {% else %}
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
+          {% endif %}
+        {% endfor %}
+      </ul>
     </div>
+  </div>
 {% endblock content %}

templates/collections/objects_list.html

@@ -2,269 +2,427 @@
 {% load static %}
 {% block content %}
 
-    {% if object_type != 'package' %}
+  {% if object_type != 'package' %}
-        <div>
+    <div>
-            <div id="load-all-error" style="display: none;">
+      <div id="load-all-error" style="display: none;">
-                <div class="alert alert-danger" role="alert">
+        <div class="alert alert-danger" role="alert">
-                    <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
+          <span
-                    <span class="sr-only">Error:</span>
+            class="glyphicon glyphicon-exclamation-sign"
-                    Getting objects failed!
+            aria-hidden="true"
-                </div>
+          ></span>
-            </div>
+          <span class="sr-only">Error:</span>
-
+          Getting objects failed!
-            <input type="text" id="object-search" class="form-control" placeholder="Search by name"
-                   style="display: none;">
-            <p></p>
         </div>
+      </div>
+
+      <input
+        type="text"
+        id="object-search"
+        class="form-control"
+        placeholder="Search by name"
+        style="display: none;"
+      />
+      <p></p>
+    </div>
+  {% endif %}
+
+  {% block action_modals %}
+    {% if object_type == 'package' %}
+      {% include "modals/collections/new_package_modal.html" %}
+      {% include "modals/collections/import_package_modal.html" %}
+      {% include "modals/collections/import_legacy_package_modal.html" %}
+    {% elif object_type == 'compound' %}
+      {% include "modals/collections/new_compound_modal.html" %}
+    {% elif object_type == 'rule' %}
+      {% include "modals/collections/new_rule_modal.html" %}
+    {% elif object_type == 'reaction' %}
+      {% include "modals/collections/new_reaction_modal.html" %}
+    {% elif object_type == 'pathway' %}
+      {# {% include "modals/collections/new_pathway_modal.html" %} #}
+    {% elif object_type == 'node' %}
+      {% include "modals/collections/new_node_modal.html" %}
+    {% elif object_type == 'edge' %}
+      {% include "modals/collections/new_edge_modal.html" %}
+    {% elif object_type == 'scenario' %}
+      {% include "modals/collections/new_scenario_modal.html" %}
+    {% elif object_type == 'model' %}
+      {% include "modals/collections/new_model_modal.html" %}
+    {% elif object_type == 'setting' %}
+      {#{% include "modals/collections/new_setting_modal.html" %}#}
+    {% elif object_type == 'user' %}
+      <div></div>
+    {% elif object_type == 'group' %}
+      {% include "modals/collections/new_group_modal.html" %}
     {% endif %}
+  {% endblock action_modals %}
 
-    {% block action_modals %}
+  <div class="panel-group" id="reviewListAccordion">
-        {% if object_type == 'package' %}
-            {% include "modals/collections/new_package_modal.html" %}
-            {% include "modals/collections/import_package_modal.html" %}
-            {% include "modals/collections/import_legacy_package_modal.html" %}
-        {% elif object_type == 'compound' %}
-            {% include "modals/collections/new_compound_modal.html" %}
-        {% elif object_type == 'rule' %}
-            {% include "modals/collections/new_rule_modal.html" %}
-        {% elif object_type == 'reaction' %}
-            {% include "modals/collections/new_reaction_modal.html" %}
-        {% elif object_type == 'pathway' %}
-            {# {% include "modals/collections/new_pathway_modal.html" %} #}
-        {% elif object_type == 'node' %}
-            {% include "modals/collections/new_node_modal.html" %}
-        {% elif object_type == 'edge' %}
-            {% include "modals/collections/new_edge_modal.html" %}
-        {% elif object_type == 'scenario' %}
-            {% include "modals/collections/new_scenario_modal.html" %}
-        {% elif object_type == 'model' %}
-            {% include "modals/collections/new_model_modal.html" %}
-        {% elif object_type == 'setting' %}
-            {#{% include "modals/collections/new_setting_modal.html" %}#}
-        {% elif object_type == 'user' %}
-            <div></div>
-        {% elif object_type == 'group' %}
-            {% include "modals/collections/new_group_modal.html" %}
-        {% endif %}
-    {% endblock action_modals %}
-
-<div class="panel-group" id="reviewListAccordion">
     <div class="panel panel-default">
-        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+      <div
-            {% if object_type == 'package' %}
+        class="panel-heading"
-            Packages
+        id="headingPanel"
-            {% elif object_type == 'compound' %}
+        style="font-size:2rem;height: 46px"
-            Compounds
+      >
-            {% elif object_type == 'structure' %}
+        {% if object_type == 'package' %}
-            Compound structures
+          Packages
-            {% elif object_type == 'rule' %}
+        {% elif object_type == 'compound' %}
-            Rules
+          Compounds
-            {% elif object_type == 'reaction' %}
+        {% elif object_type == 'structure' %}
-            Reactions
+          Compound structures
-            {% elif object_type == 'pathway' %}
+        {% elif object_type == 'rule' %}
-            Pathways
+          Rules
-            {% elif object_type == 'node' %}
+        {% elif object_type == 'reaction' %}
-            Nodes
+          Reactions
-            {% elif object_type == 'edge' %}
+        {% elif object_type == 'pathway' %}
-            Edges
+          Pathways
-            {% elif object_type == 'scenario' %}
+        {% elif object_type == 'node' %}
-            Scenarios
+          Nodes
-            {% elif object_type == 'model' %}
+        {% elif object_type == 'edge' %}
-            Model
+          Edges
-            {% elif object_type == 'setting' %}
+        {% elif object_type == 'scenario' %}
-            Settings
+          Scenarios
-            {% elif object_type == 'user' %}
+        {% elif object_type == 'model' %}
-            Users
+          Model
-            {% elif object_type == 'group' %}
+        {% elif object_type == 'setting' %}
-            Groups
+          Settings
-            {% endif %}
+        {% elif object_type == 'user' %}
-            <div id="actionsButton"
+          Users
-                 style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
+        {% elif object_type == 'group' %}
-                 class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
+          Groups
-                                     aria-haspopup="true" aria-expanded="false"><span
+        {% endif %}
-                    class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
+        <div
-                    style="padding-right:1em"></span></a>
+          id="actionsButton"
-                <ul id="actionsList" class="dropdown-menu">
+          style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
-                    {% block actions %}
+          class="dropdown"
-                        {% if object_type == 'package' %}
+        >
-                            {% include "actions/collections/package.html" %}
+          <a
-                        {% elif object_type == 'compound' %}
+            href="#"
-                            {% include "actions/collections/compound.html" %}
+            class="dropdown-toggle"
-                        {% elif object_type == 'structure' %}
+            data-toggle="dropdown"
-                            {% include "actions/collections/compound_structure.html" %}
+            role="button"
-                        {% elif object_type == 'rule' %}
+            aria-haspopup="true"
-                            {% include "actions/collections/rule.html" %}
+            aria-expanded="false"
-                        {% elif object_type == 'reaction' %}
+            ><span class="glyphicon glyphicon-wrench"></span> Actions
-                            {% include "actions/collections/reaction.html" %}
+            <span class="caret"></span><span style="padding-right:1em"></span
-                        {% elif object_type == 'setting' %}
+          ></a>
-                            {% include "actions/collections/setting.html" %}
+          <ul id="actionsList" class="dropdown-menu">
-                        {% elif object_type == 'scenario' %}
+            {% block actions %}
-                            {% include "actions/collections/scenario.html" %}
+              {% if object_type == 'package' %}
-                        {% elif object_type == 'model' %}
+                {% include "actions/collections/package.html" %}
-                            {% include "actions/collections/model.html" %}
+              {% elif object_type == 'compound' %}
-                        {% elif object_type == 'pathway' %}
+                {% include "actions/collections/compound.html" %}
-                            {% include "actions/collections/pathway.html" %}
+              {% elif object_type == 'structure' %}
-                        {% elif object_type == 'node' %}
+                {% include "actions/collections/compound_structure.html" %}
-                            {% include "actions/collections/node.html" %}
+              {% elif object_type == 'rule' %}
-                        {% elif object_type == 'edge' %}
+                {% include "actions/collections/rule.html" %}
-                            {% include "actions/collections/edge.html" %}
+              {% elif object_type == 'reaction' %}
-                        {% elif object_type == 'group' %}
+                {% include "actions/collections/reaction.html" %}
-                            {% include "actions/collections/group.html" %}
+              {% elif object_type == 'setting' %}
-                        {% endif %}
+                {% include "actions/collections/setting.html" %}
-                    {% endblock %}
+              {% elif object_type == 'scenario' %}
-                </ul>
+                {% include "actions/collections/scenario.html" %}
-            </div>
+              {% elif object_type == 'model' %}
+                {% include "actions/collections/model.html" %}
+              {% elif object_type == 'pathway' %}
+                {% include "actions/collections/pathway.html" %}
+              {% elif object_type == 'node' %}
+                {% include "actions/collections/node.html" %}
+              {% elif object_type == 'edge' %}
+                {% include "actions/collections/edge.html" %}
+              {% elif object_type == 'group' %}
+                {% include "actions/collections/group.html" %}
+              {% endif %}
+            {% endblock %}
+          </ul>
         </div>
-        <div class="panel-body">
+      </div>
-            <!-- Set Text above links -->
+      <div class="panel-body">
-            {% if object_type == 'package' %}
+        <!-- Set Text above links -->
-            <p>A package contains pathways, rules, etc. and can reflect specific experimental
+        {% if object_type == 'package' %}
-                conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
+          <p>
-                    more &gt;&gt;</a></p>
+            A package contains pathways, rules, etc. and can reflect specific
-            {% elif object_type == 'compound' %}
+            experimental conditions.
-            <p>A compound stores the structure of a molecule and can include meta-information.
+            <a
-                <a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
+              target="_blank"
-                    &gt;&gt;</a></p>
+              href="https://wiki.envipath.org/index.php/packages"
-            {% elif object_type == 'structure' %}
+              role="button"
-            <p>The structures stored in this compound
+              >Learn more &gt;&gt;</a
-                <a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
+            >
-                    &gt;&gt;</a></p>
+          </p>
-            {% elif object_type == 'rule' %}
+        {% elif object_type == 'compound' %}
-            <p>A rule describes a biotransformation reaction template that is defined as SMIRKS.
+          <p>
-                <a target="_blank" href="https://wiki.envipath.org/index.php/Rules" role="button">Learn more
+            A compound stores the structure of a molecule and can include
-                    &gt;&gt;</a></p>
+            meta-information.
-            {% elif object_type == 'reaction' %}
+            <a
-            <p>A reaction is a specific biotransformation from educt compounds to product compounds.
+              target="_blank"
-                <a target="_blank" href="https://wiki.envipath.org/index.php/reactions" role="button">Learn more
+              href="https://wiki.envipath.org/index.php/compounds"
-                    &gt;&gt;</a></p>
+              role="button"
-            {% elif object_type == 'pathway' %}
+              >Learn more &gt;&gt;</a
-            <p>A pathway displays the (predicted) biodegradation of a compound as graph.
+            >
-                <a target="_blank" href="https://wiki.envipath.org/index.php/pathways" role="button">Learn more
+          </p>
-                    &gt;&gt;</a></p>
+        {% elif object_type == 'structure' %}
-            {% elif object_type == 'node' %}
+          <p>
-            <p>Nodes represent the (predicted) compounds in a graph.
+            The structures stored in this compound
-                <a target="_blank" href="https://wiki.envipath.org/index.php/nodes" role="button">Learn more
+            <a
-                    &gt;&gt;</a></p>
+              target="_blank"
-            {% elif object_type == 'edge' %}
+              href="https://wiki.envipath.org/index.php/compounds"
-            <p>Edges represent the links between Nodes in a graph
+              role="button"
-                <a target="_blank" href="https://wiki.envipath.org/index.php/edges" role="button">Learn more
+              >Learn more &gt;&gt;</a
-                    &gt;&gt;</a></p>
+            >
-            {% elif object_type == 'scenario' %}
+          </p>
-            <p>A scenario contains meta-information that can be attached to other data (compounds, rules, ..).
+        {% elif object_type == 'rule' %}
-                <a target="_blank" href="https://wiki.envipath.org/index.php/scenarios" role="button">Learn more
+          <p>
-                    &gt;&gt;</a></p>
+            A rule describes a biotransformation reaction template that is
-            {% elif object_type == 'model' %}
+            defined as SMIRKS.
-            <p>A model applies machine learning to limit the combinatorial explosion.
+            <a
-                <a target="_blank" href="https://wiki.envipath.org/index.php/relative_reasoning" role="button">Learn
+              target="_blank"
-                    more
+              href="https://wiki.envipath.org/index.php/Rules"
-                    &gt;&gt;</a></p>
+              role="button"
-            {% elif object_type == 'setting' %}
+              >Learn more &gt;&gt;</a
-            <p>A setting includes configuration parameters for pathway predictions.
+            >
-                <a target="_blank" href="https://wiki.envipath.org/index.php/settings" role="button">Learn more
+          </p>
-                    &gt;&gt;</a></p>
+        {% elif object_type == 'reaction' %}
-            {% elif object_type == 'user' %}
+          <p>
-            <p>Register now to create own packages and to submit and manage your data.
+            A reaction is a specific biotransformation from educt compounds to
-                <a target="_blank" href="https://wiki.envipath.org/index.php/users" role="button">Learn more
+            product compounds.
-                    &gt;&gt;</a></p>
+            <a
-            {% elif object_type == 'group' %}
+              target="_blank"
-            <p>Users can team up in groups to share packages.
+              href="https://wiki.envipath.org/index.php/reactions"
-                <a target="_blank" href="https://wiki.envipath.org/index.php/groups" role="button">Learn more
+              role="button"
-                    &gt;&gt;</a></p>
+              >Learn more &gt;&gt;</a
-            {% endif %}
+            >
+          </p>
+        {% elif object_type == 'pathway' %}
+          <p>
+            A pathway displays the (predicted) biodegradation of a compound as
+            graph.
+            <a
+              target="_blank"
+              href="https://wiki.envipath.org/index.php/pathways"
+              role="button"
+              >Learn more &gt;&gt;</a
+            >
+          </p>
+        {% elif object_type == 'node' %}
+          <p>
+            Nodes represent the (predicted) compounds in a graph.
+            <a
+              target="_blank"
+              href="https://wiki.envipath.org/index.php/nodes"
+              role="button"
+              >Learn more &gt;&gt;</a
+            >
+          </p>
+        {% elif object_type == 'edge' %}
+          <p>
+            Edges represent the links between Nodes in a graph
+            <a
+              target="_blank"
+              href="https://wiki.envipath.org/index.php/edges"
+              role="button"
+              >Learn more &gt;&gt;</a
+            >
+          </p>
+        {% elif object_type == 'scenario' %}
+          <p>
+            A scenario contains meta-information that can be attached to other
+            data (compounds, rules, ..).
+            <a
+              target="_blank"
+              href="https://wiki.envipath.org/index.php/scenarios"
+              role="button"
+              >Learn more &gt;&gt;</a
+            >
+          </p>
+        {% elif object_type == 'model' %}
+          <p>
+            A model applies machine learning to limit the combinatorial
+            explosion.
+            <a
+              target="_blank"
+              href="https://wiki.envipath.org/index.php/relative_reasoning"
+              role="button"
+              >Learn more &gt;&gt;</a
+            >
+          </p>
+        {% elif object_type == 'setting' %}
+          <p>
+            A setting includes configuration parameters for pathway predictions.
+            <a
+              target="_blank"
+              href="https://wiki.envipath.org/index.php/settings"
+              role="button"
+              >Learn more &gt;&gt;</a
+            >
+          </p>
+        {% elif object_type == 'user' %}
+          <p>
+            Register now to create own packages and to submit and manage your
+            data.
+            <a
+              target="_blank"
+              href="https://wiki.envipath.org/index.php/users"
+              role="button"
+              >Learn more &gt;&gt;</a
+            >
+          </p>
+        {% elif object_type == 'group' %}
+          <p>
+            Users can team up in groups to share packages.
+            <a
+              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 theres nothing to show extend the text above -->
-            {% if reviewed_objects and unreviewed_objects %}
+        {% if reviewed_objects and unreviewed_objects %}
-            {% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %}
+          {% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %}
-            <p>Nothing found. There are two possible reasons: <br><br>1. There is no content yet.<br>2. You have no
+            <p>
-                reading permissions.<br><br>Please be sure you have at least reading permissions.</p>
+              Nothing found. There are two possible reasons: <br /><br />1.
-            {% endif %}
+              There is no content yet.<br />2. You have no reading
-            {% endif %}
+              permissions.<br /><br />Please be sure you have at least reading
-        </div>
+              permissions.
-        {% if reviewed_objects %}
+            </p>
+          {% endif %}
+        {% endif %}
+      </div>
+      {% if reviewed_objects %}
         {% if reviewed_objects|length > 0 %}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+          <div
+            class="panel panel-default panel-heading list-group-item"
+            style="background-color:silver"
+          >
             <h4 class="panel-title">
-                <a id="ReviewedLink" data-toggle="collapse" data-parent="#reviewListAccordion"
+              <a
-                   href="#Reviewed">Reviewed</a>
+                id="ReviewedLink"
+                data-toggle="collapse"
+                data-parent="#reviewListAccordion"
+                href="#Reviewed"
+                >Reviewed</a
+              >
             </h4>
-        </div>
+          </div>
-        <div id="Reviewed" class="panel-collapse collapse in">
+          <div id="Reviewed" class="panel-collapse in collapse">
             <div class="panel-body list-group-item" id="ReviewedContent">
-                {% if object_type == 'package' %}
+              {% if object_type == 'package' %}
                 {% for obj in reviewed_objects %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}
+                  <a class="list-group-item" href="{{ obj.url }}"
-                    <span class="glyphicon glyphicon-star" aria-hidden="true"
+                    >{{ obj.name|safe }}
-                          style="float:right" data-toggle="tooltip"
+                    <span
-                          data-placement="top" title="" data-original-title="Reviewed">
+                      class="glyphicon glyphicon-star"
-                        </span>
+                      aria-hidden="true"
-                </a>
+                      style="float:right"
+                      data-toggle="tooltip"
+                      data-placement="top"
+                      title=""
+                      data-original-title="Reviewed"
+                    >
+                    </span>
+                  </a>
                 {% endfor %}
-                {% else %}
+              {% else %}
                 {% for obj in reviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
+                  <a class="list-group-item" href="{{ obj.url }}"
-                    <span class="glyphicon glyphicon-star" aria-hidden="true"
+                    >{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
-                          style="float:right" data-toggle="tooltip"
+                    <span
-                          data-placement="top" title="" data-original-title="Reviewed">
+                      class="glyphicon glyphicon-star"
-                        </span>
+                      aria-hidden="true"
-                </a>
+                      style="float:right"
+                      data-toggle="tooltip"
+                      data-placement="top"
+                      title=""
+                      data-original-title="Reviewed"
+                    >
+                    </span>
+                  </a>
                 {% endfor %}
-                {% endif %}
+              {% endif %}
             </div>
+          </div>
+        {% endif %}
+      {% endif %}
+      {% if unreviewed_objects %}
+        <div
+          class="panel panel-default panel-heading list-group-item"
+          style="background-color:silver"
+        >
+          <h4 class="panel-title">
+            <a
+              id="UnreviewedLink"
+              data-toggle="collapse"
+              data-parent="#unReviewListAccordion"
+              href="#Unreviewed"
+              >Unreviewed</a
+            >
+          </h4>
         </div>
-        {% endif %}
+        <div
-        {% endif %}
+          id="Unreviewed"
-        {% if unreviewed_objects %}
+          class="panel-collapse {% if reviewed_objects|length == 0 or object_type == 'package' %}in{% endif %} collapse"
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver"><h4
+        >
-                class="panel-title"><a id="UnreviewedLink" data-toggle="collapse" data-parent="#unReviewListAccordion"
+          <div class="panel-body list-group-item" id="UnreviewedContent">
-                                       href="#Unreviewed">Unreviewed</a></h4></div>
+            {% if object_type == 'package' %}
-        <div id="Unreviewed" class="panel-collapse collapse {% if reviewed_objects|length == 0 or object_type == 'package' %}in{% endif %}">
+              {% for obj in unreviewed_objects %}
-            <div class="panel-body list-group-item" id="UnreviewedContent">
+                <a class="list-group-item" href="{{ obj.url }}"
-                {% if object_type == 'package' %}
+                  >{{ obj.name|safe }}</a
-                {% for obj in unreviewed_objects %}
+                >
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
+              {% endfor %}
-                {% endfor %}
-                {% else %}
-                {% for obj in unreviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
-                {% endfor %}
-                {% endif %}
-            </div>
-        </div>
-        {% endif %}
-        {% if objects %}
-        <!-- Unreviewable objects such as User / Group / Setting -->
-        <ul class='list-group'>
-            {% for obj in objects %}
-            {% if object_type == 'user' %}
-            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username|safe }}</a>
             {% else %}
-            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
+              {% for obj in unreviewed_objects|slice:":50" %}
+                <a class="list-group-item" href="{{ obj.url }}"
+                  >{{ obj.name|safe }}</a
+                >
+              {% endfor %}
             {% endif %}
-            {% endfor %}
+          </div>
+        </div>
+      {% endif %}
+      {% if objects %}
+        <!-- Unreviewable objects such as User / Group / Setting -->
+        <ul class="list-group">
+          {% for obj in objects %}
+            {% if object_type == 'user' %}
+              <a class="list-group-item" href="{{ obj.url }}"
+                >{{ obj.username|safe }}</a
+              >
+            {% else %}
+              <a class="list-group-item" href="{{ obj.url }}"
+                >{{ obj.name|safe }}</a
+              >
+            {% endif %}
+          {% endfor %}
         </ul>
-        {% endif %}
+      {% endif %}
     </div>
     <style>
-        .spinner-widget {
+      .spinner-widget {
-            position: fixed; /* stays in place on scroll */
+        position: fixed; /* stays in place on scroll */
-            bottom: 20px; /* distance from bottom */
+        bottom: 20px; /* distance from bottom */
-            right: 20px; /* distance from right */
+        right: 20px; /* distance from right */
-            z-index: 9999; /* above most elements */
+        z-index: 9999; /* above most elements */
-            width: 60px; /* adjust to gif size */
+        width: 60px; /* adjust to gif size */
-            height: 60px;
+        height: 60px;
-        }
+      }
 
-        .spinner-widget img {
+      .spinner-widget img {
-            width: 100%;
+        width: 100%;
-            height: auto;
+        height: auto;
-        }
+      }
     </style>
 
     <div id="load-all-loading" class="spinner-widget" style="display: none">
-        <img id="loading-gif" src="{% static '/images/wait.gif' %}" alt="Loading...">
+      <img
+        id="loading-gif"
+        src="{% static '/images/wait.gif' %}"
+        alt="Loading..."
+      />
     </div>
-
+  </div>
-</div>
+  {# prettier-ignore-start #}
     <script>
         $(function () {
 
