mrg

templates/collections/joblog.html

@@ -1,6 +1,5 @@
 {% extends "framework.html" %}
 {% load static %}
-{% load envipytags %}
 {% block content %}
   <div class="panel-group" id="reviewListAccordion">
     <div class="panel panel-default">

templates/framework.html

@@ -151,6 +151,11 @@
                   >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

templates/framework_modern.html

@@ -113,7 +113,7 @@
 
           {# License - inside paper if present #}
           {% if meta.url_contains_package and meta.current_package.license %}
-            <div class="collapse-arrow bg-base-200 collapse p-8">
+            <div class="collapse-arrow bg-base-200 collapse m-8">
               <input type="checkbox" checked />
               <div class="collapse-title text-xl font-medium">License</div>
               <div class="collapse-content">

templates/includes/navbar.html

@@ -27,7 +27,7 @@
           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>
+            <a href="{{ meta.server_url }}/Package" id="packageLink">Package</a>
           </li>
           <li>
             <a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a>

templates/index/index.html

@@ -119,9 +119,7 @@
                       >Ibuprofen</a
                     >
                   </div>
-                  <a
+                  <a class="absolute top-0 left-[calc(100%-5.4rem)]" href="#"
-                    class="absolute top-0 left-[calc(100%-5.4rem)]"
-                    href="/predict"
                     >Advanced</a
                   >
                 </div>
@@ -258,31 +256,6 @@
   <script language="javascript">
     var currentPackage = "{{ meta.current_package.url }}";
 
-    // Helper function to safely get Ketcher instance from iframe
-    function getKetcherInstance(iframeId) {
-      const ketcherFrame = document.getElementById(iframeId);
-      if (!ketcherFrame) {
-        console.error("Ketcher iframe not found:", iframeId);
-        return null;
-      }
-
-      try {
-        if (
-          "contentWindow" in ketcherFrame &&
-          ketcherFrame.contentWindow.ketcher
-        ) {
-          return ketcherFrame.contentWindow.ketcher;
-        }
-      } catch (err) {
-        console.error(
-          "Cannot access Ketcher iframe - possible CORS issue:",
-          err,
-        );
-      }
-
-      return null;
-    }
-
     // Discourse API integration is now handled by discourse-api.js
 
     // Function to render Discourse topics into cards
@@ -386,16 +359,10 @@
         }, 300);
 
         // Transfer SMILES from Ketcher to text input if available
-        const ketcher = getKetcherInstance("index-ketcher");
+        if (window.indexKetcher && window.indexKetcher.getSmiles) {
-        if (ketcher && ketcher.getSmiles) {
+          const smiles = window.indexKetcher.getSmiles();
-          try {
+          if (smiles && smiles.trim() !== "") {
-            const smiles = ketcher.getSmiles();
+            $("#index-form-text-input").val(smiles);
-            if (smiles && smiles.trim() !== "") {
-              $("#index-form-text-input").val(smiles);
-            }
-          } catch (err) {
-            console.error("Failed to sync Ketcher to text input:", err);
-            // Non-critical error, just log it
           }
         }
       }
@@ -464,32 +431,13 @@
         var textSmiles = "";
 
         // Check if we're in Ketcher mode and extract SMILES
-        if ($('input[type="checkbox"]').is(":checked")) {
+        if ($('input[type="checkbox"]').is(":checked") && window.indexKetcher) {
-          // Use the robust getter function
+          textSmiles = window.indexKetcher.getSmiles().trim();
-          const ketcher = getKetcherInstance("index-ketcher");
-          if (ketcher && ketcher.getSmiles) {
-            try {
-              textSmiles = ketcher.getSmiles().trim();
-            } catch (err) {
-              console.error("Failed to get SMILES from Ketcher:", err);
-              alert(
-                "Unable to extract structure from the drawing editor. Please try again or switch to SMILES input mode.",
-              );
-              return;
-            }
-          } else {
-            console.warn("Ketcher not available, possibly still loading");
-            alert(
-              "The drawing editor is still loading. Please wait a moment and try again.",
-            );
-            return;
-          }
         } else {
           textSmiles = $("#index-form-text-input").val().trim();
         }
 
