[Feature] Leftovers after Release (#303)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#303

epapi/v1/endpoints/settings.py

@@ -0,0 +1,23 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+
+from epdb.logic import SettingManager
+
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import SettingOutSchema
+
+router = Router()
+
+
+@router.get("/settings/", response=EnhancedPageNumberPagination.Output[SettingOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+)
+def list_all_pathways(request):
+    """
+    List all pathways from reviewed packages.
+    """
+    user = request.user
+    return SettingManager.get_all_settings(user)

epapi/v1/router.py

@@ -1,7 +1,18 @@
 from ninja import Router
 from ninja.security import SessionAuth
+
 from .auth import BearerTokenAuth
-from .endpoints import packages, scenarios, compounds, rules, reactions, pathways, models, structure
+from .endpoints import (
+    compounds,
+    models,
+    packages,
+    pathways,
+    reactions,
+    rules,
+    scenarios,
+    settings,
+    structure,
+)
 
 # Main router with authentication
 router = Router(
@@ -20,3 +31,4 @@ router.add_router("", reactions.router)
 router.add_router("", pathways.router)
 router.add_router("", models.router)
 router.add_router("", structure.router)
+router.add_router("", settings.router)

epapi/v1/schemas.py

@@ -102,3 +102,10 @@ class PackageOutSchema(Schema):
     @staticmethod
     def resolve_review_status(obj):
         return "reviewed" if obj.reviewed else "unreviewed"
+
+
+class SettingOutSchema(Schema):
+    uuid: UUID
+    url: str = ""
+    name: str
+    description: str

epdb/admin.py

@@ -28,7 +28,7 @@ Package = s.GET_PACKAGE_MODEL()
 
 
 class UserAdmin(admin.ModelAdmin):
-    list_display = ["username", "email", "is_active"]
+    list_display = ["username", "email", "is_active", "is_staff", "is_superuser"]
 
 
 class UserPackagePermissionAdmin(admin.ModelAdmin):
@@ -48,7 +48,7 @@ class JobLogAdmin(admin.ModelAdmin):
 
 
 class EPAdmin(admin.ModelAdmin):
-    search_fields = ["name", "description"]
+    search_fields = ["name", "description", "url", "uuid"]
     list_display = ["name", "url", "created"]
     ordering = ["-created"]
 

epdb/legacy_api.py

@@ -18,6 +18,8 @@ from .models import (
     Edge,
     EnviFormer,
     EPModel,
+    Group,
+    GroupPackagePermission,
     MLRelativeReasoning,
     Node,
     PackageBasedModel,
@@ -204,6 +206,82 @@ def get_user(request, user_uuid):
         }
 
 
+########
+# Group #
+########
+
+
+class GroupMember(Schema):
+    id: str = Field(None, alias="url")
+    identifier: str
+    name: str
+
+
+class GroupWrapper(Schema):
+    group: List[SimpleGroup]
+
+
+class GroupSchema(Schema):
+    description: str
+    id: str = Field(None, alias="url")
+    identifier: str = "group"
+    members: List[GroupMember] = Field([], alias="members")
+    name: str = Field(None, alias="name")
+    ownerid: str = Field(None, alias="owner.url")
+    ownername: str = Field(None, alias="owner.name")
+    packages: List["SimplePackage"] = Field([], alias="packages")
+    readers: List[GroupMember] = Field([], alias="readers")
+    writers: List[GroupMember] = Field([], alias="writers")
+
+    @staticmethod
+    def resolve_members(obj: Group):
+        res = []
+        for member in obj.user_member.all():
+            res.append(GroupMember(id=member.url, identifier="usermember", name=member.username))
+
+        for member in obj.group_member.all():
+            res.append(GroupMember(id=member.url, identifier="groupmember", name=member.name))
+
+        return res
+
+    @staticmethod
+    def resolve_packages(obj: Group):
+        return Package.objects.filter(
+            id__in=[
+                GroupPackagePermission.objects.filter(group=obj).values_list(
+                    "package_id", flat=True
+                )
+            ]
+        )
+
+    @staticmethod
+    def resolve_readers(obj: Group):
+        return GroupSchema.resolve_members(obj)
+
+    @staticmethod
+    def resolve_writers(obj: Group):
+        return [GroupMember(id=obj.owner.url, identifier="usermember", name=obj.owner.username)]
+
+
+@router.get("/group", response={200: GroupWrapper, 403: Error})
+def get_groups(request):
+    return {"group": GroupManager.get_groups(request.user)}
+
+
+@router.get("/group/{uuid:group_uuid}", response={200: GroupSchema, 403: Error})
+def get_group(request, group_uuid):
+    try:
+        g = GroupManager.get_group_by_id(request.user, group_uuid)
+        return g
+    except ValueError:
+        return 403, {
+            "message": f"Getting Group with id {group_uuid} failed due to insufficient rights!"
+        }
+
+
+##########
+# Search #
+##########
 class Search(Schema):
     packages: List[str] = Field(alias="packages[]")
     search: str

