missing import

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

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More on PES

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minor

PW interactions

API PES

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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

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Dockerfile

@@ -37,7 +37,7 @@ RUN mkdir -p -m 0700 /root/.ssh \
 # We'll need access to private repos, let docker make use of host ssh agent and use it like:
 # docker build --ssh default -t envipath/envipy-bayer:1.0 .
 RUN --mount=type=ssh \
-    uv sync --locked --extra ms-login --extra pepper-plugin
+    uv sync --locked --extra pepper-plugin
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable

bridge/contracts.py

@@ -261,7 +261,6 @@ class Classifier(Plugin):
             for k, v in data.items():
                 if v != "":
                     cpy[k] = v
-
         return cls.Config(**cpy)
 
     @classmethod

epdb/models.py

@@ -2359,8 +2359,8 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
     def get_timeseries_data(self):
         for ai in self.additional_information.all():
-            if ai.__class__.__name__ == "OECD301FTimeSeries":
-                return ai.model_dump(mode="json")
+            if ai.type == "OECD301FTimeSeries":
+                return ai.get().model_dump(mode="json")
 
         return None
 

migration/views.py

@@ -65,6 +65,24 @@ def run_both_engines(SMILES, SMIRKS):
 
 
 def migration(request):
+    accepted_diffs = [
+        "bt0055-3469.1",
+        "bt0056-2685",
+        "bt0193-4263",
+        "bt0231-1871.1",
+        "bt0242-3803",
+        "bt0254-4224.1",
+        "bt0254-4224.2",
+        "bt0291-1129",
+        "bt0337-3543",
+        "bt0391-4285",
+        "bt0402-3576",
+        "bt0404-3928",
+        "bt0416-4269",
+        "bt0432-4254",
+        "bt0337-4117",
+    ]
+
     if request.method == "GET":
         context = get_base_context(request)
 
@@ -109,11 +127,11 @@ def migration(request):
                         ),
                         "id": str(r.uuid),
                         "url": r.url,
-                        "status": res,
+                        "status": res or r.name in accepted_diffs,
                     }
                 )
 
-                if res:
+                if res or r.name in accepted_diffs:
                     success += 1
                 else:
                     error += 1
@@ -135,7 +153,16 @@ def migration(request):
 
         for r in migration_status["results"]:
             r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
+            if r["name"] in accepted_diffs:
+                r["status"] = True
 
+        migration_status["results"] = sorted(
+            migration_status["results"], key=lambda x: (x["status"], x["name"])
+        )
+
+        num_success = sum([int(x["status"]) for x in migration_status["results"]])
+        migration_status["success"] = num_success
+        migration_status["error"] = migration_status["total"] - num_success
         context.update(**migration_status)
 
         return render(request, "migration.html", context)

static/js/pw.js

@@ -22,6 +22,7 @@ function predictFromNode(url) {
 // data = {{ pathway.d3_json | safe }};
 // elem = 'vizdiv'
 function draw(pathway, elem) {
+
     const initialzoom = 2.5
     const nodeRadius = 20;
     const linkDistance = 100;
@@ -572,12 +573,13 @@ function draw(pathway, elem) {
         .scaleExtent([0.5, 5])
         .on("zoom", (event) => {
             zoomable.attr("transform", event.transform);
-        })
-
+        });
 
     // Apply zoom to the SVG element - this enables wheel zoom
     svg.call(zoom);
+
     svg.call(zoom.scaleBy, initialzoom);
+
     // Also apply zoom to container to catch events that might not reach SVG
     // This ensures drag-to-pan works even when clicking on empty space
     container.call(zoom);

templates/collections/packages_paginated.html

@@ -3,73 +3,73 @@
 {% block page_title %}Packages{% endblock %}
 
 {% block action_button %}
-    <div class="flex items-center gap-2">
-      <button
-        type="button"
-        class="btn btn-primary btn-sm"
-        id="new-package-button"
-        onclick="document.getElementById('new_package_modal').showModal(); return false;"
+  <div class="flex items-center gap-2">
+    <button
+      type="button"
+      class="btn btn-primary btn-sm"
+      id="new-package-button"
+      onclick="document.getElementById('new_package_modal').showModal(); return false;"
+    >
+      <svg
+        xmlns="http://www.w3.org/2000/svg"
+        width="24"
+        height="24"
+        viewBox="0 0 24 24"
+        fill="none"
+        stroke="currentColor"
+        stroke-width="2"
+        stroke-linecap="round"
+        stroke-linejoin="round"
+        class="lucide lucide-folder-plus-icon lucide-folder-plus"
       >
+        <path d="M12 10v6" />
+        <path d="M9 13h6" />
+        <path
+          d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
+        />
+      </svg>
+    </button>
+    <div class="dropdown dropdown-end">
+      <div tabindex="0" role="button" class="btn btn-sm">
+        Import
         <svg
           xmlns="http://www.w3.org/2000/svg"
-          width="24"
-          height="24"
+          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-folder-plus-icon lucide-folder-plus"
+          class="lucide lucide-chevron-down ml-1"
         >
-          <path d="M12 10v6" />
-          <path d="M9 13h6" />
-          <path
-            d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
-          />
+          <path d="m6 9 6 6 6-6" />
         </svg>
-      </button>
-      <div class="dropdown dropdown-end">
-        <div tabindex="0" role="button" class="btn btn-sm">
-          Import
-          <svg
-            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-chevron-down ml-1"
-          >
-            <path d="m6 9 6 6 6-6" />
-          </svg>
-        </div>
-        <ul
-          tabindex="-1"
-          class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
-        >
-          <li>
-            <a
-              role="button"
-              onclick="document.getElementById('import_package_modal').showModal(); return false;"
-            >
-              Import Package from JSON
-            </a>
-          </li>
-          <li>
-            <a
-              role="button"
-              onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
-            >
-              Import Package from legacy JSON
-            </a>
-          </li>
-        </ul>
       </div>
+      <ul
+        tabindex="-1"
+        class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
+      >
+        <li>
+          <a
+            role="button"
+            onclick="document.getElementById('import_package_modal').showModal(); return false;"
+          >
+            Import Package from JSON
+          </a>
+        </li>
+        <li>
+          <a
+            role="button"
+            onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
+          >
+            Import Package from legacy JSON
+          </a>
+        </li>
+      </ul>
     </div>
+  </div>
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/scenarios_paginated.html

@@ -11,7 +11,7 @@
 {% endblock action_modals %}
 
 {% block action_button %}
-  {% if meta.can_edit or not meta.url_contains_package  %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/predict_pathway.html

@@ -158,7 +158,6 @@
         document.getElementById("predict-submit-button").innerText = "Predict";
       }
     }
-
     const radioButtons = document.querySelectorAll('input[name="predict"]');
     radioButtons.forEach(radio => {
       radio.addEventListener('change', radioChange);