Merge branch 'develop' into fix/missing_nav_links

[Feature] Add per-package pathway prediction (#195 )
## Major Changes - Introduces a new view for per-package predictions Co-authored-by: jebus <lorsbach@envipath.com> Reviewed-on: enviPath/enviPy#195 Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2025-11-12 22:01:46 +13:00 · 2025-11-12 22:01:34 +13:00 · 2025-11-12 21:42:02 +13:00 · 2025-11-12 20:53:52 +13:00 · 2025-11-12 18:15:33 +13:00 · 2025-11-12 11:04:00 +13:00
12 changed files with 809 additions and 748 deletions
--- a/epdb/tasks.py
+++ b/epdb/tasks.py
@ -1,15 +1,15 @@
 import csv
 import io
 import logging
-from datetime import datetime
 from typing import Any, Callable, List, Optional
 from uuid import uuid4

 from celery import shared_task
 from celery.utils.functional import LRUCache
+from django.utils import timezone

 from epdb.logic import SPathway
-from epdb.models import EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User, Edge
+from epdb.models import Edge, EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User

 logger = logging.getLogger(__name__)
 ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.
@ -29,7 +29,7 @@ def dispatch_eager(user: "User", job: Callable, *args, **kwargs):
        log.task_id = uuid4()
        log.job_name = job.__name__
        log.status = "SUCCESS"
-        log.done_at = datetime.now()
+        log.done_at = timezone.now()
        log.task_result = str(x) if x else None
        log.save()

--- a/epdb/urls.py
+++ b/epdb/urls.py
@ -142,6 +142,11 @@ urlpatterns = [
        v.package_pathway,
        name="package pathway detail",
    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/predict$",
+        v.package_predict_pathway,
+        name="package predict pathway",
+    ),
    # Pathway Nodes
    re_path(
        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",
--- a/epdb/views.py
+++ b/epdb/views.py
@ -374,6 +374,22 @@ def predict_pathway(request):
    return render(request, "predict_pathway.html", context)


+@package_permission_required()
+def package_predict_pathway(request, package_uuid):
+    """Package-specific predict pathway view."""
+    if request.method != "GET":
+        return HttpResponseNotAllowed(["GET"])
+
+    current_user = _anonymous_or_real(request)
+    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
+
+    context = get_base_context(request)
+    context["title"] = f"enviPath - {current_package.name} - Predict Pathway"
+    context["meta"]["current_package"] = current_package
+
+    return render(request, "predict_pathway.html", context)
+
+
 def packages(request):
    current_user = _anonymous_or_real(request)

@ -955,6 +971,12 @@ def package_model(request, package_uuid, model_uuid):
                ]
                dispatch(current_user, evaluate_model, current_model.pk, multigen, eval_package_ids)

+                return redirect(current_model.url)
+            elif hidden == "retrain":
+                from .tasks import dispatch, retrain
+
+                dispatch(current_user, retrain, current_model.pk)
+
                return redirect(current_model.url)
            else:
                return HttpResponseBadRequest()
--- a/templates/actions/collections/pathway.html
+++ b/templates/actions/collections/pathway.html
@ -1,6 +1,9 @@
 {% if meta.can_edit %}
-    <li>
-        <a href="{{ meta.server_url }}/predict">
-            <span class="glyphicon glyphicon-plus"></span> New Pathway</a>
-    </li>
+  <li>
+    <a
+      href="{% if meta.current_package %}{{ meta.current_package.url }}/predict{% else %}{{ meta.server_url }}/predict{% endif %}"
+    >
+      <span class="glyphicon glyphicon-plus"></span> New Pathway</a
+    >
+  </li>
 {% endif %}
--- a/templates/framework_modern.html
+++ b/templates/framework_modern.html
@ -178,6 +178,23 @@
        }
      });