epdb/migrations/0015_user_is_reviewer.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.2.7 on 2026-01-19 19:26
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0014_rename_expansion_schema_setting_expansion_scheme"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="user",
+            name="is_reviewer",
+            field=models.BooleanField(default=False),
+        ),
+    ]

epdb/models.py

@@ -72,6 +72,7 @@ class User(AbstractUser):
         null=True,
         blank=False,
     )
+    is_reviewer = models.BooleanField(default=False)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -1828,8 +1829,8 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
                         queue.append(prod)
 
         # We shouldn't lose or make up nodes...
-        assert len(nodes) == len(self.nodes)
+        if len(nodes) != len(self.nodes):
-        logger.debug(f"{self.name}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}")
+            logger.debug(f"{self.name}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}")
 
         links = [e.d3_json() for e in self.edges]
 
@@ -1880,6 +1881,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
                         "source": pseudo_idx,
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
+                        "multi_step": link["multi_step"],
                     }
                     adjusted_links.append(new_link)
 
@@ -2146,6 +2148,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
         }
 
     @staticmethod
+    @transaction.atomic
     def create(
         pathway: "Pathway",
         smiles: str,
@@ -2185,8 +2188,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
         if data:
             rule_ids = defaultdict(list)
             for e in Edge.objects.filter(start_nodes__in=[self]):
-                for r in e.edge_label.rules.all():
+                # TODO While the Pathway is being predicted we sometimes
-                    rule_ids[str(r.uuid)].append(e.simple_json())
+                # TODO receive 'NoneType' object has no attribute 'rules'
+                if e.edge_label:
+                    for r in e.edge_label.rules.all():
+                        rule_ids[str(r.uuid)].append(e.simple_json())
 
             for t in data["assessment"]["transformations"]:
                 if t["rule"]["uuid"] in rule_ids:
@@ -2230,6 +2236,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
             "reaction": {"name": self.edge_label.name, "url": self.edge_label.url}
             if self.edge_label
             else None,
+            "multi_step": self.edge_label.multi_step if self.edge_label else False,
             "reaction_probability": self.kv.get("probability"),
             "start_node_urls": [x.url for x in self.start_nodes.all()],
             "end_node_urls": [x.url for x in self.end_nodes.all()],
@@ -2270,6 +2277,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
         return edge_json
 
     @staticmethod
+    @transaction.atomic
     def create(
         pathway,
         start_nodes: List[Node],
@@ -3819,6 +3827,11 @@ class Scenario(EnviPathModel):
 
                 yield inst
 
+    def related_pathways(self):
+        return Pathway.objects.filter(
+            scenarios__in=[self], package__reviewed=True, package=self.package
+        ).distinct()
+
 
 class UserSettingPermission(Permission):
     uuid = models.UUIDField(

epdb/views.py

@@ -1352,6 +1352,14 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
     )
 
     if request.method == "GET":
+        is_image_request = request.GET.get("image")
+
+        if is_image_request:
+            if is_image_request == "svg":
+                return HttpResponse(current_structure.as_svg, content_type="image/svg+xml")
+            else:
+                return HttpResponseBadRequest("Currently only SVG as image formate supported!")
+
         context = get_base_context(request)
         context["title"] = (
             f"enviPath - {current_package.name} - {current_compound.name} - {current_structure.name}"
@@ -2569,6 +2577,28 @@ def package_scenario(request, package_uuid, scenario_uuid):
                 return redirect(current_scenario.url)
             else:
                 return HttpResponseBadRequest()
+
+        new_scenario_name = request.POST.get("scenario-name")
+
+        if new_scenario_name is not None:
+            new_scenario_name = nh3.clean(new_scenario_name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+            if new_scenario_name:
+                current_scenario.name = new_scenario_name
+
+        new_scenario_description = request.POST.get("scenario-description")
+
+        if new_scenario_description is not None:
+            new_scenario_description = nh3.clean(
+                new_scenario_description, tags=s.ALLOWED_HTML_TAGS
+            ).strip()
+
+            if new_scenario_description:
+                current_scenario.description = new_scenario_description
+
+        if any([new_scenario_name, new_scenario_description]):
+            current_scenario.save()
+            return redirect(current_scenario.url)
         else:
             return HttpResponseBadRequest()
     else:
@@ -2784,10 +2814,17 @@ def settings(request):
         context["object_type"] = "setting"
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
-            {"Group": s.SERVER_URL + "/setting"},
+            {"Setting": s.SERVER_URL + "/setting"},
         ]
 
