adjusted migration

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

Wip

minor

PW interactions

API PES

wip

Make Select Widget reflect required

make required generallay available

Update UI if pathway mode is set to build

Added ais

circle adjustments

Initial Zoom, fix AD Creation

wip

auth log, bb4g fix

missing import

Added viz hint if PES is part of reaction

Add Edge check for pes

flip boolean

...

pes

Added extra

...

In / Out Edges Viz, Submitting Button Text

...

Make PES Link clickable

Return proper http response instead of error

Fixed error return, removed unused options

Fix PES Link HTML for other entities

Fixed molfile assignment, adjusted Export

Package Export/Import cycle

highlight Description links

implemented non persistent

Harmonised proposed field in Json output

Added pesLink field to PW Api output

PES Fields in API Output

removed debug

Fix Classification import, Fix PES Deserialization

underline pes link in templates

Fix alter name/desc for node, make /node /edge funcitonal

provide setting link and copy button

Implemented Compound Names / Reaction Names View Option

Unconnected Nodes

Make links thicker, reduce timeout trigger time

Show proposed info in popover

Pathway Build no stereo removal

Include probs in reaction name option viz

Detect clicks outside nodes/edges

Provide proper Error Pages

View Package Perm

wip

sync

Auth log

auth log leftovers

...

secret packs viz

auth log for api

model stats

Fix Package Adjustment

Adjust Group Auth Log

Fix Secret image size in Navbar

leftover

...

minor

templates/actions/objects/package.html

@@ -15,6 +15,7 @@
       <i class="glyphicon glyphicon-user"></i> Edit Permissions</a
     >
   </li>
+  {% if meta.current_package.get_classification_level_display != "Secret" %}
   <li>
     <a
       role="button"
@@ -23,6 +24,8 @@
       <i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a
     >
   </li>
+  {% endif %}
+{% endif %}
   <li>
     <a
       role="button"
@@ -31,6 +34,7 @@
       <i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a
     >
   </li>
+{% if meta.can_edit %}
   <li>
     <a
       role="button"
@@ -48,3 +52,13 @@
     >
   </li>
 {% endif %}
+{% if not meta.can_edit %}
+  <li>
+    <a
+      role="button"
+      onclick="document.getElementById('view_package_permissions_modal').showModal(); return false;"
+    >
+      <i class="glyphicon glyphicon-user"></i> View Permissions</a
+    >
+  </li>
+{% endif %}

templates/components/navbar.html

@@ -35,6 +35,7 @@
             <use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
           </svg>
         </a>
+        <img src="{% static 'images/bayer-logo.svg' %}" width="40">
       </div>
 
       {% if not public_mode %}
@@ -88,12 +89,27 @@
                   >Scenario</a
                 >
               </li>
+                <hr/>
+              <li>
+                <a href="{{ meta.server_url }}/group" id="scenarioLink"
+                  >Group</a
+                >
+              </li>
             </ul>
           </div>
         </div>
       {% endif %}
 
       <div class="navbar-end">
+        {% if meta.url_contains_package and meta.current_package.get_classification_level_display == "Restricted" %}
+          <img src="{% static 'images/restricted_mid.png' %}" width="200">
+        {% elif meta.url_contains_package and meta.current_package.get_classification_level_display == "Secret" %}
+          <img src="{% static 'images/secret_mid.png' %}" width="120">
+        {% elif not meta.url_contains_package and meta.user.default_package.get_classification_level_display == "Restricted" %}
+          <img src="{% static 'images/restricted_mid.png' %}" width="200">
+        {% elif not meta.url_contains_package and meta.user.default_package.get_classification_level_display == "Secret" %}
+          <img src="{% static 'images/secret_mid.png' %}" width="120">
+        {% endif %}
         {% if not public_mode %}
           <a id="search-trigger" role="button" class="cursor-pointer">
             <div

templates/modals/objects/add_pathway_edge_modal.html

@@ -5,6 +5,7 @@
   x-data="{
     isSubmitting: false,
     reactionImageUrl: '',
+    pes: false,
 
     reset() {
       this.isSubmitting = false;
@@ -15,20 +16,30 @@
       const substratesSelect = document.getElementById('add_pathway_edge_substrates');
       const productsSelect = document.getElementById('add_pathway_edge_products');
 
