added retrain code

epdb/tasks.py

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

templates/framework_modern.html

@@ -178,23 +178,6 @@
         }
       });
 
-      // 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
@@ -215,7 +198,7 @@
 
         if (isCorrectModifier && event.key === "k") {
           event.preventDefault();
-          openSearchModal();
+          search_modal.showModal();
         }
       });
     </script>

templates/includes/navbar.html

@@ -57,7 +57,7 @@
 
   <div class="navbar-end">
     {% if not public_mode %}
-      <a id="search-trigger" role="button" class="cursor-pointer">
+      <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"
         >

templates/index/index.html

@@ -2,86 +2,74 @@
 {% load static %}
 {% block main_content %}
   <!-- Hero Section with Logo and Search -->
-  <section class="hero relative mx-auto h-fit w-full max-w-5xl shadow-none">
+  <section class="hero h-fit max-w-5xl w-full shadow-none mx-auto relative">
     <div
-      class="hero from-primary-800 to-primary-600 min-h-[calc(100vh*0.4)] bg-gradient-to-br"
+      class="hero min-h-[calc(100vh*0.4)] bg-gradient-to-br from-primary-800 to-primary-600"
       style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
     >
       <div class="hero-overlay"></div>
       <!-- Predict Pathway text over the image -->
-      <div class="absolute bottom-40 left-1/8 z-10 -translate-x-8">
+      <div class="absolute bottom-40 left-1/8 -translate-x-8 z-10">
-        <h2 class="text-base-100 text-left text-3xl text-shadow-lg">
+        <h2 class="text-3xl text-base-100 text-shadow-lg text-left">
           Predict Your Pathway
         </h2>
       </div>
     </div>
   </section>
 
-  <div class="bg-base-200 mx-auto max-w-5xl shadow-md">
+  <div class="shadow-md max-w-5xl mx-auto bg-base-200">
     <!-- Predict Pathway Section -->
     <div
-      class="relative z-20 mx-auto -mt-32 mb-10 w-full flex-col lg:flex-row-reverse"
+      class="flex-col lg:flex-row-reverse w-full mx-auto -mt-32 relative z-20 mb-10 "
     >
       <div
-        class="card bg-base-100 mx-auto w-3/4 shrink-0 shadow-xl transition-all duration-300 ease-in-out"
+        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">
-          <div class="my-4 ml-8 flex h-fit flex-row items-center justify-start">
+          <!-- Input Mode Toggle - Fixed position outside fieldset -->
-            <div class="flex items-center gap-1">
+          <div class="flex flex-row justify-start items-center h-fit ml-8 my-4">
-              <label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
+            <div class="flex items-center gap-2">
+              <!-- <span class="text-sm text-neutral-500">Input Mode:</span> -->
+              <label class="toggle text-base-content toggle-md">
                 <input type="checkbox" />
-                <span class="swap-on flex items-center gap-1">
+                <svg
-                  <div
+                  aria-label="smiles mode"
-                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
+                  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"
                   >
-                    <svg
+                    <path
-                      aria-label="smiles mode"
+                      fill-rule="evenodd"
-                      xmlns="http://www.w3.org/2000/svg"
+                      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"
-                      viewBox="0 0 20 20"
+                      clip-rule="evenodd"
-                      class="size-5"
+                    />
-                    >
+                  </g>
-                      <g
+                </svg>
-                        stroke-linejoin="round"
+                <svg
-                        stroke-linecap="round"
+                  aria-label="draw mode"
-                        stroke-width="2"
+                  xmlns="http://www.w3.org/2000/svg"
-                        fill="currentColor"
+                  viewBox="0 0 20 20"
-                        stroke="none"
+                  fill="currentColor"
-                      >
+                  stroke="none"
-                        <path
+                  class="size-5"
-                          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"
+                  <path
-                          clip-rule="evenodd"
+                    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"
-                        />
+                  />
-                      </g>
+                </svg>
-                    </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 overflow-hidden transition-all duration-300 ease-in-out"
+            class="fieldset transition-all duration-300 ease-in-out overflow-hidden"
           >
             <form
               id="index-form"
@@ -91,29 +79,29 @@
               {% csrf_token %}
               <div
                 id="text-input-container"
-                class="scale-100 transform opacity-100 transition-all duration-300 ease-in-out"
+                class="transition-all duration-300 ease-in-out opacity-100 transform scale-100"
               >
-                <div class="join mx-auto w-full">
+                <div class="join w-full mx-auto">
                   <input
                     type="text"
                     id="index-form-text-input"
                     placeholder="canonical SMILES string"
-                    class="input input-md join-item grow"
+                    class="input grow input-md join-item"
                   />
                   <button class="btn btn-neutral join-item">Predict!</button>
                 </div>
-                <div class="label relative mt-1 w-full">
+                <div class="label relative w-full mt-1">
                   <div class="flex gap-2">
                     <a
                       href="#"
-                      class="example-link hover:text-primary cursor-pointer"
+                      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 hover:text-primary cursor-pointer"
+                      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
@@ -126,7 +114,7 @@
               </div>
               <div
                 id="ketcher-container"
-                class="hidden w-full scale-95 transform opacity-0 transition-all duration-300 ease-in-out"
+                class="hidden w-full transition-all duration-300 ease-in-out opacity-0 transform scale-95"
               >
                 <iframe
                   id="index-ketcher"
@@ -136,13 +124,11 @@
                   class="rounded-lg"
                 ></iframe>
                 <button
-                  class="btn btn-lg bg-primary-950 text-primary-50 join-item mt-2 w-full"
+                  class="btn btn-lg bg-primary-950 text-primary-50 join-item w-full mt-2"
                 >
                   Predict!
                 </button>
-                <div class="mt-1 flex w-full justify-end">
+                <a class="label mx-auto w-full mt-1" href="#">Advanced</a>
-                  <a class="label justify-end" href="/predict">Advanced</a>
-                </div>
               </div>
               <input
                 type="hidden"
@@ -164,18 +150,18 @@
     </div>
 
