reintroduces envipytags

Signed-off-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

envipath/settings.py

@@ -87,7 +87,6 @@ TEMPLATES = [
                 "django.template.context_processors.request",
                 "django.contrib.auth.context_processors.auth",
                 "django.contrib.messages.context_processors.messages",
-                "epdb.context_processors.package_context",
             ],
         },
     },

epdb/admin.py

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

epdb/context_processors.py

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

epdb/management/commands/bootstrap.py

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

epdb/migrations/0010_license_cc_string.py

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

epdb/migrations/0011_auto_20251111_1413.py

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

epdb/models.py

@@ -655,7 +655,6 @@ class ScenarioMixin(models.Model):
 
 
 class License(models.Model):
-    cc_string = models.TextField(blank=False, null=False, verbose_name="CC string")
     link = models.URLField(blank=False, null=False, verbose_name="link")
     image_link = models.URLField(blank=False, null=False, verbose_name="Image link")
 

epdb/tasks.py

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

epdb/urls.py

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

epdb/views.py

@@ -362,34 +362,6 @@ def index(request):
     return render(request, "index/index.html", context)
 
 
-def predict_pathway(request):
-    """Top-level predict pathway view using user's default package."""
-    if request.method != "GET":
-        return HttpResponseNotAllowed(["GET"])
-
-    context = get_base_context(request)
-    context["title"] = "enviPath - Predict Pathway"
-    context["meta"]["current_package"] = context["meta"]["user"].default_package
-
-    return render(request, "predict_pathway.html", context)
-
-
-@package_permission_required()
-def package_predict_pathway(request, package_uuid):
-    """Package-specific predict pathway view."""
-    if request.method != "GET":
-        return HttpResponseNotAllowed(["GET"])
-
-    current_user = _anonymous_or_real(request)
-    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-
-    context = get_base_context(request)
-    context["title"] = f"enviPath - {current_package.name} - Predict Pathway"
-    context["meta"]["current_package"] = current_package
-
-    return render(request, "predict_pathway.html", context)
-
-
 def packages(request):
     current_user = _anonymous_or_real(request)
 
@@ -710,6 +682,7 @@ def search(request):
     if request.method == "GET":
         package_urls = request.GET.getlist("packages")
         searchterm = request.GET.get("search", "").strip()
+
         mode = request.GET.get("mode")
 
         # add HTTP_ACCEPT check to differentiate between index and ajax call
@@ -810,7 +783,6 @@ 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")
 
@@ -971,12 +943,6 @@ 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()
@@ -1106,7 +1072,9 @@ def package(request, package_uuid):
         write = request.POST.get("write") == "on"
         owner = request.POST.get("owner") == "on"
 
-        cc_string = request.POST.get("license")
+        license = request.POST.get("license")
+        license_link = request.POST.get("license-link")
+        license_image_link = request.POST.get("license-image-link")
 
         if new_package_name:
             current_package.name = new_package_name
@@ -1134,15 +1102,24 @@ def package(request, package_uuid):
 
             PackageManager.update_permissions(current_user, current_package, grantee, max_perm)
             return redirect(current_package.url)
+        elif license is not None:
+            if license == "no-license":
+                if current_package.license is not None:
+                    current_package.license.delete()
 
-        elif cc_string is not None:
-            cc_string = cc_string.strip()
-            if cc_string == "no-license":  # Reset the package's license
                 current_package.license = None
                 current_package.save()
                 return redirect(current_package.url)
-            else:  # Get the license and assign it to the package
+            else:
-                current_package.license = License.objects.get(cc_string=cc_string)
+                if current_package.license is not None:
+                    current_package.license.delete()
+
+                license = License()
+                license.link = license_link
+                license.image_link = license_image_link
+                license.save()
+
+                current_package.license = license
                 current_package.save()
 
                 return redirect(current_package.url)
@@ -1197,7 +1174,7 @@ def package_compounds(request, package_uuid):
 
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
-        compound_smiles = request.POST.get("compound-smiles")
+        compound_smiles = request.POST.get("compound-smiles").strip()
         compound_description = request.POST.get("compound-description")
 
         c = Compound.create(current_package, compound_smiles, compound_name, compound_description)
@@ -1324,7 +1301,7 @@ 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")
+        structure_smiles = request.POST.get("structure-smiles").strip()
         structure_description = request.POST.get("structure-description")
 
         try:
@@ -1506,11 +1483,11 @@ def package_rules(request, package_uuid):
 
         # Obtain parameters as required by rule type
         if rule_type == "SimpleAmbitRule":
-            params["smirks"] = request.POST.get("rule-smirks")
+            params["smirks"] = request.POST.get("rule-smirks").strip()
             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")
+            params["reaction_smarts"] = request.POST.get("rule-reaction-smarts").strip()
         elif rule_type == "ParallelRule":
             pass
         elif rule_type == "SequentialRule":
@@ -1707,7 +1684,8 @@ def package_reactions(request, package_uuid):
     elif request.method == "POST":
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
-        reactions_smirks = request.POST.get("reaction-smirks")
+
+        reactions_smirks = request.POST.get("reaction-smirks").strip()
         educts = reactions_smirks.split(">>")[0].split(".")
         products = reactions_smirks.split(">>")[1].split(".")
 
@@ -2281,7 +2259,6 @@ 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")
 

static/css/input.css

@@ -30,7 +30,6 @@
 /* Import DaisyUI plugin */
 @plugin "daisyui" {
   logs: true;
-  exclude: rootscrollgutter;
 }
 
 @import "./daisyui-theme.css";

templates/actions/collections/compound.html

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

templates/actions/collections/compound_structure.html

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

templates/actions/collections/edge.html

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

templates/actions/collections/group.html

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

templates/actions/collections/model.html

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

templates/actions/collections/node.html

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

templates/actions/collections/package.html

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

templates/actions/collections/pathway.html

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

templates/actions/collections/reaction.html

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

templates/actions/collections/rule.html

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

templates/actions/collections/scenario.html

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

templates/actions/collections/setting.html

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

templates/actions/objects/compound.html

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

templates/actions/objects/compound_structure.html

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

templates/actions/objects/edge.html

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

templates/actions/objects/group.html

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

templates/actions/objects/model.html

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

templates/actions/objects/node.html

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

templates/actions/objects/package.html

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

templates/actions/objects/pathway.html

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

templates/actions/objects/reaction.html

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

templates/actions/objects/rule.html

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

templates/actions/objects/scenario.html

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

templates/actions/objects/user.html

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

templates/admin.html

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

templates/collections/joblog.html

@@ -1,38 +1,30 @@
 {% extends "framework.html" %}
 {% load static %}
-{% load envipytags %}
 {% block content %}
+
     <div class="panel-group" id="reviewListAccordion">
         <div class="panel panel-default">
-      <div
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-        class="panel-heading"
-        id="headingPanel"
-        style="font-size:2rem;height: 46px"
-      >
                 Jobs
             </div>
             <div class="panel-body">
-        <p>Job Logs Desc</p>
+                <p>
+                    Job Logs Desc
+                </p>
+
             </div>
 
-      <div
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-        class="panel panel-default panel-heading list-group-item"
-        style="background-color:silver"
-      >
                 <h4 class="panel-title">
-          <a
+                    <a id="job-accordion-link" data-toggle="collapse" data-parent="#job-accordion" href="#jobs">
-            id="job-accordion-link"
-            data-toggle="collapse"
-            data-parent="#job-accordion"
-            href="#jobs"
-          >
                         Jobs
                     </a>
                 </h4>
             </div>
-      <div id="jobs" class="panel-collapse in collapse">
+            <div id="jobs"
+                 class="panel-collapse collapse in">
                 <div class="panel-body list-group-item" id="job-content">
-          <table class="table-bordered table-hover table">
+                    <table class="table table-bordered table-hover">
                         <tr style="background-color: rgba(0, 0, 0, 0.08);">
                             <th scope="col">ID</th>
                             <th scope="col">Name</th>
@@ -64,12 +56,10 @@
             </div>
 
             <!-- Unreviewable objects such as User / Group / Setting -->
-      <ul class="list-group">
+            <ul class='list-group'>
                 {% for obj in objects %}
                     {% if object_type == 'user' %}
-            <a class="list-group-item" href="{{ obj.url }}"
+                        <a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
-              >{{ obj.username }}</a
-            >
                     {% else %}
                         <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
                     {% endif %}

templates/collections/objects_list.html

@@ -6,22 +6,14 @@
         <div>
             <div id="load-all-error" style="display: none;">
                 <div class="alert alert-danger" role="alert">
-          <span
+                    <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
-            class="glyphicon glyphicon-exclamation-sign"
-            aria-hidden="true"
-          ></span>
                     <span class="sr-only">Error:</span>
                     Getting objects failed!
                 </div>
             </div>
 
-      <input
+            <input type="text" id="object-search" class="form-control" placeholder="Search by name"
-        type="text"
+                   style="display: none;">
-        id="object-search"
-        class="form-control"
-        placeholder="Search by name"
-        style="display: none;"
-      />
             <p></p>
         </div>
     {% endif %}
@@ -56,13 +48,9 @@
         {% endif %}
     {% endblock action_modals %}
 
-  <div class="panel-group" id="reviewListAccordion">
+<div class="panel-group" id="reviewListAccordion">
     <div class="panel panel-default">
-      <div
+        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-        class="panel-heading"
-        id="headingPanel"
-        style="font-size:2rem;height: 46px"
-      >
             {% if object_type == 'package' %}
             Packages
             {% elif object_type == 'compound' %}
@@ -90,21 +78,12 @@
             {% elif object_type == 'group' %}
             Groups
             {% endif %}
-        <div
+            <div id="actionsButton"
-          id="actionsButton"
                  style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
-          class="dropdown"
+                 class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
-        >
+                                     aria-haspopup="true" aria-expanded="false"><span
-          <a
+                    class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
-            href="#"
+                    style="padding-right:1em"></span></a>
-            class="dropdown-toggle"
-            data-toggle="dropdown"
-            role="button"
-            aria-haspopup="true"
-            aria-expanded="false"
-            ><span class="glyphicon glyphicon-wrench"></span> Actions
-            <span class="caret"></span><span style="padding-right:1em"></span
-          ></a>
                 <ul id="actionsList" class="dropdown-menu">
                     {% block actions %}
                         {% if object_type == 'package' %}
@@ -139,204 +118,93 @@
         <div class="panel-body">
             <!-- Set Text above links -->
             {% if object_type == 'package' %}
-          <p>
+            <p>A package contains pathways, rules, etc. and can reflect specific experimental
-            A package contains pathways, rules, etc. and can reflect specific
+                conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
-            experimental conditions.
+                    more &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/packages"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'compound' %}
-          <p>
+            <p>A compound stores the structure of a molecule and can include meta-information.
-            A compound stores the structure of a molecule and can include
+                <a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
-            meta-information.
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/compounds"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'structure' %}
-          <p>
+            <p>The structures stored in this compound
-            The structures stored in this compound
+                <a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/compounds"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'rule' %}
-          <p>
+            <p>A rule describes a biotransformation reaction template that is defined as SMIRKS.
-            A rule describes a biotransformation reaction template that is
+                <a target="_blank" href="https://wiki.envipath.org/index.php/Rules" role="button">Learn more
-            defined as SMIRKS.
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/Rules"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'reaction' %}
-          <p>
+            <p>A reaction is a specific biotransformation from educt compounds to product compounds.
-            A reaction is a specific biotransformation from educt compounds to
+                <a target="_blank" href="https://wiki.envipath.org/index.php/reactions" role="button">Learn more
-            product compounds.
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/reactions"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'pathway' %}
-          <p>
+            <p>A pathway displays the (predicted) biodegradation of a compound as graph.
-            A pathway displays the (predicted) biodegradation of a compound as
+                <a target="_blank" href="https://wiki.envipath.org/index.php/pathways" role="button">Learn more
-            graph.
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/pathways"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'node' %}
-          <p>
+            <p>Nodes represent the (predicted) compounds in a graph.
-            Nodes represent the (predicted) compounds in a graph.
+                <a target="_blank" href="https://wiki.envipath.org/index.php/nodes" role="button">Learn more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/nodes"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'edge' %}
-          <p>
+            <p>Edges represent the links between Nodes in a graph
-            Edges represent the links between Nodes in a graph
+                <a target="_blank" href="https://wiki.envipath.org/index.php/edges" role="button">Learn more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/edges"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'scenario' %}
-          <p>
+            <p>A scenario contains meta-information that can be attached to other data (compounds, rules, ..).
-            A scenario contains meta-information that can be attached to other
+                <a target="_blank" href="https://wiki.envipath.org/index.php/scenarios" role="button">Learn more
-            data (compounds, rules, ..).
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/scenarios"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'model' %}
-          <p>
+            <p>A model applies machine learning to limit the combinatorial explosion.
-            A model applies machine learning to limit the combinatorial
+                <a target="_blank" href="https://wiki.envipath.org/index.php/relative_reasoning" role="button">Learn
-            explosion.
+                    more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/relative_reasoning"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'setting' %}
-          <p>
+            <p>A setting includes configuration parameters for pathway predictions.
-            A setting includes configuration parameters for pathway predictions.
+                <a target="_blank" href="https://wiki.envipath.org/index.php/settings" role="button">Learn more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/settings"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'user' %}
-          <p>
+            <p>Register now to create own packages and to submit and manage your data.
-            Register now to create own packages and to submit and manage your
+                <a target="_blank" href="https://wiki.envipath.org/index.php/users" role="button">Learn more
-            data.
+                    &gt;&gt;</a></p>
-            <a
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/users"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% elif object_type == 'group' %}
-          <p>
+            <p>Users can team up in groups to share packages.
-            Users can team up in groups to share packages.
+                <a target="_blank" href="https://wiki.envipath.org/index.php/groups" role="button">Learn more
-            <a
+                    &gt;&gt;</a></p>
-              target="_blank"
-              href="https://wiki.envipath.org/index.php/groups"
-              role="button"
-              >Learn more &gt;&gt;</a
-            >
-          </p>
             {% endif %}
 
             <!-- If theres nothing to show extend the text above -->
             {% if reviewed_objects and unreviewed_objects %}
             {% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %}
-            <p>
+            <p>Nothing found. There are two possible reasons: <br><br>1. There is no content yet.<br>2. You have no
-              Nothing found. There are two possible reasons: <br /><br />1.
+                reading permissions.<br><br>Please be sure you have at least reading permissions.</p>
-              There is no content yet.<br />2. You have no reading
-              permissions.<br /><br />Please be sure you have at least reading
-              permissions.
-            </p>
             {% endif %}
             {% endif %}
         </div>
         {% if reviewed_objects %}
         {% if reviewed_objects|length > 0 %}
-          <div
+        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            class="panel panel-default panel-heading list-group-item"
-            style="background-color:silver"
-          >
             <h4 class="panel-title">
-              <a
+                <a id="ReviewedLink" data-toggle="collapse" data-parent="#reviewListAccordion"
-                id="ReviewedLink"
+                   href="#Reviewed">Reviewed</a>
-                data-toggle="collapse"
-                data-parent="#reviewListAccordion"
-                href="#Reviewed"
-                >Reviewed</a
-              >
             </h4>
         </div>
-          <div id="Reviewed" class="panel-collapse in collapse">
+        <div id="Reviewed" class="panel-collapse collapse in">
             <div class="panel-body list-group-item" id="ReviewedContent">
                 {% if object_type == 'package' %}
                 {% for obj in reviewed_objects %}
-                  <a class="list-group-item" href="{{ obj.url }}"
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}
-                    >{{ obj.name|safe }}
+                    <span class="glyphicon glyphicon-star" aria-hidden="true"
-                    <span
+                          style="float:right" data-toggle="tooltip"
-                      class="glyphicon glyphicon-star"
+                          data-placement="top" title="" data-original-title="Reviewed">
-                      aria-hidden="true"
-                      style="float:right"
-                      data-toggle="tooltip"
-                      data-placement="top"
-                      title=""
-                      data-original-title="Reviewed"
-                    >
                         </span>
                 </a>
                 {% endfor %}
                 {% else %}
                 {% for obj in reviewed_objects|slice:":50" %}
-                  <a class="list-group-item" href="{{ obj.url }}"
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
-                    >{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
+                    <span class="glyphicon glyphicon-star" aria-hidden="true"
-                    <span
+                          style="float:right" data-toggle="tooltip"
-                      class="glyphicon glyphicon-star"
+                          data-placement="top" title="" data-original-title="Reviewed">
-                      aria-hidden="true"
-                      style="float:right"
-                      data-toggle="tooltip"
-                      data-placement="top"
-                      title=""
-                      data-original-title="Reviewed"
-                    >
                         </span>
                 </a>
                 {% endfor %}
@@ -346,36 +214,18 @@
         {% endif %}
         {% endif %}
         {% if unreviewed_objects %}
-        <div
+        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver"><h4
-          class="panel panel-default panel-heading list-group-item"
+                class="panel-title"><a id="UnreviewedLink" data-toggle="collapse" data-parent="#unReviewListAccordion"
-          style="background-color:silver"
+                                       href="#Unreviewed">Unreviewed</a></h4></div>
-        >
+        <div id="Unreviewed" class="panel-collapse collapse {% if reviewed_objects|length == 0 or object_type == 'package' %}in{% endif %}">
-          <h4 class="panel-title">
-            <a
-              id="UnreviewedLink"
-              data-toggle="collapse"
-              data-parent="#unReviewListAccordion"
-              href="#Unreviewed"
-              >Unreviewed</a
-            >
-          </h4>
-        </div>
-        <div
-          id="Unreviewed"
-          class="panel-collapse {% if reviewed_objects|length == 0 or object_type == 'package' %}in{% endif %} collapse"
-        >
             <div class="panel-body list-group-item" id="UnreviewedContent">
                 {% if object_type == 'package' %}
                 {% for obj in unreviewed_objects %}
-                <a class="list-group-item" href="{{ obj.url }}"
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
-                  >{{ obj.name|safe }}</a
-                >
                 {% endfor %}
                 {% else %}
                 {% for obj in unreviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}"
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
-                  >{{ obj.name|safe }}</a
-                >
                 {% endfor %}
                 {% endif %}
             </div>
@@ -383,16 +233,12 @@
         {% endif %}
         {% if objects %}
         <!-- Unreviewable objects such as User / Group / Setting -->
-        <ul class="list-group">
+        <ul class='list-group'>
             {% for obj in objects %}
             {% if object_type == 'user' %}
-              <a class="list-group-item" href="{{ obj.url }}"
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username|safe }}</a>
-                >{{ obj.username|safe }}</a
-              >
             {% else %}
-              <a class="list-group-item" href="{{ obj.url }}"
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
-                >{{ obj.name|safe }}</a
-              >
             {% endif %}
             {% endfor %}
         </ul>
@@ -415,14 +261,10 @@
     </style>
 
     <div id="load-all-loading" class="spinner-widget" style="display: none">
-      <img
+        <img id="loading-gif" src="{% static '/images/wait.gif' %}" alt="Loading...">
-        id="loading-gif"
-        src="{% static '/images/wait.gif' %}"
-        alt="Loading..."
-      />
     </div>
-  </div>
+
-  {# prettier-ignore-start #}
+</div>
     <script>
         $(function () {
 
@@ -474,5 +316,4 @@
 
         });
     </script>
-    {# prettier-ignore-end #}
 {% endblock content %}

templates/compare.html

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

templates/errors/400_bad_request.html

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

templates/errors/403_access_denied.html

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

templates/errors/404_not_found.html

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

templates/errors/error.html

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

templates/errors/user_account_inactive.html

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

templates/framework.html

@@ -1,15 +1,11 @@
-<!doctype html>
+<!DOCTYPE html>
 <html data-theme="envipath">
-  {% load static %}
+{% load static %}
-  <head>
+<head>
     <title>{{ title }}</title>
-    <meta name="csrf-token" content="{{ csrf_token }}" />
+    <meta name="csrf-token" content="{{ csrf_token }}">
     {# Favicon #}
-    <link
+    <link rel="shortcut icon" type="image/png" href="{% static 'images/favicon.ico' %}"/>
-      rel="shortcut icon"
-      type="image/png"
-      href="{% static 'images/favicon.ico' %}"
-    />
 
     {# Tailwind CSS disabled for legacy Bootstrap framework #}
     {# Pages using this framework will be migrated to framework_modern.html incrementally #}
@@ -17,20 +13,12 @@
 
     {# 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
+    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
-      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
+    <link href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
-      href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css"
+    <link rel="stylesheet"
-      rel="stylesheet"
+          href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.css">
-    />
-    <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 -->
@@ -38,23 +26,22 @@
     {# Bootstrap compatibility styles #}
     <style>
         /* Ensure proper viewport behavior */
-      html,
+        html, body {
-      body {
             height: 100%; /* ensure body fills viewport */
             overflow-x: hidden; /* prevent horizontal scroll */
         }
     </style>
 
     <script>
-      const csrftoken = document.querySelector("[name=csrf-token]").content;
+        const csrftoken = document.querySelector('[name=csrf-token]').content;
 
         // Setup CSRF header for all jQuery AJAX requests
         $.ajaxSetup({
-        beforeSend: function (xhr, settings) {
+            beforeSend: function(xhr, settings) {
                 if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
                     xhr.setRequestHeader("X-CSRFToken", csrftoken);
                 }
-        },
+            }
         });
     </script>
 
@@ -63,6 +50,7 @@
     <!--    {# EP CSS #}-->
     <!--    <link id="css-pps_white_general" href="{% static 'css/epp.css' %}" rel="stylesheet" type="text/css"/>-->
 
+
     {# General EP JS #}
     <script src="{% static 'js/pps.js' %}"></script>
     {# Modal Steps for Stepwise Modal Wizards #}
@@ -71,33 +59,28 @@
     {% if not debug %}
         <!-- Matomo -->
         <script>
-        var _paq = (window._paq = window._paq || []);
+            var _paq = window._paq = window._paq || [];
             /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
-        _paq.push(["trackPageView"]);
+            _paq.push(['trackPageView']);
-        _paq.push(["enableLinkTracking"]);
+            _paq.push(['enableLinkTracking']);
             (function () {
                 var u = "//matomo.envipath.com/";
-          _paq.push(["setTrackerUrl", u + "matomo.php"]);
+                _paq.push(['setTrackerUrl', u + 'matomo.php']);
-          _paq.push(["setSiteId", "{{ meta.site_id }}"]);
+                _paq.push(['setSiteId', '{{ meta.site_id }}']);
-          var d = document,
+                var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
-            g = d.createElement("script"),
-            s = d.getElementsByTagName("script")[0];
                 g.async = true;
-          g.src = u + "matomo.js";
+                g.src = u + 'matomo.js';
                 s.parentNode.insertBefore(g, s);
             })();
         </script>
         <!-- End Matomo Code -->
     {% endif %}
-  </head>
+
-  <body>
+</head>
-    <!-- Legacy Bootstrap navbar - isolated from Tailwind -->
+<body>
-    <div class="legacy-bootstrap">
+<!-- Legacy Bootstrap navbar - isolated from Tailwind -->
-      <nav
+<div class="legacy-bootstrap">
-        class="navbar navbar-default navbar-inverse"
+<nav class="navbar navbar-default navbar-inverse" style="border-radius:0px;" role="navigation">
-        style="border-radius:0px;"
-        role="navigation"
-      >
     <div class="container-fluid">
         <!-- Brand and toggle get grouped for better mobile display -->
         <div class="navbar-header navbar-header-framework">
@@ -108,181 +91,95 @@
             <!--                <span class="icon-bar"></span>-->
             <!--                <span class="icon-bar"></span>-->
             <!--            </button>-->
-            <a
+            <a id="pictureLink" href="{{ meta.server_url }}" class="navbar-brand">
-              id="pictureLink"
+                <img id="image-logo-short-white.svg" src='{% static "/images/logo-short-white.svg" %}' width="100"
-              href="{{ meta.server_url }}"
+                     alt="enviPath">
-              class="navbar-brand"
-            >
-              <img
-                id="image-logo-short-white.svg"
-                src="{% static "/images/logo-short-white.svg" %}"
-                width="100"
-                alt="enviPath"
-              />
             </a>
         </div>
 
         <!-- Collect the nav links, forms, and other content for toggling -->
-          <div
+        <div class="collapse navbar-collapse collapse-framework navbar-collapse-framework" id="navbarCollapse">
-            class="navbar-collapse collapse-framework navbar-collapse-framework collapse"
-            id="navbarCollapse"
-          >
             <ul class="nav navbar-nav navbar-nav-framework">
                 <li>
-                <a href="{{ meta.server_url }}/predict"> Predict Pathway </a>
+                    <a href="#" data-toggle="modal" data-target="#predict_modal">
-              </li>
+                        Predict Pathway
-              {#                <li class="dropdown">#}
+                    </a>
-              {#                    <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 }}/model" id="modelLink"
-                  >Modelling</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="#"
+                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Browse Data<b class="caret"></b></a>
-                  >Browse Data<b class="caret"></b
-                ></a>
                     <ul role="menu" class="dropdown-menu">
-                  <li>
+                        <li><a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a></li>
-                    <a href="{{ meta.server_url }}/pathway" id="pathwayLink"
+                        <li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
-                      >Pathway</a
+                        <li><a href="{{ meta.server_url }}/compound" id="compoundLink">Compound</a></li>
-                    >
+                        <li><a href="{{ meta.server_url }}/reaction" id="reactionLink">Reaction</a></li>
-                  </li>
+                        <li><a href="{{ meta.server_url }}/model" id="relative-reasoningLink">Model</a></li>
-                  <li>
+                        <li><a href="{{ meta.server_url }}/scenario" id="scenarioLink">Scenario</a></li>
-                    <a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a>
-                  </li>
-                  <li>
-                    <a href="{{ meta.server_url }}/compound" id="compoundLink"
-                      >Compound</a
-                    >
-                  </li>
-                  <li>
-                    <a href="{{ meta.server_url }}/reaction" id="reactionLink"
-                      >Reaction</a
-                    >
-                  </li>
-                  <li>
-                    <a
-                      href="{{ meta.server_url }}/model"
-                      id="relative-reasoningLink"
-                      >Model</a
-                    >
-                  </li>
-                  <li>
-                    <a href="{{ meta.server_url }}/scenario" id="scenarioLink"
-                      >Scenario</a
-                    >
-                  </li>
                         {#                        <li><a href="{{ meta.server_url }}/setting" id="settingLink">Setting</a></li>#}
                         {#                        <li><a href="{{ meta.server_url }}/user" id="userLink">User</a></li>#}
                         {#                        <li><a href="{{ meta.server_url }}/group" id="groupLink">Group</a></li>#}
                     </ul>
                 </li>
+
             </ul>
 
