adjusted migration

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

wip

More on PES

wip

wip

Wip

minor

PW interactions

API PES

wip

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

wip

auth log, bb4g fix

missing import

Added viz hint if PES is part of reaction

Add Edge check for pes

flip boolean

...

pes

Added extra

...

In / Out Edges Viz, Submitting Button Text

...

Make PES Link clickable

Return proper http response instead of error

Fixed error return, removed unused options

Fix PES Link HTML for other entities

Fixed molfile assignment, adjusted Export

Package Export/Import cycle

highlight Description links

implemented non persistent

Harmonised proposed field in Json output

Added pesLink field to PW Api output

PES Fields in API Output

removed debug

Fix Classification import, Fix PES Deserialization

underline pes link in templates

Fix alter name/desc for node, make /node /edge funcitonal

provide setting link and copy button

Implemented Compound Names / Reaction Names View Option

Unconnected Nodes

Make links thicker, reduce timeout trigger time

Show proposed info in popover

Pathway Build no stereo removal

Include probs in reaction name option viz

Detect clicks outside nodes/edges

bayer/templates/objects/package.html

@@ -4,7 +4,6 @@
 
   {% block action_modals %}
     {% include "modals/objects/edit_package_modal.html" %}
-    {% include "modals/objects/view_package_permissions_modal.html" %}
     {% include "modals/objects/edit_package_permissions_modal.html" %}
     {% include "modals/objects/publish_package_modal.html" %}
     {% include "modals/objects/set_license_modal.html" %}

bayer/views.py

@@ -1,9 +1,8 @@
 import base64
-import logging
 
 import requests
 from django.conf import settings as s
-from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed
+from django.http import HttpResponse, HttpResponseBadRequest
 from django.shortcuts import redirect
 
 from bayer.models import PESCompound
@@ -15,9 +14,6 @@ from utilities.decorators import package_permission_required
 Package = s.GET_PACKAGE_MODEL()
 
 
-logger = logging.getLogger(__name__)
-
-
 @package_permission_required()
 def create_pes(request, package_uuid):
     current_user = _anonymous_or_real(request)
@@ -40,41 +36,27 @@ def create_pes(request, package_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return error(
-                    request,
-                    "Could not fetch PES",
-                    f"Could not fetch PES data for {pes_link}"
-                )
+                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return error(
-                        request,
-                        "Classification Mismatch!",
-                        "Cannot create secret PESs in non-secret packages."
-                    )
+                    return HttpResponseBadRequest("Cannot create PESs for non-secret packages.")
 
-                if not current_package.data_pool or not current_package.data_pool.secret:
-                    logger.info(f"The current package does not have a secret data pool.")
-                    return error(
-                        request,
-                        "The current package does not have a secret data pool.",
-                        "Cannot create secret PESs in package without a secret data pool."
-                    )
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return HttpResponseBadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
             return redirect(pes.url)
         else:
-            return error(
-                request,
-                "No PES link received",
-                "Please provide a PES link."
-            )
+            return HttpResponseBadRequest("Please provide a PES link.")
     else:
-        return HttpResponseNotAllowed(["POST"])
+        pass
 
 
 @package_permission_required()
@@ -100,37 +82,23 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return error(
-                    request,
-                    "Could not fetch PES",
-                    f"Could not fetch PES data for {pes_link}"
-                )
+                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return error(
-                        request,
-                        "Classification Mismatch!",
-                        "Cannot create secret PESs in non-secret packages."
-                    )
+                    return HttpResponseBadRequest("Cannot create PESs for non-secret packages.")
 
-                if not current_package.data_pool or not current_package.data_pool.secret:
-                    logger.info(f"The current package does not have a secret data pool.")
-                    return error(
-                        request,
-                        "The current package does not have a secret data pool.",
-                        "Cannot create secret PESs in package without a secret data pool."
-                    )
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return HttpResponseBadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
-            node_qs = Node.objects.filter(
-                pathway=current_pathway,
-                default_node_label=pes.default_structure
-            )
-
+            node_qs = Node.objects.filter(pathway=current_pathway, default_node_label=pes.default_structure)
             if node_qs.exists():
                 return redirect(current_pathway.url)
 
