refactor: large scale formatting/linting

This commit is contained in:
2025-11-12 15:51:13 +13:00
parent 305fdc41fb
commit 34aed2c7aa
120 changed files with 11389 additions and 7532 deletions

View File

@ -2,269 +2,427 @@
{% load static %}
{% block content %}
{% if object_type != 'package' %}
<div>
<div id="load-all-error" style="display: none;">
<div class="alert alert-danger" role="alert">
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
<span class="sr-only">Error:</span>
Getting objects failed!
</div>
</div>
<input type="text" id="object-search" class="form-control" placeholder="Search by name"
style="display: none;">
<p></p>
{% if object_type != 'package' %}
<div>
<div id="load-all-error" style="display: none;">
<div class="alert alert-danger" role="alert">
<span
class="glyphicon glyphicon-exclamation-sign"
aria-hidden="true"
></span>
<span class="sr-only">Error:</span>
Getting objects failed!
</div>
</div>
<input
type="text"
id="object-search"
class="form-control"
placeholder="Search by name"
style="display: none;"
/>
<p></p>
</div>
{% endif %}
{% block action_modals %}
{% if object_type == 'package' %}
{% include "modals/collections/new_package_modal.html" %}
{% include "modals/collections/import_package_modal.html" %}
{% include "modals/collections/import_legacy_package_modal.html" %}
{% elif object_type == 'compound' %}
{% include "modals/collections/new_compound_modal.html" %}
{% elif object_type == 'rule' %}
{% include "modals/collections/new_rule_modal.html" %}
{% elif object_type == 'reaction' %}
{% include "modals/collections/new_reaction_modal.html" %}
{% elif object_type == 'pathway' %}
{# {% include "modals/collections/new_pathway_modal.html" %} #}
{% elif object_type == 'node' %}
{% include "modals/collections/new_node_modal.html" %}
{% elif object_type == 'edge' %}
{% include "modals/collections/new_edge_modal.html" %}
{% elif object_type == 'scenario' %}
{% include "modals/collections/new_scenario_modal.html" %}
{% elif object_type == 'model' %}
{% include "modals/collections/new_model_modal.html" %}
{% elif object_type == 'setting' %}
{#{% include "modals/collections/new_setting_modal.html" %}#}
{% elif object_type == 'user' %}
<div></div>
{% elif object_type == 'group' %}
{% include "modals/collections/new_group_modal.html" %}
{% endif %}
{% endblock action_modals %}
{% block action_modals %}
{% if object_type == 'package' %}
{% include "modals/collections/new_package_modal.html" %}
{% include "modals/collections/import_package_modal.html" %}
{% include "modals/collections/import_legacy_package_modal.html" %}
{% elif object_type == 'compound' %}
{% include "modals/collections/new_compound_modal.html" %}
{% elif object_type == 'rule' %}
{% include "modals/collections/new_rule_modal.html" %}
{% elif object_type == 'reaction' %}
{% include "modals/collections/new_reaction_modal.html" %}
{% elif object_type == 'pathway' %}
{# {% include "modals/collections/new_pathway_modal.html" %} #}
{% elif object_type == 'node' %}
{% include "modals/collections/new_node_modal.html" %}
{% elif object_type == 'edge' %}
{% include "modals/collections/new_edge_modal.html" %}
{% elif object_type == 'scenario' %}
{% include "modals/collections/new_scenario_modal.html" %}
{% elif object_type == 'model' %}
{% include "modals/collections/new_model_modal.html" %}
{% elif object_type == 'setting' %}
{#{% include "modals/collections/new_setting_modal.html" %}#}
{% elif object_type == 'user' %}
<div></div>
{% elif object_type == 'group' %}
{% include "modals/collections/new_group_modal.html" %}
{% endif %}
{% endblock action_modals %}
<div class="panel-group" id="reviewListAccordion">
<div class="panel-group" id="reviewListAccordion">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{% if object_type == 'package' %}
Packages
{% elif object_type == 'compound' %}
Compounds
{% elif object_type == 'structure' %}
Compound structures
{% elif object_type == 'rule' %}
Rules
{% elif object_type == 'reaction' %}
Reactions
{% elif object_type == 'pathway' %}
Pathways
{% elif object_type == 'node' %}
Nodes
{% elif object_type == 'edge' %}
Edges
{% elif object_type == 'scenario' %}
Scenarios
{% elif object_type == 'model' %}
Model
{% elif object_type == 'setting' %}
Settings
{% elif object_type == 'user' %}
Users
{% elif object_type == 'group' %}
Groups
{% endif %}
<div id="actionsButton"
style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-haspopup="true" aria-expanded="false"><span
class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
style="padding-right:1em"></span></a>
