flip boolean

bayer/views.py

@@ -118,6 +118,9 @@ def fetch_pes(request, pes_url) -> dict:
     from epauth.views import get_access_token_from_request
     token = get_access_token_from_request(request)
 
+    if token is None:
+        token = pes_url.split('/')[-1] == 'dummy'
+
     if token:
         for k, v in s.PES_API_MAPPING.items():
             if pes_url.startswith(k):

docker-compose.dev.yml

@@ -28,17 +28,6 @@ services:
     image: git.envipath.com/envipath/biotransformer3:1.0
     container_name: epbiotransformer3
 
-#  web:
-#    image: envipath/envipy-bayer:1.0
-#    container_name: epdjango
-#    ports:
-#      - "127.0.0.1:8000:8000"
-#    env_file:
-#      - .env
-#    command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
-#    volumes:
-#      - ep_bayer_data:/opt/enviPy/
-
   celery_worker:
     image: git.envipath.com/envipath/envipy-bayer:1.0
     container_name: epcelery

epdb/models.py

@@ -576,6 +576,10 @@ class ReactionIdentifierMixin(ExternalIdentifierMixin):
     def get_uniprot_identifiers(self):
         return self.get_external_identifier("UniProt")
 
+    def contains_pes(self):
+        from bayer.models import PESStructure
+        return any([isinstance(o, PESStructure) for o in self.educts.all()]) or any(
+            [isinstance(o, PESStructure) for o in self.products.all()])
 
 ##############
 # EP Objects #

templates/modals/objects/add_pathway_edge_modal.html

@@ -5,6 +5,7 @@
   x-data="{
     isSubmitting: false,
     reactionImageUrl: '',
+    pes: false,
 
     reset() {
       this.isSubmitting = false;
@@ -15,20 +16,30 @@
       const substratesSelect = document.getElementById('add_pathway_edge_substrates');
       const productsSelect = document.getElementById('add_pathway_edge_products');
 
+      const pesLinks = [];
+
       const substrates = [];
       for (const option of substratesSelect.selectedOptions) {
         substrates.push(option.dataset.smiles);
+        if (option.dataset.pes === 'true') {
+          pesLinks.push(option.dataset.pes);
+        }
       }
 
       const products = [];
       for (const option of productsSelect.selectedOptions) {
         products.push(option.dataset.smiles);
+        if (option.dataset.pes === 'true') {
+          pesLinks.push(option.dataset.pes);
+        }
       }
 
       if (substrates.length > 0 && products.length > 0) {
         const reaction = substrates.join('.') + '>>' + products.join('.');
         this.reactionImageUrl = '{% url "depict" %}?smirks=' + encodeURIComponent(reaction);
+        this.pes = pesLinks.length > 0;
       } else {
+        this.pes = false;
         this.reactionImageUrl = '';
       }
     },
@@ -106,6 +117,7 @@
                 {% for n in pathway.nodes %}
                   <option
                     data-smiles="{{ n.default_node_label.smiles }}"
+                    data-pes="{% if n.default_node_label.pes_link %}true{% else %}false{% endif %}"
                     value="{{ n.url }}"
                   >
                     {{ n.default_node_label.name|safe }}
@@ -132,6 +144,7 @@
                 {% for n in pathway.nodes %}
                   <option
                     data-smiles="{{ n.default_node_label.smiles }}"
+                    data-pes="{% if n.default_node_label.pes_link %}true{% else %}false{% endif %}"
                     value="{{ n.url }}"
                   >
                     {{ n.default_node_label.name|safe }}
@@ -144,6 +157,9 @@
 
         <div class="mb-3" x-show="reactionImageUrl" x-cloak>
           <img :src="reactionImageUrl" class="w-full" alt="Reaction preview" />
+          <div x-show="pes">
+            <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
+          </div>
         </div>
       </form>
     </div>

templates/objects/edge.html

@@ -82,6 +82,9 @@
       <div class="collapse-content">
         <div class="flex justify-center">{{ edge.edge_label.as_svg|safe }}</div>
       </div>
+      {% if edge.edge_label.contains_pes %}
+        <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
+      {% endif %}
     </div>
 
     <!-- Reaction Description -->
@@ -92,7 +95,7 @@
         <div class="flex flex-wrap items-center justify-center gap-4">
           {% for educt in edge.start_nodes.all %}
             <a href="{{ educt.url }}" class="btn btn-outline btn-sm"
-              >{{ educt.name }}</a
+              >{{ educt.get_name }}</a
             >
           {% endfor %}
           <svg
@@ -112,7 +115,7 @@
           </svg>
           {% for product in edge.end_nodes.all %}
             <a href="{{ product.url }}" class="btn btn-outline btn-sm"
-              >{{ product.name }}</a
+              >{{ product.get_name }}</a
             >
           {% endfor %}
         </div>

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="{% if not user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}" class="hover:bg-base-300"
+                <a href="{% if 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/objects/reaction.html

@@ -79,6 +79,9 @@
       <div class="collapse-content">
         <div class="flex justify-center">{{ reaction.as_svg|safe }}</div>
       </div>
+      {% if reaction.contains_pes %}
+        <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
+      {% endif %}
     </div>
 
     <!-- Reaction Description -->

uv.lock

@@ -894,7 +894,7 @@ provides-extras = ["ms-login", "dev", "pepper-plugin"]
 [[package]]
 name = "envipy-additional-information"
 version = "0.4.2"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#f2f251e0214f016760348730c45e56183d961201" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#ad825570480bbe2f1a35c04923fede756c450751" }
 dependencies = [
     { name = "pydantic" },
 ]