Enable init call for transition

bayer/migrations/0007_alter_newsentry_publication_date.py

@@ -1,19 +0,0 @@
-# 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'),
-        ),
-    ]

epdb/logic.py

@@ -378,10 +378,6 @@ class PackageManager(object):
         # 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:
                 return False
 

epdb/models.py

@@ -2071,10 +2071,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     def empty_due_to_threshold(self):
         return self.kv.get("empty_due_to_threshold", False)
 
-    def merged_d3_json(self):
-        return self.d3_json(merged=True)
-
-    def d3_json(self, merged=False):
+    def d3_json(self):
         # 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]
@@ -2082,68 +2079,15 @@ 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)
 
-        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)
+        # 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)
@@ -2153,56 +2097,25 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
             processed.add(current)
             nodes.append(current.d3_json())
 
-            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 e in self.edges.filter(start_nodes=current).order_by("url").distinct():
                 for prod in e.end_nodes.all().order_by("url"):
-
-                    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)
+                    if prod not in queue and prod not in processed:
+                        queue.append(prod)
 
         # We shouldn't lose or make up 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)}"
-                )
+        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

@@ -2313,7 +2313,6 @@ 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},

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 w-96"> <!-- Fixed width applied via w-96 -->
+            <div class="card-body flex flex-col h-full justify-between p-5">
               <div>
                 <div class="flex items-center gap-2 mb-2">
                   <div class="bg-primary/10 text-primary rounded-lg p-1.5">
@@ -283,20 +283,10 @@
                   {{ ne.content }}
                 </p>
               </div>
-
-              <a href="{{ ne.url }}" class="btn btn-primary btn-sm w-full group-hover:btn-active mt-1">
-                Read Full
-                <svg xmlns="http://www.w3.org/2000/svg" class="h-3.5 w-3.5" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
-                  <path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"></path>
-                  <polyline points="15 3 21 3 21 9"></polyline>
-                  <line x1="10" y1="14" x2="21" y2="3"></line>
-                </svg>
-              </a>
             </div>
           {% endfor %}
         </div>
 
-
         <div class="mt-6 text-right">
           <a
             href="https://community.envipath.org/c/announcements/10"

templates/objects/pathway.html

@@ -544,11 +544,8 @@
       </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;