-            <ul
+            <ul class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework">
-              class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework"
+                <li><a href="https://community.envipath.org/" id="communityLink">Community</a></li>
-            >
-              <li>
-                <a href="https://community.envipath.org/" id="communityLink"
-                  >Community</a
-                >
-              </li>
                 <li class="dropdown">
-                <a data-toggle="dropdown" class="dropdown-toggle" href="#"
+                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Info <b class="caret"></b></a>
-                  >Info <b class="caret"></b
-                ></a>
                     <ul role="menu" class="dropdown-menu">
                         <!--<li><a href="{{ meta.server_url }}/funding" id="fundingLink">Funding</a></li>-->
-                  <li>
+                        <li><a href="https://community.envipath.org/t/envipath-license/109" id="licenceLink">Licences</a></li>
-                    <a
-                      href="https://community.envipath.org/t/envipath-license/109"
-                      id="licenceLink"
-                      >Licences</a
-                    >
-                  </li>
                         <li class="divider"></li>
-                  <li>
+                        <li><a target="_blank" href="https://wiki.envipath.org/" id="wikiLink">Documentation Wiki</a>
-                    <a
-                      target="_blank"
-                      href="https://wiki.envipath.org/"
-                      id="wikiLink"
-                      >Documentation Wiki</a
-                    >
-                  </li>
-                  <li>
-                    <a
-                      href="#"
-                      id="citeButton"
-                      data-toggle="modal"
-                      data-target="#citemodal"
-                      >How to cite enviPath</a
-                    >
                         </li>
+                        <li><a href="#" id="citeButton" data-toggle="modal" data-target="#citemodal">How to cite
+                            enviPath</a></li>
                         <li class="divider"></li>
                         <li><a>Version: {{ meta.version }}</a></li>
                     </ul>
                 </li>
                 {% if meta.user.username == 'anonymous' %}
                     <li>
-                  <a
+                        <a href="{% url 'login' %}" id="loginButton" style="margin-right:10px">Login</a>
-                    href="{% url 'login' %}"
-                    id="loginButton"
-                    style="margin-right:10px"
-                    >Login</a
-                  >
                     </li>
                 {% else %}
                     <li class="dropdown">
-                  <a
+                        <a data-toggle="dropdown" id="loggedInButton" class="dropdown-toggle" id="logedInButton"
-                    data-toggle="dropdown"
+                           href="#">
-                    id="loggedInButton"
-                    class="dropdown-toggle"
-                    id="logedInButton"
-                    href="#"
-                  >
                             <div id="username">
                                 {{ user.username }}<b class="caret"></b>
                             </div>
                         </a>
                         <ul role="menu" class="dropdown-menu">
                             <li>
-                      <a href="{{ meta.user.url }}" id="accountbutton"
+                                <a href="{{ meta.user.url }}" id="accountbutton">My Account</a>
-                        >My Account</a
-                      >
                             </li>
                             <li class="divider"></li>
-                    <form
+                            <form class="navbar-form navbar-left navbar-left-framework" role="logout"
-                      class="navbar-form navbar-left navbar-left-framework"
+                                  action="{% url 'logout' %}" method="post">
-                      role="logout"
-                      action="{% url 'logout' %}"
-                      method="post"
-                    >
                                 {% csrf_token %}
                                 <div class="form-group">
-                        <input type="hidden" name="logout" value="true" />
+                                    <input type="hidden" name="logout" value="true">
                                 </div>
-                      <button type="submit" class="btn btn-default">
+                                <button type="submit" class="btn btn-default">Logout</button>
-                        Logout
-                      </button>
                             </form>
                         </ul>
                     </li>
@@ -290,11 +187,11 @@
             </ul>
         </div>
     </div>
-      </nav>
+</nav>
-    </div>
+</div>
-    <!-- End legacy Bootstrap navbar -->
+<!-- End legacy Bootstrap navbar -->
 
-    <div id="docContent" class="content container">
+<div id="docContent" class="content container">
     {% if breadcrumbs %}
         <div id="bread">
             <ol class="breadcrumb">
@@ -313,105 +210,85 @@
         </div>
     {% endif %}
     {% if message %}
-        <div id="message">{{ message }}</div>
+        <div id="message">
+            {{ message }}
+        </div>
     {% endif %}
     {% block content %}
     {% endblock content %}
     {% if meta.url_contains_package and meta.current_package.license %}
         <p></p>
         <div class="panel-group" id="license_accordion">
-          <div
+            <div class="panel panel-default list-group-item" style="background-color:#f5f5f5">
-            class="panel panel-default list-group-item"
-            style="background-color:#f5f5f5"
-          >
                 <div class="panel-title">
-              <a
+                    <a data-toggle="collapse" data-parent="#licence_accordion" href="#license">License</a>
-                data-toggle="collapse"
-                data-parent="#licence_accordion"
-                href="#license"
-                >License</a
-              >
                 </div>
             </div>
-          <div id="license" class="panel-collapse in collapse">
+            <div id="license" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     <a target="_blank" href="{{ meta.current_package.license.link }}">
-                <img src="{{ meta.current_package.license.image_link }}" />
+                        <img src="{{ meta.current_package.license.image_link }}">
                     </a>
                 </div>
             </div>
         </div>
     {% endif %}
-    </div>
+</div>
 
-    <!-- FOOTER - Legacy Bootstrap -->
+<!-- FOOTER - Legacy Bootstrap -->
-    <div class="legacy-bootstrap">
+<div class="legacy-bootstrap">
-      <div class="container text-center">
+<div class="container text-center">
-        <hr />
+    <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
+                        <img id="image-uoalogo" height="60" src='{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}'
-                    id="image-uoalogo"
+                             alt="The Univserity of Auckland"/>
-                    height="60"
-                    src="{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}"
-                    alt="The Univserity of Auckland"
-                  />
                     </a>
                 </li>
                 <li>
                     <a href="https://eawag.ch" target="_blank">
-                  <img
+                        <img id="image-ealogo" height="60" src='{% static "/images/ealogo.gif" %}' alt="Eawag"/>
-                    id="image-ealogo"
-                    height="60"
-                    src="{% static "/images/ealogo.gif" %}"
-                    alt="Eawag"
-                  />
                     </a>
                 </li>
                 <li>
                     <a href="https://www.uzh.ch/" target="_blank">
-                  <img
+                        <img id="image-ufzlogo" height="60" src='{% static "/images/uzh-logo.svg" %}'
-                    id="image-ufzlogo"
+                             alt="University of Zurich"/>
-                    height="60"
-                    src="{% static "/images/uzh-logo.svg" %}"
-                    alt="University of Zurich"
-                  />
                     </a>
                 </li>
             </ul>
         </div>
     </div>
-      </div>
+</div>
-      <div class="row">
+<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>
+            <li><a href="mailto:admin@envipath.org" target="_blank">Contact</a></li>
-              <a href="mailto:admin@envipath.org" target="_blank">Contact</a>
-            </li>
             <!--            <li><a href="http://envipath.com" target="_blank"> enviPath UG (haftungsbeschr&auml;nkt) &amp; Co. KG &copy;-->
             <!--                {{ YEAR }}</a></li>-->
         </ul>
     </div>
-      </div>
+</div>
-    </div>
+</div>
-    <!-- End legacy Bootstrap footer -->
+<!-- End legacy Bootstrap footer -->
 
-    <script>
+<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/signup_modal.html" %}
     {% include "modals/predict_modal.html" %}
     {% include "modals/batch_predict_modal.html" %}
-    {% endblock %}
+{% endblock %}
-  </body>
+</body>
 </html>

templates/framework_modern.html

@@ -1,48 +1,37 @@
-<!doctype html>
+<!DOCTYPE html>
 <html data-theme="envipath" lang="en">
-  {% load static %}
+{% load static %}
-  <head>
+<head>
     <title>{{ title }}</title>
-    <meta charset="UTF-8" />
+    <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <meta name="csrf-token" content="{{ csrf_token }}" />
+    <meta name="csrf-token" content="{{ csrf_token }}">
 
     {# Favicon #}
-    <link
+    <link rel="shortcut icon" type="image/png" href="{% static 'images/favicon.ico' %}"/>
-      rel="shortcut icon"
-      type="image/png"
-      href="{% static 'images/favicon.ico' %}"
-    />
 
     {# Tailwind CSS + DaisyUI Output #}
-    <link
+    <link href="{% static 'css/output.css' %}" rel="stylesheet" type="text/css"/>
-      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
+    <link href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
-      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;
+        const csrftoken = document.querySelector('[name=csrf-token]').content;
 
         // Setup CSRF header for all jQuery AJAX requests
         $.ajaxSetup({
-        beforeSend: function (xhr, settings) {
+            beforeSend: function(xhr, settings) {
                 if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
                     xhr.setRequestHeader("X-CSRFToken", csrftoken);
                 }
-        },
+            }
         });
     </script>
 
@@ -54,25 +43,23 @@
     {% if not debug %}
         <!-- Matomo -->
         <script>
-        var _paq = (window._paq = window._paq || []);
+            var _paq = window._paq = window._paq || [];
-        _paq.push(["trackPageView"]);
+            _paq.push(['trackPageView']);
-        _paq.push(["enableLinkTracking"]);
+            _paq.push(['enableLinkTracking']);
             (function () {
                 var u = "//matomo.envipath.com/";
-          _paq.push(["setTrackerUrl", u + "matomo.php"]);
+                _paq.push(['setTrackerUrl', u + 'matomo.php']);
-          _paq.push(["setSiteId", "{{ meta.site_id }}"]);
+                _paq.push(['setSiteId', '{{ meta.site_id }}']);
-          var d = document,
+                var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
-            g = d.createElement("script"),
-            s = d.getElementsByTagName("script")[0];
                 g.async = true;
-          g.src = u + "matomo.js";
+                g.src = u + 'matomo.js';
                 s.parentNode.insertBefore(g, s);
             })();
         </script>
         <!-- End Matomo Code -->
     {% endif %}
-  </head>
+</head>
-  <body class="bg-base-300 min-h-screen">
+<body class="min-h-screen bg-base-300">
     {% include "includes/navbar.html" %}
 
     {# Main Content Area #}
@@ -80,8 +67,8 @@
         {% block main_content %}
             {# Breadcrumbs - outside main content, optional #}
             {% if breadcrumbs %}
-          <div id="bread" class="mx-auto max-w-7xl px-4 py-4">
+                <div id="bread" class="max-w-7xl mx-auto px-4 py-4">
-            <div class="breadcrumbs text-sm">
+                    <div class="text-sm breadcrumbs">
                         <ul>
                             {% for elem in breadcrumbs %}
                                 {% for name, url in elem.items %}
@@ -98,13 +85,12 @@
             {% endif %}
 
             {# Main content container - paper effect on medium+ screens #}
-        <div
+            <div id="docContent" class="w-full xl:w-xl md:mx-auto md:my-8 bg-base-100 md:shadow-2xl md:rounded-lg border-2">
-          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>
+                    <div id="message" class="alert alert-info m-4">
+                        {{ message }}
+                    </div>
                 {% endif %}
 
                 {# Page content - no enforced styles #}
@@ -113,18 +99,14 @@
 
                 {# 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">
+                    <div class="collapse collapse-arrow bg-base-200 m-8">
                         <input type="checkbox" checked />
-              <div class="collapse-title text-xl font-medium">License</div>
+                        <div class="collapse-title text-xl font-medium">
+                            License
+                        </div>
                         <div class="collapse-content">
-                <a
+                            <a target="_blank" href="{{ meta.current_package.license.link }}">
-                  target="_blank"
+                                <img src="{{ meta.current_package.license.image_link }}" alt="License">
-                  href="{{ meta.current_package.license.link }}"
-                >
-                  <img
-                    src="{{ meta.current_package.license.image_link }}"
-                    alt="License"
-                  />
                             </a>
                         </div>
                     </div>
@@ -137,73 +119,44 @@
 
     {# Floating Help Tab #}
     {% if not public_mode %}
-      <div class="fixed top-1/2 right-0 z-50 -translate-y-1/2">
+    <div class="fixed right-0 top-1/2 -translate-y-1/2 z-50">
-        <a
+        <a href="https://community.envipath.org/" target="_blank"
-          href="https://community.envipath.org/"
+           class="flex items-center justify-center btn btn-secondary hover:btn-secondary-focus text-secondary-content text-sm shadow-lg transition-all duration-300 hover:scale-105 hover:-translate-x-1"
-          target="_blank"
+           title="Get Help from the Community">
-          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"
+            <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"/>
-          title="Get Help from the Community"
+                <path d="M12 17h.01"/>
-        >
-          <svg
-            xmlns="http://www.w3.org/2000/svg"
-            width="24"
-            height="24"
-            viewBox="0 0 24 24"
-            fill="none"
-            stroke="currentColor"
-            stroke-width="2"
-            stroke-linecap="round"
-            stroke-linejoin="round"
-            class="lucide lucide-message-circle-question-mark-icon lucide-message-circle-question-mark"
-          >
-            <path
-              d="M2.992 16.342a2 2 0 0 1 .094 1.167l-1.065 3.29a1 1 0 0 0 1.236 1.168l3.413-.998a2 2 0 0 1 1.099.092 10 10 0 1 0-4.777-4.719"
-            />
-            <path d="M9.09 9a3 3 0 0 1 5.83 1c0 2-3 3-3 3" />
-            <path d="M12 17h.01" />
             </svg>
         </a>
     </div>
     {% endif %}
 
+    {# Modals - TODO: Convert these to DaisyUI modals #}
     {% block modals %}
-      {% include "modals/search_modal.html" %}
+        {# Note: These modals still use Bootstrap markup and will need conversion #}
+        {% include "modals/cite_modal.html" %}
+        {% include "modals/signup_modal.html" %}
+        {% include "modals/predict_modal.html" %}
+        {% include "modals/batch_predict_modal.html" %}
     {% endblock %}
 
     <script>
         $(function () {
             // Hide actionsbutton if there's no action defined
-        if ($("#actionsButton ul").children().length > 0) {
+            if ($('#actionsButton ul').children().length > 0) {
-          $("#actionsButton").show();
+                $('#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) {
+        document.addEventListener('keydown', function(event) {
             // Check if user is typing in an input field
             const activeElement = document.activeElement;
-        const isInputField =
+            const isInputField = activeElement && (
-          activeElement &&
+                activeElement.tagName === 'INPUT' ||
-          (activeElement.tagName === "INPUT" ||
+                activeElement.tagName === 'TEXTAREA' ||
-            activeElement.tagName === "TEXTAREA" ||
+                activeElement.contentEditable === 'true'
-            activeElement.contentEditable === "true");
+            );
 
             if (isInputField) {
                 return; // Don't trigger shortcut when typing in input fields
@@ -213,11 +166,11 @@
             const isMac = /Mac/.test(navigator.platform);
             const isCorrectModifier = isMac ? event.metaKey : event.ctrlKey;
 
-        if (isCorrectModifier && event.key === "k") {
+            if (isCorrectModifier && event.key === 'k') {
                 event.preventDefault();
-          openSearchModal();
+                window.location.href = '/search';
             }
         });
     </script>
-  </body>
+</body>
 </html>

templates/includes/footer.html

@@ -1,20 +1,17 @@
 {% load static %}
-<div class="bg-base-300 text-base-content mx-auto mt-10 lg:max-w-5xl">
+<div class="lg:max-w-5xl mt-10 mx-auto bg-base-300 text-base-content">
+
     <footer class="footer sm:footer-horizontal p-10">
         {% if not public_mode %}
         <nav>
             <h6 class="footer-title">Services</h6>
-        <a class="link link-hover" href="/predict">Predict</a>
+            <a class="link link-hover" href="/">Predict</a>
-        <a class="link link-hover" href="/package">Packages</a>
+            <a class="link link-hover" href="/search">Search</a>
+            <a class="link link-hover" href="/package">Browse</a>
             {% if user.is_authenticated %}
             <a class="link link-hover" href="/model">Your Collections</a>
             {% endif %}
-        <a
+            <a href="https://wiki.envipath.org/" target="_blank" class="link link-hover">Documentation</a>
-          href="https://wiki.envipath.org/"
-          target="_blank"
-          class="link link-hover"
-          >Documentation</a
-        >
     </nav>
         {% endif %}
     <nav>
@@ -32,61 +29,39 @@
       <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">
+  <footer class="footer border-neutral-300 border-t-2 px-10 py-4">
-    <div class="flex w-full flex-row items-start justify-between">
+    <div class="flex flex-row justify-between w-full items-start">
       <aside class="grid-flow-col items-center">
-        <svg
+          <svg class="fill-neutral-content flex-shrink-0 h-14 m-2" viewbox="0 0 65 65" >
-          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>
+              >
+              </use>
             </svg>
 
           enviPath Ltd.
           <br />
           Biodegredation prediction since 2015.
+        </p>
       </aside>
-      <aside class="text-base-200 mt-2 text-sm">
+      <aside class="text-sm text-base-200 mt-2"><span class="text-xs tracking-tight">Version</span> <span class="text-base font-bold">{{ meta.version }}</span></aside>
-        <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
+            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
-            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
+                <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"/>
-              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
+            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
-            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
+                <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"/>
-              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
+            <img src="{% static "/images/linkedin.png" %}" alt="LinkedIn" class="w-6 h-6">
-            src="{% static "/images/linkedin.png" %}"
-            alt="LinkedIn"
-            class="h-6 w-6"
-          />
         </a>
       </div>
     </nav>

templates/includes/navbar.html

@@ -1,58 +1,28 @@
 {% load static %}
 {# Modern DaisyUI Navbar #}
-<div class="navbar x-50 bg-neutral-50 text-neutral-950 shadow-lg">
+<div class="navbar bg-neutral-50 text-neutral-950 shadow-lg x-50">
     <div class="navbar-start">
-    <a href="{{ meta.server_url }}" class="btn btn-ghost text-xl normal-case">
+        <a href="{{ meta.server_url }}" class="btn btn-ghost normal-case text-xl">
-      <svg class="fill-base-content h-8" viewBox="0 0 104 26" role="img">
+            <svg class="h-8 fill-base-content" viewBox="0 0 104 26"  role="img">
-        <use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
+                <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
+        <a href="#" role="button" class="btn btn-ghost" id="predictLink">Predict</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
+            <ul tabindex="-1" class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm">
-          tabindex="-1"
+                <li><a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a></li>
-          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>
+                <li><a href="{{ meta.server_url }}/compound" id="compoundLink">Compound</a></li>
-            <a href="{{ meta.server_url }}/compound" id="compoundLink"
+                <li><a href="{{ meta.server_url }}/reaction" id="reactionLink">Reaction</a></li>
-              >Compound</a
+                <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>
-          <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>
@@ -60,25 +30,9 @@
 
     <div class="navbar-end">
         {% if not public_mode %}
-      <a id="search-trigger" role="button" class="cursor-pointer">
+        <a href="/search" role="button" >
-        <div
+            <div class="flex items-center badge badge-dash space-x-1 bg-base-200 text-base-content/50 p-2 m-1">
-          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>
-        >
-          <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>
@@ -87,50 +41,17 @@
             <a href="{% url 'login' %}" id="loginButton" class="p-2">Login</a>
         {% else %}
             <div class="dropdown dropdown-end">
-        <div
+                <div tabindex="0" role="button" class="btn btn-ghost m-1 btn-circle" id="loggedInButton">
-          tabindex="0"
+                    <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>
-          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
+                <ul tabindex="-1" class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2 shadow-sm">
-          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
+                        <form id="logoutForm" action="{% url 'logout' %}" method="post" style="display: none;">
-              id="logoutForm"
-              action="{% url 'logout' %}"
-              method="post"
-              style="display: none;"
-            >
                             {% csrf_token %}
-              <input type="hidden" name="logout" value="true" />
+                            <input type="hidden" name="logout" value="true">
                         </form>
-            <a
+                        <a href="#" id="logoutButton" onclick="event.preventDefault(); document.getElementById('logoutForm').submit();">Logout</a>
-              href="#"
-              id="logoutButton"
-              onclick="event.preventDefault(); document.getElementById('logoutForm').submit();"
-              >Logout</a
-            >
                     </li>
                 </ul>
             </div>
@@ -140,11 +61,11 @@
 
 <script>
     // OS-aware search shortcut display
-  (function () {
+    (function() {
         const isMac = /Mac/.test(navigator.platform);
-    const shortcutElement = document.getElementById("search-shortcut");
+        const shortcutElement = document.getElementById('search-shortcut');
         if (shortcutElement) {
-      shortcutElement.textContent = isMac ? "⌘K" : "Ctrl+K";
+            shortcutElement.textContent = isMac ? '⌘K' : 'Ctrl+K';
         }
     })();
 </script>

templates/index/index.html

@@ -1,45 +1,34 @@
 {% extends "framework_modern.html" %}
 {% load static %}
 {% block main_content %}
+
     <!-- Hero Section with Logo and Search -->
-  <section class="hero relative mx-auto h-fit w-full max-w-5xl shadow-none">
+<section class="hero h-fit max-w-5xl w-full shadow-none mx-auto relative">
-    <div
+
-      class="hero from-primary-800 to-primary-600 min-h-[calc(100vh*0.4)] bg-gradient-to-br"
+        <div class="hero min-h-[calc(100vh*0.4)] bg-gradient-to-br from-primary-800 to-primary-600"
             style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
             >
             <div class="hero-overlay"></div>
             <!-- Predict Pathway text over the image -->
-      <div class="absolute bottom-40 left-1/8 z-10 -translate-x-8">
+            <div class="absolute bottom-40 left-1/8 -translate-x-8 z-10">
-        <h2 class="text-base-100 text-left text-3xl text-shadow-lg">
+                <h2 class="text-3xl text-base-100 text-shadow-lg text-left">Predict Your Pathway</h2>
-          Predict Your Pathway
-        </h2>
             </div>
         </div>
-  </section>
+</section>
+
+<div class="shadow-md max-w-5xl mx-auto bg-base-200">
 
-  <div class="bg-base-200 mx-auto max-w-5xl shadow-md">
     <!-- Predict Pathway Section -->
-    <div
+    <div class="flex-col lg:flex-row-reverse w-full mx-auto -mt-32 relative z-20 mb-10 ">
-      class="relative z-20 mx-auto -mt-32 mb-10 w-full flex-col lg:flex-row-reverse"
+        <div class="card bg-base-100 shrink-0 shadow-xl w-3/4 mx-auto transition-all duration-300 ease-in-out">
-    >
-      <div
-        class="card bg-base-100 mx-auto w-3/4 shrink-0 shadow-xl transition-all duration-300 ease-in-out"
-      >
             <div class="card-body">
-          <div class="my-4 ml-8 flex h-fit flex-row items-center justify-start">
+                <!-- Input Mode Toggle - Fixed position outside fieldset -->
-            <div class="flex items-center gap-1">
+                <div class="flex flex-row justify-start items-center h-fit ml-8 my-4">
-              <label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
+                    <div class="flex items-center gap-2">
+                        <!-- <span class="text-sm text-neutral-500">Input Mode:</span> -->
+                        <label class="toggle text-base-content toggle-md">
                             <input type="checkbox" />
-                <span class="swap-on flex items-center gap-1">
+                            <svg aria-label="smiles mode" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 20 20" class="size-5">
-                  <div
-                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
-                  >
-                    <svg
-                      aria-label="smiles mode"
-                      xmlns="http://www.w3.org/2000/svg"
-                      viewBox="0 0 20 20"
-                      class="size-5"
-                    >
                                 <g
                                 stroke-linejoin="round"
                                 stroke-linecap="round"
@@ -47,20 +36,9 @@
                                 fill="currentColor"
                                 stroke="none"
                                 >
-                        <path
+                                    <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" />
-                          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"
@@ -69,120 +47,63 @@
                                 stroke="none"
                                 class="size-5"
                             >
-                      <path
+                                <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" />
-                        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
+                <fieldset class="fieldset transition-all duration-300 ease-in-out overflow-hidden">
-            class="fieldset overflow-hidden transition-all duration-300 ease-in-out"
+                    <form id="index-form" action="{{ meta.current_package.url }}/pathway" method="POST">
-          >
-            <form
-              id="index-form"
-              action="{{ meta.current_package.url }}/pathway"
-              method="POST"
-            >
                         {% csrf_token %}
-              <div
+                            <div id="text-input-container" class="transition-all duration-300 ease-in-out opacity-100 transform scale-100">
-                id="text-input-container"
+                                <div class="join w-full mx-auto">
-                class="scale-100 transform opacity-100 transition-all duration-300 ease-in-out"
+                                    <input type="text" id="index-form-text-input" placeholder="canonical SMILES string" class="input grow input-md join-item" />
-              >
-                <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="label relative w-full mt-1" >
                                     <div class="flex gap-2">
-                    <a
+                                        <a href="#" class="example-link cursor-pointer hover:text-primary"
-                      href="#"
-                      class="example-link hover:text-primary cursor-pointer"
                                            data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
-                      title="load example"
+                                           title="load example">Caffeine</a>
-                      >Caffeine</a
+                                        <a href="#" class="example-link cursor-pointer hover:text-primary"
-                    >
-                    <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"
+                                           title="load example">Ibuprofen</a>
-                      >Ibuprofen</a
-                    >
                                     </div>
-                  <a
+                                    <a class="absolute top-0 left-[calc(100%-5.4rem)]" href="#">Advanced</a>
-                    class="absolute top-0 left-[calc(100%-5.4rem)]"
-                    href="/predict"
-                    >Advanced</a
-                  >
                                 </div>
                             </div>
-              <div
+                             <div id="ketcher-container" class="hidden w-full transition-all duration-300 ease-in-out opacity-0 transform scale-95">
-                id="ketcher-container"
+                                 <iframe id="index-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}"
-                class="hidden w-full scale-95 transform opacity-0 transition-all duration-300 ease-in-out"
+                                 width="100%" height="400" class="rounded-lg"></iframe>
-              >
+                                 <button class="btn btn-lg bg-primary-950 text-primary-50 join-item w-full mt-2">Predict!</button>
-                <iframe
+                                 <a class="label mx-auto w-full mt-1" href="#">Advanced</a>
-                  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
+                        <input type="hidden" id="index-form-predict" name="predict" value="predict">
-                type="hidden"
+                        <input type="hidden" id="current-action" value="predict">
-                id="index-form-smiles"
-                name="smiles"
-                value="smiles"
-              />
-              <input
-                type="hidden"
-                id="index-form-predict"
-                name="predict"
-                value="predict"
-              />
-              <input type="hidden" id="current-action" value="predict" />
                     </form>
                 </fieldset>
             </div>
         </div>
     </div>
 