<ul id="actionsList" class="dropdown-menu">
{% block actions %}
{% if object_type == 'package' %}
{% include "actions/collections/package.html" %}
{% elif object_type == 'compound' %}
{% include "actions/collections/compound.html" %}
{% elif object_type == 'structure' %}
{% include "actions/collections/compound_structure.html" %}
{% elif object_type == 'rule' %}
{% include "actions/collections/rule.html" %}
{% elif object_type == 'reaction' %}
{% include "actions/collections/reaction.html" %}
{% elif object_type == 'setting' %}
{% include "actions/collections/setting.html" %}
{% elif object_type == 'scenario' %}
{% include "actions/collections/scenario.html" %}
{% elif object_type == 'model' %}
{% include "actions/collections/model.html" %}
{% elif object_type == 'pathway' %}
{% include "actions/collections/pathway.html" %}
{% elif object_type == 'node' %}
{% include "actions/collections/node.html" %}
{% elif object_type == 'edge' %}
{% include "actions/collections/edge.html" %}
{% elif object_type == 'group' %}
{% include "actions/collections/group.html" %}
{% endif %}
{% endblock %}
</ul>
</div>
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{% if object_type == 'package' %}
Packages
{% elif object_type == 'compound' %}
Compounds
{% elif object_type == 'structure' %}
Compound structures
{% elif object_type == 'rule' %}
Rules
{% elif object_type == 'reaction' %}
Reactions
{% elif object_type == 'pathway' %}
Pathways
{% elif object_type == 'node' %}
Nodes
{% elif object_type == 'edge' %}
Edges
{% elif object_type == 'scenario' %}
Scenarios
{% elif object_type == 'model' %}
Model
{% elif object_type == 'setting' %}
Settings
{% elif object_type == 'user' %}
Users
{% elif object_type == 'group' %}
Groups
{% endif %}
<div
id="actionsButton"
style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
class="dropdown"
>
<a
href="#"
class="dropdown-toggle"
data-toggle="dropdown"
role="button"
aria-haspopup="true"
aria-expanded="false"
><span class="glyphicon glyphicon-wrench"></span> Actions
<span class="caret"></span><span style="padding-right:1em"></span
></a>
<ul id="actionsList" class="dropdown-menu">
{% block actions %}
{% if object_type == 'package' %}
{% include "actions/collections/package.html" %}
{% elif object_type == 'compound' %}
{% include "actions/collections/compound.html" %}
{% elif object_type == 'structure' %}
{% include "actions/collections/compound_structure.html" %}
{% elif object_type == 'rule' %}
{% include "actions/collections/rule.html" %}
{% elif object_type == 'reaction' %}
{% include "actions/collections/reaction.html" %}
{% elif object_type == 'setting' %}
{% include "actions/collections/setting.html" %}
{% elif object_type == 'scenario' %}
{% include "actions/collections/scenario.html" %}
{% elif object_type == 'model' %}
{% include "actions/collections/model.html" %}
{% elif object_type == 'pathway' %}
{% include "actions/collections/pathway.html" %}
{% elif object_type == 'node' %}
{% include "actions/collections/node.html" %}
{% elif object_type == 'edge' %}
{% include "actions/collections/edge.html" %}
{% elif object_type == 'group' %}
{% include "actions/collections/group.html" %}
{% endif %}
{% endblock %}
</ul>
</div>
<div class="panel-body">
<!-- Set Text above links -->
{% if object_type == 'package' %}
<p>A package contains pathways, rules, etc. and can reflect specific experimental
conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
more &gt;&gt;</a></p>
{% elif object_type == 'compound' %}
<p>A compound stores the structure of a molecule and can include meta-information.
<a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'structure' %}
<p>The structures stored in this compound
<a target="_blank" href="https://wiki.envipath.org/index.php/compounds" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'rule' %}
<p>A rule describes a biotransformation reaction template that is defined as SMIRKS.
<a target="_blank" href="https://wiki.envipath.org/index.php/Rules" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'reaction' %}
<p>A reaction is a specific biotransformation from educt compounds to product compounds.
<a target="_blank" href="https://wiki.envipath.org/index.php/reactions" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'pathway' %}
<p>A pathway displays the (predicted) biodegradation of a compound as graph.
<a target="_blank" href="https://wiki.envipath.org/index.php/pathways" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'node' %}
<p>Nodes represent the (predicted) compounds in a graph.