@@ -316,4 +474,5 @@
 
         });
     </script>
+    {# prettier-ignore-end #}
 {% endblock content %}

templates/compare.html

@@ -1,55 +1,75 @@
 {% extends "framework.html" %}
 
 {% block content %}
-    <div>
+  <div>
-        <form action="" method="post">
+    <form action="" method="post">
-            {% csrf_token %}
+      {% csrf_token %}
-            <input type="text" class="form-control" id="smiles" name="smiles" placeholder="SMILES"
+      <input
-                   value="{{ smiles }}"/>
+        type="text"
-            <input type="text" class="form-control" id="smiles" name="smirks" placeholder="SMIRKS"
+        class="form-control"
-                   value="{{ smirks }}"/>
+        id="smiles"
-            <button type="submit" class="btn btn-primary">Test</button>
+        name="smiles"
-        </form>
+        placeholder="SMILES"
-    </div>
+        value="{{ smiles }}"
-    {% if result %}
+      />
-        {{ smiles }}<p></p>
+      <input
-        <img width='400' src='{% url 'depict' %}?smiles={{ smiles|urlencode }}'><br>
+        type="text"
-        <p></p>
+        class="form-control"
-        {% if rule %}
+        id="smiles"
-            {{ smirks }}
+        name="smirks"
-            <p></p>
+        placeholder="SMIRKS"
-            {{ rule.reactants_smarts }}
+        value="{{ smirks }}"
-            <p></p>
+      />
-            {{ rule.products_smarts }}
+      <button type="submit" class="btn btn-primary">Test</button>
-            <p></p>
+    </form>
-            <div>
+  </div>
-                {{ rule.as_svg|safe }}
+  {% if result %}
-            </div>
+    {{ smiles }}
-        {% endif %}
+    <p></p>
-        <h2>Diff</h2>
+    <img
-        {% if diff %}
+      width="400"
-            {% for d in diff %}
+      src="{% url 'depict' %}?smiles={{ smiles|urlencode }}"
-                {{ d }}
+    /><br />
-            {% endfor %}
+    <p></p>
-        {% else %}
+    {% if rule %}
-            {{ "No diff" }}
+      {{ smirks }}
-        {% endif %}
+      <p></p>
-        <div>
+      {{ rule.reactants_smarts }}
-            <div class="col-md-6">
+      <p></p>
-                <h2>Ambit</h2>
+      {{ rule.products_smarts }}
-                {% for p in ambit_res %}
+      <p></p>
-                    {{ p }}<br>
+      <div>{{ rule.as_svg|safe }}</div>
-                    <img 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>
-                    <img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
-                {% endfor %}
-            </div>
-        </div>
     {% endif %}
+    <h2>Diff</h2>
+    {% if diff %}
+      {% for d in diff %}
+        {{ d }}
+      {% endfor %}
+    {% else %}
+      {{ "No diff" }}
+    {% endif %}
+    <div>
+      <div class="col-md-6">
+        <h2>Ambit</h2>
+        {% for p in ambit_res %}
+          {{ p }}<br />
+          <img
+            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 />
+          <img
+            width="400"
+            src="{% url 'depict' %}?smiles={{ p|urlencode }}"
+          /><br />
+        {% endfor %}
+      </div>
+    </div>
+  {% endif %}
 {% endblock content %}

templates/errors/400_bad_request.html

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

templates/errors/403_access_denied.html

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

templates/errors/404_not_found.html

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

templates/errors/error.html

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

templates/errors/user_account_inactive.html

@@ -1,12 +1,11 @@
 {% extends "framework.html" %}
 {% load static %}
 {% block content %}
-
+  <div class="alert alert-danger" role="alert">
-    <div class="alert alert-danger" role="alert">
+    <h4 class="alert-heading">Your account has not been activated yet!</h4>
-        <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>
+    </p>
-    </div>
+  </div>
-
 {% endblock content %}

templates/framework.html

@@ -1,77 +1,106 @@
-<!DOCTYPE html>
+<!doctype html>
-<html>
+<html data-theme="envipath">
-{% load static %}
+  {% load static %}
-<head>
+  <head>
     <title>{{ title }}</title>
-    <style>
+    <meta name="csrf-token" content="{{ csrf_token }}" />
-        html, body {
+    {# Favicon #}
-            height: 100%; /* ensure body fills viewport */
+    <link
-            overflow-x: hidden; /* prevent horizontal scroll */
+      rel="shortcut icon"
-        }
+      type="image/png"
-    </style>
+      href="{% static 'images/favicon.ico' %}"
-    {# TODO use bundles from bootstrap 3.3.7 #}
+    />
+
+    {# 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">
+    <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
-    <link rel="stylesheet"
+      href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css"
-          href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.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;
 
-        // Setup CSRF header for all jQuery AJAX requests
+    {# Bootstrap compatibility styles #}
-        $.ajaxSetup({
+    <style>
-            beforeSend: function(xhr, settings) {
+      /* Ensure proper viewport behavior */
-                if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
+      html,
-                    xhr.setRequestHeader("X-CSRFToken", csrftoken);
+      body {
-                }
+        height: 100%; /* ensure body fills viewport */
-            }
+        overflow-x: hidden; /* prevent horizontal scroll */
-        });
+      }
+    </style>
+
+    <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>
-    {# 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 #}
     <script src="{% static 'js/jquery-bootstrap-modal-steps.js' %}"></script>
 
     {% if not debug %}
-        <!-- Matomo -->
+      <!-- Matomo -->
-        <script>
+      <script>
-            var _paq = window._paq = window._paq || [];
+        var _paq = (window._paq = window._paq || []);
-            /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+        /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
-            _paq.push(['trackPageView']);
+        _paq.push(["trackPageView"]);
-            _paq.push(['enableLinkTracking']);
+        _paq.push(["enableLinkTracking"]);
-            (function () {
+        (function () {
-                var u = "//matomo.envipath.com/";
+          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", "{{ meta.site_id }}"]);
-                var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
+          var d = document,
-                g.async = true;
+            g = d.createElement("script"),
-                g.src = u + 'matomo.js';
+            s = d.getElementsByTagName("script")[0];
-                s.parentNode.insertBefore(g, s);
+          g.async = true;
-            })();
+          g.src = u + "matomo.js";
-        </script>
+          s.parentNode.insertBefore(g, s);
-        <!-- End Matomo Code -->
+        })();
+      </script>
+      <!-- End Matomo Code -->
     {% endif %}
-
+  </head>
-</head>
+  <body>
-<body>
+    <!-- Legacy Bootstrap navbar - isolated from Tailwind -->
-<nav class="navbar navbar-default navbar-inverse" style="border-radius:0px;" role="navigation">
+    <div class="legacy-bootstrap">
-    <div class="container-fluid">
+      <nav
-        <!-- Brand and toggle get grouped for better mobile display -->
+        class="navbar navbar-default navbar-inverse"
-        <div class="navbar-header navbar-header-framework">
+        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">
             <!--            <button type="button" class="navbar-toggle navbar-toggle-framework" data-toggle="collapse"-->
             <!--                    data-target="#navbarCollapse">-->
             <!--                <span class="sr-only">Toggle navigation</span>-->
@@ -79,198 +108,315 @@
             <!--                <span class="icon-bar"></span>-->
             <!--                <span class="icon-bar"></span>-->
             <!--            </button>-->
-            <a id="pictureLink" href="{{ meta.server_url }}" class="navbar-brand">
+            <a
-                <img id="image-logo-short-white.svg" src='{% static "/images/logo-short-white.svg" %}' width="100"
+              id="pictureLink"
-                     alt="enviPath">
+              href="{{ meta.server_url }}"
+              class="navbar-brand"
+            >
+              <img
+                id="image-logo-short-white.svg"
+                src="{% static "/images/logo-short-white.svg" %}"
+                width="100"
+                alt="enviPath"
+              />
             </a>
-        </div>
+          </div>
 
-        <!-- Collect the nav links, forms, and other content for toggling -->
+          <!-- Collect the nav links, forms, and other content for toggling -->
-        <div class="collapse navbar-collapse collapse-framework navbar-collapse-framework" id="navbarCollapse">
+          <div
+            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>
+              </li>
+              {#                <li class="dropdown">#}
+              {#                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
+              {#                    <ul role="menu" class="dropdown-menu">#}
+              {#                        <li>#}
+              {#                            <a class="button" data-toggle="modal" data-target="#predict_modal">#}
+              {#                                <i class="	glyphicon glyphicon-tag"></i> Predict Pathway#}
+              {#                            </a>#}
+              {#                        </li>#}
+              {#                        <li>#}
+              {#                            <a class="button" data-toggle="modal" data-target="#batch_predict_modal">#}
+              {#                                <i class="	glyphicon glyphicon-tags"></i> Batch Prediction#}
+              {#                            </a>#}
+              {#                        </li>#}
+              {#                    </ul>#}
+              {#                </li>#}
+              <li>
+                <a href="{{ meta.server_url }}/package" id="packageLink"
+                  >Package</a
+                >
+              </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="#"
+                  >Browse Data<b class="caret"></b
+                ></a>
+                <ul role="menu" class="dropdown-menu">
+                  <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>
+                  {#                        <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
+              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 class="dropdown">
+                <a data-toggle="dropdown" class="dropdown-toggle" href="#"
+                  >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>
+                    <a
+                      href="https://community.envipath.org/t/envipath-license/109"
+                      id="licenceLink"
+                      >Licences</a
+                    >
+                  </li>
+                  <li class="divider"></li>
+                  <li>
+                    <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 class="divider"></li>
+                  <li><a>Version: {{ meta.version }}</a></li>
+                </ul>
+              </li>
+              {% if meta.user.username == 'anonymous' %}
                 <li>
-                    <a href="#" data-toggle="modal" data-target="#predict_modal">
+                  <a
-                        Predict Pathway
+                    href="{% url 'login' %}"
-                    </a>
+                    id="loginButton"
+                    style="margin-right:10px"
+                    >Login</a
+                  >
                 </li>
-{#                <li class="dropdown">#}
+              {% else %}
-{#                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
-{#                    <ul role="menu" class="dropdown-menu">#}
-{#                        <li>#}
-{#                            <a class="button" data-toggle="modal" data-target="#predict_modal">#}
-{#                                <i class="	glyphicon glyphicon-tag"></i> Predict Pathway#}
-{#                            </a>#}
-{#                        </li>#}
-{#                        <li>#}
-{#                            <a class="button" data-toggle="modal" data-target="#batch_predict_modal">#}
-{#                                <i class="	glyphicon glyphicon-tags"></i> Batch Prediction#}
-{#                            </a>#}
-{#                        </li>#}
-{#                    </ul>#}
-{#                </li>#}
-                <li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></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="#">Browse Data<b class="caret"></b></a>
+                  <a
-                    <ul role="menu" class="dropdown-menu">
+                    data-toggle="dropdown"
-                        <li><a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a></li>
+                    id="loggedInButton"
-                        <li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
+                    class="dropdown-toggle"
-                        <li><a href="{{ meta.server_url }}/compound" id="compoundLink">Compound</a></li>
+                    id="logedInButton"
-                        <li><a href="{{ meta.server_url }}/reaction" id="reactionLink">Reaction</a></li>
+                    href="#"
-                        <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>
+                    <div id="username">
-                        {#                        <li><a href="{{ meta.server_url }}/setting" id="settingLink">Setting</a></li>#}
+                      {{ user.username }}<b class="caret"></b>
-                        {#                        <li><a href="{{ meta.server_url }}/user" id="userLink">User</a></li>#}
+                    </div>
-                        {#                        <li><a href="{{ meta.server_url }}/group" id="groupLink">Group</a></li>#}
+                  </a>
-                    </ul>
+                  <ul role="menu" class="dropdown-menu">
-                </li>
-
-            </ul>
-
-            <ul 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 class="dropdown">
-                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">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><a href="https://community.envipath.org/t/envipath-license/109" id="licenceLink">Licences</a></li>
-                        <li class="divider"></li>
-                        <li><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 class="divider"></li>
-                        <li><a>Version: {{ meta.version }}</a></li>
-                    </ul>
-                </li>
-                {% if meta.user.username == 'anonymous' %}
                     <li>
-                        <a href="#signup" id="loginButton" data-toggle="modal" data-target="#signupmodal"
+                      <a href="{{ meta.user.url }}" id="accountbutton"
-                           style="margin-right:10px">Login</a>
+                        >My Account</a
+                      >
                     </li>
-                {% else %}
+                    <li class="divider"></li>
-                    <li class="dropdown">
+                    <form
-                        <a data-toggle="dropdown" id="loggedInButton" class="dropdown-toggle" id="logedInButton"
+                      class="navbar-form navbar-left navbar-left-framework"
-                           href="#">
+                      role="logout"
-                            <div id="username">
+                      action="{% url 'logout' %}"
-                                {{ user.username }}<b class="caret"></b>
+                      method="post"
-                            </div>
+                    >
-                        </a>
+                      {% csrf_token %}
-                        <ul role="menu" class="dropdown-menu">
+                      <div class="form-group">
-                            <li>
+                        <input type="hidden" name="logout" value="true" />
-                                <a href="{{ meta.user.url }}" id="accountbutton">My Account</a>
+                      </div>
-                            </li>
+                      <button type="submit" class="btn btn-default">
-                            <li class="divider"></li>
+                        Logout
-                            <form class="navbar-form navbar-left navbar-left-framework" role="logout"
+                      </button>
-                                  action="{% url 'logout' %}" method="post">
+                    </form>
-                                {% csrf_token %}
+                  </ul>
-                                <div class="form-group">
+                </li>
-                                    <input type="hidden" name="logout" value="true">
+              {% endif %}
-                                </div>
-                                <button type="submit" class="btn btn-default">Logout</button>
-                            </form>
-                        </ul>
-                    </li>
-                {% endif %}
             </ul>
+          </div>
         </div>
+      </nav>
     </div>
-</nav>
+    <!-- End legacy Bootstrap navbar -->
-<div id="docContent" class="content container">
+
-    {% if breadcrumbs %}
+    <div id="docContent" class="content container">
+      {% if breadcrumbs %}
         <div id="bread">
-            <ol class="breadcrumb">
+          <ol class="breadcrumb">
-                {% for elem in breadcrumbs %}
+            {% for elem in breadcrumbs %}
-                    {% for name, url in elem.items %}
+              {% for name, url in elem.items %}
-                        {% if forloop.parentloop.last %}
+                {% if forloop.parentloop.last %}
-                            <li class="active">{{ name }}</li>
+                  <li class="active">{{ name }}</li>
-                        {% else %}
+                {% else %}
-                            <li>
+                  <li>
-                                <a href="{{ url }}">{{ name }}</a>
+                    <a href="{{ url }}">{{ name }}</a>
-                            </li>
+                  </li>
-                        {% endif %}
+                {% endif %}
-                    {% endfor %}
+              {% endfor %}
-                {% endfor %}
+            {% endfor %}
-            </ol>
+          </ol>
         </div>
-    {% endif %}
+      {% endif %}
-    {% if message %}
+      {% if message %}
-        <div id="message">
+        <div id="message">{{ message }}</div>
-            {{ message }}
+      {% endif %}
-        </div>
+      {% block content %}
-    {% endif %}
+      {% endblock content %}
-    {% block content %}
+      {% if meta.url_contains_package and meta.current_package.license %}
-    {% endblock content %}
-    {% if meta.url_contains_package and meta.current_package.license %}
         <p></p>
         <div class="panel-group" id="license_accordion">
-            <div class="panel panel-default list-group-item" style="background-color:#f5f5f5">
+          <div
-                <div class="panel-title">
+            class="panel panel-default list-group-item"
-                    <a data-toggle="collapse" data-parent="#licence_accordion" href="#license">License</a>
+            style="background-color:#f5f5f5"
-                </div>
+          >
+            <div class="panel-title">
+              <a
+                data-toggle="collapse"
+                data-parent="#licence_accordion"
+                href="#license"
+                >License</a
+              >
             </div>
-            <div id="license" class="panel-collapse collapse in">
+          </div>
-                <div class="panel-body list-group-item">
+          <div id="license" class="panel-collapse in collapse">
-                    <a target="_blank" href="{{ meta.current_package.license.link }}">
+            <div class="panel-body list-group-item">
-                        <img src="{{ meta.current_package.license.image_link }}">
+              <a target="_blank" href="{{ meta.current_package.license.link }}">
-                    </a>
+                <img src="{{ meta.current_package.license.image_link }}" />
-                </div>
+              </a>
             </div>
+          </div>
         </div>
-    {% endif %}
+      {% endif %}
-</div>
-
-<!-- FOOTER -->
-<div class="container text-center">
-    <hr/>
-    <div class="row">
-        <div class="col-lg-12">
-            <ul class="nav nav-pills nav-justified">
-                <li>
-                    <a href="http://ml.auckland.ac.nz" target="_blank">
-                        <img id="image-uoalogo" 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 id="image-ealogo" height="60" src='{% static "/images/ealogo.gif" %}' alt="Eawag"/>
-                    </a>
-                </li>
-                <li>
-                    <a href="https://www.uzh.ch/" target="_blank">
-                        <img id="image-ufzlogo" height="60" src='{% static "/images/uzh-logo.svg" %}'
-                             alt="University of Zurich"/>
-                    </a>
-                </li>
-            </ul>
-        </div>
     </div>
-</div>
+
-<div class="row">
+    <!-- FOOTER - Legacy Bootstrap -->
-    <div class="col-lg-12">
+    <div class="legacy-bootstrap">
-        <ul class="nav nav-pills nav-justified">
+      <div class="container text-center">
+        <hr />
+        <div class="row">
+          <div class="col-lg-12">
+            <ul class="nav nav-pills nav-justified">
+              <li>
+                <a href="http://ml.auckland.ac.nz" target="_blank">
+                  <img
+                    id="image-uoalogo"
+                    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
+                    id="image-ealogo"
+                    height="60"
+                    src="{% static "/images/ealogo.gif" %}"
+                    alt="Eawag"
+                  />
+                </a>
+              </li>
+              <li>
+                <a href="https://www.uzh.ch/" target="_blank">
+                  <img
+                    id="image-ufzlogo"
+                    height="60"
+                    src="{% static "/images/uzh-logo.svg" %}"
+                    alt="University of Zurich"
+                  />
+                </a>
+              </li>
+            </ul>
+          </div>
+        </div>
+      </div>
+      <div class="row">
+        <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><a href="mailto:admin@envipath.org" target="_blank">Contact</a></li>
+            <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>
+          </ul>
+        </div>
+      </div>
     </div>
-</div>
+    <!-- End legacy Bootstrap footer -->
-<script>
+
-    $(function () {
+    <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>
+    </script>
-{% block modals %}
+    {% block modals %}
-    {% include "modals/cite_modal.html" %}
+      {% include "modals/cite_modal.html" %}
-    {% include "modals/signup_modal.html" %}
+      {% include "modals/predict_modal.html" %}
-    {% include "modals/predict_modal.html" %}
+      {% include "modals/batch_predict_modal.html" %}
-    {% include "modals/batch_predict_modal.html" %}
+    {% endblock %}
-{% endblock %}
+  </body>
-</body>
 </html>

templates/framework_modern.html

@@ -0,0 +1,223 @@
+<!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

@@ -0,0 +1,94 @@
+{% 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

@@ -0,0 +1,150 @@
+{% 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

@@ -1,186 +1,503 @@
-{% extends "framework.html" %}
+{% extends "framework_modern.html" %}
 {% load static %}
-{% block content %}
+{% block main_content %}
-    <!-- TODO rename ids as well as remove pathways if modal is closed!-->
+  <!-- Hero Section with Logo and Search -->
-    <div class="modal fade" tabindex="-1" id="foundMatching" role="dialog" aria-labelledby="foundModal"
+  <section class="hero relative mx-auto h-fit w-full max-w-5xl shadow-none">
-         aria-hidden="true">
+    <div
-        <div class="modal-dialog">
+      class="hero from-primary-800 to-primary-600 min-h-[calc(100vh*0.4)] bg-gradient-to-br"
-            <div class="modal-content">
+      style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
-                <div class="modal-header">
+    >
-                    <button type="button" class="close" data-dismiss="modal">
+      <div class="hero-overlay"></div>
-                        <span aria-hidden="true">&times;</span>
+      <!-- Predict Pathway text over the image -->
-                        <span class="sr-only">Close</span>
+      <div class="absolute bottom-40 left-1/8 z-10 -translate-x-8">
-                    </button>
+        <h2 class="text-base-100 text-left text-3xl text-shadow-lg">
-                    <h4 class="modal-title" id="newPackMod">Found Pathway in Database</h4>
+          Predict Your Pathway
-                </div>
+        </h2>
-                <div class="modal-body">
+      </div>
-                    <p>We found at least one pathway in the database with the given root
-                        compound. Do you want to open any of the existing pathways or
-                        predict a new one? To open an existing pathway, simply click
-                        on the pathway, to predict a new one, click Predict. The predicted
-                        pathway might differ from the ones in the database due to the
-                        settings used in the prediction.</p>
-                    <div id="foundPathways"></div>
-                </div>
-                <div class="modal-footer">
-                    <a id="modal-predict" class="btn btn-primary" href="#">Predict</a>
-                    <button type="button" id="cancel-predict" class="btn btn-default" data-dismiss="modal">Cancel
-                    </button>
-                </div>
-            </div>
-        </div>
     </div>
-    <div class="row">
+  </section>
-        <div class="col-xs-8">
+
-            <div class="jumbotron">
+  <div class="bg-base-200 mx-auto max-w-5xl shadow-md">
-                <h1>
+    <!-- Predict Pathway Section -->
-                    <img id="image-logo-long" class="img-responsive" alt="enviPath" width="1000ex"
+    <div
-                         src='{% static "/images/logo-long.svg" %}'/>
+      class="relative z-20 mx-auto -mt-32 mb-10 w-full flex-col lg:flex-row-reverse"
-                </h1>
+    >
-                <p>enviPath is a database and prediction system for the microbial
+      <div
-                    biotransformation of organic environmental contaminants. The
+        class="card bg-base-100 mx-auto w-3/4 shrink-0 shadow-xl transition-all duration-300 ease-in-out"
-                    database provides the possibility to store and view experimentally
+      >
-                    observed biotransformation pathways. The pathway prediction system
+        <div class="card-body">
-                    provides different relative reasoning models to predict likely biotransformation
+          <div class="my-4 ml-8 flex h-fit flex-row items-center justify-start">
-                    pathways and products. You can try it out below.
+            <div class="flex items-center gap-1">
-                </p>
+              <label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
-                <p>
+                <input type="checkbox" />
-                    <a class="btn" style="background-color:#222222;color:#9d9d9d" role="button" target="_blank"
+                <span class="swap-on flex items-center gap-1">
-                       href="https://wiki.envipath.org/index.php/Main_Page">Learn more &gt;&gt;</a>
+                  <div
-                </p>
+                    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">
+                  <a class="label justify-end" href="/predict">Advanced</a>
+                </div>
+              </div>
+              <input
+                type="hidden"
+                id="index-form-smiles"
+                name="smiles"
+                value="smiles"
+              />
+              <input
+                type="hidden"
+                id="index-form-predict"
+                name="predict"
+                value="predict"
+              />
+              <input type="hidden" id="current-action" value="predict" />
+            </form>
+          </fieldset>
         </div>
-        <div id="loading"></div>
+      </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">
+    <!-- Community News Section -->
-            {% csrf_token %}
+    <section class="bg-base-200 z-10 mx-8 py-16">
-            <div class="input-group" id="index-form-bar">
+      <div class="mx-auto max-w-7xl px-4">
-                <div class="input-group-btn">
+        <h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>
-                    <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
+
-                            aria-expanded="false">
+        <div id="community-news-container" class="flex justify-center gap-4">
-                        <span class="caret"></span>
+          <!-- News cards will be populated here -->
-                    </button>
+          <div id="loading" class="flex w-full justify-center">
-                    <ul class="dropdown-menu" role="menu">
+            <span class="loading loading-spinner loading-lg"></span>
-                        <li>
+          </div>
-                            <iframe id="index-form-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
+        </div>
-                                    height="510"></iframe>
+
-                        </li>
+        <div class="mt-6 text-right">
-                    </ul>
+          <a
-                </div>
+            href="https://community.envipath.org/c/announcements/10"
-                <input type="text" class="form-control" id='index-form-text-input'
+            target="_blank"
-                       placeholder="Enter a SMILES to predict a Pathway or type something to search">
+            class="btn btn-ghost btn-sm"
-                <div class="input-group-btn">
+          >
-                    <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
+            Read More Announcements
-                            aria-haspopup="true"
+          </a>
-                            aria-expanded="false" id="action-button">Predict <span class="caret"></span></button>
+        </div>
-                    <ul class="dropdown-menu">
+
-                        <li><a id="dropdown-predict">Predict</a></li>
+        <!-- Discourse API integration -->
-                        <li><a id="dropdown-search">Search</a></li>
+        <script src="{% static 'js/discourse-api.js' %}"></script>
-                    </ul>
+      </div>
-                    <button class="btn" style="background-color:#222222;color:#9d9d9d" type="button" id="run-button">Go!
+    </section>
-                    </button>
+
-                </div>
+    <!-- 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.
+            </p>
+            <p class="">
+              The pathway prediction system provides different relative
+              reasoning models to predict likely biotransformation pathways and
+              products. Explore our tools and contribute to advancing
+              environmental biotransformation research.
+            </p>
+            <div class="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>
-            <input type="hidden" id="index-form-smiles" name="smiles" value="smiles">
+          </div>
-            <input type="hidden" id="index-form-predict" name="predict" value="predict">
+        </div>
-        </form>
+      </div>
-    </div>
+    </section>
-    <p></p>
-    <script language="javascript">
-        var currentPackage = "{{ meta.current_package.url }}";
 