@@ -148,13 +116,9 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             return redirect(current_pathway.url)
 
         else:
-            return error(
-                request,
-                "No PES link received",
-                "Please provide a PES link."
-            )
+            return HttpResponseBadRequest("Please provide a PES link.")
     else:
-        return HttpResponseNotAllowed(["POST"])
+        pass
 
 
 def fetch_pes(request, pes_url) -> dict:

epapi/v1/endpoints/additional_information.py

@@ -9,8 +9,8 @@ from envipy_additional_information import registry
 from envipy_additional_information.groups import GroupEnum
 from epapi.utils.schema_transformers import build_rjsf_output
 from epapi.utils.validation_errors import handle_validation_error
-from epdb.models import AdditionalInformation, Scenario, Node
-from ..dal import get_scenario_for_read, get_scenario_for_write, get_package_for_write
+from epdb.models import AdditionalInformation
+from ..dal import get_scenario_for_read, get_scenario_for_write
 
 logger = logging.getLogger(__name__)
 
@@ -58,61 +58,6 @@ def list_scenario_info(request, scenario_uuid: UUID):
     return result
 
 
-@router.post("/information/{model_name}/")
-def add_object_info(request, model_name: str, payload: Dict[str, Any] = Body(...)):
-    from epdb.views import EPDBURLParser
-
-    cls = registry.get_model(model_name.lower())
-    if not cls:
-        raise HttpError(404, f"Unknown model: {model_name}")
-
-    try:
-        instance = cls(**payload)  # Pydantic validates
-    except ValidationError as e:
-        handle_validation_error(e)
-
-    if "attach_obj_url" in payload:
-        url_parser = EPDBURLParser(payload["attach_obj_url"])
-
-        if url_parser.contains_package_url():
-            package = get_package_for_write(request.user, url_parser.get_objects()[0].uuid)
-            attach_obj = url_parser.get_object()
-
-            if "scenario_uuid" in payload:
-                scenario = get_scenario_for_read(request.user, payload["scenario_uuid"])
-            else:
-                scenario = Scenario.create(
-                    package,
-                    name=f"Scenario {Scenario.objects.filter(package=package).count() + 1}",
-                    description="no description",
-                    scenario_date=None,
-                    scenario_type=None,
-                    additional_information=[],
-                )
-
-            if isinstance(attach_obj, Node):
-                ai = add_info_to_node(package, instance, scenario, attach_obj)
-            else:
-                raise HttpError(404, f"Bad request - Not implemented for {type(attach_obj)}!")
-
-            return {"status": "created", "uuid": ai.uuid}
-
-    raise HttpError(404, "Bad request!")
-
-
-def add_info_to_node(package, add_inf, scenario, node):
-    ai = AdditionalInformation.create(
-        package,
-        add_inf,
-        scenario=scenario,
-        content_object=node,
-    )
-
-    node.pathway.scenarios.add(scenario)
-
-    return ai
-
-
 @router.post("/scenario/{uuid:scenario_uuid}/information/{model_name}/")
 def add_scenario_info(
     request, scenario_uuid: UUID, model_name: str, payload: Dict[str, Any] = Body(...)

epdb/legacy_api.py

@@ -881,11 +881,12 @@ def create_package_compound(
             if "secret" == classification.lower():
 
                 if p.classification_level != Package.Classification.SECRET:
-                    return 400, {"message": "Cannot create secret PESs in non-secret packages."}
-
-                if not p.data_pool or not p.data_pool.secret:
-                    return 400, {"message": "Cannot create secret PESs in package without a secret data pool."}
+                    return 400, {"Cannot create PESs for non-secret packages."}
 
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
 
             c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
         else:
@@ -1704,7 +1705,7 @@ class PathwayNode(Schema):
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
-    proposed: List[Dict[str, Any]] = []
+    proposed: List[Dict[str, str]] = []
     smiles: str = Field(None, alias="smiles")
     pseudo: bool = Field(False, alias="pseudo")
     pesLink: str | None = Field(None, alias="pes_link")
@@ -1974,7 +1975,7 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
 
 class CreateNode(Schema):
-    nodeAsSmiles: str | None = None
+    nodeAsSmiles: str
     nodeAsMolFile: str | None = None
     nodeName: str | None = None
     nodeReason: str | None = None
@@ -2006,10 +2007,14 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
             if "secret" == classification.lower():
 
                 if p.classification_level != Package.Classification.SECRET:
-                    return 400, {"message": "Cannot create secret PESs in non-secret packages."}
+                    return 400, "Cannot create PESs for non-secret packages."
 
