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

epdb/migrations/0026_auto_20260602_1718.py

@@ -0,0 +1,48 @@
+# Generated by Django 6.0.3 on 2026-06-02 17:18
+
+from django.db import migrations
+from envipy_additional_information import DOI
+
+
+def forward_func(apps, schema_editor):
+    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
+
+    refs = AdditionalInformation.objects.filter(type="Reference")
+
+    remaining = []
+
+    for ref in refs:
+        r = ref.data["reference"]
+        try:
+            # PubMed IDs are plain ints, try parsing
+            _ = int(r)
+            # Nothing to do
+        except ValueError:
+            DOMAINS = [
+                "http://dx.doi.org/",
+                "https://dx.doi.org/",
+                "http://doi.org/",
+                "https://doi.org/",
+            ]
+            for d in DOMAINS:
+                r = r.replace(d, "")
+
+            if r.startswith("10."):
+                ref.type = DOI.__name__
+                ref.data = {"doi": r}
+                ref.save()
+            else:
+                remaining.append(ref)
+
+    if len(remaining) > 0:
+        raise ValueError(f"Could not parse {len(remaining)} references")
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0025_auto_20260511_2025"),
+    ]
+
+    operations = [
+        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
+    ]

epdb/models.py

@@ -1781,7 +1781,7 @@ class Reaction(
         return new_reaction
 
     def smirks(self):
-        return f"{'.'.join([cs.smiles for cs in self.educts.all()])}>>{'.'.join([cs.smiles for cs in self.products.all()])}"
+        return f"{'.'.join([cs.smiles for cs in self.educts.all().order_by('-pk')])}>>{'.'.join([cs.smiles for cs in self.products.all().order_by('-pk')])}"
 
     @property
     def as_svg(self):
@@ -1894,6 +1894,9 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 if n not in queue:
                     queue.append(n)
 
+        for i in queue:
+            processed.add(i)
+
         while len(queue):
             current = queue.pop()
             processed.add(current)
@@ -2202,17 +2205,8 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         depth_map[0] = list()
         processed = set()
 
-        for n in self.nodes:
-            num_parents = in_count[str(n.uuid)]
-            if num_parents == 0:
-                # must be a root node or unconnected node
-                if n.depth != 0:
-                    n.depth = 0
-                    n.save()
-
-                # Only root node may have children
-                if out_count[str(n.uuid)] > 0:
-                    depth_map[0].append(n)
+        for n in self.root_nodes:
+            depth_map[0].append(n)
 
         # At most depth len(nodes) is possible
         for i in range(self.nodes.count()):
@@ -2235,7 +2229,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
 
         for depth, nodes in depth_map.items():
             for n in nodes:
-                if n.depth != depth:
+                if n.depth != depth and depth != 0:
                     n.depth = depth
                     n.save()
 

static/js/alpine/components/widgets.js

@@ -293,6 +293,34 @@ document.addEventListener("alpine:init", () => {
     }),
   );
 
+    // PubMed link widget
+  Alpine.data(
+    "doiWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get value() {
+        return this.data[this.fieldName] || "";
+      },
+      set value(v) {
+        this.data[this.fieldName] = v;
+      },
+      get doiUrl() {
+        return this.value
+          ? `https://dx.doi.org/${this.value}`
+          : null;
+      },
+    }),
+  );
+
   // Compound link widget
   Alpine.data(
     "compoundWidget",

static/js/pw.js

@@ -581,11 +581,11 @@ function draw(pathway, elem) {
         for (idx in parents) {
             p = nodes[parents[idx]]
             // console.log(p.depth)
-            if (p.depth >= n.depth) {
-                // keep the .5 steps for pseudo nodes
-                n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
-                // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
-            }
+            // if (p.depth >= n.depth) {
+            //     // keep the .5 steps for pseudo nodes
+            //     n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
+            //     // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
+            // }
         }
     });
 

templates/components/schema_form.html

@@ -123,6 +123,17 @@
             </div>
           </template>
 
+          <!-- DOI link widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'doi-link'"
+          >
+            <div
+              x-data="doiWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/doi_link_widget.html" %}
+            </div>
+          </template>
+
           <!-- Compound link widget -->
           <template
             x-if="getWidget(fieldName, schema.properties[fieldName]) === 'compound-link'"

templates/components/widgets/doi_link_widget.html

@@ -0,0 +1,69 @@
+{# DOI link widget - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode: display as link -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <template x-if="value && doiUrl">
+            <a
+              :href="doiUrl"
+              class="link link-primary"
+              target="_blank"
+              x-text="value"
+            ></a>
+          </template>
+          <template x-if="!value">
+            <span class="text-base-content/50">—</span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Edit mode -->
+      <template x-if="isEditMode">
+        <input
+          type="text"
+          class="input input-bordered w-full"
+          :class="{ 'input-error': $store.validationErrors.hasError(fieldName, context) }"
+          placeholder="DOI e.g. 10.1016/j.jhazmat.2016.08.036"
+          x-model="value"
+        />
+      </template>
+
+      <!-- Errors -->
+      <template x-if="$store.validationErrors.hasError(fieldName, context)">
+        <div class="label">
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

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#79285f522e0a6ed3f2e805dfeeb6b9fa5cea4323" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#f2f251e0214f016760348730c45e56183d961201" }
 dependencies = [
     { name = "pydantic" },
 ]