-    <!-- Community News Section -->
-    <section class="bg-base-200 z-10 mx-8 py-16">
-      <div class="mx-auto max-w-7xl px-4">
-        <h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>
 
-        <div id="community-news-container" class="flex justify-center gap-4">
+    <!-- Community News Section -->
+    <section class="py-16 bg-base-200 z-10 mx-8">
+        <div class="max-w-7xl mx-auto px-4">
+            <h2 class="h2 font-bold text-left mb-8">Community Updates</h2>
+
+            <div id="community-news-container" class="flex gap-4 justify-center">
                 <!-- News cards will be populated here -->
-          <div id="loading" class="flex w-full justify-center">
+                <div id="loading" class="flex justify-center w-full">
                     <span class="loading loading-spinner loading-lg"></span>
                 </div>
             </div>
 
-        <div class="mt-6 text-right">
+            <div class="text-right mt-6">
-          <a
+                <a href="https://community.envipath.org/c/announcements/10" target="_blank" class="btn btn-ghost btn-sm">
-            href="https://community.envipath.org/c/announcements/10"
-            target="_blank"
-            class="btn btn-ghost btn-sm"
-          >
                     Read More Announcements
                 </a>
             </div>
@@ -193,18 +114,14 @@
     </section>
 
     <!-- Mission Statement Section -->
-    <section class="from-base-200 to-base-100 bg-gradient-to-b py-16">
+    <section class="py-16 from-base-200 to-base-100 bg-gradient-to-b">
         <div class="mx-auto px-8 md:px-12">
             <div class="flex flex-row gap-4">
                 <div class="w-1/3">
-            <img
+                    <img src="{% static "/images/ep-rule-artwork.png" %}" alt="rule-based iterative tree greneration" class="w-full h-full object-contain" />
-              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">
+                <div class="space-y-4 text-left w-2/3 mr-8">
-            <h2 class="h2 mb-8 font-bold">About enviPath</h2>
+                    <h2 class="h2 font-bold mb-8">About enviPath</h2>
                     <p class="">
                         enviPath is a database and prediction system for the microbial
                         biotransformation of organic environmental contaminants. The
@@ -212,91 +129,54 @@
                         observed biotransformation pathways.
                     </p>
                     <p class="">
-              The pathway prediction system provides different relative
+                        The pathway prediction system provides different relative reasoning models
-              reasoning models to predict likely biotransformation pathways and
+                        to predict likely biotransformation pathways and products. Explore our tools
-              products. Explore our tools and contribute to advancing
+                        and contribute to advancing environmental biotransformation research.
-              environmental biotransformation research.
                     </p>
-            <div class="float-right flex flex-row gap-4">
+                    <div class="flex flex-row gap-4 float-right">
                         <a href="/about" class="btn btn-ghost-neutral">Read More</a>
                         <a href="/about" class="btn btn-neutral">Publications</a>
                     </div>
                 </div>
             </div>
+
         </div>
     </section>
 
     <!-- Partners Section -->
-    <section class="bg-base-100 py-14 sm:py-12">
+    <section class="py-14 sm:py-12 bg-base-100">
         <div class="mx-auto px-6 lg:px-8">
-        <div class="divider">
+            <div class="divider"><h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2></div>
-          <h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2>
+            <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">
-        </div>
+                <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" />
-        <div
+                <img src="{% static "/images/logo-eawag.svg" %}" alt="Eawag" class=" max-h-12 w-full object-contain lg:col-span-1" />
-          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/uzh-logo.svg" %}" alt="University of Zurich" class="2 max-h-16 w-full object-contain lg:col-span-1" />
-        >
-          <img
-            src="{% static "/images/uoa-logo-small.png" %}"
-            alt="The University of Auckland"
-            class="max-h-20 w-full object-contain lg:col-span-1"
-          />
-          <img
-            src="{% static "/images/logo-eawag.svg" %}"
-            alt="Eawag"
-            class="max-h-12 w-full object-contain lg:col-span-1"
-          />
-          <img
-            src="{% static "/images/uzh-logo.svg" %}"
-            alt="University of Zurich"
-            class="2 max-h-16 w-full object-contain lg:col-span-1"
-          />
             </div>
         </div>
     </section>
-  </div>
+
+
+
+
+</div>
 
     <script language="javascript">
         var currentPackage = "{{ meta.current_package.url }}";
 
-    // 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;
-      }
-
-      try {
-        if (
-          "contentWindow" in ketcherFrame &&
-          ketcherFrame.contentWindow.ketcher
-        ) {
-          return ketcherFrame.contentWindow.ketcher;
-        }
-      } catch (err) {
-        console.error(
-          "Cannot access Ketcher iframe - possible CORS issue:",
-          err,
-        );
-      }
-
-      return null;
-    }
-
         // Discourse API integration is now handled by discourse-api.js
 
         // Function to render Discourse topics into cards
         function renderDiscourseTopics(topics) {
-      const container = document.getElementById("community-news-container");
+            const container = document.getElementById('community-news-container');
             if (!container) return;
 
             // Clear container
-      container.innerHTML = "";
+            container.innerHTML = '';
 
             // Create cards for each topic
-      topics.forEach((topic) => {
+            topics.forEach(topic => {
                 const card = createDiscourseCard(topic);
-        container.insertAdjacentHTML("beforeend", card);
+                container.insertAdjacentHTML('beforeend', card);
             });
         }
 
@@ -343,59 +223,53 @@
         // Toggle functionality with smooth animations
         function toggleInputMode() {
             const toggle = $('input[type="checkbox"]');
-      const textContainer = $("#text-input-container");
+            const textContainer = $('#text-input-container');
-      const ketcherContainer = $("#ketcher-container");
+            const ketcherContainer = $('#ketcher-container');
-      const formCard = $(".card");
+            const formCard = $('.card');
-      const fieldset = $(".fieldset");
+            const fieldset = $('.fieldset');
 
-      if (toggle.is(":checked")) {
+            if (toggle.is(':checked')) {
                 // Draw mode - show Ketcher, hide text input
-        textContainer.addClass("opacity-0 transform scale-95");
+                textContainer.addClass('opacity-0 transform scale-95');
-        textContainer.removeClass("opacity-100 transform scale-100");
+                textContainer.removeClass('opacity-100 transform scale-100');
 
                 // Adjust fieldset padding for Ketcher mode - reduce padding and make more compact
-        fieldset.removeClass("p-8");
+                fieldset.removeClass('p-8');
-        fieldset.addClass("p-4");
+                fieldset.addClass('p-4');
 
                 // Wait for fade out to complete, then hide and show new content
                 setTimeout(() => {
-          textContainer.addClass("hidden");
+                    textContainer.addClass('hidden');
-          ketcherContainer.removeClass("hidden opacity-0 transform scale-95");
+                    ketcherContainer.removeClass('hidden opacity-0 transform scale-95');
-          ketcherContainer.addClass("opacity-100 transform scale-100");
+                    ketcherContainer.addClass('opacity-100 transform scale-100');
 
                     // Force re-evaluation of iframe size
-          const iframe = document.getElementById("index-ketcher");
+                    const iframe = document.getElementById('index-ketcher');
                     if (iframe) {
-            iframe.style.height = "400px";
+                        iframe.style.height = '400px';
                     }
                 }, 300);
             } else {
                 // SMILES mode - show text input, hide Ketcher
-        ketcherContainer.addClass("opacity-0 transform scale-95");
+                ketcherContainer.addClass('opacity-0 transform scale-95');
-        ketcherContainer.removeClass("opacity-100 transform scale-100");
+                ketcherContainer.removeClass('opacity-100 transform scale-100');
 
                 // Restore fieldset padding for text input mode
-        fieldset.removeClass("p-4");
+                fieldset.removeClass('p-4');
-        fieldset.addClass("p-8");
+                fieldset.addClass('p-8');
 
                 // Wait for fade out to complete, then hide and show new content
                 setTimeout(() => {
-          ketcherContainer.addClass("hidden");
+                    ketcherContainer.addClass('hidden');
-          textContainer.removeClass("hidden opacity-0 transform scale-95");
+                    textContainer.removeClass('hidden opacity-0 transform scale-95');
-          textContainer.addClass("opacity-100 transform scale-100");
+                    textContainer.addClass('opacity-100 transform scale-100');
                 }, 300);
 
                 // Transfer SMILES from Ketcher to text input if available
-        const ketcher = getKetcherInstance("index-ketcher");
+                if (window.indexKetcher && window.indexKetcher.getSmiles) {
-        if (ketcher && ketcher.getSmiles) {
+                    const smiles = window.indexKetcher.getSmiles();
-          try {
+                    if (smiles && smiles.trim() !== '') {
-            const smiles = ketcher.getSmiles();
+                        $('#index-form-text-input').val(smiles);
-            if (smiles && smiles.trim() !== "") {
-              $("#index-form-text-input").val(smiles);
-            }
-          } catch (err) {
-            console.error("Failed to sync Ketcher to text input:", err);
-            // Non-critical error, just log it
                     }
                 }
             }
@@ -403,27 +277,27 @@
 
         // Ketcher integration
         function indexKetcherToTextInput() {
-      $("#index-form-smiles").val(this.ketcher.getSmiles());
+            $('#index-form-smiles').val(this.ketcher.getSmiles());
         }
 
         $(function () {
             // Initialize fieldset with proper padding
-      $(".fieldset").addClass("p-8");
+            $('.fieldset').addClass('p-8');
 
             // Toggle event listener
-      $('input[type="checkbox"]').on("change", toggleInputMode);
+            $('input[type="checkbox"]').on('change', toggleInputMode);
 
             // Ketcher iframe load handler
-      $("#index-ketcher").on("load", function () {
+            $('#index-ketcher').on('load', function() {
                 const checkKetcherReady = () => {
                     const win = this.contentWindow;
-          if (win.ketcher && "editor" in win.ketcher) {
+                    if (win.ketcher && 'editor' in win.ketcher) {
                         window.indexKetcher = win.ketcher;
                         win.ketcher.editor.event.change.handlers.push({
                             once: false,
                             priority: 0,
                             f: indexKetcherToTextInput,
-              ketcher: win.ketcher,
+                            ketcher: win.ketcher
                         });
                     } else {
                         setTimeout(checkKetcherReady, 100);
@@ -433,20 +307,20 @@
             });
 
             // Handle example link clicks
-      $(".example-link").on("click", function (e) {
+            $('.example-link').on('click', function(e) {
                 e.preventDefault();
-        const smiles = $(this).data("smiles");
+                const smiles = $(this).data('smiles');
-        const title = $(this).attr("title");
+                const title = $(this).attr('title');
 
                 // Check if we're in Ketcher mode or text input mode
-        if ($('input[type="checkbox"]').is(":checked")) {
+                if ($('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);
+                    $('#index-form-text-input').val(smiles);
                 }
 
                 // Show a brief feedback
@@ -458,44 +332,25 @@
             });
 
             // Handle form submission on Enter
-      $("#index-form").on("submit", function (e) {
+            $('#index-form').on("submit", function (e) {
                 e.preventDefault();
 
-        var textSmiles = "";
+                var textSmiles = '';
 
                 // Check if we're in Ketcher mode and extract SMILES
-        if ($('input[type="checkbox"]').is(":checked")) {
+                if ($('input[type="checkbox"]').is(':checked') && window.indexKetcher) {
-          // Use the robust getter function
+                    textSmiles = window.indexKetcher.getSmiles().trim();
-          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");
+                    textSmiles = $('#index-form-text-input').val().trim();
-            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 === "") {
+                if (textSmiles === '') {
-          alert("Please enter a SMILES string or draw a structure.");
                     return;
                 }
 
-        $("#index-form-smiles").val(textSmiles);
+                $('#index-form-smiles').val(textSmiles);
                 $("#index-form").attr("action", currentPackage + "/pathway");
-        $("#index-form").attr("method", "POST");
+                $("#index-form").attr("method", 'POST');
                 this.submit();
             });
 

templates/migration.html

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

templates/migration_detail.html

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

templates/modals/cite_modal.html

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

templates/modals/collections/import_legacy_package_modal.html

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

templates/modals/collections/import_package_modal.html

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

templates/modals/collections/new_compound_modal.html

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

templates/modals/collections/new_group_modal.html

@@ -1,11 +1,5 @@
-<div
+<div class="modal fade" tabindex="-1" id="new_group_modal" role="dialog" aria-labelledby="new_group_modal"
-  class="modal fade"
+     aria-hidden="true">
-  tabindex="-1"
-  id="new_group_modal"
-  role="dialog"
-  aria-labelledby="new_group_modal"
-  aria-hidden="true"
->
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
@@ -16,44 +10,25 @@
                 <h4 class="modal-title">New Group</h4>
             </div>
             <div class="modal-body">
-        <p>
+                <p>Create new Group. You can assign users to the group once
-          Create new Group. You can assign users to the group once it is
+                    it is created. Description can be changed after creation.</p>
-          created. Description can be changed after creation.
+                <form id="new_group_modal_form" accept-charset="UTF-8" action="{{ SERVER_BASE }}/group"
-        </p>
-        <form
-          id="new_group_modal_form"
-          accept-charset="UTF-8"
-          action="{{ SERVER_BASE }}/group"
                       data-remote="true"
-          method="post"
+                      method="post">
-        >
                     {% csrf_token %}
                     <p>
                         <label for="name">Name</label>
-            <input
+                        <input id="name" type="text" name="group-name" class="form-control" placeholder="Name"/>
-              id="name"
-              type="text"
-              name="group-name"
-              class="form-control"
-              placeholder="Name"
-            />
                     </p>
                     <p>
                         <label for="description">Description</label>
-            <input
+                        <input id="description" type="text" class="form-control" placeholder="Description..."
-              id="description"
+                               name="group-description"/>
-              type="text"
-              class="form-control"
-              placeholder="Description..."
-              name="group-description"
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <a id="new_group_modal_form_submit" class="btn btn-primary" href="#"
+                <a id="new_group_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-          >Submit</a
-        >
                 <button type="button" class="btn btn-default" data-dismiss="modal">
                     Cancel
                 </button>
@@ -62,9 +37,9 @@
     </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

@@ -1,11 +1,6 @@
-<div
+
-  class="modal fade"
+<div class="modal fade" tabindex="-1" id="new_model_modal" role="dialog" aria-labelledby="new_model_modal"
-  tabindex="-1"
+     aria-hidden="true">
-  id="new_model_modal"
-  role="dialog"
-  aria-labelledby="new_model_modal"
-  aria-hidden="true"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
@@ -16,52 +11,29 @@
                 <h4 class="modal-title">New Model</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="new_model_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/model"
-          id="new_model_form"
+                      data-remote="true" method="post">
-          accept-charset="UTF-8"
-          action="{{ meta.current_package.url }}/model"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <div class="jumbotron">
+                    <div class="jumbotron">Create a new Model to
-            Create a new Model to limit the number of degradation products in
+                        limit the number of degradation products in the
-            the prediction. You just need to set a name and the packages you
+                        prediction. You just need to set a name and the packages
-            want the object to be based on. There are multiple types of models
+                        you want the object to be based on. There are multiple types of models available.
-            available. For additional information have a look at our
+                        For additional information have a look at our
-            <a
+                        <a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki
-              target="_blank"
+                            &gt;&gt;</a>
-              href="https://wiki.envipath.org/index.php/relative-reasoning"
-              role="button"
-              >wiki &gt;&gt;</a
-            >
                     </div>
                     <!-- Name -->
                     <label for="model-name">Name</label>
-          <input
+                    <input id="model-name" name="model-name" class="form-control" placeholder="Name"/>
-            id="model-name"
-            name="model-name"
-            class="form-control"
-            placeholder="Name"
-          />
 
                     <!-- Description -->
                     <label for="model-description">Description</label>
-          <input
+                    <input id="model-description" name="model-description" class="form-control"
-            id="model-description"
+                           placeholder="Description"/>
-            name="model-description"
-            class="form-control"
-            placeholder="Description"
-          />
 
                     <!-- Model Type -->
                     <label for="model-type">Model Type</label>
-          <select
+                    <select id="model-type" name="model-type" class="form-control" data-width='100%'>
-            id="model-type"
-            name="model-type"
-            class="form-control"
-            data-width="100%"
-          >
                         <option disabled selected>Select Model Type</option>
                         {% for k, v in model_types.items %}
                             <option value="{{ v }}">{{ k }}</option>
@@ -71,14 +43,8 @@
                     <!-- Rule Packages -->
                     <div id="rule-packages" class="ep-model-param mlrr rbrr">
                         <label for="model-rule-packages">Rule Packages</label>
-            <select
+                        <select id="model-rule-packages" name="model-rule-packages" data-actions-box='true'
-              id="model-rule-packages"
+                                class="form-control" multiple data-width='100%'>
-              name="model-rule-packages"
-              data-actions-box="true"
-              class="form-control"
-              multiple
-              data-width="100%"
-            >
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if obj.reviewed %}
@@ -98,14 +64,8 @@
                     <!-- Data Packages -->
                     <div id="data-packages" class="ep-model-param mlrr rbrr enviformer">
                         <label for="model-data-packages">Data Packages</label>
-            <select
+                        <select id="model-data-packages" name="model-data-packages" data-actions-box='true'
-              id="model-data-packages"
+                                class="form-control" multiple data-width='100%'>
-              name="model-data-packages"
-              data-actions-box="true"
-              class="form-control"
-              multiple
-              data-width="100%"
-            >
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if obj.reviewed %}
@@ -125,19 +85,11 @@
                     <!-- Fingerprinter -->
                     <div id="fingerprinter" class="ep-model-param mlrr">
                         <label for="model-fingerprinter">Fingerprinter</label>
-            <select
+                        <select id="model-fingerprinter" name="model-fingerprinter" data-actions-box='true'
-              id="model-fingerprinter"
+                                class="form-control" multiple data-width='100%'>
-              name="model-fingerprinter"
-              data-actions-box="true"
-              class="form-control"
-              multiple
-              data-width="100%"
-            >
                             <option value="MACCS" selected>MACCS Fingerprinter</option>
                             {% if meta.enabled_features.PLUGINS and additional_descriptors %}
-                <option disabled selected>
+                                <option disabled selected>Select Additional Fingerprinter / Descriptor</option>
-                  Select Additional Fingerprinter / Descriptor
-                </option>
                                 {% for k, v in additional_descriptors.items %}
                                     <option value="{{ v }}">{{ k }}</option>
                                 {% endfor %}
@@ -148,16 +100,8 @@
                     <!-- Threshold -->
                     <div id="threshold" class="ep-model-param mlrr enviformer">
                         <label for="model-threshold">Threshold</label>
-            <input
+                        <input type="number" min="0" max="1" step="0.05" value="0.5" id="model-threshold"
-              type="number"
+                               name="model-threshold" class="form-control">
-              min="0"
-              max="1"
-              step="0.05"
-              value="0.5"
-              id="model-threshold"
-              name="model-threshold"
-              class="form-control"
-            />
                     </div>
 
                     <div id="appdomain" class="ep-model-param mlrr">
@@ -165,64 +109,33 @@
                             <!-- Build AD? -->
                             <div class="checkbox">
                                 <label>
-                  <input
+                                    <input type="checkbox" id="build-app-domain" name="build-app-domain">Also build an
-                    type="checkbox"
+                                    Applicability Domain?
-                    id="build-app-domain"
-                    name="build-app-domain"
-                  />Also build an Applicability Domain?
                                 </label>
                             </div>
                             <div id="ad-params" style="display:none">
                                 <!-- Num Neighbors -->
                                 <label for="num-neighbors">Number of Neighbors</label>
-                <input
+                                <input id="num-neighbors" name="num-neighbors" type="number" class="form-control"
-                  id="num-neighbors"
-                  name="num-neighbors"
-                  type="number"
-                  class="form-control"
                                        value="5"
-                  step="1"
+                                       step="1" min="0" max="10">
-                  min="0"
-                  max="10"
-                />
                                 <!-- Local Compatibility -->
-                <label for="local-compatibility-threshold"
+                                <label for="local-compatibility-threshold">Local Compatibility Threshold</label>
-                  >Local Compatibility Threshold</label
+                                <input id="local-compatibility-threshold" name="local-compatibility-threshold"
-                >
-                <input
-                  id="local-compatibility-threshold"
-                  name="local-compatibility-threshold"
                                        type="number"
-                  class="form-control"
+                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
-                  value="0.5"
-                  step="0.01"
-                  min="0"
-                  max="1"
-                />
                                 <!-- Reliability -->
                                 <label for="reliability-threshold">Reliability Threshold</label>
-                <input
+                                <input id="reliability-threshold" name="reliability-threshold" type="number"
-                  id="reliability-threshold"
+                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
-                  name="reliability-threshold"
-                  type="number"
-                  class="form-control"
-                  value="0.5"
-                  step="0.01"
-                  min="0"
-                  max="1"
-                />
                             </div>
                         {% endif %}
                     </div>
                 </form>
             </div>
             <div class="modal-footer">
-        <a id="new_model_modal_form_submit" class="btn btn-primary" href="#"
+                <a id="new_model_modal_form_submit" class="btn btn-primary" href="#">Submit</a>
-          >Submit</a
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-        >
-        <button type="button" class="btn btn-default" data-dismiss="modal">
-          Cancel
-        </button>
             </div>
         </div>
     </div>
@@ -231,40 +144,45 @@
 <script>
     $(function () {
         // Built in Model Types
-    var nativeModelTypes = ["mlrr", "rbrr", "enviformer"];
+        var nativeModelTypes = [
+            "mlrr",
+            "rbrr",
+            "enviformer",
+        ]
 
         // Initially hide all "specific" forms
         $(".ep-model-param").each(function () {
             $(this).hide();
         });
 
-    $("#model-type").selectpicker();
+        $('#model-type').selectpicker();
         $("#model-fingerprinter").selectpicker();
         $("#model-rule-packages").selectpicker();
         $("#model-data-packages").selectpicker();
 
         $("#build-app-domain").change(function () {
             if ($(this).is(":checked")) {
-        $("#ad-params").show();
+                $('#ad-params').show();
             } else {
-        $("#ad-params").hide();
+                $('#ad-params').hide();
             }
         });
 
         // On change hide all and show only selected
         $("#model-type").change(function () {
-      $(".ep-model-param").hide();
+            $('.ep-model-param').hide();
-      var modelType = $("#model-type").val();
+            var modelType = $('#model-type').val();
             if (nativeModelTypes.indexOf(modelType) !== -1) {
-        $("." + modelType).show();
+                $('.' + modelType).show();
             } else {
                 // do nothing
             }
         });
 