-                if not p.data_pool or not p.data_pool.secret:
-                    return 400, {"message": "Cannot create secret PESs in package without a secret data pool."}
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, {
+                            "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"
+                        }
 
             c = PESCompound.create(p, pes_data, n.nodeName, n.nodeReason)
 

epdb/models.py

@@ -2466,7 +2466,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "name": self.get_name(),
             "plain_name": self.get_name(include_suffix=False),
             "smiles": self.default_node_label.smiles,
-            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.get_scenarios()],
+            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
                 "inside_app_domain": app_domain_data["assessment"]["inside_app_domain"]
                 if app_domain_data
@@ -2594,15 +2594,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return list(collected.values())
 
-    def get_scenarios(self):
-        qs = self.scenarios.all()
-        qs |= Scenario.objects.filter(
-            id__in=self.additional_information.filter(scenario__isnull=False)
-            .values_list("scenario", flat=True)
-            .distinct()
-        )
-        return qs.distinct()
-
 
 class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(

static/js/api/additional-information.js

@@ -186,40 +186,6 @@ window.AdditionalInformationApi = {
     return this._handleResponse(response, "createItem");
   },
 
-    /**
-   * Create new additional information and attach it to an object.
-
-   * @param {string} modelName - Name/type of the additional information model
-   * @param {Object} data - Data for the new item
-   * @param {string} attachObjectUrl - UUID of the object this data should be attached to
-   * @param {string} scenarioUuid - UUID of the scenario
-   * @returns {Promise<{status: string, uuid: string}>}
-   */
-  async createItemOnNonScenarioObject(modelName, data, attachObjectUrl, scenarioUuid) {
-    const sanitizedData = this.sanitizePayload(data);
-    this._log("createItemOnNonScenarioObject", { modelName, data: sanitizedData, attachObjectUrl, scenarioUuid });
-
-    sanitizedData.attach_obj_url = attachObjectUrl;
-    if (scenarioUuid) {
-      sanitizedData.scenario_uuid = scenarioUuid;
-    }
-
-
-    // Normalize model name to lowercase
-    const normalizedName = modelName.toLowerCase();
-
-    const response = await fetch(
-      `/api/v1/information/${normalizedName}/`,
-      {
-        method: "POST",
-        headers: this._buildHeaders(),
-        body: JSON.stringify(sanitizedData),
-      },
-    );
-
-    return this._handleResponse(response, "createItemOnNonScenarioObject");
-  },
-
   /**
    * Delete additional information from a scenario
    * @param {string} scenarioUuid - UUID of the scenario

templates/actions/objects/package.html

@@ -23,7 +23,6 @@
       <i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a
     >
   </li>
-{% endif %}
   <li>
     <a
       role="button"
@@ -32,7 +31,6 @@
       <i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a
     >
   </li>
-{% if meta.can_edit %}
   <li>
     <a
       role="button"
@@ -50,13 +48,3 @@
     >
   </li>
 {% endif %}
-{% if not meta.can_edit %}
-  <li>
-    <a
-      role="button"
-      onclick="document.getElementById('view_package_permissions_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-user"></i> View Permissions</a
-    >
-  </li>
-{% endif %}

templates/actions/objects/pathway.html

@@ -83,19 +83,6 @@
       <i class="glyphicon glyphicon-edit"></i> Edit Pathway</a
     >
   </li>
-  <li>
-    <a
-      class="button"
-      onclick="
-      const modal = document.getElementById('edit_pathway_node_modal');
-      modal.showModal();
-      window.dispatchEvent(new Event('modal-opened'));
-      return false;
-      "
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Compound</a
-    >
-  </li>
   <li>
     <a
       role="button"

templates/actions/objects/scenario.html

@@ -10,7 +10,7 @@
   <li>
     <a
       class="button"
-      onclick="document.getElementById('add_scenario_additional_information_modal').showModal(); return false;"
+      onclick="document.getElementById('add_additional_information_modal').showModal(); return false;"
     >
       <i class="glyphicon glyphicon-trash"></i> Add Additional Information</a
     >

templates/modals/objects/add_additional_information_modal.html

@@ -1,7 +1,7 @@
 {% load static %}
 <!-- Add Additional Information -->
 <dialog
-  id="add_scenario_additional_information_modal"
+  id="add_additional_information_modal"
   class="modal"
   x-data="{
     isSubmitting: false,
@@ -98,7 +98,7 @@
         );
 
