exclude groups

bayer/migrations/0004_package_shareable.py

@@ -0,0 +1,18 @@
+# Generated by Django 6.0.3 on 2026-09-08 08:54
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('bayer', '0003_pescompound_pesstructure_package_data_pool'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='package',
+            name='shareable',
+            field=models.BooleanField(default=True, verbose_name='Shareable'),
+        ),
+    ]

bayer/models.py

@@ -23,6 +23,7 @@ class Package(EnviPathModel):
     license = models.ForeignKey(
         "epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
     )
+    shareable = models.BooleanField(verbose_name="Shareable", default=True)
 
     class Classification(models.IntegerChoices):
         INTERNAL = 0, "Internal"

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>`;
       };
     },

bayer/views.py

@@ -119,8 +119,8 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             except ValueError as e:
                 return error(
                     request,
-                    "Could not fetch PES",
+                    "Failed to fetch this PES",
-                    f"Could not fetch PES data for {pes_link}"
+                    "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."
                 )
 
             classification = pes_data.get("classificationLevel", "")
@@ -177,7 +177,7 @@ def create_pes_node(request, package_uuid, pathway_uuid):
 def get_application_token(prod: bool) -> str:
     scope = f"{s.PROD_PES_SCOPE if prod else s.NON_PROD_PES_SCOPE}/.default"
 
-    url = f"https://login.microsoftonline.com/{s.MS_TENANT_ID}/oauth2/v2.0/token"
+    url = f"https://login.microsoftonline.com/{s.MS_ENTRA_TENANT_ID}/oauth2/v2.0/token"
     data = {
         "grant_type": "client_credentials",
         "client_id": s.MS_ENTRA_CLIENT_ID,

envipath/settings.py

@@ -445,6 +445,8 @@ if MS_ENTRA_ENABLED:
     MS_ENTRA_AUTHORITY = f"https://login.microsoftonline.com/{MS_ENTRA_TENANT_ID}"
     MS_ENTRA_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
     MS_ENTRA_SCOPES = os.environ.get("MS_SCOPES", "").split(",")
+    NON_PROD_PES_SCOPE = os.environ.get("NON_PROD_PES_SCOPE")
+    PROD_PES_SCOPE = os.environ.get("PROD_PES_SCOPE")
 
 # Site ID 10 -> beta.envipath.org
 MATOMO_SITE_ID = os.environ.get("MATOMO_SITE_ID", "10")

epauth/views.py

@@ -77,7 +77,7 @@ def entra_callback(request):
         return error(
             request,
             "Login Failed",
-            "The user is not authenticated. A reason for this might be a missing assignment to the respective enviPath group.",
+            "Request access to role 1230/MON/APPS/Envipath/Envipath_Prod on go/idnow",
             403,
         )
 
@@ -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)}")
@@ -139,10 +139,16 @@ def entra_callback(request):
                 auth_log.info(f"Login Group Sync: Adding {u.username} to Group {g.name} ({ uuid })")
         else:
             g = Group.objects.get(uuid=uuid)
-            if g.user_member.contains(u):
+            # Do not remove users from All enviPath Users
+            if g.user_member.contains(u) and g.name != 'All enviPath Users':
                 g.user_member.remove(u)
                 auth_log.info(f"Login Group Sync: Removing {u.username} from Group {g.name} ({ uuid })")
 
+    # Ensure people are part of All enviPath Users -> they have to as, envipath_registered_user is granted
+    all_envipath_users = Group.objects.get(name="All enviPath Users")
+    if not all_envipath_users.user_member.contains(u):
+        all_envipath_users.user_member.add(u)
+
     if registered:
         # #72 make package secret if user is part of a secret group
         for id, name in s.ENTRA_SECRET_GROUPS.items():

epdb/admin.py

@@ -11,6 +11,7 @@ from .models import (
     CompoundStructure,
     Edge,
     EnviFormer,
+    EnzymeLink,
     ExternalDatabase,
     ExternalIdentifier,
     Group,
@@ -212,6 +213,10 @@ class CompoundStructureAdmin(EPAdmin):
     pass
 
 
+class EnzymeLinkAdmin(EPAdmin):
+    pass
+
+
 class SimpleAmbitRuleAdmin(EPAdmin):
     pass
 
@@ -266,6 +271,7 @@ admin.site.register(License, LicenseAdmin)
 admin.site.register(ClassifierPluginModel, ClassifierPluginModelAdmin)
 admin.site.register(Compound, CompoundAdmin)
 admin.site.register(CompoundStructure, CompoundStructureAdmin)
+admin.site.register(EnzymeLink, EnzymeLinkAdmin)
 admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)
 admin.site.register(ParallelRule, ParallelRuleAdmin)
 admin.site.register(Reaction, ReactionAdmin)

epdb/logic.py

@@ -211,7 +211,7 @@ class UserManager(object):
         # Create package
         package_name = f"{u.username}{'’' if u.username[-1] in 'sxzß' else 's'} Package"
         package_description = "This package was generated during registration."
-        p = PackageManager.create_package(u, package_name, package_description)
+        p = PackageManager.create_package(u, package_name, package_description, shareable=False)
         u.default_package = p
         u.save()
 