+      // Open search modal function
+      function openSearchModal() {
+        const searchModal = document.getElementById("search_modal");
+        if (searchModal) {
+          searchModal.showModal();
+        }
+      }
+
+      // Click handler for search badge
+      const searchTrigger = document.getElementById("search-trigger");
+      if (searchTrigger) {
+        searchTrigger.addEventListener("click", function (event) {
+          event.preventDefault();
+          openSearchModal();
+        });
+      }
+
      // Global keyboard shortcut for search (Cmd+K on Mac, Ctrl+K on Windows/Linux)
      document.addEventListener("keydown", function (event) {
        // Check if user is typing in an input field
@ -198,7 +215,7 @@

        if (isCorrectModifier && event.key === "k") {
          event.preventDefault();
-          search_modal.showModal();
+          openSearchModal();
        }
      });
    </script>
--- a/templates/includes/footer.html
+++ b/templates/includes/footer.html
@ -1,19 +1,22 @@
 {% load static %}
-<div class="lg:max-w-5xl mt-10 mx-auto bg-base-300 text-base-content">
-
-    <footer class="footer sm:footer-horizontal p-10">
-        {% if not public_mode %}
-        <nav>
-            <h6 class="footer-title">Services</h6>
-            <a class="link link-hover" href="/">Predict</a>
-            <a class="link link-hover" href="/search">Search</a>
-            <a class="link link-hover" href="/package">Browse</a>
-            {% if user.is_authenticated %}
-            <a class="link link-hover" href="/model">Your Collections</a>
-            {% endif %}
-            <a href="https://wiki.envipath.org/" target="_blank" class="link link-hover">Documentation</a>
-    </nav>
+<div class="bg-base-300 text-base-content mx-auto mt-10 lg:max-w-5xl">
+  <footer class="footer sm:footer-horizontal p-10">
+    {% if not public_mode %}
+      <nav>
+        <h6 class="footer-title">Services</h6>
+        <a class="link link-hover" href="/predict">Predict</a>
+        <a class="link link-hover" href="/package">Packages</a>
+        {% if user.is_authenticated %}
+          <a class="link link-hover" href="/model">Your Collections</a>
        {% endif %}
+        <a
+          href="https://wiki.envipath.org/"
+          target="_blank"
+          class="link link-hover"
+          >Documentation</a
+        >
+      </nav>
+    {% endif %}
    <nav>
      <h6 class="footer-title">Company</h6>
      <a class="link link-hover" href="/about">About us</a>
@ -29,39 +32,61 @@
      <a class="link link-hover" href="/cite">Cite enviPath</a>
    </nav>
  </footer>
-  <footer class="footer border-neutral-300 border-t-2 px-10 py-4">
-    <div class="flex flex-row justify-between w-full items-start">
+  <footer class="footer border-t-2 border-neutral-300 px-10 py-4">
+    <div class="flex w-full flex-row items-start justify-between">
      <aside class="grid-flow-col items-center">
-          <svg class="fill-neutral-content flex-shrink-0 h-14 m-2" viewbox="0 0 65 65" >
-              <use
-                href="{% static "/images/logo-square.svg" %}#ep-logo-square"
-              >
-              </use>
-            </svg>
+        <svg
+          class="fill-neutral-content m-2 h-14 flex-shrink-0"
+          viewbox="0 0 65 65"
+        >
+          <use
+            href="{% static "/images/logo-square.svg" %}#ep-logo-square"
+          ></use>
+        </svg>

