minor

## Major Changes
- Predict Pathway is now a separate view as it is meant as adavanced prediction interface

## Current status
![image.png](/attachments/c5bc3f5c-cf30-4b5f-acb3-a70117a96dae)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#188
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>

.gitea/workflows/ci.yaml

@@ -105,7 +105,7 @@ jobs:
           until pg_isready -h postgres -U postgres; do sleep 2; done
           # until redis-cli -h redis ping; do sleep 2; done
 
-      - name: Run Django migrations
+      - name: Run Django Migrations
         run: |
           source .venv/bin/activate
           python manage.py migrate --noinput

envipath/settings.py

@@ -87,6 +87,7 @@ 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

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

epdb/context_processors.py

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

epdb/management/commands/bootstrap.py

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

epdb/migrations/0010_license_cc_string.py

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

epdb/migrations/0011_auto_20251111_1413.py

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

epdb/models.py

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

epdb/urls.py

@@ -48,6 +48,7 @@ urlpatterns = [
     re_path(r"^user$", v.users, name="users"),
     re_path(r"^group$", v.groups, name="groups"),
     re_path(r"^search$", v.search, name="search"),
+    re_path(r"^predict$", v.predict_pathway, name="predict_pathway"),
     # User Detail
     re_path(rf"^user/(?P<user_uuid>{UUID})", v.user, name="user"),
     # Group Detail

epdb/views.py

@@ -362,6 +362,18 @@ 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)
+
+
 def packages(request):
     current_user = _anonymous_or_real(request)
 
@@ -682,7 +694,6 @@ 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
@@ -783,6 +794,7 @@ def package_models(request, package_uuid):
 
     elif request.method == "POST":
         log_post_params(request)
+
         name = request.POST.get("model-name")
         description = request.POST.get("model-description")
 
@@ -1072,9 +1084,7 @@ def package(request, package_uuid):
         write = request.POST.get("write") == "on"
         owner = request.POST.get("owner") == "on"
 
-        license = request.POST.get("license")
+        cc_string = request.POST.get("license")
-        license_link = request.POST.get("license-link")
-        license_image_link = request.POST.get("license-image-link")
 
         if new_package_name:
             current_package.name = new_package_name
@@ -1102,24 +1112,15 @@ def package(request, package_uuid):
 
             PackageManager.update_permissions(current_user, current_package, grantee, max_perm)
             return redirect(current_package.url)
-        elif license is not None:
-            if license == "no-license":
-                if current_package.license is not None:
-                    current_package.license.delete()
 
+        elif cc_string is not None:
+            cc_string = cc_string.strip()
+            if cc_string == "no-license":  # Reset the package's license
                 current_package.license = None
                 current_package.save()
                 return redirect(current_package.url)
-            else:
+            else:  # Get the license and assign it to the package
-                if current_package.license is not None:
+                current_package.license = License.objects.get(cc_string=cc_string)
-                    current_package.license.delete()
-
-                license = License()
-                license.link = license_link
-                license.image_link = license_image_link
-                license.save()
-
-                current_package.license = license
                 current_package.save()
 
                 return redirect(current_package.url)
@@ -1174,7 +1175,7 @@ def package_compounds(request, package_uuid):
 
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
-        compound_smiles = request.POST.get("compound-smiles").strip()
+        compound_smiles = request.POST.get("compound-smiles")
         compound_description = request.POST.get("compound-description")
 
         c = Compound.create(current_package, compound_smiles, compound_name, compound_description)
@@ -1301,7 +1302,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
 
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
-        structure_smiles = request.POST.get("structure-smiles").strip()
+        structure_smiles = request.POST.get("structure-smiles")
         structure_description = request.POST.get("structure-description")
 
         try:
@@ -1483,11 +1484,11 @@ def package_rules(request, package_uuid):
 
         # Obtain parameters as required by rule type
         if rule_type == "SimpleAmbitRule":
-            params["smirks"] = request.POST.get("rule-smirks").strip()
+            params["smirks"] = request.POST.get("rule-smirks")
             params["reactant_filter_smarts"] = request.POST.get("rule-reactant-smarts")
             params["product_filter_smarts"] = request.POST.get("rule-product-smarts")
         elif rule_type == "SimpleRDKitRule":
-            params["reaction_smarts"] = request.POST.get("rule-reaction-smarts").strip()
+            params["reaction_smarts"] = request.POST.get("rule-reaction-smarts")
         elif rule_type == "ParallelRule":
             pass
         elif rule_type == "SequentialRule":
@@ -1684,8 +1685,7 @@ def package_reactions(request, package_uuid):
     elif request.method == "POST":
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
-
+        reactions_smirks = request.POST.get("reaction-smirks")
-        reactions_smirks = request.POST.get("reaction-smirks").strip()
         educts = reactions_smirks.split(">>")[0].split(".")
         products = reactions_smirks.split(">>")[1].split(".")
 
@@ -2259,6 +2259,7 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
 
     elif request.method == "POST":
         log_post_params(request)
+
         edge_name = request.POST.get("edge-name")
         edge_description = request.POST.get("edge-description")
 

static/css/input.css

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

templates/actions/collections/pathway.html

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

templates/framework.html

@@ -1,11 +1,15 @@
-<!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 rel="shortcut icon" type="image/png" href="{% static 'images/favicon.ico' %}"/>
+    <link
+      rel="shortcut icon"
+      type="image/png"
+      href="{% static 'images/favicon.ico' %}"
+    />
 
     {# Tailwind CSS disabled for legacy Bootstrap framework #}
     {# Pages using this framework will be migrated to framework_modern.html incrementally #}
@@ -13,36 +17,45 @@
 
     {# Legacy Bootstrap 3.3.7 - scoped to .legacy-bootstrap #}
     <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
-    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
+    <link
+      rel="stylesheet"
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+    />
     <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
     <script src="https://ajax.aspnetcdn.com/ajax/jquery.templates/beta1/jquery.tmpl.js"></script>
-    <link href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
+    <link
-    <link rel="stylesheet"
+      href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css"
-          href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.css">
+      rel="stylesheet"
+    />
+    <link
+      rel="stylesheet"
+      href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.css"
+    />
     <script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/js/bootstrap-select.min.js"></script>
     <script src="https://community.envipath.org/javascripts/embed-topics.js"></script>
     <!-- CDN END -->
 
     {# Bootstrap compatibility styles #}
     <style>
-        /* Ensure proper viewport behavior */
+      /* Ensure proper viewport behavior */
-        html, body {
+      html,
-            height: 100%; /* ensure body fills viewport */
+      body {
-            overflow-x: hidden; /* prevent horizontal scroll */
+        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
+      // Setup CSRF header for all jQuery AJAX requests
-        $.ajaxSetup({
+      $.ajaxSetup({
-            beforeSend: function(xhr, settings) {
+        beforeSend: function (xhr, settings) {
-                if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
+          if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
-                    xhr.setRequestHeader("X-CSRFToken", csrftoken);
+            xhr.setRequestHeader("X-CSRFToken", csrftoken);
-                }
+          }
-            }
+        },
-        });
+      });
     </script>
 
     <!--    {# C3 CSS #}-->
@@ -50,40 +63,44 @@
     <!--    {# EP CSS #}-->
     <!--    <link id="css-pps_white_general" href="{% static 'css/epp.css' %}" rel="stylesheet" type="text/css"/>-->
 
-
     {# General EP JS #}
     <script src="{% static 'js/pps.js' %}"></script>
     {# Modal Steps for Stepwise Modal Wizards #}
     <script src="{% static 'js/jquery-bootstrap-modal-steps.js' %}"></script>
 
     {% if not debug %}
-        <!-- Matomo -->
+      <!-- Matomo -->
-        <script>
+      <script>
-            var _paq = window._paq = window._paq || [];
+        var _paq = (window._paq = window._paq || []);
-            /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+        /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
-            _paq.push(['trackPageView']);
+        _paq.push(["trackPageView"]);
-            _paq.push(['enableLinkTracking']);
+        _paq.push(["enableLinkTracking"]);
-            (function () {
+        (function () {
-                var u = "//matomo.envipath.com/";
+          var u = "//matomo.envipath.com/";
-                _paq.push(['setTrackerUrl', u + 'matomo.php']);
+          _paq.push(["setTrackerUrl", u + "matomo.php"]);
-                _paq.push(['setSiteId', '{{ meta.site_id }}']);
+          _paq.push(["setSiteId", "{{ meta.site_id }}"]);
-                var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
+          var d = document,
-                g.async = true;
+            g = d.createElement("script"),
-                g.src = u + 'matomo.js';
+            s = d.getElementsByTagName("script")[0];
-                s.parentNode.insertBefore(g, s);
+          g.async = true;
-            })();
+          g.src = u + "matomo.js";
-        </script>
+          s.parentNode.insertBefore(g, s);
-        <!-- End Matomo Code -->
+        })();
+      </script>
+      <!-- End Matomo Code -->
     {% endif %}
-
+  </head>
-</head>
+  <body>
-<body>
+    <!-- Legacy Bootstrap navbar - isolated from Tailwind -->
-<!-- Legacy Bootstrap navbar - isolated from Tailwind -->
+    <div class="legacy-bootstrap">
-<div class="legacy-bootstrap">
+      <nav
-<nav class="navbar navbar-default navbar-inverse" style="border-radius:0px;" role="navigation">
+        class="navbar navbar-default navbar-inverse"
-    <div class="container-fluid">
+        style="border-radius:0px;"
-        <!-- Brand and toggle get grouped for better mobile display -->
+        role="navigation"
-        <div class="navbar-header navbar-header-framework">
+      >
+        <div class="container-fluid">
+          <!-- Brand and toggle get grouped for better mobile display -->
+          <div class="navbar-header navbar-header-framework">
             <!--            <button type="button" class="navbar-toggle navbar-toggle-framework" data-toggle="collapse"-->
             <!--                    data-target="#navbarCollapse">-->
             <!--                <span class="sr-only">Toggle navigation</span>-->
@@ -91,204 +108,315 @@
             <!--                <span class="icon-bar"></span>-->
             <!--                <span class="icon-bar"></span>-->
             <!--            </button>-->
-            <a id="pictureLink" href="{{ meta.server_url }}" class="navbar-brand">
+            <a
-                <img id="image-logo-short-white.svg" src='{% static "/images/logo-short-white.svg" %}' width="100"
+              id="pictureLink"
-                     alt="enviPath">
+              href="{{ meta.server_url }}"
+              class="navbar-brand"
+            >
+              <img
+                id="image-logo-short-white.svg"
+                src="{% static "/images/logo-short-white.svg" %}"
+                width="100"
+                alt="enviPath"
+              />
             </a>
-        </div>
+          </div>
 