         if (textSmiles === "") {
-          alert("Please enter a SMILES string or draw a structure.");
           return;
         }
 

templates/predict_pathway.html

@@ -26,7 +26,6 @@
               placeholder="Name"
               id="name"
               class="input input-md w-full"
-              autofocus
             />
             <span>Name</span>
           </label>
@@ -138,25 +137,6 @@
   </div>
   {# prettier-ignore-start #}
   <script>
-    // Helper function to safely get Ketcher instance from iframe
-    function getKetcherInstance(iframeId) {
-      const ketcherFrame = document.getElementById(iframeId);
-      if (!ketcherFrame) {
-        console.error("Ketcher iframe not found:", iframeId);
-        return null;
-      }
-
-      try {
-        if ('contentWindow' in ketcherFrame && ketcherFrame.contentWindow.ketcher) {
-          return ketcherFrame.contentWindow.ketcher;
-        }
-      } catch (err) {
-        console.error("Cannot access Ketcher iframe - possible CORS issue:", err);
-      }
-
-      return null;
-    }
-
     function predictKetcherToTextInput() {
       $("#predict-smiles").val(this.ketcher.getSmiles());
     }
@@ -191,21 +171,10 @@
         let smiles = $("#predict-smiles").val().trim();
 
         // If SMILES input is empty, try to get from Ketcher
-        if (!smiles) {
+        if (!smiles && window.predictKetcher) {
-          const ketcher = getKetcherInstance('predict-ketcher');
+          smiles = window.predictKetcher.getSmiles().trim();
-          if (ketcher && ketcher.getSmiles) {
+          if (smiles) {
-            try {
+            $("#predict-smiles").val(smiles);
-              smiles = ketcher.getSmiles().trim();
-              if (smiles) {
-                $("#predict-smiles").val(smiles);
-              }
-            } catch (err) {
-              console.error("Failed to get SMILES from Ketcher:", err);
-              alert("Unable to extract structure from the drawing editor. Please enter a SMILES string instead.");
-              button.prop("disabled", false);
-              button.text("Predict");
-              return;
-            }
           }
         }
 

templates/static/login.html

@@ -3,31 +3,12 @@
 {% block title %}enviPath - Sign In{% endblock %}
 
 {% block extra_styles %}
-  <style>
+  /* Tab styling */ .tab-content { display: none; } .tab-content.active {
-    /* Tab styling */
+  display: block; } input[type="radio"].tab-radio { display: none; } .tab-label
-    .tab-content {
+  { cursor: pointer; padding: 0.75rem 1.5rem; border-bottom: 2px solid
-      display: none;
+  transparent; transition: all 0.3s ease; } .tab-label:hover { background-color:
-    }
+  rgba(0, 0, 0, 0.05); } input[type="radio"].tab-radio:checked + .tab-label {
-    .tab-content.active {
+  border-bottom-color: #3b82f6; font-weight: 600; }
-      display: block;
-    }
-    input[type="radio"].tab-radio {
-      display: none;
-    }
-    .tab-label {
-      cursor: pointer;
-      padding: 0.75rem 1.5rem;
-      border-bottom: 2px solid transparent;
-      transition: all 0.3s ease;
-    }
-    .tab-label:hover {
-      background-color: rgba(0, 0, 0, 0.05);
-    }
-    input[type="radio"].tab-radio:checked + .tab-label {
-      border-bottom-color: #3b82f6;
-      font-weight: 600;
-    }
-  </style>
 {% endblock %}
 
 {% block content %}

templates/static/login_base.html

@@ -18,8 +18,6 @@
       rel="stylesheet"
       type="text/css"
     />
-
-    {% block extra_styles %}{% endblock %}
   </head>
   <body class="bg-base-100">
     <div class="flex h-screen">