+      const pesLinks = [];
+
       const substrates = [];
       for (const option of substratesSelect.selectedOptions) {
         substrates.push(option.dataset.smiles);
+        if (option.dataset.pes === 'true') {
+          pesLinks.push(option.dataset.pes);
+        }
       }
 
       const products = [];
       for (const option of productsSelect.selectedOptions) {
         products.push(option.dataset.smiles);
+        if (option.dataset.pes === 'true') {
+          pesLinks.push(option.dataset.pes);
+        }
       }
 
       if (substrates.length > 0 && products.length > 0) {
         const reaction = substrates.join('.') + '>>' + products.join('.');
         this.reactionImageUrl = '{% url "depict" %}?smirks=' + encodeURIComponent(reaction);
+        this.pes = pesLinks.length > 0;
       } else {
+        this.pes = false;
         this.reactionImageUrl = '';
       }
     },
@@ -106,6 +117,7 @@
                 {% for n in pathway.nodes %}
                   <option
                     data-smiles="{{ n.default_node_label.smiles }}"
+                    data-pes="{% if n.default_node_label.pes_link %}true{% else %}false{% endif %}"
                     value="{{ n.url }}"
                   >
                     {{ n.default_node_label.name|safe }}
@@ -132,6 +144,7 @@
                 {% for n in pathway.nodes %}
                   <option
                     data-smiles="{{ n.default_node_label.smiles }}"
+                    data-pes="{% if n.default_node_label.pes_link %}true{% else %}false{% endif %}"
                     value="{{ n.url }}"
                   >
                     {{ n.default_node_label.name|safe }}
@@ -144,6 +157,9 @@
 
         <div class="mb-3" x-show="reactionImageUrl" x-cloak>
           <img :src="reactionImageUrl" class="w-full" alt="Reaction preview" />
+          <div x-show="pes">
+            <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
+          </div>
         </div>
       </form>
     </div>

templates/modals/objects/view_package_permissions_modal.html

@@ -0,0 +1,147 @@
+{% load static %}
+<!-- Edit Package Permissions -->
+<dialog
+  id="view_package_permissions_modal"
+  class="modal"
+  x-data="{}"
+>
+  <div class="modal-box max-w-2xl">
+    <!-- Header -->
+    <h3 class="text-lg font-bold">Current Permissions</h3>
+
+    <!-- Close button (X) -->
+    <form method="dialog">
+      <button class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2">
+        ✕
+      </button>
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <p class="mb-4">
+        Current permissions for this package.
+      </p>
+
+      <!-- User Permissions -->
+      {% if user_permissions %}
+        <div class="divider">User Permissions</div>
+        <div class="space-y-2">
+        <div class="grid grid-cols-12 gap-2 items-center">
+          <div class="col-span-5 truncate"></div>
+          <div class="col-span-2 text-center">Read</div>
+          <div class="col-span-2 text-center">Write</div>
+          <div class="col-span-2 text-center">Owner</div>
+          <div class="col-span-1"></div>
+        </div>
+          {% for up in user_permissions %}
+              <div class="grid grid-cols-12 gap-2 items-center">
+                <div class="col-span-5 truncate">
+                  {{ up.user.username }}
+                  {% if not up.user.is_active %}<i>(inactive)</i>{% endif %}
+                </div>
+                <div class="col-span-2 text-center">
+                  <input
+                    type="checkbox"
+                    name="read"
+                    id="read_{{ up.user.uuid }}"
+                    class="checkbox"
+                    {% if up.has_read %}checked{% endif %}
+                    onclick="return false;"
+                  />
+                </div>
+                <div class="col-span-2 text-center">
+                  <input
+                    type="checkbox"
+                    name="write"
+                    id="write_{{ up.user.uuid }}"
+                    class="checkbox"
+                    {% if up.has_write %}checked{% endif %}
+                    onclick="return false;"
+                  />
+                </div>
+                <div class="col-span-2 text-center">
+                  <input
+                    type="checkbox"
+                    name="owner"
+                    id="owner_{{ up.user.uuid }}"
+                    class="checkbox"
+                    {% if up.has_all %}checked{% endif %}
+                    onclick="return false;"
+                  />
+                </div>
+              </div>
+
+          {% endfor %}
+        </div>
+      {% endif %}
+
+      <!-- Group Permissions -->
+      {% if group_permissions %}
+        <div class="divider">Group Permissions</div>
+        <div class="space-y-2">
+        <div class="grid grid-cols-12 gap-2 items-center">
+          <div class="col-span-5 truncate"></div>
+          <div class="col-span-2 text-center">Read</div>
+          <div class="col-span-2 text-center">Write</div>
+          <div class="col-span-2 text-center">Owner</div>
+          <div class="col-span-1"></div>
+        </div>
+          {% for gp in group_permissions %}
+
+              <div class="grid grid-cols-12 gap-2 items-center">
+                <div class="col-span-5 truncate">
+                  {{ gp.group.name|safe }}
+                </div>
+                <div class="col-span-2 text-center">
+                  <input
+                    type="checkbox"
+                    name="read"
+                    id="read_{{ gp.group.uuid }}"
+                    class="checkbox"
+                    {% if gp.has_read %}checked{% endif %}
+                    onclick="return false;"
+                  />
+                </div>
+                <div class="col-span-2 text-center">
+                  <input
+                    type="checkbox"
+                    name="write"
+                    id="write_{{ gp.group.uuid }}"
+                    class="checkbox"
+                    {% if gp.has_write %}checked{% endif %}
+                    onclick="return false;"
+                  />
+                </div>
+                <div class="col-span-2 text-center">
+                  <input
+                    type="checkbox"
+                    name="owner"
+                    id="owner_{{ gp.group.uuid }}"
+                    class="checkbox"
+                    {% if gp.has_all %}checked{% endif %}
+                    onclick="return false;"
+                  />
+                </div>
+              </div>
+          {% endfor %}
+        </div>
+      {% endif %}
+    </div>
+
+    <!-- Footer -->
+    <div class="modal-action">
+      <button
+        type="button"
+        class="btn"
+        onclick="this.closest('dialog').close()"
+      >
+        Close
+      </button>
+    </div>
+  </div>
+
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button>close</button>
+  </form>
+</dialog>