-        <!-- Collect the nav links, forms, and other content for toggling -->
+          <!-- Collect the nav links, forms, and other content for toggling -->
-        <div class="collapse navbar-collapse collapse-framework navbar-collapse-framework" id="navbarCollapse">
+          <div
+            class="collapse navbar-collapse collapse-framework navbar-collapse-framework"
+            id="navbarCollapse"
+          >
             <ul class="nav navbar-nav navbar-nav-framework">
+              <li>
+                <a href="{{ meta.server_url }}/predict"> Predict Pathway </a>
+              </li>
+              {#                <li class="dropdown">#}
+              {#                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
+              {#                    <ul role="menu" class="dropdown-menu">#}
+              {#                        <li>#}
+              {#                            <a class="button" data-toggle="modal" data-target="#predict_modal">#}
+              {#                                <i class="	glyphicon glyphicon-tag"></i> Predict Pathway#}
+              {#                            </a>#}
+              {#                        </li>#}
+              {#                        <li>#}
+              {#                            <a class="button" data-toggle="modal" data-target="#batch_predict_modal">#}
+              {#                                <i class="	glyphicon glyphicon-tags"></i> Batch Prediction#}
+              {#                            </a>#}
+              {#                        </li>#}
+              {#                    </ul>#}
+              {#                </li>#}
+              <li>
+                <a href="{{ meta.server_url }}/package" id="packageLink"
+                  >Package</a
+                >
+              </li>
+              <li>
+                <a href="{{ meta.server_url }}/search" id="searchLink"
+                  >Search</a
+                >
+              </li>
+              <li>
+                <a href="{{ meta.server_url }}/model" id="modelLink"
+                  >Modelling</a
+                >
+              </li>
+              <li class="dropdown">
+                <a data-toggle="dropdown" class="dropdown-toggle" href="#"
+                  >Browse Data<b class="caret"></b
+                ></a>
+                <ul role="menu" class="dropdown-menu">
+                  <li>
+                    <a href="{{ meta.server_url }}/pathway" id="pathwayLink"
+                      >Pathway</a
+                    >
+                  </li>
+                  <li>
+                    <a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a>
+                  </li>
+                  <li>
+                    <a href="{{ meta.server_url }}/compound" id="compoundLink"
+                      >Compound</a
+                    >
+                  </li>
+                  <li>
+                    <a href="{{ meta.server_url }}/reaction" id="reactionLink"
+                      >Reaction</a
+                    >
+                  </li>
+                  <li>
+                    <a
+                      href="{{ meta.server_url }}/model"
+                      id="relative-reasoningLink"
+                      >Model</a
+                    >
+                  </li>
+                  <li>
+                    <a href="{{ meta.server_url }}/scenario" id="scenarioLink"
+                      >Scenario</a
+                    >
+                  </li>
+                  {#                        <li><a href="{{ meta.server_url }}/setting" id="settingLink">Setting</a></li>#}
+                  {#                        <li><a href="{{ meta.server_url }}/user" id="userLink">User</a></li>#}
+                  {#                        <li><a href="{{ meta.server_url }}/group" id="groupLink">Group</a></li>#}
+                </ul>
+              </li>
+            </ul>
+
+            <ul
+              class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework"
+            >
+              <li>
+                <a href="https://community.envipath.org/" id="communityLink"
+                  >Community</a
+                >
+              </li>
+              <li class="dropdown">
+                <a data-toggle="dropdown" class="dropdown-toggle" href="#"
+                  >Info <b class="caret"></b
+                ></a>
+                <ul role="menu" class="dropdown-menu">
+                  <!--<li><a href="{{ meta.server_url }}/funding" id="fundingLink">Funding</a></li>-->
+                  <li>
+                    <a
+                      href="https://community.envipath.org/t/envipath-license/109"
+                      id="licenceLink"
+                      >Licences</a
+                    >
+                  </li>
+                  <li class="divider"></li>
+                  <li>
+                    <a
+                      target="_blank"
+                      href="https://wiki.envipath.org/"
+                      id="wikiLink"
+                      >Documentation Wiki</a
+                    >
+                  </li>
+                  <li>
+                    <a
+                      href="#"
+                      id="citeButton"
+                      data-toggle="modal"
+                      data-target="#citemodal"
+                      >How to cite enviPath</a
+                    >
+                  </li>
+                  <li class="divider"></li>
+                  <li><a>Version: {{ meta.version }}</a></li>
+                </ul>
+              </li>
+              {% if meta.user.username == 'anonymous' %}
                 <li>
-                    <a href="#" data-toggle="modal" data-target="#predict_modal">
+                  <a
-                        Predict Pathway
+                    href="{% url 'login' %}"
-                    </a>
+                    id="loginButton"
+                    style="margin-right:10px"
+                    >Login</a
+                  >
                 </li>
-{#                <li class="dropdown">#}
+              {% else %}
-{#                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
-{#                    <ul role="menu" class="dropdown-menu">#}
-{#                        <li>#}
-{#                            <a class="button" data-toggle="modal" data-target="#predict_modal">#}
-{#                                <i class="	glyphicon glyphicon-tag"></i> Predict Pathway#}
-{#                            </a>#}
-{#                        </li>#}
-{#                        <li>#}
-{#                            <a class="button" data-toggle="modal" data-target="#batch_predict_modal">#}
-{#                                <i class="	glyphicon glyphicon-tags"></i> Batch Prediction#}
-{#                            </a>#}
-{#                        </li>#}
-{#                    </ul>#}
-{#                </li>#}
-                <li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li>
-                <li><a href="{{ meta.server_url }}/search" id="searchLink">Search</a></li>
-                <li><a href="{{ meta.server_url }}/model" id="modelLink">Modelling</a></li>
                 <li class="dropdown">
-                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Browse Data<b class="caret"></b></a>
+                  <a
-                    <ul role="menu" class="dropdown-menu">
+                    data-toggle="dropdown"
-                        <li><a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a></li>
+                    id="loggedInButton"
-                        <li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
+                    class="dropdown-toggle"
-                        <li><a href="{{ meta.server_url }}/compound" id="compoundLink">Compound</a></li>
+                    id="logedInButton"
-                        <li><a href="{{ meta.server_url }}/reaction" id="reactionLink">Reaction</a></li>
+                    href="#"
-                        <li><a href="{{ meta.server_url }}/model" id="relative-reasoningLink">Model</a></li>
+                  >
-                        <li><a href="{{ meta.server_url }}/scenario" id="scenarioLink">Scenario</a></li>
+                    <div id="username">
-                        {#                        <li><a href="{{ meta.server_url }}/setting" id="settingLink">Setting</a></li>#}
+                      {{ user.username }}<b class="caret"></b>
-                        {#                        <li><a href="{{ meta.server_url }}/user" id="userLink">User</a></li>#}
+                    </div>
-                        {#                        <li><a href="{{ meta.server_url }}/group" id="groupLink">Group</a></li>#}
+                  </a>
-                    </ul>
+                  <ul role="menu" class="dropdown-menu">
-                </li>
-
-            </ul>
-
-            <ul class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework">
-                <li><a href="https://community.envipath.org/" id="communityLink">Community</a></li>
-                <li class="dropdown">
-                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Info <b class="caret"></b></a>
-                    <ul role="menu" class="dropdown-menu">
-                        <!--<li><a href="{{ meta.server_url }}/funding" id="fundingLink">Funding</a></li>-->
-                        <li><a href="https://community.envipath.org/t/envipath-license/109" id="licenceLink">Licences</a></li>
-                        <li class="divider"></li>
-                        <li><a target="_blank" href="https://wiki.envipath.org/" id="wikiLink">Documentation Wiki</a>
-                        </li>
-                        <li><a href="#" id="citeButton" data-toggle="modal" data-target="#citemodal">How to cite
-                            enviPath</a></li>
-                        <li class="divider"></li>
-                        <li><a>Version: {{ meta.version }}</a></li>
-                    </ul>
-                </li>
-                {% if meta.user.username == 'anonymous' %}
                     <li>
-                        <a href="{% url 'login' %}" id="loginButton" style="margin-right:10px">Login</a>
+                      <a href="{{ meta.user.url }}" id="accountbutton"
+                        >My Account</a
+                      >
                     </li>
-                {% else %}
+                    <li class="divider"></li>
-                    <li class="dropdown">
+                    <form
-                        <a data-toggle="dropdown" id="loggedInButton" class="dropdown-toggle" id="logedInButton"
+                      class="navbar-form navbar-left navbar-left-framework"
-                           href="#">
+                      role="logout"
-                            <div id="username">
+                      action="{% url 'logout' %}"
-                                {{ user.username }}<b class="caret"></b>
+                      method="post"
-                            </div>
+                    >
-                        </a>
+                      {% csrf_token %}
-                        <ul role="menu" class="dropdown-menu">
+                      <div class="form-group">
-                            <li>
+                        <input type="hidden" name="logout" value="true" />
-                                <a href="{{ meta.user.url }}" id="accountbutton">My Account</a>
+                      </div>
-                            </li>
+                      <button type="submit" class="btn btn-default">
-                            <li class="divider"></li>
+                        Logout
-                            <form class="navbar-form navbar-left navbar-left-framework" role="logout"
+                      </button>
-                                  action="{% url 'logout' %}" method="post">
+                    </form>
-                                {% csrf_token %}
+                  </ul>
-                                <div class="form-group">
+                </li>
-                                    <input type="hidden" name="logout" value="true">
+              {% endif %}
-                                </div>
-                                <button type="submit" class="btn btn-default">Logout</button>
-                            </form>
-                        </ul>
-                    </li>
-                {% endif %}
             </ul>
+          </div>
         </div>
+      </nav>
     </div>
-</nav>
+    <!-- End legacy Bootstrap navbar -->
-</div>
-<!-- End legacy Bootstrap navbar -->
 