-        function goButtonClicked() {
+    <!-- Partners Section -->
-            $(this).prop("disabled", true);
+    <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>
 
-            var action = $('#action-button').text().trim();
+  <script language="javascript">
+    var currentPackage = "{{ meta.current_package.url }}";
 
-            var textSmiles = $('#index-form-text-input').val().trim();
+    // Helper function to safely get Ketcher instance from iframe
+    function getKetcherInstance(iframeId) {
+      const ketcherFrame = document.getElementById(iframeId);
+      if (!ketcherFrame) {
+        console.error("Ketcher iframe not found:", iframeId);
+        return null;
+      }
 
-            if (textSmiles === '') {
+      try {
-                $(this).prop("disabled", false);
+        if (
-                return;
+          "contentWindow" in ketcherFrame &&
-            }
+          ketcherFrame.contentWindow.ketcher
-
+        ) {
-            var ketcherSmiles = getKetcher('index-form-ketcher').getSmiles().trim();
+          return ketcherFrame.contentWindow.ketcher;
-
-            if (action !== 'Search' && ketcherSmiles !== '' && textSmiles !== ketcherSmiles) {
-                console.log("Ketcher and TextInput differ!");
-            }
-
-            if (action === 'Search') {
-                var par = {};
-                par['search'] = textSmiles;
-                par['mode'] = 'text';
-                var queryString = $.param(par, true);
-                window.location.href = "/search?" + queryString;
-            } else {
-                $('#index-form-smiles').val(textSmiles);
-                $('#index-form').submit();
-            }
         }
+      } catch (err) {
+        console.error(
+          "Cannot access Ketcher iframe - possible CORS issue:",
+          err,
+        );
+      }
 
-        function actionDropdownClicked() {
+      return null;
-            var suffix = ' <span class="caret"></span>';
+    }
-            var dropdownVal = $(this).text();
 
-            if (dropdownVal === 'Search') {
+    // Discourse API integration is now handled by discourse-api.js
-                $("#index-form").attr("action", '/search');
+
-                $("#index-form").attr("method", 'GET');
+    // Function to render Discourse topics into cards
-            } else {
+    function renderDiscourseTopics(topics) {
-                $("#index-form").attr("action", currentPackage + "/pathway");
+      const container = document.getElementById("community-news-container");
+      if (!container) return;
+
+      // Clear container
+      container.innerHTML = "";
+
+      // Create cards for each topic
+      topics.forEach((topic) => {
+        const card = createDiscourseCard(topic);
+        container.insertAdjacentHTML("beforeend", card);
+      });
+    }
+
+    // Function to create HTML card for a topic
+    function createDiscourseCard(topic) {
+      const date = new Date(topic.created_at).toLocaleDateString();
+
+      return `
+                <div class="card bg-white shadow-xs hover:shadow-lg transition-shadow duration-300 h-64 w-75 flex-shrink-0">
+                    <div class="card-body flex flex-col h-full">
+                        <h3 class="card-title leading-tight font-normal tracking-tight h-12 mb-2 line-clamp-2 text-ellipsis wrap-break-word overflow-hidden">
+                            <a href="${topic.url}" target="_blank" class="hover:text-primary">
+                                ${topic.title}
+                            </a>
+                        </h3>
+                        <div class="text-sm line-clamp-4 break-words" >
+                            ${topic.excerpt}
+                        </div>
+
+                        <div class="flex flex-row items-center justify-between">
+                            <div class="flex items-center gap-2">
+                                <div class="avatar tooltip tooltip-right" data-tip="${topic.author}">
+                                    <div class="w-8 rounded-full">
+                                        <img src="${topic.author_avatar}" alt="${topic.author}" />
+                                    </div>
+                                </div>
+                                <span class="text-xs text-gray-500">${date}</span>
+                            </div>
+                            <a href="${topic.url}" target="_blank" class="btn btn-ghost text-neutral-500 rounded-full p-2">
+                                <svg xmlns="http://www.w3.org/2000/svg" class="h-5 w-5" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
+                                    <path d="M12 7v14"/>
+                                    <path d="M3 18a1 1 0 0 1-1-1V4a1 1 0 0 1 1-1h5a4 4 0 0 1 4 4 4 4 0 0 1 4-4h5a1 1 0 0 1 1 1v13a1 1 0 0 1-1 1h-6a3 3 0 0 0-3 3 3 3 0 0 0-3-3z"/>
+                                </svg>
+                            </a>
+                        </div>
+                    </div>
+                </div>
+            `;
+    }
+
+    // Make render function globally available
+    window.renderDiscourseTopics = renderDiscourseTopics;
+
+    // Toggle functionality with smooth animations
+    function toggleInputMode() {
+      const toggle = $('input[type="checkbox"]');
+      const textContainer = $("#text-input-container");
+      const ketcherContainer = $("#ketcher-container");
+      const formCard = $(".card");
+      const fieldset = $(".fieldset");
+
+      if (toggle.is(":checked")) {
+        // Draw mode - show Ketcher, hide text input
+        textContainer.addClass("opacity-0 transform scale-95");
+        textContainer.removeClass("opacity-100 transform scale-100");
+
+        // Adjust fieldset padding for Ketcher mode - reduce padding and make more compact
+        fieldset.removeClass("p-8");
+        fieldset.addClass("p-4");
+
+        // Wait for fade out to complete, then hide and show new content
+        setTimeout(() => {
+          textContainer.addClass("hidden");
+          ketcherContainer.removeClass("hidden opacity-0 transform scale-95");
+          ketcherContainer.addClass("opacity-100 transform scale-100");
+
+          // Force re-evaluation of iframe size
+          const iframe = document.getElementById("index-ketcher");
+          if (iframe) {
+            iframe.style.height = "400px";
+          }
+        }, 300);
+      } else {
+        // SMILES mode - show text input, hide Ketcher
+        ketcherContainer.addClass("opacity-0 transform scale-95");
+        ketcherContainer.removeClass("opacity-100 transform scale-100");
+
+        // Restore fieldset padding for text input mode
+        fieldset.removeClass("p-4");
+        fieldset.addClass("p-8");
+
+        // Wait for fade out to complete, then hide and show new content
+        setTimeout(() => {
+          ketcherContainer.addClass("hidden");
+          textContainer.removeClass("hidden opacity-0 transform scale-95");
+          textContainer.addClass("opacity-100 transform scale-100");
+        }, 300);
+
+        // Transfer SMILES from Ketcher to text input if available
+        const ketcher = getKetcherInstance("index-ketcher");
+        if (ketcher && ketcher.getSmiles) {
+          try {
+            const smiles = ketcher.getSmiles();
+            if (smiles && smiles.trim() !== "") {
+              $("#index-form-text-input").val(smiles);
             }
-
+          } catch (err) {
-            $('#action-button').html(dropdownVal + suffix);
+            console.error("Failed to sync Ketcher to text input:", err);
+            // Non-critical error, just log it
+          }
         }
+      }
+    }
 
-        function ketcherToTextInput() {
+    // Ketcher integration
-            $('#index-form-text-input').val(this.ketcher.getSmiles());
+    function indexKetcherToTextInput() {
-        }
+      $("#index-form-smiles").val(this.ketcher.getSmiles());
+    }
 
-        $(function () {
+    $(function () {
+      // Initialize fieldset with proper padding
+      $(".fieldset").addClass("p-8");
 
-            $('#index-form').on("keydown", function (e) {
+      // Toggle event listener
-                if (e.key === "Enter") {
+      $('input[type="checkbox"]').on("change", toggleInputMode);
-                    e.preventDefault();
+
-                    goButtonClicked();
+      // Ketcher iframe load handler
-                }
+      $("#index-ketcher").on("load", function () {
+        const checkKetcherReady = () => {
+          const win = this.contentWindow;
+          if (win.ketcher && "editor" in win.ketcher) {
+            window.indexKetcher = win.ketcher;
+            win.ketcher.editor.event.change.handlers.push({
+              once: false,
+              priority: 0,
+              f: indexKetcherToTextInput,
+              ketcher: win.ketcher,
             });
+          } else {
+            setTimeout(checkKetcherReady, 100);
+          }
+        };
+        checkKetcherReady();
+      });
 
-            // Code that should be executed once DOM is ready goes here
+      // Handle example link clicks
-            $('#dropdown-predict').on('click', actionDropdownClicked);
+      $(".example-link").on("click", function (e) {
-            $('#dropdown-search').on('click', actionDropdownClicked);
+        e.preventDefault();
+        const smiles = $(this).data("smiles");
+        const title = $(this).attr("title");
 
-            $('#run-button').on('click', goButtonClicked);
+        // Check if we're in Ketcher mode or text input mode
+        if ($('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);
+        }
 
-            // Update Ketcher Width
+        // Show a brief feedback
-            var fullWidth = $('#index-form-bar').width();
+        const originalText = $(this).text();
-            $('#index-form-ketcher').width(fullWidth);
+        $(this).text(`loaded!`);
+        setTimeout(() => {
+          $(this).text(originalText);
+        }, 1000);
+      });
 
-            // add a listener that gets triggered whenever the structure in ketcher has changed
+      // Handle form submission on Enter
-            $('#index-form-ketcher').on('load', function () {
+      $("#index-form").on("submit", function (e) {
-                const checkKetcherReady = () => {
+        e.preventDefault();
-                    win = this.contentWindow
-                    if (win.ketcher && 'editor' in win.ketcher) {
-                        win.ketcher.editor.event.change.handlers.push({
-                            once: false,
-                            priority: 0,
-                            f: ketcherToTextInput,
-                            ketcher: win.ketcher
-                        });
-                    } else {
-                        setTimeout(checkKetcherReady, 100);
-                    }
-                };
 
-                checkKetcherReady();
+        var textSmiles = "";
-            });
 
-        });
+        // Check if we're in Ketcher mode and extract SMILES
-    </script>
+        if ($('input[type="checkbox"]').is(":checked")) {
-{% endblock content %}
+          // Use the robust getter function
+          const ketcher = getKetcherInstance("index-ketcher");
+          if (ketcher && ketcher.getSmiles) {
+            try {
+              textSmiles = ketcher.getSmiles().trim();
+            } catch (err) {
+              console.error("Failed to get SMILES from Ketcher:", err);
+              alert(
+                "Unable to extract structure from the drawing editor. Please try again or switch to SMILES input mode.",
+              );
+              return;
+            }
+          } else {
+            console.warn("Ketcher not available, possibly still loading");
+            alert(
+              "The drawing editor is still loading. Please wait a moment and try again.",
+            );
+            return;
+          }
+        } else {
+          textSmiles = $("#index-form-text-input").val().trim();
+        }
+
+        if (textSmiles === "") {
+          alert("Please enter a SMILES string or draw a structure.");
+          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 %}

templates/migration.html

@@ -1,44 +1,71 @@
 {% extends "framework.html" %}
 
 {% block content %}
-<div class="panel-group" id="migration-detail">
+  <div class="panel-group" id="migration-detail">
     <div class="panel panel-default">
-        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+      <div
-            Migration Status BT Rules
+        class="panel-heading"
-        </div>
+        id="headingPanel"
-        <div class="panel-body">
+        style="font-size:2rem;height: 46px"
-            <p>Rules with Error: {{ error }}/{{ total }} </p>
+      >
-            <p>Rules without Error: {{ success }}/{{ total }}</p>
+        Migration Status BT Rules
-        </div>
+      </div>
+      <div class="panel-body">
+        <p>Rules with Error: {{ error }}/{{ total }}</p>
+        <p>Rules without Error: {{ success }}/{{ total }}</p>
+      </div>
 
-        {% for obj in results %}
+      {% for obj in results %}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+        <div
-            {% if obj.status %}
+          class="panel panel-default panel-heading list-group-item"
-            <span class="glyphicon glyphicon-ok" aria-hidden="true"
+          style="background-color:silver"
-                  style="float:right" data-toggle="tooltip"
+        >
-                  data-placement="top" title="" data-original-title="Reviewed">
+          {% if obj.status %}
+            <span
+              class="glyphicon glyphicon-ok"
+              aria-hidden="true"
+              style="float:right"
+              data-toggle="tooltip"
+              data-placement="top"
+              title=""
+              data-original-title="Reviewed"
+            >
             </span>
-            {% else %}
+          {% else %}
-            <span class="glyphicon glyphicon-remove" aria-hidden="true"
+            <span
-                  style="float:right" data-toggle="tooltip"
+              class="glyphicon glyphicon-remove"
-                  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>
-            {% endif %}
+          {% endif %}
-            <h4 class="panel-title">
+          <h4 class="panel-title">
-                <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
+            <a
-                   href="#{{ obj.id }}">{{ obj.name|safe }}</a>
+              id="{{ obj.id }}-link"
-            </h4>
+              data-toggle="collapse"
+              data-parent="#migration-detail"
+              href="#{{ obj.id }}"
+              >{{ obj.name|safe }}</a
+            >
+          </h4>
         </div>
-        <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
+        <div
-            <div class="panel-body list-group-item">
+          id="{{ obj.id }}"
-                <a class="list-group-item" href="{{ obj.detail_url }}">{{ obj.name|safe }} Migration Detail Page</a>
+          class="panel-collapse {% if not obj.status %}in{% endif %} collapse"
-            </div>
+        >
+          <div class="panel-body list-group-item">
+            <a class="list-group-item" href="{{ obj.detail_url }}"
+              >{{ obj.name|safe }} Migration Detail Page</a
+            >
+          </div>
         </div>
-        {% endfor %}
+      {% endfor %}
     </div>
-</div>
+  </div>
 
-<script>
+  <script></script>
-
-</script>
 {% endblock content %}

templates/migration_detail.html

@@ -1,45 +1,77 @@
 {% extends "framework.html" %}
 
 {% block content %}
-    <div class="panel-group" id="migration-detail">
+  <div class="panel-group" id="migration-detail">
-        <div class="panel panel-default">
+    <div class="panel panel-default">
-            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+      <div
-                Migration Status for {{ bt_rule_name }}
+        class="panel-heading"
-            </div>
+        id="headingPanel"
-            <div class="panel-body">
+        style="font-size:2rem;height: 46px"
-                <p>A package contains pathways, rules, etc. and can reflect specific experimental
+      >
-                    conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
+        Migration Status for {{ bt_rule_name }}
-                        more &gt;&gt;</a></p>
+      </div>
-            </div>
+      <div class="panel-body">
+        <p>
+          A package contains pathways, rules, etc. and can reflect specific
+          experimental conditions.
+          <a
+            target="_blank"
+            href="https://wiki.envipath.org/index.php/packages"
+            role="button"
+            >Learn more &gt;&gt;</a
+          >
+        </p>
+      </div>
 
-            {% for obj in results %}
+      {% for obj in results %}
-                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+        <div
-                    {% if obj.status %}
+          class="panel panel-default panel-heading list-group-item"
-                        <span class="glyphicon glyphicon-ok" aria-hidden="true"
+          style="background-color:silver"
-                              style="float:right" data-toggle="tooltip"
+        >
-                              data-placement="top" title="" data-original-title="Reviewed">
+          {% if obj.status %}
-                        </span>
+            <span
-                    {% else %}
+              class="glyphicon glyphicon-ok"
-                        <span class="glyphicon glyphicon-remove" aria-hidden="true"
+              aria-hidden="true"
-                              style="float:right" data-toggle="tooltip"
+              style="float:right"
-                              data-placement="top" title="" data-original-title="Reviewed">
+              data-toggle="tooltip"
-                        </span>
+              data-placement="top"
-                    {% endif %}
+              title=""
-                    <h4 class="panel-title">
+              data-original-title="Reviewed"
-                        <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
+            >
-                           href="#{{ obj.id }}">{{ obj.name|safe }}</a>
+            </span>
-                    </h4>
+          {% else %}
-                </div>
+            <span
-                <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
+              class="glyphicon glyphicon-remove"
-                    <div class="panel-body list-group-item">
+              aria-hidden="true"
-                        <pre>{{ obj.detail }}</pre>
+              style="float:right"
-                    </div>
+              data-toggle="tooltip"
-                </div>
+              data-placement="top"
-            {% endfor %}
+              title=""
+              data-original-title="Reviewed"
+            >
+            </span>
+          {% endif %}
+          <h4 class="panel-title">
+            <a
+              id="{{ obj.id }}-link"
+              data-toggle="collapse"
+              data-parent="#migration-detail"
+              href="#{{ obj.id }}"
+              >{{ obj.name|safe }}</a
+            >
+          </h4>
         </div>
+        <div
+          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>
+        </div>
+      {% endfor %}
     </div>
+  </div>
 
-    <script>
+  <script></script>
-
-    </script>
 {% endblock content %}

templates/modals/cite_modal.html

@@ -1,31 +1,48 @@
-<div class="modal fade bs-modal-lg" id="citemodal" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel"
+<div
-     aria-hidden="true">
+  class="modal fade bs-modal-lg"
-    <div class="modal-dialog modal-lg">
+  id="citemodal"
-        <div class="modal-content">
+  tabindex="-1"
-            <div class="modal-header">
+  role="dialog"
-                <h3>How to cite enviPath</h3>
+  aria-labelledby="myLargeModalLabel"
-            </div>
+  aria-hidden="true"
-            <div class="modal-body">
+>
-                <ol class="list-group list-group-numbered">
+  <div class="modal-dialog modal-lg">
-                    <li class="list-group-item">
+    <div class="modal-content">
-                        Hafner, J., Lorsbach, T., Schmidt, S. <em>et al.</em>
+      <div class="modal-header">
-                        <cite>Advancements in biotransformation pathway prediction: enhancements, datasets, and novel
+        <h3>How to cite enviPath</h3>
-                            functionalities in enviPath.</cite>
+      </div>
-                        <a href="https://doi.org/10.1186/s13321-024-00881-6" target="_blank">J Cheminform 16, 93
+      <div class="modal-body">
-                            (2024)</a>
+        <ol class="list-group list-group-numbered">
-                    </li>
+          <li class="list-group-item">
-                    <li class="list-group-item">
+            Hafner, J., Lorsbach, T., Schmidt, S. <em>et al.</em>
-                        Wicker, J., Lorsbach, T., Gütlein, M., Schmid, E., Latino, D., Kramer, S., Fenner, K.
+            <cite
-                        <cite>enviPath - The environmental contaminant biotransformation pathway resource</cite>
+              >Advancements in biotransformation pathway prediction:
-                        <a href="https://doi.org/10.1093/nar/gkv1229" target="_blank">
+              enhancements, datasets, and novel functionalities in
-                            Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D502-D508
+              enviPath.</cite
-                        </a>
+            >
-                    </li>
+            <a href="https://doi.org/10.1186/s13321-024-00881-6" target="_blank"
-                </ol>
+              >J Cheminform 16, 93 (2024)</a
-            </div>
+            >
-            <div class="modal-footer">
+          </li>
-                <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+          <li class="list-group-item">
-            </div>
+            Wicker, J., Lorsbach, T., Gütlein, M., Schmid, E., Latino, D.,
-        </div>
+            Kramer, S., Fenner, K.
+            <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
+              D502-D508
+            </a>
+          </li>
+        </ol>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-default" data-dismiss="modal">
+          Close
+        </button>
+      </div>
     </div>
+  </div>
 </div>