templates/objects/edge.html

@@ -82,6 +82,9 @@
       <div class="collapse-content">
         <div class="flex justify-center">{{ edge.edge_label.as_svg|safe }}</div>
       </div>
+      {% if edge.edge_label.contains_pes %}
+        <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
+      {% endif %}
     </div>
 
     <!-- Reaction Description -->

templates/objects/model/_model_base.html

@@ -117,6 +117,38 @@
           </div>
         </div>
       {% endif %}
+
+      <!-- Model Parameters Panel -->
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" checked />
+        <div class="collapse-title text-xl font-medium">Model Parameters</div>
+        <div class="collapse-content">
+          <div class="flex justify-center">
+            <div
+              id="model-stats"
+              class="overflow-x-auto rounded-box shadow-md bg-base-100"
+            >
+              <table class="table table-fixed w-full">
+                <thead class="text-base">
+                  <tr>
+                    <th class="w-3/5">Parameter</th>
+                    <th>Value</th>
+                  </tr>
+                </thead>
+                <tbody>
+                  {% for param, value in model.parameters.items %}
+                    <tr>
+                      <td>{{ param }}</td>
+                      <td>{{ value }}</td>
+                    </tr>
+                  {% endfor %}
+                </tbody>
+              </table>
+            </div>
+          </div>
+        </div>
+      </div>
+
     {% endblock %}
 