-<div id="docContent" class="content container">
+    <div id="docContent" class="content container">
-    {% if breadcrumbs %}
+      {% if breadcrumbs %}
         <div id="bread">
-            <ol class="breadcrumb">
+          <ol class="breadcrumb">
-                {% for elem in breadcrumbs %}
+            {% for elem in breadcrumbs %}
-                    {% for name, url in elem.items %}
+              {% for name, url in elem.items %}
-                        {% if forloop.parentloop.last %}
+                {% if forloop.parentloop.last %}
-                            <li class="active">{{ name }}</li>
+                  <li class="active">{{ name }}</li>
-                        {% else %}
+                {% else %}
-                            <li>
+                  <li>
-                                <a href="{{ url }}">{{ name }}</a>
+                    <a href="{{ url }}">{{ name }}</a>
-                            </li>
+                  </li>
-                        {% endif %}
+                {% endif %}
-                    {% endfor %}
+              {% endfor %}
-                {% endfor %}
+            {% endfor %}
-            </ol>
+          </ol>
         </div>
-    {% endif %}
+      {% endif %}
-    {% if message %}
+      {% if message %}
-        <div id="message">
+        <div id="message">{{ message }}</div>
-            {{ message }}
+      {% endif %}
-        </div>
+      {% block content %}
-    {% endif %}
+      {% endblock content %}
-    {% block content %}
+      {% if meta.url_contains_package and meta.current_package.license %}
-    {% endblock content %}
-    {% if meta.url_contains_package and meta.current_package.license %}
         <p></p>
         <div class="panel-group" id="license_accordion">
-            <div class="panel panel-default list-group-item" style="background-color:#f5f5f5">
+          <div
-                <div class="panel-title">
+            class="panel panel-default list-group-item"
-                    <a data-toggle="collapse" data-parent="#licence_accordion" href="#license">License</a>
+            style="background-color:#f5f5f5"
-                </div>
+          >
+            <div class="panel-title">
+              <a
+                data-toggle="collapse"
+                data-parent="#licence_accordion"
+                href="#license"
+                >License</a
+              >
             </div>
-            <div id="license" class="panel-collapse collapse in">
+          </div>
-                <div class="panel-body list-group-item">
+          <div id="license" class="panel-collapse collapse in">
-                    <a target="_blank" href="{{ meta.current_package.license.link }}">
+            <div class="panel-body list-group-item">
-                        <img src="{{ meta.current_package.license.image_link }}">
+              <a target="_blank" href="{{ meta.current_package.license.link }}">
-                    </a>
+                <img src="{{ meta.current_package.license.image_link }}" />
-                </div>
+              </a>
             </div>
+          </div>
         </div>
-    {% endif %}
+      {% endif %}
-</div>
-
-<!-- FOOTER - Legacy Bootstrap -->
-<div class="legacy-bootstrap">
-<div class="container text-center">
-    <hr/>
-    <div class="row">
-        <div class="col-lg-12">
-            <ul class="nav nav-pills nav-justified">
-                <li>
-                    <a href="http://ml.auckland.ac.nz" target="_blank">
-                        <img id="image-uoalogo" height="60" src='{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}'
-                             alt="The Univserity of Auckland"/>
-                    </a>
-                </li>
-                <li>
-                    <a href="https://eawag.ch" target="_blank">
-                        <img id="image-ealogo" height="60" src='{% static "/images/ealogo.gif" %}' alt="Eawag"/>
-                    </a>
-                </li>
-                <li>
-                    <a href="https://www.uzh.ch/" target="_blank">
-                        <img id="image-ufzlogo" height="60" src='{% static "/images/uzh-logo.svg" %}'
-                             alt="University of Zurich"/>
-                    </a>
-                </li>
-            </ul>
-        </div>
     </div>
-</div>
+
-<div class="row">
+    <!-- FOOTER - Legacy Bootstrap -->
-    <div class="col-lg-12">
+    <div class="legacy-bootstrap">
-        <ul class="nav nav-pills nav-justified">
+      <div class="container text-center">
+        <hr />
+        <div class="row">
+          <div class="col-lg-12">
+            <ul class="nav nav-pills nav-justified">
+              <li>
+                <a href="http://ml.auckland.ac.nz" target="_blank">
+                  <img
+                    id="image-uoalogo"
+                    height="60"
+                    src="{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}"
+                    alt="The Univserity of Auckland"
+                  />
+                </a>
+              </li>
+              <li>
+                <a href="https://eawag.ch" target="_blank">
+                  <img
+                    id="image-ealogo"
+                    height="60"
+                    src="{% static "/images/ealogo.gif" %}"
+                    alt="Eawag"
+                  />
+                </a>
+              </li>
+              <li>
+                <a href="https://www.uzh.ch/" target="_blank">
+                  <img
+                    id="image-ufzlogo"
+                    height="60"
+                    src="{% static "/images/uzh-logo.svg" %}"
+                    alt="University of Zurich"
+                  />
+                </a>
+              </li>
+            </ul>
+          </div>
+        </div>
+      </div>
+      <div class="row">
+        <div class="col-lg-12">
+          <ul class="nav nav-pills nav-justified">
             <!--            <li><a href="https://envipath.com/imprint/" target="_blank">Impressum/Imprint</a></li>-->
-            <li><a href="mailto:admin@envipath.org" target="_blank">Contact</a></li>
+            <li>
+              <a href="mailto:admin@envipath.org" target="_blank">Contact</a>
+            </li>
             <!--            <li><a href="http://envipath.com" target="_blank"> enviPath UG (haftungsbeschr&auml;nkt) &amp; Co. KG &copy;-->
             <!--                {{ YEAR }}</a></li>-->
-        </ul>
+          </ul>
+        </div>
+      </div>
     </div>
-</div>
+    <!-- End legacy Bootstrap footer -->
-</div>
-<!-- End legacy Bootstrap footer -->
 
-<script>
+    <script>
-    $(function () {
+      $(function () {
         // Hide actionsbutton if theres no action defined
-        if ($('#actionsButton ul').children().length > 0) {
+        if ($("#actionsButton ul").children().length > 0) {
-            $('#actionsButton').show();
+          $("#actionsButton").show();
         }
-    });
+      });
-</script>
+    </script>
-{% block modals %}
+    {% block modals %}
-    {% include "modals/cite_modal.html" %}
+      {% include "modals/cite_modal.html" %}
-    {% include "modals/signup_modal.html" %}
+      {% include "modals/predict_modal.html" %}
-    {% include "modals/predict_modal.html" %}
+      {% include "modals/batch_predict_modal.html" %}
-    {% include "modals/batch_predict_modal.html" %}
+    {% endblock %}
-{% endblock %}
+  </body>
-</body>
 </html>

templates/framework_modern.html

@@ -1,38 +1,49 @@
-<!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 rel="shortcut icon" type="image/png" href="{% static 'images/favicon.ico' %}"/>
+    <link
+      rel="shortcut icon"
+      type="image/png"
+      href="{% static 'images/favicon.ico' %}"
+    />
 
     {# Tailwind CSS + DaisyUI Output #}
-    <link href="{% static 'css/output.css' %}" rel="stylesheet" type="text/css"/>
+    <link
+      href="{% static 'css/output.css' %}"
+      rel="stylesheet"
+      type="text/css"
+    />
 
     {# jQuery - Keep for compatibility with existing JS #}
     <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
 
     {# Font Awesome #}
-    <link href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
+    <link
+      href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css"
+      rel="stylesheet"
+    />
 
     {# Discourse embed for community #}
     <script src="https://community.envipath.org/javascripts/embed-topics.js"></script>
 
     <script>
-        const csrftoken = document.querySelector('[name=csrf-token]').content;
+      const csrftoken = document.querySelector("[name=csrf-token]").content;
 
-        // Setup CSRF header for all jQuery AJAX requests
+      // Setup CSRF header for all jQuery AJAX requests
-        $.ajaxSetup({
+      $.ajaxSetup({
-            beforeSend: function(xhr, settings) {
+        beforeSend: function (xhr, settings) {
-                if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
+          if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
-                    xhr.setRequestHeader("X-CSRFToken", csrftoken);
+            xhr.setRequestHeader("X-CSRFToken", csrftoken);
-                }
+          }
-            }
+        },
-        });
+      });
     </script>
 
     {# General EP JS #}
@@ -41,136 +52,155 @@
     <script src="{% static 'js/jquery-bootstrap-modal-steps.js' %}"></script>
 
     {% if not debug %}
-        <!-- Matomo -->
+      <!-- Matomo -->
-        <script>
+      <script>
-            var _paq = window._paq = window._paq || [];
+        var _paq = (window._paq = window._paq || []);
-            _paq.push(['trackPageView']);
+        _paq.push(["trackPageView"]);
-            _paq.push(['enableLinkTracking']);
+        _paq.push(["enableLinkTracking"]);
-            (function () {
+        (function () {
-                var u = "//matomo.envipath.com/";
+          var u = "//matomo.envipath.com/";
-                _paq.push(['setTrackerUrl', u + 'matomo.php']);
+          _paq.push(["setTrackerUrl", u + "matomo.php"]);
-                _paq.push(['setSiteId', '{{ meta.site_id }}']);
+          _paq.push(["setSiteId", "{{ meta.site_id }}"]);
-                var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
+          var d = document,
-                g.async = true;
+            g = d.createElement("script"),
-                g.src = u + 'matomo.js';
+            s = d.getElementsByTagName("script")[0];
-                s.parentNode.insertBefore(g, s);
+          g.async = true;
-            })();
+          g.src = u + "matomo.js";
-        </script>
+          s.parentNode.insertBefore(g, s);
-        <!-- End Matomo Code -->
+        })();
+      </script>
+      <!-- End Matomo Code -->
     {% endif %}
-</head>
+  </head>
-<body class="min-h-screen bg-base-300">
+  <body class="bg-base-300 min-h-screen">
     {% include "includes/navbar.html" %}
 