-          enviPath Ltd.
-          <br />
-          Biodegredation prediction since 2015.
-        </p>
+        enviPath Ltd.
+        <br />
+        Biodegredation prediction since 2015.
+      </aside>
+      <aside class="text-base-200 mt-2 text-sm">
+        <span class="text-xs tracking-tight">Version</span>
+        <span class="text-base font-bold">{{ meta.version }}</span>
      </aside>
-      <aside class="text-sm text-base-200 mt-2"><span class="text-xs tracking-tight">Version</span> <span class="text-base font-bold">{{ meta.version }}</span></aside>
    </div>
    <nav class="md:place-self-center md:justify-self-end">
      <div class="grid grid-flow-col gap-4">
        <a href="https://www.youtube.com/@envipath7231" target="_blank">
-            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
-                <title>YouTube</title>
-                <path d="M23.498 6.186a3.016 3.016 0 0 0-2.122-2.136C19.505 3.545 12 3.545 12 3.545s-7.505 0-9.377.505A3.017 3.017 0 0 0 .502 6.186C0 8.07 0 12 0 12s0 3.93.502 5.814a3.016 3.016 0 0 0 2.122 2.136c1.871.505 9.376.505 9.376.505s7.505 0 9.377-.505a3.015 3.015 0 0 0 2.122-2.136C24 15.93 24 12 24 12s0-3.93-.502-5.814zM9.545 15.568V8.432L15.818 12l-6.273 3.568z"/>
-            </svg>
+          <svg
+            role="img"
+            viewBox="0 0 24 24"
+            xmlns="http://www.w3.org/2000/svg"
+            class="h-6 w-6 fill-current"
+          >
+            <title>YouTube</title>
+            <path
+              d="M23.498 6.186a3.016 3.016 0 0 0-2.122-2.136C19.505 3.545 12 3.545 12 3.545s-7.505 0-9.377.505A3.017 3.017 0 0 0 .502 6.186C0 8.07 0 12 0 12s0 3.93.502 5.814a3.016 3.016 0 0 0 2.122 2.136c1.871.505 9.376.505 9.376.505s7.505 0 9.377-.505a3.015 3.015 0 0 0 2.122-2.136C24 15.93 24 12 24 12s0-3.93-.502-5.814zM9.545 15.568V8.432L15.818 12l-6.273 3.568z"
+            />
+          </svg>
        </a>
        <a href="https://community.envipath.org/" target="_blank">
-            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
-                <title>Discourse</title>
-                <path d="M12.103 0C18.666 0 24 5.485 24 11.997c0 6.51-5.33 11.99-11.9 11.99L0 24V11.79C0 5.28 5.532 0 12.103 0zm.116 4.563c-2.593-.003-4.996 1.352-6.337 3.57-1.33 2.208-1.387 4.957-.148 7.22L4.4 19.61l4.794-1.074c2.745 1.225 5.965.676 8.136-1.39 2.17-2.054 2.86-5.228 1.737-7.997-1.135-2.778-3.84-4.59-6.84-4.585h-.008z"/>
-            </svg>
+          <svg
+            role="img"
+            viewBox="0 0 24 24"
+            xmlns="http://www.w3.org/2000/svg"
+            class="h-6 w-6 fill-current"
+          >
+            <title>Discourse</title>
+            <path
+              d="M12.103 0C18.666 0 24 5.485 24 11.997c0 6.51-5.33 11.99-11.9 11.99L0 24V11.79C0 5.28 5.532 0 12.103 0zm.116 4.563c-2.593-.003-4.996 1.352-6.337 3.57-1.33 2.208-1.387 4.957-.148 7.22L4.4 19.61l4.794-1.074c2.745 1.225 5.965.676 8.136-1.39 2.17-2.054 2.86-5.228 1.737-7.997-1.135-2.778-3.84-4.59-6.84-4.585h-.008z"
+            />
+          </svg>
        </a>
        <a href="https://www.linkedin.com/company/envipath/" target="_blank">
-            <img src="{% static "/images/linkedin.png" %}" alt="LinkedIn" class="w-6 h-6">
+          <img
+            src="{% static "/images/linkedin.png" %}"
+            alt="LinkedIn"
+            class="h-6 w-6"
+          />
        </a>
      </div>
    </nav>
--- a/templates/includes/navbar.html
+++ b/templates/includes/navbar.html
@ -1,9 +1,9 @@
 {% load static %}
 {# Modern DaisyUI Navbar #}
-<div class="navbar bg-neutral-50 text-neutral-950 shadow-lg x-50">
+<div class="navbar x-50 bg-neutral-50 text-neutral-950 shadow-lg">
  <div class="navbar-start">
-    <a href="{{ meta.server_url }}" class="btn btn-ghost normal-case text-xl">
-      <svg class="h-8 fill-base-content" viewBox="0 0 104 26" role="img">
+    <a href="{{ meta.server_url }}" class="btn btn-ghost text-xl normal-case">
+      <svg class="fill-base-content h-8" viewBox="0 0 104 26" role="img">
        <use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
      </svg>
    </a>
@ -26,6 +26,9 @@
          tabindex="-1"
          class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm"
        >
+          <li>
+            <a href="{{ meta.server_url }}/Package" id="packageLink">Package</a>
+          </li>
          <li>
            <a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a>
          </li>
@ -57,9 +60,9 @@