<a target="_blank" href="https://wiki.envipath.org/index.php/nodes" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'edge' %}
<p>Edges represent the links between Nodes in a graph
<a target="_blank" href="https://wiki.envipath.org/index.php/edges" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'scenario' %}
<p>A scenario contains meta-information that can be attached to other data (compounds, rules, ..).
<a target="_blank" href="https://wiki.envipath.org/index.php/scenarios" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'model' %}
<p>A model applies machine learning to limit the combinatorial explosion.
<a target="_blank" href="https://wiki.envipath.org/index.php/relative_reasoning" role="button">Learn
more
&gt;&gt;</a></p>
{% elif object_type == 'setting' %}
<p>A setting includes configuration parameters for pathway predictions.
<a target="_blank" href="https://wiki.envipath.org/index.php/settings" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'user' %}
<p>Register now to create own packages and to submit and manage your data.
<a target="_blank" href="https://wiki.envipath.org/index.php/users" role="button">Learn more
&gt;&gt;</a></p>
{% elif object_type == 'group' %}
<p>Users can team up in groups to share packages.
<a target="_blank" href="https://wiki.envipath.org/index.php/groups" role="button">Learn more
&gt;&gt;</a></p>
{% endif %}
</div>
<div class="panel-body">
<!-- Set Text above links -->
{% if object_type == 'package' %}
<p>
A package contains pathways, rules, etc. and can reflect specific
experimental conditions.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/packages"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'compound' %}
<p>
A compound stores the structure of a molecule and can include
meta-information.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/compounds"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'structure' %}
<p>
The structures stored in this compound
<a
target="_blank"
href="https://wiki.envipath.org/index.php/compounds"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'rule' %}
<p>
A rule describes a biotransformation reaction template that is
defined as SMIRKS.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/Rules"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'reaction' %}
<p>
A reaction is a specific biotransformation from educt compounds to
product compounds.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/reactions"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'pathway' %}
<p>
A pathway displays the (predicted) biodegradation of a compound as
graph.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/pathways"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'node' %}
<p>
Nodes represent the (predicted) compounds in a graph.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/nodes"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'edge' %}
<p>
Edges represent the links between Nodes in a graph
<a
target="_blank"
href="https://wiki.envipath.org/index.php/edges"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'scenario' %}
<p>
A scenario contains meta-information that can be attached to other
data (compounds, rules, ..).
<a
target="_blank"
href="https://wiki.envipath.org/index.php/scenarios"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'model' %}
<p>
A model applies machine learning to limit the combinatorial
explosion.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/relative_reasoning"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'setting' %}
<p>
A setting includes configuration parameters for pathway predictions.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/settings"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'user' %}
<p>
Register now to create own packages and to submit and manage your
data.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/users"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% elif object_type == 'group' %}
<p>
Users can team up in groups to share packages.
<a
target="_blank"
href="https://wiki.envipath.org/index.php/groups"
role="button"
>Learn more &gt;&gt;</a
>
</p>
{% endif %}
<!-- If theres nothing to show extend the text above -->
{% if reviewed_objects and unreviewed_objects %}
{% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %}
<p>Nothing found. There are two possible reasons: <br><br>1. There is no content yet.<br>2. You have no
reading permissions.<br><br>Please be sure you have at least reading permissions.</p>
{% endif %}
{% endif %}
</div>
{% if reviewed_objects %}
<!-- If theres nothing to show extend the text above -->
{% if reviewed_objects and unreviewed_objects %}
{% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %}
<p>
Nothing found. There are two possible reasons: <br /><br />1.
There is no content yet.<br />2. You have no reading
permissions.<br /><br />Please be sure you have at least reading
permissions.