     {# Main Content Area #}
     <main class="w-full">
-        {% block main_content %}
+      {% block main_content %}
-            {# Breadcrumbs - outside main content, optional #}
+        {# Breadcrumbs - outside main content, optional #}
-            {% if breadcrumbs %}
+        {% if breadcrumbs %}
-                <div id="bread" class="max-w-7xl mx-auto px-4 py-4">
+          <div id="bread" class="max-w-7xl mx-auto px-4 py-4">
-                    <div class="text-sm breadcrumbs">
+            <div class="breadcrumbs text-sm">
-                        <ul>
+              <ul>
-                            {% for elem in breadcrumbs %}
+                {% for elem in breadcrumbs %}
-                                {% for name, url in elem.items %}
+                  {% for name, url in elem.items %}
-                                    {% if forloop.parentloop.last %}
+                    {% if forloop.parentloop.last %}
-                                        <li>{{ name }}</li>
+                      <li>{{ name }}</li>
-                                    {% else %}
+                    {% else %}
-                                        <li><a href="{{ url }}">{{ name }}</a></li>
+                      <li><a href="{{ url }}">{{ name }}</a></li>
-                                    {% endif %}
+                    {% endif %}
-                                {% endfor %}
+                  {% endfor %}
-                            {% endfor %}
+                {% endfor %}
-                        </ul>
+              </ul>
-                    </div>
-                </div>
-            {% endif %}
-
-            {# Main content container - paper effect on medium+ screens #}
-            <div id="docContent" class="w-full xl:w-xl md:mx-auto md:my-8 bg-base-100 md:shadow-2xl md:rounded-lg border-2">
-                {# Messages - inside paper #}
-                {% if message %}
-                    <div id="message" class="alert alert-info m-4">
-                        {{ message }}
-                    </div>
-                {% endif %}
-
-                {# Page content - no enforced styles #}
-                {% block content %}
-                {% endblock content %}
-
-                {# License - inside paper if present #}
-                {% if meta.url_contains_package and meta.current_package.license %}
-                    <div class="collapse collapse-arrow bg-base-200 m-8">
-                        <input type="checkbox" checked />
-                        <div class="collapse-title text-xl font-medium">
-                            License
-                        </div>
-                        <div class="collapse-content">
-                            <a target="_blank" href="{{ meta.current_package.license.link }}">
-                                <img src="{{ meta.current_package.license.image_link }}" alt="License">
-                            </a>
-                        </div>
-                    </div>
-                {% endif %}
             </div>
-        {% endblock main_content %}
+          </div>
+        {% endif %}
+
+        {# Main content container - paper effect on medium+ screens #}
+        <div
+          id="docContent"
+          class="bg-base-100 mx-auto md:my-8 md:max-w-6xl md:rounded-lg md:shadow-xl"
+        >
+          {# Messages - inside paper #}
+          {% if message %}
+            <div id="message" class="alert alert-info m-4">{{ message }}</div>
+          {% endif %}
+
+          {# Page content - no enforced styles #}
+          {% block content %}
+          {% endblock content %}
+
+          {# License - inside paper if present #}
+          {% if meta.url_contains_package and meta.current_package.license %}
+            <div class="collapse collapse-arrow bg-base-200 m-8">
+              <input type="checkbox" checked />
+              <div class="collapse-title text-xl font-medium">License</div>
+              <div class="collapse-content">
+                <a
+                  target="_blank"
+                  href="{{ meta.current_package.license.link }}"
+                >
+                  <img
+                    src="{{ meta.current_package.license.image_link }}"
+                    alt="License"
+                  />
+                </a>
+              </div>
+            </div>
+          {% endif %}
+        </div>
+      {% endblock main_content %}
     </main>
 
     {% include "includes/footer.html" %}
 
     {# Floating Help Tab #}
     {% if not public_mode %}
-    <div class="fixed right-0 top-1/2 -translate-y-1/2 z-50">
+      <div class="fixed right-0 top-1/2 -translate-y-1/2 z-50">
-        <a href="https://community.envipath.org/" target="_blank"
+        <a
-           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"
+          href="https://community.envipath.org/"
-           title="Get Help from the Community">
+          target="_blank"
-            <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"/>
+          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"
-                <path d="M12 17h.01"/>
+          title="Get Help from the Community"
-            </svg>
+        >
+          <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>
+      </div>
     {% endif %}
 
-    {# Modals - TODO: Convert these to DaisyUI modals #}
     {% block modals %}
-        {# Note: These modals still use Bootstrap markup and will need conversion #}
+      {% include "modals/search_modal.html" %}
-        {% include "modals/cite_modal.html" %}
-        {% include "modals/signup_modal.html" %}
-        {% include "modals/predict_modal.html" %}
-        {% include "modals/batch_predict_modal.html" %}
     {% endblock %}
 
     <script>
-        $(function () {
+      $(function () {
-            // Hide actionsbutton if there's no action defined
+        // Hide actionsbutton if there's no action defined
-            if ($('#actionsButton ul').children().length > 0) {
+        if ($("#actionsButton ul").children().length > 0) {
-                $('#actionsButton').show();
+          $("#actionsButton").show();
-            }
+        }
+      });
 
-        });
+      // Global keyboard shortcut for search (Cmd+K on Mac, Ctrl+K on Windows/Linux)
+      document.addEventListener("keydown", function (event) {
+        // Check if user is typing in an input field
+        const activeElement = document.activeElement;
+        const isInputField =
+          activeElement &&
+          (activeElement.tagName === "INPUT" ||
+            activeElement.tagName === "TEXTAREA" ||
+            activeElement.contentEditable === "true");
 
-        // Global keyboard shortcut for search (Cmd+K on Mac, Ctrl+K on Windows/Linux)
+        if (isInputField) {
-        document.addEventListener('keydown', function(event) {
+          return; // Don't trigger shortcut when typing in input fields
-            // Check if user is typing in an input field
+        }
-            const activeElement = document.activeElement;
-            const isInputField = activeElement && (
-                activeElement.tagName === 'INPUT' ||
-                activeElement.tagName === 'TEXTAREA' ||
-                activeElement.contentEditable === 'true'
-            );
 
-            if (isInputField) {
+        // Check for Cmd+K (Mac) or Ctrl+K (Windows/Linux)
-                return; // Don't trigger shortcut when typing in input fields
+        const isMac = /Mac/.test(navigator.platform);
-            }
+        const isCorrectModifier = isMac ? event.metaKey : event.ctrlKey;
 
-            // Check for Cmd+K (Mac) or Ctrl+K (Windows/Linux)
+        if (isCorrectModifier && event.key === "k") {
-            const isMac = /Mac/.test(navigator.platform);
+          event.preventDefault();
-            const isCorrectModifier = isMac ? event.metaKey : event.ctrlKey;
+          search_modal.showModal();
-
+        }
-            if (isCorrectModifier && event.key === 'k') {
+      });
-                event.preventDefault();
-                window.location.href = '/search';
-            }
-        });
     </script>
-</body>
+  </body>
 </html>

templates/includes/navbar.html

@@ -1,71 +1,147 @@
 {% load static %}
 {# Modern DaisyUI Navbar #}
 <div class="navbar bg-neutral-50 text-neutral-950 shadow-lg x-50">
-    <div class="navbar-start">
+  <div class="navbar-start">
-        <a href="{{ meta.server_url }}" class="btn btn-ghost normal-case text-xl">
+    <a href="{{ meta.server_url }}" class="btn btn-ghost normal-case text-xl">
-            <svg class="h-8 fill-base-content" viewBox="0 0 104 26"  role="img">
+      <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>
+      </svg>
-        </a>
+    </a>
-    </div>
+  </div>
 
-    {% if not public_mode %}
+  {% if not public_mode %}
     <div class="navbar-center hidden lg:flex">
-        <a href="#" role="button" class="btn btn-ghost" id="predictLink">Predict</a>
+      <a
-        <!-- <li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li> -->
+        href="{{ meta.server_url }}/predict"
-        <!--<li><a href="{{ meta.server_url }}/browse" id="browseLink">Browse</a></li>-->
+        role="button"
-        <div class="dropdown dropdown-center">
+        class="btn btn-ghost"
-            <div tabindex="0" role="button" class="btn btn-ghost">Browse</div>
+        id="predictLink"
-            <ul tabindex="-1" class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm">
+        >Predict</a
-                <li><a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a></li>
+      >
-                <li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
+      <!-- <li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li> -->
-                <li><a href="{{ meta.server_url }}/compound" id="compoundLink">Compound</a></li>
+      <!--<li><a href="{{ meta.server_url }}/browse" id="browseLink">Browse</a></li>-->
-                <li><a href="{{ meta.server_url }}/reaction" id="reactionLink">Reaction</a></li>
+      <div class="dropdown dropdown-center">
-                <li><a href="{{ meta.server_url }}/model" id="relative-reasoningLink">Model</a></li>
+        <div tabindex="0" role="button" class="btn btn-ghost">Browse</div>
-                <li><a href="{{ meta.server_url }}/scenario" id="scenarioLink">Scenario</a></li>
+        <ul
-            </ul>
+          tabindex="-1"
-        </div>
+          class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm"
+        >
+          <li>
+            <a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a>
+          </li>
+          <li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
+          <li>
+            <a href="{{ meta.server_url }}/compound" id="compoundLink"
+              >Compound</a
+            >
+          </li>
+          <li>
+            <a href="{{ meta.server_url }}/reaction" id="reactionLink"
+              >Reaction</a
+            >
+          </li>
+          <li>
+            <a href="{{ meta.server_url }}/model" id="relative-reasoningLink"
+              >Model</a
+            >
+          </li>
+          <li>
+            <a href="{{ meta.server_url }}/scenario" id="scenarioLink"
+              >Scenario</a
+            >
+          </li>
+        </ul>
+      </div>
     </div>
-    {% endif %}
+  {% endif %}
 
-    <div class="navbar-end">
+  <div class="navbar-end">
-        {% if not public_mode %}
+    {% if not public_mode %}
-        <a href="/search" role="button" >
+      <a href="/search" role="button">
-            <div class="flex items-center badge badge-dash space-x-1 bg-base-200 text-base-content/50 p-2 m-1">
+        <div
-                <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>
+          class="flex items-center badge badge-dash space-x-1 bg-base-200 text-base-content/50 p-2 m-1"
-                <span id="search-shortcut">⌘K</span>
+        >
-            </div>
+          <svg
-        </a>
+            xmlns="http://www.w3.org/2000/svg"
-        {% endif %}
+            width="16"
-            {% if meta.user.username == 'anonymous' or public_mode %}
+            height="16"
-            <a href="{% url 'login' %}" id="loginButton" class="p-2">Login</a>
+            viewBox="0 0 24 24"
-        {% else %}
+            fill="none"
-            <div class="dropdown dropdown-end">
+            stroke="currentColor"
-                <div tabindex="0" role="button" class="btn btn-ghost m-1 btn-circle" id="loggedInButton">
+            stroke-width="2"
-                    <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>
+            stroke-linecap="round"
-                </div>
+            stroke-linejoin="round"
-                <ul tabindex="-1" class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2 shadow-sm">
+            class="lucide lucide-search-icon lucide-search"
-                    <li><a href="{{ meta.user.url }}" id="accountbutton">Settings</a></li>
+          >
-                    <li>
+            <path d="m21 21-4.34-4.34" />
-                        <form id="logoutForm" action="{% url 'logout' %}" method="post" style="display: none;">
+            <circle cx="11" cy="11" r="8" />
-                            {% csrf_token %}
+          </svg>
-                            <input type="hidden" name="logout" value="true">
+          <span id="search-shortcut">⌘K</span>
-                        </form>
+        </div>
-                        <a href="#" id="logoutButton" onclick="event.preventDefault(); document.getElementById('logoutForm').submit();">Logout</a>
+      </a>
-                    </li>
+    {% endif %}
-                </ul>
+    {% if meta.user.username == 'anonymous' or public_mode %}
-            </div>
+      <a href="{% url 'login' %}" id="loginButton" class="p-2">Login</a>
-        {% endif %}
+    {% else %}
-    </div>
+      <div class="dropdown dropdown-end">
+        <div
+          tabindex="0"
+          role="button"
+          class="btn btn-ghost m-1 btn-circle"
+          id="loggedInButton"
+        >
+          <svg
+            xmlns="http://www.w3.org/2000/svg"
+            width="24"
+            height="24"
+            viewBox="0 0 24 24"
+            fill="none"
+            stroke="currentColor"
+            stroke-width="2"
+            stroke-linecap="round"
+            stroke-linejoin="round"
+            class="lucide lucide-circle-user-icon lucide-circle-user"
+          >
+            <circle cx="12" cy="12" r="10" />
+            <circle cx="12" cy="10" r="3" />
+            <path d="M7 20.662V19a2 2 0 0 1 2-2h6a2 2 0 0 1 2 2v1.662" />
+          </svg>
+        </div>
+        <ul
+          tabindex="-1"
+          class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2 shadow-sm"
+        >
+          <li><a href="{{ meta.user.url }}" id="accountbutton">Settings</a></li>
+          <li>
+            <form
+              id="logoutForm"
+              action="{% url 'logout' %}"
+              method="post"
+              style="display: none;"
+            >
+              {% csrf_token %}
+              <input type="hidden" name="logout" value="true" />
+            </form>
+            <a
+              href="#"
+              id="logoutButton"
+              onclick="event.preventDefault(); document.getElementById('logoutForm').submit();"
+              >Logout</a
+            >
+          </li>
+        </ul>
+      </div>
+    {% endif %}
+  </div>
 </div>
 