     {% block usemodel %}

templates/objects/model/classification_model.html

@@ -313,6 +313,44 @@
                 </div>
             </div>
         {% endif %}
+
+      <!-- Model Statistics Panel -->
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" checked />
+        <div class="collapse-title text-xl font-medium">Model Statistics for threshold {{ model.threshold }}</div>
+        <div class="collapse-content">
+          <div class="flex justify-center">
+            <div
+              id="model-stats"
+              class="overflow-x-auto rounded-box shadow-md bg-base-100"
+            >
+              <table class="table table-fixed w-full">
+                <thead class="text-base">
+                  <tr>
+                    <th class="w-1/5">Metric</th>
+                    <th>Single Gen Value</th>
+                    {% if model.multigen_eval %}
+                      <th>Multi Gen Value</th>
+                    {% endif %}
+                  </tr>
+                </thead>
+                <tbody>
+                  {% for metric, value in model.statistics.items %}
+                    <tr>
+                      <td>{{ metric|upper }}</td>
+                      <td>{{ value.0|floatformat:3 }}</td>
+                      {% if model.multigen_eval %}
+                        <td>{{ value.1|floatformat:3 }}</td>
+                      {% endif %}
+                    </tr>
+                  {% endfor %}
+                </tbody>
+              </table>
+            </div>
+          </div>
+        </div>
+      </div>
+
     {% endif %}
     <script>
         function makeChart(selector, data) {

templates/objects/pathway.html

@@ -252,6 +252,7 @@
                       </a>
                     </li>
                   {% endif %}
+                  {% if 1 == 0 %}
                   <li>
                     <a id="timeseries-toggle-button" class="cursor-pointer">
                       <svg
@@ -302,6 +303,7 @@
                       Show Predicted Properties
                     </a>
                   </li>
+                  {% endif %}
                 </ul>
               </div>
             </div>
@@ -535,7 +537,7 @@
         <input type="checkbox" />
         <div class="collapse-title text-xl font-medium">Setting</div>
         <div class="collapse-content">
-          {% with setting_to_render=pathway.setting can_be_default=False %}
+          {% with setting_to_render=pathway.setting_with_overrides can_be_default=False %}
             {% include "objects/setting_template.html" %}
           {% endwith %}
         </div>

templates/objects/reaction.html

@@ -79,6 +79,9 @@
       <div class="collapse-content">
         <div class="flex justify-center">{{ reaction.as_svg|safe }}</div>
       </div>
+      {% if reaction.contains_pes %}
+        <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
+      {% endif %}
     </div>
 
     <!-- Reaction Description -->

templates/objects/setting_template.html

@@ -24,6 +24,76 @@
         <td>Setting Name</td>
         <td>{{ setting_to_render.name }}</td>
       </tr>
+      <tr>
+        <td>Setting URL</td>
+        <td>
+          <a href="{{ setting_to_render.url }}" class="link link-primary">{{ setting_to_render.url }}</a>
+          <div
+            x-data="{
+              value: '{{ setting_to_render.url }}',
+              copied: false,
+
+              async copy() {
+                await navigator.clipboard.writeText(this.value)
+                this.copied = true
+
+                setTimeout(() => {
+                  this.copied = false
+                }, 1500)
+              }
+            }"
+            class="join"
+          >
+          <button
+            type="button"
+            class="btn btn-ghost"
+            :data-tip="copied ? 'Copied!' : 'Copy'"
+            @click="copy"
+            aria-label="Copy to clipboard"
+          >
+            <svg
+              x-show="!copied"
+              xmlns="http://www.w3.org/2000/svg"
+              class="h-4 w-4"
+              fill="none"
+              viewBox="0 0 24 24"
+              stroke="currentColor"
+              stroke-width="2"
+            >
+              <path
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                d="M8 16H6a2 2 0 01-2-2V6a2 2 0 012-2h8a2 2 0 012 2v2"
+              />
+              <rect
+                width="12"
+                height="12"
+                x="8"
+                y="8"
+                rx="2"
+                ry="2"
+              />
+            </svg>
+
+            <svg
+              x-show="copied"
+              xmlns="http://www.w3.org/2000/svg"
+              class="h-4 w-4"
+              fill="none"
+              viewBox="0 0 24 24"
+              stroke="currentColor"
+              stroke-width="2"
+            >
+              <path
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                d="M5 13l4 4L19 7"
+              />
+            </svg>
+            </button>
+          </div>
+        </td>
+      </tr>
       {% if setting_to_render.description %}
         <tr>
           <td>Setting Description</td>

templates/objects/user.html

@@ -95,6 +95,7 @@
     </div>
 
     <!-- Other Prediction Settings -->
+    {% if meta.available_settings|length > 1 %}
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" />
       <div class="collapse-title text-xl font-medium">
@@ -110,6 +111,7 @@
         {% endfor %}
       </div>
     </div>
+  {% endif %}
   </div>
 
   <script>