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

...

epdb/views.py

@@ -19,6 +19,7 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
+from .exceptions import InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -388,6 +389,9 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
             "debug": s.DEBUG,
             "external_databases": ExternalDatabase.get_databases(),
             "site_id": s.MATOMO_SITE_ID,
+            # EDIT START
+            "secret_groups": Group.objects.filter(secret=True),
+            # EDIT END
         },
     }
 
@@ -587,10 +591,38 @@ def packages(request):
                 "package-description", s.DEFAULT_VALUES["description"]
             )
 
+            # EDIT START
+            data_pool = None
+            package_classification = request.POST.get("package-classification")
+            classification = Package.Classification(int(package_classification))
+            # For SECRET we'll need a data pool which will be an additional perm check later
+            if classification == Package.Classification.SECRET:
+                package_data_pool = request.POST.get("package-data-pool")
+
+                if package_data_pool is None:
+                    return error(request, "Invalid data pool.", "Data Pool is required!")
+
+                data_pool = GroupManager.get_group_by_url(current_user, package_data_pool)
+
+                if data_pool is None:
+                    return error(request, "Invalid data pool.", "Data Pool does not exist or no access!")
+
+                if not data_pool.secret:
+                    return error(request, "Invalid data pool.", "Data Pool is not a secret group!")
+
             created_package = PackageManager.create_package(
                 current_user, package_name, package_description
             )
 
+            created_package.classification_level = classification
+
+            # Set previously determined data pool
+            if classification == Package.Classification.SECRET:
+                created_package.data_pool = data_pool
+
+            created_package.save()
+            # EDIT END
+
             return redirect(created_package.url)
 
     elif request.method == "OPTIONS":
@@ -753,6 +785,10 @@ def models(request):
             {"Home": s.SERVER_URL},
             {"Model": s.SERVER_URL + "/model"},
         ]
+        context["entity_type"] = "model"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "models"
 
         # Keep model_types for potential modal/action use
         context["model_types"] = {
@@ -766,12 +802,14 @@ def models(request):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-            "EnviFormer": {
+        }
+
+        if s.ENVIFORMER_PRESENT:
+            context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
             },
-        }
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -779,6 +817,9 @@ def models(request):
                     "type": k,
                     "requires_rule_packages": v.requires_rule_packages(),
                     "requires_data_packages": v.requires_data_packages(),
+                    "additional_parameters": v.Config.__name__.lower()
+                    if v.Config.__name__ != ""
+                    else None,
                 }
             for k, v in s.PROPERTY_PLUGINS.items():
                 context["model_types"][v.display()] = {
@@ -787,12 +828,6 @@ def models(request):
                     "requires_data_packages": v.requires_data_packages(),
                 }
 
-        # Context for paginated template
-        context["entity_type"] = "model"
-        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "models"
-
         return render(request, "collections/models_paginated.html", context)
 
     elif request.method == "POST":
@@ -906,12 +941,14 @@ def package_models(request, package_uuid):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-            "EnviFormer": {
+        }
+
+        if s.ENVIFORMER_PRESENT:
+            context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
             },
-        }
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -1087,6 +1124,9 @@ def package_model(request, package_uuid, model_uuid):
                             }
                         )
 
+                # Sort data by prob desc
+                res["pred"] = sorted(res["pred"], key=lambda x: x["probability"], reverse=True)
+
                 return JsonResponse(res, safe=False)
 
             elif half_life:
@@ -2328,7 +2368,10 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_description = request.POST.get("node-description")
 
         node_smiles = request.POST.get("node-smiles").strip()
-        current_pathway.add_node(node_smiles, name=node_name, description=node_description)
+        try:
+            current_pathway.add_node(node_smiles, name=node_name, description=node_description)
+        except InvalidSMILESException as e:
+            return error(request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid")
 
         return redirect(current_pathway.url)
 
@@ -2968,9 +3011,15 @@ def settings(request):
         new_default = request.POST.get("prediction-setting-new-default", "off") == "on"
 
         # min 2, max s.DEFAULT_MAX_NUMBER_OF_NODES
+        temp_max_nodes = request.POST.get("prediction-setting-max-nodes")
+        if temp_max_nodes is None or temp_max_nodes == "" or int(temp_max_nodes) == -1:
+            temp_max_nodes = s.DEFAULT_MAX_NUMBER_OF_NODES
+        else:
+            temp_max_nodes = int(request.POST.get("prediction-setting-max-nodes", 1))
+
         max_nodes = min(
             max(
-                int(request.POST.get("prediction-setting-max-nodes", 1)),
+                temp_max_nodes,
                 2,
             ),
             s.DEFAULT_MAX_NUMBER_OF_NODES,
@@ -2991,6 +3040,7 @@ def settings(request):
 
             model_uuid = model_url.split("/")[-1]
             params["model"] = EPModel.objects.get(uuid=model_uuid)
+            # TODO Check if removed if request contains "" or not at all
             params["model_threshold"] = request.POST.get(
                 "model-based-prediction-setting-threshold", s.DEFAULT_MODEL_THRESHOLD
             )