-    $("#new_model_modal_form_submit").on("click", function (e) {
+        $('#new_model_modal_form_submit').on('click', function (e) {
             e.preventDefault();
-      $("#new_model_form").submit();
+            $('#new_model_form').submit();
         });
+
     });
 </script>

templates/modals/collections/new_package_modal.html

@@ -1,15 +1,15 @@
-<div
+<div class="modal fade"
-  class="modal fade"
      tabindex="-1"
      id="new_package_modal"
      role="dialog"
      aria-labelledby="new_package_modal"
-  aria-hidden="true"
+     aria-hidden="true">
->
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-        <button type="button" class="close" data-dismiss="modal">
+                <button type="button"
+                        class="close"
+                        data-dismiss="modal">
                     <span aria-hidden="true">&times;</span>
                     <span class="sr-only">Close</span>
                 </button>
@@ -17,52 +17,46 @@
             </div>
             <div class="modal-body">
                 <p>Create new package. Description can be changed later.</p>
-        <form
+                <form id="new_package_modal_form"
-          id="new_package_modal_form"
                       accept-charset="UTF-8"
                       action=""
                       data-remote="true"
-          method="post"
+                      method="post">
-        >
                     {% csrf_token %}
                     <p>
                         <label for="name">Name</label>
-            <input
+                        <input id="name" class="form-control"
-              id="name"
-              class="form-control"
                                name="package-name"
-              placeholder="Name"
+                               placeholder="Name"/>
-            />
                     </p>
                     <p>
                         <label for="description">Description</label>
-            <input
+                        <input id="description"
-              id="description"
                                type="text"
                                rows="3"
                                class="form-control"
                                placeholder="Description..."
-              name="package-description"
+                               name="package-description"/>
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <a id="new_package_modal_form_submit" class="btn btn-primary" href="#"
+                <a id="new_package_modal_form_submit"
-          >Submit</a
+                   class="btn btn-primary"
-        >
+                   href="#">Submit</a>
-        <button type="button" class="btn btn-default" data-dismiss="modal">
+                <button type="button"
-          Cancel
+                        class="btn btn-default"
+                        data-dismiss="modal">Cancel
                 </button>
             </div>
         </div>
     </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();
-      $("#new_package_modal_form").submit();
+        $('#new_package_modal_form').submit();
-    });
     });
+});
 </script>

templates/modals/collections/new_pathway_modal.html

@@ -1,57 +1,40 @@
+
 {% load static %}
-<div
+<div class="modal fade" tabindex="-1" id="new_pathway_modal" role="dialog" aria-labelledby="new_pathway_modal"
-  class="modal fade"
+     aria-hidden="true" style="overflow-y: auto;">
-  tabindex="-1"
-  id="new_pathway_modal"
-  role="dialog"
-  aria-labelledby="new_pathway_modal"
-  aria-hidden="true"
-  style="overflow-y: auto;"
->
     <!-- FIXME: make width dynamic-->
     <div class="modal-dialog" id="new_pathway_modal_dialog" style="width:900px">
         <div class="modal-content">
             <div class="modal-header">
                 <button type="button" class="close" data-dismiss="modal">
-          <span aria-hidden="true">&times;</span>
+                    <span aria-hidden="true">&times;</span> <span class="sr-only">Close</span>
-          <span class="sr-only">Close</span>
                 </button>
                 <h4 class="js-title-step"></h4>
             </div>
             <div class="modal-body hide" data-step="1" data-title="New Pathway">
-        <div class="jumbotron">
+                <div class="jumbotron">Create a new pathway by entering
-          Create a new pathway by entering the root compound and a name. Then
+                    the root compound and a name. Then select if you want to
-          select if you want to use the prediction engine to generate a
+                    use the prediction engine to generate a predicted pathway or
-          predicted pathway or create an empty pathway that you fill in by
+                    create an empty pathway that you fill in by yourself. If
-          yourself. If you choose to predict a pathway, you can modify the
+                    you choose to predict a pathway, you can modify the
-          settings for the prediction, or use the default settings and just
+                    settings for the prediction, or use the default settings
-          click Submit.
+                    and just click Submit.
                 </div>
                 <div class="modal-body">
                     {% if current_user.name == 'anonymous' %}
                     <div class="alert alert-warning">
-              You are currently logged in as Anonymous. Please note: Pathways
+                        You are currently logged in as Anonymous. Please note:
-              entered or predicted as anonymous user will be deleted after 30
+                        Pathways entered or predicted as anonymous user will be deleted after 30 days.
-              days. Please log in to save your results.
+                        Please log in to save your results.
                     </div>
                     {% endif %}
                 </div>
                 <div class="row">
                     <div class="col-md-6">
                         <label for="name">Name</label>
-            <input
+                        <input id="name" class="form-control" name="name" placeholder="Name"/>
-              id="name"
-              class="form-control"
-              name="name"
-              placeholder="Name"
-            />
                         <label for="description">Description</label>
-            <input
+                        <input id="description" class="form-control" name="description" placeholder="no description"/>
-              id="description"
-              class="form-control"
-              name="description"
-              placeholder="no description"
-            />
                     </div>
 
                     <div class="col-md-6">
@@ -59,33 +42,17 @@
                         <div class="radio" id="predict">
                             <p>
                                 <label>
-                  <input
+                                    <input type="radio" name="predict" id="radioPredict" value="predict" checked/>Predict pathway
-                    type="radio"
-                    name="predict"
-                    id="radioPredict"
-                    value="predict"
-                    checked
-                  />Predict pathway
                                 </label>
                             </p>
                             <p>
                                 <label>
-                  <input
+                                    <input type="radio" name="predict" id="radioIncremental"value="incremental"/>Incremental prediction
-                    type="radio"
-                    name="predict"
-                    id="radioIncremental"
-                    value="incremental"
-                  />Incremental prediction
                                 </label>
                             </p>
                             <p>
                                 <label>
-                  <input
+                                    <input type="radio" name="predict" id="radioBuild" value="build"/>Build pathway
-                    type="radio"
-                    name="predict"
-                    id="radioBuild"
-                    value="build"
-                  />Build pathway
                                 </label>
                             </p>
                         </div>
@@ -94,18 +61,13 @@
                 <label for="smilesinput">SMILES</label>
                 <table style="width: 100%">
                     <colgroup>
-            <col span="1" style="width: 90%;" />
+                        <col span="1" style="width: 90%;">
-            <col span="1" style="width: 10%;" />
+                        <col span="1" style="width: 10%;">
                     </colgroup>
                     <tr>
                         <td>
-              <input
+                            <input id="smilesinput" class="form-control" name="smilesinput" placeholder="C1CCCCC1"
-                id="smilesinput"
+                                   autocapitalize="none"/>
-                class="form-control"
-                name="smilesinput"
-                placeholder="C1CCCCC1"
-                autocapitalize="none"
-              />
                         </td>
                         <td>
                             <button type="button" class="btn btn-default" id="render-button">
@@ -116,57 +78,33 @@
                 </table>
                 <p id="ketcher_container"></p>
                 <div>
-          <iframe
+                    <iframe id="ifKetcher" src="{% static '/js/ketcher/ketcher.html' %}" width="850"
-            id="ifKetcher"
+                            height="510"></iframe>
-            src="{% static '/js/ketcher/ketcher.html' %}"
-            width="850"
-            height="510"
-          ></iframe>
                 </div>
             </div>
-      <div
+            <div class="modal-body hide" data-step="2" data-title="New Pathway - Advanced Settings">
-        class="modal-body hide"
+                <div class="jumbotron">Choose if you want to use an existing
-        data-step="2"
+                    setting, or create a new one for this pathway
-        data-title="New Pathway - Advanced Settings"
+                    prediction. Then click Submit to use the specified setting,
-      >
+                    or click next to set the parameters.
-        <div class="jumbotron">
-          Choose if you want to use an existing setting, or create a new one for
-          this pathway prediction. Then click Submit to use the specified
-          setting, or click next to set the parameters.
                 </div>
                 <div id="settings">
                     <div class="radio" id="settingRadio">
                         <p>
                             <label>
-                <input
+                                <input type="radio" name="existing" id="radioDefault" value="exisiting" checked/>
-                  type="radio"
-                  name="existing"
-                  id="radioDefault"
-                  value="exisiting"
-                  checked
-                />
                                 Use Default
                             </label>
                         </p>
                         <p>
                             <label>
-                <input
+                                <input type="radio" name="existing" id="radioExists" value="exisiting"/>
-                  type="radio"
-                  name="existing"
-                  id="radioExists"
-                  value="exisiting"
-                />
                                 Select Existing
                             </label>
                         </p>
                         <p>
                             <label>
-                <input
+                                <input type="radio" name="existing" id="radioNew" value="temporary"/>
-                  type="radio"
-                  name="existing"
-                  id="radioNew"
-                  value="temporary"
-                />
                                 Create New
                             </label>
                         </p>
@@ -184,25 +122,12 @@
             {% include "templates/modals/collections/new_setting_modal_body.html" %}
             {% endwith %}
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-default js-btn-step pull-left" data-orientation="cancel"
-          type="button"
+                        onclick="reset()" data-dismiss="modal"></button>
-          class="btn btn-default js-btn-step pull-left"
+                <button type="button" class="btn btn-default js-btn-step" data-orientation="previous"
-          data-orientation="cancel"
+                        id="backbutton"></button>
-          onclick="reset()"
+                <button type="button" class="btn btn-default js-btn-step" data-orientation="next"
-          data-dismiss="modal"
+                        id="nextbutton"></button>
-        ></button>
-        <button
-          type="button"
-          class="btn btn-default js-btn-step"
-          data-orientation="previous"
-          id="backbutton"
-        ></button>
-        <button
-          type="button"
-          class="btn btn-default js-btn-step"
-          data-orientation="next"
-          id="nextbutton"
-        ></button>
                 <a id="modal-form-submit" class="btn btn-primary" href="#">Submit</a>
             </div>
         </div>
@@ -210,87 +135,87 @@
 </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) {
-        syncKetcherAndTextInput("text", "ifKetcher", "smilesinput");
+            syncKetcherAndTextInput('text', 'ifKetcher', 'smilesinput');
         }
     });
 
     // Show forms depending on the selected TS
-    $("#availableTS").on("change", function (e) {
+    $('#availableTS').on('change', function(e) {
         e.preventDefault();
 
         var type = $(this).val();
         // hide current content
-      $("#forms").children().hide();
+        $('#forms').children().hide()
 
-      if (type === "") {
+        if(type === '') {
             return;
         }
 
-      $("#" + type + "_form").show();
+        $('#' + type + '_form').show()
     });
 
-    $("#modelSelect").on("change", function () {
+    $("#modelSelect").on("change", function() {
         setCutoff = function (thresh) {
             $("#cutoff").val(thresh);
-      };
+        }
 
         var modelUri = $("#modelSelect :selected").val();
         fillPRCurve(modelUri, setCutoff);
     });
 
     // Add a TS to the setting
-    $("#add-ts-button").on("click", function (e) {
+    $('#add-ts-button').on('click', function(e) {
         e.preventDefault();
         s.addTruncator();
     });
 
-    $("input[type=radio][name=predict]").change(function () {
+    $('input[type=radio][name=predict]').change(function() {
-      if (this.id == "radioBuild") {
+        if (this.id == 'radioBuild') {
           $("#nextbutton").prop("disabled", true);
         } else {
           $("#nextbutton").prop("disabled", false);
         }
     });
 
-    $("input[type=radio][name=existing]").change(function () {
+    $('input[type=radio][name=existing]').change(function() {
-      if (this.id == "radioDefault" || this.id == "radioExists") {
+        if (this.id == 'radioDefault' || this.id == 'radioExists') {
-        if (this.id == "radioDefault") {
+          if(this.id == 'radioDefault') {
             $("#settingSelect").prop("disabled", true);
           } else {
             $("#settingSelect").prop("disabled", false);
@@ -303,74 +228,75 @@
         }
     });
 
-    var pwStep1 = function () {
+    var pwStep1 = function() {
         console.log("pw step 1");
         // Make "Next" to "Advanced"
-      $("#nextbutton").val("Advanced");
+        $('#nextbutton').val("Advanced");
-    };
+    }
 
-    var pwStep2 = function () {
+    var pwStep2 = function() {
         console.log("pw step 2");
         // Make "Advanced" to "Next"
-      $("#nextbutton").val("Next");
+        $('#nextbutton').val("Next");
         // As "Use default is preselected" disable "Next" button
-      $("#nextbutton").prop("disabled", true);
+        $("#nextbutton").prop("disabled",true);
         // Disable setting dropdown as long as the correspndonding radio isnt checked
-      $("#settingSelect").prop("disabled", true);
+        $("#settingSelect").prop("disabled",true);
         // Show submit button
         $("#modal-form-submit").show();
-    };
+    }
 
-    var settingStep1 = function () {
+    var settingStep1 = function (){
         // First step sets name and packages
         s.extractName();
         s.extractSelectedPackages();
-    };
+    }
 
-    var settingStep2 = function () {
+    var settingStep2 = function (){
         // Seconds step gathers relative reasoning params
         s.extractRelativeReasoning();
         s.extractCutoff();
         s.extractEvaluationType();
-    };
+    }
 
-    var settingStep3 = function () {
+    var settingStep3 = function() {
         s.updateTable();
         s.updateSummaryTable();
         // hide duplicate submit...
         $("#nextbutton").hide();
-    };
+    }
 
-    var postPathway = function () {
+    var postPathway = function(){
         console.log("Complete!");
         console.log(s.tsParams);
         console.log("Getting SMILES");
-    };
+    }
 
     function dummy() {
         console.log("dummy");
     }
 
-    $("#new_pathway_modal").modalSteps({
+    $('#new_pathway_modal').modalSteps({
-      btnCancelHtml: "Cancel",
+      btnCancelHtml: 'Cancel',
-      btnPreviousHtml: "Back",
+      btnPreviousHtml: 'Back',
-      btnNextHtml: "Next",
+      btnNextHtml: 'Next',
-      btnLastStepHtml: "Submit",
+      btnLastStepHtml: 'Submit',
       disableNextButton: false,
       completeCallback: postPathway,
       callbacks: {
-        1: pwStep1,
+        '1': pwStep1,
-        2: pwStep2,
+        '2' : pwStep2,
-        3: dummy,
+        '3' : dummy,
-        4: settingStep1,
+        '4' : settingStep1,
-        5: settingStep2,
+        '5' : settingStep2,
-        6: settingStep3,
+        '6' : settingStep3,
-      },
+      }
     });
 
-    $("#modal-form-submit").on("click", function () {
+   $('#modal-form-submit').on('click', function() {
       e.preventDefault();
       postPathway();
    });
-  });
+});
+
 </script>

templates/modals/collections/new_prediction_setting_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 
 <div id="new_prediction_setting_modal" class="modal" tabindex="-1">
@@ -5,88 +6,38 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Create a Prediction Setting</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-        <p>
+                <p>To create a Prediction Setting fill the form below and click "Create"</p>
-          To create a Prediction Setting fill the form below and click "Create"
+                <form id="new-prediction-setting-modal-form" accept-charset="UTF-8" action="" data-remote="true"
-        </p>
+                      method="post">
-        <form
-          id="new-prediction-setting-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
 
                     <label for="prediction-setting-name">Name</label>
-          <input
+                    <input id="prediction-setting-name" name="prediction-setting-name" class="form-control" placeholder="Name"/>
-            id="prediction-setting-name"
-            name="prediction-setting-name"
-            class="form-control"
-            placeholder="Name"
-          />
                     <label for="prediction-setting-description">Description</label>
-          <input
+                    <input id="prediction-setting-description" name="prediction-setting-description" class="form-control"
-            id="prediction-setting-description"
+                           placeholder="Description"/>
-            name="prediction-setting-description"
-            class="form-control"
-            placeholder="Description"
-          />
 
                     <label for="prediction-setting-max-nodes">Max #Nodes</label>
-          <input
+                    <input id="prediction-setting-max-nodes" type="number" class="form-control" name="prediction-setting-max-nodes" value="30" min="1" max="50" step="1">
-            id="prediction-setting-max-nodes"
-            type="number"
-            class="form-control"
-            name="prediction-setting-max-nodes"
-            value="30"
-            min="1"
-            max="50"
-            step="1"
-          />
                     <label for="prediction-setting-max-depth">Max Depth</label>
-          <input
+                    <input id="prediction-setting-max-depth" type="number" class="form-control" name="prediction-setting-max-depth" value="5" min="1" max="8" step="1">
-            id="prediction-setting-max-depth"
-            type="number"
-            class="form-control"
-            name="prediction-setting-max-depth"
-            value="5"
-            min="1"
-            max="8"
-            step="1"
-          />
 
                     <label for="tp-generation-method">TP Generation Method</label>
-          <select
+                    <select id="tp-generation-method" name="tp-generation-method" class="form-control" data-width='100%'>
-            id="tp-generation-method"
-            name="tp-generation-method"
-            class="form-control"
-            data-width="100%"
-          >
                         <option disabled selected>Select how TPs are generated</option>
                         <option value="rule-based-prediction-setting">Rule Based</option>
                         <option value="model-based-prediction-setting">Model Based</option>
                     </select>
                     <div id="rule-based-prediction-setting-specific-form">
                         <!-- Rule Packages -->
-            <label>Rule Packages</label><br />
+                        <label>Rule Packages</label><br>
-            <select
+                        <select id="rule-based-prediction-setting-packages" name="rule-based-prediction-setting-packages"
-              id="rule-based-prediction-setting-packages"
+                                data-actions-box='true' class="form-control" multiple data-width='100%'>
-              name="rule-based-prediction-setting-packages"
-              data-actions-box="true"
-              class="form-control"
-              multiple
-              data-width="100%"
-            >
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                             {% if obj.reviewed %}
@@ -103,83 +54,56 @@
                         </select>
                     </div>
                     <div id="model-based-prediction-setting-specific-form">
-            <label>Select Model</label><br />
+                        <label>Select Model</label><br>
-            <select
+                        <select id="model-based-prediction-setting-model" name="model-based-prediction-setting-model" class="form-control" data-width='100%'>
-              id="model-based-prediction-setting-model"
-              name="model-based-prediction-setting-model"
-              class="form-control"
-              data-width="100%"
-            >
                         <option disabled selected>Select the model</option>
                         {% for m in models %}
                         <option value="{{ m.url }}">{{ m.name|safe }}</option>
                         {% endfor %}
                         </select>
-            <label for="model-based-prediction-setting-threshold"
+                        <label for="model-based-prediction-setting-threshold">Threshold</label>
-              >Threshold</label
+                        <input id="model-based-prediction-setting-threshold" name="model-based-prediction-setting-threshold" class="form-control" placeholder="0.25" type="number"/>
-            >
-            <input
-              id="model-based-prediction-setting-threshold"
-              name="model-based-prediction-setting-threshold"
-              class="form-control"
-              placeholder="0.25"
-              type="number"
-            />
                     </div>
 
-          <input
+                    <input class="form-check-input" type="checkbox" value="on" id="prediction-setting-new-default" name="prediction-setting-new-default">
-            class="form-check-input"
+                    <label class="form-check-label" for="prediction-setting-new-default">Set this setting as new default</label>
-            type="checkbox"
+
-            value="on"
-            id="prediction-setting-new-default"
-            name="prediction-setting-new-default"
-          />
-          <label class="form-check-label" for="prediction-setting-new-default"
-            >Set this setting as new default</label
-          >
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="new-prediction-setting-modal-submit">Create</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="new-prediction-setting-modal-submit"
-        >
-          Create
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+    $(function() {
+
         // Initially hide all "specific" forms
-    $("div[id$='-specific-form']").each(function () {
+        $("div[id$='-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 () {
+        $("#tp-generation-method").change(function() {
-      $("div[id$='-specific-form']").each(function () {
+            $("div[id$='-specific-form']").each( function() {
                 $(this).hide();
             });
-      val = $("option:selected", this).val();
+            val = $('option:selected', this).val();
             $("#" + val + "-specific-form").show();
         });
 
-    $("#new-prediction-setting-modal-submit").click(function (e) {
+        $('#new-prediction-setting-modal-submit').click(function(e){
             e.preventDefault();
             // $('#new-prediction-setting-modal-form').submit();
 
-      const formData = $("#new-prediction-setting-modal-form").serialize();
+            const formData = $('#new-prediction-setting-modal-form').serialize();
-      $.post("/setting", formData, function (response) {
+            $.post('/setting', formData, function(response) {
                 location.reload();
             });
         });
-  });
+    })
 </script>

templates/modals/collections/new_reaction_modal.html

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

templates/modals/collections/new_rule_modal.html

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

templates/modals/collections/new_scenario_modal.html

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

templates/modals/objects/add_additional_information_modal.html

@@ -4,89 +4,58 @@
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
                 <h3 class="modal-title">Add Additional Information</h3>
             </div>
             <div class="modal-body">
-        <select
+                <select id="select-additional-information-type" data-actions-box='true' class="form-control" data-width='100%'>
-          id="select-additional-information-type"
-          data-actions-box="true"
-          class="form-control"
-          data-width="100%"
-        >
                     <option selected disabled>Select the type to add</option>
                     {% for add_inf in available_additional_information %}
-            <option value="{{ add_inf.name }}">
+                        <option value="{{ add_inf.name }}">{{ add_inf.display_name }}</option>
-              {{ add_inf.display_name }}
-            </option>
                     {% endfor %}
                 </select>
                 {% for add_inf in available_additional_information %}
                     <div class="aiform {{ add_inf.name }}" style="display: none;">
-            <form
+                        <form id="add_{{ add_inf.name }}_add-additional-information-modal-form" accept-charset="UTF-8"
-              id="add_{{ add_inf.name }}_add-additional-information-modal-form"
+                              action="" data-remote="true" method="post">
-              accept-charset="UTF-8"
-              action=""
-              data-remote="true"
-              method="post"
-            >
                             {% csrf_token %}
                             {{ add_inf.widget|safe }}
-              <input
+                            <input type="hidden" name="hidden" value="add-additional-information">
-                type="hidden"
-                name="hidden"
-                value="add-additional-information"
-              />
                         </form>
                     </div>
                 {% endfor %}
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="add-additional-information-modal-submit">Add
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="add-additional-information-modal-submit"
-        >
-          Add
                 </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#select-additional-information-type").change(function (e) {
-      var selectedType = $(
-        "#select-additional-information-type :selected",
-      ).val();
-      $(".aiform").hide();
-      $("." + selectedType).show();
-    });
 
-    $("#add-additional-information-modal-submit").click(function (e) {
+    $('#select-additional-information-type').change(function(e){
+        var selectedType = $("#select-additional-information-type :selected").val();
+        $('.aiform').hide();
+        $('.' + selectedType).show();
+    })
+
+    $('#add-additional-information-modal-submit').click(function(e){
         e.preventDefault();
 
-      var selectedType = $(
+        var selectedType = $("#select-additional-information-type :selected").val();
-        "#select-additional-information-type :selected",
-      ).val();
         console.log(selectedType);
-      if (
+        if (selectedType !== null && selectedType !== undefined && selectedType !== '') {
-        selectedType !== null &&
+            $('.' + selectedType + ' >form').submit();
-        selectedType !== undefined &&
-        selectedType !== ""
-      ) {
-        $("." + selectedType + " >form").submit();
         }
+
     });
-  });
+
+});
+
+
 </script>

templates/modals/objects/add_pathway_edge_modal.html

@@ -1,150 +1,95 @@
+
 {% load static %}
-<div
+<div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_modal"
-  class="modal fade bs-modal-lg"
-  id="add_pathway_edge_modal"
-  tabindex="-1"
-  aria-labelledby="add_pathway_edge_modal"
      aria-modal="true"
-  role="dialog"
+     role="dialog">
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
                 <h4 class="modal-title">Add a Reaction</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="add_pathway_edge_modal_form" accept-charset="UTF-8"
-          id="add_pathway_edge_modal_form"
-          accept-charset="UTF-8"
                       action="{% url 'package pathway edge list' meta.current_package.uuid pathway.uuid %}"
-          data-remote="true"
+                      data-remote="true" method="post">
-          method="post"
-        >
                     {% csrf_token %}
                     <label for="edge-name">Name</label>
-          <input
+                    <input id="edge-name" class="form-control" name="edge-name" placeholder="Name"/>
-            id="edge-name"
-            class="form-control"
-            name="edge-name"
-            placeholder="Name"
-          />
                     <label for="edge-description">Description</label>
-          <input
+                    <input id="edge-description" class="form-control" name="edge-description" placeholder="Description"/>
-            id="edge-description"
-            class="form-control"
-            name="edge-description"
-            placeholder="Description"
-          />
                     <p></p>
                     <div class="row">
                         <div class="col-xs-5">
                             <legend>Substrate(s)</legend>
                         </div>
-            <div class="col-xs-2"></div>
+                        <div class="col-xs-2">
+
+                        </div>
                         <div class="col-xs-5">
                             <legend>Product(s)</legend>
                         </div>
                     </div>
                     <div class="row">
                         <div class="col-xs-5">
-              <select
+                            <select id="add_pathway_edge_substrates" name="edge-substrates"
-                id="add_pathway_edge_substrates"
+                                    data-actions-box='true' class="form-control" multiple data-width='100%'>
-                name="edge-substrates"
-                data-actions-box="true"
-                class="form-control"
-                multiple
-                data-width="100%"
-              >
                                 {% for n in pathway.nodes %}
-                  <option
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
-                    data-smiles="{{ n.default_node_label.smiles }}"
-                    value="{{ n.url }}"
-                  >
-                    {{ n.default_node_label.name|safe }}
-                  </option>
                                 {% endfor %}
                             </select>
                         </div>
-            <div
+                        <div class="col-xs-2" style="display: flex; justify-content: center; align-items: center;">
-              class="col-xs-2"
-              style="display: flex; justify-content: center; align-items: center;"
-            >
                             <i class="glyphicon glyphicon-arrow-right"></i>
                         </div>
                         <div class="col-xs-5">
-              <select
+                            <select id="add_pathway_edge_products" name="edge-products"
-                id="add_pathway_edge_products"
+                                    data-actions-box='true' class="form-control" multiple data-width='100%'>
-                name="edge-products"
-                data-actions-box="true"
-                class="form-control"
-                multiple
-                data-width="100%"
-              >
                                 {% for n in pathway.nodes %}
-                  <option
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
-                    data-smiles="{{ n.default_node_label.smiles }}"
-                    value="{{ n.url }}"
-                  >
-                    {{ n.default_node_label.name|safe }}
-                  </option>
                                 {% endfor %}
                             </select>
                         </div>
                     </div>
                     <div class="row">
                         <p></p>
-            <div class="col-xs-12" id="reaction_image"></div>
+                        <div class="col-xs-12" id="reaction_image">
+
+                        </div>
                     </div>
                 </form>
             </div>
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-          type="button"
-          class="btn btn-secondary pull-left"
-          data-dismiss="modal"
-        >
-          Close
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="add_pathway_edge_modal_form_submit"
-        >
-          Submit
                 </button>
+                <button type="button" class="btn btn-primary" id="add_pathway_edge_modal_form_submit">Submit</button>
             </div>
         </div>
     </div>
+
 </div>
 <script>
+
     function reactionImage() {
         var substrates = [];
-    $("#add_pathway_edge_substrates option:selected").each(function () {
+        $('#add_pathway_edge_substrates option:selected').each(function () {
-      var smiles = $(this).data("smiles"); // read data-smiles attribute
+          var smiles = $(this).data('smiles'); // read data-smiles attribute
           substrates.push(smiles);
         });
 
