jebus/enviPy-bayer
1
0
Fork 0
forked from enviPath/enviPy
Code Issues Pull Requests 1 Actions Releases Activity

adjusted migration
Some checks failed
CI / test (pull_request) Failing after 17s
Details
API CI / api-tests (pull_request) Failing after 29s
Details

Browse Source 
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

Wip

minor

PW interactions

API PES

wip

Make Select Widget reflect required

make required generallay available

Update UI if pathway mode is set to build

Added ais

circle adjustments

Initial Zoom, fix AD Creation

wip

auth log, bb4g fix

missing import

Added viz hint if PES is part of reaction

Add Edge check for pes

flip boolean

...

pes

Added extra

...

In / Out Edges Viz, Submitting Button Text

...

Make PES Link clickable

Return proper http response instead of error

Fixed error return, removed unused options

Fix PES Link HTML for other entities

Fixed molfile assignment, adjusted Export

Package Export/Import cycle

highlight Description links

implemented non persistent

Harmonised proposed field in Json output

Added pesLink field to PW Api output

PES Fields in API Output

removed debug

Fix Classification import, Fix PES Deserialization

underline pes link in templates

Fix alter name/desc for node, make /node /edge funcitonal

provide setting link and copy button

Implemented Compound Names / Reaction Names View Option

Unconnected Nodes

Make links thicker, reduce timeout trigger time

Show proposed info in popover

Pathway Build no stereo removal

Include probs in reaction name option viz

Detect clicks outside nodes/edges
This commit is contained in:
Tim Lorsbach
2026-03-06 15:15:08 +01:00
parent 2c2437e3f5
commit 1d2bb85c90
81 changed files with 1614857 additions and 3531 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
templates/components/navbar.html
View File

@ -35,6 +35,7 @@
<use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
</svg>
</a>
<img src="{% static 'images/bayer-logo.svg' %}" width="40">
</div>
{% if not public_mode %}
@ -88,12 +89,23 @@
>Scenario</a
>
</li>
<hr/>
<li>
<a href="{{ meta.server_url }}/group" id="scenarioLink"
>Group</a
>
</li>
</ul>
</div>
</div>
{% endif %}
<div class="navbar-end">
{% if meta.url_contains_package and meta.current_package.get_classification_level_display == "Restricted" %}
<img src="{% static 'images/restricted_mid.png' %}" width="200">
{% elif meta.url_contains_package and meta.current_package.get_classification_level_display == "Secret" %}
<img src="{% static 'images/secret_mid.png' %}" width="120">
{% endif %}
{% if not public_mode %}
<a id="search-trigger" role="button" class="cursor-pointer">
<div

16
templates/modals/objects/add_pathway_edge_modal.html
View File

@ -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>

3
templates/objects/edge.html
View File

@ -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 -->

9
templates/objects/node.html
View File

@ -55,6 +55,15 @@
</div>
</div>
<!-- Description -->
{% if node.description and node.description != "no description" %}
<div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked />
<div class="collapse-title text-xl font-medium">Description</div>
<div class="collapse-content">{{ node.description }}</div>
</div>
{% endif %}
{% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}
{% for tpl in viz_templates %}

