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[Feature] Integrate DOI Links, Handle Cycles in Pathway Viz (#407)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#407
This commit is contained in:
jebus
2026-06-03 06:00:38 +12:00
parent 868bbf5c05
commit 14cfc1e4d7
7 changed files with 169 additions and 19 deletions
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48
epdb/migrations/0026_auto_20260602_1718.py Normal file
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@ -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),
]

18
epdb/models.py
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@ -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)
@ -2194,16 +2197,7 @@ 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:
for n in self.root_nodes:
depth_map[0].append(n)
# At most depth len(nodes) is possible
@ -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()

28
static/js/alpine/components/widgets.js
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@ -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",

10
static/js/pw.js
View File

@ -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));
// }
}
});

11
templates/components/schema_form.html
View File

@ -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'"

69
templates/components/widgets/doi_link_widget.html Normal file
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@ -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>

2
uv.lock generated
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@ -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" },
]