wip

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}"

bayer/models.py

@@ -232,5 +232,6 @@ class PESStructure(CompoundStructure):
             "is_pes": True,
             "pes_link": self.pes_link,
             # Will overwrite image from Node
-            "image": f"{reverse("depict_pes")}?pesLink={urllib.parse.quote(self.pes_link)}"
+            "image": f"{reverse('depict_pes')}?pesLink={urllib.parse.quote(self.pes_link)}",
+            "image_type": "png",
         }

bayer/views.py

@@ -75,6 +75,10 @@ def create_pes_node(request, package_uuid, pathway_uuid):
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
+
+                if current_package.classification_level != Package.Classification.SECRET:
+                    return BadRequest("Cannot create PESs for non-secret packages.")
+
                 data_pools = pes_data.get("dataPools")
                 if data_pools:
                     if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
@@ -83,6 +87,10 @@ def create_pes_node(request, package_uuid, pathway_uuid):
 
             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)
+            if node_qs.exists():
+                return redirect(current_pathway.url)
+
             n = Node()
             n.stereo_removed = False
             n.pathway = current_pathway

envipath/settings.py

@@ -491,3 +491,5 @@ BB4G_TENANT_ID = os.environ.get("BB4G_TENANT_ID")
 BB4G_CLIENT_ID = os.environ.get("BB4G_CLIENT_ID")
 BB4G_CLIENT_SECRET = os.environ.get("BB4G_CLIENT_SECRET")
 BB4G_SCOPE = os.environ.get("BB4G_SCOPE")
+
+os.environ["NO_PROXY"] = "localhost,127.0.0.1,epbiotransformer3"

epdb/legacy_api.py

@@ -1980,30 +1980,42 @@ class CreateNode(Schema):
 
 @router.post(
     "/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node",
-    response={200: str | Any, 403: Error},
+    response={200: str | Any, 400: Error, 403: Error},
 )
 def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
     try:
         p = get_package_for_write(request.user, package_uuid)
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
+        # TODO Code Dup from bayer.views
+
         if n.pesLink:
             from bayer.views import fetch_pes
             from bayer.models import PESCompound
 
             try:
-                pes_data = fetch_pes(request, c.pesLink)
+                pes_data = fetch_pes(request, n.pesLink)
             except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
+                return 400, {"message": f"Could not fetch PES data for {n.pesLink}"}
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
+
+                if p.classification_level != Package.Classification.SECRET:
+                    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"}
+                        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)
+            c = PESCompound.create(p, pes_data, n.nodeName, n.nodeReason)
+
+            node_qs = Node.objects.filter(pathway=pw, default_node_label=c.default_structure)
+            if node_qs.exists():
+                return redirect(pw.url)
 
             node = Node()
             node.stereo_removed = False

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'

templates/objects/group.html

@@ -56,7 +56,7 @@
         <ul class="menu bg-base-200 rounded-box">
           {% for um in group.user_member.all %}
             <li>
-              <a href="{{ um.url }}" class="hover:bg-base-300"
+                <a href="{% if not user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}" class="hover:bg-base-300"
                   >{{ um.username }}
                 {% if not um.is_active %}<i>(inactive)</i>{% endif %}</a
               >

templates/static/login_base.html

@@ -110,8 +110,6 @@
           <div
             class="text-base-content/50 flex items-center justify-center space-x-6 text-sm"
           >
-            <a href="/legal" class="link link-hover">Legal</a>
-            <span class="text-base-content/30">•</span>
             <a href="/terms" class="link link-hover">Terms of Use</a>
             <span class="text-base-content/30">•</span>
             <a href="/privacy" class="link link-hover">Privacy Policy</a>