App Integration Secret Packages

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: #2

bayer/migrations/0007_alter_newsentry_publication_date.py

@@ -0,0 +1,19 @@
+# Generated by Django 6.0.3 on 2026-11-09 21:43
+
+import django.utils.timezone
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('bayer', '0006_remove_newsentry_url'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='newsentry',
+            name='publication_date',
+            field=models.DateTimeField(default=django.utils.timezone.now, verbose_name='Date'),
+        ),
+    ]

bayer/views.py

@@ -272,7 +272,6 @@ def visualize_pes(request):
                 return HttpResponse(image_data, content_type="image/png")
 
 
-@package_permission_required()
 def news_detail(request, news_entry_uuid):
     current_user = _anonymous_or_real(request)
     context = get_base_context(request, current_user)

bb4g/__init__.py

@@ -29,6 +29,8 @@ class SamplingAlgorithm(enum.Enum):
 class BB4GConfig(EnviPyModel):
     sampling_algorithm: SamplingAlgorithm = SamplingAlgorithm.EXACT
     cutoff: int = -5
+    model: str = "rat"
+    mode: str | None = None
 
     class UI:
         title = "BB4G Configuration"
@@ -44,6 +46,18 @@ class BB4GConfig(EnviPyModel):
             order=2,
             placeholder="If unset defaults to -5"
         )
+        model = UIConfig(
+            widget=WidgetType.TEXT,
+            label="BB4G Model",
+            order=3,
+            placeholder="If unset defaults to rat"
+        )
+        mode = UIConfig(
+            widget=WidgetType.TEXT,
+            label="BB4G Mode",
+            order=4,
+            placeholder="If unset defaults to None"
+        )
 
 
 # Once stable these will be exposed by enviPy-plugins lib
@@ -167,6 +181,8 @@ class BB4G(Classifier):
                 "smiles": smi,
                 "sampling_alg": self.config.sampling_algorithm.value,
                 "cutoff": self.config.cutoff,
+                "model": self.config.model,
+                "mode": self.config.mode,
             }
 
             retries = 0

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

@@ -376,9 +376,12 @@ class PackageManager(object):
         groups = GroupManager.get_groups(user)
 
         # EDIT START
-
         if package.classification_level == Package.Classification.SECRET:
-            if package.data_pool not in groups:
+            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
+
+            elif package.data_pool not in groups:
                 return False
 
         # EDIT END
@@ -440,6 +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
 

epdb/models.py

@@ -2071,7 +2071,10 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     def empty_due_to_threshold(self):
         return self.kv.get("empty_due_to_threshold", False)
 
-    def d3_json(self):
+    def merged_d3_json(self):
+        return self.d3_json(merged=True)
+
+    def d3_json(self, merged=False):
         # Ideally it would be something like this but
         # to reduce crossing in edges do a DFS
         # nodes = [n.d3_json() for n in self.nodes]
@@ -2079,15 +2082,68 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         nodes = []
         processed = set()
 
+        structure_to_combined_nodes = dict()
+        node_to_combined_node = dict()
         queue = list()
-        for n in self.root_nodes:
-            queue.append(n)
 
-        # Add unconnected nodes
-        for n in self.nodes.order_by("url"):
-            if len(n.out_edges.all()) == 0:
-                if n not in queue:
-                    queue.append(n)
+        class CombinedNode(object):
+
+            def __init__(self, representative: "Node"):
+                self.representative = representative
+                self.nodes = set([self.representative])
+
+            def ids(self):
+                return [n.id for n in self.nodes]
+
+            def d3_json(self):
+                d3_json = self.representative.d3_json()
+                compound = self.representative.default_node_label.compound
+                d3_json["name"] = compound.get_name()
+                d3_json["smiles"] = compound.default_structure.smiles
+                d3_json["node_label_id"] = compound.default_structure.url
+                d3_json["image"] = f"{compound.default_structure.url}?image=svg",
+                d3_json["image_svg"] = IndigoUtils.mol_to_svg(
+                    compound.default_structure.molfile
+                    if compound.default_structure.molfile is not None
+                       and compound.default_structure.molfile.strip()
+                    else compound.default_structure.smiles,
+                    width=40,
+                    height=40,
+                ),
+
+                return d3_json
+
+            def __repr__(self):
+                return f"CombinedNode({self.nodes})"
+
+        if merged:
+            for n in self.nodes:
+                def_struct = n.default_node_label.compound.default_structure
+                if def_struct in structure_to_combined_nodes:
+                    structure_to_combined_nodes[def_struct].nodes.add(n)
+                else:
+                    cn = CombinedNode(n)
+                    structure_to_combined_nodes[def_struct] = cn
+
+            # for n in self.nodes.order_by("url"):
+            #     if len(n.out_edges.all()) == 0:
+            #         if n not in queue:
+            #             queue.append(n)
+
+            for cn in structure_to_combined_nodes.values():
+                for n in cn.nodes:
+                    node_to_combined_node[n] = cn
+
+            queue = list(structure_to_combined_nodes.values())
+        else:
+            for n in self.nodes:
+                queue.append(n)
+
+            # Add unconnected nodes
+            for n in self.nodes.order_by("url"):
+                if len(n.out_edges.all()) == 0:
+                    if n not in queue:
+                        queue.append(n)
 