templates/modals/collections/import_legacy_package_modal.html

@@ -1,42 +1,70 @@
-<div class="modal fade" tabindex="-1" id="import_legacy_package_modal" role="dialog"
+<div
-     aria-labelledby="import_legacy_package_modal" aria-hidden="true">
+  class="modal fade"
-    <div class="modal-dialog">
+  tabindex="-1"
-        <div class="modal-content">
+  id="import_legacy_package_modal"
-            <div class="modal-header">
+  role="dialog"
-                <button type="button" class="close" data-dismiss="modal">
+  aria-labelledby="import_legacy_package_modal"
-                    <span aria-hidden="true">&times;</span>
+  aria-hidden="true"
-                    <span class="sr-only">Close</span>
+>
-                </button>
+  <div class="modal-dialog">
-                <h4 class="modal-title">Import Package from legacy System</h4>
+    <div class="modal-content">
-            </div>
+      <div class="modal-header">
-            <div class="modal-body">
+        <button type="button" class="close" data-dismiss="modal">
-                <p>Create a Package based on the JSON Export of the legacy system.</p>
+          <span aria-hidden="true">&times;</span>
-                <form id="import-legacy-package-modal-form" accept-charset="UTF-8" data-remote="true" method="post"
+          <span class="sr-only">Close</span>
-                      enctype="multipart/form-data">
+        </button>
-                    {% csrf_token %}
+        <h4 class="modal-title">Import Package from legacy System</h4>
-                    <p>
+      </div>
-                        <label class="btn btn-primary" for="legacyJsonFile">
+      <div class="modal-body">
-                            <input id="legacyJsonFile" name="file" type="file" style="display:none;"
+        <p>Create a Package based on the JSON Export of the legacy system.</p>
-                                   onchange="$('#upload-legacy-file-info').html(this.files[0].name)">
+        <form
-                            Choose JSON File
+          id="import-legacy-package-modal-form"
-                        </label>
+          accept-charset="UTF-8"
-                        <span class="label label-info" id="upload-legacy-file-info"></span>
+          data-remote="true"
-                        <input type="hidden" value="import-legacy-package-json" name="hidden" readonly="">
+          method="post"
-                    </p>
+          enctype="multipart/form-data"
-                </form>
+        >
-            </div>
+          {% csrf_token %}
-            <div class="modal-footer">
+          <p>
-                <a id="import-legacy-package-modal-form-submit" class="btn btn-primary" href="#">Submit</a>
+            <label class="btn btn-primary" for="legacyJsonFile">
-                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
+              <input
-            </div>
+                id="legacyJsonFile"
-        </div>
+                name="file"
+                type="file"
+                style="display:none;"
+                onchange="$('#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
+              type="hidden"
+              value="import-legacy-package-json"
+              name="hidden"
+              readonly=""
+            />
+          </p>
+        </form>
+      </div>
+      <div class="modal-footer">
+        <a
+          id="import-legacy-package-modal-form-submit"
+          class="btn btn-primary"
+          href="#"
+          >Submit</a
+        >
+        <button type="button" class="btn btn-default" data-dismiss="modal">
+          Cancel
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-    $(function () {
+  $(function () {
-        $('#import-legacy-package-modal-form-submit').on('click', function (e) {
+    $("#import-legacy-package-modal-form-submit").on("click", function (e) {
-            e.preventDefault();
+      e.preventDefault();
-            $('#import-legacy-package-modal-form').submit();
+      $("#import-legacy-package-modal-form").submit();
-        });
     });
+  });
 </script>

templates/modals/collections/import_package_modal.html

@@ -1,42 +1,70 @@
-<div class="modal fade" tabindex="-1" id="import_package_modal" role="dialog"
+<div
-     aria-labelledby="import_package_modal" aria-hidden="true">
+  class="modal fade"
-    <div class="modal-dialog">
+  tabindex="-1"
-        <div class="modal-content">
+  id="import_package_modal"
-            <div class="modal-header">
+  role="dialog"
-                <button type="button" class="close" data-dismiss="modal">
+  aria-labelledby="import_package_modal"
-                    <span aria-hidden="true">&times;</span>
+  aria-hidden="true"
-                    <span class="sr-only">Close</span>
+>
-                </button>
+  <div class="modal-dialog">
-                <h4 class="modal-title">Import Package</h4>
+    <div class="modal-content">
-            </div>
+      <div class="modal-header">
-            <div class="modal-body">
+        <button type="button" class="close" data-dismiss="modal">
-                <p>Create a Package based on a JSON Export.</p>
+          <span aria-hidden="true">&times;</span>
-                <form id="import-package-modal-form" accept-charset="UTF-8" data-remote="true" method="post"
+          <span class="sr-only">Close</span>
-                      enctype="multipart/form-data">
+        </button>
-                    {% csrf_token %}
+        <h4 class="modal-title">Import Package</h4>
-                    <p>
+      </div>
-                        <label class="btn btn-primary" for="jsonFile">
+      <div class="modal-body">
-                            <input id="jsonFile" name="file" type="file" style="display:none;"
+        <p>Create a Package based on a JSON Export.</p>
-                                   onchange="$('#upload-file-info').html(this.files[0].name)">
+        <form
-                            Choose JSON File
+          id="import-package-modal-form"
-                        </label>
+          accept-charset="UTF-8"
-                        <span class="label label-info" id="upload-file-info"></span>
+          data-remote="true"
-                        <input type="hidden" value="import-package-json" name="hidden" readonly="">
+          method="post"
-                    </p>
+          enctype="multipart/form-data"
-                </form>
+        >
-            </div>
+          {% csrf_token %}
-            <div class="modal-footer">
+          <p>
-                <a id="import-package-modal-form-submit" class="btn btn-primary" href="#">Submit</a>
+            <label class="btn btn-primary" for="jsonFile">
-                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
+              <input
-            </div>
+                id="jsonFile"
-        </div>
+                name="file"
+                type="file"
+                style="display:none;"
+                onchange="$('#upload-file-info').html(this.files[0].name)"
+              />
+              Choose JSON File
+            </label>
+            <span class="label label-info" id="upload-file-info"></span>
+            <input
+              type="hidden"
+              value="import-package-json"
+              name="hidden"
+              readonly=""
+            />
+          </p>
+        </form>
+      </div>
+      <div class="modal-footer">
+        <a
+          id="import-package-modal-form-submit"
+          class="btn btn-primary"
+          href="#"
+          >Submit</a
+        >
+        <button type="button" class="btn btn-default" data-dismiss="modal">
+          Cancel
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-    $(function () {
+  $(function () {
-        $('#import-package-modal-form-submit').on('click', function (e) {
+    $("#import-package-modal-form-submit").on("click", function (e) {
-            e.preventDefault();
+      e.preventDefault();
-            $('#import-package-modal-form').submit();
+      $("#import-package-modal-form").submit();
-        });
     });
+  });
 </script>

templates/modals/collections/new_compound_modal.html

@@ -1,78 +1,119 @@
 {% load static %}
-<div class="modal fade bs-modal-lg" id="new_compound_modal" tabindex="-1" aria-labelledby="new_compound_modal" aria-modal="true"
+<div
-     role="dialog">
+  class="modal fade bs-modal-lg"
-    <div class="modal-dialog modal-lg">
+  id="new_compound_modal"
-        <div class="modal-content">
+  tabindex="-1"
-            <div class="modal-header">
+  aria-labelledby="new_compound_modal"
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+  aria-modal="true"
-                    <span aria-hidden="true">×</span>
+  role="dialog"
-                </button>
+>
-                <h4 class="modal-title">Create a new Compound</h4>
+  <div class="modal-dialog modal-lg">
-            </div>
+    <div class="modal-content">
-            <div class="modal-body">
+      <div class="modal-header">
-                <form id="new_compound_modal_form" accept-charset="UTF-8" action="{% url 'package compound list' meta.current_package.uuid %}" data-remote="true" method="post">
+        <button
-                    {% csrf_token %}
+          type="button"
-                    <label for="compound-name">Name</label>
+          class="close"
-                    <input id="compound-name" class="form-control" name="compound-name" placeholder="Name"/>
+          data-dismiss="modal"
-                    <label for="compound-description">Description</label>
+          aria-label="Close"
-                    <input id="compound-description" class="form-control" name="compound-description" placeholder="Description"/>
+        >
-                    <label for="compound-smiles">SMILES</label>
+          <span aria-hidden="true">×</span>
-                    <input type="text" class="form-control" name="compound-smiles" placeholder="SMILES" id="compound-smiles">
+        </button>
-                    <p></p>
+        <h4 class="modal-title">Create a new Compound</h4>
-                    <div>
+      </div>
-                        <iframe id="new_compound_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
+      <div class="modal-body">
-                                height="510"></iframe>
+        <form
-                    </div>
+          id="new_compound_modal_form"
-                    <p></p>
+          accept-charset="UTF-8"
-                </form>
+          action="{% url 'package compound list' meta.current_package.uuid %}"
-            </div>
+          data-remote="true"
-            <div class="modal-footer">
+          method="post"
-                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+        >
-                </button>
+          {% csrf_token %}
-                <button type="button" class="btn btn-primary" id="new_compound_modal_form_submit">Submit</button>
+          <label for="compound-name">Name</label>
-            </div>
+          <input
-        </div>
+            id="compound-name"
+            class="form-control"
+            name="compound-name"
+            placeholder="Name"
+          />
+          <label for="compound-description">Description</label>
+          <input
+            id="compound-description"
+            class="form-control"
+            name="compound-description"
+            placeholder="Description"
+          />
+          <label for="compound-smiles">SMILES</label>
+          <input
+            type="text"
+            class="form-control"
+            name="compound-smiles"
+            placeholder="SMILES"
+            id="compound-smiles"
+          />
+          <p></p>
+          <div>
+            <iframe
+              id="new_compound_ketcher"
+              src="{% static '/js/ketcher2/ketcher.html' %}"
+              width="100%"
+              height="510"
+            ></iframe>
+          </div>
+          <p></p>
+        </form>
+      </div>
+      <div class="modal-footer">
+        <button
+          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>
+      </div>
     </div>
-
+  </div>
 </div>
 <script>
+  function newCompoundModalketcherToNewCompoundModalTextInput() {
+    $("#compound-smiles").val(this.ketcher.getSmiles());
+  }
 
-function newCompoundModalketcherToNewCompoundModalTextInput() {
+  $(function () {
-    $('#compound-smiles').val(this.ketcher.getSmiles());
+    $("#new_compound_ketcher").on("load", function () {
-}
+      const checkKetcherReady = () => {
+        win = this.contentWindow;
+        if (win.ketcher && "editor" in win.ketcher) {
+          win.ketcher.editor.event.change.handlers.push({
+            once: false,
+            priority: 0,
+            f: newCompoundModalketcherToNewCompoundModalTextInput,
+            ketcher: win.ketcher,
+          });
+        } else {
+          setTimeout(checkKetcherReady, 100);
+        }
+      };
 
-$(function() {
+      checkKetcherReady();
-
-    $('#new_compound_ketcher').on('load', function() {
-        const checkKetcherReady = () => {
-            win = this.contentWindow
-            if (win.ketcher && 'editor' in win.ketcher) {
-                win.ketcher.editor.event.change.handlers.push({
-                    once: false,
-                    priority: 0,
-                    f: newCompoundModalketcherToNewCompoundModalTextInput,
-                    ketcher: win.ketcher
-                });
-            } else {
-                setTimeout(checkKetcherReady, 100);
-            }
-        };
-
-        checkKetcherReady();
-    })
-
-    $(function() {
-        $('#new_compound_modal_form_submit').on('click', function(e) {
-            e.preventDefault();
-            $(this).prop("disabled",true);
-
-
-
-            // submit form
-            $('#new_compound_modal_form').submit();
-        });
     });
 
-});
+    $(function () {
+      $("#new_compound_modal_form_submit").on("click", function (e) {
+        e.preventDefault();
+        $(this).prop("disabled", true);
 
+        // submit form
+        $("#new_compound_modal_form").submit();
+      });
+    });
+  });
 </script>

templates/modals/collections/new_group_modal.html

@@ -1,45 +1,70 @@
-<div class="modal fade" tabindex="-1" id="new_group_modal" role="dialog" aria-labelledby="new_group_modal"
+<div
-     aria-hidden="true">
+  class="modal fade"
-    <div class="modal-dialog">
+  tabindex="-1"
-        <div class="modal-content">
+  id="new_group_modal"
-            <div class="modal-header">
+  role="dialog"
-                <button type="button" class="close" data-dismiss="modal">
+  aria-labelledby="new_group_modal"
-                    <span aria-hidden="true">&times;</span>
+  aria-hidden="true"
-                    <span class="sr-only">Close</span>
+>
-                </button>
+  <div class="modal-dialog">
-                <h4 class="modal-title">New Group</h4>
+    <div class="modal-content">
-            </div>
+      <div class="modal-header">
-            <div class="modal-body">
+        <button type="button" class="close" data-dismiss="modal">
-                <p>Create new Group. You can assign users to the group once
+          <span aria-hidden="true">&times;</span>
-                    it is created. Description can be changed after creation.</p>
+          <span class="sr-only">Close</span>
-                <form id="new_group_modal_form" accept-charset="UTF-8" action="{{ SERVER_BASE }}/group"
+        </button>
-                      data-remote="true"
+        <h4 class="modal-title">New Group</h4>
-                      method="post">
+      </div>
-                    {% csrf_token %}
+      <div class="modal-body">
-                    <p>
+        <p>
-                        <label for="name">Name</label>
+          Create new Group. You can assign users to the group once it is
-                        <input id="name" type="text" name="group-name" class="form-control" placeholder="Name"/>
+          created. Description can be changed after creation.
-                    </p>
+        </p>
-                    <p>
+        <form
-                        <label for="description">Description</label>
+          id="new_group_modal_form"
-                        <input id="description" type="text" class="form-control" placeholder="Description..."
+          accept-charset="UTF-8"
-                               name="group-description"/>
+          action="{{ SERVER_BASE }}/group"
-                    </p>
+          data-remote="true"
-                </form>
+          method="post"
-            </div>
+        >
-            <div class="modal-footer">
+          {% csrf_token %}
-                <a id="new_group_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
+          <p>
-                <button type="button" class="btn btn-default" data-dismiss="modal">
+            <label for="name">Name</label>
-                    Cancel
+            <input
-                </button>
+              id="name"
-            </div>
+              type="text"
-        </div>
+              name="group-name"
+              class="form-control"
+              placeholder="Name"
+            />
+          </p>
+          <p>
+            <label for="description">Description</label>
+            <input
+              id="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="#"
+          >Submit</a
+        >
+        <button type="button" class="btn btn-default" data-dismiss="modal">
+          Cancel
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-$(function() {
+  $(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

@@ -1,188 +1,270 @@
+<div
+  class="modal fade"
+  tabindex="-1"
+  id="new_model_modal"
+  role="dialog"
+  aria-labelledby="new_model_modal"
+  aria-hidden="true"
+>
+  <div class="modal-dialog modal-lg">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal">
+          <span aria-hidden="true">&times;</span>
+          <span class="sr-only">Close</span>
+        </button>
+        <h4 class="modal-title">New Model</h4>
+      </div>
+      <div class="modal-body">
+        <form
+          id="new_model_form"
+          accept-charset="UTF-8"
+          action="{{ meta.current_package.url }}/model"
+          data-remote="true"
+          method="post"
+        >
+          {% csrf_token %}
+          <div class="jumbotron">
+            Create a new Model to limit the number of degradation products in
+            the prediction. You just need to set a name and the packages you
+            want the object to be based on. There are multiple types of models
+            available. For additional information have a look at our
+            <a
+              target="_blank"
+              href="https://wiki.envipath.org/index.php/relative-reasoning"
+              role="button"
+              >wiki &gt;&gt;</a
+            >
+          </div>
+          <!-- Name -->
+          <label for="model-name">Name</label>
+          <input
+            id="model-name"
+            name="model-name"
+            class="form-control"
+            placeholder="Name"
+          />
 
-<div class="modal fade" tabindex="-1" id="new_model_modal" role="dialog" aria-labelledby="new_model_modal"
+          <!-- Description -->
-     aria-hidden="true">
+          <label for="model-description">Description</label>
-    <div class="modal-dialog modal-lg">
+          <input
-        <div class="modal-content">
+            id="model-description"
-            <div class="modal-header">
+            name="model-description"
-                <button type="button" class="close" data-dismiss="modal">
+            class="form-control"
-                    <span aria-hidden="true">&times;</span>
+            placeholder="Description"
-                    <span class="sr-only">Close</span>
+          />
-                </button>
-                <h4 class="modal-title">New Model</h4>
-            </div>
-            <div class="modal-body">
-                <form id="new_model_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/model"
-                      data-remote="true" method="post">
-                    {% csrf_token %}
-                    <div class="jumbotron">Create a new Model to
-                        limit the number of degradation products in the
-                        prediction. You just need to set a name and the packages
-                        you want the object to be based on. There are multiple types of models available.
-                        For additional information have a look at our
-                        <a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki
-                            &gt;&gt;</a>
-                    </div>
-                    <!-- Name -->
-                    <label for="model-name">Name</label>
-                    <input id="model-name" name="model-name" class="form-control" placeholder="Name"/>
 
-                    <!-- Description -->
+          <!-- Model Type -->
-                    <label for="model-description">Description</label>
+          <label for="model-type">Model Type</label>
-                    <input id="model-description" name="model-description" class="form-control"
+          <select
-                           placeholder="Description"/>
+            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>
+            {% endfor %}
+          </select>
 
-                    <!-- Model Type -->
+          <!-- Rule Packages -->
-                    <label for="model-type">Model Type</label>
+          <div id="rule-packages" class="ep-model-param mlrr rbrr">
-                    <select id="model-type" name="model-type" class="form-control" data-width='100%'>
+            <label for="model-rule-packages">Rule Packages</label>
-                        <option disabled selected>Select Model Type</option>
+            <select
-                        {% for k, v in model_types.items %}
+              id="model-rule-packages"
-                            <option value="{{ v }}">{{ k }}</option>
+              name="model-rule-packages"
-                        {% endfor %}
+              data-actions-box="true"
-                    </select>
+              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>
+                {% endif %}
+              {% endfor %}
 
-                    <!-- Rule Packages -->
+              <option disabled>Unreviewed Packages</option>
-                    <div id="rule-packages" class="ep-model-param mlrr rbrr">
+              {% for obj in meta.readable_packages %}
-                        <label for="model-rule-packages">Rule Packages</label>
+                {% if not obj.reviewed %}
-                        <select id="model-rule-packages" name="model-rule-packages" data-actions-box='true'
+                  <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
-                                class="form-control" multiple data-width='100%'>
+                {% endif %}
-                            <option disabled>Reviewed Packages</option>
+              {% endfor %}
-                            {% for obj in meta.readable_packages %}
+            </select>
-                                {% if obj.reviewed %}
+          </div>
-                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
-                                {% endif %}
-                            {% endfor %}
 
-                            <option disabled>Unreviewed Packages</option>
+          <!-- Data Packages -->
-                            {% for obj in meta.readable_packages %}
+          <div id="data-packages" class="ep-model-param mlrr rbrr enviformer">
-                                {% if not obj.reviewed %}
+            <label for="model-data-packages">Data Packages</label>
-                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+            <select
-                                {% endif %}
+              id="model-data-packages"
-                            {% endfor %}
+              name="model-data-packages"
-                        </select>
+              data-actions-box="true"
-                    </div>
+              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>
+                {% endif %}
+              {% endfor %}
 
-                    <!-- Data Packages -->
+              <option disabled>Unreviewed Packages</option>
-                    <div id="data-packages" class="ep-model-param mlrr rbrr enviformer">
+              {% for obj in meta.readable_packages %}
-                        <label for="model-data-packages">Data Packages</label>
+                {% if not obj.reviewed %}
-                        <select id="model-data-packages" name="model-data-packages" data-actions-box='true'
+                  <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
-                                class="form-control" multiple data-width='100%'>
+                {% endif %}
-                            <option disabled>Reviewed Packages</option>
+              {% endfor %}
-                            {% for obj in meta.readable_packages %}
+            </select>
-                                {% if obj.reviewed %}
+          </div>
-                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
-                                {% endif %}
-                            {% endfor %}
 
-                            <option disabled>Unreviewed Packages</option>
+          <!-- Fingerprinter -->
-                            {% for obj in meta.readable_packages %}
+          <div id="fingerprinter" class="ep-model-param mlrr">
-                                {% if not obj.reviewed %}
+            <label for="model-fingerprinter">Fingerprinter</label>
-                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+            <select
-                                {% endif %}
+              id="model-fingerprinter"
-                            {% endfor %}
+              name="model-fingerprinter"
-                        </select>
+              data-actions-box="true"
-                    </div>
+              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>
+                  Select Additional Fingerprinter / Descriptor
+                </option>
+                {% for k, v in additional_descriptors.items %}
+                  <option value="{{ v }}">{{ k }}</option>
+                {% endfor %}
+              {% endif %}
+            </select>
+          </div>
 
-                    <!-- Fingerprinter -->
+          <!-- Threshold -->
-                    <div id="fingerprinter" class="ep-model-param mlrr">
+          <div id="threshold" class="ep-model-param mlrr enviformer">
-                        <label for="model-fingerprinter">Fingerprinter</label>
+            <label for="model-threshold">Threshold</label>
-                        <select id="model-fingerprinter" name="model-fingerprinter" data-actions-box='true'
+            <input
-                                class="form-control" multiple data-width='100%'>
+              type="number"
-                            <option value="MACCS" selected>MACCS Fingerprinter</option>
+              min="0"
-                            {% if meta.enabled_features.PLUGINS and additional_descriptors %}
+              max="1"
-                                <option disabled selected>Select Additional Fingerprinter / Descriptor</option>
+              step="0.05"
-                                {% for k, v in additional_descriptors.items %}
+              value="0.5"
-                                    <option value="{{ v }}">{{ k }}</option>
+              id="model-threshold"
-                                {% endfor %}
+              name="model-threshold"
-                            {% endif %}
+              class="form-control"
-                        </select>
+            />
-                    </div>
+          </div>
 
-                    <!-- Threshold -->
+          <div id="appdomain" class="ep-model-param mlrr">
-                    <div id="threshold" class="ep-model-param mlrr enviformer">
+            {% if meta.enabled_features.APPLICABILITY_DOMAIN %}
-                        <label for="model-threshold">Threshold</label>
+              <!-- Build AD? -->
-                        <input type="number" min="0" max="1" step="0.05" value="0.5" id="model-threshold"
+              <div class="checkbox">
-                               name="model-threshold" class="form-control">
+                <label>
-                    </div>
+                  <input
-
+                    type="checkbox"
-                    <div id="appdomain" class="ep-model-param mlrr">
+                    id="build-app-domain"
-                        {% if meta.enabled_features.APPLICABILITY_DOMAIN %}
+                    name="build-app-domain"
-                            <!-- Build AD? -->
+                  />Also build an Applicability Domain?
-                            <div class="checkbox">
+                </label>
-                                <label>
+              </div>
-                                    <input type="checkbox" id="build-app-domain" name="build-app-domain">Also build an
+              <div id="ad-params" style="display:none">
-                                    Applicability Domain?
+                <!-- Num Neighbors -->
-                                </label>
+                <label for="num-neighbors">Number of Neighbors</label>
-                            </div>
+                <input
-                            <div id="ad-params" style="display:none">
+                  id="num-neighbors"
-                                <!-- Num Neighbors -->
+                  name="num-neighbors"
-                                <label for="num-neighbors">Number of Neighbors</label>
+                  type="number"
-                                <input id="num-neighbors" name="num-neighbors" type="number" class="form-control"
+                  class="form-control"
-                                       value="5"
+                  value="5"
-                                       step="1" min="0" max="10">
+                  step="1"
-                                <!-- Local Compatibility -->
+                  min="0"
-                                <label for="local-compatibility-threshold">Local Compatibility Threshold</label>
+                  max="10"
-                                <input id="local-compatibility-threshold" name="local-compatibility-threshold"
+                />
-                                       type="number"
+                <!-- Local Compatibility -->
-                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
+                <label for="local-compatibility-threshold"
-                                <!-- Reliability -->
+                  >Local Compatibility Threshold</label
-                                <label for="reliability-threshold">Reliability Threshold</label>
+                >
-                                <input id="reliability-threshold" name="reliability-threshold" type="number"
+                <input
-                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
+                  id="local-compatibility-threshold"
-                            </div>
+                  name="local-compatibility-threshold"
-                        {% endif %}
+                  type="number"
-                    </div>
+                  class="form-control"
-                </form>
+                  value="0.5"
-            </div>
+                  step="0.01"
-            <div class="modal-footer">
+                  min="0"
-                <a id="new_model_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
+                  max="1"
-                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
+                />
-            </div>
+                <!-- Reliability -->
-        </div>
+                <label for="reliability-threshold">Reliability Threshold</label>
+                <input
+                  id="reliability-threshold"
+                  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="#"
+          >Submit</a
+        >
+        <button type="button" class="btn btn-default" data-dismiss="modal">
+          Cancel
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 
 <script>
-    $(function () {
+  $(function () {
-        // Built in Model Types
+    // Built in Model Types
-        var nativeModelTypes = [
+    var nativeModelTypes = ["mlrr", "rbrr", "enviformer"];
-            "mlrr",
-            "rbrr",
-            "enviformer",
-        ]
-
-        // Initially hide all "specific" forms
-        $(".ep-model-param").each(function () {
-            $(this).hide();
-        });
-
-        $('#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();
-            } else {
-                $('#ad-params').hide();
-            }
-        });
-
-        // On change hide all and show only selected
-        $("#model-type").change(function () {
-            $('.ep-model-param').hide();
-            var modelType = $('#model-type').val();
-            if (nativeModelTypes.indexOf(modelType) !== -1) {
-                $('.' + modelType).show();
-            } else {
-                // do nothing
-            }
-        });
-
-        $('#new_model_modal_form_submit').on('click', function (e) {
-            e.preventDefault();
-            $('#new_model_form').submit();
-        });
 