@@ -547,7 +547,7 @@ class PackageManager(object):
 
     @staticmethod
     @transaction.atomic
-    def create_package(current_user, name: str, description: str = None):
+    def create_package(current_user, name: str, description: str = None, *args, **kwargs):
         p = Package()
 
         # Clean for potential XSS
@@ -556,6 +556,9 @@ class PackageManager(object):
         if description is not None and description.strip() != "":
             p.description = nh3.clean(description.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
 
+        if "shareable" in kwargs:
+            p.shareable = kwargs["shareable"]
+
         p.save()
 
         up = UserPackagePermission()
@@ -578,6 +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,
         }
@@ -623,6 +629,10 @@ class PackageManager(object):
     def grant_write(caller: User, package: Package, grantee: Union[User, Group]):
         PackageManager.update_permissions(caller, package, grantee, Permission.WRITE[0])
 
+    @staticmethod
+    def grant_owner(caller: User, package: Package, grantee: Union[User, Group]):
+        PackageManager.update_permissions(caller, package, grantee, Permission.ALL[0])
+
     @staticmethod
     @transaction.atomic
     def import_legacy_package(
@@ -665,11 +675,11 @@ class PackageManager(object):
         # EDIT START
         if data.get("classification"):
             if data["classification"] == "INTERNAL":
-                pack.classification = Package.Classification.RESTRICTED
+                pack.classification_level = Package.Classification.RESTRICTED
             elif data["classification"] == "RESTRICTED":
-                pack.classification = Package.Classification.RESTRICTED
+                pack.classification_level = Package.Classification.RESTRICTED
             elif data["classification"] == "SECRET":
-                pack.classification = Package.Classification.SECRET
+                pack.classification_level = Package.Classification.SECRET
 
                 if not "datapool" in data:
                     raise ValueError("Missing datapool in package")
@@ -821,7 +831,14 @@ class PackageManager(object):
             r.name = rule["name"]
             r.description = rule["description"]
             r.aliases = rule.get("aliases", [])
-            r.smirks = rule["smirks"]
+
+            if rule.get("smirks") is not None:
+                r.smirks = rule["smirks"]
+            elif rule.get("reactionSmarts") is not None:
+                r.smirks = rule["reactionSmarts"]
+            else:
+                raise ValueError(f"No SMIRKS or reactionSmarts found for rule {rule['id']}")
+
             r.reactant_filter_smarts = rule.get("reactantFilterSmarts", None)
             r.product_filter_smarts = rule.get("productFilterSmarts", None)
             r.save()

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

@@ -1292,14 +1292,18 @@ 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(
+
-            id__in=GroupPackagePermission.objects.filter(package=current_package).values_list(
+        if current_package.classification_level == current_package.Classification.SECRET:
-                "group_id", flat=True
+            groups = Group.objects.none()
+        else:
+            groups = Group.objects.exclude(
+                id__in=GroupPackagePermission.objects.filter(package=current_package).values_list(
+                    "group_id", flat=True
+                )
             )
-        )
 
         context["users"] = users
         context["groups"] = groups
@@ -1324,6 +1328,12 @@ 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 +3324,11 @@ 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/actions/objects/package.html

@@ -7,6 +7,7 @@
       <i class="glyphicon glyphicon-edit"></i> Edit Package</a
     >
   </li>
+  {% if meta.current_package.shareable  %}
   <li>
     <a
       role="button"
@@ -15,6 +16,7 @@
       <i class="glyphicon glyphicon-user"></i> Edit Permissions</a
     >
   </li>
+  {% endif %}
   {% if meta.current_package.get_classification_level_display != "Secret" %}
   <li>
     <a
@@ -52,7 +54,7 @@
     >
   </li>
 {% endif %}
-{% if not meta.can_edit %}
+{% if not meta.can_edit and meta.current_package.shareable %}
   <li>
     <a
       role="button"

templates/actions/objects/user.html

@@ -7,6 +7,7 @@
       <i class="glyphicon glyphicon-edit"></i> Update</a
     >
   </li>
+  {% if 1 == 0 %}
   <li>
     <a
       role="button"
@@ -15,6 +16,7 @@
       <i class="glyphicon glyphicon-lock"></i> Update Password</a
     >
   </li>
+  {% endif %}
   <li>
     <a
       role="button"