 <script>
-    // OS-aware search shortcut display
+  // OS-aware search shortcut display
-    (function() {
+  (function () {
-        const isMac = /Mac/.test(navigator.platform);
+    const isMac = /Mac/.test(navigator.platform);
-        const shortcutElement = document.getElementById('search-shortcut');
+    const shortcutElement = document.getElementById("search-shortcut");
-        if (shortcutElement) {
+    if (shortcutElement) {
-            shortcutElement.textContent = isMac ? '⌘K' : 'Ctrl+K';
+      shortcutElement.textContent = isMac ? "⌘K" : "Ctrl+K";
-        }
+    }
-    })();
+  })();
 </script>

templates/index/index.html

@@ -1,190 +1,269 @@
 {% extends "framework_modern.html" %}
 {% load static %}
 {% block main_content %}
-
+  <!-- Hero Section with Logo and Search -->
-    <!-- Hero Section with Logo and Search -->
+  <section class="hero h-fit max-w-5xl w-full shadow-none mx-auto relative">
-<section class="hero h-fit max-w-5xl w-full shadow-none mx-auto relative">
+    <div
-
+      class="hero min-h-[calc(100vh*0.4)] bg-gradient-to-br from-primary-800 to-primary-600"
-        <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;"
-            style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
+    >
-            >
+      <div class="hero-overlay"></div>
-            <div class="hero-overlay"></div>
+      <!-- Predict Pathway text over the image -->
-            <!-- Predict Pathway text over the image -->
+      <div class="absolute bottom-40 left-1/8 -translate-x-8 z-10">
-            <div class="absolute bottom-40 left-1/8 -translate-x-8 z-10">
+        <h2 class="text-3xl text-base-100 text-shadow-lg text-left">
-                <h2 class="text-3xl text-base-100 text-shadow-lg text-left">Predict Your Pathway</h2>
+          Predict Your Pathway
-            </div>
+        </h2>
-        </div>
+      </div>
-</section>
-
-<div class="shadow-md max-w-5xl mx-auto bg-base-200">
-
-    <!-- Predict Pathway Section -->
-    <div class="flex-col lg:flex-row-reverse w-full mx-auto -mt-32 relative z-20 mb-10 ">
-        <div class="card bg-base-100 shrink-0 shadow-xl w-3/4 mx-auto transition-all duration-300 ease-in-out">
-            <div class="card-body">
-                <!-- Input Mode Toggle - Fixed position outside fieldset -->
-                <div class="flex flex-row justify-start items-center h-fit ml-8 my-4">
-                    <div class="flex items-center gap-2">
-                        <!-- <span class="text-sm text-neutral-500">Input Mode:</span> -->
-                        <label class="toggle text-base-content toggle-md">
-                            <input type="checkbox" />
-                            <svg aria-label="smiles mode" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 20 20" class="size-5">
-                                <g
-                                stroke-linejoin="round"
-                                stroke-linecap="round"
-                                stroke-width="2"
-                                fill="currentColor"
-                                stroke="none"
-                                >
-                                    <path fill-rule="evenodd" d="M8 2.75A.75.75 0 0 1 8.75 2h7.5a.75.75 0 0 1 0 1.5h-3.215l-4.483 13h2.698a.75.75 0 0 1 0 1.5h-7.5a.75.75 0 0 1 0-1.5h3.215l4.483-13H8.75A.75.75 0 0 1 8 2.75Z" clip-rule="evenodd" />
-                                </g>
-                            </svg>
-                            <svg
-                                aria-label="draw mode"
-                                xmlns="http://www.w3.org/2000/svg"
-                                viewBox="0 0 20 20"
-                                fill="currentColor"
-                                stroke="none"
-                                class="size-5"
-                            >
-                                <path d="m2.695 14.762-1.262 3.155a.5.5 0 0 0 .65.65l3.155-1.262a4 4 0 0 0 1.343-.886L17.5 5.501a2.121 2.121 0 0 0-3-3L3.58 13.419a4 4 0 0 0-.885 1.343Z" />
-
-                            </svg>
-                        </label>
-                    </div>
-                </div>
-
-                <fieldset class="fieldset transition-all duration-300 ease-in-out overflow-hidden">
-                    <form id="index-form" action="{{ meta.current_package.url }}/pathway" method="POST">
-                        {% csrf_token %}
-                            <div id="text-input-container" class="transition-all duration-300 ease-in-out opacity-100 transform scale-100">
-                                <div class="join w-full mx-auto">
-                                    <input type="text" id="index-form-text-input" placeholder="canonical SMILES string" class="input grow input-md join-item" />
-                                    <button class="btn btn-neutral join-item">Predict!</button>
-                                </div>
-                                <div class="label relative w-full mt-1" >
-                                    <div class="flex gap-2">
-                                        <a href="#" class="example-link cursor-pointer hover:text-primary"
-                                           data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
-                                           title="load example">Caffeine</a>
-                                        <a href="#" class="example-link cursor-pointer hover:text-primary"
-                                           data-smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
-                                           title="load example">Ibuprofen</a>
-                                    </div>
-                                    <a class="absolute top-0 left-[calc(100%-5.4rem)]" href="#">Advanced</a>
-                                </div>
-                            </div>
-                             <div id="ketcher-container" class="hidden w-full transition-all duration-300 ease-in-out opacity-0 transform scale-95">
-                                 <iframe id="index-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}"
-                                 width="100%" height="400" class="rounded-lg"></iframe>
-                                 <button class="btn btn-lg bg-primary-950 text-primary-50 join-item w-full mt-2">Predict!</button>
-                                 <a class="label mx-auto w-full mt-1" href="#">Advanced</a>
-                             </div>
-                        <input type="hidden" id="index-form-smiles" name="smiles" value="smiles">
-                        <input type="hidden" id="index-form-predict" name="predict" value="predict">
-                        <input type="hidden" id="current-action" value="predict">
-                    </form>
-                </fieldset>
-            </div>
-        </div>
     </div>
+  </section>
 
+  <div class="shadow-md max-w-5xl mx-auto bg-base-200">
+    <!-- Predict Pathway Section -->
+    <div
+      class="flex-col lg:flex-row-reverse w-full mx-auto -mt-32 relative z-20 mb-10 "
+    >
+      <div
+        class="card bg-base-100 shrink-0 shadow-xl w-3/4 mx-auto transition-all duration-300 ease-in-out"
+      >
+        <div class="card-body">
+          <!-- Input Mode Toggle - Fixed position outside fieldset -->
+          <div class="flex flex-row justify-start items-center h-fit ml-8 my-4">
+            <div class="flex items-center gap-2">
+              <!-- <span class="text-sm text-neutral-500">Input Mode:</span> -->
+              <label class="toggle text-base-content toggle-md">
+                <input type="checkbox" />
+                <svg
+                  aria-label="smiles mode"
+                  xmlns="http://www.w3.org/2000/svg"
+                  viewBox="0 0 20 20"
+                  class="size-5"
+                >
+                  <g
+                    stroke-linejoin="round"
+                    stroke-linecap="round"
+                    stroke-width="2"
+                    fill="currentColor"
+                    stroke="none"
+                  >
+                    <path
+                      fill-rule="evenodd"
+                      d="M8 2.75A.75.75 0 0 1 8.75 2h7.5a.75.75 0 0 1 0 1.5h-3.215l-4.483 13h2.698a.75.75 0 0 1 0 1.5h-7.5a.75.75 0 0 1 0-1.5h3.215l4.483-13H8.75A.75.75 0 0 1 8 2.75Z"
+                      clip-rule="evenodd"
+                    />
+                  </g>
+                </svg>
+                <svg
+                  aria-label="draw mode"
+                  xmlns="http://www.w3.org/2000/svg"
+                  viewBox="0 0 20 20"
+                  fill="currentColor"
+                  stroke="none"
+                  class="size-5"
+                >
+                  <path
+                    d="m2.695 14.762-1.262 3.155a.5.5 0 0 0 .65.65l3.155-1.262a4 4 0 0 0 1.343-.886L17.5 5.501a2.121 2.121 0 0 0-3-3L3.58 13.419a4 4 0 0 0-.885 1.343Z"
+                  />
+                </svg>
+              </label>
+            </div>
+          </div>
+
+          <fieldset
+            class="fieldset transition-all duration-300 ease-in-out overflow-hidden"
+          >
+            <form
+              id="index-form"
+              action="{{ meta.current_package.url }}/pathway"
+              method="POST"
+            >
+              {% csrf_token %}
+              <div
+                id="text-input-container"
+                class="transition-all duration-300 ease-in-out opacity-100 transform scale-100"
+              >
+                <div class="join w-full mx-auto">
+                  <input
+                    type="text"
+                    id="index-form-text-input"
+                    placeholder="canonical SMILES string"
+                    class="input grow input-md join-item"
+                  />
+                  <button class="btn btn-neutral join-item">Predict!</button>
+                </div>
+                <div class="label relative w-full mt-1">
+                  <div class="flex gap-2">
+                    <a
+                      href="#"
+                      class="example-link cursor-pointer hover:text-primary"
+                      data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
+                      title="load example"
+                      >Caffeine</a
+                    >
+                    <a
+                      href="#"
+                      class="example-link cursor-pointer hover:text-primary"
+                      data-smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
+                      title="load example"
+                      >Ibuprofen</a
+                    >
+                  </div>
+                  <a class="absolute top-0 left-[calc(100%-5.4rem)]" href="#"
+                    >Advanced</a
+                  >
+                </div>
+              </div>
+              <div
+                id="ketcher-container"
+                class="hidden w-full transition-all duration-300 ease-in-out opacity-0 transform scale-95"
+              >
+                <iframe
+                  id="index-ketcher"
+                  src="{% static '/js/ketcher2/ketcher.html' %}"
+                  width="100%"
+                  height="400"
+                  class="rounded-lg"
+                ></iframe>
+                <button
+                  class="btn btn-lg bg-primary-950 text-primary-50 join-item w-full mt-2"
+                >
+                  Predict!
+                </button>
+                <a class="label mx-auto w-full mt-1" href="#">Advanced</a>
+              </div>
+              <input
+                type="hidden"
+                id="index-form-smiles"
+                name="smiles"
+                value="smiles"
+              />
+              <input
+                type="hidden"
+                id="index-form-predict"
+                name="predict"
+                value="predict"
+              />
+              <input type="hidden" id="current-action" value="predict" />
+            </form>
+          </fieldset>
+        </div>
+      </div>
+    </div>
 