115
templates/objects/pathway.html
View File

@ -21,12 +21,14 @@
.link {
stroke: #999;
stroke-opacity: 0.6;
stroke-width: 1.5px;
/* marker-end: url(#arrow); */
}
.link_no_arrow {
stroke: #999;
stroke-opacity: 0.6;
stroke-width: 1.5px;
}
.node image {
@ -177,6 +179,52 @@
tabindex="0"
class="dropdown-content menu bg-base-100 rounded-box z-50 w-60 p-2"
>
<li>
<a id="compound-names-toggle-button" class="cursor-pointer">
<svg
id="compound-names-icon"
xmlns="http://www.w3.org/2000/svg"
width="16"
height="16"
viewBox="0 0 24 24"
fill="none"
stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
class="lucide lucide-eye"
>
<path
d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
/>
<circle cx="12" cy="12" r="3" />
</svg>
Compound Names
</a>
</li>
<li>
<a id="reaction-names-toggle-button" class="cursor-pointer">
<svg
id="reaction-names-icon"
xmlns="http://www.w3.org/2000/svg"
width="16"
height="16"
viewBox="0 0 24 24"
fill="none"
stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
class="lucide lucide-eye"
>
<path
d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
/>
<circle cx="12" cy="12" r="3" />
</svg>
Reaction Names
</a>
</li>
{% if pathway.setting.model.app_domain %}
<li>
<a id="app-domain-toggle-button" class="cursor-pointer">
@ -202,6 +250,7 @@
</a>
</li>
{% endif %}
{% if 1 == 0 %}
<li>
<a id="timeseries-toggle-button" class="cursor-pointer">
<svg
@ -252,6 +301,7 @@
Show Predicted Properties
</a>
</li>
{% endif %}
</ul>
</div>
</div>
@ -495,6 +545,10 @@
{{ pathway.d3_json|json_script:"pathway" }}
<script>
// Global switch for compound names view
var compoundNamesViewEnabled = false;
// Gloabl switch for reaction names view
var reactionNamesViewEnabled = false;
// Global switch for app domain view
var appDomainViewEnabled = false;
// Global switch for timeseries view
@ -530,6 +584,67 @@
descContent.innerHTML = newDesc;
}
const compoundNamesBtn = document.getElementById("compound-names-toggle-button");
if (compoundNamesBtn) {
compoundNamesBtn.addEventListener("click", function () {
compoundNamesViewEnabled = !compoundNamesViewEnabled;
const icon = document.getElementById("compound-names-icon");
if (compoundNamesViewEnabled) {
// Change to eye-off icon
icon.innerHTML =
'<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
nodes.forEach((x) => {
if (x.name) {
d3.select(x.el)
.append("text")
.text(d => d.name)
.attr("text-anchor", "middle")
.attr("y", -20)
.style("font-size", "4px");
}
});
} else {
// Change back to eye icon
icon.innerHTML =
'<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
nodes.forEach((x) => {
d3.select(x.el)
.select("text")
.remove()
})
}
});
}
const reactionNamesBtn = document.getElementById("reaction-names-toggle-button");
if (reactionNamesBtn) {
reactionNamesBtn.addEventListener("click", function () {
reactionNamesViewEnabled = !reactionNamesViewEnabled;
const icon = document.getElementById("reaction-names-icon");
if (reactionNamesViewEnabled) {
// Change to eye-off icon
icon.innerHTML =
'<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
d3.selectAll(".link-label")
.style("display", null);
} else {
// Change back to eye icon
icon.innerHTML =
'<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
d3.selectAll(".link-label")
.style("display", "none");
}
});
}
// App domain toggle
const appDomainBtn = document.getElementById("app-domain-toggle-button");
if (appDomainBtn) {

3
templates/objects/reaction.html
View File

@ -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 -->

70
templates/objects/setting_template.html
View File

@ -24,6 +24,76 @@
<td>Setting Name</td>
<td>{{ setting_to_render.name }}</td>
</tr>
<tr>
<td>Setting URL</td>
<td>
<a href="{{ setting_to_render.url }}" class="link link-primary">{{ setting_to_render.url }}</a>
<div
x-data="{
value: '{{ setting_to_render.url }}',
copied: false,
async copy() {
await navigator.clipboard.writeText(this.value)
this.copied = true
setTimeout(() => {
this.copied = false
}, 1500)
}
}"
class="join"
>
<button
type="button"
class="btn btn-ghost"
:data-tip="copied ? 'Copied!' : 'Copy'"
@click="copy"
aria-label="Copy to clipboard"
>
<svg
x-show="!copied"
xmlns="http://www.w3.org/2000/svg"
class="h-4 w-4"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
stroke-width="2"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
d="M8 16H6a2 2 0 01-2-2V6a2 2 0 012-2h8a2 2 0 012 2v2"
/>
<rect
width="12"
height="12"
x="8"
y="8"
rx="2"
ry="2"
/>
</svg>
<svg
x-show="copied"
xmlns="http://www.w3.org/2000/svg"
class="h-4 w-4"
fill="none"
viewBox="0 0 24 24"
stroke="currentColor"
stroke-width="2"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
d="M5 13l4 4L19 7"
/>
</svg>
</button>
</div>
</td>
</tr>
{% if setting_to_render.description %}
<tr>
<td>Setting Description</td>

2
templates/static/login_base.html
View File

@ -110,8 +110,6 @@
<div
class="text-base-content/50 flex items-center justify-center space-x-6 text-sm"
>
<a href="/legal" class="link link-hover">Legal</a>
<span class="text-base-content/30">•</span>
<a href="/terms" class="link link-hover">Terms of Use</a>
<span class="text-base-content/30">•</span>
<a href="/privacy" class="link link-hover">Privacy Policy</a>