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refactor: large scale formatting/linting

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Tobias O
2025-11-12 15:51:13 +13:00
parent 305fdc41fb
commit 34aed2c7aa
120 changed files with 11389 additions and 7532 deletions
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templates/objects/simple_rule.html
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@ -2,242 +2,367 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/edit_rule_modal.html" %}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/generic_copy_object_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
{% block action_modals %}
{% include "modals/objects/edit_rule_modal.html" %}
{% include "modals/objects/generic_set_aliases_modal.html" %}
{% include "modals/objects/generic_set_scenario_modal.html" %}
{% include "modals/objects/generic_copy_object_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
{% endblock action_modals %}
<div class="panel-group" id="rule-detail">
<div class="panel panel-default">
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
{{ rule.name|safe }}
<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 %}
{% include "actions/objects/rule.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-body">
<p>
{{ rule.description|safe }}
</p>
</div>
{% if rule.aliases %}
<!-- Aliases -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-aliases-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-aliases">Aliases</a>
</h4>
</div>
<div id="rule-aliases" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for alias in rule.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Representation -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-image-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-image">Image Representation</a>
</h4>
</div>
<div id="rule-image" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<div id="image-div" align="center">
{{ rule.as_svg|safe }}
</div>
</div>
</div>
<!-- SMIRKS -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-smirks-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-smirks">SMIRKS Representation</a>
</h4>
</div>
<div id="rule-smirks" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<p> {{ rule.smirks }} </p>
</div>
</div>
<!-- Reactants SMARTS -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-reactants-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-reactants-smarts">Reactant SMARTS</a>
</h4>
</div>
<div id="rule-reactants-smarts" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<p> {{ rule.reactants_smarts }} </p>
</div>
</div>
<!-- Reactant Filter SMARTS -->
{% if rule.reactant_filter_smarts %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-reactant-filter-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-reactant-filter-smarts">Reactant Filter SMARTS</a>
</h4>
</div>
<div id="rule-reactant-filter-smarts" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<p> {{ rule.reactant_filter_smarts }} </p>
</div>
</div>
{% endif %}
<!-- Products SMARTS -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-products-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-products-smarts">Reactant SMARTS</a>
</h4>
</div>
<div id="rule-products-smarts" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<p> {{ rule.products_smarts }} </p>
</div>
</div>
<!-- Product Filter SMARTS -->
{% if rule.product_filter_smarts %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-product-filter-smarts-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-product-filter-smarts">Product Filter SMARTS</a>
</h4>
</div>
<div id="rule-product-filter-smarts" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
<p> {{ rule.product_filter_smarts }} </p>
</div>
</div>
{% endif %}
<!-- Included in Composite Rules -->
{% if rule.parallelrule_set.all %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-composite-rule-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-composite-rule">Included in Composite Rules</a>
</h4>
</div>
<div id="rule-composite-rule" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for cr in rule.parallelrule_set.all %}
<a class="list-group-item" href="{{ cr.url }}">{{ cr.name|safe }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Scenarios -->
{% if rule.scenarios.all %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-scenario-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-scenario">Scenarios</a>
</h4>
</div>
<div id="rule-scenario" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for s in rule.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Reactions -->
{% if rule.related_reactions %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-reaction-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-reaction">Reactions</a>
</h4>
</div>
<div id="rule-reaction" class="panel-collapse collapse">
<div class="panel-body list-group-item">
{% for r in rule.related_reactions %}
<a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Pathways -->
{% if rule.related_pathways %}
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-pathway-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-pathway">Pathways</a>
</h4>
</div>
<div id="rule-pathway" class="panel-collapse collapse">
<div class="panel-body list-group-item">
{% for r in rule.related_pathways %}
<a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
{% endfor %}
</div>
</div>
{% endif %}
{% if rule.enzymelinks %}
<!-- EC Numbers -->
<div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
<h4 class="panel-title">
<a id="rule-ec-numbers-link" data-toggle="collapse" data-parent="#rule-detail"
href="#rule-ec-numbers">EC Numbers</a>
</h4>
</div>
<div id="rule-ec-numbers" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for k, v in rule.get_grouped_enzymelinks.items %}
<div class="panel panel-default panel-heading list-group-item"
style="background-color:silver">
<h4 class="panel-title">
<a id="{{ k|slugify }}_Link" data-toggle="collapse"
data-parent="#{{ k|slugify }}_Accordion"
href="#{{ k|slugify }}">
{{ k }}
</a>
</h4>
</div>
<div id="{{ k|slugify }}" class="panel-collapse collapse in">