  <div class="navbar-end">
    {% if not public_mode %}
-      <a href="/search" role="button">
+      <a id="search-trigger" role="button" class="cursor-pointer">
        <div
-          class="flex items-center badge badge-dash space-x-1 bg-base-200 text-base-content/50 p-2 m-1"
+          class="badge badge-dash bg-base-200 text-base-content/50 m-1 flex items-center space-x-1 p-2"
        >
          <svg
            xmlns="http://www.w3.org/2000/svg"
@ -87,7 +90,7 @@
        <div
          tabindex="0"
          role="button"
-          class="btn btn-ghost m-1 btn-circle"
+          class="btn btn-ghost btn-circle m-1"
          id="loggedInButton"
        >
          <svg
--- a/templates/index/index.html
+++ b/templates/index/index.html
@ -2,74 +2,86 @@
 {% load static %}
 {% block main_content %}
  <!-- Hero Section with Logo and Search -->
-  <section class="hero h-fit max-w-5xl w-full shadow-none mx-auto relative">
+  <section class="hero relative mx-auto h-fit w-full max-w-5xl shadow-none">
    <div
-      class="hero min-h-[calc(100vh*0.4)] bg-gradient-to-br from-primary-800 to-primary-600"
+      class="hero from-primary-800 to-primary-600 min-h-[calc(100vh*0.4)] bg-gradient-to-br"
      style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
    >
      <div class="hero-overlay"></div>
      <!-- Predict Pathway text over the image -->
-      <div class="absolute bottom-40 left-1/8 -translate-x-8 z-10">
-        <h2 class="text-3xl text-base-100 text-shadow-lg text-left">
+      <div class="absolute bottom-40 left-1/8 z-10 -translate-x-8">
+        <h2 class="text-base-100 text-left text-3xl text-shadow-lg">
          Predict Your Pathway
        </h2>
      </div>
    </div>
  </section>

-  <div class="shadow-md max-w-5xl mx-auto bg-base-200">
+  <div class="bg-base-200 mx-auto max-w-5xl shadow-md">
    <!-- Predict Pathway Section -->
    <div
-      class="flex-col lg:flex-row-reverse w-full mx-auto -mt-32 relative z-20 mb-10 "
+      class="relative z-20 mx-auto -mt-32 mb-10 w-full flex-col lg:flex-row-reverse"
    >
      <div
-        class="card bg-base-100 shrink-0 shadow-xl w-3/4 mx-auto transition-all duration-300 ease-in-out"
+        class="card bg-base-100 mx-auto w-3/4 shrink-0 shadow-xl transition-all duration-300 ease-in-out"
      >
        <div class="card-body">
-          <!-- 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">
+          <div class="my-4 ml-8 flex h-fit flex-row items-center justify-start">
+            <div class="flex items-center gap-1">
+              <label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
                <input type="checkbox" />
-                <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"
+                <span class="swap-on flex items-center gap-1">
+                  <div
+                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
                  >
-                    <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>
+                    <svg
+                      aria-label="smiles mode"
+                      xmlns="http://www.w3.org/2000/svg"
+                      viewBox="0 0 20 20"
+                      class="size-5"
+                    >
+                      <g
+                        stroke-linejoin="round"
+                        stroke-linecap="round"
+                        stroke-width="2"
+                        fill="currentColor"
+                        stroke="none"
+                      >
+                        <path
+                          fill-rule="evenodd"
+                          d="M8 2.75A.75.75 0 0 1 8.75 2h7.5a.75.75 0 0 1 0 1.5h-3.215l-4.483 13h2.698a.75.75 0 0 1 0 1.5h-7.5a.75.75 0 0 1 0-1.5h3.215l4.483-13H8.75A.75.75 0 0 1 8 2.75Z"
+                          clip-rule="evenodd"
+                        />
+                      </g>
+                    </svg>
+                  </div>
+                  <span class="ext-xs">SMILES</span>
+                </span>
+                <span class="swap-off flex items-center gap-1">
+                  <div
+                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
+                  >
+                    <svg
+                      aria-label="draw mode"
+                      xmlns="http://www.w3.org/2000/svg"
+                      viewBox="0 0 20 20"
+                      fill="currentColor"
+                      stroke="none"
+                      class="size-5"
+                    >
+                      <path
+                        d="m2.695 14.762-1.262 3.155a.5.5 0 0 0 .65.65l3.155-1.262a4 4 0 0 0 1.343-.886L17.5 5.501a2.121 2.121 0 0 0-3-3L3.58 13.419a4 4 0 0 0-.885 1.343Z"
+                      />
+                    </svg>
+                  </div>
+                  <span class="text-base/50 text-xs">Draw</span>
+                </span>
              </label>
            </div>
          </div>