     <!-- Community News Section -->
     <section class="py-16 bg-base-200 z-10 mx-8">
-        <div class="max-w-7xl mx-auto px-4">
+      <div class="max-w-7xl mx-auto px-4">
-            <h2 class="h2 font-bold text-left mb-8">Community Updates</h2>
+        <h2 class="h2 font-bold text-left mb-8">Community Updates</h2>
 
-            <div id="community-news-container" class="flex gap-4 justify-center">
+        <div id="community-news-container" class="flex gap-4 justify-center">
-                <!-- News cards will be populated here -->
+          <!-- News cards will be populated here -->
-                <div id="loading" class="flex justify-center w-full">
+          <div id="loading" class="flex justify-center w-full">
-                    <span class="loading loading-spinner loading-lg"></span>
+            <span class="loading loading-spinner loading-lg"></span>
-                </div>
+          </div>
-            </div>
-
-            <div class="text-right mt-6">
-                <a href="https://community.envipath.org/c/announcements/10" target="_blank" class="btn btn-ghost btn-sm">
-                    Read More Announcements
-                </a>
-            </div>
-
-            <!-- Discourse API integration -->
-            <script src="{% static 'js/discourse-api.js' %}"></script>
         </div>
+
+        <div class="text-right mt-6">
+          <a
+            href="https://community.envipath.org/c/announcements/10"
+            target="_blank"
+            class="btn btn-ghost btn-sm"
+          >
+            Read More Announcements
+          </a>
+        </div>
+
+        <!-- Discourse API integration -->
+        <script src="{% static 'js/discourse-api.js' %}"></script>
+      </div>
     </section>
 
     <!-- Mission Statement Section -->
     <section class="py-16 from-base-200 to-base-100 bg-gradient-to-b">
-        <div class="mx-auto px-8 md:px-12">
+      <div class="mx-auto px-8 md:px-12">
-            <div class="flex flex-row gap-4">
+        <div class="flex flex-row gap-4">
-                <div class="w-1/3">
+          <div class="w-1/3">
-                    <img src="{% static "/images/ep-rule-artwork.png" %}" alt="rule-based iterative tree greneration" class="w-full h-full object-contain" />
+            <img
-                </div>
+              src="{% static "/images/ep-rule-artwork.png" %}"
-                <div class="space-y-4 text-left w-2/3 mr-8">
+              alt="rule-based iterative tree greneration"
-                    <h2 class="h2 font-bold mb-8">About enviPath</h2>
+              class="w-full h-full object-contain"
-                    <p class="">
+            />
-                        enviPath is a database and prediction system for the microbial
+          </div>
-                        biotransformation of organic environmental contaminants. The
+          <div class="space-y-4 text-left w-2/3 mr-8">
-                        database provides the possibility to store and view experimentally
+            <h2 class="h2 font-bold mb-8">About enviPath</h2>
-                        observed biotransformation pathways.
+            <p class="">
-                    </p>
+              enviPath is a database and prediction system for the microbial
-                    <p class="">
+              biotransformation of organic environmental contaminants. The
-                        The pathway prediction system provides different relative reasoning models
+              database provides the possibility to store and view experimentally
-                        to predict likely biotransformation pathways and products. Explore our tools
+              observed biotransformation pathways.
-                        and contribute to advancing environmental biotransformation research.
+            </p>
-                    </p>
+            <p class="">
-                    <div class="flex flex-row gap-4 float-right">
+              The pathway prediction system provides different relative
-                        <a href="/about" class="btn btn-ghost-neutral">Read More</a>
+              reasoning models to predict likely biotransformation pathways and
-                        <a href="/about" class="btn btn-neutral">Publications</a>
+              products. Explore our tools and contribute to advancing
-                    </div>
+              environmental biotransformation research.
-                </div>
+            </p>
+            <div class="flex flex-row gap-4 float-right">
+              <a href="/about" class="btn btn-ghost-neutral">Read More</a>
+              <a href="/about" class="btn btn-neutral">Publications</a>
             </div>
-
+          </div>
         </div>
+      </div>
     </section>
 
     <!-- Partners Section -->
     <section class="py-14 sm:py-12 bg-base-100">
-        <div class="mx-auto px-6 lg:px-8">
+      <div class="mx-auto px-6 lg:px-8">
-            <div class="divider"><h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2></div>
+        <div class="divider">
-            <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">
+          <h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2>
-                <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>
+        <div
+          class="mx-auto mt-10 grid max-w-lg grid-cols-4 items-center gap-x-8 gap-y-10 sm:max-w-xl sm:grid-cols-6 sm:gap-x-10 lg:mx-0 lg:max-w-none lg:grid-cols-3"
+        >
+          <img
+            src="{% static "/images/uoa-logo-small.png" %}"
+            alt="The University of Auckland"
+            class=" max-h-20 w-full object-contain lg:col-span-1"
+          />
+          <img
+            src="{% static "/images/logo-eawag.svg" %}"
+            alt="Eawag"
+            class=" max-h-12 w-full object-contain lg:col-span-1"
+          />
+          <img
+            src="{% static "/images/uzh-logo.svg" %}"
+            alt="University of Zurich"
+            class="2 max-h-16 w-full object-contain lg:col-span-1"
+          />
+        </div>
+      </div>
     </section>
+  </div>
 
+  <script language="javascript">
+    var currentPackage = "{{ meta.current_package.url }}";
 
+    // 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");
+      if (!container) return;
 
-</div>
+      // Clear container
+      container.innerHTML = "";
 
-    <script language="javascript">
+      // Create cards for each topic
-        var currentPackage = "{{ meta.current_package.url }}";
+      topics.forEach((topic) => {
+        const card = createDiscourseCard(topic);
+        container.insertAdjacentHTML("beforeend", card);
+      });
+    }
 
-        // Discourse API integration is now handled by discourse-api.js
+    // Function to create HTML card for a topic
+    function createDiscourseCard(topic) {
+      const date = new Date(topic.created_at).toLocaleDateString();
 
-        // Function to render Discourse topics into cards
+      return `
-        function renderDiscourseTopics(topics) {
-            const container = document.getElementById('community-news-container');
-            if (!container) return;
-
-            // Clear container
-            container.innerHTML = '';
-
-            // Create cards for each topic
-            topics.forEach(topic => {
-                const card = createDiscourseCard(topic);
-                container.insertAdjacentHTML('beforeend', card);
-            });
-        }
-
-        // Function to create HTML card for a topic
-        function createDiscourseCard(topic) {
-            const date = new Date(topic.created_at).toLocaleDateString();
-
-            return `
                 <div class="card bg-white shadow-xs hover:shadow-lg transition-shadow duration-300 h-64 w-75 flex-shrink-0">
                     <div class="card-body flex flex-col h-full">
                         <h3 class="card-title leading-tight font-normal tracking-tight h-12 mb-2 line-clamp-2 text-ellipsis wrap-break-word overflow-hidden">
@@ -215,146 +294,146 @@
                     </div>
                 </div>
             `;
+    }
+
+    // Make render function globally available
+    window.renderDiscourseTopics = renderDiscourseTopics;
+
+    // Toggle functionality with smooth animations
+    function toggleInputMode() {
+      const toggle = $('input[type="checkbox"]');
+      const textContainer = $("#text-input-container");
+      const ketcherContainer = $("#ketcher-container");
+      const formCard = $(".card");
+      const fieldset = $(".fieldset");
+
+      if (toggle.is(":checked")) {
+        // Draw mode - show Ketcher, hide text input
+        textContainer.addClass("opacity-0 transform scale-95");
+        textContainer.removeClass("opacity-100 transform scale-100");
+
+        // Adjust fieldset padding for Ketcher mode - reduce padding and make more compact
+        fieldset.removeClass("p-8");
+        fieldset.addClass("p-4");
+
+        // Wait for fade out to complete, then hide and show new content
+        setTimeout(() => {
+          textContainer.addClass("hidden");
+          ketcherContainer.removeClass("hidden opacity-0 transform scale-95");
+          ketcherContainer.addClass("opacity-100 transform scale-100");
+
+          // Force re-evaluation of iframe size
+          const iframe = document.getElementById("index-ketcher");
+          if (iframe) {
+            iframe.style.height = "400px";
+          }
+        }, 300);
+      } else {
+        // SMILES mode - show text input, hide Ketcher
+        ketcherContainer.addClass("opacity-0 transform scale-95");
+        ketcherContainer.removeClass("opacity-100 transform scale-100");
+
+        // Restore fieldset padding for text input mode
+        fieldset.removeClass("p-4");
+        fieldset.addClass("p-8");
+
+        // Wait for fade out to complete, then hide and show new content
+        setTimeout(() => {
+          ketcherContainer.addClass("hidden");
+          textContainer.removeClass("hidden opacity-0 transform scale-95");
+          textContainer.addClass("opacity-100 transform scale-100");
+        }, 300);
+
+        // Transfer SMILES from Ketcher to text input if available
+        if (window.indexKetcher && window.indexKetcher.getSmiles) {
+          const smiles = window.indexKetcher.getSmiles();
+          if (smiles && smiles.trim() !== "") {
+            $("#index-form-text-input").val(smiles);
+          }
+        }
+      }
+    }
+
+    // Ketcher integration
+    function indexKetcherToTextInput() {
+      $("#index-form-smiles").val(this.ketcher.getSmiles());
+    }
+
+    $(function () {
+      // Initialize fieldset with proper padding
+      $(".fieldset").addClass("p-8");
+
+      // Toggle event listener
+      $('input[type="checkbox"]').on("change", toggleInputMode);
+
+      // Ketcher iframe load handler
+      $("#index-ketcher").on("load", function () {
+        const checkKetcherReady = () => {
+          const win = this.contentWindow;
+          if (win.ketcher && "editor" in win.ketcher) {
+            window.indexKetcher = win.ketcher;
+            win.ketcher.editor.event.change.handlers.push({
+              once: false,
+              priority: 0,
+              f: indexKetcherToTextInput,
+              ketcher: win.ketcher,
+            });
+          } else {
+            setTimeout(checkKetcherReady, 100);
+          }
+        };
+        checkKetcherReady();
+      });
+
+      // Handle example link clicks
+      $(".example-link").on("click", function (e) {
+        e.preventDefault();
+        const smiles = $(this).data("smiles");
+        const title = $(this).attr("title");
+
+        // Check if we're in Ketcher mode or text input mode
+        if ($('input[type="checkbox"]').is(":checked")) {
+          // In Ketcher mode - set the SMILES in Ketcher
+          if (window.indexKetcher && window.indexKetcher.setMolecule) {
+            window.indexKetcher.setMolecule(smiles);
+          }
+        } else {
+          // In text input mode - set the SMILES in the text input
+          $("#index-form-text-input").val(smiles);
         }
 