-        context["objects"] = SettingManager.get_all_settings(current_user)
+        # Context for paginated template
+        context["entity_type"] = "setting"
+        context["api_endpoint"] = "/api/v1/settings/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "settings"
+        context["list_mode"] = "combined"
+
+        return render(request, "collections/settings_paginated.html", context)
 
         return render(request, "collections/objects_list.html", context)
     elif request.method == "POST":
@@ -2867,7 +2904,26 @@ def settings(request):
 
 
 def setting(request, setting_uuid):
-    pass
+    current_user = _anonymous_or_real(request)
+    current_setting = SettingManager.get_setting_by_id(current_user, setting_uuid)
+
+    if request.method == "GET":
+        context = get_base_context(request)
+        context["title"] = f"enviPath - {current_setting.name}"
+
+        context["object_type"] = "setting"
+        context["breadcrumbs"] = [
+            {"Home": s.SERVER_URL},
+            {"Setting": s.SERVER_URL + "/setting"},
+            {f"{current_setting.name}": current_setting.url},
+        ]
+
+        context["setting"] = current_setting
+        context["current_object"] = current_setting
+
+        return render(request, "objects/setting.html", context)
+    else:
+        return HttpResponseNotAllowed(["GET"])
 
 
 def jobs(request):

static/js/pw.js

@@ -498,7 +498,8 @@ function draw(pathway, elem) {
         .enter().append("line")
         // Check if target is pseudo and draw marker only if not pseudo
         .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-        .attr("marker-end", d => d.target.pseudo ? '' : 'url(#arrow)')
+        .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
+
 
     // add element to links array
     link.each(function (d) {

templates/actions/objects/scenario.html

@@ -1,4 +1,12 @@
 {% if meta.can_edit %}
+  <li>
+    <a
+      class="button"
+      onclick="document.getElementById('edit_scenario_modal').showModal(); return false;"
+    >
+      <i class="glyphicon glyphicon-trash"></i> Edit Scenario</a
+    >
+  </li>
   <li>
     <a
       class="button"

templates/collections/settings_paginated.html

@@ -0,0 +1,20 @@
+{% extends "collections/paginated_base.html" %}
+
+{% block page_title %}Settings{% endblock %}
+
+{% block action_button %}
+{% endblock action_button %}
+
+{% block action_modals %}
+{% endblock action_modals %}
+
+{% block description %}
+  <p>A setting includes configuration parameters for pathway predictions.</p>
+  <a
+    target="_blank"
+    href="https://wiki.envipath.org/index.php/Setting"
+    class="link link-primary"
+  >
+    Learn more &gt;&gt;
+  </a>
+{% endblock description %}

templates/modals/objects/edit_scenario_modal.html

@@ -0,0 +1,91 @@
+{% load static %}
+
+<dialog
+  id="edit_scenario_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- Header -->
+    <h3 class="font-bold text-lg">Edit Scenario</h3>
+
+    <!-- Close button (X) -->
+    <form method="dialog">
+      <button
+        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
+        :disabled="isSubmitting"
+      >
+        ✕
+      </button>
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <form
+        id="edit-scenario-modal-form"
+        accept-charset="UTF-8"
+        action=""
+        method="post"
+      >
+        {% csrf_token %}
+
+        <div class="form-control mb-3">
+          <label class="label" for="scenario-name">
+            <span class="label-text">Name</span>
+          </label>
+          <input
+            id="scenario-name"
+            class="input input-bordered w-full"
+            name="scenario-name"
+            value="{{ scenario.name|safe }}"
+            required
+          />
+        </div>
+
+        <div class="form-control mb-3">
+          <label class="label" for="scenario-description">
+            <span class="label-text">Description</span>
+          </label>
+          <input
+            id="scenario-description"
+            type="text"
+            class="input input-bordered w-full"
+            value="{{ scenario.description|safe }}"
+            name="scenario-description"
+          />
+        </div>
+      </form>
+    </div>
+
+    <!-- Footer -->
+    <div class="modal-action">
+      <button
+        type="button"
+        class="btn"
+        onclick="this.closest('dialog').close()"
+        :disabled="isSubmitting"
+      >
+        Close
+      </button>
+      <button
+        type="button"
+        class="btn btn-primary"
+        @click="submit('edit-scenario-modal-form')"
+        :disabled="isSubmitting"
+      >
+        <span x-show="!isSubmitting">Update</span>
+        <span
+          x-show="isSubmitting"
+          class="loading loading-spinner loading-sm"
+        ></span>
+        <span x-show="isSubmitting">Updating...</span>
+      </button>
+    </div>
+  </div>
+
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/objects/pathway.html

