App Integration Secret Packages

epdb/legacy_api.py

@@ -2159,6 +2159,7 @@ class CreateEdge(Schema):
     products: str | None = None  # Node URIs comma sep
     multistep: str | None = None
     edgeReason: str | None = None
+    probability: float | None = None
 
 
 @router.post(
@@ -2226,6 +2227,10 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             multi_step=multi_step,
         )
 
+        if e.probability:
+            new_e.kv["probability"] = e.probability
+            new_e.save()
+
         # Update depths as sideeffect of above operation
         pw.update_depths()
 

epdb/logic.py

@@ -376,13 +376,12 @@ class PackageManager(object):
         groups = GroupManager.get_groups(user)
 
         # EDIT START
-
         if package.classification_level == Package.Classification.SECRET:
             if user.principal_type == user.PrincipalType.APP:
                 if not user.app_details.secret_allowed or package.data_pool != user.app_details.data_pool:
                     return False
 
-            if package.data_pool not in groups:
+            elif package.data_pool not in groups:
                 return False
 
         # EDIT END
@@ -444,6 +443,10 @@ class PackageManager(object):
     @staticmethod
     def check_package_classification(user, pack: Package):
         if pack.classification_level == Package.Classification.SECRET:
+            if user.principal_type == user.PrincipalType.APP:
+                if pack.data_pool == user.app_details.data_pool:
+                    return pack
+
             if pack.data_pool.user_member.filter(id=user.id).exists():
                 return pack
 

pyproject.toml

@@ -15,7 +15,6 @@ dependencies = [
     "django-polymorphic>=4.1.0",
     "enviformer",
     "envipy-additional-information",
-    "envipy-ambit>=0.1.0",
     "envipy-plugins",
     "epam-indigo>=1.30.1",
     "gunicorn>=23.0.0",

templates/objects/pathway.html

@@ -227,6 +227,29 @@
                       Reaction Names
                     </a>
                   </li>
+                  <li>
+                    <a href="{% if merged %}{{ current_object.url }}{% else %}{{ current_object.url }}?merged=true{% endif %}" id="merged-toggle-button" class="cursor-pointer">
+                      <svg
+                        id="merged-icon"
+                        xmlns="http://www.w3.org/2000/svg"
+                        width="16"
+                        height="16"
+                        viewBox="0 0 24 24"
+                        fill="none"
+                        stroke="currentColor"
+                        stroke-width="2"
+                        stroke-linecap="round"
+                        stroke-linejoin="round"
+                        class="lucide lucide-eye"
+                      >
+                        <path
+                          d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
+                        />
+                        <circle cx="12" cy="12" r="3" />
+                      </svg>
+                      Merged View
+                    </a>
+                  </li>
                   {% if pathway.setting.model.app_domain %}
                     <li>
                       <a id="app-domain-toggle-button" class="cursor-pointer">
@@ -560,6 +583,8 @@
     var timeseriesViewEnabled = false;
     // Predicted Property View
     var predictedPropertyViewEnabled = false;
+    // Merged View
+    var mergedViewEnabled = new URLSearchParams(window.location.search).get("merged") !== null;
 
     function goFullscreen(id) {
       var element = document.getElementById(id);
@@ -705,6 +730,23 @@
         });
       }
 
+      const mergedViewBtn = document.getElementById(
+        "merged-toggle-button",
+      );
+      if (mergedViewBtn) {
+          const icon = document.getElementById("merged-icon");
+          if (mergedViewEnabled) {
+            // Change to eye-off icon
+            icon.innerHTML =
+              '<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
+          } else {
+            // Change back to eye icon
+            icon.innerHTML =
+              '<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
+        }
+      };
+
+
       // Timeseries toggle
       const timeseriesBtn = document.getElementById("timeseries-toggle-button");
       if (timeseriesBtn) {

utilities/misc.py

@@ -214,6 +214,7 @@ class EdgeExportSchema(RefEdgeExportSchema):
     start_nodes: List[RefNodeExportSchema]
     end_nodes: List[RefNodeExportSchema]
     scenarios: List[RefScenarioExportSchema]
+    kv: Optional[dict]
 
 
 class PathwayExportSchema(RefPathwayExportSchema):
@@ -623,6 +624,7 @@ class PackageImporter:
                 new_e.description = e.description
                 new_e.aliases = e.aliases
                 new_e.edge_label = self._cache[e.edge_label.uuid]
+                new_e.kv = e.kv
                 new_e.save()
 
                 for sn in e.start_nodes:

uv.lock

@@ -802,7 +802,6 @@ dependencies = [
     { name = "django-polymorphic" },
     { name = "enviformer" },
     { name = "envipy-additional-information" },
-    { name = "envipy-ambit" },
     { name = "envipy-plugins" },
     { name = "epam-indigo" },
     { name = "gunicorn" },
@@ -859,7 +858,6 @@ requires-dist = [
     { name = "emcee", marker = "extra == 'pepper-plugin'", specifier = ">=3.1.6" },
     { name = "enviformer", git = "ssh://git@git.envipath.com/enviPath/enviformer.git?rev=main" },
     { name = "envipy-additional-information", git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop" },
-    { name = "envipy-ambit", git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" },
     { name = "envipy-plugins", git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git?rev=v0.1.0" },
     { name = "epam-indigo", specifier = ">=1.30.1" },
     { name = "gunicorn", specifier = ">=23.0.0" },
@@ -899,14 +897,6 @@ dependencies = [
     { name = "pydantic" },
 ]
 
-[[package]]
-name = "envipy-ambit"
-version = "0.1.0"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git#0c424ba153105a54f758569a784d5871989338d8" }
-dependencies = [
-    { name = "jpype1" },
-]
-
 [[package]]
 name = "envipy-plugins"
 version = "0.1.0"
@@ -1190,30 +1180,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/1e/e8/685f47e0d754320684db4425a0967f7d3fa70126bffd76110b7009a0090f/joblib-1.5.2-py3-none-any.whl", hash = "sha256:4e1f0bdbb987e6d843c70cf43714cb276623def372df3c22fe5266b2670bc241", size = 308396, upload-time = "2025-08-27T12:15:45.188Z" },
 ]
 
-[[package]]
-name = "jpype1"
-version = "1.6.0"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "packaging" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/34/49/6090a131d84b22c6aae13b1853092028b060fd17da1af87c0e42ad69d50f/jpype1-1.6.0.tar.gz", hash = "sha256:2d46b2a14f8f0e6f17d8aa22b4fc3a64b2790851ebf1409ad79a37c698fd6e9a", size = 1057888, upload-time = "2025-07-07T14:04:11.244Z" }
-wheels = [
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-    { url = "https://files.pythonhosted.org/packages/6b/5d/51bde8695cc3eabcc465779f6dc23b149194bbcdcb8d221a9572422053f4/jpype1-1.6.0-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:cf646459023a0dd71b3cc3aeeb977225a93f94c97839bb4e6146977b166c7caf", size = 468341, upload-time = "2025-07-07T13:50:40.739Z" },
-    { url = "https://files.pythonhosted.org/packages/7a/a1/50cdc2bf9e51c0828faabec6fad50d61aada5a57d0bc435f4db0c16eb2ca/jpype1-1.6.0-cp312-cp312-manylinux2014_i686.manylinux_2_17_i686.whl", hash = "sha256:7a98b34bc68a117881382dffa9b02d5e1d0d94325f85d7f564c33cc9e9d2916b", size = 511724, upload-time = "2025-07-07T13:50:42.479Z" },
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-]
-
 [[package]]
 name = "jsonref"
 version = "1.1.0"