-    var products = [];
+        var products = []
-    $("#add_pathway_edge_products option:selected").each(function () {
+        $('#add_pathway_edge_products option:selected').each(function () {
-      var smiles = $(this).data("smiles"); // read data-smiles attribute
+          var smiles = $(this).data('smiles'); // read data-smiles attribute
           products.push(smiles);
         });
 
         if (substrates.length > 0 && products.length > 0) {
-      reaction = substrates.join(".") + ">>" + products.join(".");
+            reaction = substrates.join('.') + ">>" + products.join('.');
-      $("#reaction_image").empty();
+            $('#reaction_image').empty();
-      $("#reaction_image").append(
+            $('#reaction_image').append(
-        "<img width='100%' src='{% url 'depict' %}?smirks=" +
+                "<img width='100%' src='{% url 'depict' %}?smirks=" + encodeURIComponent(reaction) +"'>"
-          encodeURIComponent(reaction) +
-          "'>",
             );
         }
     }
@@ -153,22 +98,30 @@
         $("#add_pathway_edge_substrates").selectpicker();
         $("#add_pathway_edge_products").selectpicker();
 
-    $("#add_pathway_edge_substrates").on("change", function (e) {
+        $("#add_pathway_edge_substrates").on('change', function (e) {
             reactionImage();
-    });
+        })
 
-    $("#add_pathway_edge_products").on("change", function (e) {
+        $("#add_pathway_edge_products").on('change', function (e) {
             reactionImage();
-    });
+        })
 
         $(function () {
-      $("#add_pathway_edge_modal_form_submit").on("click", function (e) {
+            $('#add_pathway_edge_modal_form_submit').on('click', function (e) {
                 e.preventDefault();
                 $(this).prop("disabled", true);
 
+
                 // submit form
-        $("#add_pathway_edge_modal_form").submit();
+                $('#add_pathway_edge_modal_form').submit();
             });
         });
+
     });
+
 </script>
+
+
+
+
+

templates/modals/objects/add_pathway_node_modal.html

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

templates/modals/objects/add_structure_modal.html

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

templates/modals/objects/delete_pathway_edge_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Delete Edge -->
 <div id="delete_pathway_edge_modal" class="modal" tabindex="-1">
@@ -5,56 +6,31 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h3 class="modal-title">Delete Edge</h3>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 Deletes the Edge. Nodes referenced by this edge will remain.
                 <p></p>
-        <form
+                <form id="delete-pathway-edge-modal-form" accept-charset="UTF-8" action="" data-remote="true"
-          id="delete-pathway-edge-modal-form"
+                      method="post">
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <select
+                    <select id="delete_pathway_edge_edges" name="edge-url"
-            id="delete_pathway_edge_edges"
+                            data-actions-box='true' class="form-control" data-width='100%'>
-            name="edge-url"
+                        <option value="" disabled selected>Select Reaction to delete</option>
-            data-actions-box="true"
-            class="form-control"
-            data-width="100%"
-          >
-            <option value="" disabled selected>
-              Select Reaction to delete
-            </option>
                         {% for e in pathway.edges %}
                             <option value="{{ e.url }}">{{ e.edge_label.name|safe }}</option>
                         {% endfor %}
                     </select>
-          <input type="hidden" id="hidden" name="hidden" value="delete" />
+                    <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">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="delete-pathway-edge-modal-submit">Delete</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="delete-pathway-edge-modal-submit"
-        >
-          Delete
-        </button>
             </div>
         </div>
     </div>
@@ -63,27 +39,28 @@
     $(function () {
         $("#delete_pathway_edge_edges").selectpicker();
 
-    $("#delete_pathway_edge_edges").on("change", function (e) {
+        $("#delete_pathway_edge_edges").on('change', function (e) {
-      edge_url = $("#delete_pathway_edge_edges option:selected").val();
+            edge_url = $('#delete_pathway_edge_edges option:selected').val()
 
             if (edge_url !== "") {
-        $("#delete_pathway_edge_image").empty();
+                $('#delete_pathway_edge_image').empty();
-        $("#delete_pathway_edge_image").append(
+                $('#delete_pathway_edge_image').append(
-          "<img width='100%' src='" + edge_url + "?image=svg'>",
+                    "<img width='100%' src='" + edge_url + "?image=svg'>"
                 );
             }
-    });
+        })
 
-    $("#delete-pathway-edge-modal-submit").click(function (e) {
+        $('#delete-pathway-edge-modal-submit').click(function (e) {
             e.preventDefault();
-      edge_url = $("#delete_pathway_edge_edges option:selected").val();
+            edge_url = $('#delete_pathway_edge_edges option:selected').val()
 
             if (edge_url === "") {
                 return;
             }
 
-      $("#delete-pathway-edge-modal-form").attr("action", edge_url);
+            $('#delete-pathway-edge-modal-form').attr('action', edge_url)
-      $("#delete-pathway-edge-modal-form").submit();
+            $('#delete-pathway-edge-modal-form').submit();
-    });
         });
+
+    })
 </script>

templates/modals/objects/delete_pathway_node_modal.html

@@ -6,59 +6,31 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h3 class="modal-title">Delete Node</h3>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-        Deletes the Node. Edges having this Node as Substrate or Product will be
+                Deletes the Node. Edges having this Node as Substrate or Product will be removed as well.
-        removed as well.
                 <p></p>
-        <form
+                <form id="delete-pathway-node-modal-form" accept-charset="UTF-8" action="" data-remote="true"
-          id="delete-pathway-node-modal-form"
+                      method="post">
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <select
+                    <select id="delete_pathway_node_nodes" name="node-url"
-            id="delete_pathway_node_nodes"
+                            data-actions-box='true' class="form-control" data-width='100%'>
-            name="node-url"
+                        <option value="" disabled selected>Select Compound to delete</option>
-            data-actions-box="true"
-            class="form-control"
-            data-width="100%"
-          >
-            <option value="" disabled selected>
-              Select Compound to delete
-            </option>
                         {% for n in pathway.nodes %}
-              <option value="{{ n.url }}">
+                            <option value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
-                {{ n.default_node_label.name|safe }}
-              </option>
                         {% endfor %}
                     </select>
-          <input type="hidden" id="hidden" name="hidden" value="delete" />
+                    <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">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="delete-pathway-node-modal-submit">Delete</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="delete-pathway-node-modal-submit"
-        >
-          Delete
-        </button>
             </div>
         </div>
     </div>
@@ -67,27 +39,28 @@
     $(function () {
         $("#delete_pathway_node_nodes").selectpicker();
 
-    $("#delete_pathway_node_nodes").on("change", function (e) {
+        $("#delete_pathway_node_nodes").on('change', function (e) {
-      node_url = $("#delete_pathway_node_nodes option:selected").val();
+            node_url = $('#delete_pathway_node_nodes option:selected').val()
 
             if (node_url !== "") {
-        $("#delete_pathway_node_image").empty();
+                $('#delete_pathway_node_image').empty();
-        $("#delete_pathway_node_image").append(
+                $('#delete_pathway_node_image').append(
-          "<img width='100%' src='" + node_url + "?image=svg'>",
+                    "<img width='100%' src='" + node_url + "?image=svg'>"
                 );
             }
-    });
+        })
 
-    $("#delete-pathway-node-modal-submit").click(function (e) {
+        $('#delete-pathway-node-modal-submit').click(function (e) {
             e.preventDefault();
-      node_url = $("#delete_pathway_node_nodes option:selected").val();
+            node_url = $('#delete_pathway_node_nodes option:selected').val()
 
             if (node_url === "") {
                 return;
             }
 
-      $("#delete-pathway-node-modal-form").attr("action", node_url);
+            $('#delete-pathway-node-modal-form').attr('action', node_url)
-      $("#delete-pathway-node-modal-form").submit();
+            $('#delete-pathway-node-modal-form').submit();
-    });
         });
+
+    })
 </script>

templates/modals/objects/download_pathway_csv_modal.html

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

templates/modals/objects/download_pathway_image_modal.html

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

templates/modals/objects/edit_compound_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Compound -->
 <div id="edit_compound_modal" class="modal" tabindex="-1">
@@ -5,66 +6,42 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Edit Compound</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>Edit Compound.</p>
-        <form
+                <form id="edit-compound-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-compound-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="compound-name">Name</label>
-            <input
+                        <input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name|safe}}">
-              id="compound-name"
-              class="form-control"
-              name="compound-name"
-              value="{{ compound.name|safe }}"
-            />
                     </p>
                     <p>
                         <label for="compound-description">Description</label>
-            <input
+                        <input id="compound-description" type="text" class="form-control"
-              id="compound-description"
-              type="text"
-              class="form-control"
                                value="{{ compound.description|safe }}"
-              name="compound-description"
+                               name="compound-description">
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-compound-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-compound-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#edit-compound-modal-submit").click(function (e) {
+
+    $('#edit-compound-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-compound-modal-form").submit();
+        $('#edit-compound-modal-form').submit();
-    });
     });
+
+});
+
+
 </script>

templates/modals/objects/edit_compound_structure_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Compound -->
 <div id="edit_compound_structure_modal" class="modal" tabindex="-1">
@@ -5,66 +6,41 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Create a Compound</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>Edit a Compound Structure.</p>
-        <form
+                <form id="edit-compound-structure-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-compound-structure-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="compound-structure-name">Name</label>
-            <input
+                        <input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name|safe }}">
-              id="compound-structure-name"
-              class="form-control"
-              name="compound-structure-name"
-              value="{{ compound_structure.name|safe }}"
-            />
                     </p>
                     <p>
                         <label for="compound-structure-description">Description</label>
-            <input
+                        <input id="compound-structure-description" type="text" class="form-control"
-              id="compound-structure-description"
+                               value="{{ compound_structure.description|safe }}" name="compound-structure-description">
-              type="text"
-              class="form-control"
-              value="{{ compound_structure.description|safe }}"
-              name="compound-structure-description"
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-compound-structure-modal-submit">Create</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-compound-structure-modal-submit"
-        >
-          Create
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#edit-compound-structure-modal-submit").click(function (e) {
+
+    $('#edit-compound-structure-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-compound-structure-modal-form").submit();
+        $('#edit-compound-structure-modal-form').submit();
-    });
     });
+
+});
+
+
 </script>

templates/modals/objects/edit_group_member_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Package Permission -->
 <div id="edit_group_member_modal" class="modal" tabindex="-1">
@@ -5,20 +6,15 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Add or Remove Group Member</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>
-          To add member (either User or entire Groups) to this group select the
+                    To add member (either User or entire Groups) to this group select the entity you want to add below
-          entity you want to add below and click the check mark.
+                    and click the check mark.
-          <br />
+                    <br>
                     To remove member simply click the <code>X</code> next to the member.
                 </p>
 
@@ -32,24 +28,12 @@
 				</div>
 
                 <div class="row">
-          <form
+                    <form id="modal-form-group-member" class="form-inline" role="form" accept-charset="UTF-8" action=""
-            id="modal-form-group-member"
+                          data-remote="true" method="post">
-            class="form-inline"
-            role="form"
-            accept-charset="UTF-8"
-            action=""
-            data-remote="true"
-            method="post"
-          >
                         {% csrf_token %}
                         <div class="col-xs-8">
-              <select
+                            <select id="select_member" name="member" data-actions-box='true'
-                id="select_member"
+                                    class="selPackages" data-width='100%'>
-                name="member"
-                data-actions-box="true"
-                class="selPackages"
-                data-width="100%"
-              >
                                 <option disabled selected>User</option>
                                 {% for u in users %}
                                 <option value="{{ u.url }}">{{ u.username }}</option>
@@ -59,9 +43,10 @@
                                 <option value="{{ g.url }}">{{ g.name|safe }}</option>
                                 {% endfor %}
                             </select>
-              <input type="hidden" name="action" value="add" />
+                            <input type="hidden" name="action" value="add">
+                        </div>
+                        <div class="col-xs-2">
                         </div>
-            <div class="col-xs-2"></div>
                         <div class="col-xs-2">
                             <button type="submit" style="width:60%;" class="btn col-xs-2">
                                 <span class="glyphicon glyphicon-ok"></span>
@@ -72,22 +57,16 @@
                 <p></p>
                 {% for u in group.user_member.all %}
                 <div class="row">
-            <form
+                    <form id="modal-form-group-member_{{ u.uuid }}" class="form-inline" role="form"
-              id="modal-form-group-member_{{ u.uuid }}"
+                          accept-charset="UTF-8" action="" data-remote="true" method="post">
-              class="form-inline"
-              role="form"
-              accept-charset="UTF-8"
-              action=""
-              data-remote="true"
-              method="post"
-            >
                         {% csrf_token %}
                         <div class="col-xs-8">
                             {{ u.username }}
-                <input type="hidden" name="member" value="{{ u.url }}" />
+                            <input type="hidden" name="member" value="{{ u.url }}"/>
-                <input type="hidden" name="action" value="remove" />
+                            <input type="hidden" name="action" value="remove">
+                        </div>
+                        <div class="col-xs-2">
                         </div>
-              <div class="col-xs-2"></div>
                         <div class="col-xs-2">
                             <button type="submit" style="width:60%;" class="btn col-xs-2">
                                 <span class="glyphicon glyphicon-trash"></span>
@@ -99,22 +78,16 @@
                 <p></p>
                 {% for g in group.group_member.all %}
                 <div class="row">
-            <form
+                    <form id="modal-form-group-member_{{ g.uuid }}" class="form-inline" role="form"
-              id="modal-form-group-member_{{ g.uuid }}"
+                          accept-charset="UTF-8" action="" data-remote="true" method="post">
-              class="form-inline"
-              role="form"
-              accept-charset="UTF-8"
-              action=""
-              data-remote="true"
-              method="post"
-            >
                         {% csrf_token %}
                         <div class="col-xs-8">
                             {{ g.name|safe }}
-                <input type="hidden" name="member" value="{{ g.url }}" />
+                            <input type="hidden" name="member" value="{{ g.url }}"/>
-                <input type="hidden" name="action" value="remove" />
+                            <input type="hidden" name="action" value="remove">
+                        </div>
+                        <div class="col-xs-2">
                         </div>
-              <div class="col-xs-2"></div>
                         <div class="col-xs-2">
                             <button type="submit" style="width:60%;" class="btn col-xs-2">
                                 <span class="glyphicon glyphicon-trash"></span>
@@ -123,29 +96,26 @@
                     </form>
                 </div>
                 {% endfor %}
+
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-package-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+
-    $("#edit-package-modal-submit").click(function (e) {
+
+$(function() {
+
+    $('#edit-package-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-package-modal-form").submit();
+        $('#edit-package-modal-form').submit();
     });
 
     $("#select_member").selectpicker();
-  });
+
+})
 </script>

templates/modals/objects/edit_model_modal.html

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

templates/modals/objects/edit_node_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Node -->
 <div id="edit_node_modal" class="modal" tabindex="-1">
@@ -5,66 +6,42 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Edit Node</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>Edit Node.</p>
-        <form
+                <form id="edit-node-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-node-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="node-name">Name</label>
-            <input
+                        <input id="node-name" class="form-control" name="node-name" value="{{ node.name|safe}}">
-              id="node-name"
-              class="form-control"
-              name="node-name"
-              value="{{ node.name|safe }}"
-            />
                     </p>
                     <p>
                         <label for="node-description">Description</label>
-            <input
+                        <input id="node-description" type="text" class="form-control"
-              id="node-description"
-              type="text"
-              class="form-control"
                                value="{{ node.description|safe }}"
-              name="node-description"
+                               name="node-description">
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-node-modal-submit">Create</button>
-        </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();
-      $("#edit-node-modal-form").submit();
+        $('#edit-node-modal-form').submit();
-    });
     });
+
+});
+
+
 </script>

templates/modals/objects/edit_package_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Package -->
 <div id="edit_package_modal" class="modal" tabindex="-1">
@@ -5,66 +6,40 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Update Package</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>Edit a Package.</p>
-        <form
+                <form id="edit-package-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-package-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="package-name">Name</label>
-            <input
+                        <input id="package-name" class="form-control" name="package-name" value="{{ package.name|safe}}">
-              id="package-name"
-              class="form-control"
-              name="package-name"
-              value="{{ package.name|safe }}"
-            />
                     </p>
                     <p>
                         <label for="package-description">Description</label>
-            <input
+                        <input id="package-description" type="text" class="form-control"
-              id="package-description"
-              type="text"
-              class="form-control"
                                value="{{ package.description|safe }}"
-              name="package-description"
+                               name="package-description">
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-package-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#edit-package-modal-submit").click(function (e) {
+
+    $('#edit-package-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-package-modal-form").submit();
+        $('#edit-package-modal-form').submit();
-    });
     });
+
+})
 </script>

templates/modals/objects/edit_package_permissions_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Package Permission -->
 <div id="edit_package_permissions_modal" class="modal" tabindex="-1">
@@ -5,23 +6,16 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Grant or Revoke Permissions</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>
-          Modify permissions for this package. Note that if you give
+                    Modify permissions for this package. Note that if you give <code>write</code>
-          <code>write</code> permissions to a user or group,
+                    permissions to a user or group, <code>read</code> permissions will be granted automatically.
-          <code>read</code> permissions will be granted automatically.
+                    <br>
-          <br />
+                    To allow users to perform destructive actions, such as deleting the package, <code>owner</code>
-          To allow users to perform destructive actions, such as deleting the
-          package, <code>owner</code>
                     permissions must be granted.
                 </p>
 
@@ -41,24 +35,12 @@
 				</div>
 
                 <div class="row">
-          <form
+                    <form id="modal-form-permissions" class="form-inline" role="form" accept-charset="UTF-8" action=""
-            id="modal-form-permissions"
+                          data-remote="true" method="post">
-            class="form-inline"
-            role="form"
-            accept-charset="UTF-8"
-            action=""
-            data-remote="true"
-            method="post"
-          >
                         {% csrf_token %}
                         <div class="col-xs-4">
-              <select
+                            <select id="select_grantee" name="grantee" data-actions-box='true'
-                id="select_grantee"
+                                    class="selPackages" data-width='100%'>
-                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>
@@ -70,20 +52,16 @@
                             </select>
                         </div>
                         <div class="col-xs-2">
-              <input type="checkbox" name="read" id="read_new" />
+                            <input type="checkbox" name="read" id="read_new"/>
                         </div>
                         <div class="col-xs-2">
-              <input type="checkbox" name="write" id="write_new" />
+                            <input type="checkbox" name="write" id="write_new"/>
                         </div>
                         <div class="col-xs-2">
-              <input type="checkbox" name="owner" id="owner_new" />
+                            <input type="checkbox" name="owner" id="owner_new"/>
                         </div>
                         <div class="col-xs-2">
-              <button
+                            <button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
-                type="submit"
-                style="width:60%;"
-                class="btn col-xs-2 modify-perm-button"
-              >
                                 <span class="glyphicon glyphicon-plus"></span>
                             </button>
                         </div>
@@ -92,50 +70,24 @@
                 <p></p>
                 {% for up in user_permissions %}
                 <div class="row">
-            <form
+                    <form id="modal-form-permissions_{{ up.user.uuid }}" class="form-inline" role="form"
-              id="modal-form-permissions_{{ up.user.uuid }}"
+                          accept-charset="UTF-8" action="" data-remote="true" method="post">
-              class="form-inline"
-              role="form"
-              accept-charset="UTF-8"
-              action=""
-              data-remote="true"
-              method="post"
-            >
                         {% csrf_token %}
                         <div class="col-xs-4">
                             {{ up.user.username }}
-                <input type="hidden" name="grantee" value="{{ up.user.url }}" />
+                            <input type="hidden" name="grantee" value="{{ up.user.url }}"/>
                         </div>
                         <div class="col-xs-2">
-                <input
+                            <input type="checkbox" name="read" id="read_{{ up.user.uuid }}" {% if up.has_read %} checked {% endif %}/>
-                  type="checkbox"
-                  name="read"
-                  id="read_{{ up.user.uuid }}"
-                  {% if up.has_read %}checked{% endif %}
-                />
                         </div>
                         <div class="col-xs-2">
-                <input
+                            <input type="checkbox" name="write" id="write_{{ up.user.uuid }}" {% if up.has_write %} checked {% endif %}/>
-                  type="checkbox"
-                  name="write"
-                  id="write_{{ up.user.uuid }}"
-                  {% if up.has_write %}checked{% endif %}
-                />
                         </div>
                         <div class="col-xs-2">
-                <input
+                            <input type="checkbox" name="owner" id="owner_{{ up.user.uuid }}" {% if up.has_all %} checked {% endif %}/>
-                  type="checkbox"
-                  name="owner"
-                  id="owner_{{ up.user.uuid }}"
-                  {% if up.has_all %}checked{% endif %}
-                />
                         </div>
                         <div class="col-xs-2">
-                <button
+                            <button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-button">
-                  type="submit"
-                  style="width:60%;"
-                  class="btn col-xs-2 modify-perm-button"
-                >
                                 <span class="glyphicon glyphicon-ok"></span>
                             </button>
                         </div>
@@ -145,93 +97,58 @@
                 <p></p>
                 {% for gp in group_permissions %}
                 <div class="row">
-            <form
+                    <form id="modal-form-permissions_{{ gp.user.uuid }}" class="form-inline" role="form"
-              id="modal-form-permissions_{{ gp.user.uuid }}"
+                          accept-charset="UTF-8" action="" data-remote="true" method="post">
-              class="form-inline"
-              role="form"
-              accept-charset="UTF-8"
-              action=""
-              data-remote="true"
-              method="post"
-            >
                         {% csrf_token %}
                         <div class="col-xs-4">
                             {{ gp.group.name|safe }}
-                <input
+                            <input type="hidden" name="grantee" value="{{ gp.group.url }}"/>
-                  type="hidden"
-                  name="grantee"
-                  value="{{ gp.group.url }}"
-                />
                         </div>
                         <div class="col-xs-2">
-                <input
+                            <input type="checkbox" name="read" id="read_{{ gp.group.uuid }}" {% if gp.has_read %} checked {% endif %}/>
-                  type="checkbox"
-                  name="read"
-                  id="read_{{ gp.group.uuid }}"
-                  {% if gp.has_read %}checked{% endif %}
-                />
                         </div>
                         <div class="col-xs-2">
-                <input
+                            <input type="checkbox" name="write" id="write_{{ gp.group.uuid }}" {% if gp.has_write %} checked {% endif %}/>
-                  type="checkbox"
-                  name="write"
-                  id="write_{{ gp.group.uuid }}"
-                  {% if gp.has_write %}checked{% endif %}
-                />
                         </div>
                         <div class="col-xs-2">
-                <input
+                            <input type="checkbox" name="owner" id="owner_{{ gp.group.uuid }}" {% if gp.has_all %} checked {% endif %}/>
-                  type="checkbox"
-                  name="owner"
-                  id="owner_{{ gp.group.uuid }}"
-                  {% if gp.has_all %}checked{% endif %}
-                />
                         </div>
                         <div class="col-xs-2">
-                <button
+                            <button type="submit" style="width:60%;" class="btn col-xs-2 modify-perm-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">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-package-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-package-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  function 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" && !$(readbox).prop("checked")) {
+
+    if (perm == 'read' && !$(readbox).prop("checked")) {
         $(writebox).prop("checked", false);
         $(ownerbox).prop("checked", false);
     }
 
-    if (perm == "write") {
+    if (perm == 'write') {
         if ($(writebox).prop("checked")) {
             $(readbox).prop("checked", true);
         }
@@ -240,25 +157,27 @@
         }
     }
 
-    if (perm == "owner") {
+    if (perm == 'owner') {
         if ($(ownerbox).prop("checked")) {
             $(readbox).prop("checked", true);
             $(writebox).prop("checked", true);
         }
     }
-  }
+}
 
-  $(function () {
+$(function() {
-    $("#edit-package-modal-submit").click(function (e) {
+
+    $('#edit-package-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-package-modal-form").submit();
+        $('#edit-package-modal-form').submit();
     });
 