         for i in queue:
             processed.add(i)
@@ -2097,25 +2153,56 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
             processed.add(current)
             nodes.append(current.d3_json())
 
-            for e in self.edges.filter(start_nodes=current).order_by("url").distinct():
+            if merged:
+                q = Q(start_nodes__in=current.ids())
+            else:
+                q = Q(start_nodes=current)
+
+            for e in self.edges.filter(q).order_by("url").distinct():
                 for prod in e.end_nodes.all().order_by("url"):
-                    if prod not in queue and prod not in processed:
-                        queue.append(prod)
+
+                    if merged:
+                        def_struct = n.default_node_label.compound.default_structure
+                        if def_struct in structure_to_combined_nodes:
+                            structure_to_combined_nodes[def_struct].nodes.add(n)
+                        else:
+                            cn = CombinedNode(n)
+                            structure_to_combined_nodes[def_struct] = cn
+                            if cn not in queue and cn not in processed:
+                                queue.append(cn)
+                    else:
+                        if prod not in queue and prod not in processed:
+                            queue.append(prod)
 
         # We shouldn't lose or make up nodes...
-        if len(nodes) != len(self.nodes):
-            logger.debug(
-                f"{self.get_name()}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}"
-            )
+        if not merged:
+            if len(nodes) != len(self.nodes):
+                logger.debug(
+                    f"{self.get_name()}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}"
+                )
 
         links = [e.d3_json() for e in self.edges]
 
         # D3 links Nodes based on indices in nodes array
+        combined_node_depth_to_idx = dict()
         node_url_to_idx = dict()
         for i, n in enumerate(nodes):
             n["id"] = i
             node_url_to_idx[n["url"]] = i
 
+        # Add potential missing mappings
+        if merged:
+            cn_idx_mapping = dict()
+            for n in nodes:
+                for cn in processed:
+                    for sub_n in cn.nodes:
+                        if n["url"] == sub_n.url:
+                            cn_idx_mapping[cn] = n["id"]
+
+            for n in processed:
+                for sub_n in n.nodes:
+                    node_url_to_idx[sub_n.url] = cn_idx_mapping[n]
+
         adjusted_links = []
         for link in links:
             # Check if we'll need pseudo nodes

epdb/views.py

@@ -2313,6 +2313,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
 
         context["pathway"] = current_pathway
         context["current_object"] = current_pathway
+        context["merged"] = request.GET.get("merged", False) == "true"
 
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},

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/index/index.html

@@ -266,7 +266,7 @@
 
         <div id="services-container" class="flex justify-center gap-4">
           {% for ne in news_entries %}
-            <div class="card-body flex flex-col h-full justify-between p-5">
+            <div class="card-body flex flex-col h-full justify-between p-5 w-96"> <!-- Fixed width applied via w-96 -->
               <div>
                 <div class="flex items-center gap-2 mb-2">
                   <div class="bg-primary/10 text-primary rounded-lg p-1.5">
@@ -296,6 +296,7 @@
           {% endfor %}
         </div>
 
+
         <div class="mt-6 text-right">
           <a
             href="https://community.envipath.org/c/announcements/10"

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">
@@ -544,8 +567,11 @@
       </div>
     {% endif %}
   </div>
+  {% if merged %}
+  {{ pathway.merged_d3_json|json_script:"pathway" }}
+  {% else %}
   {{ pathway.d3_json|json_script:"pathway" }}
-
+  {% endif %}
   <script>
     // Global switch for compound names view
     var compoundNamesViewEnabled = false;
@@ -557,6 +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);
@@ -702,6 +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 = [
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 ]
 
-[[package]]
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-version = "1.6.0"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "packaging" },
-]
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-]
-
 [[package]]
 name = "jsonref"
 version = "1.1.0"