...

bayer/templates/modals/collections/new_pes_modal.html

@@ -36,8 +36,8 @@
       img.onerror = () => {
         this.pesVizHtml = `
           <div class='alert alert-error' role='alert'>
-            <h4 class='alert-heading'>Could not render PES!</h4>
+            <h4 class='alert-heading'>Failed to fetch this PES!</h4>
-            <p>Could not render PES - Do you have access?</p>
+            <p>Either the PES-ID is incorrect, or you're missing sufficient permissions to access this (potentially secret) item. In case you're missing permissions you can request the entitlement cs.u.enviPath_secret_data_user_group on go/idnow to gain access.</p>
           </div>`;
       };
     },

epauth/views.py

@@ -102,7 +102,7 @@ def entra_callback(request):
 
     else:
         auth_log.info(f"Registering {user_name} with OID {user_oid}")
-        u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True)
+        u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True, add_to_group=False)
         registered = True
 
     auth_log.info(f"User {user_name} {'(admin) ' if u.is_superuser else ''}with OID {user_oid} successfully logged in as {u.username} from {get_remote_address(request)}")

epdb/logic.py

@@ -581,6 +581,9 @@ class PackageManager(object):
         if caller_perm != Permission.ALL[0] and not caller.is_superuser:
             raise ValueError("Only owner are allowed to modify permissions")
 
+        if isinstance(grantee, Group) and package.classification_level == package.Classification.SECRET:
+            raise ValueError("Cannot grant permissions to a Group on a secret package")
+
         data = {
             "package": package,
         }

epdb/models.py

@@ -2456,6 +2456,20 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             else:
                 return self.default_node_label.name
 
+    def get_description(self, include_suffix=True):
+        default_desc = False
+
+        if self.description == "no description":
+            default_desc = True
+
+        if not default_desc:
+            return self.description
+        else:
+            if include_suffix:
+                return f"{self.default_node_label.description} (taken from underlying structure)"
+            else:
+                return self.default_node_label.description
+
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
 
@@ -2773,6 +2787,20 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             else:
                 return self.edge_label.name
 
+    def get_description(self, include_suffix=True):
+        default_desc = False
+
+        if self.description == "no description":
+            default_desc = True
+
+        if not default_desc:
+            return self.description
+        else:
+            if include_suffix:
+                return f"{self.edge_label.description} (taken from underlying reaction)"
+            else:
+                return self.edge_label.description
+
 
 class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):
     package = models.ForeignKey(

epdb/views.py

@@ -1292,7 +1292,7 @@ def package(request, package_uuid):
                 "user_id", flat=True
             )
         )
-        users = users.filter(is_active=True)
+        users = users.filter(is_active=True).exclude(username="anonymous")
 
         group_perms = GroupPackagePermission.objects.filter(package=current_package)
         groups = Group.objects.exclude(
@@ -1324,6 +1324,12 @@ def package(request, package_uuid):
 
                 return redirect(s.SERVER_URL + "/package")
             elif hidden == "publish-package":
+                if current_package.classification_level == current_package.Classification.SECRET:
+                    return error(
+                        request,
+                        "Cannot publish a secret package",
+                        "You cannot publish a secret package.",
+                    )
                 for g in Group.objects.filter(public=True):
                     PackageManager.grant_read(current_user, current_package, g)
                 return redirect(current_package.url)
@@ -3314,6 +3320,11 @@ def jobs(request):
                 "This Package was generated automatically for the batch prediction task.",
             )
 
+            if current_user.default_package.classification_level == current_user.default_package.Classification.SECRET:
+                target_package.classification_level = current_user.default_package.Classification.SECRET
+                target_package.data_pool = current_user.default_package.data_pool
+                target_package.save()
+
             from .tasks import batch_predict, dispatch
 