         // Close modal and reload page to show new item
-        document.getElementById('add_scenario_additional_information_modal').close();
+        document.getElementById('add_additional_information_modal').close();
         window.location.reload();
       } catch (err) {
         if (err.isValidationError && err.fieldErrors) {

templates/modals/objects/edit_pathway_node_modal.html

@@ -1,276 +0,0 @@
-{% load static %}
-<!-- Add Additional Information -->
-<dialog
-  id="edit_pathway_node_modal"
-  class="modal"
-  x-data="{
-    isSubmitting: false,
-    selectedType: '',
-    selectedScenario: '',
-    selectedNode: '',
-    schemas: {},
-    loadingSchemas: false,
-    error: null,
-    formData: null,  // Store reference to form data
-    formRenderKey: 0,  // Counter to force form re-render
-    allowedTypes: ['halflife', 'halflifews', 'proposedintermediate', 'transformationproductimportance', 'confidence'],
-    scenarios: [],
-    scenariosLoaded: false,
-
-    // Get sorted unique schema names for dropdown, excluding already-added types
-    get sortedSchemaNames() {
-      const names = Object.keys(this.schemas);
-      // Remove duplicates, exclude existing types, and sort alphabetically by display title
-      const unique = [...new Set(names)];
-      const available = unique.filter(name =>
-        this.allowedTypes.includes(name)
-      );
-      return available.sort((a, b) => {
-        const titleA = (this.schemas[a]?.schema?.['x-title'] || a).toLowerCase();
-        const titleB = (this.schemas[b]?.schema?.['x-title'] || b).toLowerCase();
-        return titleA.localeCompare(titleB);
-      });
-    },
-
-    async init() {
-      // Watch for selectedType changes
-      this.$watch('selectedType', (value) => {
-        // Reset formData when type changes and increment key to force re-render
-        this.formData = null;
-        this.formRenderKey++;
-        // Clear previous errors
-        this.error = null;
-        Alpine.store('validationErrors').clearErrors(); // No context - clears all
-      });
-
-      // Load schemas and existing items
-      try {
-        this.loadingSchemas = true;
-        const [schemasRes, scenarioRes] = await Promise.all([
-          fetch('/api/v1/information/schema/'),
-          fetch('{% url "package scenario list" meta.current_package.uuid %}', { headers: {'Accept': 'application/json' }}),
-        ]);
-
-        if (!schemasRes.ok) throw new Error('Failed to load schemas');
-        if (!scenarioRes.ok) throw new Error('Failed to load scenarios');
-
-        this.schemas = await schemasRes.json();
-        this.scenarios = await scenarioRes.json();
-        // Get unique existing types (normalize to lowercase)
-      } catch (err) {
-        this.error = err.message;
-      } finally {
-        this.loadingSchemas = false;
-      }
-    },
-
-    reset() {
-      this.isSubmitting = false;
-      this.selectedType = '';
-      this.error = null;
-      this.formData = null;
-      this.selectedScenario = '';
-      Alpine.store('validationErrors').clearErrors(); // No context - clears all
-    },
-
-    setFormData(data) {
-      // Fired from schemaRenderer
-      this.formData = data;
-    },
-
-    async submit() {
-      if (!this.selectedType) return;
-      const payload = window.AdditionalInformationApi.sanitizePayload(this.formData || {});
-
-      // Validate that form has data
-      if (!payload || Object.keys(payload).length === 0) {
-        // proposedintermediate is parameterless
-        if (!this.selectedType === 'proposedintermediate') {
-          this.error = 'Please fill in at least one field';
-          return;
-        }
-      }
-
-      this.isSubmitting = true;
-      this.error = null;
-
-      try {
-      // TODO
-        await window.AdditionalInformationApi.createItemOnNonScenarioObject(
-          this.selectedType,
-          payload,
-          this.selectedNode,
-          this.selectedScenario
-        );
-
-        // Close modal and reload page to show new item
-        document.getElementById('edit_pathway_node_modal').close();
-        window.location.reload();
-      } catch (err) {
-        if (err.isValidationError && err.fieldErrors) {
-          // No context for add modal - simple flat errors
-          Alpine.store('validationErrors').setErrors(err.fieldErrors);
-          this.error = err.message || 'Please correct the errors in the form';
-        } else {