          <fieldset
-            class="fieldset transition-all duration-300 ease-in-out overflow-hidden"
+            class="fieldset overflow-hidden transition-all duration-300 ease-in-out"
          >
            <form
              id="index-form"
@ -79,29 +91,29 @@
              {% csrf_token %}
              <div
                id="text-input-container"
-                class="transition-all duration-300 ease-in-out opacity-100 transform scale-100"
+                class="scale-100 transform opacity-100 transition-all duration-300 ease-in-out"
              >
-                <div class="join w-full mx-auto">
+                <div class="join mx-auto w-full">
                  <input
                    type="text"
                    id="index-form-text-input"
                    placeholder="canonical SMILES string"
-                    class="input grow input-md join-item"
+                    class="input input-md join-item grow"
                  />
                  <button class="btn btn-neutral join-item">Predict!</button>
                </div>
-                <div class="label relative w-full mt-1">
+                <div class="label relative mt-1 w-full">
                  <div class="flex gap-2">
                    <a
                      href="#"
-                      class="example-link cursor-pointer hover:text-primary"
+                      class="example-link hover:text-primary cursor-pointer"
                      data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
                      title="load example"
                      >Caffeine</a
                    >
                    <a
                      href="#"
-                      class="example-link cursor-pointer hover:text-primary"
+                      class="example-link hover:text-primary cursor-pointer"
                      data-smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
                      title="load example"
                      >Ibuprofen</a
@ -114,7 +126,7 @@
              </div>
              <div
                id="ketcher-container"
-                class="hidden w-full transition-all duration-300 ease-in-out opacity-0 transform scale-95"
+                class="hidden w-full scale-95 transform opacity-0 transition-all duration-300 ease-in-out"
              >
                <iframe
                  id="index-ketcher"
@ -124,11 +136,13 @@
                  class="rounded-lg"
                ></iframe>
                <button
-                  class="btn btn-lg bg-primary-950 text-primary-50 join-item w-full mt-2"
+                  class="btn btn-lg bg-primary-950 text-primary-50 join-item mt-2 w-full"
                >
                  Predict!
                </button>
-                <a class="label mx-auto w-full mt-1" href="#">Advanced</a>
+                <div class="mt-1 flex w-full justify-end">
+                  <a class="label justify-end" href="/predict">Advanced</a>
+                </div>
              </div>
              <input
                type="hidden"
@ -150,18 +164,18 @@
    </div>

    <!-- Community News Section -->
-    <section class="py-16 bg-base-200 z-10 mx-8">
-      <div class="max-w-7xl mx-auto px-4">
-        <h2 class="h2 font-bold text-left mb-8">Community Updates</h2>
+    <section class="bg-base-200 z-10 mx-8 py-16">
+      <div class="mx-auto max-w-7xl px-4">
+        <h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>

-        <div id="community-news-container" class="flex gap-4 justify-center">
+        <div id="community-news-container" class="flex justify-center gap-4">
          <!-- News cards will be populated here -->
-          <div id="loading" class="flex justify-center w-full">
+          <div id="loading" class="flex w-full justify-center">
            <span class="loading loading-spinner loading-lg"></span>
          </div>
        </div>

-        <div class="text-right mt-6">
+        <div class="mt-6 text-right">
          <a
            href="https://community.envipath.org/c/announcements/10"
            target="_blank"
@ -177,18 +191,18 @@
    </section>

    <!-- Mission Statement Section -->
-    <section class="py-16 from-base-200 to-base-100 bg-gradient-to-b">
+    <section class="from-base-200 to-base-100 bg-gradient-to-b py-16">
      <div class="mx-auto px-8 md:px-12">
        <div class="flex flex-row gap-4">
          <div class="w-1/3">
            <img
              src="{% static "/images/ep-rule-artwork.png" %}"
              alt="rule-based iterative tree greneration"
-              class="w-full h-full object-contain"
+              class="h-full w-full object-contain"
            />
          </div>
-          <div class="space-y-4 text-left w-2/3 mr-8">
-            <h2 class="h2 font-bold mb-8">About enviPath</h2>
+          <div class="mr-8 w-2/3 space-y-4 text-left">
+            <h2 class="h2 mb-8 font-bold">About enviPath</h2>
            <p class="">
              enviPath is a database and prediction system for the microbial
              biotransformation of organic environmental contaminants. The
@ -201,7 +215,7 @@
              products. Explore our tools and contribute to advancing
              environmental biotransformation research.
            </p>
-            <div class="flex flex-row gap-4 float-right">
+            <div class="float-right flex flex-row gap-4">
              <a href="/about" class="btn btn-ghost-neutral">Read More</a>
              <a href="/about" class="btn btn-neutral">Publications</a>
            </div>
@ -211,7 +225,7 @@
    </section>