templates/index/index.html

@@ -180,12 +180,25 @@
                       >Aspartame</a
                     >
                   </div>
-                  <a
-                    class="absolute top-0 left-[calc(100%-5.4rem)]"
-                    href="/predict"
-                    >Advanced</a
-                  >
                 </div>
+                  {% 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 Package
+                    <strong class="text-base-content"
+                    ><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"
+                      ><a class="link" href="{{ meta.user.default_setting.url}}">{{ meta.user.default_setting.name|safe }}</a></strong
+                      >
+                    {% endif %}
+                    To use a different setting click
+                    <a class="link" href="/predict">here</a>
+                  </div>
+                {% endif %}
               </div>
               <div
                 id="ketcher-container"
@@ -208,9 +221,24 @@
                 >
                   Predict!
                 </button>
-                <div class="mt-1 flex w-full justify-end">
+                  {% if meta.current_package %}
-                  <a class="label justify-end" href="/predict">Advanced</a>
+                  <div
-                </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 Package
+                    <strong class="text-base-content"
+                    ><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"
+                      ><a class="link" href="{{ meta.user.default_setting.url}}">{{ meta.user.default_setting.name|safe }}</a></strong
+                      >
+                    {% endif %}
+                    To use a different setting click
+                    <a class="link" href="/predict">here</a>
+                  </div>
+                {% endif %}
               </div>
               <input
                 type="hidden"

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>
 

utilities/misc.py

@@ -21,6 +21,8 @@ from epdb.models import (
     Compound,
     CompoundStructure,
     Edge,
+    EnzymeLink,
+    Group,
     License,
     Node,
     ParallelRule,
@@ -150,6 +152,8 @@ class ReactionExportSchema(RefReactionExportSchema):
 # Rules #
 #########
 class EnzymeExportSchema(RefEnzymeExportSchema):
+    name: str
+    description: str
     ec_number: str
     classification_level: int
     linking_method: str
@@ -162,12 +166,12 @@ class EnzymeRuleExportSchema(RefRuleExportSchema):
 
     @staticmethod
     def resolve_enzymes(obj):
-        if isinstance(obj, dict):
+        if isinstance(obj, EnzymeRuleExportSchema):
-            res = []
+            return obj.enzymes
-            for e in obj.get("enzymes", []):
+        elif isinstance(obj, dict):
-                res.append(EnzymeExportSchema.model_validate(e))
+            return obj.get("enzymes", [])
-            return res
+        else:
-        return obj.enzymelink_set.all()
+            return obj.enzymelink_set.all()
 
 
 class RuleExportSchema(EnzymeRuleExportSchema):
@@ -271,7 +275,7 @@ class PackageExportSchema(Schema):
     @staticmethod
     def resolve_classification_level(obj):
         if isinstance(obj, dict):
-            return obj["classification_level"]
+            return obj.get("classification_level", "Internal")
         return obj.Classification(obj.classification_level).name
 
 
@@ -679,6 +683,27 @@ class PackageImporter:
                 for scen in elem.scenarios:
                     elem_obj.scenarios.add(self._cache[scen.uuid])
 
+    def _import_enzyme(self, rule: Rule, enzyme: EnzymeExportSchema):
+        e = EnzymeLink()
+        e.uuid = str(uuid.uuid4()) if not self.preserve_uuids else enzyme.uuid
+        e.rule = rule
+        e.name = enzyme.name
+        e.description = enzyme.description
+        e.ec_number = enzyme.ec_number
+        e.classification_level = enzyme.classification_level
+        e.linking_method = enzyme.linking_method
+        e.save()
+        for reaction in enzyme.reaction_evidence:
+            e.reaction_evidence.add(self._cache[reaction.uuid])
+        for edge in enzyme.edge_evidence:
+            e.edge_evidence.add(self._cache[edge.uuid])
+        self._cache[enzyme.uuid] = e
+
+    def _import_and_link_enzymes(self, data: PackageExportSchema):
+        for rule in data.composite_rules:
+            for enzyme in rule.enzymes:
+                self._import_enzyme(self._cache[rule.uuid], enzyme)
+
     def _import_package_from_json(
         self,
     ) -> Package:
@@ -717,6 +742,7 @@ class PackageImporter:
         self._import_scenarios(package, parsed.scenarios)
         self._import_additional_information(package, parsed.additional_information)
         self._link_scenarios_after_import(parsed)
+        self._import_and_link_enzymes(parsed)
 
         return package
 

uv.lock

@@ -894,7 +894,7 @@ provides-extras = ["ms-login", "dev", "pepper-plugin"]
 [[package]]
 name = "envipy-additional-information"
 version = "0.4.2"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#ad825570480bbe2f1a35c04923fede756c450751" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#4909e35aac5a0a3969ac2a01f8d4ad8bdadae04c" }
 dependencies = [
     { name = "pydantic" },
 ]