diff --git a/epdb/migrations/0026_auto_20260602_1718.py b/epdb/migrations/0026_auto_20260602_1718.py
new file mode 100644
index 00000000..da3bd22e
--- /dev/null
+++ b/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),
+ ]
diff --git a/epdb/models.py b/epdb/models.py
index b1b1bb20..3acad772 100644
--- a/epdb/models.py
+++ b/epdb/models.py
@@ -1773,7 +1773,7 @@ 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):
@@ -1886,6 +1886,9 @@ 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)
@@ -2194,17 +2197,8 @@ 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()):
@@ -2227,7 +2221,7 @@ 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()
diff --git a/static/js/alpine/components/widgets.js b/static/js/alpine/components/widgets.js
index 9da8c22d..a0577b2e 100644
--- a/static/js/alpine/components/widgets.js
+++ b/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",
diff --git a/static/js/pw.js b/static/js/pw.js
index 7bf7fff7..de259beb 100644
--- a/static/js/pw.js
+++ b/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));
+ // }
}
});
diff --git a/templates/components/schema_form.html b/templates/components/schema_form.html
index 75cc9591..37050c26 100644
--- a/templates/components/schema_form.html
+++ b/templates/components/schema_form.html
@@ -123,6 +123,17 @@
+
+
+
+ {% include "components/widgets/doi_link_widget.html" %}
+
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