    <!-- Partners Section -->
-    <section class="py-14 sm:py-12 bg-base-100">
+    <section class="bg-base-100 py-14 sm:py-12">
      <div class="mx-auto px-6 lg:px-8">
        <div class="divider">
          <h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2>
@ -222,12 +236,12 @@
          <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"
+            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"
+            class="max-h-12 w-full object-contain lg:col-span-1"
          />
          <img
            src="{% static "/images/uzh-logo.svg" %}"
--- a/templates/modals/objects/retrain_model_modal.html
+++ b/templates/modals/objects/retrain_model_modal.html
@ -1,43 +1,55 @@
-<div class="modal fade" tabindex="-1" id="retrain_model_modal" role="dialog" aria-labelledby="retrain_model_modal"
-     aria-hidden="true">
-    <div class="modal-dialog modal-lg">
-        <div class="modal-content">
-            <div class="modal-header">
-                <button type="button" class="close" data-dismiss="modal">
-                    <span aria-hidden="true">&times;</span>
-                    <span class="sr-only">Close</span>
-                </button>
-                <h4 class="modal-title">Retrain Model</h4>
-            </div>
-            <div class="modal-body">
-                <form id="retrain_model_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/model"
-                      data-remote="true" method="post">
-                    <div class="jumbotron">
-                        To reflect changes in the rule or data packages, you can use the "Retrain" button,
-                        to let the model reflect the changes without creating a new model.
-                        While the model is retraining, it will be unavailable for prediction.
-                    </div>
-                    {% csrf_token %}
-                    <input type="hidden" name="action" value="retrain">
-                </form>
-            </div>
-            <div class="modal-footer">
-                <a id="retrain_model_form_submit" class="btn btn-primary" href="#">Retrain</a>
-                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-            </div>
-        </div>
+<div
+  class="modal fade"
+  tabindex="-1"
+  id="retrain_model_modal"
+  role="dialog"
+  aria-labelledby="retrain_model_modal"
+  aria-hidden="true"
+>
+  <div class="modal-dialog modal-lg">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal">
+          <span aria-hidden="true">&times;</span>
+          <span class="sr-only">Close</span>
+        </button>
+        <h4 class="modal-title">Retrain Model</h4>
+      </div>
+      <div class="modal-body">
+        <form
+          id="retrain_model_form"
+          accept-charset="UTF-8"
+          action="{{ meta.current_object.url }}"
+          data-remote="true"
+          method="post"
+        >
+          <div class="jumbotron">
+            To reflect changes in the rule or data packages, you can use the
+            "Retrain" button, to let the model reflect the changes without
+            creating a new model. While the model is retraining, it will be
+            unavailable for prediction.
+          </div>
+          {% csrf_token %}
+          <input type="hidden" name="hidden" value="retrain" />
+        </form>
+      </div>
+      <div class="modal-footer">
+        <a id="retrain_model_form_submit" class="btn btn-primary" href="#"
+          >Retrain</a
+        >
+        <button type="button" class="btn btn-default" data-dismiss="modal">
+          Cancel
+        </button>
+      </div>
    </div>
+  </div>
 </div>

 <script>
-
-    $(function () {
-
-        $('#retrain_model_form_submit').on('click', function (e) {
-            e.preventDefault();
-            $('#retrain_model_form').submit();
-        });
-
+  $(function () {
+    $("#retrain_model_form_submit").on("click", function (e) {
+      e.preventDefault();
+      $("#retrain_model_form").submit();
    });
-
+  });
 </script>
--- a/templates/modals/search_modal.html
+++ b/templates/modals/search_modal.html
--- a/templates/predict_pathway.html
+++ b/templates/predict_pathway.html
@ -2,7 +2,13 @@
 {% 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>
+    <h1 class="h1 mb-4 text-3xl font-bold">
+      Predict a Pathway
+
+      <span class="text-base-content/50 text-xs"
+        >in <strong>{{ meta.current_package.name|safe }}</strong>
+      </span>
+    </h1>