@@ -306,6 +306,21 @@
               >
                 <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
               </marker>
+              <marker
+                id="doublearrow"
+                viewBox="0 0 20 30"
+                refX="53"
+                refY="5"
+                markerWidth="18"
+                markerHeight="18"
+                orient="auto-start-reverse"
+                markerUnits="userSpaceOnUse"
+              >
+                <!-- first triangle -->
+                <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
+                <!-- second triangle -->
+                <path d="M 10 0 L 20 5 L 10 10 Z" fill="#999" />
+              </marker>
               <marker
                 id="arrow_passes_app_domain"
                 viewBox="0 0 10 10"

templates/objects/scenario.html

@@ -3,6 +3,7 @@
 {% block content %}
 
   {% block action_modals %}
+    {% include "modals/objects/edit_scenario_modal.html" %}
     {% include "modals/objects/add_additional_information_modal.html" %}
     {% include "modals/objects/update_scenario_additional_information_modal.html" %}
     {% include "modals/objects/generic_delete_modal.html" %}
@@ -160,6 +161,25 @@
         </div>
       </div>
     </div>
+
+    <!-- Pathways -->
+    {% if scenario.related_pathways %}
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" checked />
+        <div class="collapse-title text-xl font-medium">Pathways</div>
+        <div class="collapse-content">
+          <ul class="menu bg-base-100 rounded-box">
+            {% for p in scenario.related_pathways %}
+              <li>
+                <a href="{{ p.url }}" class="hover:bg-base-200"
+                  >{{ p.name }} <i>({{ p.package.name }})</i></a
+                >
+              </li>
+            {% endfor %}
+          </ul>
+        </div>
+      </div>
+    {% endif %}
   </div>
 
   <script>

templates/objects/setting.html

@@ -0,0 +1,67 @@
+{% extends "framework_modern.html" %}
+
+{% block content %}
+
+  {% block action_modals %}
+  {% endblock action_modals %}
+
+  <div class="space-y-2 p-4">
+    <!-- Header Section -->
+    <div class="card bg-base-100">
+      <div class="card-body">
+        <div class="flex items-center justify-between">
+          <h2 class="card-title text-2xl">{{ setting.name }}</h2>
+          <div id="actionsButton" class="dropdown dropdown-end hidden">
+            <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
+              <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-wrench"
+              >
+                <path
+                  d="M14.7 6.3a1 1 0 0 0 0 1.4l1.6 1.6a1 1 0 0 0 1.4 0l3.77-3.77a6 6 0 0 1-7.94 7.94l-6.91 6.91a2.12 2.12 0 0 1-3-3l6.91-6.91a6 6 0 0 1 7.94-7.94l-3.76 3.76z"
+                />
+              </svg>
+              Actions
+            </div>
+            <ul
+              tabindex="-1"
+              class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+            >
+              {% block actions %}
+              {% endblock %}
+            </ul>
+          </div>
+        </div>
+      </div>
+    </div>
+
+    <!-- The actual setting -->
+    <div class="collapse-arrow bg-base-200 collapse">
+      <input type="checkbox" checked />
+      <div class="collapse-content">
+        {% with setting_to_render=setting can_be_default=False %}
+          {% include "objects/setting_template.html" %}
+        {% endwith %}
+      </div>
+    </div>
+  </div>
+
+  <script>
+    // Show actions button if there are actions
+    document.addEventListener("DOMContentLoaded", function () {
+      const actionsButton = document.getElementById("actionsButton");
+      const actionsList = actionsButton?.querySelector("ul");
+      if (actionsList && actionsList.children.length > 0) {
+        actionsButton?.classList.remove("hidden");
+      }
+    });
+  </script>
+{% endblock content %}

templates/static/login.html

@@ -31,6 +31,32 @@
 {% endblock %}
 
 {% block content %}
+  <div class="card bg-base-200 mb-6 ">
+    <div class="card-body">
+      <h3 class="card-title">Welcome to the new enviPath!</h3>
+      <p class="mb-4 text-sm">
+        Rebuilt from the ground up for faster predictions, greater stability,
+        and powerful scalability. Explore a decade of research on a modern,
+        reliable platform.<br />
+        The old system is still accessible but will be shut down at a later
+        date. If you want to back up your data, download it from the
+        <a
+          href="https://legacy.envipath.org"
+          class="link link-primary"
+          target="_blank"
+          >old system</a
+        >
+        or contact us via the
+        <a
+          href="https://community.envipath.org/"
+          class="link link-primary"
+          target="_blank"
+          >community forum</a
+        >
+        for assistance.
+      </p>
+    </div>
+  </div>
   <!-- Tab Navigation -->
   <div class="border-base-300 mb-6 border-b">
     <div class="flex justify-start">