-        // Make render function globally available
+        // Show a brief feedback
-        window.renderDiscourseTopics = renderDiscourseTopics;
+        const originalText = $(this).text();
+        $(this).text(`loaded!`);
+        setTimeout(() => {
+          $(this).text(originalText);
+        }, 1000);
+      });
 
-        // Toggle functionality with smooth animations
+      // Handle form submission on Enter
-        function toggleInputMode() {
+      $("#index-form").on("submit", function (e) {
-            const toggle = $('input[type="checkbox"]');
+        e.preventDefault();
-            const textContainer = $('#text-input-container');
-            const ketcherContainer = $('#ketcher-container');
-            const formCard = $('.card');
-            const fieldset = $('.fieldset');
 
-            if (toggle.is(':checked')) {
+        var textSmiles = "";
-                // Draw mode - show Ketcher, hide text input
-                textContainer.addClass('opacity-0 transform scale-95');
-                textContainer.removeClass('opacity-100 transform scale-100');
 
-                // Adjust fieldset padding for Ketcher mode - reduce padding and make more compact
+        // Check if we're in Ketcher mode and extract SMILES
-                fieldset.removeClass('p-8');
+        if ($('input[type="checkbox"]').is(":checked") && window.indexKetcher) {
-                fieldset.addClass('p-4');
+          textSmiles = window.indexKetcher.getSmiles().trim();
-
+        } else {
-                // Wait for fade out to complete, then hide and show new content
+          textSmiles = $("#index-form-text-input").val().trim();
-                setTimeout(() => {
-                    textContainer.addClass('hidden');
-                    ketcherContainer.removeClass('hidden opacity-0 transform scale-95');
-                    ketcherContainer.addClass('opacity-100 transform scale-100');
-
-                    // Force re-evaluation of iframe size
-                    const iframe = document.getElementById('index-ketcher');
-                    if (iframe) {
-                        iframe.style.height = '400px';
-                    }
-                }, 300);
-            } else {
-                // SMILES mode - show text input, hide Ketcher
-                ketcherContainer.addClass('opacity-0 transform scale-95');
-                ketcherContainer.removeClass('opacity-100 transform scale-100');
-
-                // Restore fieldset padding for text input mode
-                fieldset.removeClass('p-4');
-                fieldset.addClass('p-8');
-
-                // Wait for fade out to complete, then hide and show new content
-                setTimeout(() => {
-                    ketcherContainer.addClass('hidden');
-                    textContainer.removeClass('hidden opacity-0 transform scale-95');
-                    textContainer.addClass('opacity-100 transform scale-100');
-                }, 300);
-
-                // Transfer SMILES from Ketcher to text input if available
-                if (window.indexKetcher && window.indexKetcher.getSmiles) {
-                    const smiles = window.indexKetcher.getSmiles();
-                    if (smiles && smiles.trim() !== '') {
-                        $('#index-form-text-input').val(smiles);
-                    }
-                }
-            }
         }
 
-        // Ketcher integration
+        if (textSmiles === "") {
-        function indexKetcherToTextInput() {
+          return;
-            $('#index-form-smiles').val(this.ketcher.getSmiles());
         }
 
-        $(function () {
+        $("#index-form-smiles").val(textSmiles);
-            // Initialize fieldset with proper padding
+        $("#index-form").attr("action", currentPackage + "/pathway");
-            $('.fieldset').addClass('p-8');
+        $("#index-form").attr("method", "POST");
+        this.submit();
+      });
 
-            // Toggle event listener
+      // Discourse topics are now loaded automatically by discourse-api.js
-            $('input[type="checkbox"]').on('change', toggleInputMode);
+    });
-
+  </script>
-            // Ketcher iframe load handler
-            $('#index-ketcher').on('load', function() {
-                const checkKetcherReady = () => {
-                    const win = this.contentWindow;
-                    if (win.ketcher && 'editor' in win.ketcher) {
-                        window.indexKetcher = win.ketcher;
-                        win.ketcher.editor.event.change.handlers.push({
-                            once: false,
-                            priority: 0,
-                            f: indexKetcherToTextInput,
-                            ketcher: win.ketcher
-                        });
-                    } else {
-                        setTimeout(checkKetcherReady, 100);
-                    }
-                };
-                checkKetcherReady();
-            });
-
-            // Handle example link clicks
-            $('.example-link').on('click', function(e) {
-                e.preventDefault();
-                const smiles = $(this).data('smiles');
-                const title = $(this).attr('title');
-
-                // Check if we're in Ketcher mode or text input mode
-                if ($('input[type="checkbox"]').is(':checked')) {
-                    // In Ketcher mode - set the SMILES in Ketcher
-                    if (window.indexKetcher && window.indexKetcher.setMolecule) {
-                        window.indexKetcher.setMolecule(smiles);
-                    }
-                } else {
-                    // In text input mode - set the SMILES in the text input
-                    $('#index-form-text-input').val(smiles);
-                }
-
-                // Show a brief feedback
-                const originalText = $(this).text();
-                $(this).text(`loaded!`);
-                setTimeout(() => {
-                    $(this).text(originalText);
-                }, 1000);
-            });
-
-            // Handle form submission on Enter
-            $('#index-form').on("submit", function (e) {
-                e.preventDefault();
-
-                var textSmiles = '';
-
-                // Check if we're in Ketcher mode and extract SMILES
-                if ($('input[type="checkbox"]').is(':checked') && window.indexKetcher) {
-                    textSmiles = window.indexKetcher.getSmiles().trim();
-                } else {
-                    textSmiles = $('#index-form-text-input').val().trim();
-                }
-
-                if (textSmiles === '') {
-                    return;
-                }
-
-                $('#index-form-smiles').val(textSmiles);
-                $("#index-form").attr("action", currentPackage + "/pathway");
-                $("#index-form").attr("method", 'POST');
-                this.submit();
-            });
-
-            // Discourse topics are now loaded automatically by discourse-api.js
-        });
-    </script>
 {% endblock main_content %}

templates/modals/objects/set_license_modal.html

@@ -52,8 +52,6 @@
                         </div>
                     </div>
                     <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">
@@ -128,8 +126,6 @@ function cc() {
 
         $('#ccfig').append(img_tpl);
         $('#license').val(ccstr);
-        $('#license-link').val(link);
-        $('#license-image-link').val(imageLink);
     } else {
         $('#ccfig').empty();
         $('#set_license_form_submit').prop('disabled', true);

templates/modals/search_modal.html

@@ -0,0 +1,535 @@
+{% load static %}
+<dialog id="search_modal" class="modal @max-sm:modal-top justify-center">
+    <div class="modal-box w-lvw sm:w-[85vw] sm:max-w-5xl h-full sm:h-8/12 p-1" >
+
+        <!-- Search Input and Mode Selector -->
+        <div class="form-control mb-4 flex-shrink-0 w-full">
+            <div class="join w-full m-0 p-3 items-center">
+                <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:--anchor-1"
+                            class="btn join-item btn-ghost">
+                        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>
+                    </button>
+                    <ul tabindex="0"" class="dropdown dropdown-end menu bg-base-200 rounded-box  z-[100] w-64 p-2 shadow-lg" popover id="search_dropdown_menu" style="position-anchor:--anchor-1">
+                        <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 p-1 text-base-content/50">
+                        <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 flex-shrink-0">
+            <!-- Pills Container -->
+            <div id="modal_package_pills_container"
+                 class="flex flex-wrap gap-2 p-3 border-2 border-dashed border-base-300 rounded-lg m-3 min-h-[3rem] items-center">
+                <!-- Pills will be added here dynamically -->
+
+            </div>
+
+            <!-- Package Dropdown Menu -->
+            <ul class="dropdown dropdown-end menu bg-base-200 rounded-box z-[100] w-80 max-h-96 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 justify-between items-center"
+                           data-package-url="{{ obj.url }}"
+                           data-package-name="{{ obj.name }}">
+                            <span>{{ obj.name }}</span>
+                            <svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4 package-checkmark hidden" 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 justify-between items-center"
+                           data-package-url="{{ obj.url }}"
+                           data-package-name="{{ obj.name }}">
+                            <span>{{ obj.name }}</span>
+                            <svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4 package-checkmark hidden" 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 justify-between items-center"
+                           data-package-url="{{ obj.url }}"
+                           data-package-name="{{ obj.name }}">
+                            <span>{{ obj.name }}</span>
+                            <svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4 package-checkmark hidden" 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 justify-center py-8 flex-shrink-0">
+            <span class="loading loading-spinner loading-lg text-primary"></span>
+        </div>
+
+        <!-- Results Container - scrollable -->
+        <div id="search_results" class="flex-1 overflow-y-auto min-h-0 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 });
+
+    // 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>