    <form
      id="predict_form"
--- a/templates/search.html
+++ b/templates/search.html
@ -1,197 +0,0 @@
-{% extends "framework.html" %}
-{% load static %}
-{% block content %}
-
-    <div id=searchContent>
-        <div id="packSelector">
-            <label>Select Packages</label><br>
-            <select id="selPackages" name="selPackages" data-actions-box='true' class="selPackages" multiple
-                    data-width='100%'>
-                {% if unreviewed_objects %}
-                    <option disabled>Reviewed Packages</option>
-                {% endif %}
-                {% for obj in reviewed_objects %}
-                    <option value="{{ obj.url }}" selected>{{ obj.name|safe }}</option>
-                {% endfor %}
-                {% if unreviewed_objects %}
-                    <option disabled>Unreviewed Packages</option>
-                {% endif %}
-                {% for obj in unreviewed_objects %}
-                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
-                {% endfor %}
-            </select>
-        </div>
-        <p></p>
-        <div>
-            <label>Search Term</label><br>
-            <div class="input-group" id="index-form-bar">
-                <input type="text" class="form-control" id='searchbar' placeholder="Benfuracarb">
-                <div class="input-group-btn">
-                    <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
-                            id="mode-button"
-                            aria-haspopup="true" aria-expanded="false">Text <span class="caret"></span></button>
-                    <ul class="dropdown-menu">
-                        <li class="dropdown-header">Text</li>
-                        <li><a id="dropdown-predict-text-text">Text</a></li>
-                        <li class="dropdown-header">SMILES</li>
-                        <li><a id="dropdown-search-smiles-default" data-toggle="tooltip">Default</a></li>
-                        <li><a id="dropdown-search-smiles-canonical">Canonical</a></li>
-                        <li><a id="dropdown-search-smiles-exact">Exact</a></li>
-                        <li class="dropdown-header">InChI</li>
-                        <li><a id="dropdown-search-inchi-inchikey">InChIKey</a></li>
-                    </ul>
-                    <button class="btn" style="background-color:#222222;color:#9d9d9d" type="button" id="search-button">
-                        Go!
-                    </button>
-                </div>
-            </div>
-            <p></p>
-            <div id="results"></div>
-            <p></p>
-            <div id="loading"></div>
-        </div>
-    </div>
-    <script>
-        function modeDropdownClicked() {
-            var suffix = ' <span class="caret"></span>';
-            var dropdownVal = $(this).text();
-            $('#mode-button').html(dropdownVal + suffix);
-        }
-
-        function handleSearchResponse(id, data) {
-            content = `
-                <div class='panel-group' id='search-accordion'>
-                    <div class='panel panel-default'>
-                        <div class='panel-heading' id='headingPanel' style='font-size:2rem;height: 46px'>
-                        Results
-                        </div>
-                        <div id='descDiv'></div>
-                    </div>`;
-
-            function makeContent(objs) {
-                links = "";
-                for (idx in objs) {
-                    obj = objs[idx];
-                    links += `<a class='list-group-item' href='${obj.url}'>${obj.name}</a>`
-                }
-                return links;
-            }
-
-            allEmpty = true;
-            for (key in data) {
-                if (key === 'searchterm') {
-                    continue;
-                }
-
-                if (data[key].length < 1) {
-                    continue;
-                }
-                allEmpty = false;
-                content += `
-                    <div class='panel panel-default panel-heading list-group-item' style='background-color:silver'>
-                        <h4 class='panel-title'>
-                            <a id='${key}_link' data-toggle='collapse' data-parent='#search-accordion' href='#${key}_panel'>
-                                ${key}
-                            </a>
-                        </h4>
-                    </div>
-                    <div id='${key}_panel' class='panel-collapse collapse in'>
-                        <div class='panel-body list-group-item'>
-                        ${makeContent(data[key])}
-                        </div>
-                    </div>
-
-        `;
-            }
-            if (allEmpty) {