     $("#select_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>

templates/modals/objects/edit_password_modal.html

@@ -5,78 +5,42 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Update your Password</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>To change your password please fill out the following inputs</p>
-        <form
+                <form id="edit-password-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-password-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="old-password">Old Password</label>
-            <input
+                        <input id="old-password" class="form-control" name="old-password" type="password" autocomplete="current-password">
-              id="old-password"
-              class="form-control"
-              name="old-password"
-              type="password"
-              autocomplete="current-password"
-            />
                     </p>
                     <p>
                         <label for="new-password">New Password</label>
-            <input
+                        <input id="new-password" class="form-control" name="new-password" type="password", autocomplete="new-password">
-              id="new-password"
-              class="form-control"
-              name="new-password"
-              type="password"
-              ,
-              autocomplete="new-password"
-            />
                     </p>
                     <p>
                         <label for="new-password-repeat">Repeat New Password</label>
-            <input
+                        <input id="new-password-repeat" class="form-control" name="new-password-repeat" type="password" autocomplete="new-password">
-              id="new-password-repeat"
-              class="form-control"
-              name="new-password-repeat"
-              type="password"
-              autocomplete="new-password"
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-password-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-password-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#edit-password-modal-submit").click(function (e) {
+
+    $('#edit-password-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-password-modal-form").submit();
+        $('#edit-password-modal-form').submit();
-    });
     });
+
+})
 </script>

templates/modals/objects/edit_pathway_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Pathway -->
 <div id="edit_pathway_modal" class="modal" tabindex="-1">
@@ -5,68 +6,39 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Edit Pathway</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>Edit Pathway.</p>
-        <form
+                <form id="edit-pathway-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-pathway-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="pathway-name">Name</label>
-            <input
+                        <input id="pathway-name" class="form-control" name="pathway-name" value="{{ pathway.name|safe }}">
-              id="pathway-name"
-              class="form-control"
-              name="pathway-name"
-              value="{{ pathway.name|safe }}"
-            />
                     </p>
                     <p>
                         <label for="pathway-description">Description</label>
-            <textarea
+                        <textarea id="pathway-description" type="text" class="form-control" name="pathway-description"
-              id="pathway-description"
+                                  rows="10">{{ pathway.description|safe }}</textarea>
-              type="text"
-              class="form-control"
-              name="pathway-description"
-              rows="10"
-            >
-{{ pathway.description|safe }}</textarea
-            >
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-pathway-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-pathway-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#edit-pathway-modal-submit").click(function (e) {
+
+    $('#edit-pathway-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-pathway-modal-form").submit();
+        $('#edit-pathway-modal-form').submit();
-    });
     });
+
+})
 </script>

templates/modals/objects/edit_prediction_setting_modal.html

@@ -5,31 +5,18 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Update Prediction Setting</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-        <p>
+                <p>To update your prediction setting modify parameters in the form below und click "Update"</p>
-          To update your prediction setting modify parameters in the form below
+                <form id="edit-prediction-setting-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          und click "Update"
-        </p>
-        <form
-          id="edit-prediction-setting-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <div id="prediction-setting" class="panel-collapse in collapse">
+                    <div id="prediction-setting" class="panel-collapse collapse in">
                         <div class="panel-body list-group-item">
-              <table class="table-bordered table-hover table">
+
+                            <table class="table table-bordered table-hover">
                                 <tr style="background-color: rgba(0, 0, 0, 0.08);">
                                     <th scope="col" width="20%">Parameter</th>
                                     <th scope="col" width="80%">Value</th>
@@ -39,26 +26,13 @@
                                 <tr>
                                     <td width="20%">Model</td>
                                     <td width="80%">
-                        <table
+                                        <table width="100%" class="table table-bordered table-hover">
-                          width="100%"
-                          class="table-bordered table-hover table"
-                        >
                                             <tbody>
                                             <tr>
                                                 <td colspan="2">
-                                <select
+                                                    <select id="model" name="model" class="form-control" data-width='100%'>
-                                  id="model"
-                                  name="model"
-                                  class="form-control"
-                                  data-width="100%"
-                                >
                                                     {% for m in models %}
-                                    <option
+                                                    <option value="{{ m.id }}" {% if user.prediction_settings.model.url == m.url %}selected{% endif %}>{{ m.name|safe }}</option>
-                                      value="{{ m.id }}"
-                                      {% if user.prediction_settings.model.url == m.url %}selected{% endif %}
-                                    >
-                                      {{ m.name|safe }}
-                                    </option>
                                                     {% endfor %}
                                                     </select>
                                                 </td>
@@ -76,15 +50,8 @@
                                                 </td>
                                                 <td width="80%">
                                                     {% if k == 'threshold' %}
-                                    <input
+                                                    <input type="number" class="form-control" name="{{k}}" value="{{v}}"
-                                      type="number"
+                                                           min="0" max="1" step="0.05">
-                                      class="form-control"
-                                      name="{{ k }}"
-                                      value="{{ v }}"
-                                      min="0"
-                                      max="1"
-                                      step="0.05"
-                                    />
                                                     {% endif %}
                                                 </td>
                                             </tr>
@@ -96,40 +63,22 @@
                                 {% endif %}
                                 {% for k, v in user.prediction_settings.truncator.items %}
                                 <tr>
-                      <td>
+                                    <td><p>
-                        <p>
                                         {% if k == 'max_nodes' %}
                                         Max Nodes
                                         {% elif k == 'max_depth' %}
                                         Max Depth
                                         {% endif %}
-                        </p>
+                                    </p></td>
-                      </td>
+                                    <td><p>
-                      <td>
-                        <p>
                                         {% if k == 'max_nodes' %}
-                            <input
+                                        <input type="number" class="form-control" name="{{k}}" value="{{v}}" min="1"
-                              type="number"
+                                               max="50" step="1">
-                              class="form-control"
-                              name="{{ k }}"
-                              value="{{ v }}"
-                              min="1"
-                              max="50"
-                              step="1"
-                            />
                                         {% elif k == 'max_depth' %}
-                            <input
+                                        <input type="number" class="form-control" name="{{k}}" value="{{v}}" min="1"
-                              type="number"
+                                               max="8" step="1">
-                              class="form-control"
-                              name="{{ k }}"
-                              value="{{ v }}"
-                              min="1"
-                              max="8"
-                              step="1"
-                            />
                                         {% endif %}
-                        </p>
+                                    </p></td>
-                      </td>
                                 </tr>
                                 {% endfor %}
                                 </tbody>
@@ -139,25 +88,19 @@
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-prediction-setting-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-prediction-setting-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+    $(function() {
-    $("#edit-prediction-setting-modal-submit").click(function (e) {
+
+        $('#edit-prediction-setting-modal-submit').click(function(e){
             e.preventDefault();
-      $("#edit-prediction-setting-modal-form").submit();
+            $('#edit-prediction-setting-modal-form').submit();
-    });
         });
+
+    })
 </script>

templates/modals/objects/edit_reaction_modal.html

@@ -1,69 +1,45 @@
+
 {% load static %}
 <!-- Edit Reaction -->
 <div id="edit_reaction_modal" class="modal" tabindex="-1">
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
                 <h3 class="modal-title">Update Reaction</h3>
             </div>
             <div class="modal-body">
-        <form
+                <form id="edit-reaction-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-reaction-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="reaction-name">Name</label>
-            <input
+                        <input id="reaction-name" class="form-control" name="reaction-name" value="{{ reaction.name|safe }}">
-              id="reaction-name"
-              class="form-control"
-              name="reaction-name"
-              value="{{ reaction.name|safe }}"
-            />
                     </p>
                     <p>
                         <label for="reaction-description">Description</label>
-            <input
+                        <input id="reaction-description" type="text" class="form-control"
-              id="reaction-description"
+                               value="{{ reaction.description|safe }}" name="reaction-description">
-              type="text"
-              class="form-control"
-              value="{{ reaction.description|safe }}"
-              name="reaction-description"
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-reaction-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-reaction-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#edit-reaction-modal-submit").click(function (e) {
+
+    $('#edit-reaction-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-reaction-modal-form").submit();
+        $('#edit-reaction-modal-form').submit();
-    });
     });
+
+});
+
+
 </script>

templates/modals/objects/edit_rule_modal.html

@@ -1,69 +1,45 @@
+
 {% load static %}
 <!-- Edit Rule -->
 <div id="edit_rule_modal" class="modal" tabindex="-1">
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
                 <h3 class="modal-title">Update Rule</h3>
             </div>
             <div class="modal-body">
-        <form
+                <form id="edit-rule-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-rule-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="rule-name">Name</label>
-            <input
+                        <input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name|safe }}">
-              id="rule-name"
-              class="form-control"
-              name="rule-name"
-              value="{{ rule.name|safe }}"
-            />
                     </p>
                     <p>
                         <label for="rule-description">Description</label>
-            <input
+                        <input id="rule-description" type="text" class="form-control"
-              id="rule-description"
+                               value="{{ rule.description|safe }}" name="rule-description">
-              type="text"
-              class="form-control"
-              value="{{ rule.description|safe }}"
-              name="rule-description"
-            />
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-rule-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-rule-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#edit-rule-modal-submit").click(function (e) {
+
+    $('#edit-rule-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-rule-modal-form").submit();
+        $('#edit-rule-modal-form').submit();
-    });
     });
+
+});
+
+
 </script>

templates/modals/objects/edit_user_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit User -->
 <div id="edit_user_modal" class="modal" tabindex="-1">
@@ -5,106 +6,57 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Update User Defaults</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>Edit User Defaults.</p>
-        <form
+                <form id="edit-user-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-user-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <p>
                         <label for="default-package">Default Package</label>
-            <select
+                        <select id="default-package" name="default-package" class="form-control" data-width='100%'>
-              id="default-package"
-              name="default-package"
-              class="form-control"
-              data-width="100%"
-            >
                             <option disabled>Select a Package</option>
                             {% for p in meta.writeable_packages %}
-                <option
+                            <option value="{{ p.url }}" {% if p.id == meta.user.default_package.id %}selected{% endif %}>{{ p.name|safe }}</option>
-                  value="{{ p.url }}"
-                  {% if p.id == meta.user.default_package.id %}selected{% endif %}
-                >
-                  {{ p.name|safe }}
-                </option>
                             {% endfor %}
                         </select>
                     </p>
                     <p>
                         <label for="default-group">Default Group</label>
-            <select
+                        <select id="default-group" name="default-group" class="form-control" data-width='100%'>
-              id="default-group"
-              name="default-group"
-              class="form-control"
-              data-width="100%"
-            >
                             <option disabled>Select a Group</option>
                             {% for g in meta.available_groups %}
-                <option
+                            <option value="{{ g.url }}" {% if g.id == meta.user.default_group.id %}selected{% endif %}>{{ g.name|safe }}</option>
-                  value="{{ g.url }}"
-                  {% if g.id == meta.user.default_group.id %}selected{% endif %}
-                >
-                  {{ g.name|safe }}
-                </option>
                             {% endfor %}
                         </select>
                     </p>
                     <p>
-            <label for="default-prediction-setting"
+                        <label for="default-prediction-setting">Default Prediction Setting</label>
-              >Default Prediction Setting</label
+                        <select id="default-prediction-setting" name="default-prediction-setting" class="form-control" data-width='100%'>
-            >
-            <select
-              id="default-prediction-setting"
-              name="default-prediction-setting"
-              class="form-control"
-              data-width="100%"
-            >
                             <option disabled>Select a Setting</option>
                             {% for s in meta.available_settings %}
-                <option
+                            <option value="{{ s.url }}" {% if s.id == meta.user.default_setting.id %}selected{% endif %}>{{ s.name|safe }}</option>
-                  value="{{ s.url }}"
-                  {% if s.id == meta.user.default_setting.id %}selected{% endif %}
-                >
-                  {{ s.name|safe }}
-                </option>
                             {% endfor %}
                         </select>
                     </p>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-user-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-user-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#edit-user-modal-submit").click(function (e) {
+
+    $('#edit-user-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-user-modal-form").submit();
+        $('#edit-user-modal-form').submit();
-    });
     });
+
+})
 </script>

templates/modals/objects/evaluate_model_modal.html

@@ -1,11 +1,6 @@
-<div
+
-  class="modal fade"
+<div class="modal fade" tabindex="-1" id="evaluate_model_modal" role="dialog" aria-labelledby="evaluate_model_modal"
-  tabindex="-1"
+     aria-hidden="true">
-  id="evaluate_model_modal"
-  role="dialog"
-  aria-labelledby="evaluate_model_modal"
-  aria-hidden="true"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
@@ -16,29 +11,17 @@
                 <h4 class="modal-title">Evaluate Model</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="evaluate_model_form" accept-charset="UTF-8" action="{{ current_object.url }}"
-          id="evaluate_model_form"
+                      data-remote="true" method="post">
-          accept-charset="UTF-8"
-          action="{{ current_object.url }}"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <div class="jumbotron">
                         For evaluation, you need to select the packages you want to use.
-            While the model is evaluating, you can use the model for
+                        While the model is evaluating, you can use the model for predictions.
-            predictions.
                     </div>
                     <!-- Evaluation Packages -->
                     <label for="model-evaluation-packages">Evaluation Packages</label>
-          <select
+                    <select id="model-evaluation-packages" name="model-evaluation-packages" data-actions-box='true'
-            id="model-evaluation-packages"
+                            class="form-control" multiple data-width='100%'>
-            name="model-evaluation-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 %}
@@ -56,38 +39,35 @@
 
                     <!-- Eval Type -->
                     <label for="model-evaluation-type">Evaluation Type</label>
-          <select
+                    <select id="model-evaluation-type" name="model-evaluation-type" class="form-control">
-            id="model-evaluation-type"
-            name="model-evaluation-type"
-            class="form-control"
-          >
                         <option disabled selected>Select evaluation type</option>
                         <option value="sg">Single Generation</option>
                         <option value="mg">Multiple Generations</option>
                     </select>
 
-          <input type="hidden" name="hidden" value="evaluate" />
+                    <input type="hidden" name="hidden" value="evaluate">
                 </form>
             </div>
             <div class="modal-footer">
-        <a id="evaluate_model_form_submit" class="btn btn-primary" href="#"
+                <a id="evaluate_model_form_submit" class="btn btn-primary" href="#">Evaluate</a>
-          >Evaluate</a
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-        >
-        <button type="button" class="btn btn-default" data-dismiss="modal">
-          Cancel
-        </button>
             </div>
         </div>
     </div>
 </div>
 
 <script>
+
     $(function () {
+
         $("#model-evaluation-packages").selectpicker();
 
-    $("#evaluate_model_form_submit").on("click", function (e) {
+        $('#evaluate_model_form_submit').on('click', function (e) {
             e.preventDefault();
-      $("#evaluate_model_form").submit();
+            $('#evaluate_model_form').submit();
         });
+
     });
+
+
 </script>

templates/modals/objects/export_package_modal.html

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

templates/modals/objects/generic_copy_object_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Copy Object -->
 <div id="generic_copy_object_modal" class="modal" tabindex="-1">
@@ -5,58 +6,30 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h3 class="modal-title">Copy {{ object_type|capfirst }}</h3>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-        <form
+                <form id="generic-copy-object-modal-form" accept-charset="UTF-8" data-remote="true" method="post">
-          id="generic-copy-object-modal-form"
-          accept-charset="UTF-8"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <label for="target-package"
+                    <label for="target-package">Select the Target Package you want to copy this {{ object_type }}
-            >Select the Target Package you want to copy this {{ object_type }}
+                        into</label>
-            into</label
+                    <select id="target-package" name="target-package" data-actions-box='true' class="form-control"
-          >
+                            data-width='100%'>
-          <select
-            id="target-package"
-            name="target-package"
-            data-actions-box="true"
-            class="form-control"
-            data-width="100%"
-          >
                         <option disabled selected>Select Target Package</option>
                         {% for p in meta.writeable_packages %}
-              <option value="{{ p.url }}">{{ p.name|safe }}</option>
+                            <option value="{{ p.url }}">{{ p.name|safe }}</option>`
-              `
                         {% endfor %}
                     </select>
-          <input type="hidden" name="hidden" value="copy" />
+                    <input type="hidden" name="hidden" value="copy">
                 </form>
-        <div
+                <div id="copy-object-error-message" class="alert alert-danger" role="alert" style="display: none">
-          id="copy-object-error-message"
+                </div>
-          class="alert alert-danger"
-          role="alert"
-          style="display: none"
-        ></div>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="generic-copy-object-modal-form-submit">
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="generic-copy-object-modal-form-submit"
-        >
                     Copy
                 </button>
             </div>
@@ -65,45 +38,38 @@
 </div>
 <script>
     $(function () {
-    $("#generic-copy-object-modal-form-submit").click(function (e) {
+
+        $('#generic-copy-object-modal-form-submit').click(function (e) {
             e.preventDefault();
-      $("#copy-object-error-message").hide();
+            $('#copy-object-error-message').hide()
 
-      const packageUrl = $("#target-package").find(":selected").val();
+            const packageUrl = $('#target-package').find(":selected").val();
 
-      if (
+            if (packageUrl === 'Select Target Package' || packageUrl === '' || packageUrl === null || packageUrl === undefined) {
-        packageUrl === "Select Target Package" ||
-        packageUrl === "" ||
-        packageUrl === null ||
-        packageUrl === undefined
-      ) {
                 return;
             }
             const formData = {
-        hidden: "copy",
+                hidden: 'copy',
-        object_to_copy: "{{ current_object.url }}",
+                object_to_copy: '{{ current_object.url }}',
-      };
+            }
 
             $.ajax({
-        type: "post",
+                type: 'post',
                 data: formData,
                 url: packageUrl,
                 success: function (data, textStatus) {
                     window.location.href = data.success;
                 },
                 error: function (jqXHR, textStatus, errorThrown) {
-          if (jqXHR.responseJSON.error.indexOf("to the same package") > -1) {
+                    if (jqXHR.responseJSON.error.indexOf('to the same package') > -1) {
-            $("#copy-object-error-message").append(
+                        $('#copy-object-error-message').append('<p>The target Package is the same as the source Package. Please select another target!</p>');
-              "<p>The target Package is the same as the source Package. Please select another target!</p>",
-            );
                     } else {
-            $("#copy-object-error-message").append(
+                        $('#copy-object-error-message').append('<p>' + jqXHR.responseJSON.error + '</p>');
-              "<p>" + jqXHR.responseJSON.error + "</p>",
+                    }
-            );
+                    $('#copy-object-error-message').show();
                 }
-          $("#copy-object-error-message").show();
-        },
-      });
             });
         });
+
+    })
 </script>

templates/modals/objects/generic_delete_modal.html

@@ -5,54 +5,38 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h3 class="modal-title">Delete {{ object_type|capfirst }}</h3>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 {% if object_type == 'user' %}
-          Clicking "Delete" will <strong>permanently</strong> delete the User
+                    Clicking "Delete" will <strong>permanently</strong> delete the User and associated data.
-          and associated data. This action can't be undone!
+                    This action can't be undone!
                 {% else %}
-          Deletes the {{ object_type|capfirst }}. Related objects that depend on
+                    Deletes the {{ object_type|capfirst }}. Related objects that depend on this {{ object_type|capfirst }}
-          this {{ object_type|capfirst }} will be deleted as well.
+                    will be deleted as well.
                 {% endif %}
-        <form
+                <form id="generic-delete-modal-form" accept-charset="UTF-8" action="{{ current_object.url }}"
-          id="generic-delete-modal-form"
+                      data-remote="true" method="post">
-          accept-charset="UTF-8"
-          action="{{ current_object.url }}"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <input type="hidden" id="hidden" name="hidden" value="delete" />
+                    <input type="hidden" id="hidden" name="hidden" value="delete"/>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="generic-delete-modal-form-submit">Delete</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="generic-delete-modal-form-submit"
-        >
-          Delete
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
     $(function () {
-    $("#generic-delete-modal-form-submit").click(function (e) {
+
+        $('#generic-delete-modal-form-submit').click(function (e) {
             e.preventDefault();
-      $("#generic-delete-modal-form").submit();
+            $('#generic-delete-modal-form').submit();
-    });
         });
+
+    })
 </script>

templates/modals/objects/generic_set_aliases_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 
 <style>
@@ -47,110 +48,66 @@
     }
 </style>
 
-<div
+<div class="modal fade bs-modal-lg" id="set_aliases_modal" tabindex="-1" aria-labelledby="set_aliases_modal"
-  class="modal fade bs-modal-lg"
+     aria-modal="true" role="dialog">
-  id="set_aliases_modal"
-  tabindex="-1"
-  aria-labelledby="set_aliases_modal"
-  aria-modal="true"
-  role="dialog"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">×</span>
                 </button>
-        <h4 class="modal-title">
+                <h4 class="modal-title">Set Aliases for {{ current_object.name|safe }}</h4>
-          Set Aliases for {{ current_object.name|safe }}
-        </h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="set_aliases_modal_form" accept-charset="UTF-8" action="{{ current_object.url }}"
-          id="set_aliases_modal_form"
+                      data-remote="true" method="post">
-          accept-charset="UTF-8"
-          action="{{ current_object.url }}"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <label for="alias-input">Aliases:</label>
                     <div class="form-control alias-container" id="alias-box">
                         {% for alias in current_object.aliases %}
-              <span class="alias"
+                        <span class="alias">{{ alias|escape }}<span class="remove">&times;</span></span>
-                >{{ alias|escape }}<span class="remove">&times;</span></span
-              >
                         {% endfor %}
-            <input
+                        <input type="text" id="alias-input" class="alias-input" placeholder="Add Alias...">
-              type="text"
-              id="alias-input"
-              class="alias-input"
-              placeholder="Add Alias..."
-            />
                     </div>
                 </form>
-        <div
+                <div id="add-alias-error-message" class="alert alert-danger" role="alert" style="display: none">
-          id="add-alias-error-message"
+                </div>
-          class="alert alert-danger"
-          role="alert"
-          style="display: none"
-        ></div>
             </div>
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close</button>
-          type="button"
+                <button type="button" class="btn btn-primary" id="set_aliases_modal_form_submit">Submit</button>
-          class="btn btn-secondary pull-left"
-          data-dismiss="modal"
-        >
-          Close
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="set_aliases_modal_form_submit"
-        >
-          Submit
-        </button>
             </div>
         </div>
     </div>
+
 </div>
 <script>
     $(function () {
+
         function addAlias(aliasText) {
             aliasText = aliasText.trim();
-      if (aliasText === "") return;
+            if (aliasText === '') return;
 
             // Avoid duplicate aliass
             var exists = false;
-      $("#alias-box .alias").each(function () {
+            $('#alias-box .alias').each(function () {
-        if (
+                if ($(this).text().replace('×', '').trim().toLowerCase() === aliasText.toLowerCase()) {
-          $(this).text().replace("×", "").trim().toLowerCase() ===
-          aliasText.toLowerCase()
-        ) {
                     exists = true;
                     return false;
                 }
             });
 
             if (!exists) {
-        var aliasHtml =
+                var aliasHtml = '<span class="alias">' + $('<div>').text(aliasText).html() +
-          '<span class="alias">' +
-          $("<div>").text(aliasText).html() +
                     '<span class="remove">&times;</span></span>';
-        $(aliasHtml).insertBefore("#alias-input");
+                $(aliasHtml).insertBefore('#alias-input');
             }
 
-      $("#alias-input").val("");
+            $('#alias-input').val('');
         }
 
         // Add alias when Enter is pressed
-    $("#alias-input").on("keypress", function (e) {
+        $('#alias-input').on('keypress', function (e) {
             if (e.which === 13) {
                 e.preventDefault();
                 addAlias($(this).val());
@@ -158,56 +115,56 @@
         });
 
         // Add alias when input loses focus
-    $("#alias-input").on("blur", function () {
+        $('#alias-input').on('blur', function () {
             var val = $(this).val();
-      if (val.trim() !== "") {
+            if (val.trim() !== '') {
                 addAlias(val);
             }
         });
 
         // Remove alias when clicking ×
-    $("#alias-box").on("click", ".remove", function () {
+        $('#alias-box').on('click', '.remove', function () {
-      $(this).closest(".alias").remove();
+            $(this).closest('.alias').remove();
         });
 
         // Focus input when clicking the container
-    $("#alias-box").on("click", function () {
+        $('#alias-box').on('click', function () {
-      $("#alias-input").focus();
+            $('#alias-input').focus();
         });
 
-    $("#set_aliases_modal_form_submit").on("click", function (e) {
+
+        $('#set_aliases_modal_form_submit').on('click', function (e) {
             e.preventDefault();
 
             let aliases = [];
-      $("#alias-box .alias").each(function () {
+            $('#alias-box .alias').each(function () {
-        aliases.push($(this).text().replace("×", "").trim());
+                aliases.push($(this).text().replace('×', '').trim())
             });
 
             if (aliases.length === 0) {
                 // Set empty string for deletion of all aliases
                 // If empty list is sent, its gets removed entirely from post data
-        aliases = [""];
+                aliases = ['']
             }
 
             formData = {
-        aliases: aliases,
+                'aliases': aliases
-      };
+            }
 