templates/modals/signup_modal.html

@@ -1,110 +0,0 @@
-<div class="modal fade bs-modal-sm" id="signupmodal" tabindex="-1" role="dialog" aria-labelledby="mySmallModalLabel"
-     aria-hidden="true">
-    <div class="modal-dialog modal-sm">
-        <div class="modal-content">
-            <br>
-            <div class="bs-example bs-example-tabs">
-                <ul id="myTab" class="nav nav-tabs">
-                    <li class="active">
-                        <a href="#signin" data-toggle="tab">Sign In</a>
-                    </li>
-                    <li class="">
-                        <a href="#signup" data-toggle="tab">Register</a>
-                    </li>
-                    <li class="">
-                        <a href="#why" data-toggle="tab">Why?</a>
-                    </li>
-                </ul>
-            </div>
-            <div class="modal-body">
-                <div id="myTabContent" class="tab-content">
-                    <div class="tab-pane fade active in" id="signin">
-                        <form class="form-horizontal" method="post" action="{% url 'login' %}">
-                            {% csrf_token %}
-                            <fieldset>
-                                <input type="hidden" name="login" id="login" value="true"/>
-                                <div class="control-group">
-                                    <label class="control-label" for="username">Username:</label>
-                                    <div class="controls">
-                                        <input required id="username" name="username" type="text" class="form-control"
-                                               placeholder="username" autocomplete="username">
-                                    </div>
-                                    <label class="control-label" for="passwordinput">Password:</label>
-                                    <div class="controls">
-                                        <input required id="passwordinput" name="password" class="form-control"
-                                               type="password" placeholder="********" autocomplete="current-password">
-                                    </div>
-                                </div>
-
-                                <!-- Button -->
-                                <div class="control-group">
-                                    <label class="control-label" for="signin"></label>
-                                    <div class="controls">
-                                        <button id="signin" name="signin" class="btn btn-success">Sign In</button>
-                                    </div>
-                                </div>
-                            </fieldset>
-                        </form>
-                    </div>
-
-                    <!-- Why tab -->
-                    <div class="tab-pane fade in" id="why">
-                        <p>After you register, you have more permissions on
-                            this site, e.g., can create your own
-                            packages, submit data for review, and set access
-                            permissions to your data.</p>
-                        <p></p>
-                        <p>
-                            <br> Please
-                            contact <a href="mailto:admin@envipath.org">admin@envipath.org</a>
-                            if you have any questions.</p>
-                    </div>
-
-
-                    <!-- Register -->
-                    <div class="tab-pane fade"
-                         id="signup">
-                        <div id="passwordGuideline" class="alert alert-info">
-                            The password must contain 8 to 30 characters<br>
-                            The following characters are allowed:
-                            - Upper and lower case characters<br>
-                            - Digits<br>
-                            - Special characters _, -, +<br>
-
-                        </div>
-
-                        <form id="signup-action" class="form-horizontal" action="{% url 'login' %}" method="post">
-                            {% csrf_token %}
-                            <input type="hidden" name="register" id="register" value="true"/>
-
-                            <label class="control-label" for="userid">Username:</label>
-                            <input id="userid" name="username" class="form-control" type="text" placeholder="user" required autocomplete="username">
-
-                            <label class="control-label" for="email">Email:</label>
-                            <input id="email" name="email" class="form-control" type="email" placeholder="user@envipath.org" required>
-
-                            <label class="control-label" for="password">Password:</label>
-                            <input id="password" name="password" class="form-control" type="password" placeholder="********" required autocomplete="new-password">
-
-                            <label class="control-label" for="rpassword">Repeat Password:</label>
-                            <input id="rpassword" name="rpassword" class="form-control" type="password" placeholder="********" required autocomplete="new-password">
-
-                            <div class="control-group">
-                                <label class="control-label" for="confirmsignup"></label>
-                                <div class="controls">
-                                    <button id="confirmsignup" name="confirmsignup" class="btn btn-success">Sign Up
-                                    </button>
-                                </div>
-                            </div>
-                        </form>
-                    </div>
-                </div>
-            </div>
-            <div class="modal-footer">
-                <center>
-                    <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
-                </center>
-            </div>
-        </div>
-    </div>
-</div>

templates/predict_pathway.html

@@ -0,0 +1,188 @@
+{% extends "framework_modern.html" %}
+{% load static %}
+{% block content %}
+  <div class="mx-auto w-full p-8">
+    <h1 class="h1 mb-4 text-3xl font-bold">Predict a Pathway</h1>
+
+    <form
+      id="predict_form"
+      accept-charset="UTF-8"
+      action="{{ meta.current_package.url }}/pathway"
+      method="post"
+    >
+      {% csrf_token %}
+      <div class="mb-8 flex flex-col gap-8 md:flex-row md:items-end">
+        <fieldset class="flex flex-col gap-4 md:flex-3/4">
+          <label class="floating-label" for="name">
+            <input
+              type="text"
+              name="name"
+              placeholder="Name"
+              id="name"
+              class="input input-md w-full"
+            />
+            <span>Name</span>
+          </label>
+
+          <label class="floating-label" for="description">
+            <input
+              type="text"
+              name="description"
+              placeholder="Description"
+              id="description"
+              class="input input-md w-full"
+            />
+            <span>Description</span>
+          </label>
+        </fieldset>
+        <fieldset
+          class="fieldset flex shrink-0 flex-row items-start gap-3 md:flex-1/4 md:flex-col"
+        >
+          <label class="fieldset-label text-base-content/50">Mode</label>
+          <label class="label">
+            <input
+              type="radio"
+              name="predict"
+              id="radioPredict"
+              value="predict"
+              checked
+              class="radio radio-neutral"
+            />
+            Predict
+          </label>
+          <label class="label">
+            <input
+              type="radio"
+              name="predict"
+              id="radioIncremental"
+              value="incremental"
+              class="radio radio-neutral"
+            />
+            Incremental
+          </label>
+          <label class="label">
+            <input
+              type="radio"
+              name="predict"
+              id="radioBuild"
+              value="build"
+              class="radio radio-neutral"
+            />
+            Build
+          </label>
+        </fieldset>
+      </div>
+
+      <label class="floating-label" for="predict-smiles">
+        <input
+          type="text"
+          name="smiles"
+          placeholder="SMILES"
+          id="predict-smiles"
+          class="input input-md w-full"
+        />
+        <span>SMILES</span>
+      </label>
+
+      <div class="divider text-base-content/50">OR</div>
+
+      <div class="mb-8 w-full">
+        <label class="text-base-content/50 mb-4 text-xs font-medium"
+          >Draw Structure</label
+        >
+        <iframe
+          id="predict-ketcher"
+          src="{% static '/js/ketcher2/ketcher.html' %}"
+          width="100%"
+          height="510"
+        ></iframe>
+      </div>
+
+      <label class="select mb-8 w-full">
+        <span class="label">Predictor</span>
+        <select id="prediction-setting" name="prediction-setting">
+          <option disabled>Select a Setting</option>
+          {% for s in meta.available_settings %}
+            <option
+              value="{{ s.url }}"
+              {% if s.id == meta.user.default_setting.id %}selected{% endif %}
+            >
+              {{ s.name }}{% if s.id == meta.user.default_setting.id %}
+                (User default)
+              {% endif %}
+            </option>
+          {% endfor %}
+        </select>
+      </label>
+
+      <div class="flex justify-end gap-2">
+        <a href="{{ meta.current_package.url }}/pathway" class="btn btn-outline"
+          >Cancel</a
+        >
+        <button
+          type="submit"
+          id="predict-submit-button"
+          class="btn btn-primary"
+        >
+          Predict
+        </button>
+      </div>
+    </form>
+  </div>
+
+  <script>
+    function predictKetcherToTextInput() {
+      $("#predict-smiles").val(this.ketcher.getSmiles());
+    }
+
+    $(function () {
+      $("#predict-ketcher").on("load", function () {
+        const checkKetcherReady = () => {
+          const win = this.contentWindow;
+          if (win.ketcher && "editor" in win.ketcher) {
+            window.predictKetcher = win.ketcher;
+            win.ketcher.editor.event.change.handlers.push({
+              once: false,
+              priority: 0,
+              f: predictKetcherToTextInput,
+              ketcher: win.ketcher,
+            });
+          } else {
+            setTimeout(checkKetcherReady, 100);
+          }
+        };
+
+        checkKetcherReady();
+      });
+
+      $("#predict-submit-button").on("click", function (e) {
+        e.preventDefault();
+        const button = $(this);
+        button.prop("disabled", true);
+        button.text("Predicting...");
+
+        // Get SMILES from either input or Ketcher
+        let smiles = $("#predict-smiles").val().trim();
+
+        // If SMILES input is empty, try to get from Ketcher
+        if (!smiles && window.predictKetcher) {
+          smiles = window.predictKetcher.getSmiles().trim();
+          if (smiles) {
+            $("#predict-smiles").val(smiles);
+          }
+        }
+
+        // Basic validation
+        if (!smiles) {
+          alert("Please enter a SMILES string or draw a structure.");
+          button.prop("disabled", false);
+          button.text("Predict");
+          return;
+        }
+
+        // Submit form
+        $("#predict_form").submit();
+      });
+    });
+  </script>
+{% endblock content %}

templates/static/login.html

@@ -105,7 +105,7 @@
       </div>
     </div>
 
-    <form method="post" action="{% url 'register' %}" class="space-y-4">
+    <form method="post" action="{% url 'login' %}" class="space-y-4">
       {% csrf_token %}
       <input type="hidden" name="register" value="true" />
 

tests/views/test_package_views.py

@@ -4,7 +4,14 @@ from django.test import TestCase, tag
 from django.urls import reverse
 
 from epdb.logic import UserManager
-from epdb.models import Package, UserPackagePermission, Permission, GroupPackagePermission, Group
+from epdb.models import (
+    Package,
+    UserPackagePermission,
+    Permission,
+    GroupPackagePermission,
+    Group,
+    License,
+)
 
 
 class PackageViewTest(TestCase):
@@ -29,6 +36,15 @@ class PackageViewTest(TestCase):
             add_to_group=True,
             is_active=True,
         )
+        # Create the default license set.
+        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 setUp(self):
         self.client.force_login(self.user1)
@@ -188,7 +204,28 @@ class PackageViewTest(TestCase):
         self.client.post(package_url, {"license": "no-license"})
 
         self.assertIsNone(p.license)
-        # TODO test others
+
+        # Test other possible licenses
+        cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
+        for cc_string in cc_strings:
+            self.client.post(package_url, {"license": cc_string})
+            # Without this, the instance of p doesn't have the license. However, the one retrieved with get does
+            p = Package.objects.get(url=package_url)
+            self.assertEqual(
+                p.license.link, f"https://creativecommons.org/licenses/{cc_string}/4.0/"
+            )
+
+        # Test again to ensure that Licenses are reused
+        cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
+        for cc_string in cc_strings:
+            self.client.post(package_url, {"license": cc_string})
+            # Without this, the instance of p doesn't have the license. However, the one retrieved with get does
+            p = Package.objects.get(url=package_url)
+            self.assertEqual(
+                p.license.link, f"https://creativecommons.org/licenses/{cc_string}/4.0/"
+            )
+
+        self.assertEqual(License.objects.count(), len(cc_strings))
 
     def test_delete_package(self):
         response = self.client.post(

utilities/misc.py

@@ -714,6 +714,7 @@ class PackageImporter:
             license_obj, _ = License.objects.get_or_create(
                 name=license_data["name"],
                 defaults={
+                    "cc_string": license_data.get("cc_string", ""),
                     "link": license_data.get("link", ""),
                     "image_link": license_data.get("image_link", ""),
                 },