wip

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

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 epdb.models import AdditionalInformation
-from ..dal import get_scenario_for_read, get_scenario_for_write, get_package_for_write
+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/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/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/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 %}