+    // Initially hide all "specific" forms
+    $(".ep-model-param").each(function () {
+      $(this).hide();
     });
+
+    $("#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();
+      } else {
+        $("#ad-params").hide();
+      }
+    });
+
+    // On change hide all and show only selected
+    $("#model-type").change(function () {
+      $(".ep-model-param").hide();
+      var modelType = $("#model-type").val();
+      if (nativeModelTypes.indexOf(modelType) !== -1) {
+        $("." + modelType).show();
+      } else {
+        // do nothing
+      }
+    });
+
+    $("#new_model_modal_form_submit").on("click", function (e) {
+      e.preventDefault();
+      $("#new_model_form").submit();
+    });
+  });
 </script>

templates/modals/collections/new_package_modal.html

@@ -1,62 +1,68 @@
-<div class="modal fade"
+<div
-     tabindex="-1"
+  class="modal fade"
-     id="new_package_modal"
+  tabindex="-1"
-     role="dialog"
+  id="new_package_modal"
-     aria-labelledby="new_package_modal"
+  role="dialog"
-     aria-hidden="true">
+  aria-labelledby="new_package_modal"
-    <div class="modal-dialog">
+  aria-hidden="true"
-        <div class="modal-content">
+>
-            <div class="modal-header">
+  <div class="modal-dialog">
-                <button type="button"
+    <div class="modal-content">
-                        class="close"
+      <div class="modal-header">
-                        data-dismiss="modal">
+        <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>
+        </button>
-                <h4 class="modal-title">New Package</h4>
+        <h4 class="modal-title">New Package</h4>
-            </div>
+      </div>
-            <div class="modal-body">
+      <div class="modal-body">
-                <p>Create new package. Description can be changed later.</p>
+        <p>Create new package. Description can be changed later.</p>
-                <form id="new_package_modal_form"
+        <form
-                      accept-charset="UTF-8"
+          id="new_package_modal_form"
-                      action=""
+          accept-charset="UTF-8"
-                      data-remote="true"
+          action=""
-                      method="post">
+          data-remote="true"
-                    {% csrf_token %}
+          method="post"
-                    <p>
+        >
-                        <label for="name">Name</label>
+          {% csrf_token %}
-                        <input id="name" class="form-control"
+          <p>
-                               name="package-name"
+            <label for="name">Name</label>
-                               placeholder="Name"/>
+            <input
-                    </p>
+              id="name"
-                    <p>
+              class="form-control"
-                        <label for="description">Description</label>
+              name="package-name"
-                        <input id="description"
+              placeholder="Name"
-                               type="text"
+            />
-                               rows="3"
+          </p>
-                               class="form-control"
+          <p>
-                               placeholder="Description..."
+            <label for="description">Description</label>
-                               name="package-description"/>
+            <input
-                    </p>
+              id="description"
-                </form>
+              type="text"
-            </div>
+              rows="3"
-            <div class="modal-footer">
+              class="form-control"
-                <a id="new_package_modal_form_submit"
+              placeholder="Description..."
-                   class="btn btn-primary"
+              name="package-description"
-                   href="#">Submit</a>
+            />
-                <button type="button"
+          </p>
-                        class="btn btn-default"
+        </form>
-                        data-dismiss="modal">Cancel
+      </div>
-                </button>
+      <div class="modal-footer">
-            </div>
+        <a id="new_package_modal_form_submit" class="btn btn-primary" href="#"
-        </div>
+          >Submit</a
+        >
+        <button type="button" class="btn btn-default" data-dismiss="modal">
+          Cancel
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-$(function() {
+  $(function () {
-    $('#new_package_modal_form_submit').on('click', function (e) {
+    $("#new_package_modal_form_submit").on("click", function (e) {
-        e.preventDefault();
+      e.preventDefault();
-        $('#new_package_modal_form').submit();
+      $("#new_package_modal_form").submit();
     });
-});
+  });
 </script>

templates/modals/collections/new_pathway_modal.html

@@ -1,302 +1,376 @@
-
 {% load static %}
-<div class="modal fade" tabindex="-1" id="new_pathway_modal" role="dialog" aria-labelledby="new_pathway_modal"
+<div
-     aria-hidden="true" style="overflow-y: auto;">
+  class="modal fade"
-    <!-- FIXME: make width dynamic-->
+  tabindex="-1"
-    <div class="modal-dialog" id="new_pathway_modal_dialog" style="width:900px">
+  id="new_pathway_modal"
-        <div class="modal-content">
+  role="dialog"
-            <div class="modal-header">
+  aria-labelledby="new_pathway_modal"
-                <button type="button" class="close" data-dismiss="modal">
+  aria-hidden="true"
-                    <span aria-hidden="true">&times;</span> <span class="sr-only">Close</span>
+  style="overflow-y: auto;"
-                </button>
+>
-                <h4 class="js-title-step"></h4>
+  <!-- FIXME: make width dynamic-->
-            </div>
+  <div class="modal-dialog" id="new_pathway_modal_dialog" style="width:900px">
-            <div class="modal-body hide" data-step="1" data-title="New Pathway">
+    <div class="modal-content">
-                <div class="jumbotron">Create a new pathway by entering
+      <div class="modal-header">
-                    the root compound and a name. Then select if you want to
+        <button type="button" class="close" data-dismiss="modal">
-                    use the prediction engine to generate a predicted pathway or
+          <span aria-hidden="true">&times;</span>
-                    create an empty pathway that you fill in by yourself. If
+          <span class="sr-only">Close</span>
-                    you choose to predict a pathway, you can modify the
+        </button>
-                    settings for the prediction, or use the default settings
+        <h4 class="js-title-step"></h4>
-                    and just click Submit.
+      </div>
-                </div>
+      <div class="modal-body hide" data-step="1" data-title="New Pathway">
-                <div class="modal-body">
+        <div class="jumbotron">
-                    {% if current_user.name == 'anonymous' %}
+          Create a new pathway by entering the root compound and a name. Then
-                    <div class="alert alert-warning">
+          select if you want to use the prediction engine to generate a
-                        You are currently logged in as Anonymous. Please note:
+          predicted pathway or create an empty pathway that you fill in by
-                        Pathways entered or predicted as anonymous user will be deleted after 30 days.
+          yourself. If you choose to predict a pathway, you can modify the
-                        Please log in to save your results.
+          settings for the prediction, or use the default settings and just
-                    </div>
+          click Submit.
-                    {% endif %}
-                </div>
-                <div class="row">
-                    <div class="col-md-6">
-                        <label for="name">Name</label>
-                        <input id="name" class="form-control" name="name" placeholder="Name"/>
-                        <label for="description">Description</label>
-                        <input id="description" class="form-control" name="description" placeholder="no description"/>
-                    </div>
-
-                    <div class="col-md-6">
-                        <label for="predict">Predict pathway or build yourself?</label>
-                        <div class="radio" id="predict">
-                            <p>
-                                <label>
-                                    <input type="radio" name="predict" id="radioPredict" value="predict" checked/>Predict pathway
-                                </label>
-                            </p>
-                            <p>
-                                <label>
-                                    <input type="radio" name="predict" id="radioIncremental"value="incremental"/>Incremental prediction
-                                </label>
-                            </p>
-                            <p>
-                                <label>
-                                    <input type="radio" name="predict" id="radioBuild" value="build"/>Build pathway
-                                </label>
-                            </p>
-                        </div>
-                    </div>
-                </div>
-                <label for="smilesinput">SMILES</label>
-                <table style="width: 100%">
-                    <colgroup>
-                        <col span="1" style="width: 90%;">
-                        <col span="1" style="width: 10%;">
-                    </colgroup>
-                    <tr>
-                        <td>
-                            <input id="smilesinput" class="form-control" name="smilesinput" placeholder="C1CCCCC1"
-                                   autocapitalize="none"/>
-                        </td>
-                        <td>
-                            <button type="button" class="btn btn-default" id="render-button">
-                                Render
-                            </button>
-                        </td>
-                    </tr>
-                </table>
-                <p id="ketcher_container"></p>
-                <div>
-                    <iframe id="ifKetcher" src="{% static '/js/ketcher/ketcher.html' %}" width="850"
-                            height="510"></iframe>
-                </div>
-            </div>
-            <div class="modal-body hide" data-step="2" data-title="New Pathway - Advanced Settings">
-                <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 type="radio" name="existing" id="radioDefault" value="exisiting" checked/>
-                                Use Default
-                            </label>
-                        </p>
-                        <p>
-                            <label>
-                                <input type="radio" name="existing" id="radioExists" value="exisiting"/>
-                                Select Existing
-                            </label>
-                        </p>
-                        <p>
-                            <label>
-                                <input type="radio" name="existing" id="radioNew" value="temporary"/>
-                                Create New
-                            </label>
-                        </p>
-                    </div>
-
-                    <select id="settingSelect" name="settingSelect" class="form-control">
-                        {% for setting in available_settings %}
-                        <option value="{{ setting.id }}">{{ setting.name|safe }}</option>
-                        {% endfor %}
-                    </select>
-                    <p></p>
-                </div>
-            </div>
-            {% with step_offset=1 %}
-            {% include "templates/modals/collections/new_setting_modal_body.html" %}
-            {% endwith %}
-            <div class="modal-footer">
-                <button type="button" class="btn btn-default js-btn-step pull-left" data-orientation="cancel"
-                        onclick="reset()" data-dismiss="modal"></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>
+        <div class="modal-body">
+          {% if current_user.name == 'anonymous' %}
+            <div class="alert alert-warning">
+              You are currently logged in as Anonymous. Please note: Pathways
+              entered or predicted as anonymous user will be deleted after 30
+              days. Please log in to save your results.
+            </div>
+          {% endif %}
+        </div>
+        <div class="row">
+          <div class="col-md-6">
+            <label for="name">Name</label>
+            <input
+              id="name"
+              class="form-control"
+              name="name"
+              placeholder="Name"
+            />
+            <label for="description">Description</label>
+            <input
+              id="description"
+              class="form-control"
+              name="description"
+              placeholder="no description"
+            />
+          </div>
+
+          <div class="col-md-6">
+            <label for="predict">Predict pathway or build yourself?</label>
+            <div class="radio" id="predict">
+              <p>
+                <label>
+                  <input
+                    type="radio"
+                    name="predict"
+                    id="radioPredict"
+                    value="predict"
+                    checked
+                  />Predict pathway
+                </label>
+              </p>
+              <p>
+                <label>
+                  <input
+                    type="radio"
+                    name="predict"
+                    id="radioIncremental"
+                    value="incremental"
+                  />Incremental prediction
+                </label>
+              </p>
+              <p>
+                <label>
+                  <input
+                    type="radio"
+                    name="predict"
+                    id="radioBuild"
+                    value="build"
+                  />Build pathway
+                </label>
+              </p>
+            </div>
+          </div>
+        </div>
+        <label for="smilesinput">SMILES</label>
+        <table style="width: 100%">
+          <colgroup>
+            <col span="1" style="width: 90%;" />
+            <col span="1" style="width: 10%;" />
+          </colgroup>
+          <tr>
+            <td>
+              <input
+                id="smilesinput"
+                class="form-control"
+                name="smilesinput"
+                placeholder="C1CCCCC1"
+                autocapitalize="none"
+              />
+            </td>
+            <td>
+              <button type="button" class="btn btn-default" id="render-button">
+                Render
+              </button>
+            </td>
+          </tr>
+        </table>
+        <p id="ketcher_container"></p>
+        <div>
+          <iframe
+            id="ifKetcher"
+            src="{% static '/js/ketcher/ketcher.html' %}"
+            width="850"
+            height="510"
+          ></iframe>
+        </div>
+      </div>
+      <div
+        class="modal-body hide"
+        data-step="2"
+        data-title="New Pathway - Advanced Settings"
+      >
+        <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
+                  type="radio"
+                  name="existing"
+                  id="radioDefault"
+                  value="exisiting"
+                  checked
+                />
+                Use Default
+              </label>
+            </p>
+            <p>
+              <label>
+                <input
+                  type="radio"
+                  name="existing"
+                  id="radioExists"
+                  value="exisiting"
+                />
+                Select Existing
+              </label>
+            </p>
+            <p>
+              <label>
+                <input
+                  type="radio"
+                  name="existing"
+                  id="radioNew"
+                  value="temporary"
+                />
+                Create New
+              </label>
+            </p>
+          </div>
+
+          <select id="settingSelect" name="settingSelect" class="form-control">
+            {% for setting in available_settings %}
+              <option value="{{ setting.id }}">{{ setting.name|safe }}</option>
+            {% endfor %}
+          </select>
+          <p></p>
+        </div>
+      </div>
+      {% with step_offset=1 %}
+        {% include "templates/modals/collections/new_setting_modal_body.html" %}
+      {% endwith %}
+      <div class="modal-footer">
+        <button
+          type="button"
+          class="btn btn-default js-btn-step pull-left"
+          data-orientation="cancel"
+          onclick="reset()"
+          data-dismiss="modal"
+        ></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>
+  </div>
 </div>
 
 <script>
-s = new Setting(
+  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() {
+  $(function () {
     // hide all forms
-    $('#forms').children().hide()
+    $("#forms").children().hide();
 
-    $("#render-button").on("click", function() {
+    $("#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() {
+    setInterval(function () {
-        syncKetcherAndTextInput('ketcher', 'ifKetcher', 'smilesinput');
+      syncKetcherAndTextInput("ketcher", "ifKetcher", "smilesinput");
     }, 250);
 
-    $("#smilesinput").on("blur", function() {
+    $("#smilesinput").on("blur", function () {
-        syncKetcherAndTextInput('text', 'ifKetcher', 'smilesinput');
+      syncKetcherAndTextInput("text", "ifKetcher", "smilesinput");
     });
 
-    $("#smilesinput").on("keypress", function(event) {
+    $("#smilesinput").on("keypress", function (event) {
-        if (event.keyCode == 13) {
+      if (event.keyCode == 13) {
-            syncKetcherAndTextInput('text', 'ifKetcher', 'smilesinput');
+        syncKetcherAndTextInput("text", "ifKetcher", "smilesinput");
-        }
-    });
-
-    // Show forms depending on the selected TS
-    $('#availableTS').on('change', function(e) {
-        e.preventDefault();
-
-        var type = $(this).val();
-        // hide current content
-        $('#forms').children().hide()
-
-        if(type === '') {
-            return;
-        }
-
-        $('#' + 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) {
-        e.preventDefault();
-        s.addTruncator();
-    });
-
-    $('input[type=radio][name=predict]').change(function() {
-        if (this.id == 'radioBuild') {
-          $("#nextbutton").prop("disabled", true);
-        } else {
-          $("#nextbutton").prop("disabled", false);
-        }
-    });
-
-    $('input[type=radio][name=existing]').change(function() {
-        if (this.id == 'radioDefault' || this.id == 'radioExists') {
-          if(this.id == 'radioDefault') {
-            $("#settingSelect").prop("disabled", true);
-          } else {
-            $("#settingSelect").prop("disabled", false);
-          }
-          $("#nextbutton").prop("disabled", true);
-        } else {
-          // build...
-	  	  $("#settingSelect").prop("disabled", true);
-          $("#nextbutton").prop("disabled", false);
-        }
-    });
-
-    var pwStep1 = function() {
-        console.log("pw step 1");
-        // Make "Next" to "Advanced"
-        $('#nextbutton').val("Advanced");
-    }
-
-    var pwStep2 = function() {
-        console.log("pw step 2");
-        // Make "Advanced" to "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({
-      btnCancelHtml: 'Cancel',
-      btnPreviousHtml: 'Back',
-      btnNextHtml: 'Next',
-      btnLastStepHtml: 'Submit',
-      disableNextButton: false,
-      completeCallback: postPathway,
-      callbacks: {
-        '1': pwStep1,
-        '2' : pwStep2,
-        '3' : dummy,
-        '4' : settingStep1,
-        '5' : settingStep2,
-        '6' : settingStep3,
       }
     });
 
-   $('#modal-form-submit').on('click', function() {
+    // Show forms depending on the selected TS
+    $("#availableTS").on("change", function (e) {
+      e.preventDefault();
+
+      var type = $(this).val();
+      // hide current content
+      $("#forms").children().hide();
+
+      if (type === "") {
+        return;
+      }
+
+      $("#" + 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) {
+      e.preventDefault();
+      s.addTruncator();
+    });
+
+    $("input[type=radio][name=predict]").change(function () {
+      if (this.id == "radioBuild") {
+        $("#nextbutton").prop("disabled", true);
+      } else {
+        $("#nextbutton").prop("disabled", false);
+      }
+    });
+
+    $("input[type=radio][name=existing]").change(function () {
+      if (this.id == "radioDefault" || this.id == "radioExists") {
+        if (this.id == "radioDefault") {
+          $("#settingSelect").prop("disabled", true);
+        } else {
+          $("#settingSelect").prop("disabled", false);
+        }
+        $("#nextbutton").prop("disabled", true);
+      } else {
+        // build...
+        $("#settingSelect").prop("disabled", true);
+        $("#nextbutton").prop("disabled", false);
+      }
+    });
+
+    var pwStep1 = function () {
+      console.log("pw step 1");
+      // Make "Next" to "Advanced"
+      $("#nextbutton").val("Advanced");
+    };
+
+    var pwStep2 = function () {
+      console.log("pw step 2");
+      // Make "Advanced" to "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({
+      btnCancelHtml: "Cancel",
+      btnPreviousHtml: "Back",
+      btnNextHtml: "Next",
+      btnLastStepHtml: "Submit",
+      disableNextButton: false,
+      completeCallback: postPathway,
+      callbacks: {
+        1: pwStep1,
+        2: pwStep2,
+        3: dummy,
+        4: settingStep1,
+        5: settingStep2,
+        6: settingStep3,
+      },
+    });
+
+    $("#modal-form-submit").on("click", function () {
       e.preventDefault();
       postPathway();
-   });
+    });
-});
+  });
-
 </script>

templates/modals/collections/new_prediction_setting_modal.html

@@ -1,109 +1,185 @@
-
 {% load static %}
 
 <div id="new_prediction_setting_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h5 class="modal-title">Create a Prediction Setting</h5>
+        <h5 class="modal-title">Create a Prediction Setting</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                <p>To create a Prediction Setting fill the form below and click "Create"</p>
+        >
-                <form id="new-prediction-setting-modal-form" accept-charset="UTF-8" action="" data-remote="true"
+          <span aria-hidden="true">&times;</span>
-                      method="post">
+        </button>
-                    {% csrf_token %}
+      </div>
+      <div class="modal-body">
+        <p>
+          To create a Prediction Setting fill the form below and click "Create"
+        </p>
+        <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>
+          <label for="prediction-setting-name">Name</label>
-                    <input id="prediction-setting-name" name="prediction-setting-name" class="form-control" placeholder="Name"/>
+          <input
-                    <label for="prediction-setting-description">Description</label>
+            id="prediction-setting-name"
-                    <input id="prediction-setting-description" name="prediction-setting-description" class="form-control"
+            name="prediction-setting-name"
-                           placeholder="Description"/>
+            class="form-control"
+            placeholder="Name"
+          />
+          <label for="prediction-setting-description">Description</label>
+          <input
+            id="prediction-setting-description"
+            name="prediction-setting-description"
+            class="form-control"
+            placeholder="Description"
+          />
 
-                    <label for="prediction-setting-max-nodes">Max #Nodes</label>
+          <label for="prediction-setting-max-nodes">Max #Nodes</label>
-                    <input id="prediction-setting-max-nodes" type="number" class="form-control" name="prediction-setting-max-nodes" value="30" min="1" max="50" step="1">
+          <input
-                    <label for="prediction-setting-max-depth">Max Depth</label>
+            id="prediction-setting-max-nodes"
-                    <input id="prediction-setting-max-depth" type="number" class="form-control" name="prediction-setting-max-depth" value="5" min="1" max="8" step="1">
+            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
+            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>
+          <label for="tp-generation-method">TP Generation Method</label>
-                    <select id="tp-generation-method" name="tp-generation-method" class="form-control" data-width='100%'>
+          <select
-                        <option disabled selected>Select how TPs are generated</option>
+            id="tp-generation-method"
-                        <option value="rule-based-prediction-setting">Rule Based</option>
+            name="tp-generation-method"
-                        <option value="model-based-prediction-setting">Model Based</option>
+            class="form-control"
-                    </select>
+            data-width="100%"
-                    <div id="rule-based-prediction-setting-specific-form">
+          >
-                        <!-- Rule Packages -->
+            <option disabled selected>Select how TPs are generated</option>
-                        <label>Rule Packages</label><br>
+            <option value="rule-based-prediction-setting">Rule Based</option>
-                        <select id="rule-based-prediction-setting-packages" name="rule-based-prediction-setting-packages"
+            <option value="model-based-prediction-setting">Model Based</option>
-                                data-actions-box='true' class="form-control" multiple data-width='100%'>
+          </select>
-                            <option disabled>Reviewed Packages</option>
+          <div id="rule-based-prediction-setting-specific-form">
-                            {% for obj in meta.readable_packages %}
+            <!-- Rule Packages -->
-                            {% if obj.reviewed %}
+            <label>Rule Packages</label><br />
-                            <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+            <select
-                            {% endif %}
+              id="rule-based-prediction-setting-packages"
-                            {% endfor %}
+              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>
+                {% endif %}
+              {% endfor %}
 