             $.ajax({
-        type: "post",
+                type: 'post',
                 data: formData,
-        url: "{{ current_object.url }}",
+                url: '{{ current_object.url }}',
                 traditional: true,
                 success: function (data, textStatus) {
                     window.location.href = data.success;
                 },
                 error: function (jqXHR, textStatus, errorThrown) {
-          $("#add-alias-error-message").append(
+                    $('#add-alias-error-message').append('<p>Setting aliases failed!</p>');
-            "<p>Setting aliases failed!</p>",
+                    $('#add-alias-error-message').show();                }
-          );
-          $("#add-alias-error-message").show();
-        },
             });
+
         });
+
     });
 </script>

templates/modals/objects/generic_set_external_reference_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Delete Object -->
 <div id="generic_set_external_reference_modal" class="modal" tabindex="-1">
@@ -5,93 +6,56 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h3 class="modal-title">Add External References</h3>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-        <form
+                <form id="generic-set-external-reference-modal-form" accept-charset="UTF-8"
-          id="generic-set-external-reference-modal-form"
-          accept-charset="UTF-8"
                       action="{{ current_object.url }}"
-          data-remote="true"
+                      data-remote="true" method="post">
-          method="post"
-        >
                     {% csrf_token %}
-          <label for="database-select"
+                    <label for="database-select">Select the Database you want to attach an External Reference
-            >Select the Database you want to attach an External Reference
+                        for</label>
-            for</label
+                    <select id="database-select" name="selected-database" data-actions-box='true' class="form-control"
-          >
+                            data-width='100%'>
-          <select
-            id="database-select"
-            name="selected-database"
-            data-actions-box="true"
-            class="form-control"
-            data-width="100%"
-          >
                         <option disabled selected>Select Database</option>
                         {% for entity, databases in meta.external_databases.items %}
                             {% if entity == object_type %}
                                 {% for db in databases %}
-                  <option
+                                    <option id="db-select-{{ db.database.pk }}" data-input-placeholder="{{ db.placeholder }}"
-                    id="db-select-{{ db.database.pk }}"
+                                            value="{{ db.database.id }}">{{ db.database.name|safe }}</option>`
-                    data-input-placeholder="{{ db.placeholder }}"
-                    value="{{ db.database.id }}"
-                  >
-                    {{ db.database.name|safe }}
-                  </option>
-                  `
                                 {% endfor %}
                             {% endif %}
                         {% endfor %}
                     </select>
                     <p></p>
                     <div id="input-div" style="display: none">
-            <label for="identifier">The reference</label>
+                        <label for="identifier" >The reference</label>
-            <input
+                        <input type="text" id="identifier" name="identifier" class="form-control" placeholder="">
-              type="text"
-              id="identifier"
-              name="identifier"
-              class="form-control"
-              placeholder=""
-            />
                     </div>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="generic-set-external-reference-modal-form-submit">Submit</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="generic-set-external-reference-modal-form-submit"
-        >
-          Submit
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
     $(function () {
+
         $("#database-select").on("change", function () {
             let selected = $(this).val();
-      $("#identifier").attr(
+            $("#identifier").attr("placeholder", $('#db-select-' + selected).data('input-placeholder'));
-        "placeholder",
-        $("#db-select-" + selected).data("input-placeholder"),
-      );
             $("#input-div").show();
         });
 
-    $("#generic-set-external-reference-modal-form-submit").click(function (e) {
+        $('#generic-set-external-reference-modal-form-submit').click(function (e) {
             e.preventDefault();
-      $("#generic-set-external-reference-modal-form").submit();
+            $('#generic-set-external-reference-modal-form').submit();
-    });
         });
+
+    })
 </script>

templates/modals/objects/generic_set_scenario_modal.html

@@ -1,71 +1,37 @@
+
 {% load static %}
-<div
+<div class="modal fade bs-modal-lg" id="set_scenario_modal" tabindex="-1" aria-labelledby="set_scenario_modal"
-  class="modal fade bs-modal-lg"
+     aria-modal="true" role="dialog">
-  id="set_scenario_modal"
-  tabindex="-1"
-  aria-labelledby="set_scenario_modal"
-  aria-modal="true"
-  role="dialog"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">×</span>
                 </button>
-        <h4 class="modal-title">
+                <h4 class="modal-title">Set Scenarios for {{ current_object.name|safe }}</h4>
-          Set Scenarios for {{ current_object.name|safe }}
-        </h4>
             </div>
             <div class="modal-body">
                 <div id="loading_scenario_div" class="text-center"></div>
-        <form
+                <form id="set_scenario_modal_form" accept-charset="UTF-8" action="{{ current_object.url }}"
-          id="set_scenario_modal_form"
+                      data-remote="true" method="post">
-          accept-charset="UTF-8"
-          action="{{ current_object.url }}"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <label for="scenario-select">Scenarios</label>
-          <select
+                    <select id="scenario-select" name="selected-scenarios" data-actions-box='true' class="form-control"
-            id="scenario-select"
+                            multiple data-width='100%'>
-            name="selected-scenarios"
-            data-actions-box="true"
-            class="form-control"
-            multiple
-            data-width="100%"
-          >
                         <option disabled>Select Scenarios</option>
                         <option value="" hidden></option>
                     </select>
                 </form>
             </div>
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-          type="button"
-          class="btn btn-secondary pull-left"
-          data-dismiss="modal"
-        >
-          Close
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="set_scenario_modal_form_submit"
-        >
-          Submit
                 </button>
+                <button type="button" class="btn btn-primary" id="set_scenario_modal_form_submit">Submit</button>
             </div>
         </div>
     </div>
+
 </div>
-{# prettier-ignore-start #}
 <script>
 
     $(function () {
@@ -109,4 +75,3 @@
     });
 
 </script>
-{# prettier-ignore-end #}

templates/modals/objects/identify_missing_rules_modal.html

@@ -5,33 +5,18 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h3 class="modal-title">Identify Missing Rules</h3>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
-        By clicking on Download we'll search the Pathway for Reactions that are
+                By clicking on Download we'll search the Pathway for Reactions that are not backed by
-        not backed by a Rule or which can be assembled by chaining two rules.
+                a Rule or which can be assembled by chaining two rules.
-        <form
+                <form id="identify-missing-rules-modal-form" accept-charset="UTF-8" action="{{ pathway.url }}"
-          id="identify-missing-rules-modal-form"
+                      data-remote="true" method="GET">
-          accept-charset="UTF-8"
-          action="{{ pathway.url }}"
-          data-remote="true"
-          method="GET"
-        >
                     <label for="rule-package">Select the Rule Package</label>
-          <select
+                    <select id="rule-package" name="rule-package" data-actions-box='true' class="form-control"
-            id="rule-package"
+                            data-width='100%'>
-            name="rule-package"
-            data-actions-box="true"
-            class="form-control"
-            data-width="100%"
-          >
                         <option disabled>Reviewed Packages</option>
                         {% for obj in meta.readable_packages %}
                             {% if obj.reviewed %}
@@ -46,30 +31,24 @@
                             {% endif %}
                         {% endfor %}
                     </select>
-          <input type="hidden" name="identify-missing-rules" value="true" />
+                    <input type="hidden" name="identify-missing-rules" value="true"/>
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="identify-missing-rules-modal-submit">Download</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="identify-missing-rules-modal-submit"
-        >
-          Download
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
     $(function () {
-    $("#identify-missing-rules-modal-submit").click(function (e) {
+
+        $('#identify-missing-rules-modal-submit').click(function (e) {
             e.preventDefault();
-      $("#identify-missing-rules-modal-form").submit();
+            $('#identify-missing-rules-modal-form').submit();
-      $("#identify_missing_rules_modal").modal("hide");
+            $('#identify_missing_rules_modal').modal('hide');
-    });
         });
+
+    })
 </script>

templates/modals/objects/manage_api_token_modal.html

@@ -1,52 +1,35 @@
-<div
+
-  class="modal fade"
+<div class="modal fade"
      tabindex="-1"
      id="manage_api_token_modal"
      role="dialog"
      aria-labelledby="manage_api_token_modal"
-  aria-hidden="true"
+     aria-hidden="true">
->
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-        <button type="button" class="close" data-dismiss="modal">
+                <button type="button"
+                        class="close"
+                        data-dismiss="modal">
                     <span aria-hidden="true">&times;</span>
                     <span class="sr-only">Close</span>
                 </button>
                 <h3 class="modal-title">Manage API Token</h3>
             </div>
             <div class="modal-body">
-        <p>
+                <p>Requesting a Token will invalidate all potential existing tokens. The new token will only be shown once, so ensure to store it in secure place</p>
-          Requesting a Token will invalidate all potential existing tokens. The
+                <form id="request_api_token_form"
-          new token will only be shown once, so ensure to store it in secure
-          place
-        </p>
-        <form
-          id="request_api_token_form"
                       accept-charset="UTF-8"
                       action=""
                       data-remote="true"
-          method="post"
+                      method="post">
-        >
                     {% csrf_token %}
                     <p>
                         <label for="token-name">Name</label>
-            <input
+                        <input type="text" id="token-name" class="form-control" name="name" placeholder="Generic Token for {{ meta.user.username }}"/>
-              type="text"
-              id="token-name"
-              class="form-control"
-              name="name"
-              placeholder="Generic Token for {{ meta.user.username }}"
-            />
                         <label for="valid-for">Valid for (in days)</label>
-            <input
+                        <input type="number" id="valid-for" class="form-control" name="valid-for" value="90"/>
-              type="number"
+                        <input type="hidden" name="hidden" value="request-api-token">
-              id="valid-for"
-              class="form-control"
-              name="valid-for"
-              value="90"
-            />
-            <input type="hidden" name="hidden" value="request-api-token" />
                     </p>
                 </form>
                 <div id="new-token">
@@ -54,23 +37,12 @@
                 </div>
                 <div id="existing-tokens">
                     {% for t in tokens %}
-            <form
+                    <form id="delete-token-{{ forloop.counter0 }}" accept-charset="UTF-8" action="{{ meta.user.url }}" data-remote="true" method="post">
-              id="delete-token-{{ forloop.counter0 }}"
-              accept-charset="UTF-8"
-              action="{{ meta.user.url }}"
-              data-remote="true"
-              method="post"
-            >
                         {% csrf_token %}
                         <div class="input-group">
-                <input type="hidden" name="hidden" value="delete" />
+                            <input type="hidden" name="hidden" value="delete">
-                <input type="hidden" name="token-id" value="{{ t.pk }}" />
+                            <input type="hidden" name="token-id" value="{{ t.pk }}">
-                <input
+                            <input type="text" class="form-control" value="{{ t.name|safe }}" disabled>
-                  type="text"
-                  class="form-control"
-                  value="{{ t.name|safe }}"
-                  disabled
-                />
                             <span class="input-group-btn">
                                 <button type="submit" class="btn btn-danger">Delete</button>
                             </span>
@@ -80,39 +52,41 @@
                 </div>
             </div>
             <div class="modal-footer">
-        <a id="manage_api_token_form_submit" class="btn btn-primary" href="#"
+                <a id="manage_api_token_form_submit"
-          >Submit</a
+                   class="btn btn-primary"
-        >
+                   href="#">Submit</a>
-        <button type="button" class="btn btn-default" data-dismiss="modal">
+                <button type="button"
-          Cancel
+                        class="btn btn-default"
+                        data-dismiss="modal">Cancel
                 </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#new-token").hide();
+    $('#new-token').hide()
 
-    $("#manage_api_token_form_submit").on("click", function (e) {
+    $('#manage_api_token_form_submit').on('click', function (e) {
         e.preventDefault();
 
-      const formData = $("#request_api_token_form").serialize();
+        const formData = $('#request_api_token_form').serialize();
-      $.post("", formData, function (response) {
+        $.post('', formData, function(response) {
-        $("#new-token-pre").text(response.raw_token);
+            $('#new-token-pre').text(response.raw_token);
-        $("#new-token").show();
+            $('#new-token').show();
         });
     });
 
     // Select all elements that start with 'delete-token-'
-    $("[id^='delete-token-']").on("submit", function (e) {
+    $("[id^='delete-token-']").on("submit", function(e) {
         e.preventDefault();
         const formData = $(this).serialize();
         const form = $(this);
-      $.post(this.action, formData, function (response) {
+        $.post(this.action, formData, function(response) {
             console.log(this);
             form.remove();
         });
     });
-  });
+
+});
 </script>

templates/modals/objects/publish_package_modal.html

@@ -5,48 +5,31 @@
         <div class="modal-content">
             <div class="modal-header">
                 <h5 class="modal-title">Publish Package</h5>
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
             </div>
             <div class="modal-body">
                 <p>Clicking on Publish will make this Package publicly available!</p>
-        <form
+                <form id="publish-package-modal-form" accept-charset="UTF-8" action="{{ current_package.url }}" data-remote="true" method="post">
-          id="publish-package-modal-form"
-          accept-charset="UTF-8"
-          action="{{ current_package.url }}"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
-          <input type="hidden" name="hidden" value="publish-package" />
+                    <input type="hidden" name="hidden" value="publish-package">
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="publish-package-modal-form-submit">Publish</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="publish-package-modal-form-submit"
-        >
-          Publish
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#publish-package-modal-form-submit").click(function (e) {
+
+    $('#publish-package-modal-form-submit').click(function(e){
         e.preventDefault();
-      $("#publish-package-modal-form").submit();
+        $('#publish-package-modal-form').submit();
-    });
     });
+
+})
 </script>

templates/modals/objects/retrain_model_modal.html

@@ -1,11 +1,5 @@
-<div
+<div class="modal fade" tabindex="-1" id="retrain_model_modal" role="dialog" aria-labelledby="retrain_model_modal"
-  class="modal fade"
+     aria-hidden="true">
-  tabindex="-1"
-  id="retrain_model_modal"
-  role="dialog"
-  aria-labelledby="retrain_model_modal"
-  aria-hidden="true"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
@@ -16,40 +10,34 @@
                 <h4 class="modal-title">Retrain Model</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="retrain_model_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/model"
-          id="retrain_model_form"
+                      data-remote="true" method="post">
-          accept-charset="UTF-8"
-          action="{{ meta.current_object.url }}"
-          data-remote="true"
-          method="post"
-        >
                     <div class="jumbotron">
-            To reflect changes in the rule or data packages, you can use the
+                        To reflect changes in the rule or data packages, you can use the "Retrain" button,
-            "Retrain" button, to let the model reflect the changes without
+                        to let the model reflect the changes without creating a new model.
-            creating a new model. While the model is retraining, it will be
+                        While the model is retraining, it will be unavailable for prediction.
-            unavailable for prediction.
                     </div>
                     {% csrf_token %}
-          <input type="hidden" name="hidden" value="retrain" />
+                    <input type="hidden" name="action" value="retrain">
                 </form>
             </div>
             <div class="modal-footer">
-        <a id="retrain_model_form_submit" class="btn btn-primary" href="#"
+                <a id="retrain_model_form_submit" class="btn btn-primary" href="#">Retrain</a>
-          >Retrain</a
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-        >
-        <button type="button" class="btn btn-default" data-dismiss="modal">
-          Cancel
-        </button>
             </div>
         </div>
     </div>
 </div>
 
 <script>
+
     $(function () {
-    $("#retrain_model_form_submit").on("click", function (e) {
+
+        $('#retrain_model_form_submit').on('click', function (e) {
             e.preventDefault();
-      $("#retrain_model_form").submit();
+            $('#retrain_model_form').submit();
         });
+
     });
+
 </script>

templates/modals/objects/set_license_modal.html

@@ -1,15 +1,15 @@
-<div
+<div class="modal fade"
-  class="modal fade"
      tabindex="-1"
      id="set_license_modal"
      role="dialog"
      aria-labelledby="set_license_modal"
-  aria-hidden="true"
+     aria-hidden="true">
->
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-        <button type="button" class="close" data-dismiss="modal">
+                <button type="button"
+                        class="close"
+                        data-dismiss="modal">
                     <span aria-hidden="true">&times;</span>
                     <span class="sr-only">Close</span>
                 </button>
@@ -21,152 +21,103 @@
                     <div class="col-md-9">
                         <p>
                             Set the license for all data in this package:
-              <br />
+                            <br> <br>
-              <br />
+                            (For more information please visit our <a target="#"
-              (For more information please visit our
+                                                                      href="https://wiki.envipath.org/index.php/License">wiki</a>.)
-              <a target="#" href="https://wiki.envipath.org/index.php/License"
-                >wiki</a
-              >.)
                         </p>
                     </div>
                     <div class="col-md-3">
                         <div id="ccfig"></div>
                     </div>
                 </div>
-        <form
+                <form id="set_license_form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="set_license_form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <div class="input-group">
                         <div class="radio">
-              <label
+                            <label><input type="radio" name="optlicense" onclick="cc()" id="ccradio">Creative commons license</label>
-                ><input
-                  type="radio"
-                  name="optlicense"
-                  onclick="cc()"
-                  id="ccradio"
-                />Creative commons license</label
-              >
                         </div>
                         <div>
                             <div class="checkbox">
-                <label
+                                <label><input type="checkbox" value="" onclick="cc()" id="ccremix" disabled>Allow adaptations of your work to be shared</label>
-                  ><input
-                    type="checkbox"
-                    value=""
-                    onclick="cc()"
-                    id="ccremix"
-                    disabled
-                  />Allow adaptations of your work to be shared</label
-                >
                             </div>
                             <div class="checkbox">
-                <label
+                                <label><input type="checkbox" value="" onclick="cc()" id="ccnocom" disabled>Prohibit commercial use</label>
-                  ><input
-                    type="checkbox"
-                    value=""
-                    onclick="cc()"
-                    id="ccnocom"
-                    disabled
-                  />Prohibit commercial use</label
-                >
                             </div>
                             <div class="checkbox">
-                <label
+                                <label><input type="checkbox" value="" onclick="cc()" id="ccalike" disabled>Share only if others share alike</label>
-                  ><input
-                    type="checkbox"
-                    value=""
-                    onclick="cc()"
-                    id="ccalike"
-                    disabled
-                  />Share only if others share alike</label
-                >
                             </div>
                         </div>
                         <div class="radio">
-              <label
+                            <label><input type="radio" name="optlicense" onclick="cc()" id="noccradio">No creative commons license, contact package owner for license information</label>
-                ><input
-                  type="radio"
-                  name="optlicense"
-                  onclick="cc()"
-                  id="noccradio"
-                />No creative commons license, contact package owner for license
-                information</label
-              >
                         </div>
                     </div>
-          <input type="hidden" id="license" name="license" />
+                    <input type="hidden" id="license" name="license">
+                    <input type="hidden" id="license-link" name="license-link">
+                    <input type="hidden" id="license-image-link" name="license-image-link">
                 </form>
             </div>
             <div class="modal-footer">
-        <button id="set_license_form_submit" class="btn btn-primary">
+                <button id="set_license_form_submit" class="btn btn-primary">Submit</button>
-          Submit
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-        </button>
-        <button type="button" class="btn btn-default" data-dismiss="modal">
-          Cancel
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  function ccstring(ccremix, ccnocom, ccalike) {
+
+function ccstring(ccremix, ccnocom, ccalike){
     var ccstring = "by";
 
-    if (ccnocom) {
+    if(ccnocom){
-      ccstring += "-nc";
+        ccstring +="-nc";
     }
 
-    if (!ccremix) {
+    if(!ccremix){
-      ccstring += "-nd";
+        ccstring +="-nd";
-    } else {
+    } else{
-      if (ccalike) {
+        if(ccalike){
-        ccstring += "-sa";
+            ccstring +="-sa";
         }
     }
     return ccstring;
-  }
+}
 
-  function cc() {
+function cc() {
-    var nocc = $("#noccradio").prop("checked");
+    var nocc = $('#noccradio').prop('checked')
-    var iscc = $("#ccradio").prop("checked");
+    var iscc = $('#ccradio').prop('checked');
 
-    if (nocc) {
+    if(nocc) {
-      $("#ccradio").prop("checked", false);
+        $('#ccradio').prop('checked', false);
-      $("#ccremix").prop("checked", false);
+        $('#ccremix').prop('checked', false);
-      $("#ccnocom").prop("checked", false);
+        $('#ccnocom').prop('checked', false);
-      $("#ccalike").prop("checked", false);
+        $('#ccalike').prop('checked', false);
 
-      $("#ccremix").prop("disabled", true);
+        $('#ccremix').prop('disabled', true);
-      $("#ccnocom").prop("disabled", true);
+        $('#ccnocom').prop('disabled', true);
-      $("#ccalike").prop("disabled", true);
+        $('#ccalike').prop('disabled', true);
     } else if (iscc) {
-      $("#ccremix").prop("disabled", false);
+        $('#ccremix').prop('disabled', false);
-      $("#ccnocom").prop("disabled", false);
+        $('#ccnocom').prop('disabled', false);
 
-      if ($("#ccremix").prop("checked")) {
+        if ($('#ccremix').prop('checked')) {
-        $("#ccalike").prop("disabled", false);
+            $('#ccalike').prop('disabled', false);
         } else {
-        $("#ccalike").prop("disabled", true);
+            $('#ccalike').prop('disabled', true);
         }
     }
 
-    var remix = $("#ccremix").prop("checked");
+    var remix = $('#ccremix').prop('checked');
-    var nocom = $("#ccnocom").prop("checked");
+    var nocom = $('#ccnocom').prop('checked');
-    var alike = $("#ccalike").prop("checked");
+    var alike = $('#ccalike').prop('checked');
 
-    if (nocc) {
+    if(nocc) {
-      $("#set_license_form_submit").prop("disabled", false);
+        $('#set_license_form_submit').prop('disabled', false);
-      $("#ccfig").empty();
+        $('#ccfig').empty();
-      $("#license").val("no-license");
+        $('#license').val('no-license')
-    } else if (iscc) {
+    } else if(iscc) {
-      $("#set_license_form_submit").prop("disabled", false);
+        $('#set_license_form_submit').prop('disabled', false);
-      $("#ccfig").empty();
+        $('#ccfig').empty();
-      var ccstr = ccstring(remix, nocom, alike);
+        var ccstr = ccstring(remix, nocom, alike)
 
         var link = `https://creativecommons.org/licenses/${ccstr}/4.0/`;
         var imageLink = `https://licensebuttons.net/l/${ccstr}/4.0/88x31.png`;
@@ -175,24 +126,28 @@
                        <img src='${imageLink}'>
                        </a>`;
 
-      $("#ccfig").append(img_tpl);
+        $('#ccfig').append(img_tpl);
-      $("#license").val(ccstr);
+        $('#license').val(ccstr);
+        $('#license-link').val(link);
+        $('#license-image-link').val(imageLink);
     } else {
-      $("#ccfig").empty();
+        $('#ccfig').empty();
-      $("#set_license_form_submit").prop("disabled", true);
+        $('#set_license_form_submit').prop('disabled', true);
-      $("#license").val("no-license");
+        $('#license').val('no-license')
-    }
     }
 
-  $(function () {
+}
+
+$(function() {
     // Disable by default as nothing is selected
 
     cc();
-    $("#set_license_form_submit").prop("disabled", true);
+    $('#set_license_form_submit').prop('disabled', true);
 
-    $("#set_license_form_submit").on("click", function (e) {
+     $('#set_license_form_submit').on('click', function (e) {
         e.preventDefault();
-      $("#set_license_form").submit();
+        $('#set_license_form').submit();
-    });
     });
+});
+
 </script>

templates/modals/objects/update_scenario_additional_information_modal.html

@@ -1,62 +1,39 @@
 {% load static %}
 <!-- Update Scenario Additional Information-->
-<div
+<div id="update_scenario_additional_information_modal" class="modal" tabindex="-1">
-  id="update_scenario_additional_information_modal"
-  class="modal"
-  tabindex="-1"
->
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">&times;</span>
                 </button>
                 <h3 class="modal-title">Update Additional Information</h3>
             </div>
             <div class="modal-body">
-        <form
+                <form id="edit-scenario-additional-information-modal-form" accept-charset="UTF-8" action="" data-remote="true" method="post">
-          id="edit-scenario-additional-information-modal-form"
-          accept-charset="UTF-8"
-          action=""
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     {% for widget in update_widgets %}
                         {{ widget|safe }}
                     {% endfor %}
-          <input
+                <input type="hidden" name="hidden" value="set-additional-information">
-            type="hidden"
-            name="hidden"
-            value="set-additional-information"
-          />
                 </form>
             </div>
             <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          Close
+                <button type="button" class="btn btn-primary" id="edit-scenario-additional-information-modal-submit">Update</button>
-        </button>
-        <button
-          type="button"
-          class="btn btn-primary"
-          id="edit-scenario-additional-information-modal-submit"
-        >
-          Update
-        </button>
             </div>
         </div>
     </div>
 </div>
 <script>
-  $(function () {
+$(function() {
-    $("#edit-scenario-additional-information-modal-submit").click(function (e) {
+
+    $('#edit-scenario-additional-information-modal-submit').click(function(e){
         e.preventDefault();
-      $("#edit-scenario-additional-information-modal-form").submit();
+        $('#edit-scenario-additional-information-modal-form').submit();
-    });
     });
+
+});
+
+
 </script>

templates/modals/predict_modal.html

@@ -1,157 +1,94 @@
 {% load static %}
-<div
+<div class="modal fade bs-modal-lg" id="predict_modal" tabindex="-1" aria-labelledby="predict_modal" aria-modal="true"
-  class="modal fade bs-modal-lg"
+     role="dialog">
-  id="predict_modal"
-  tabindex="-1"
-  aria-labelledby="predict_modal"
-  aria-modal="true"
-  role="dialog"
->
     <div class="modal-dialog modal-lg">
         <div class="modal-content">
             <div class="modal-header">
-        <button
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-          type="button"
-          class="close"
-          data-dismiss="modal"
-          aria-label="Close"
-        >
                     <span aria-hidden="true">×</span>
                 </button>
                 <h4 class="modal-title">Predict a Pathway</h4>
             </div>
             <div class="modal-body">
-        <form
+                <form id="predict_modal_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/pathway" data-remote="true" method="post">
-          id="predict_modal_form"
-          accept-charset="UTF-8"
-          action="{{ meta.current_package.url }}/pathway"
-          data-remote="true"
-          method="post"
-        >
                     {% csrf_token %}
                     <div class="row">
                         <div class="col-md-6">
                             <label for="name">Name</label>
-              <input
+                            <input id="name" class="form-control" name="name" placeholder="Name"/>
-                id="name"
-                class="form-control"
-                name="name"
-                placeholder="Name"
-              />
                             <label for="description">Description</label>
-              <input
+                            <input id="description" class="form-control" name="description" placeholder="Description"/>
-                id="description"
-                class="form-control"
-                name="description"
-                placeholder="Description"
-              />
                         </div>
                         <div class="col-md-6">
                             <label for="predict">Predict pathway or build yourself?</label>
                             <div class="radio" id="predict">
                                 <p>
                                     <label>
-                    <input
+                                        <input type="radio" name="predict" id="radioPredict" value="predict" checked/>Predict
-                      type="radio"
+                                        pathway
-                      name="predict"
-                      id="radioPredict"
-                      value="predict"
-                      checked
-                    />Predict pathway
                                     </label>
                                 </p>
                                 <p>
                                     <label>
-                    <input
+                                        <input type="radio" name="predict" id="radioIncremental" value="incremental"/>Incremental
-                      type="radio"
+                                        prediction
-                      name="predict"
-                      id="radioIncremental"
-                      value="incremental"
-                    />Incremental prediction
                                     </label>
                                 </p>
                                 <p>
                                     <label>
-                    <input
+                                        <input type="radio" name="predict" id="radioBuild" value="build"/>Build pathway
-                      type="radio"
-                      name="predict"
-                      id="radioBuild"
-                      value="build"
-                    />Build pathway
                                     </label>
                                 </p>
                             </div>
                         </div>
                     </div>
                     <label for="predict-modal-smiles">SMILES</label>
-          <input
+                    <input type="text" class="form-control" name="smiles" placeholder="SMILES" id="predict-modal-smiles">
-            type="text"
-            class="form-control"
-            name="smiles"
-            placeholder="SMILES"
-            id="predict-modal-smiles"
-          />
                     <p id="ketcher_container"></p>
                     <div>
-            <iframe
+                        <iframe id="predict-modal-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
-              id="predict-modal-ketcher"
+                                height="510"></iframe>
-              src="{% static '/js/ketcher2/ketcher.html' %}"
-              width="100%"
-              height="510"
-            ></iframe>
                     </div>
 
