forked from enviPath/enviPy
[Feature] Integrate DOI Links, Handle Cycles in Pathway Viz (#407)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#407
This commit is contained in:
48
epdb/migrations/0026_auto_20260602_1718.py
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48
epdb/migrations/0026_auto_20260602_1718.py
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@ -0,0 +1,48 @@
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# Generated by Django 6.0.3 on 2026-06-02 17:18
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from django.db import migrations
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from envipy_additional_information import DOI
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def forward_func(apps, schema_editor):
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AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
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refs = AdditionalInformation.objects.filter(type="Reference")
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remaining = []
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for ref in refs:
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r = ref.data["reference"]
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try:
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# PubMed IDs are plain ints, try parsing
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_ = int(r)
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# Nothing to do
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except ValueError:
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DOMAINS = [
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"http://dx.doi.org/",
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"https://dx.doi.org/",
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"http://doi.org/",
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"https://doi.org/",
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]
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for d in DOMAINS:
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r = r.replace(d, "")
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if r.startswith("10."):
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ref.type = DOI.__name__
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ref.data = {"doi": r}
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ref.save()
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else:
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remaining.append(ref)
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if len(remaining) > 0:
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raise ValueError(f"Could not parse {len(remaining)} references")
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class Migration(migrations.Migration):
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dependencies = [
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("epdb", "0025_auto_20260511_2025"),
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]
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operations = [
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migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
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]
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@ -1773,7 +1773,7 @@ class Reaction(
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return new_reaction
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def smirks(self):
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return f"{'.'.join([cs.smiles for cs in self.educts.all()])}>>{'.'.join([cs.smiles for cs in self.products.all()])}"
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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')])}"
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@property
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def as_svg(self):
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@ -1886,6 +1886,9 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
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if n not in queue:
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queue.append(n)
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for i in queue:
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processed.add(i)
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while len(queue):
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current = queue.pop()
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processed.add(current)
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@ -2194,17 +2197,8 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
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depth_map[0] = list()
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processed = set()
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for n in self.nodes:
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num_parents = in_count[str(n.uuid)]
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if num_parents == 0:
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# must be a root node or unconnected node
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if n.depth != 0:
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n.depth = 0
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n.save()
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# Only root node may have children
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if out_count[str(n.uuid)] > 0:
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depth_map[0].append(n)
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for n in self.root_nodes:
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depth_map[0].append(n)
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# At most depth len(nodes) is possible
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for i in range(self.nodes.count()):
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@ -2227,7 +2221,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
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for depth, nodes in depth_map.items():
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for n in nodes:
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if n.depth != depth:
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if n.depth != depth and depth != 0:
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n.depth = depth
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n.save()
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@ -293,6 +293,34 @@ document.addEventListener("alpine:init", () => {
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}),
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);
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// PubMed link widget
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Alpine.data(
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"doiWidget",
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(fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
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...baseWidget(
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fieldName,
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data,
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schema,
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uiSchema,
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mode,
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debugErrors,
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context,
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),
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get value() {
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return this.data[this.fieldName] || "";
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},
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set value(v) {
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this.data[this.fieldName] = v;
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},
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get doiUrl() {
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return this.value
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? `https://dx.doi.org/${this.value}`
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: null;
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},
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}),
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);
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// Compound link widget
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Alpine.data(
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"compoundWidget",
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@ -581,11 +581,11 @@ function draw(pathway, elem) {
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for (idx in parents) {
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p = nodes[parents[idx]]
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// console.log(p.depth)
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if (p.depth >= n.depth) {
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// keep the .5 steps for pseudo nodes
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n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
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// console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
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}
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// if (p.depth >= n.depth) {
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// // keep the .5 steps for pseudo nodes
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// n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
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// // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
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// }
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}
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});
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@ -123,6 +123,17 @@
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</div>
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</template>
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<!-- DOI link widget -->
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<template
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x-if="getWidget(fieldName, schema.properties[fieldName]) === 'doi-link'"
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>
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<div
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x-data="doiWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
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>
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{% include "components/widgets/doi_link_widget.html" %}
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</div>
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</template>
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<!-- Compound link widget -->
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<template
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x-if="getWidget(fieldName, schema.properties[fieldName]) === 'compound-link'"
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69
templates/components/widgets/doi_link_widget.html
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69
templates/components/widgets/doi_link_widget.html
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{# DOI link widget - pure HTML template #}
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<div class="form-control">
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<div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
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<!-- Label -->
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<label class="label sm:w-48 sm:shrink-0">
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<span
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class="label-text"
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:class="{
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'text-error': $store.validationErrors.hasError(fieldName, context),
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'text-sm text-base-content/60': isViewMode
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}"
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x-text="label"
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></span>
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</label>
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<!-- Input column -->
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<div class="flex-1">
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<!-- Help text -->
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<template x-if="helpText">
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<div class="label">
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<span
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class="label-text-alt text-base-content/60"
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x-text="helpText"
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></span>
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</div>
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</template>
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<!-- View mode: display as link -->
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<template x-if="isViewMode">
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<div class="mt-1">
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<template x-if="value && doiUrl">
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<a
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:href="doiUrl"
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class="link link-primary"
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target="_blank"
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x-text="value"
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></a>
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</template>
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<template x-if="!value">
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<span class="text-base-content/50">—</span>
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</template>
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</div>
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</template>
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<!-- Edit mode -->
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<template x-if="isEditMode">
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<input
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type="text"
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class="input input-bordered w-full"
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:class="{ 'input-error': $store.validationErrors.hasError(fieldName, context) }"
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placeholder="DOI e.g. 10.1016/j.jhazmat.2016.08.036"
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x-model="value"
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/>
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</template>
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<!-- Errors -->
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<template x-if="$store.validationErrors.hasError(fieldName, context)">
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<div class="label">
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<template
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x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
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:key="errMsg"
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>
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<span class="label-text-alt text-error" x-text="errMsg"></span>
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</template>
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</div>
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</template>
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</div>
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</div>
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</div>
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2
uv.lock
generated
2
uv.lock
generated
@ -894,7 +894,7 @@ provides-extras = ["ms-login", "dev", "pepper-plugin"]
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[[package]]
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name = "envipy-additional-information"
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version = "0.4.2"
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source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#79285f522e0a6ed3f2e805dfeeb6b9fa5cea4323" }
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source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#f2f251e0214f016760348730c45e56183d961201" }
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dependencies = [
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{ name = "pydantic" },
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]
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