-                            <option disabled>Unreviewed Packages</option>
+              <option disabled>Unreviewed Packages</option>
-                            {% for obj in meta.readable_packages %}
+              {% for obj in meta.readable_packages %}
-                            {% if not obj.reviewed %}
+                {% if not obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                  <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
-                            {% endif %}
+                {% endif %}
-                            {% endfor %}
+              {% endfor %}
-                        </select>
+            </select>
-                    </div>
+          </div>
-                    <div id="model-based-prediction-setting-specific-form">
+          <div id="model-based-prediction-setting-specific-form">
-                        <label>Select Model</label><br>
+            <label>Select Model</label><br />
-                        <select id="model-based-prediction-setting-model" name="model-based-prediction-setting-model" class="form-control" data-width='100%'>
+            <select
-                        <option disabled selected>Select the model</option>
+              id="model-based-prediction-setting-model"
-                        {% for m in models %}
+              name="model-based-prediction-setting-model"
-                        <option value="{{ m.url }}">{{ m.name|safe }}</option>
+              class="form-control"
-                        {% endfor %}
+              data-width="100%"
-                        </select>
+            >
-                        <label for="model-based-prediction-setting-threshold">Threshold</label>
+              <option disabled selected>Select the model</option>
-                        <input id="model-based-prediction-setting-threshold" name="model-based-prediction-setting-threshold" class="form-control" placeholder="0.25" type="number"/>
+              {% for m in models %}
-                    </div>
+                <option value="{{ m.url }}">{{ m.name|safe }}</option>
+              {% endfor %}
+            </select>
+            <label for="model-based-prediction-setting-threshold"
+              >Threshold</label
+            >
+            <input
+              id="model-based-prediction-setting-threshold"
+              name="model-based-prediction-setting-threshold"
+              class="form-control"
+              placeholder="0.25"
+              type="number"
+            />
+          </div>
 
-                    <input class="form-check-input" type="checkbox" value="on" id="prediction-setting-new-default" name="prediction-setting-new-default">
+          <input
-                    <label class="form-check-label" for="prediction-setting-new-default">Set this setting as new default</label>
+            class="form-check-input"
-
+            type="checkbox"
-                </form>
+            value="on"
-            </div>
+            id="prediction-setting-new-default"
-            <div class="modal-footer">
+            name="prediction-setting-new-default"
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+          />
-                <button type="button" class="btn btn-primary" id="new-prediction-setting-modal-submit">Create</button>
+          <label class="form-check-label" for="prediction-setting-new-default"
-            </div>
+            >Set this setting as new default</label
-        </div>
+          >
+        </form>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="new-prediction-setting-modal-submit"
+        >
+          Create
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-    $(function() {
+  $(function () {
+    // Initially hide all "specific" forms
+    $("div[id$='-specific-form']").each(function () {
+      $(this).hide();
+    });
 
-        // Initially hide all "specific" forms
+    $("#rule-based-prediction-setting-packages").selectpicker();
-        $("div[id$='-specific-form']").each( function() {
-            $(this).hide();
-        });
 
-        $("#rule-based-prediction-setting-packages").selectpicker();
+    // On change hide all and show only selected
+    $("#tp-generation-method").change(function () {
+      $("div[id$='-specific-form']").each(function () {
+        $(this).hide();
+      });
+      val = $("option:selected", this).val();
+      $("#" + val + "-specific-form").show();
+    });
 
-        // On change hide all and show only selected
+    $("#new-prediction-setting-modal-submit").click(function (e) {
-        $("#tp-generation-method").change(function() {
+      e.preventDefault();
-            $("div[id$='-specific-form']").each( function() {
+      // $('#new-prediction-setting-modal-form').submit();
-                $(this).hide();
-            });
-            val = $('option:selected', this).val();
-            $("#" + val + "-specific-form").show();
-        });
 
-        $('#new-prediction-setting-modal-submit').click(function(e){
+      const formData = $("#new-prediction-setting-modal-form").serialize();
-            e.preventDefault();
+      $.post("/setting", formData, function (response) {
-            // $('#new-prediction-setting-modal-form').submit();
+        location.reload();
-
+      });
-            const formData = $('#new-prediction-setting-modal-form').serialize();
+    });
-            $.post('/setting', formData, function(response) {
+  });
-                location.reload();
-            });
-        });
-    })
 </script>

templates/modals/collections/new_reaction_modal.html

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

templates/modals/collections/new_rule_modal.html

@@ -1,72 +1,120 @@
 {% load static %}
-<div class="modal fade bs-modal-lg" id="new_rule_modal" tabindex="-1" aria-labelledby="new_rule_modal" aria-modal="true"
+<div
-     role="dialog">
+  class="modal fade bs-modal-lg"
-    <div class="modal-dialog modal-lg">
+  id="new_rule_modal"
-        <div class="modal-content">
+  tabindex="-1"
-            <div class="modal-header">
+  aria-labelledby="new_rule_modal"
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+  aria-modal="true"
-                    <span aria-hidden="true">×</span>
+  role="dialog"
-                </button>
+>
-                <h4 class="modal-title">Create a new Rule</h4>
+  <div class="modal-dialog modal-lg">
-            </div>
+    <div class="modal-content">
-            <div class="modal-body">
+      <div class="modal-header">
-                <form id="new_rule_modal_form" accept-charset="UTF-8" action="{% url 'package rule list' meta.current_package.uuid %}" data-remote="true" method="post">
+        <button
-                    {% csrf_token %}
+          type="button"
-                    <label for="rule-name">Name</label>
+          class="close"
-                    <input id="rule-name" class="form-control" name="rule-name" placeholder="Name"/>
+          data-dismiss="modal"
-                    <label for="rule-description">Description</label>
+          aria-label="Close"
-                    <input id="rule-description" class="form-control" name="rule-description" placeholder="Description"/>
+        >
-                    <label for="rule-smirks">SMIRKS</label>
+          <span aria-hidden="true">×</span>
-                    <input id="rule-smirks" class="form-control" name="rule-smirks" placeholder="SMIRKS"/>
+        </button>
-                    <p></p>
+        <h4 class="modal-title">Create a new Rule</h4>
-                    <div id="rule-smirks-viz"></div>
+      </div>
-                    <input type="hidden" name="rule-type" id="rule-type" value="SimpleAmbitRule">
+      <div class="modal-body">
-                    <p></p>
+        <form
-                </form>
+          id="new_rule_modal_form"
-            </div>
+          accept-charset="UTF-8"
-            <div class="modal-footer">
+          action="{% url 'package rule list' meta.current_package.uuid %}"
-                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+          data-remote="true"
-                </button>
+          method="post"
-                <button type="button" class="btn btn-primary" id="new_rule_modal_form_submit">Submit</button>
+        >
-            </div>
+          {% csrf_token %}
-        </div>
+          <label for="rule-name">Name</label>
+          <input
+            id="rule-name"
+            class="form-control"
+            name="rule-name"
+            placeholder="Name"
+          />
+          <label for="rule-description">Description</label>
+          <input
+            id="rule-description"
+            class="form-control"
+            name="rule-description"
+            placeholder="Description"
+          />
+          <label for="rule-smirks">SMIRKS</label>
+          <input
+            id="rule-smirks"
+            class="form-control"
+            name="rule-smirks"
+            placeholder="SMIRKS"
+          />
+          <p></p>
+          <div id="rule-smirks-viz"></div>
+          <input
+            type="hidden"
+            name="rule-type"
+            id="rule-type"
+            value="SimpleAmbitRule"
+          />
+          <p></p>
+        </form>
+      </div>
+      <div class="modal-footer">
+        <button
+          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>
+      </div>
     </div>
-
+  </div>
 </div>
 <script>
-$(function() {
+  $(function () {
+    $("#rule-smirks").on("input", function (e) {
+      $("#rule-smirks-viz").empty();
 
-    $('#rule-smirks').on('input', function(e) {
+      smirks = $("#rule-smirks").val();
-        $('#rule-smirks-viz').empty()
 
-        smirks = $('#rule-smirks').val()
+      const img = new Image();
+      img.src =
+        "{% url 'depict' %}?is_query_smirks=true&smirks=" +
+        encodeURIComponent(smirks);
+      img.style.width = "100%";
+      img.style.height = "100%";
+      img.style.objectFit = "cover";
 
-        const img = new Image();
+      img.onload = function () {
-        img.src = "{% url 'depict' %}?is_query_smirks=true&smirks=" + encodeURIComponent(smirks);
+        $("#rule-smirks-viz").append(img);
-        img.style.width = '100%';
+      };
-        img.style.height = '100%';
-        img.style.objectFit = 'cover';
 
-        img.onload = function () {
+      img.onerror = function () {
-            $('#rule-smirks-viz').append(img);
+        error_tpl = `
-        };
-
-        img.onerror = function () {
-            error_tpl = `
                 <div class="alert alert-error" role="alert">
                     <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();
+      e.preventDefault();
-        $(this).prop("disabled",true);
+      $(this).prop("disabled", true);
-        // submit form
+      // submit form
-        $('#new_rule_modal_form').submit();
+      $("#new_rule_modal_form").submit();
     });
-});
+  });
 </script>

templates/modals/collections/new_scenario_modal.html

@@ -1,102 +1,153 @@
-<div class="modal fade" tabindex="-1" id="new_scenario_modal" role="dialog" aria-labelledby="new_scenario_modal"
+<div
-     aria-hidden="true">
+  class="modal fade"
-    <div class="modal-dialog modal-lg">
+  tabindex="-1"
-        <div class="modal-content">
+  id="new_scenario_modal"
-            <div class="modal-header">
+  role="dialog"
-                <button type="button" class="close" data-dismiss="modal">
+  aria-labelledby="new_scenario_modal"
-                    <span aria-hidden="true">&times;</span>
+  aria-hidden="true"
-                    <span class="sr-only">Close</span>
+>
-                </button>
+  <div class="modal-dialog modal-lg">
-                <h4 class="modal-title">New Scenario</h4>
+    <div class="modal-content">
-            </div>
+      <div class="modal-header">
-            <div class="modal-body">
+        <button type="button" class="close" data-dismiss="modal">
-                <form id="new_scenario_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/scenario"
+          <span aria-hidden="true">&times;</span>
-                      data-remote="true" method="post">
+          <span class="sr-only">Close</span>
-                    {% csrf_token %}
+        </button>
-                    <div class="jumbotron">Please enter name, description, and date of scenario. Date should be
+        <h4 class="modal-title">New Scenario</h4>
-                        associated to the data, not the current date. For example, this could reflect the publishing
+      </div>
-                        date of a study. You can leave all fields but the name empty and fill them in later.
+      <div class="modal-body">
-                        <a target="_blank" href="https://wiki.envipath.org/index.php/scenario" role="button">wiki
+        <form
-                            &gt;&gt;</a>
+          id="new_scenario_form"
-                    </div>
+          accept-charset="UTF-8"
-                    <label for="scenario-name">Name</label>
+          action="{{ meta.current_package.url }}/scenario"
-                    <input id="scenario-name" name="scenario-name" class="form-control" placeholder="Name"/>
+          data-remote="true"
-                    <label for="scenario-description">Description</label>
+          method="post"
-                    <input id="scenario-description" name="scenario-description" class="form-control"
+        >
-                           placeholder="Description"/>
+          {% csrf_token %}
-                    <label id="dateField" for="dateYear">Date</label>
+          <div class="jumbotron">
-                    <table>
+            Please enter name, description, and date of scenario. Date should be
-                        <tr>
+            associated to the data, not the current date. For example, this
-                            <th>
+            could reflect the publishing date of a study. You can leave all
-                                <input type="number" id="dateYear" name="scenario-date-year" class="form-control"
+            fields but the name empty and fill them in later.
-                                       placeholder="YYYY" max="{% now "Y" %}">
+            <a
-                            </th>
+              target="_blank"
-                            <th>
+              href="https://wiki.envipath.org/index.php/scenario"
-                                <input type="number" id="dateMonth" name="scenario-date-month" min="1" max="12"
+              role="button"
-                                       class="form-control" placeholder="MM" >
+              >wiki &gt;&gt;</a
-                            </th>
+            >
-                            <th>
+          </div>
-                                <input type="number" id="dateDay" name="scenario-date-day" min="1" max="31" class="form-control"
+          <label for="scenario-name">Name</label>
-                                       placeholder="DD">
+          <input
-                            </th>
+            id="scenario-name"
-                        </tr>
+            name="scenario-name"
-                    </table>
+            class="form-control"
-                    <label for="scenario-type">Scenario Type</label>
+            placeholder="Name"
-                    <select id="scenario-type" name="scenario-type" class="form-control" data-width='100%'>
+          />
-                        <option value="empty" selected>Empty Scenario</option>
+          <label for="scenario-description">Description</label>
-                        {% for k, v in scenario_types.items %}
+          <input
-                            <option value="{{ v.name }}">{{ k }}</option>
+            id="scenario-description"
-                        {% endfor %}
+            name="scenario-description"
-                    </select>
+            class="form-control"
+            placeholder="Description"
+          />
+          <label id="dateField" for="dateYear">Date</label>
+          <table>
+            <tr>
+              <th>
+                <input
+                  type="number"
+                  id="dateYear"
+                  name="scenario-date-year"
+                  class="form-control"
+                  placeholder="YYYY"
+                  max="{% now "Y" %}"
+                />
+              </th>
+              <th>
+                <input
+                  type="number"
+                  id="dateMonth"
+                  name="scenario-date-month"
+                  min="1"
+                  max="12"
+                  class="form-control"
+                  placeholder="MM"
+                />
+              </th>
+              <th>
+                <input
+                  type="number"
+                  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
+            id="scenario-type"
+            name="scenario-type"
+            class="form-control"
+            data-width="100%"
+          >
+            <option value="empty" selected>Empty Scenario</option>
+            {% for k, v in scenario_types.items %}
+              <option value="{{ v.name }}">{{ k }}</option>
+            {% endfor %}
+          </select>
 
-                    {% for type in scenario_types.values %}
+          {% for type in scenario_types.values %}
-                        <div id="{{ type.name }}-specific-inputs">
+            <div id="{{ type.name }}-specific-inputs">
-                            {% for widget in type.widgets %}
+              {% for widget in type.widgets %}
-                                {{ widget|safe }}
+                {{ widget|safe }}
-                            {% endfor %}
+              {% endfor %}
-                        </div>
-                    {% endfor %}
-
-                </form>
             </div>
-            <div class="modal-footer">
+          {% endfor %}
-                <a id="new_scenario_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
+        </form>
-                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
+      </div>
-            </div>
+      <div class="modal-footer">
-        </div>
+        <a id="new_scenario_modal_form_submit" class="btn btn-primary" href="#"
+          >Submit</a
+        >
+        <button type="button" class="btn btn-default" data-dismiss="modal">
+          Cancel
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 
 <script>
-    $(function () {
+  $(function () {
-        // Initially hide all "specific" forms
+    // Initially hide all "specific" forms
-        $("div[id$='-specific-inputs']").each(function () {
+    $("div[id$='-specific-inputs']").each(function () {
-            $(this).hide();
+      $(this).hide();
-        });
-
-        // On change hide all and show only selected
-        $("#scenario-type").change(function () {
-            $("div[id$='-specific-inputs']").each(function () {
-                $(this).hide();
-            });
-            val = $('option:selected', this).val();
-            $("#" + val + "-specific-inputs").show();
-        });
-
-        $('#new_scenario_modal_form_submit').on('click', function (e) {
-            e.preventDefault();
-            $('#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 = {% now "Y" %};
-            }
-        });
-
     });
 
-</script>
+    // On change hide all and show only selected
+    $("#scenario-type").change(function () {
+      $("div[id$='-specific-inputs']").each(function () {
+        $(this).hide();
+      });
+      val = $("option:selected", this).val();
+      $("#" + val + "-specific-inputs").show();
+    });
 
+    $("#new_scenario_modal_form_submit").on("click", function (e) {
+      e.preventDefault();
+      $("#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();
+      }
+    });
+  });
+</script>

templates/modals/objects/add_additional_information_modal.html

@@ -1,61 +1,92 @@
 {% load static %}
 <!-- Add Additional Information-->
 <div id="add_additional_information_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-                <h3 class="modal-title">Add Additional Information</h3>
+          data-dismiss="modal"
-            </div>
+          aria-label="Close"
-            <div class="modal-body">
+        >
-                <select id="select-additional-information-type" data-actions-box='true' class="form-control" data-width='100%'>
+          <span aria-hidden="true">&times;</span>
-                    <option selected disabled>Select the type to add</option>
+        </button>
-                    {% for add_inf in available_additional_information %}
+        <h3 class="modal-title">Add Additional Information</h3>
-                        <option value="{{ add_inf.name }}">{{ add_inf.display_name }}</option>
+      </div>
-                    {% endfor %}
+      <div class="modal-body">
-                </select>
+        <select
-                {% for add_inf in available_additional_information %}
+          id="select-additional-information-type"
-                    <div class="aiform {{ add_inf.name }}" style="display: none;">
+          data-actions-box="true"
-                        <form id="add_{{ add_inf.name }}_add-additional-information-modal-form" accept-charset="UTF-8"
+          class="form-control"
-                              action="" data-remote="true" method="post">
+          data-width="100%"
-                            {% csrf_token %}
+        >
-                            {{ add_inf.widget|safe }}
+          <option selected disabled>Select the type to add</option>
-                            <input type="hidden" name="hidden" value="add-additional-information">
+          {% for add_inf in available_additional_information %}
-                        </form>
+            <option value="{{ add_inf.name }}">
-                    </div>
+              {{ add_inf.display_name }}
-                {% endfor %}
+            </option>
-            </div>
+          {% endfor %}
-            <div class="modal-footer">
+        </select>
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+        {% for add_inf in available_additional_information %}
-                <button type="button" class="btn btn-primary" id="add-additional-information-modal-submit">Add
+          <div class="aiform {{ add_inf.name }}" style="display: none;">
-                </button>
+            <form
-            </div>
+              id="add_{{ add_inf.name }}_add-additional-information-modal-form"
-        </div>
+              accept-charset="UTF-8"
+              action=""
+              data-remote="true"
+              method="post"
+            >
+              {% csrf_token %}
+              {{ add_inf.widget|safe }}
+              <input
+                type="hidden"
+                name="hidden"
+                value="add-additional-information"
+              />
+            </form>
+          </div>
+        {% endfor %}
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="add-additional-information-modal-submit"
+        >
+          Add
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-$(function() {
+  $(function () {
-
+    $("#select-additional-information-type").change(function (e) {
-    $('#select-additional-information-type').change(function(e){
+      var selectedType = $(
-        var selectedType = $("#select-additional-information-type :selected").val();
+        "#select-additional-information-type :selected",
-        $('.aiform').hide();
+      ).val();
-        $('.' + selectedType).show();
+      $(".aiform").hide();
-    })
+      $("." + selectedType).show();
-
-    $('#add-additional-information-modal-submit').click(function(e){
-        e.preventDefault();
-
-        var selectedType = $("#select-additional-information-type :selected").val();
-        console.log(selectedType);
-        if (selectedType !== null && selectedType !== undefined && selectedType !== '') {
-            $('.' + selectedType + ' >form').submit();
-        }
-
     });
 
-});
+    $("#add-additional-information-modal-submit").click(function (e) {
-
+      e.preventDefault();
 
+      var selectedType = $(
+        "#select-additional-information-type :selected",
+      ).val();
+      console.log(selectedType);
+      if (
+        selectedType !== null &&
+        selectedType !== undefined &&
+        selectedType !== ""
+      ) {
+        $("." + selectedType + " >form").submit();
+      }
+    });
+  });
 </script>

templates/modals/objects/add_pathway_edge_modal.html

@@ -1,127 +1,174 @@
-
 {% load static %}
-<div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_modal"
+<div
-     aria-modal="true"
+  class="modal fade bs-modal-lg"
-     role="dialog">
+  id="add_pathway_edge_modal"
-    <div class="modal-dialog modal-lg">
+  tabindex="-1"
-        <div class="modal-content">
+  aria-labelledby="add_pathway_edge_modal"
-            <div class="modal-header">
+  aria-modal="true"
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+  role="dialog"
-                    <span aria-hidden="true">&times;</span>
+>
-                </button>
+  <div class="modal-dialog modal-lg">
-                <h4 class="modal-title">Add a Reaction</h4>
+    <div class="modal-content">
+      <div class="modal-header">
+        <button
+          type="button"
+          class="close"
+          data-dismiss="modal"
+          aria-label="Close"
+        >
+          <span aria-hidden="true">&times;</span>
+        </button>
+        <h4 class="modal-title">Add a Reaction</h4>
+      </div>
+      <div class="modal-body">
+        <form
+          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"
+          method="post"
+        >
+          {% csrf_token %}
+          <label for="edge-name">Name</label>
+          <input
+            id="edge-name"
+            class="form-control"
+            name="edge-name"
+            placeholder="Name"
+          />
+          <label for="edge-description">Description</label>
+          <input
+            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="modal-body">
+            <div class="col-xs-2"></div>
-                <form id="add_pathway_edge_modal_form" accept-charset="UTF-8"
+            <div class="col-xs-5">
-                      action="{% url 'package pathway edge list' meta.current_package.uuid pathway.uuid %}"
+              <legend>Product(s)</legend>
-                      data-remote="true" method="post">
-                    {% csrf_token %}
-                    <label for="edge-name">Name</label>
-                    <input id="edge-name" class="form-control" name="edge-name" placeholder="Name"/>
-                    <label for="edge-description">Description</label>
-                    <input 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-5">
-                            <legend>Product(s)</legend>
-                        </div>
-                    </div>
-                    <div class="row">
-                        <div class="col-xs-5">
-                            <select id="add_pathway_edge_substrates" name="edge-substrates"
-                                    data-actions-box='true' class="form-control" multiple data-width='100%'>
-                                {% for n in pathway.nodes %}
-                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
-                                {% endfor %}
-                            </select>
-                        </div>
-                        <div 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 id="add_pathway_edge_products" name="edge-products"
-                                    data-actions-box='true' class="form-control" multiple data-width='100%'>
-                                {% for n in pathway.nodes %}
-                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
-                                {% endfor %}
-                            </select>
-                        </div>
-                    </div>
-                    <div class="row">
-                        <p></p>
-                        <div class="col-xs-12" id="reaction_image">
-
-                        </div>
-                    </div>
-                </form>
             </div>
-            <div class="modal-footer">
+          </div>
-                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+          <div class="row">
-                </button>
+            <div class="col-xs-5">
-                <button type="button" class="btn btn-primary" id="add_pathway_edge_modal_form_submit">Submit</button>
+              <select
+                id="add_pathway_edge_substrates"
+                name="edge-substrates"
+                data-actions-box="true"
+                class="form-control"
+                multiple
+                data-width="100%"
+              >
+                {% for n in pathway.nodes %}
+                  <option
+                    data-smiles="{{ n.default_node_label.smiles }}"
+                    value="{{ n.url }}"
+                  >
+                    {{ n.default_node_label.name|safe }}
+                  </option>
+                {% endfor %}
+              </select>
             </div>
-        </div>
+            <div
+              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
+                id="add_pathway_edge_products"
+                name="edge-products"
+                data-actions-box="true"
+                class="form-control"
+                multiple
+                data-width="100%"
+              >
+                {% for n in pathway.nodes %}
+                  <option
+                    data-smiles="{{ n.default_node_label.smiles }}"
+                    value="{{ n.url }}"
+                  >
+                    {{ n.default_node_label.name|safe }}
+                  </option>
+                {% endfor %}
+              </select>
+            </div>
+          </div>
+          <div class="row">
+            <p></p>
+            <div class="col-xs-12" id="reaction_image"></div>
+          </div>
+        </form>
+      </div>
+      <div class="modal-footer">
+        <button
+          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>
+      </div>
     </div>
-
+  </div>
 </div>
 <script>
-
+  function reactionImage() {
-    function reactionImage() {
+    var substrates = [];
-        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);
-          substrates.push(smiles);
-        });
-
-        var products = []
-        $('#add_pathway_edge_products option:selected').each(function () {
-          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_image').empty();
-            $('#reaction_image').append(
-                "<img width='100%' src='{% url 'depict' %}?smirks=" + encodeURIComponent(reaction) +"'>"
-            );
-        }
-    }
-
-    $(function () {
-        $("#add_pathway_edge_substrates").selectpicker();
-        $("#add_pathway_edge_products").selectpicker();
-
-        $("#add_pathway_edge_substrates").on('change', function (e) {
-            reactionImage();
-        })
-
-        $("#add_pathway_edge_products").on('change', function (e) {
-            reactionImage();
-        })
-
-        $(function () {
-            $('#add_pathway_edge_modal_form_submit').on('click', function (e) {
-                e.preventDefault();
-                $(this).prop("disabled", true);
-
-
-                // submit form
-                $('#add_pathway_edge_modal_form').submit();
-            });
-        });
-
     });
 