                     <label for="prediction-setting">Default Prediction Setting</label>
-          <select
+                    <select id="prediction-setting" name="prediction-setting" class="form-control"
-            id="prediction-setting"
+                            data-width='100%'>
-            name="prediction-setting"
-            class="form-control"
-            data-width="100%"
-          >
                         <option disabled>Select a Setting</option>
                         {% for s in meta.available_settings %}
-              <option
+                            <option value="{{ s.url }}"{% if s.id == meta.user.default_setting.id %}selected{% endif %}>
-                value="{{ s.url }}"
+                                {{ s.name|safe }}{% if s.id == meta.user.default_setting.id %} <i>(User default)</i>{% endif %}
-                {% if s.id == meta.user.default_setting.id %}selected{% endif %}
-              >
-                {{ s.name|safe }}{% if s.id == meta.user.default_setting.id %}
-                  <i>(User default)</i>
-                {% endif %}
                             </option>
                         {% endfor %}
                     </select>
+
                 </form>
             </div>
             <div class="modal-footer">
-        <button
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close
-          type="button"
-          class="btn btn-secondary pull-left"
-          data-dismiss="modal"
-        >
-          Close
-        </button>
-        <button type="button" class="btn btn-primary" id="predictButton">
-          Predict
                 </button>
+                <button type="button" class="btn btn-primary" id="predictButton">Predict</button>
             </div>
         </div>
     </div>
+
 </div>
 <script>
-  function predictModalketcherToPredictModalTextInput() {
-    $("#predict-modal-smiles").val(this.ketcher.getSmiles());
-  }
 
-  $(function () {
+function predictModalketcherToPredictModalTextInput() {
-    $("#predict-modal-ketcher").on("load", function () {
+    $('#predict-modal-smiles').val(this.ketcher.getSmiles());
+}
+
+$(function() {
+
+    $('#predict-modal-ketcher').on('load', function() {
         const checkKetcherReady = () => {
-        win = this.contentWindow;
+            win = this.contentWindow
-        if (win.ketcher && "editor" in win.ketcher) {
+            if (win.ketcher && 'editor' in win.ketcher) {
                 win.ketcher.editor.event.change.handlers.push({
                     once: false,
                     priority: 0,
                     f: predictModalketcherToPredictModalTextInput,
-            ketcher: win.ketcher,
+                    ketcher: win.ketcher
                 });
             } else {
                 setTimeout(checkKetcherReady, 100);
@@ -159,9 +96,9 @@
         };
 
         checkKetcherReady();
-    });
+    })
 
-    $("#predictButton").on("click", function (e) {
+    $('#predictButton').on('click', function(e) {
         e.preventDefault();
         $(this).prop("disabled", true);
 
@@ -172,7 +109,7 @@
         // existing pws...
 
         // submit form
-      $("#predict_modal_form").submit();
+        $('#predict_modal_form').submit();
-    });
     });
+});
 </script>

templates/modals/search_modal.html

@@ -1,686 +0,0 @@
-{% load static %}
-<dialog id="search_modal" class="modal @max-sm:modal-top justify-center">
-  <div class="modal-box h-full w-lvw p-1 sm:h-8/12 sm:w-[85vw] sm:max-w-5xl">
-    <!-- Search Input and Mode Selector -->
-    <div class="form-control mb-4 w-full shrink-0">
-      <div class="join m-0 w-full items-center p-3">
-        <label class="input join-item input-ghost grow">
-          <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>
-          <input
-            type="text"
-            autofocus
-            id="modal_searchbar"
-            placeholder="Benfuracarb"
-            class="grow"
-            aria-label="Search"
-          />
-        </label>
-
-        <!-- Mode Dropdown -->
-        <div>
-          <button
-            type="button"
-            tabindex="0"
-            id="modal_mode_button"
-            popovertarget="search_dropdown_menu"
-            style="anchor-name:--1"
-            class="btn join-item btn-ghost"
-          >
-            Text
-            <svg
-              class="ml-1 h-4 w-4"
-              fill="none"
-              stroke="currentColor"
-              viewBox="0 0 24 24"
-            >
-              <path
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                stroke-width="2"
-                d="M19 9l-7 7-7-7"
-              />
-            </svg>
-          </button>
-          <ul
-            tabindex="0"
-            class="dropdown dropdown-end menu bg-base-200 rounded-box w-64 p-2 shadow-lg"
-            popover
-            id="search_dropdown_menu"
-            style="position-anchor:--anchor-2"
-          >
-            <li class="menu-title">Text</li>
-            <li>
-              <a
-                id="modal_dropdown_text"
-                class="tooltip tooltip-left"
-                data-tip="Search on object names and descriptions"
-              >
-                Text
-              </a>
-            </li>
-            <li class="menu-title">SMILES</li>
-            <li>
-              <a
-                id="modal_dropdown_smiles_default"
-                class="tooltip tooltip-left"
-                data-tip="Ignores stereochemistry and charge"
-              >
-                Default
-              </a>
-            </li>
-            <li>
-              <a
-                id="modal_dropdown_smiles_canonical"
-                class="tooltip tooltip-left"
-                data-tip="Ignores stereochemistry, preserves charge"
-              >
-                Canonical
-              </a>
-            </li>
-            <li>
-              <a
-                id="modal_dropdown_smiles_exact"
-                class="tooltip tooltip-left"
-                data-tip="Exact match for stereochemistry and charge"
-              >
-                Exact
-              </a>
-            </li>
-            <li class="menu-title">InChI</li>
-            <li>
-              <a
-                id="modal_dropdown_inchikey"
-                class="tooltip tooltip-left"
-                data-tip="Search by InChIKey"
-              >
-                InChIKey
-              </a>
-            </li>
-          </ul>
-        </div>
-
-        <button
-          type="button"
-          id="modal_search_button"
-          class="btn btn-xs btn-ghost join-item"
-        >
-          <kbd class="kbd kbd-sm text-base-content/50 p-1">
-            <svg
-              xmlns="http://www.w3.org/2000/svg"
-              width="16"
-              height="16"
-              viewBox="0 0 24 24"
-              fill="none"
-              stroke="currentColor"
-              stroke-width="2"
-              stroke-linecap="round"
-              stroke-linejoin="round"
-              class="lucide lucide-corner-down-left-icon lucide-corner-down-left"
-            >
-              <path d="M20 4v7a4 4 0 0 1-4 4H4" />
-              <path d="m9 10-5 5 5 5" />
-            </svg>
-          </kbd>
-        </button>
-      </div>
-    </div>
-
-    <!-- Package Selector with Pills -->
-    <div class="form-control mb-4 shrink-0">
-      <!-- Pills Container -->
-      <div
-        id="modal_package_pills_container"
-        class="border-base-300 m-3 flex min-h-12 flex-wrap items-center gap-2 rounded-lg border-2 border-dashed p-3"
-      >
-        <!-- Pills will be added here dynamically -->
-      </div>
-
-      <!-- Package Dropdown Menu -->
-      <ul
-        class="dropdown dropdown-center menu bg-base-200 rounded-box max-h-96 w-80 overflow-y-auto p-2 shadow-lg"
-        popover
-        id="package_dropdown_menu"
-        style="position-anchor:--anchor-packages"
-      >
-        {% if unreviewed_packages %}
-          <li class="menu-title">Reviewed Packages</li>
-          {% for obj in reviewed_packages %}
-            <li>
-              <a
-                class="package-option flex items-center justify-between"
-                data-package-url="{{ obj.url }}"
-                data-package-name="{{ obj.name }}"
-              >
-                <span>{{ obj.name }}</span>
-                <svg
-                  xmlns="http://www.w3.org/2000/svg"
-                  class="package-checkmark hidden h-4 w-4"
-                  fill="none"
-                  viewBox="0 0 24 24"
-                  stroke="currentColor"
-                >
-                  <path
-                    stroke-linecap="round"
-                    stroke-linejoin="round"
-                    stroke-width="2"
-                    d="M5 13l4 4L19 7"
-                  />
-                </svg>
-              </a>
-            </li>
-          {% endfor %}
-          <li class="menu-title">Unreviewed Packages</li>
-          {% for obj in unreviewed_packages %}
-            <li>
-              <a
-                class="package-option flex items-center justify-between"
-                data-package-url="{{ obj.url }}"
-                data-package-name="{{ obj.name }}"
-              >
-                <span>{{ obj.name }}</span>
-                <svg
-                  xmlns="http://www.w3.org/2000/svg"
-                  class="package-checkmark hidden h-4 w-4"
-                  fill="none"
-                  viewBox="0 0 24 24"
-                  stroke="currentColor"
-                >
-                  <path
-                    stroke-linecap="round"
-                    stroke-linejoin="round"
-                    stroke-width="2"
-                    d="M5 13l4 4L19 7"
-                  />
-                </svg>
-              </a>
-            </li>
-          {% endfor %}
-        {% else %}
-          <li class="menu-title">Reviewed Packages</li>
-          {% for obj in reviewed_packages %}
-            <li>
-              <a
-                class="package-option flex items-center justify-between"
-                data-package-url="{{ obj.url }}"
-                data-package-name="{{ obj.name }}"
-              >
-                <span>{{ obj.name }}</span>
-                <svg
-                  xmlns="http://www.w3.org/2000/svg"
-                  class="package-checkmark hidden h-4 w-4"
-                  fill="none"
-                  viewBox="0 0 24 24"
-                  stroke="currentColor"
-                >
-                  <path
-                    stroke-linecap="round"
-                    stroke-linejoin="round"
-                    stroke-width="2"
-                    d="M5 13l4 4L19 7"
-                  />
-                </svg>
-              </a>
-            </li>
-          {% endfor %}
-        {% endif %}
-      </ul>
-    </div>
-
-    <!-- Loading Indicator -->
-    <div id="search_loading" class="hidden shrink-0 justify-center py-8">
-      <span class="loading loading-spinner loading-lg text-primary"></span>
-    </div>
-
-    <!-- Results Container - scrollable -->
-    <div id="search_results" class="min-h-0 flex-1 overflow-y-auto p-2"></div>
-  </div>
-
-  <!-- Backdrop to close -->
-  <form method="dialog" class="modal-backdrop">
-    <button>close</button>
-  </form>
-</dialog>
-
-<script>
-  (function () {
-    // Package Selector Module - Data-driven multiselect package selection
-    const PackageSelector = {
-      // Single source of truth: array of selected packages
-      selectedPackages: [],
-
-      elements: {
-        pillsContainer: null,
-        packageDropdown: null,
-        packageOptions: null,
-      },
-
-      init() {
-        this.cacheElements();
-        this.loadInitialSelection();
-        this.attachEventListeners();
-        this.render();
-      },
-
-      cacheElements() {
-        this.elements.pillsContainer = document.getElementById(
-          "modal_package_pills_container",
-        );
-        this.elements.packageDropdown = document.getElementById(
-          "package_dropdown_menu",
-        );
-        this.elements.packageOptions =
-          document.querySelectorAll(".package-option");
-      },
-
-      loadInitialSelection() {
-        // Load pre-selected packages from server-rendered pills
-        const existingPills =
-          this.elements.pillsContainer.querySelectorAll(".badge");
-        existingPills.forEach((pill) => {
-          this.selectedPackages.push({
-            url: pill.dataset.packageUrl,
-            name: pill.dataset.packageName,
-          });
-        });
-
-        // If no pills found, select all reviewed packages by default
-        if (this.selectedPackages.length === 0) {
-          // Iterate through all menu items and collect reviewed packages
-          const menuItems =
-            this.elements.packageDropdown.querySelectorAll("li");
-
-          for (const item of menuItems) {
-            // Check if this is the "Unreviewed Packages" menu title
-            if (
-              item.classList.contains("menu-title") &&
-              item.textContent.trim() === "Unreviewed Packages"
-            ) {
-              break; // Stop processing after this point
-            }
-
-            // Check for package options (only reviewed packages reach here)
-            const packageOption = item.querySelector(".package-option");
-            if (packageOption) {
-              this.selectedPackages.push({
-                url: packageOption.dataset.packageUrl,
-                name: packageOption.dataset.packageName,
-              });
-            }
-          }
-        }
-      },
-
-      attachEventListeners() {
-        // Toggle package selection on dropdown item click
-        this.elements.packageOptions.forEach((option) => {
-          option.addEventListener("click", (e) => {
-            e.preventDefault();
-            e.stopPropagation(); // Prevent dropdown from closing
-            const packageUrl = option.dataset.packageUrl;
-            const packageName = option.dataset.packageName;
-            this.togglePackageSelection(packageUrl, packageName);
-          });
-        });
-
-        // Remove package when X is clicked (using event delegation)
-        this.elements.pillsContainer.addEventListener("click", (e) => {
-          if (
-            e.target.classList.contains("package-remove-btn") ||
-            e.target.closest(".package-remove-btn")
-          ) {
-            const pill = e.target.closest(".badge");
-            if (pill) {
-              const packageUrl = pill.dataset.packageUrl;
-              this.removePackage(packageUrl);
-            }
-          }
-        });
-      },
-
-      togglePackageSelection(packageUrl, packageName) {
-        const index = this.selectedPackages.findIndex(
-          (pkg) => pkg.url === packageUrl,
-        );
-
-        if (index !== -1) {
-          // Remove from selection
-          this.selectedPackages.splice(index, 1);
-        } else {
-          // Add to selection
-          this.selectedPackages.push({ url: packageUrl, name: packageName });
-        }
-
-        this.render();
-      },
-
-      removePackage(packageUrl) {
-        const index = this.selectedPackages.findIndex(
-          (pkg) => pkg.url === packageUrl,
-        );
-        if (index !== -1) {
-          this.selectedPackages.splice(index, 1);
-          this.render();
-        }
-      },
-
-      render() {
-        this.renderPills();
-        this.renderAddButton();
-        this.renderCheckmarks();
-      },
-
-      renderPills() {
-        // Clear existing pills and button (except placeholder)
-        const pills = this.elements.pillsContainer.querySelectorAll(".badge");
-        pills.forEach((pill) => pill.remove());
-
-        const existingButton = this.elements.pillsContainer.querySelector(
-          "#modal_package_add_button",
-        );
-        if (existingButton) {
-          existingButton.remove();
-        }
-
-        // Create pills from data
-        this.selectedPackages.forEach((pkg) => {
-          const pill = this.createPillElement(pkg.url, pkg.name);
-          this.elements.pillsContainer.appendChild(pill);
-        });
-      },
-
-      renderAddButton() {
-        // Only render button if there are packages available
-        if (this.elements.packageOptions.length === 0) {
-          return;
-        }
-
-        const button = document.createElement("button");
-        button.type = "button";
-        button.id = "modal_package_add_button";
-        button.setAttribute("popovertarget", "package_dropdown_menu");
-        button.style.cssText = "anchor-name:--anchor-packages";
-        button.className = "btn btn-sm btn-ghost gap-2 text-base-content/50";
-
-        button.innerHTML = `
-                <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-plus-icon lucide-plus"><path d="M5 12h14"/><path d="M12 5v14"/></svg>
-                Add Package
-            `;
-
-        this.elements.pillsContainer.appendChild(button);
-      },
-
-      createPillElement(packageUrl, packageName) {
-        const pill = document.createElement("span");
-        pill.className = "badge badge-outline gap-2 max-w-xs";
-        pill.dataset.packageUrl = packageUrl;
-        pill.dataset.packageName = packageName;
-
-        pill.innerHTML = `
-                <span class="truncate" title="${packageName}">${packageName}</span>
-
-                <svg xmlns="http://www.w3.org/2000/svg"
-                class="h-4 w-4 cursor-pointer hover:text-error package-remove-btn flex-shrink-0 rotate-45"
-                viewBox="0 0 24 24"
-                fill="none" stroke="currentColor"
-                stroke-width="2"
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                >
-                <path d="M5 12h14"/><path d="M12 5v14"/>
-                </svg>
-            `;
-
-        return pill;
-      },
-
-      renderCheckmarks() {
-        // Update all checkmarks based on selected packages
-        this.elements.packageOptions.forEach((option) => {
-          const packageUrl = option.dataset.packageUrl;
-          const isSelected = this.selectedPackages.some(
-            (pkg) => pkg.url === packageUrl,
-          );
-          const checkmark = option.querySelector(".package-checkmark");
-
-          if (checkmark) {
-            checkmark.classList.toggle("hidden", !isSelected);
-          }
-        });
-      },
-
-      getSelectedPackages() {
-        return this.selectedPackages.map((pkg) => pkg.url);
-      },
-    };
-
-    // Modal and Search Management
-    const modal = document.getElementById("search_modal");
-    const searchbar = document.getElementById("modal_searchbar");
-    const searchButton = document.getElementById("modal_search_button");
-    const modeButton = document.getElementById("modal_mode_button");
-    const resultsDiv = document.getElementById("search_results");
-    const loadingDiv = document.getElementById("search_loading");
-
-    // MutationObserver to detect when modal opens
-    const observer = new MutationObserver((mutations) => {
-      mutations.forEach((mutation) => {
-        if (mutation.attributeName === "open" && modal.open) {
-          PackageSelector.render();
-          // Delay focus to allow CSS transitions to complete (modal has 0.3s transition)
-          setTimeout(() => {
-            searchbar.focus();
-          }, 320);
-        }
-      });
-    });
-
-    observer.observe(modal, { attributes: true });
-
-    // Close modal when clicking outside (on the backdrop)
-    // According to DaisyUI docs: https://daisyui.com/components/modal/
-    // The backdrop form with method="dialog" should handle closing automatically when its button is clicked.
-    // We also handle clicks directly on the dialog element (backdrop area) or the backdrop form.
-    modal.addEventListener("click", function (event) {
-      const backdrop = modal.querySelector(".modal-backdrop");
-      const modalBox = modal.querySelector(".modal-box");
-
-      // Close if clicking directly on the dialog element (backdrop area)
-      // or on the backdrop form (but ensure we're not clicking on modal-box content)
-      if (
-        event.target === modal ||
-        (backdrop &&
-          (event.target === backdrop || backdrop.contains(event.target)) &&
-          !modalBox.contains(event.target))
-      ) {
-        modal.close();
-      }
-    });
-
-    // Clear results when modal closes
-    modal.addEventListener("close", function () {
-      resultsDiv.innerHTML = "";
-      loadingDiv.classList.add("hidden");
-      searchbar.value = "";
-    });
-
-    // Mode dropdown handlers
-    const dropdownMenu = document.getElementById("search_dropdown_menu");
-
-    const modeButtons = [
-      { id: "modal_dropdown_text", text: "Text" },
-      { id: "modal_dropdown_smiles_default", text: "Default" },
-      { id: "modal_dropdown_smiles_canonical", text: "Canonical" },
-      { id: "modal_dropdown_smiles_exact", text: "Exact" },
-      { id: "modal_dropdown_inchikey", text: "InChIKey" },
-    ];
-
-    modeButtons.forEach(({ id, text }) => {
-      document.getElementById(id).addEventListener("click", function (e) {
-        e.preventDefault();
-        modeButton.innerHTML =
-          text +
-          ` <svg class="w-4 h-4 ml-1" fill="none" stroke="currentColor" viewBox="0 0 24 24">
-                <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M19 9l-7 7-7-7"/>
-            </svg>`;
-        // Close dropdown using popover API
-        if (dropdownMenu && typeof dropdownMenu.hidePopover === "function") {
-          dropdownMenu.hidePopover();
-        }
-      });
-    });
-
-    // Initialize Package Selector
-    PackageSelector.init();
-
-    // Search Response Handler
-    function handleSearchResponse(data) {
-      resultsDiv.innerHTML = "";
-
-      function makeContent(objs) {
-        let links = "";
-        objs.forEach((obj) => {
-          links += `<a href="${obj.url}" class="block px-4 py-2 hover:bg-base-300 rounded-lg transition-colors">${obj.name}</a>`;
-        });
-        return links;
-      }
-
-      let allEmpty = true;
-      let content = "";
-
-      // Category order for better UX
-      const categoryOrder = [
-        "Compounds",
-        "Compound Structures",
-        "Rules",
-        "Reactions",
-        "Pathways",
-      ];
-
-      categoryOrder.forEach((key) => {
-        if (!data[key] || data[key].length < 1) {
-          return;
-        }
-        allEmpty = false;
-
-        content += `
-                <div class="collapse collapse-arrow bg-base-200 mb-2">
-                    <input type="checkbox" checked />
-                    <div class="collapse-title font-medium">
-                        ${key} <span class="badge badge-neutral badge-sm ml-2">${data[key].length}</span>
-                    </div>
-                    <div class="collapse-content">
-                        ${makeContent(data[key])}
-                    </div>
-                </div>
-            `;
-      });
-
-      if (allEmpty) {
-        resultsDiv.innerHTML = `
-                <div class="alert alert-warning">
-                    <svg class="w-6 h-6" fill="none" stroke="currentColor" viewBox="0 0 24 24">
-                        <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M12 9v2m0 4h.01m-6.938 4h13.856c1.54 0 2.502-1.667 1.732-3L13.732 4c-.77-1.333-2.694-1.333-3.464 0L3.34 16c-.77 1.333.192 3 1.732 3z"/>
-                    </svg>
-                    <span>No results found</span>
-                </div>
-            `;
-      } else {
-        resultsDiv.innerHTML = `
-                <div class="mb-2">
-                    <div class="text-sm font-semibold text-base-content/70 mb-2">Results</div>
-                    ${content}
-                </div>
-            `;
-      }
-    }
-
-    // Search Execution
-    function performSearch(e) {
-      e.preventDefault();
-
-      const query = searchbar.value.trim();
-
-      if (!query) {
-        console.log("Search phrase empty, won't do search");
-        return;
-      }
-
-      const selPacks = PackageSelector.getSelectedPackages();
-
-      if (selPacks.length < 1) {
-        console.log("No package selected, won't do search");
-        resultsDiv.innerHTML = `
-                <div class="alert alert-info">
-                    <svg class="w-6 h-6" fill="none" stroke="currentColor" viewBox="0 0 24 24">
-                        <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"/>
-                    </svg>
-                    <span>Please select at least one package</span>
-                </div>
-            `;
-        return;
-      }
-
-      const mode = modeButton.textContent.trim().toLowerCase();
-
-      const params = new URLSearchParams();
-      selPacks.forEach((pack) => params.append("packages", pack));
-      params.append("search", query);
-      params.append("mode", mode);
-
-      // Show loading
-      loadingDiv.classList.remove("hidden");
-      resultsDiv.innerHTML = "";
-
-      fetch(`{{ SERVER_BASE }}/search?${params.toString()}`, {
-        method: "GET",
-        headers: {
-          Accept: "application/json",
-        },
-      })
-        .then((response) => {
-          if (!response.ok) {
-            throw new Error("Search request failed");
-          }
-          return response.json();
-        })
-        .then((result) => {
-          loadingDiv.classList.add("hidden");
-          handleSearchResponse(result);
-        })
-        .catch((error) => {
-          loadingDiv.classList.add("hidden");
-          console.error("Search error:", error);
-          resultsDiv.innerHTML = `
-                <div class="alert alert-error">
-                    <svg class="w-6 h-6" fill="none" stroke="currentColor" viewBox="0 0 24 24">
-                        <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M12 8v4m0 4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"/>
-                    </svg>
-                    <span>Search failed. Please try again.</span>
-                </div>
-            `;
-        });
-    }
-
-    // Event listeners for search
-    searchButton.addEventListener("click", performSearch);
-    searchbar.addEventListener("keydown", function (e) {
-      if (e.key === "Enter") {
-        performSearch(e);
-      }
-    });
-  })();
-</script>