minor

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()
 

epdb/views.py

@@ -955,12 +955,6 @@ 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()

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/modals/objects/retrain_model_modal.html

@@ -1,55 +1,43 @@
-<div
+<div class="modal fade" tabindex="-1" id="retrain_model_modal" role="dialog" aria-labelledby="retrain_model_modal"
-  class="modal fade"
+     aria-hidden="true">
-  tabindex="-1"
+    <div class="modal-dialog modal-lg">
-  id="retrain_model_modal"
+        <div class="modal-content">
-  role="dialog"
+            <div class="modal-header">
-  aria-labelledby="retrain_model_modal"
+                <button type="button" class="close" data-dismiss="modal">
-  aria-hidden="true"
+                    <span aria-hidden="true">&times;</span>
->
+                    <span class="sr-only">Close</span>
-  <div class="modal-dialog modal-lg">
+                </button>
-    <div class="modal-content">
+                <h4 class="modal-title">Retrain Model</h4>
-      <div class="modal-header">
+            </div>
-        <button type="button" class="close" data-dismiss="modal">
+            <div class="modal-body">
-          <span aria-hidden="true">&times;</span>
+                <form id="retrain_model_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/model"
-          <span class="sr-only">Close</span>
+                      data-remote="true" method="post">
-        </button>
+                    <div class="jumbotron">
-        <h4 class="modal-title">Retrain Model</h4>
+                        To reflect changes in the rule or data packages, you can use the "Retrain" button,
-      </div>
+                        to let the model reflect the changes without creating a new model.
-      <div class="modal-body">
+                        While the model is retraining, it will be unavailable for prediction.
-        <form
+                    </div>
-          id="retrain_model_form"
+                    {% csrf_token %}
-          accept-charset="UTF-8"
+                    <input type="hidden" name="action" value="retrain">
-          action="{{ meta.current_object.url }}"
+                </form>
-          data-remote="true"
+            </div>
-          method="post"
+            <div class="modal-footer">
-        >
+                <a id="retrain_model_form_submit" class="btn btn-primary" href="#">Retrain</a>
-          <div class="jumbotron">
+                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-            To reflect changes in the rule or data packages, you can use the
+            </div>
-            "Retrain" button, to let the model reflect the changes without
+        </div>
-            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) {
+    $(function () {
-      e.preventDefault();
+
-      $("#retrain_model_form").submit();
+        $('#retrain_model_form_submit').on('click', function (e) {
+            e.preventDefault();
+            $('#retrain_model_form').submit();
+        });
+
     });
-  });
+
 </script>

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 %}