+    var products = [];
+    $("#add_pathway_edge_products option:selected").each(function () {
+      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_image").empty();
+      $("#reaction_image").append(
+        "<img width='100%' src='{% url 'depict' %}?smirks=" +
+          encodeURIComponent(reaction) +
+          "'>",
+      );
+    }
+  }
+
+  $(function () {
+    $("#add_pathway_edge_substrates").selectpicker();
+    $("#add_pathway_edge_products").selectpicker();
+
+    $("#add_pathway_edge_substrates").on("change", function (e) {
+      reactionImage();
+    });
+
+    $("#add_pathway_edge_products").on("change", function (e) {
+      reactionImage();
+    });
+
+    $(function () {
+      $("#add_pathway_edge_modal_form_submit").on("click", function (e) {
+        e.preventDefault();
+        $(this).prop("disabled", true);
+
+        // submit form
+        $("#add_pathway_edge_modal_form").submit();
+      });
+    });
+  });
 </script>
-
-
-
-
-

templates/modals/objects/add_pathway_node_modal.html

@@ -1,78 +1,119 @@
 {% load static %}
-<div class="modal fade bs-modal-lg" id="add_pathway_node_modal" tabindex="-1" aria-labelledby="add_pathway_node_modal" aria-modal="true"
+<div
-     role="dialog">
+  class="modal fade bs-modal-lg"
-    <div class="modal-dialog modal-lg">
+  id="add_pathway_node_modal"
-        <div class="modal-content">
+  tabindex="-1"
-            <div class="modal-header">
+  aria-labelledby="add_pathway_node_modal"
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+  aria-modal="true"
-                    <span aria-hidden="true">&times;</span>
+  role="dialog"
-                </button>
+>
-                <h4 class="modal-title">Add a Node</h4>
+  <div class="modal-dialog modal-lg">
-            </div>
+    <div class="modal-content">
-            <div class="modal-body">
+      <div class="modal-header">
-                <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">
+        <button
-                    {% csrf_token %}
+          type="button"
-                    <label for="node-name">Name</label>
+          class="close"
-                    <input id="node-name" class="form-control" name="node-name" placeholder="Name"/>
+          data-dismiss="modal"
-                    <label for="node-description">Description</label>
+          aria-label="Close"
-                    <input id="node-description" class="form-control" name="node-description" placeholder="Description"/>
+        >
-                    <label for="node-smiles">SMILES</label>
+          <span aria-hidden="true">&times;</span>
-                    <input type="text" class="form-control" name="node-smiles" placeholder="SMILES" id="node-smiles">
+        </button>
-                    <p></p>
+        <h4 class="modal-title">Add a Node</h4>
-                    <div>
+      </div>
-                        <iframe id="add_node_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
+      <div class="modal-body">
-                                height="510"></iframe>
+        <form
-                    </div>
+          id="add_pathway_node_modal_form"
-                    <p></p>
+          accept-charset="UTF-8"
-                </form>
+          action="{% url 'package pathway node list' meta.current_package.uuid pathway.uuid %}"
-            </div>
+          data-remote="true"
-            <div class="modal-footer">
+          method="post"
-                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+        >
-                </button>
+          {% csrf_token %}
-                <button type="button" class="btn btn-primary" id="add_pathway_node_modal_form_submit">Submit</button>
+          <label for="node-name">Name</label>
-            </div>
+          <input
-        </div>
+            id="node-name"
+            class="form-control"
+            name="node-name"
+            placeholder="Name"
+          />
+          <label for="node-description">Description</label>
+          <input
+            id="node-description"
+            class="form-control"
+            name="node-description"
+            placeholder="Description"
+          />
+          <label for="node-smiles">SMILES</label>
+          <input
+            type="text"
+            class="form-control"
+            name="node-smiles"
+            placeholder="SMILES"
+            id="node-smiles"
+          />
+          <p></p>
+          <div>
+            <iframe
+              id="add_node_ketcher"
+              src="{% static '/js/ketcher2/ketcher.html' %}"
+              width="100%"
+              height="510"
+            ></iframe>
+          </div>
+          <p></p>
+        </form>
+      </div>
+      <div class="modal-footer">
+        <button
+          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>
+      </div>
     </div>
-
+  </div>
 </div>
 <script>
+  function newStructureModalketcherToNewStructureModalTextInput() {
+    $("#node-smiles").val(this.ketcher.getSmiles());
+  }
 
-function newStructureModalketcherToNewStructureModalTextInput() {
+  $(function () {
-    $('#node-smiles').val(this.ketcher.getSmiles());
+    $("#add_node_ketcher").on("load", function () {
-}
+      const checkKetcherReady = () => {
+        win = this.contentWindow;
+        if (win.ketcher && "editor" in win.ketcher) {
+          win.ketcher.editor.event.change.handlers.push({
+            once: false,
+            priority: 0,
+            f: newStructureModalketcherToNewStructureModalTextInput,
+            ketcher: win.ketcher,
+          });
+        } else {
+          setTimeout(checkKetcherReady, 100);
+        }
+      };
 
-$(function() {
+      checkKetcherReady();
-
-    $('#add_node_ketcher').on('load', function() {
-        const checkKetcherReady = () => {
-            win = this.contentWindow
-            if (win.ketcher && 'editor' in win.ketcher) {
-                win.ketcher.editor.event.change.handlers.push({
-                    once: false,
-                    priority: 0,
-                    f: newStructureModalketcherToNewStructureModalTextInput,
-                    ketcher: win.ketcher
-                });
-            } else {
-                setTimeout(checkKetcherReady, 100);
-            }
-        };
-
-        checkKetcherReady();
-    })
-
-    $(function() {
-        $('#add_pathway_node_modal_form_submit').on('click', function(e) {
-            e.preventDefault();
-            $(this).prop("disabled",true);
-
-
-
-            // submit form
-            $('#add_pathway_node_modal_form').submit();
-        });
     });
 
-});
+    $(function () {
+      $("#add_pathway_node_modal_form_submit").on("click", function (e) {
+        e.preventDefault();
+        $(this).prop("disabled", true);
 
+        // submit form
+        $("#add_pathway_node_modal_form").submit();
+      });
+    });
+  });
 </script>

templates/modals/objects/add_structure_modal.html

@@ -1,78 +1,119 @@
 {% load static %}
-<div class="modal fade bs-modal-lg" id="add_structure_modal" tabindex="-1" aria-labelledby="add_structure_modal" aria-modal="true"
+<div
-     role="dialog">
+  class="modal fade bs-modal-lg"
-    <div class="modal-dialog modal-lg">
+  id="add_structure_modal"
-        <div class="modal-content">
+  tabindex="-1"
-            <div class="modal-header">
+  aria-labelledby="add_structure_modal"
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+  aria-modal="true"
-                    <span aria-hidden="true">×</span>
+  role="dialog"
-                </button>
+>
-                <h4 class="modal-title">Create a new Structure</h4>
+  <div class="modal-dialog modal-lg">
-            </div>
+    <div class="modal-content">
-            <div class="modal-body">
+      <div class="modal-header">
-                <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">
+        <button
-                    {% csrf_token %}
+          type="button"
-                    <label for="structure-name">Name</label>
+          class="close"
-                    <input id="structure-name" class="form-control" name="structure-name" placeholder="Name"/>
+          data-dismiss="modal"
-                    <label for="structure-description">Description</label>
+          aria-label="Close"
-                    <input id="structure-description" class="form-control" name="structure-description" placeholder="Description"/>
+        >
-                    <label for="structure-smiles">SMILES</label>
+          <span aria-hidden="true">×</span>
-                    <input type="text" class="form-control" name="structure-smiles" placeholder="SMILES" id="structure-smiles">
+        </button>
-                    <p></p>
+        <h4 class="modal-title">Create a new Structure</h4>
-                    <div>
+      </div>
-                        <iframe id="add_structure_ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
+      <div class="modal-body">
-                                height="510"></iframe>
+        <form
-                    </div>
+          id="add_structure_modal_form"
-                    <p></p>
+          accept-charset="UTF-8"
-                </form>
+          action="{% url 'package compound structure list' meta.current_package.uuid compound.uuid %}"
-            </div>
+          data-remote="true"
-            <div class="modal-footer">
+          method="post"
-                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
+        >
-                </button>
+          {% csrf_token %}
-                <button type="button" class="btn btn-primary" id="add_structure_modal_form_submit">Submit</button>
+          <label for="structure-name">Name</label>
-            </div>
+          <input
-        </div>
+            id="structure-name"
+            class="form-control"
+            name="structure-name"
+            placeholder="Name"
+          />
+          <label for="structure-description">Description</label>
+          <input
+            id="structure-description"
+            class="form-control"
+            name="structure-description"
+            placeholder="Description"
+          />
+          <label for="structure-smiles">SMILES</label>
+          <input
+            type="text"
+            class="form-control"
+            name="structure-smiles"
+            placeholder="SMILES"
+            id="structure-smiles"
+          />
+          <p></p>
+          <div>
+            <iframe
+              id="add_structure_ketcher"
+              src="{% static '/js/ketcher2/ketcher.html' %}"
+              width="100%"
+              height="510"
+            ></iframe>
+          </div>
+          <p></p>
+        </form>
+      </div>
+      <div class="modal-footer">
+        <button
+          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>
+      </div>
     </div>
-
+  </div>
 </div>
 <script>
+  function newStructureModalketcherToNewStructureModalTextInput() {
+    $("#structure-smiles").val(this.ketcher.getSmiles());
+  }
 
-function newStructureModalketcherToNewStructureModalTextInput() {
+  $(function () {
-    $('#structure-smiles').val(this.ketcher.getSmiles());
+    $("#add_structure_ketcher").on("load", function () {
-}
+      const checkKetcherReady = () => {
+        win = this.contentWindow;
+        if (win.ketcher && "editor" in win.ketcher) {
+          win.ketcher.editor.event.change.handlers.push({
+            once: false,
+            priority: 0,
+            f: newStructureModalketcherToNewStructureModalTextInput,
+            ketcher: win.ketcher,
+          });
+        } else {
+          setTimeout(checkKetcherReady, 100);
+        }
+      };
 
-$(function() {
+      checkKetcherReady();
-
-    $('#add_structure_ketcher').on('load', function() {
-        const checkKetcherReady = () => {
-            win = this.contentWindow
-            if (win.ketcher && 'editor' in win.ketcher) {
-                win.ketcher.editor.event.change.handlers.push({
-                    once: false,
-                    priority: 0,
-                    f: newStructureModalketcherToNewStructureModalTextInput,
-                    ketcher: win.ketcher
-                });
-            } else {
-                setTimeout(checkKetcherReady, 100);
-            }
-        };
-
-        checkKetcherReady();
-    })
-
-    $(function() {
-        $('#add_structure_modal_form_submit').on('click', function(e) {
-            e.preventDefault();
-            $(this).prop("disabled",true);
-
-
-
-            // submit form
-            $('#add_structure_modal_form').submit();
-        });
     });
 
-});
+    $(function () {
+      $("#add_structure_modal_form_submit").on("click", function (e) {
+        e.preventDefault();
+        $(this).prop("disabled", true);
 
+        // submit form
+        $("#add_structure_modal_form").submit();
+      });
+    });
+  });
 </script>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -1,66 +1,89 @@
-
 {% load static %}
 <!-- Delete Edge -->
 <div id="delete_pathway_edge_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h3 class="modal-title">Delete Edge</h3>
+        <h3 class="modal-title">Delete Edge</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                Deletes the Edge. Nodes referenced by this edge will remain.
+        >
-                <p></p>
+          <span aria-hidden="true">&times;</span>
-                <form id="delete-pathway-edge-modal-form" accept-charset="UTF-8" action="" data-remote="true"
+        </button>
-                      method="post">
+      </div>
-                    {% csrf_token %}
+      <div class="modal-body">
-                    <select id="delete_pathway_edge_edges" name="edge-url"
+        Deletes the Edge. Nodes referenced by this edge will remain.
-                            data-actions-box='true' class="form-control" data-width='100%'>
+        <p></p>
-                        <option value="" disabled selected>Select Reaction to delete</option>
+        <form
-                        {% for e in pathway.edges %}
+          id="delete-pathway-edge-modal-form"
-                            <option value="{{ e.url }}">{{ e.edge_label.name|safe }}</option>
+          accept-charset="UTF-8"
-                        {% endfor %}
+          action=""
-                    </select>
+          data-remote="true"
-                    <input type="hidden" id="hidden" name="hidden" value="delete"/>
+          method="post"
-                </form>
+        >
-                <p></p>
+          {% csrf_token %}
-                <div id="delete_pathway_edge_image"></div>
+          <select
-            </div>
+            id="delete_pathway_edge_edges"
-            <div class="modal-footer">
+            name="edge-url"
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+            data-actions-box="true"
-                <button type="button" class="btn btn-primary" id="delete-pathway-edge-modal-submit">Delete</button>
+            class="form-control"
-            </div>
+            data-width="100%"
-        </div>
+          >
+            <option value="" disabled selected>
+              Select Reaction to delete
+            </option>
+            {% for e in pathway.edges %}
+              <option value="{{ e.url }}">{{ e.edge_label.name|safe }}</option>
+            {% endfor %}
+          </select>
+          <input type="hidden" id="hidden" name="hidden" value="delete" />
+        </form>
+        <p></p>
+        <div id="delete_pathway_edge_image"></div>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="delete-pathway-edge-modal-submit"
+        >
+          Delete
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-    $(function () {
+  $(function () {
-        $("#delete_pathway_edge_edges").selectpicker();
+    $("#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 !== "") {
+      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();
+      e.preventDefault();
-            edge_url = $('#delete_pathway_edge_edges option:selected').val()
+      edge_url = $("#delete_pathway_edge_edges option:selected").val();
 
-            if (edge_url === "") {
+      if (edge_url === "") {
-                return;
+        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

@@ -2,65 +2,92 @@
 
 <!-- Delete Node -->
 <div id="delete_pathway_node_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h3 class="modal-title">Delete Node</h3>
+        <h3 class="modal-title">Delete Node</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                Deletes the Node. Edges having this Node as Substrate or Product will be removed as well.
+        >
-                <p></p>
+          <span aria-hidden="true">&times;</span>
-                <form id="delete-pathway-node-modal-form" accept-charset="UTF-8" action="" data-remote="true"
+        </button>
-                      method="post">
+      </div>
-                    {% csrf_token %}
+      <div class="modal-body">
-                    <select id="delete_pathway_node_nodes" name="node-url"
+        Deletes the Node. Edges having this Node as Substrate or Product will be
-                            data-actions-box='true' class="form-control" data-width='100%'>
+        removed as well.
-                        <option value="" disabled selected>Select Compound to delete</option>
+        <p></p>
-                        {% for n in pathway.nodes %}
+        <form
-                            <option value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
+          id="delete-pathway-node-modal-form"
-                        {% endfor %}
+          accept-charset="UTF-8"
-                    </select>
+          action=""
-                    <input type="hidden" id="hidden" name="hidden" value="delete"/>
+          data-remote="true"
-                </form>
+          method="post"
-                <p></p>
+        >
-                <div id="delete_pathway_node_image"></div>
+          {% csrf_token %}
-            </div>
+          <select
-            <div class="modal-footer">
+            id="delete_pathway_node_nodes"
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+            name="node-url"
-                <button type="button" class="btn btn-primary" id="delete-pathway-node-modal-submit">Delete</button>
+            data-actions-box="true"
-            </div>
+            class="form-control"
-        </div>
+            data-width="100%"
+          >
+            <option value="" disabled selected>
+              Select Compound to delete
+            </option>
+            {% for n in pathway.nodes %}
+              <option value="{{ n.url }}">
+                {{ n.default_node_label.name|safe }}
+              </option>
+            {% endfor %}
+          </select>
+          <input type="hidden" id="hidden" name="hidden" value="delete" />
+        </form>
+        <p></p>
+        <div id="delete_pathway_node_image"></div>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="delete-pathway-node-modal-submit"
+        >
+          Delete
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-    $(function () {
+  $(function () {
-        $("#delete_pathway_node_nodes").selectpicker();
+    $("#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 !== "") {
+      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();
+      e.preventDefault();
-            node_url = $('#delete_pathway_node_nodes option:selected').val()
+      node_url = $("#delete_pathway_node_nodes option:selected").val();
 
-            if (node_url === "") {
+      if (node_url === "") {
-                return;
+        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

@@ -1,36 +1,53 @@
 {% load static %}
 <!-- Download Pathway -->
 <div id="download_pathway_csv_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h3 class="modal-title">Download Pathway as CSV</h3>
+        <h3 class="modal-title">Download Pathway as CSV</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                By clicking on Download the Pathway will be converted into a CSV and directly downloaded.
+        >
-                <form id="download-pathway-csv-modal-form" accept-charset="UTF-8" action="{{ pathway.url }}"
+          <span aria-hidden="true">&times;</span>
-                      data-remote="true" method="GET">
+        </button>
-                    <input type="hidden" name="download" value="true"/>
+      </div>
-                </form>
+      <div class="modal-body">
-            </div>
+        By clicking on Download the Pathway will be converted into a CSV and
-            <div class="modal-footer">
+        directly downloaded.
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+        <form
-                <button type="button" class="btn btn-primary" id="download-pathway-csv-modal-submit">Download</button>
+          id="download-pathway-csv-modal-form"
-            </div>
+          accept-charset="UTF-8"
-        </div>
+          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">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="download-pathway-csv-modal-submit"
+        >
+          Download
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-    $(function () {
+  $(function () {
-
+    $("#download-pathway-csv-modal-submit").click(function (e) {
-        $('#download-pathway-csv-modal-submit').click(function (e) {
+      e.preventDefault();
-            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

@@ -1,32 +1,43 @@
 {% load static %}
 <!-- Download Pathway -->
 <div id="download_pathway_image_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h3 class="modal-title">Download Pathway as Image</h3>
+        <h3 class="modal-title">Download Pathway as Image</h3>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                By clicking on Download the Pathway will be saved as SVG.
+        >
-            </div>
+          <span aria-hidden="true">&times;</span>
-            <div class="modal-footer">
+        </button>
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+      </div>
-                <button type="button" class="btn btn-primary" id="download-pathway-image-modal-submit">Download</button>
+      <div class="modal-body">
-            </div>
+        By clicking on Download the Pathway will be saved as SVG.
-        </div>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="download-pathway-image-modal-submit"
+        >
+          Download
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-    $(function () {
+  $(function () {
-
+    $("#download-pathway-image-modal-submit").click(function (e) {
-        $('#download-pathway-image-modal-submit').click(function (e) {
+      e.preventDefault();
-            e.preventDefault();
+      downloadSVG($("#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

@@ -1,47 +1,70 @@
-
 {% load static %}
 <!-- Edit Compound -->
 <div id="edit_compound_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h5 class="modal-title">Edit Compound</h5>
+        <h5 class="modal-title">Edit Compound</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                <p>Edit Compound.</p>
+        >
-                <form id="edit-compound-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+          <span aria-hidden="true">&times;</span>
-                    {% csrf_token %}
+        </button>
-                    <p>
+      </div>
-                        <label for="compound-name">Name</label>
+      <div class="modal-body">
-                        <input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name|safe}}">
+        <p>Edit Compound.</p>
-                    </p>
+        <form
-                    <p>
+          id="edit-compound-modal-form"
-                        <label for="compound-description">Description</label>
+          accept-charset="UTF-8"
-                        <input id="compound-description" type="text" class="form-control"
+          action=""
-                               value="{{ compound.description|safe }}"
+          data-remote="true"
-                               name="compound-description">
+          method="post"
-                    </p>
+        >
-                </form>
+          {% csrf_token %}
-            </div>
+          <p>
-            <div class="modal-footer">
+            <label for="compound-name">Name</label>
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+            <input
-                <button type="button" class="btn btn-primary" id="edit-compound-modal-submit">Update</button>
+              id="compound-name"
-            </div>
+              class="form-control"
-        </div>
+              name="compound-name"
+              value="{{ compound.name|safe }}"
+            />
+          </p>
+          <p>
+            <label for="compound-description">Description</label>
+            <input
+              id="compound-description"
+              type="text"
+              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">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="edit-compound-modal-submit"
+        >
+          Update
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-$(function() {
+  $(function () {
-
+    $("#edit-compound-modal-submit").click(function (e) {
-    $('#edit-compound-modal-submit').click(function(e){
+      e.preventDefault();
-        e.preventDefault();
+      $("#edit-compound-modal-form").submit();
-        $('#edit-compound-modal-form').submit();
     });
-
+  });
-});
-
-
 </script>

templates/modals/objects/edit_compound_structure_modal.html

@@ -1,46 +1,70 @@
-
 {% load static %}
 <!-- Edit Compound -->
 <div id="edit_compound_structure_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h5 class="modal-title">Create a Compound</h5>
+        <h5 class="modal-title">Create a Compound</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                <p>Edit a Compound Structure.</p>
+        >
-                <form id="edit-compound-structure-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+          <span aria-hidden="true">&times;</span>
-                    {% csrf_token %}
+        </button>
-                    <p>
+      </div>
-                        <label for="compound-structure-name">Name</label>
+      <div class="modal-body">
-                        <input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name|safe }}">
+        <p>Edit a Compound Structure.</p>
-                    </p>
+        <form
-                    <p>
+          id="edit-compound-structure-modal-form"
-                        <label for="compound-structure-description">Description</label>
+          accept-charset="UTF-8"
-                        <input id="compound-structure-description" type="text" class="form-control"
+          action=""
-                               value="{{ compound_structure.description|safe }}" name="compound-structure-description">
+          data-remote="true"
-                    </p>
+          method="post"
-                </form>
+        >
-            </div>
+          {% csrf_token %}
-            <div class="modal-footer">
+          <p>
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+            <label for="compound-structure-name">Name</label>
-                <button type="button" class="btn btn-primary" id="edit-compound-structure-modal-submit">Create</button>
+            <input
-            </div>
+              id="compound-structure-name"
-        </div>
+              class="form-control"
+              name="compound-structure-name"
+              value="{{ compound_structure.name|safe }}"
+            />
+          </p>
+          <p>
+            <label for="compound-structure-description">Description</label>
+            <input
+              id="compound-structure-description"
+              type="text"
+              class="form-control"
+              value="{{ compound_structure.description|safe }}"
+              name="compound-structure-description"
+            />
+          </p>
+        </form>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="edit-compound-structure-modal-submit"
+        >
+          Create
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-$(function() {
+  $(function () {
-
+    $("#edit-compound-structure-modal-submit").click(function (e) {
-    $('#edit-compound-structure-modal-submit').click(function(e){
+      e.preventDefault();
-        e.preventDefault();
+      $("#edit-compound-structure-modal-form").submit();
-        $('#edit-compound-structure-modal-form').submit();
     });
-
+  });
-});
-
-
 </script>

templates/modals/objects/edit_group_member_modal.html

@@ -1,121 +1,151 @@
-
 {% load static %}
 <!-- Edit Package Permission -->
 <div id="edit_group_member_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h5 class="modal-title">Add or Remove Group Member</h5>
+        <h5 class="modal-title">Add or Remove Group Member</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                <p>
+        >
-                    To add member (either User or entire Groups) to this group select the entity you want to add below
+          <span aria-hidden="true">&times;</span>
-                    and click the check mark.
+        </button>
-                    <br>
+      </div>
-                    To remove member simply click the <code>X</code> next to the member.
+      <div class="modal-body">
-                </p>
+        <p>
+          To add member (either User or entire Groups) to this group select the
+          entity you want to add below and click the check mark.
+          <br />
+          To remove member simply click the <code>X</code> next to the member.
+        </p>
 
