[Fix] Collection of minor Bugfixes (#417)

User feedback from on-prem installation

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#417

bridge/contracts.py

@@ -254,7 +254,14 @@ class Classifier(Plugin):
     def parse_config(cls, data: dict | None = None) -> EnviPyModel | None:
         if cls.Config is None:
             return None
-        return cls.Config(**(data or {}))
+
+        # remove empty strings a.k.a unset params to not overwrite defaults
+        cpy = {}
+        if data is not None:
+            for k, v in data.items():
+                if v != "":
+                    cpy[k] = v
+        return cls.Config(**cpy)
 
     @classmethod
     def create(cls, data: dict | None = None):

epdb/models.py

@@ -2335,8 +2335,8 @@ 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/alpine/components/widgets.js

@@ -59,6 +59,9 @@ document.addEventListener("alpine:init", () => {
     get isEditMode() {
       return this.mode === "edit";
     },
+    get isRequired() {
+      return (this.schema.required || []).indexOf(this.fieldName) > -1
+    }
   });
 
   // Text widget

static/js/pw.js

@@ -23,6 +23,7 @@ function predictFromNode(url) {
 // elem = 'vizdiv'
 function draw(pathway, elem) {
 
+    const initialzoom = 2.5
     const nodeRadius = 20;
     const linkDistance = 100;
     const chargeStrength = -200;
@@ -63,7 +64,7 @@ function draw(pathway, elem) {
                 node.fx = width / 2 + depthMap.get(node.depth) * horizontalSpacing - ((nodesInLevel - 1) * horizontalSpacing) / 2;
             }
 
-            node.fy = node.depth * levelSpacing + 50;
+            node.fy = (node.depth + initialzoom + 0.5) * levelSpacing + 50;
             depthMap.set(node.depth, depthMap.get(node.depth) + 1);
         });
     }
@@ -577,6 +578,8 @@ function draw(pathway, elem) {
     // 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/compounds_paginated.html

@@ -5,7 +5,7 @@
 
 {% block action_button %}
   <div class="flex items-center gap-2">
-    {% if meta.can_edit %}
+    {% if meta.can_edit or not meta.url_contains_package %}
       <button
         type="button"
         class="btn btn-primary btn-sm"

templates/collections/models_paginated.html

@@ -3,7 +3,8 @@
 {% block page_title %}Models{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
+  {% if meta.can_edit or not meta.url_contains_package %}
+    {% if meta.enabled_features.MODEL_BUILDING %}
       <button
         type="button"
         class="btn btn-primary btn-sm"
@@ -12,6 +13,7 @@
         New Model
       </button>
     {% endif %}
+  {% endif %}
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/packages_paginated.html

@@ -3,7 +3,6 @@
 {% block page_title %}Packages{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
   <div class="flex items-center gap-2">
     <button
       type="button"
@@ -71,7 +70,6 @@
       </ul>
     </div>
   </div>
-  {% endif %}
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/pathways_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Pathways{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <div class="flex items-center gap-2">
       <a
         class="btn btn-primary btn-sm"

templates/collections/reactions_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Reactions{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/rules_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Rules{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/scenarios_paginated.html

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

templates/collections/structures_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}{{ page_title|default:"Structures" }}{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/components/widgets/select_widget.html

@@ -44,6 +44,7 @@
           :class="{ 'select-error': $store.validationErrors.hasError(fieldName, context) }"
           x-model="value"
           :multiple="multiple"
+          :required="isRequired"
         >
           <option value="" :selected="!value">Select...</option>
 

templates/modals/collections/new_model_modal.html

@@ -65,11 +65,11 @@
     },
 
     get showMlrr() {
-      return this.selectedType === 'mlrr';
+      return this.selectedType === 'ml-relative-reasoning';
     },
 
     get showRbrr() {
-      return this.selectedType === 'rbrr';
+      return this.selectedType === 'rule-based-relative-reasoning';
     },
 
     get showEnviformer() {

templates/modals/collections/new_prediction_setting_modal.html

@@ -203,11 +203,11 @@
               id="model-based-prediction-setting-threshold"
               name="model-based-prediction-setting-threshold"
               class="input input-bordered w-full"
-              placeholder="0.25"
+              value="0.25"
               type="number"
               min="0"
               max="1"
-              step="0.05"
+              step="any"
             />
           </div>
 

templates/predict_pathway.html

@@ -105,7 +105,7 @@
         ></iframe>
       </div>
 
-      <label class="select mb-8 w-full">
+      <label class="select mb-8 w-full" id="prediction-setting-label">
         <span class="label">Predictor</span>
         <select id="prediction-setting" name="prediction-setting">
           <option disabled>Select a Setting</option>
@@ -148,6 +148,21 @@
   </div>
   {# prettier-ignore-start #}
   <script>
+    // Hide predictor selection and update button text if mode is "build"
+    function radioChange(event) {
+      if (event.target.value === "build") {
+        document.getElementById("prediction-setting-label").hidden = true;
+        document.getElementById("predict-submit-button").innerText = "Build";
+      } else {
+        document.getElementById("prediction-setting-label").hidden = false;
+        document.getElementById("predict-submit-button").innerText = "Predict";
+      }
+    }
+    const radioButtons = document.querySelectorAll('input[name="predict"]');
+    radioButtons.forEach(radio => {
+      radio.addEventListener('change', radioChange);
+    });
+
     // Helper function to safely get Ketcher instance from iframe
     function getKetcherInstance(iframeId) {
       const ketcherFrame = document.getElementById(iframeId);