<div class="panel-body list-group-item">
{% for enzyme in v %}
<a class="list-group-item" href="{{ enzyme.url }}">
{{ enzyme.ec_number }}
<div style="position:absolute;bottom:10px;left:100px;">{{ enzyme.name }}</div>
<div style="float:right;">{{ enzyme.linking_method }}</div>
</a>
{% endfor %}
</div>
</div>
{% endfor %}
</div>
</div>
{% endif %}
<div class="panel-group" id="rule-detail">
<div class="panel panel-default">
<div
class="panel-heading"
id="headingPanel"
style="font-size:2rem;height: 46px"
>
{{ rule.name|safe }}
<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 %}
{% include "actions/objects/rule.html" %}
{% endblock %}
</ul>
</div>
</div>
<div class="panel-body">
<p>{{ rule.description|safe }}</p>
</div>
{% if rule.aliases %}
<!-- Aliases -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-aliases-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-aliases"
>Aliases</a
>
</h4>
</div>
<div id="rule-aliases" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for alias in rule.aliases %}
<a class="list-group-item">{{ alias }}</a>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Representation -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-image-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-image"
>Image Representation</a
>
</h4>
</div>
<div id="rule-image" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<div id="image-div" align="center">{{ rule.as_svg|safe }}</div>
</div>
</div>
<!-- SMIRKS -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-smirks-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-smirks"
>SMIRKS Representation</a
>
</h4>
</div>
<div id="rule-smirks" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<p>{{ rule.smirks }}</p>
</div>
</div>
<!-- Reactants SMARTS -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-reactants-smarts-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-reactants-smarts"
>Reactant SMARTS</a
>
</h4>
</div>
<div id="rule-reactants-smarts" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<p>{{ rule.reactants_smarts }}</p>
</div>
</div>
<!-- Reactant Filter SMARTS -->
{% if rule.reactant_filter_smarts %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-reactant-filter-smarts-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-reactant-filter-smarts"
>Reactant Filter SMARTS</a
>
</h4>
</div>
<div
id="rule-reactant-filter-smarts"
class="panel-collapse in collapse"
>
<div class="panel-body list-group-item">
<p>{{ rule.reactant_filter_smarts }}</p>
</div>
</div>
{% endif %}
<!-- Products SMARTS -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-products-smarts-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-products-smarts"
>Reactant SMARTS</a
>
</h4>
</div>
<div id="rule-products-smarts" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<p>{{ rule.products_smarts }}</p>
</div>
</div>
<!-- Product Filter SMARTS -->
{% if rule.product_filter_smarts %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-product-filter-smarts-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-product-filter-smarts"
>Product Filter SMARTS</a
>
</h4>
</div>
<div id="rule-product-filter-smarts" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
<p>{{ rule.product_filter_smarts }}</p>
</div>
</div>
{% endif %}
<!-- Included in Composite Rules -->
{% if rule.parallelrule_set.all %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-composite-rule-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-composite-rule"
>Included in Composite Rules</a
>
</h4>
</div>
<div id="rule-composite-rule" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for cr in rule.parallelrule_set.all %}
<a class="list-group-item" href="{{ cr.url }}"
>{{ cr.name|safe }}</a
>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Scenarios -->
{% if rule.scenarios.all %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-scenario-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-scenario"
>Scenarios</a
>
</h4>
</div>
<div id="rule-scenario" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for s in rule.scenarios.all %}
<a class="list-group-item" href="{{ s.url }}"
>{{ s.name|safe }}</a
>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Reactions -->
{% if rule.related_reactions %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-reaction-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-reaction"
>Reactions</a
>
</h4>
</div>
<div id="rule-reaction" class="panel-collapse collapse">
<div class="panel-body list-group-item">
{% for r in rule.related_reactions %}
<a class="list-group-item" href="{{ r.url }}"
>{{ r.name|safe }}</a
>
{% endfor %}
</div>
</div>
{% endif %}
<!-- Pathways -->
{% if rule.related_pathways %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-pathway-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-pathway"
>Pathways</a
>
</h4>
</div>
<div id="rule-pathway" class="panel-collapse collapse">
<div class="panel-body list-group-item">
{% for r in rule.related_pathways %}
<a class="list-group-item" href="{{ r.url }}"
>{{ r.name|safe }}</a
>
{% endfor %}
</div>
</div>
{% endif %}
{% if rule.enzymelinks %}
<!-- EC Numbers -->
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="rule-ec-numbers-link"
data-toggle="collapse"
data-parent="#rule-detail"
href="#rule-ec-numbers"
>EC Numbers</a
>
</h4>
</div>
<div id="rule-ec-numbers" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for k, v in rule.get_grouped_enzymelinks.items %}
<div
class="panel panel-default panel-heading list-group-item"
style="background-color:silver"
>
<h4 class="panel-title">
<a
id="{{ k|slugify }}_Link"
data-toggle="collapse"
data-parent="#{{ k|slugify }}_Accordion"
href="#{{ k|slugify }}"
>
{{ k }}
</a>
</h4>
</div>
<div id="{{ k|slugify }}" class="panel-collapse in collapse">
<div class="panel-body list-group-item">
{% for enzyme in v %}
<a class="list-group-item" href="{{ enzyme.url }}">
{{ enzyme.ec_number }}
<div style="position:absolute;bottom:10px;left:100px;">
{{ enzyme.name }}
</div>
<div style="float:right;">
{{ enzyme.linking_method }}
</div>
</a>
{% endfor %}
</div>
</div>
{% endfor %}
</div>
</div>
{% endif %}
</div>
</div>
{% endblock content %}