-          this.error = err.message || 'An error occurred. Please try again.';
-        }
-      } finally {
-        this.isSubmitting = false;
-      }
-    }
-  }"
-  @close="reset()"
-  @form-data-ready="setFormData($event.detail)"
-  @modal-opened.window="
-   const el = d3.select('circle.highlighted').node();
-   if (el !== null) {
-    const selectElement = document.getElementById('edit_pathway_nodes_node');
-    for (let option of selectElement.options) {
-        if (option.value === el.__data__.url) {
-            option.selected = true;
-            break;
-        }
-    }
-    selectElement.dispatchEvent(new Event('change'));
-   }
-  "
->
-  <div class="modal-box max-w-2xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Edit Compound</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <!-- Loading state -->
-      <template x-if="loadingSchemas">
-        <div class="flex items-center justify-center p-4">
-          <span class="loading loading-spinner loading-md"></span>
-        </div>
-      </template>
-
-      <!-- Error state -->
-      <template x-if="error">
-        <div class="alert alert-error mb-4">
-          <span x-text="error"></span>
-        </div>
-      </template>
-      <div class="form-control">
-        <p>
-          If no Scenario is selected a new Scenario will be created and attached
-          to this Pathway
-        </p>
-        <label class="label" for="edit_pathway_nodes_node">
-          <span class="label-text">Select Node</span>
-        </label>
-        <select
-          id="edit_pathway_nodes_node"
-          name="node"
-          class="select select-bordered w-full"
-          x-model="selectedNode"
-        >
-          {% for n in pathway.nodes %}
-            <option value="{{ n.url }}">
-              {{ n.default_node_label.name|safe }}
-            </option>
-          {% endfor %}
-        </select>
-
-        <label class="label" for="scenario-select">
-          <span class="label-text">Scenarios</span>
-        </label>
-        <select
-          id="scenario-select"
-          name="selected-scenarios"
-          class="select select-bordered w-full"
-          x-model="selectedScenario"
-        >
-          <option value="" selected disabled>Select Scenario</option>
-          <template x-for="scenario in scenarios" :key="scenario.url">
-            <option :value="scenario.url" x-text="scenario.name"></option>
-          </template>
-        </select>
-      </div>
-
-      <!-- Schema selection -->
-      <template x-if="!loadingSchemas">
-        <div>
-          <div class="form-control mb-4">
-            <label class="label" for="select-additional-information-type">
-              <span class="label-text">Select the type to add</span>
-            </label>
-            <select
-              id="select-additional-information-type"
-              class="select select-bordered w-full"
-              x-model="selectedType"
-            >
-              <option value="" selected disabled>Select the type to add</option>
-              <template x-for="name in sortedSchemaNames" :key="name">
-                <option
-                  :value="name"
-                  x-text="(schemas[name].schema && (schemas[name].schema['x-title'] || schemas[name].schema.title)) || name"
-                ></option>
-              </template>
-            </select>
-          </div>
-
-          <!-- Form renderer for selected type -->
-          <!-- Use unique key per type to force re-render -->
-          <template x-for="renderKey in [formRenderKey]" :key="renderKey">
-            <div x-show="selectedType && schemas[selectedType]">
-              <div
-                x-data="schemaRenderer({
-                  rjsf: schemas[selectedType],
-                  mode: 'edit'
-                  // No context - single form, backward compatible
-                })"
-                x-init="await init(); $dispatch('form-data-ready', data)"
-              >
-                {% include "components/schema_form.html" %}
-              </div>
-            </div>
-          </template>
-        </div>
-      </template>
-    </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()"
-        :disabled="isSubmitting || loadingSchemas || !selectedType || !selectedNode"
-      >
-        <span x-show="!isSubmitting">Add</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Adding...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

