[Chore] Updated Dockerfile (#418)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#418

Dockerfile

@@ -6,18 +6,23 @@ ENV PYTHONDONTWRITEBYTECODE=1 \
 
 WORKDIR /app
 
+
 RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential \
     libpq-dev \
     curl \
     openssh-client \
     git \
-    nodejs \
-    npm \
+    ca-certificates \
     && rm -rf /var/lib/apt/lists/*
 
-# Install pnpm
-RUN npm install -g pnpm
+# Install Node 22 + pnpm
+RUN curl -fsSL https://deb.nodesource.com/setup_22.x | bash - \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends nodejs \
+    && corepack enable \
+    && corepack prepare pnpm@latest --activate \
+    && rm -rf /var/lib/apt/lists/*
 
 RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 ENV PATH="/root/.local/bin:${PATH}"
@@ -32,7 +37,7 @@ RUN mkdir -p -m 0700 /root/.ssh \
 # We'll need access to private repos, let docker make use of host ssh agent and use it like:
 # docker build --ssh default -t envipath/envipy:1.0 .
 RUN --mount=type=ssh \
-    uv sync --locked --extra ms-login --extra pepper-plugin
+    uv sync --locked --extra pepper-plugin
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable

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)

package.json

@@ -21,5 +21,11 @@
     "django",
     "tailwindcss",
     "daisyui"
-  ]
+  ],
+  "pnpm": {
+    "onlyBuiltDependencies": [
+      "@parcel/watcher",
+      "@tailwindcss/oxide"
+    ]
+  }
 }

pnpm-workspace.yaml

@@ -1,3 +1,5 @@
+allowBuilds:
+  '@parcel/watcher': true
 onlyBuiltDependencies:
   - '@parcel/watcher'
   - '@tailwindcss/oxide'

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

@@ -3,14 +3,16 @@
 {% block page_title %}Models{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
-    <button
-      type="button"
-      class="btn btn-primary btn-sm"
-      onclick="document.getElementById('new_model_modal').showModal(); return false;"
-    >
-      New Model
-    </button>
+  {% 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"
+        onclick="document.getElementById('new_model_modal').showModal(); return false;"
+      >
+        New Model
+      </button>
+    {% endif %}
   {% endif %}
 {% endblock action_button %}
 

templates/collections/packages_paginated.html

@@ -3,75 +3,73 @@
 {% block page_title %}Packages{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
-    <div class="flex items-center gap-2">
-      <button
-        type="button"
-        class="btn btn-primary btn-sm"
-        id="new-package-button"
-        onclick="document.getElementById('new_package_modal').showModal(); return false;"
+  <div class="flex items-center gap-2">
+    <button
+      type="button"
+      class="btn btn-primary btn-sm"
+      id="new-package-button"
+      onclick="document.getElementById('new_package_modal').showModal(); return false;"
+    >
+      <svg
+        xmlns="http://www.w3.org/2000/svg"
+        width="24"
+        height="24"
+        viewBox="0 0 24 24"
+        fill="none"
+        stroke="currentColor"
+        stroke-width="2"
+        stroke-linecap="round"
+        stroke-linejoin="round"
+        class="lucide lucide-folder-plus-icon lucide-folder-plus"
       >
+        <path d="M12 10v6" />
+        <path d="M9 13h6" />
+        <path
+          d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
+        />
+      </svg>
+    </button>
+    <div class="dropdown dropdown-end">
+      <div tabindex="0" role="button" class="btn btn-sm">
+        Import
         <svg
           xmlns="http://www.w3.org/2000/svg"
-          width="24"
-          height="24"
+          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-folder-plus-icon lucide-folder-plus"
+          class="lucide lucide-chevron-down ml-1"
         >
-          <path d="M12 10v6" />
-          <path d="M9 13h6" />
-          <path
-            d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
-          />
+          <path d="m6 9 6 6 6-6" />
         </svg>
-      </button>
-      <div class="dropdown dropdown-end">
-        <div tabindex="0" role="button" class="btn btn-sm">
-          Import
-          <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-chevron-down ml-1"
-          >
-            <path d="m6 9 6 6 6-6" />
-          </svg>
-        </div>
-        <ul
-          tabindex="-1"
-          class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
-        >
-          <li>
-            <a
-              role="button"
-              onclick="document.getElementById('import_package_modal').showModal(); return false;"
-            >
-              Import Package from JSON
-            </a>
-          </li>
-          <li>
-            <a
-              role="button"
-              onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
-            >
-              Import Package from legacy JSON
-            </a>
-          </li>
-        </ul>
       </div>
+      <ul
+        tabindex="-1"
+        class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
+      >
+        <li>
+          <a
+            role="button"
+            onclick="document.getElementById('import_package_modal').showModal(); return false;"
+          >
+            Import Package from JSON
+          </a>
+        </li>
+        <li>
+          <a
+            role="button"
+            onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
+          >
+            Import Package from legacy JSON
+          </a>
+        </li>
+      </ul>
     </div>
-  {% endif %}
+  </div>
 {% 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);