     <!-- Community News Section -->
-    <section class="bg-base-200 z-10 mx-8 py-16">
+    <section class="py-16 bg-base-200 z-10 mx-8">
-      <div class="mx-auto max-w-7xl px-4">
+      <div class="max-w-7xl mx-auto px-4">
-        <h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>
+        <h2 class="h2 font-bold text-left mb-8">Community Updates</h2>
 
-        <div id="community-news-container" class="flex justify-center gap-4">
+        <div id="community-news-container" class="flex gap-4 justify-center">
           <!-- News cards will be populated here -->
-          <div id="loading" class="flex w-full justify-center">
+          <div id="loading" class="flex justify-center w-full">
             <span class="loading loading-spinner loading-lg"></span>
           </div>
         </div>
 
-        <div class="mt-6 text-right">
+        <div class="text-right mt-6">
           <a
             href="https://community.envipath.org/c/announcements/10"
             target="_blank"
@@ -191,18 +177,18 @@
     </section>
 
     <!-- Mission Statement Section -->
-    <section class="from-base-200 to-base-100 bg-gradient-to-b py-16">
+    <section class="py-16 from-base-200 to-base-100 bg-gradient-to-b">
       <div class="mx-auto px-8 md:px-12">
         <div class="flex flex-row gap-4">
           <div class="w-1/3">
             <img
               src="{% static "/images/ep-rule-artwork.png" %}"
               alt="rule-based iterative tree greneration"
-              class="h-full w-full object-contain"
+              class="w-full h-full object-contain"
             />
           </div>
-          <div class="mr-8 w-2/3 space-y-4 text-left">
+          <div class="space-y-4 text-left w-2/3 mr-8">
-            <h2 class="h2 mb-8 font-bold">About enviPath</h2>
+            <h2 class="h2 font-bold mb-8">About enviPath</h2>
             <p class="">
               enviPath is a database and prediction system for the microbial
               biotransformation of organic environmental contaminants. The
@@ -215,7 +201,7 @@
               products. Explore our tools and contribute to advancing
               environmental biotransformation research.
             </p>
-            <div class="float-right flex flex-row gap-4">
+            <div class="flex flex-row gap-4 float-right">
               <a href="/about" class="btn btn-ghost-neutral">Read More</a>
               <a href="/about" class="btn btn-neutral">Publications</a>
             </div>
@@ -225,7 +211,7 @@
     </section>
 
     <!-- Partners Section -->
-    <section class="bg-base-100 py-14 sm:py-12">
+    <section class="py-14 sm:py-12 bg-base-100">
       <div class="mx-auto px-6 lg:px-8">
         <div class="divider">
           <h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2>
@@ -236,12 +222,12 @@
           <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/search.html

@@ -0,0 +1,197 @@
+{% 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 %}