-                $('#' + id).append('<div class="alert alert-danger" role="alert"><p>' + "No results..." + '</p></div>');
-            } else {
-                $('#' + id).append(content);
-            }
-        }
-
-        function search(e) {
-            e.preventDefault();
-
-            query = $("#searchbar").val()
-
-            if (!query) {
-                // Nothing to search...
-                console.log("Search phrase empty, won't do search")
-                return;
-            }
-
-            var selPacks = [];
-            $("#selPackages :selected").each(function () {
-                var id = this.value;
-                selPacks.push(id);
-            });
-
-            if (selPacks.length < 1) {
-                console.log("No package selected, won't do search")
-                return;
-            }
-
-            var mode = $('#mode-button').text().trim().toLowerCase();
-
-            var par = {};
-            par['packages'] = selPacks;
-            par['search'] = query;
-            par['mode'] = mode;
-
-            console.log(par);
-
-            var queryString = $.param(par, true);
-
-            makeLoadingGif("#loading", "{% static '/images/wait.gif' %}");
-
-            $("#results").empty();
-
-            $.getJSON("{{ SERVER_BASE }}/search?" + queryString, function (result) {
-                handleSearchResponse("results", result);
-                $("#loading").empty();
-            }).fail(function (d) {
-                $("#loading").empty();
-                console.log(d.responseText);
-                handleError(JSON.parse(d.responseText));
-            });
-        }
-
-
-        $(function () {
-
-            tooltips = {
-                'dropdown-predict-text-text': 'The inserted pattern will be searched on all enviPath object names and descriptions',
-                'dropdown-search-smiles-default': 'Search by SMILES, stereochemistry and charge are ignored',
-                'dropdown-search-smiles-canonical': 'Search by SMILES, stereochemistry is ignored but charge is preserved',
-                'dropdown-search-smiles-exact': 'Search by SMILES, exact match for stereochemistry and charge',
-                'dropdown-search-inchi-inchikey': 'Search by InChIKey',
-            }
-
-            Object.keys(tooltips).forEach(key => {
-                $('#' + key).tooltip({
-                    placement: "top",
-                    title: tooltips[key]
-                });
-
-                $('#' + key).on('click', modeDropdownClicked);
-            });
-
-            $("#selPackages").selectpicker();
-            $("#search-button").on("click", search);
-
-            $("#searchbar").on("keydown", function (e) {
-                if (e.key === "Enter") {
-                    e.preventDefault();
-                    search(e);
-                }
-            });
-
-        });
-        {% if search_result %}
-            $('#searchbar').val('{{ search_result.searchterm }}')
-            handleSearchResponse("results", {{ search_result|safe }});
-        {% endif %}
-    </script>
-
-{% endblock content %}
Author	SHA1	Message	Date
jebus	db286d14ec	Merge branch 'develop' into fix/missing_nav_links	2025-11-12 22:01:46 +13:00
Tobias O	d20a705011	[Feature] Add per-package pathway prediction (#195 ) ## Major Changes - Introduces a new view for per-package predictions Co-authored-by: jebus <lorsbach@envipath.com> Reviewed-on: enviPath/enviPy#195 Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-committed-by: Tobias O <tobias.olenyi@envipath.com>	2025-11-12 22:01:34 +13:00
Tobias O	debbef8158	[Enhancement] Cleanup Landing Page Form (#194 ) I changed the toggle style to be more self evident. Do you think this is enough, or should I add an (ugly) label? ![image.png](/attachments/0e4ce043-7544-4852-9db9-460517b36d64) Co-authored-by: jebus <lorsbach@envipath.com> Reviewed-on: enviPath/enviPy#194 Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-committed-by: Tobias O <tobias.olenyi@envipath.com>	2025-11-12 21:42:02 +13:00
Tobias O	2799718951	fix: open and close search modal (#192 ) Modal now opens on badge click. Modal now closes on random click around Reviewed-on: enviPath/enviPy#192 Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-committed-by: Tobias O <tobias.olenyi@envipath.com>	2025-11-12 20:53:52 +13:00
Tobias O	999dc15189	fix: add/update missing nav links	2025-11-12 18:15:33 +13:00
jebus	305fdc41fb	[Fix] Replace datetime.now() with Djangos timezone.now() to get rid of NaiveTimestamp warning (#191 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#191	2025-11-12 11:04:00 +13:00
jebus	9deca8867e	[Feature] Possibility to Retrain Models (#190 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#190	2025-11-12 10:28:35 +13:00