</p>
{% endif %}
{% endif %}
</div>
{% if reviewed_objects %}
{% if reviewed_objects|length > 0 %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a id="ReviewedLink" data-toggle="collapse" data-parent="#reviewListAccordion"
href="#Reviewed">Reviewed</a>
<a
id="ReviewedLink"
data-toggle="collapse"
data-parent="#reviewListAccordion"
href="#Reviewed"
>Reviewed</a
>
</h4>
</div>
<div id="Reviewed" class="panel-collapse collapse in">
</div>
<div id="Reviewed" class="panel-collapse in collapse">
<div class="panel-body list-group-item" id="ReviewedContent">
{% if object_type == 'package' %}
{% if object_type == 'package' %}
{% for obj in reviewed_objects %}
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}
<span class="glyphicon glyphicon-star" aria-hidden="true"
style="float:right" data-toggle="tooltip"
data-placement="top" title="" data-original-title="Reviewed">
</span>
</a>
<a class="list-group-item" href="{{ obj.url }}"
>{{ obj.name|safe }}
<span
class="glyphicon glyphicon-star"
aria-hidden="true"
style="float:right"
data-toggle="tooltip"
data-placement="top"
title=""
data-original-title="Reviewed"
>
</span>
</a>
{% endfor %}
{% else %}
{% else %}
{% for obj in reviewed_objects|slice:":50" %}
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
<span class="glyphicon glyphicon-star" aria-hidden="true"
style="float:right" data-toggle="tooltip"
data-placement="top" title="" data-original-title="Reviewed">
</span>
</a>
<a class="list-group-item" href="{{ obj.url }}"
>{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
<span
class="glyphicon glyphicon-star"
aria-hidden="true"
style="float:right"
data-toggle="tooltip"
data-placement="top"
title=""
data-original-title="Reviewed"
>
</span>
</a>
{% endfor %}
{% endif %}
{% endif %}
</div>
</div>
{% endif %}
{% endif %}
{% if unreviewed_objects %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="UnreviewedLink"
data-toggle="collapse"
data-parent="#unReviewListAccordion"
href="#Unreviewed"
>Unreviewed</a
>
</h4>
</div>
{% endif %}
{% endif %}
{% if unreviewed_objects %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver"><h4
class="panel-title"><a id="UnreviewedLink" data-toggle="collapse" data-parent="#unReviewListAccordion"
href="#Unreviewed">Unreviewed</a></h4></div>
<div id="Unreviewed" class="panel-collapse collapse {% if reviewed_objects|length == 0 or object_type == 'package' %}in{% endif %}">
<div class="panel-body list-group-item" id="UnreviewedContent">
{% if object_type == 'package' %}
{% for obj in unreviewed_objects %}
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
{% endfor %}
{% else %}
{% for obj in unreviewed_objects|slice:":50" %}
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
{% endfor %}
{% endif %}
</div>
</div>
{% endif %}
{% if objects %}
<!-- Unreviewable objects such as User / Group / Setting -->
<ul class='list-group'>
{% for obj in objects %}
{% if object_type == 'user' %}
<a class="list-group-item" href="{{ obj.url }}">{{ obj.username|safe }}</a>
<div
id="Unreviewed"
class="panel-collapse {% if reviewed_objects|length == 0 or object_type == 'package' %}in{% endif %} collapse"
>
<div class="panel-body list-group-item" id="UnreviewedContent">
{% if object_type == 'package' %}
{% for obj in unreviewed_objects %}
<a class="list-group-item" href="{{ obj.url }}"
>{{ obj.name|safe }}</a
>
{% endfor %}
{% else %}
<a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
{% for obj in unreviewed_objects|slice:":50" %}
<a class="list-group-item" href="{{ obj.url }}"
>{{ obj.name|safe }}</a
>
{% endfor %}
{% endif %}
{% endfor %}
</div>
</div>
{% endif %}
{% if objects %}
<!-- Unreviewable objects such as User / Group / Setting -->
<ul class="list-group">
{% for obj in objects %}
{% if object_type == 'user' %}
<a class="list-group-item" href="{{ obj.url }}"
>{{ obj.username|safe }}</a
>
{% else %}
<a class="list-group-item" href="{{ obj.url }}"
>{{ obj.name|safe }}</a
>
{% endif %}
{% endfor %}
</ul>
{% endif %}
{% endif %}
</div>
<style>
.spinner-widget {
position: fixed; /* stays in place on scroll */
bottom: 20px; /* distance from bottom */
right: 20px; /* distance from right */
z-index: 9999; /* above most elements */
width: 60px; /* adjust to gif size */
height: 60px;
}
.spinner-widget {
position: fixed; /* stays in place on scroll */
bottom: 20px; /* distance from bottom */
right: 20px; /* distance from right */
z-index: 9999; /* above most elements */
width: 60px; /* adjust to gif size */
height: 60px;
}
.spinner-widget img {
width: 100%;
height: auto;
}
.spinner-widget img {
width: 100%;
height: auto;
}
</style>
<div id="load-all-loading" class="spinner-widget" style="display: none">
<img id="loading-gif" src="{% static '/images/wait.gif' %}" alt="Loading...">
<img
id="loading-gif"
src="{% static '/images/wait.gif' %}"
alt="Loading..."
/>
</div>
</div>
</div>
{# prettier-ignore-start #}
<script>
$(function () {
@ -300,7 +458,7 @@
}, 2500);
{% endif %}
{% endif %}
$('#modal-form-delete-submit').on('click', function (e) {
e.preventDefault();
$('#modal-form-delete').submit();
@ -316,4 +474,5 @@
});
</script>
{# prettier-ignore-end #}
{% endblock content %}