             res = dispatch(

templates/index/index.html

@@ -185,19 +185,18 @@
                   <div
                     class="mt-4 rounded-lg border border-base-300 bg-base-50 px-4 py-2.5 text-sm text-base-content/70"
                   >
-                    Prediction will be stored in
+                    Prediction will be stored in Package
                     <strong class="text-base-content"
-                      >{{ meta.current_package.name|safe }}</strong
+                    ><a class="link" href="{{ meta.current_package.url }}">{{ meta.current_package.name|safe }}</a></strong
                     >
                     {% if meta.user.default_setting %}
                       using setting
                       <strong class="text-base-content"
-                        >{{ meta.user.default_setting.name|safe }}</strong
+                      ><a class="link" href="{{ meta.user.default_setting.url}}">{{ meta.user.default_setting.name|safe }}</a></strong
                       >
                     {% endif %}
-                    <br />
                     To use a different setting click
-                    <a class="label link" href="/predict">here</a>
+                    <a class="link" href="/predict">here</a>
                   </div>
                 {% endif %}
               </div>
@@ -222,23 +221,22 @@
                 >
                   Predict!
                 </button>
-                {% if meta.current_package %}
+                  {% if meta.current_package %}
                   <div
                     class="mt-4 rounded-lg border border-base-300 bg-base-50 px-4 py-2.5 text-sm text-base-content/70"
                   >
-                    Prediction will be stored in
+                    Prediction will be stored in Package
                     <strong class="text-base-content"
-                      >{{ meta.current_package.name|safe }}</strong
+                    ><a class="link" href="{{ meta.current_package.url }}">{{ meta.current_package.name|safe }}</a></strong
                     >
                     {% if meta.user.default_setting %}
                       using setting
                       <strong class="text-base-content"
-                        >{{ meta.user.default_setting.name|safe }}</strong
+                      ><a class="link" href="{{ meta.user.default_setting.url}}">{{ meta.user.default_setting.name|safe }}</a></strong
                       >
                     {% endif %}
-                    <br />
                     To use a different setting click
-                    <a class="label link" href="/predict">here</a>
+                    <a class="link" href="/predict">here</a>
                   </div>
                 {% endif %}
               </div>

templates/modals/objects/edit_user_modal.html

@@ -31,6 +31,7 @@
         {% csrf_token %}
 
         <div class="form-control mb-3">
+          {% if 1 == 0 %}
           <label class="label" for="default-package">
             <span class="label-text">Default Package</span>
           </label>
@@ -50,7 +51,7 @@
             {% endfor %}
           </select>
         </div>
-
+        {% endif %}
         <div class="form-control mb-3">
           <label class="label" for="default-group">
             <span class="label-text">Default Group</span>

templates/objects/edge.html

@@ -57,7 +57,7 @@
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />
       <div class="collapse-title text-xl font-medium">Description</div>
-      <div class="collapse-content">{{ edge.description }}</div>
+      <div class="collapse-content">{{ edge.get_description }}</div>
     </div>
 
     {% if edge.aliases %}

templates/objects/node.html

@@ -60,7 +60,7 @@
       <div class="collapse-arrow bg-base-200 collapse">
         <input type="checkbox" checked />
         <div class="collapse-title text-xl font-medium">Description</div>
-        <div class="collapse-content">{{ node.description }}</div>
+        <div class="collapse-content">{{ node.get_description }}</div>
       </div>
     {% endif %}
     {% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}

templates/predict_pathway.html

@@ -2,11 +2,23 @@
 {% load static %}
 {% block content %}
   <div class="mx-auto w-full p-8">
-    <h1 class="h1 mb-4 text-3xl font-bold">
+    <h1 class="h1 mb-4 flex items-center gap-2 text-3xl font-bold">
       Predict a Pathway
 
-      <span class="text-base-content/50 text-xs"
+      <span class="inline-flex items-center gap-1 text-base-content/50 text-xs"
-        >in <strong>{{ meta.current_package.name|safe }}</strong>
+        >in <strong>{{ meta.current_package.name|safe }}</strong>{% if meta.url_contains_package %}
+      {% if meta.current_package.get_classification_level_display == "Restricted" %}
+        <img src="{% static 'images/restricted_mid.png' %}" width="100">
+      {% elif meta.current_package.get_classification_level_display == "Secret" %}
+        <img src="{% static 'images/secret_mid.png' %}" width="60">
+      {% endif %}
+    {% else %}
+      {% if meta.user.default_package.get_classification_level_display == "Restricted" %}
+        <img src="{% static 'images/restricted_mid.png' %}" width="100">
+      {% elif meta.user.default_package.get_classification_level_display == "Secret" %}
+        <img src="{% static 'images/secret_mid.png' %}" width="60">
+      {% endif %}
+    {% endif %}
       </span>
     </h1>