-                <div class="row">
+        <div class="row">
-					<div class="col-xs-8">
+          <div class="col-xs-8">
-						<legend>User or Group</legend>
+            <legend>User or Group</legend>
-					</div>
+          </div>
-					<div class="col-xs-4">
+          <div class="col-xs-4">
-						<legend>Add/Remove</legend>
+            <legend>Add/Remove</legend>
-					</div>
+          </div>
-				</div>
-
-                <div class="row">
-                    <form id="modal-form-group-member" class="form-inline" role="form" accept-charset="UTF-8" action=""
-                          data-remote="true" method="post">
-                        {% csrf_token %}
-                        <div class="col-xs-8">
-                            <select id="select_member" 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>
-                                {% endfor %}
-                            </select>
-                            <input type="hidden" name="action" value="add">
-                        </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>
-                            </button>
-                        </div>
-                    </form>
-                </div>
-                <p></p>
-                {% for u in group.user_member.all %}
-                <div class="row">
-                    <form id="modal-form-group-member_{{ u.uuid }}" 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">
-                        </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>
-                            </button>
-                        </div>
-                    </form>
-                </div>
-                {% endfor %}
-                <p></p>
-                {% for g in group.group_member.all %}
-                <div class="row">
-                    <form id="modal-form-group-member_{{ g.uuid }}" 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 }}
-                            <input type="hidden" name="member" value="{{ g.url }}"/>
-                            <input type="hidden" name="action" value="remove">
-                        </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>
-                            </button>
-                        </div>
-                    </form>
-                </div>
-                {% endfor %}
-
-            </div>
-            <div class="modal-footer">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
-            </div>
         </div>
+
+        <div class="row">
+          <form
+            id="modal-form-group-member"
+            class="form-inline"
+            role="form"
+            accept-charset="UTF-8"
+            action=""
+            data-remote="true"
+            method="post"
+          >
+            {% csrf_token %}
+            <div class="col-xs-8">
+              <select
+                id="select_member"
+                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>
+                {% endfor %}
+              </select>
+              <input type="hidden" name="action" value="add" />
+            </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>
+              </button>
+            </div>
+          </form>
+        </div>
+        <p></p>
+        {% for u in group.user_member.all %}
+          <div class="row">
+            <form
+              id="modal-form-group-member_{{ u.uuid }}"
+              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" />
+              </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>
+                </button>
+              </div>
+            </form>
+          </div>
+        {% endfor %}
+        <p></p>
+        {% for g in group.group_member.all %}
+          <div class="row">
+            <form
+              id="modal-form-group-member_{{ g.uuid }}"
+              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 }}
+                <input type="hidden" name="member" value="{{ g.url }}" />
+                <input type="hidden" name="action" value="remove" />
+              </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>
+                </button>
+              </div>
+            </form>
+          </div>
+        {% endfor %}
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="edit-package-modal-submit"
+        >
+          Update
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-
+  $(function () {
-
+    $("#edit-package-modal-submit").click(function (e) {
-$(function() {
+      e.preventDefault();
-
+      $("#edit-package-modal-form").submit();
-    $('#edit-package-modal-submit').click(function(e){
-        e.preventDefault();
-        $('#edit-package-modal-form').submit();
     });
 
     $("#select_member").selectpicker();
-
+  });
-})
 </script>

templates/modals/objects/edit_model_modal.html

@@ -1,45 +1,71 @@
-
 {% load static %}
 <!-- Edit Model -->
 <div id="edit_model_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-                <h3 class="modal-title">Update Model</h3>
+          data-dismiss="modal"
-            </div>
+          aria-label="Close"
-            <div class="modal-body">
+        >
-                <p>Alter Name and Description of the Model.</p>
+          <span aria-hidden="true">&times;</span>
-                <form id="edit-model-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+        </button>
-                    {% csrf_token %}
+        <h3 class="modal-title">Update Model</h3>
-                    <p>
+      </div>
-                        <label for="model-name">Name</label>
+      <div class="modal-body">
-                        <input id="model-name" type="text" class="form-control" name="model-name"
+        <p>Alter Name and Description of the Model.</p>
-                               value="{{ model.name|safe }}">
+        <form
-                    </p>
+          id="edit-model-modal-form"
-                    <p>
+          accept-charset="UTF-8"
-                        <label for="model-description">Description</label>
+          action=""
-                        <input id="model-description" type="text" class="form-control" name="model-description"
+          data-remote="true"
-                               value="{{ model.description|safe }}">
+          method="post"
-                    </p>
+        >
-                </form>
+          {% csrf_token %}
-            </div>
+          <p>
-            <div class="modal-footer">
+            <label for="model-name">Name</label>
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+            <input
-                <button type="button" class="btn btn-primary" id="edit-model-modal-submit">Update</button>
+              id="model-name"
-            </div>
+              type="text"
-        </div>
+              class="form-control"
+              name="model-name"
+              value="{{ model.name|safe }}"
+            />
+          </p>
+          <p>
+            <label for="model-description">Description</label>
+            <input
+              id="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">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="edit-model-modal-submit"
+        >
+          Update
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-    $(function () {
+  $(function () {
-
+    $("#edit-model-modal-submit").click(function (e) {
-        $('#edit-model-modal-submit').click(function (e) {
+      e.preventDefault();
-            e.preventDefault();
+      $("#edit-model-modal-form").submit();
-            $('#edit-model-modal-form').submit();
+    });
-        });
+  });
-
-    })
 </script>

templates/modals/objects/edit_node_modal.html

@@ -1,47 +1,70 @@
-
 {% load static %}
 <!-- Edit Node -->
 <div id="edit_node_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h5 class="modal-title">Edit Node</h5>
+        <h5 class="modal-title">Edit Node</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                <p>Edit Node.</p>
+        >
-                <form id="edit-node-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+          <span aria-hidden="true">&times;</span>
-                    {% csrf_token %}
+        </button>
-                    <p>
+      </div>
-                        <label for="node-name">Name</label>
+      <div class="modal-body">
-                        <input id="node-name" class="form-control" name="node-name" value="{{ node.name|safe}}">
+        <p>Edit Node.</p>
-                    </p>
+        <form
-                    <p>
+          id="edit-node-modal-form"
-                        <label for="node-description">Description</label>
+          accept-charset="UTF-8"
-                        <input id="node-description" type="text" class="form-control"
+          action=""
-                               value="{{ node.description|safe }}"
+          data-remote="true"
-                               name="node-description">
+          method="post"
-                    </p>
+        >
-                </form>
+          {% csrf_token %}
-            </div>
+          <p>
-            <div class="modal-footer">
+            <label for="node-name">Name</label>
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+            <input
-                <button type="button" class="btn btn-primary" id="edit-node-modal-submit">Create</button>
+              id="node-name"
-            </div>
+              class="form-control"
-        </div>
+              name="node-name"
+              value="{{ node.name|safe }}"
+            />
+          </p>
+          <p>
+            <label for="node-description">Description</label>
+            <input
+              id="node-description"
+              type="text"
+              class="form-control"
+              value="{{ node.description|safe }}"
+              name="node-description"
+            />
+          </p>
+        </form>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="edit-node-modal-submit"
+        >
+          Create
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-$(function() {
+  $(function () {
-
+    $("#edit-node-modal-submit").click(function (e) {
-    $('#edit-node-modal-submit').click(function(e){
+      e.preventDefault();
-        e.preventDefault();
+      $("#edit-node-modal-form").submit();
-        $('#edit-node-modal-form').submit();
     });
-
+  });
-});
-
-
 </script>

templates/modals/objects/edit_package_modal.html

@@ -1,45 +1,70 @@
-
 {% load static %}
 <!-- Edit Package -->
 <div id="edit_package_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h5 class="modal-title">Update Package</h5>
+        <h5 class="modal-title">Update Package</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                <p>Edit a Package.</p>
+        >
-                <form id="edit-package-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
+          <span aria-hidden="true">&times;</span>
-                    {% csrf_token %}
+        </button>
-                    <p>
+      </div>
-                        <label for="package-name">Name</label>
+      <div class="modal-body">
-                        <input id="package-name" class="form-control" name="package-name" value="{{ package.name|safe}}">
+        <p>Edit a Package.</p>
-                    </p>
+        <form
-                    <p>
+          id="edit-package-modal-form"
-                        <label for="package-description">Description</label>
+          accept-charset="UTF-8"
-                        <input id="package-description" type="text" class="form-control"
+          action=""
-                               value="{{ package.description|safe }}"
+          data-remote="true"
-                               name="package-description">
+          method="post"
-                    </p>
+        >
-                </form>
+          {% csrf_token %}
-            </div>
+          <p>
-            <div class="modal-footer">
+            <label for="package-name">Name</label>
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+            <input
-                <button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
+              id="package-name"
-            </div>
+              class="form-control"
-        </div>
+              name="package-name"
+              value="{{ package.name|safe }}"
+            />
+          </p>
+          <p>
+            <label for="package-description">Description</label>
+            <input
+              id="package-description"
+              type="text"
+              class="form-control"
+              value="{{ package.description|safe }}"
+              name="package-description"
+            />
+          </p>
+        </form>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="edit-package-modal-submit"
+        >
+          Update
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-$(function() {
+  $(function () {
-
+    $("#edit-package-modal-submit").click(function (e) {
-    $('#edit-package-modal-submit').click(function(e){
+      e.preventDefault();
-        e.preventDefault();
+      $("#edit-package-modal-form").submit();
-        $('#edit-package-modal-form').submit();
     });
-
+  });
-})
 </script>

templates/modals/objects/edit_package_permissions_modal.html

@@ -1,183 +1,264 @@
-
 {% load static %}
 <!-- Edit Package Permission -->
 <div id="edit_package_permissions_modal" class="modal" tabindex="-1">
-    <div class="modal-dialog">
+  <div class="modal-dialog">
-        <div class="modal-content">
+    <div class="modal-content">
-            <div class="modal-header">
+      <div class="modal-header">
-                <h5 class="modal-title">Grant or Revoke Permissions</h5>
+        <h5 class="modal-title">Grant or Revoke Permissions</h5>
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+        <button
-                    <span aria-hidden="true">&times;</span>
+          type="button"
-                </button>
+          class="close"
-            </div>
+          data-dismiss="modal"
-            <div class="modal-body">
+          aria-label="Close"
-                <p>
+        >
-                    Modify permissions for this package. Note that if you give <code>write</code>
+          <span aria-hidden="true">&times;</span>
-                    permissions to a user or group, <code>read</code> permissions will be granted automatically.
+        </button>
-                    <br>
+      </div>
-                    To allow users to perform destructive actions, such as deleting the package, <code>owner</code>
+      <div class="modal-body">
-                    permissions must be granted.
+        <p>
-                </p>
+          Modify permissions for this package. Note that if you give
+          <code>write</code> permissions to a user or group,
+          <code>read</code> permissions will be granted automatically.
+          <br />
+          To allow users to perform destructive actions, such as deleting the
+          package, <code>owner</code>
+          permissions must be granted.
+        </p>
 
-                <div class="row">
+        <div class="row">
-					<div class="col-xs-4">
+          <div class="col-xs-4">
-						<legend>User or Group</legend>
+            <legend>User or Group</legend>
-					</div>
+          </div>
-					<div class="col-xs-2">
+          <div class="col-xs-2">
-						<legend>Read</legend>
+            <legend>Read</legend>
-					</div>
+          </div>
-					<div class="col-xs-2">
+          <div class="col-xs-2">
-						<legend>Write</legend>
+            <legend>Write</legend>
-					</div>
+          </div>
-					<div class="col-xs-2">
+          <div class="col-xs-2">
-						<legend>Owner</legend>
+            <legend>Owner</legend>
-					</div>
+          </div>
-				</div>
-
-                <div class="row">
-                    <form id="modal-form-permissions" class="form-inline" role="form" accept-charset="UTF-8" action=""
-                          data-remote="true" method="post">
-                        {% csrf_token %}
-                        <div class="col-xs-4">
-                            <select id="select_grantee" name="grantee" 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>
-                                {% endfor %}
-                            </select>
-                        </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="read" id="read_new"/>
-                        </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="write" id="write_new"/>
-                        </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="owner" id="owner_new"/>
-                        </div>
-                        <div class="col-xs-2">
-                            <button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
-                                <span class="glyphicon glyphicon-plus"></span>
-                            </button>
-                        </div>
-                    </form>
-                </div>
-                <p></p>
-                {% for up in user_permissions %}
-                <div class="row">
-                    <form id="modal-form-permissions_{{ up.user.uuid }}" class="form-inline" role="form"
-                          accept-charset="UTF-8" action="" data-remote="true" method="post">
-                        {% csrf_token %}
-                        <div class="col-xs-4">
-                            {{ up.user.username }}
-                            <input type="hidden" name="grantee" value="{{ up.user.url }}"/>
-                        </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="read" id="read_{{ up.user.uuid }}" {% if up.has_read %} checked {% endif %}/>
-                        </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="write" id="write_{{ up.user.uuid }}" {% if up.has_write %} checked {% endif %}/>
-                        </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="owner" id="owner_{{ up.user.uuid }}" {% if up.has_all %} checked {% endif %}/>
-                        </div>
-                        <div class="col-xs-2">
-                            <button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
-                                <span class="glyphicon glyphicon-ok"></span>
-                            </button>
-                        </div>
-                    </form>
-                </div>
-                {% endfor %}
-                <p></p>
-                {% for gp in group_permissions %}
-                <div class="row">
-                    <form id="modal-form-permissions_{{ gp.user.uuid }}" class="form-inline" role="form"
-                          accept-charset="UTF-8" action="" data-remote="true" method="post">
-                        {% csrf_token %}
-                        <div class="col-xs-4">
-                            {{ gp.group.name|safe }}
-                            <input type="hidden" name="grantee" value="{{ gp.group.url }}"/>
-                        </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="read" id="read_{{ gp.group.uuid }}" {% if gp.has_read %} checked {% endif %}/>
-                        </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="write" id="write_{{ gp.group.uuid }}" {% if gp.has_write %} checked {% endif %}/>
-                        </div>
-                        <div class="col-xs-2">
-                            <input type="checkbox" name="owner" id="owner_{{ gp.group.uuid }}" {% if gp.has_all %} checked {% endif %}/>
-                        </div>
-                        <div class="col-xs-2">
-                            <button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
-                                <span class="glyphicon glyphicon-ok"></span>
-                            </button>
-                        </div>
-                    </form>
-                </div>
-                {% endfor %}
-
-            </div>
-            <div class="modal-footer">
-                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-                <button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
-            </div>
         </div>
+
+        <div class="row">
+          <form
+            id="modal-form-permissions"
+            class="form-inline"
+            role="form"
+            accept-charset="UTF-8"
+            action=""
+            data-remote="true"
+            method="post"
+          >
+            {% csrf_token %}
+            <div class="col-xs-4">
+              <select
+                id="select_grantee"
+                name="grantee"
+                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>
+                {% endfor %}
+              </select>
+            </div>
+            <div class="col-xs-2">
+              <input type="checkbox" name="read" id="read_new" />
+            </div>
+            <div class="col-xs-2">
+              <input type="checkbox" name="write" id="write_new" />
+            </div>
+            <div class="col-xs-2">
+              <input type="checkbox" name="owner" id="owner_new" />
+            </div>
+            <div class="col-xs-2">
+              <button
+                type="submit"
+                style="width:60%;"
+                class="btn col-xs-2 modify-perm-button"
+              >
+                <span class="glyphicon glyphicon-plus"></span>
+              </button>
+            </div>
+          </form>
+        </div>
+        <p></p>
+        {% for up in user_permissions %}
+          <div class="row">
+            <form
+              id="modal-form-permissions_{{ up.user.uuid }}"
+              class="form-inline"
+              role="form"
+              accept-charset="UTF-8"
+              action=""
+              data-remote="true"
+              method="post"
+            >
+              {% csrf_token %}
+              <div class="col-xs-4">
+                {{ up.user.username }}
+                <input type="hidden" name="grantee" value="{{ up.user.url }}" />
+              </div>
+              <div class="col-xs-2">
+                <input
+                  type="checkbox"
+                  name="read"
+                  id="read_{{ up.user.uuid }}"
+                  {% if up.has_read %}checked{% endif %}
+                />
+              </div>
+              <div class="col-xs-2">
+                <input
+                  type="checkbox"
+                  name="write"
+                  id="write_{{ up.user.uuid }}"
+                  {% if up.has_write %}checked{% endif %}
+                />
+              </div>
+              <div class="col-xs-2">
+                <input
+                  type="checkbox"
+                  name="owner"
+                  id="owner_{{ up.user.uuid }}"
+                  {% if up.has_all %}checked{% endif %}
+                />
+              </div>
+              <div class="col-xs-2">
+                <button
+                  type="submit"
+                  style="width:60%;"
+                  class="btn col-xs-2 modify-perm-button"
+                >
+                  <span class="glyphicon glyphicon-ok"></span>
+                </button>
+              </div>
+            </form>
+          </div>
+        {% endfor %}
+        <p></p>
+        {% for gp in group_permissions %}
+          <div class="row">
+            <form
+              id="modal-form-permissions_{{ gp.user.uuid }}"
+              class="form-inline"
+              role="form"
+              accept-charset="UTF-8"
+              action=""
+              data-remote="true"
+              method="post"
+            >
+              {% csrf_token %}
+              <div class="col-xs-4">
+                {{ gp.group.name|safe }}
+                <input
+                  type="hidden"
+                  name="grantee"
+                  value="{{ gp.group.url }}"
+                />
+              </div>
+              <div class="col-xs-2">
+                <input
+                  type="checkbox"
+                  name="read"
+                  id="read_{{ gp.group.uuid }}"
+                  {% if gp.has_read %}checked{% endif %}
+                />
+              </div>
+              <div class="col-xs-2">
+                <input
+                  type="checkbox"
+                  name="write"
+                  id="write_{{ gp.group.uuid }}"
+                  {% if gp.has_write %}checked{% endif %}
+                />
+              </div>
+              <div class="col-xs-2">
+                <input
+                  type="checkbox"
+                  name="owner"
+                  id="owner_{{ gp.group.uuid }}"
+                  {% if gp.has_all %}checked{% endif %}
+                />
+              </div>
+              <div class="col-xs-2">
+                <button
+                  type="submit"
+                  style="width:60%;"
+                  class="btn col-xs-2 modify-perm-button"
+                >
+                  <span class="glyphicon glyphicon-ok"></span>
+                </button>
+              </div>
+            </form>
+          </div>
+        {% endfor %}
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          id="edit-package-modal-submit"
+        >
+          Update
+        </button>
+      </div>
     </div>
+  </div>
 </div>
 <script>
-
+  function checkboxClick() {
-function checkboxClick() {
     // id looks like read_3cadef24-220e-4587-9fa5-0e9a17aca2da
-    parts = this.id.split('_');
+    parts = this.id.split("_");
     perm = parts[0];
     id = parts[1];
 
-    readbox = '#read_' + id;
+    readbox = "#read_" + id;
-    writebox = '#write_' + id;
+    writebox = "#write_" + id;
-    ownerbox = '#owner_' + id;
+    ownerbox = "#owner_" + id;
 
+    if (perm == "read" && !$(readbox).prop("checked")) {
+      $(writebox).prop("checked", false);
+      $(ownerbox).prop("checked", false);
+    }
 
-    if (perm == 'read' && !$(readbox).prop("checked")) {
+    if (perm == "write") {
-        $(writebox).prop("checked", false);
+      if ($(writebox).prop("checked")) {
+        $(readbox).prop("checked", true);
+      }
+      if (!$(writebox).prop("checked")) {
         $(ownerbox).prop("checked", false);
+      }
     }
 
-    if (perm == 'write') {
+    if (perm == "owner") {
-        if ($(writebox).prop("checked")) {
+      if ($(ownerbox).prop("checked")) {
-            $(readbox).prop("checked", true);
+        $(readbox).prop("checked", true);
-        }
+        $(writebox).prop("checked", true);
-        if (!$(writebox).prop("checked")) {
+      }
-            $(ownerbox).prop("checked", false);
-        }
     }
+  }
 
-    if (perm == 'owner') {
+  $(function () {
-        if ($(ownerbox).prop("checked")) {
+    $("#edit-package-modal-submit").click(function (e) {
-            $(readbox).prop("checked", true);
+      e.preventDefault();
-            $(writebox).prop("checked", true);
+      $("#edit-package-modal-form").submit();
-        }
-    }
-}
-
-$(function() {
-
-    $('#edit-package-modal-submit').click(function(e){
-        e.preventDefault();
-        $('#edit-package-modal-form').submit();
     });
 
     $("#select_grantee").selectpicker();
 
     // Add click functions to permission checkboxes
-    $('[id^="read_"]').on('click', checkboxClick);
+    $('[id^="read_"]').on("click", checkboxClick);
-    $('[id^="write_"]').on('click', checkboxClick);
+    $('[id^="write_"]').on("click", checkboxClick);
-    $('[id^="owner_"]').on('click', checkboxClick);
+    $('[id^="owner_"]').on("click", checkboxClick);
-
+  });
-})
 </script>