templates/modals/objects/view_package_permissions_modal.html

@@ -1,147 +0,0 @@
-{% load static %}
-<!-- Edit Package Permissions -->
-<dialog
-  id="view_package_permissions_modal"
-  class="modal"
-  x-data="{}"
->
-  <div class="modal-box max-w-2xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Current Permissions</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2">
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <p class="mb-4">
-        Current permissions for this package.
-      </p>
-
-      <!-- User Permissions -->
-      {% if user_permissions %}
-        <div class="divider">User Permissions</div>
-        <div class="space-y-2">
-        <div class="grid grid-cols-12 gap-2 items-center">
-          <div class="col-span-5 truncate"></div>
-          <div class="col-span-2 text-center">Read</div>
-          <div class="col-span-2 text-center">Write</div>
-          <div class="col-span-2 text-center">Owner</div>
-          <div class="col-span-1"></div>
-        </div>
-          {% for up in user_permissions %}
-              <div class="grid grid-cols-12 gap-2 items-center">
-                <div class="col-span-5 truncate">
-                  {{ up.user.username }}
-                  {% if not up.user.is_active %}<i>(inactive)</i>{% endif %}
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="read"
-                    id="read_{{ up.user.uuid }}"
-                    class="checkbox"
-                    {% if up.has_read %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="write"
-                    id="write_{{ up.user.uuid }}"
-                    class="checkbox"
-                    {% if up.has_write %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="owner"
-                    id="owner_{{ up.user.uuid }}"
-                    class="checkbox"
-                    {% if up.has_all %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-              </div>
-
-          {% endfor %}
-        </div>
-      {% endif %}
-
-      <!-- Group Permissions -->
-      {% if group_permissions %}
-        <div class="divider">Group Permissions</div>
-        <div class="space-y-2">
-        <div class="grid grid-cols-12 gap-2 items-center">
-          <div class="col-span-5 truncate"></div>
-          <div class="col-span-2 text-center">Read</div>
-          <div class="col-span-2 text-center">Write</div>
-          <div class="col-span-2 text-center">Owner</div>
-          <div class="col-span-1"></div>
-        </div>
-          {% for gp in group_permissions %}
-
-              <div class="grid grid-cols-12 gap-2 items-center">
-                <div class="col-span-5 truncate">
-                  {{ gp.group.name|safe }}
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="read"
-                    id="read_{{ gp.group.uuid }}"
-                    class="checkbox"
-                    {% if gp.has_read %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="write"
-                    id="write_{{ gp.group.uuid }}"
-                    class="checkbox"
-                    {% if gp.has_write %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="owner"
-                    id="owner_{{ gp.group.uuid }}"
-                    class="checkbox"
-                    {% if gp.has_all %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-              </div>
-          {% endfor %}
-        </div>
-      {% endif %}
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-      >
-        Close
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button>close</button>
-  </form>
-</dialog>

templates/objects/pathway.html

@@ -4,8 +4,6 @@
 
 {% block content %}
   <script src="https://d3js.org/d3.v7.min.js"></script>
-  <script src="{% static 'js/api/additional-information.js' %}"></script>
-
   <style>
     #vizdiv {
       width: 100%;
@@ -99,7 +97,6 @@
     {% include "modals/objects/identify_missing_rules_modal.html" %}
     {% include "modals/objects/generic_copy_object_modal.html" %}
     {% include "modals/objects/edit_pathway_modal.html" %}
-    {% include "modals/objects/edit_pathway_node_modal.html" %}
     {% include "modals/objects/generic_set_aliases_modal.html" %}
     {% include "modals/objects/generic_set_scenario_modal.html" %}
     {% include "modals/objects/delete_pathway_node_modal.html" %}

templates/objects/scenario.html

@@ -7,7 +7,7 @@
 
   {% block action_modals %}
     {% include "modals/objects/edit_scenario_modal.html" %}
-    {% include "modals/objects/add_scenario_additional_information_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" %}
   {% endblock action_modals %}