Merge branch 'develop' into fix/missing_nav_links

## 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>

epdb/urls.py

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

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)
 

templates/actions/collections/pathway.html

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

templates/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">
+<div class="bg-base-300 text-base-content mx-auto mt-10 lg:max-w-5xl">
-
+  <footer class="footer sm:footer-horizontal p-10">
-    <footer class="footer sm:footer-horizontal p-10">
+    {% if not public_mode %}
-        {% if not public_mode %}
+      <nav>
-        <nav>
+        <h6 class="footer-title">Services</h6>
-            <h6 class="footer-title">Services</h6>
+        <a class="link link-hover" href="/predict">Predict</a>
-            <a class="link link-hover" href="/">Predict</a>
+        <a class="link link-hover" href="/package">Packages</a>
-            <a class="link link-hover" href="/search">Search</a>
+        {% if user.is_authenticated %}
-            <a class="link link-hover" href="/package">Browse</a>
+          <a class="link link-hover" href="/model">Your Collections</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 %}
+        <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">
+  <footer class="footer border-t-2 border-neutral-300 px-10 py-4">
-    <div class="flex flex-row justify-between w-full items-start">
+    <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" >
+        <svg
-              <use
+          class="fill-neutral-content m-2 h-14 flex-shrink-0"
-                href="{% static "/images/logo-square.svg" %}#ep-logo-square"
+          viewbox="0 0 65 65"
-              >
+        >
-              </use>
+          <use
-            </svg>
+            href="{% static "/images/logo-square.svg" %}#ep-logo-square"
+          ></use>
+        </svg>
 
-          enviPath Ltd.
+        enviPath Ltd.
-          <br />
+        <br />
-          Biodegredation prediction since 2015.
+        Biodegredation prediction since 2015.
-        </p>
+      </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">
+          <svg
-                <title>YouTube</title>
+            role="img"
-                <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"/>
+            viewBox="0 0 24 24"
-            </svg>
+            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">
+          <svg
-                <title>Discourse</title>
+            role="img"
-                <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"/>
+            viewBox="0 0 24 24"
-            </svg>
+            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>

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">
+    <a href="{{ meta.server_url }}" class="btn btn-ghost text-xl normal-case">
-      <svg class="h-8 fill-base-content" viewBox="0 0 104 26" role="img">
+      <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>
@@ -59,7 +62,7 @@
     {% if not public_mode %}
       <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

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">
+      <div class="absolute bottom-40 left-1/8 z-10 -translate-x-8">
-        <h2 class="text-3xl text-base-100 text-shadow-lg text-left">
+        <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="my-4 ml-8 flex h-fit flex-row items-center justify-start">
-          <div class="flex flex-row justify-start items-center h-fit ml-8 my-4">
+            <div class="flex items-center gap-1">
-            <div class="flex items-center gap-2">
+              <label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
-              <!-- <span class="text-sm text-neutral-500">Input Mode:</span> -->
-              <label class="toggle text-base-content toggle-md">
                 <input type="checkbox" />
-                <svg
+                <span class="swap-on flex items-center gap-1">
-                  aria-label="smiles mode"
+                  <div
-                  xmlns="http://www.w3.org/2000/svg"
+                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
-                  viewBox="0 0 20 20"
-                  class="size-5"
-                >
-                  <g
-                    stroke-linejoin="round"
-                    stroke-linecap="round"
-                    stroke-width="2"
-                    fill="currentColor"
-                    stroke="none"
                   >
-                    <path
+                    <svg
-                      fill-rule="evenodd"
+                      aria-label="smiles mode"
-                      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"
+                      xmlns="http://www.w3.org/2000/svg"
-                      clip-rule="evenodd"
+                      viewBox="0 0 20 20"
-                    />
+                      class="size-5"
-                  </g>
+                    >
-                </svg>
+                      <g
-                <svg
+                        stroke-linejoin="round"
-                  aria-label="draw mode"
+                        stroke-linecap="round"
-                  xmlns="http://www.w3.org/2000/svg"
+                        stroke-width="2"
-                  viewBox="0 0 20 20"
+                        fill="currentColor"
-                  fill="currentColor"
+                        stroke="none"
-                  stroke="none"
+                      >
-                  class="size-5"
+                        <path
-                >
+                          fill-rule="evenodd"
-                  <path
+                          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"
-                    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"
+                          clip-rule="evenodd"
-                  />
+                        />
-                </svg>
+                      </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">
+    <section class="bg-base-200 z-10 mx-8 py-16">
-      <div class="max-w-7xl mx-auto px-4">
+      <div class="mx-auto max-w-7xl px-4">
-        <h2 class="h2 font-bold text-left mb-8">Community Updates</h2>
+        <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">
+          <div class="mr-8 w-2/3 space-y-4 text-left">
-            <h2 class="h2 font-bold mb-8">About enviPath</h2>
+            <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" %}"

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"